Glycidyl methacrylate-co-N-vinyl-2-pyrrolidone coated polypropylene strips: Synthesis, characterization and standardization for dot-enzyme linked immunosorbent assay

Energy Technology Data Exchange (ETDEWEB)

Tyagi, Charu; Tomar, Lomas [Centre for Biomedical Engineering, Indian Institute of Technology, Delhi 110016 (India); Singh, Harpal [Centre for Biomedical Engineering, Indian Institute of Technology, Delhi 110016 (India)], E-mail: tyagicharu11@rediffmail.com

2009-01-26

Glycidyl methacrylate and N-vinyl-2-pyrrolidone (GMA-co-NVP) copolymers with various GMA:NVP ratios were synthesized by solution polymerization technique in toluene using 2,2'-azobisisobutyronitrile (AIBN) as free radical initiator and dip coated onto polypropylene strips. The copolymer composition in polymeric coatings was confirmed by proton NMR spectroscopy. Various techniques like FTIR, SEM and contact angle were used for surface characterization of the polymer coatings. These polymer coated strips were evaluated and standardized for their application in dot-ELISA in two steps. In first step, specificity, sensitivity and reproducibility of the assay on developed polymer coated strips was evaluated through a model system using rabbit anti-goat IgG, goat anti-rabbit IgG and goat anti-rabbit IgG HRP (horseradish peroxidase)-conjugate. Polymer coating with GMA-NVP mol% ratio of 78:22 was able to detect rabbit anti-goat IgG antibody at a concentration as low as 2 ng mL{sup -1} with 1% BSA as blocking agent using antispecies IgG peroxidase conjugate diluted 1500 times. In the second step, the sensitivity and specificity of the developed system was established with human blood and finally used to identify the source of mosquito blood meal which is an important parameter in epidemiological studies, particularly in determining the role of mosquito in malaria transmission. The time duration of standardized assay with developed polymer coated strips was cut down to one hour compared to the 3-4 h required in usual dot-ELISA.

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.

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 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.

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

A new DPYD genotyping assay for improving the safety of 5-fluorouracil therapy.

Science.gov (United States)

Sistonen, Johanna; Smith, Chingying; Fu, Yung-Kang; Largiadèr, Carlo R

2012-12-24

Chemotherapeutic use of 5-fluorouracil (5FU) is compromised by 10-20% of patients developing severe toxicity. Recently described genetic variation in dihydropyrimidine dehydrogenase (DPYD) has been shown to be a major predictor of 5FU toxicity. Here, we describe a new genotyping assay for routine clinical use that covers all the major DPYD risk variants. Genomic regions targeting DPYD risk variants (c.1129-5923C>G, c.1679T>G/A, c.1905+1G>A, c.2846A>T) and additional markers (c.234-123G>C, c.496A>G, c.775A>G) were amplified in a multiplex PCR reaction. The subsequent steps including allele-specific primer extension, hybridization of the primers to a microarray, scanning of the array, and data analysis were automated within the INFINITI® Analyzer (AutoGenomics). The assay was validated by analyzing 107 blood samples obtained from patients previously re-sequenced for the DPYD. The genotypes obtained with the developed assay were 100% concordant with the re-sequencing. The procedure is suitable for routine clinical use since the results are obtained within one day. For heterozygous risk variant carriers (~7% of Europeans), the treatment can be adjusted by 5FU dose reduction, whereas carriers of two risk alleles should be treated with an alternative therapy. The developed assay provides a novel tool to improve the safety of commonly used 5FU-based chemotherapies. Copyright © 2012 Elsevier B.V. All rights reserved.

Genotyping three SNPs affecting warfarin drug response by isothermal real-time HDA assays.

Science.gov (United States)

Li, Ying; Jortani, Saeed A; Ramey-Hartung, Bronwyn; Hudson, Elizabeth; Lemieux, Bertrand; Kong, Huimin

2011-01-14

The response to the anticoagulant drug warfarin is greatly affected by genetic polymorphisms in the VKORC1 and CYP2C9 genes. Genotyping these polymorphisms has been shown to be important in reducing the time of the trial and error process for finding the maintenance dose of warfarin thus reducing the risk of adverse effects of the drug. We developed a real-time isothermal DNA amplification system for genotyping three single nucleotide polymorphisms (SNPs) that influence warfarin response. For each SNP, real-time isothermal Helicase Dependent Amplification (HDA) reactions were performed to amplify a DNA fragment containing the SNP. Amplicons were detected by fluorescently labeled allele specific probes during real-time HDA amplification. Fifty clinical samples were analyzed by the HDA-based method, generating a total of 150 results. Of these, 148 were consistent between the HDA-based assays and a reference method. The two samples with unresolved HDA-based test results were repeated and found to be consistent with the reference method. The HDA-based assays demonstrated a clinically acceptable performance for genotyping the VKORC1 -1639G>A SNP and two SNPs (430C>T and 1075A>C) for the CYP2C9 enzyme (CYP2C9*2 and CYP2C9*3), all of which are relevant in warfarin pharmacogenentics. Copyright © 2010 Elsevier B.V. All rights reserved.

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.

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.

The loss-of-allele assay for ES cell screening and mouse genotyping.

Science.gov (United States)

Frendewey, David; Chernomorsky, Rostislav; Esau, Lakeisha; Om, Jinsop; Xue, Yingzi; Murphy, Andrew J; Yancopoulos, George D; Valenzuela, David M

2010-01-01

Targeting vectors used to create directed mutations in mouse embryonic stem (ES) cells consist, in their simplest form, of a gene for drug selection flanked by mouse genomic sequences, the so-called homology arms that promote site-directed homologous recombination between the vector and the target gene. The VelociGene method for the creation of targeted mutations in ES cells employs targeting vectors, called BACVecs, that are based on bacterial artificial chromosomes. Compared with conventional short targeting vectors, BacVecs provide two major advantages: (1) their much larger homology arms promote high targeting efficiencies without the need for isogenicity or negative selection strategies; and (2) they enable deletions and insertions of up to 100kb in a single targeting event, making possible gene-ablating definitive null alleles and other large-scale genomic modifications. Because of their large arm sizes, however, BACVecs do not permit screening by conventional assays, such as long-range PCR or Southern blotting, that link the inserted targeting vector to the targeted locus. To exploit the advantages of BACVecs for gene targeting, we inverted the conventional screening logic in developing the loss-of-allele (LOA) assay, which quantifies the number of copies of the native locus to which the mutation was directed. In a correctly targeted ES cell clone, the LOA assay detects one of the two native alleles (for genes not on the X or Y chromosome), the other allele being disrupted by the targeted modification. We apply the same principle in reverse as a gain-of-allele assay to quantify the copy number of the inserted targeting vector. The LOA assay reveals a correctly targeted clone as having lost one copy of the native target gene and gained one copy of the drug resistance gene or other inserted marker. The combination of these quantitative assays makes LOA genotyping unequivocal and amenable to automated scoring. We use the quantitative polymerase chain reaction

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.

Integrated cryptosporidium assay to determine oocyst density, infectivity, and genotype for risk assessment of source and reuse water.

Science.gov (United States)

King, Brendon; Fanok, Stella; Phillips, Renae; Swaffer, Brooke; Monis, Paul

2015-05-15

Cryptosporidium continues to be problematic for the water industry, with risk assessments often indicating that treatment barriers may fail under extreme conditions. However, risk analyses have historically used oocyst densities and not considered either oocyst infectivity or species/genotype, which can result in an overestimation of risk if the oocysts are not human infective. We describe an integrated assay for determining oocyst density, infectivity, and genotype from a single-sample concentrate, an important advance that overcomes the need for processing multiple-grab samples or splitting sample concentrates for separate analyses. The assay incorporates an oocyst recovery control and is compatible with standard primary concentration techniques. Oocysts were purified from primary concentrates using immunomagnetic separation prior to processing by an infectivity assay. Plate-based cell culture was used to detect infectious foci, with a monolayer washing protocol developed to allow recovery and enumeration of oocysts. A simple DNA extraction protocol was developed to allow typing of any wells containing infectious Cryptosporidium. Water samples from a variety of source water and wastewater matrices, including a semirural catchment, wastewater, an aquifer recharge site, and storm water, were analyzed using the assay. Results demonstrate that the assay can reliably determine oocyst densities, infectivity, and genotype from single-grab samples for a variety of water matrices and emphasize the varying nature of Cryptosporidium risk extant throughout source waters and wastewaters. This assay should therefore enable a more comprehensive understanding of Cryptosporidium risk for different water sources, assisting in the selection of appropriate risk mitigation measures. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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

Development and evaluation of novel one-step TaqMan realtime RT-PCR assays for the detection and direct genotyping of genogroup I and II noroviruses

DEFF Research Database (Denmark)

Schultz, Anna Charlotte; Vega, Everado; Dalsgaard, Anders

2011-01-01

BackgroundCurrent detection and genotyping methods of genogroup (G) I and II noroviruses (NoVs) consist of a 2-step approach including detection of viral RNA by TaqMan realtime RT-PCR (RT-qPCR) followed by conventional RT-PCR and sequencing of partial regions of ORF1 or ORF2. ObjectiveTo develop ......Man RT-qPCR assays for the sensitive detection and direct genotyping of GI and GII NoVs from clinical and environmental matrices...... novel long-template one-step TaqMan assays (L-RT-qPCR) for the rapid detection and direct genotyping of GI and GII NoVs and to evaluate the sensitivity and specificity of the assays. Study designGI and GII-specific broadly reactive L-RT-qPCR assays were developed by combining existing NoV primers...... and probes targeting the open reading frame (ORF)1–ORF2 junction as well as region C at the 5′–ORF2. The assays were validated using GI and GII RNA transcripts and a coded panel of 75 stool samples containing NoV strains representing 9 GI genotypes and 12 GII genotypes, as well as sapoviruses, astroviruses...

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.

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)

Utility and diagnostic performance of Mycobacterium tuberculosis complex by two immunochromatographic assays as compared with the molecular Genotype assay in Nigeria

Directory of Open Access Journals (Sweden)

Benjamin Thumamo Pokam

2013-01-01

Full Text Available Among the disadvantages of smear microscopy for detection of tuberculosis cases is its inability to differentiate between Mycobacterium tuberculosis (MTB and non-tuberculous mycobacteria (NTM. This study evaluated two, new immunochromatographic assays – Capilia TB-Neo and SD Bioline – on unheated and heated cultures at 80 °C for 30 min respectively for their ability to discriminate between MTB complex and NTM as compared with the molecular Genotype assay. Mycobacteria used in the study were obtained from smear-positive specimens collected from patients at four major hospitals in Cross River State, Nigeria. Capilia TB-Neo and SD Bioline showed sensitivities of 98.8% and 93.8% respectively and 100% specificity for both assays. Heating the isolates did not significantly impact the test performance. Both tests are recommended for use in rapid differentiation of strains isolated in Nigeria.

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.

High performance of a new PCR-based urine assay for HPV-DNA detection and genotyping.

Science.gov (United States)

Tanzi, Elisabetta; Bianchi, Silvia; Fasolo, Maria Michela; Frati, Elena R; Mazza, Francesca; Martinelli, Marianna; Colzani, Daniela; Beretta, Rosangela; Zappa, Alessandra; Orlando, Giovanna

2013-01-01

Human papillomavirus (HPV) testing has been proposed as a means of replacing or supporting conventional cervical screening (Pap test). However, both methods require the collection of cervical samples. Urine sample is easier and more acceptable to collect and could be helpful in facilitating cervical cancer screening. The aim of this study was to evaluate the sensitivity and specificity of urine testing compared to conventional cervical smear testing using a PCR-based method with a new, designed specifically primer set. Paired cervical and first voided urine samples collected from 107 women infected with HIV were subjected to HPV-DNA detection and genotyping using a PCR-based assay and a restriction fragment length polymorphism method. Sensitivity, specificity, Positive Predictive Value (PPV), and Negative Predictive Value (NPV) were calculated using the McNemar's test for differences. Concordance between tests was assessed using the Cohen's unweighted Kappa (k). HPV DNA was detected in 64.5% (95% CI: 55.1-73.1%) of both cytobrush and urine samples. High concordance rates of HPV-DNA detection (k = 0.96; 95% CI: 0.90-1.0) and of high risk-clade and low-risk genotyping in paired samples (k = 0.80; 95% CI: 0.67-0.92 and k = 0.74; 95% CI: 0.60-0.88, respectively) were observed. HPV-DNA detection in urine versus cervix testing revealed a sensitivity of 98.6% (95% CI: 93.1-99.9%) and a specificity of 97.4% (95% CI: 87.7-99.9%), with a very high NPV (97.4%; 95% CI: 87.7-99.9%). The PCR-based assay utilized in this study proved highly sensitive and specific for HPV-DNA detection and genotyping in urine samples. These data suggest that a urine-based assay would be a suitable and effective tool for epidemiological surveillance and, most of all, screening programs. Copyright © 2012 Wiley Periodicals, Inc.

Multiplex pyrosequencing assay using AdvISER-MH-PYRO algorithm: a case for rapid and cost-effective genotyping analysis of prostate cancer risk-associated SNPs.

Science.gov (United States)

Ambroise, Jérôme; Butoescu, Valentina; Robert, Annie; Tombal, Bertrand; Gala, Jean-Luc

2015-06-25

Single Nucleotide Polymorphisms (SNPs) identified in Genome Wide Association Studies (GWAS) have generally moderate association with related complex diseases. Accordingly, Multilocus Genetic Risk Scores (MGRSs) have been computed in previous studies in order to assess the cumulative association of multiple SNPs. When several SNPs have to be genotyped for each patient, using successive uniplex pyrosequencing reactions increases analytical reagent expenses and Turnaround Time (TAT). While a set of several pyrosequencing primers could theoretically be used to analyze multiplex amplicons, this would generate overlapping primer-specific pyro-signals that are visually uninterpretable. In the current study, two multiplex assays were developed consisting of a quadruplex (n=4) and a quintuplex (n=5) polymerase chain reaction (PCR) each followed by multiplex pyrosequencing analysis. The aim was to reliably but rapidly genotype a set of prostate cancer-related SNPs (n=9). The nucleotide dispensation order was selected using SENATOR software. Multiplex pyro-signals were analyzed using the new AdvISER-MH-PYRO software based on a sparse representation of the signal. Using uniplex assays as gold standard, the concordance between multiplex and uniplex assays was assessed on DNA extracted from patient blood samples (n = 10). All genotypes (n=90) generated with the quadruplex and the quintuplex pyroquencing assays were perfectly (100 %) concordant with uniplex pyrosequencing. Using multiplex genotyping approach for analyzing a set of 90 patients allowed reducing TAT by approximately 75 % (i.e., from 2025 to 470 min) while reducing reagent consumption and cost by approximately 70 % (i.e., from ~229 US$ /patient to ~64 US$ /patient). This combination of quadruplex and quintuplex pyrosequencing and PCR assays enabled to reduce the amount of DNA required for multi-SNP analysis, and to lower the global TAT and costs of SNP genotyping while providing results as reliable as uniplex

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.

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.

Evaluation of genotype MTBDRplus assay for rapid detection of isoniazid and rifampicin resistance in Mycobacterium tuberculosis clinical isolates from Pakistan

Directory of Open Access Journals (Sweden)

Hasnain Javed

2016-01-01

Conclusions: As evidenced in this study, the major concern with the GenoType MTBDRplus assay were false negative results. In comparison to conventional drug susceptibility testing, the assay was unable to detect 30 (30/100; 30% strains resistant to INH and 23 (23/100; 23% strains resistant to RMP. The GenoType MTBDRplus failed to identify 38 MDR (38/100; 38% strains. Resistance in those strains probably originate from mutations in other codons and/or genes than those covered by the test. For detecting INH and RMP resistance in TB cases, especially in high TB incidence countries, such as Pakistan, molecular approaches should still be a complement rather than areplacement to conventional drug susceptibility testing.

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

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.

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.)

A Dual Electrochemical Sensor Based on a Test-strip Assay for the Quantitative Determination of Albumin and Creatinine.

Science.gov (United States)

Yasukawa, Tomoyuki; Kiba, Yuya; Mizutani, Fumio

2015-01-01

A dual-electrochemical sensor based on a test-strip assay with immunochemistry and enzyme reactions has been developed for the determination of albumin and creatinine. Each nitrocellulose membrane with an immobilization area of an anti-albumin antibody or three enzymes was prepared in the device with three working electrodes for measuring albumin, creatinine, and ascorbic acid, as well as an Ag/AgCl electrode used as a counter/pseudo-reference electrode. The reactions of three enzymes were initiated by flowing a solution containing creatinine to detect an oxidation current of hydrogen peroxide. A sandwich-type immunocomplex was formed by albumin and antibody labeled with glucose oxidase (GOx). Captured GOx catalyzed the reduction of Fe(CN)6(3-) to Fe(CN)6(4-), which was oxidized electrochemically to determine the captured albumin. The responses for creatinine and albumin increased with the concentrations in millimolar order and over the range 18.75 - 150 μg mL(-1), respectively. The present sensor would be a distinct demonstration for producing quantitative dual-assays for various biomolecules used for clinical diagnoses.

Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies.

Science.gov (United States)

McGovern, Rachel A; Thielen, Alexander; Mo, Theresa; Dong, Winnie; Woods, Conan K; Chapman, Douglass; Lewis, Marilyn; James, Ian; Heera, Jayvant; Valdez, Hernan; Harrigan, P Richard

2010-10-23

The MOTIVATE-1 and 2 studies compared maraviroc (MVC) along with optimized background therapy (OBT) vs. placebo along with OBT in treatment-experienced patients screened as having R5-HIV (original Monogram Trofile). A subset screened with non-R5 HIV were treated with MVC or placebo along with OBT in a sister safety trial, A4001029. This analysis retrospectively examined the performance of population-based sequence analysis of HIV-1 env V3-loop to predict coreceptor tropism. Triplicate V3-loop sequences were generated using stored screening plasma samples and data was processed using custom software ('ReCall'), blinded to clinical response. Tropism was inferred using geno2pheno ('g2p'; 5% false positive rate). Primary outcomes were viral load changes after starting maraviroc; and concordance with prior screening Trofile results. Genotype and Trofile results were available for 1164 individuals with virological outcome data (N = 169 non-R5 by Trofile). Compared with Trofile, V3 genotyping had a specificity of 92.6% and a sensitivity of 67.4% for detecting non-R5 virus. However, when compared with clinical outcome, virological responses were consistently similar between Trofile and V3 genotype at weeks 8 and 24 following the initiation of therapy for patients categorized as R5. Despite differences in sensitivity for predicting non-R5 HIV, week 8 and 24 week virological responses were similar in this treatment-experienced population. These findings suggest the potential utility of V3 genotyping as an accessible assay to select patients who may benefit from maraviroc treatment. Optimization of the predictive tropism algorithm may lead to further improvement in the clinical utility of HIV genotypic tropism assays.

[Evaluation of hepatitis B virus genotyping EIA kit].

Science.gov (United States)

Tanaka, Yasuhito; Sugauchi, Fuminaka; Matsuuraa, Kentaro; Naganuma, Hatsue; Tatematsu, Kanako; Takagi, Kazumi; Hiramatsu, Kumiko; Kani, Satomi; Gotoh, Takaaki; Wakimoto, Yukio; Mizokami, Masashi

2009-01-01

Clinical significance of Hepatitis B virus(HBV) genotyping is increasingly recognized. The aim of this study was to evaluate reproducibility, accuracy, and sensitivity of an enzyme immunoassay (EIA) based HBV genotyping kit, which designed to discriminate between genotypes to A, B, C, or D by detecting genotype-specific epitopes in PreS2 region. Using the four genotypes panels, the EIA demonstrated complete inter and intra-assay genotyping reproducibility. Serum specimens had stable results after 8 days at 4 degrees C, or 10 cycles of freezing-thawing. In 91 samples that have been genotyped by DNA sequencing, 87(95.6%) were in complete accordance with EIA genotyping. Of examined 344 HBsAg-positive serum specimens, genotypes A, B, C and D were determined in 26 (7.6%), 62 (18.0%), 228 (66.3%), and 9 (2.6%) cases, respectively. Of 19 (5.5%) specimens unclassified by the EIA, 13 were found to have low titer of HBsAg concentration (< 3 IU/ml), and the other 5 had amino acid mutations or deletions within targeted PreS2 epitopes. The EIA allowed genotyping even in HBV DNA negative samples (96.2%). In conclusion, HBV genotype EIA is reliable, sensitive and easy assay for HBV genotyping. The assay would be useful for clinical use.

Noninvasive Personalization of Lung Cancer Therapy Using a New, Clinical-Grade Assay for Plasma-Based Measurement and Monitoring of Tumor Genotype

Science.gov (United States)

2016-12-01

funding to launch our plasma assay as a clinical test at Brigham and Women’s Hospital . With this assay, I have launched an investigator-sponsored trial...Manager [Recently Completed] Phi Beta Psi Charity Trust (Oxnard) 08/15/14 – 08/14/16 *0.00 CM Non-invasive genotyping realized at last...Harvard University, MA BA 06/1999 Chemistry University of Chicago, Pritzker School of Medicine, IL MD 06/2005 Medicine Massachusetts General Hospital

Strip interpolation in silicon and germanium strip detectors

International Nuclear Information System (INIS)

Wulf, E. A.; Phlips, B. F.; Johnson, W. N.; Kurfess, J. D.; Lister, C. J.; Kondev, F.; Physics; Naval Research Lab.

2004-01-01

The position resolution of double-sided strip detectors is limited by the strip pitch and a reduction in strip pitch necessitates more electronics. Improved position resolution would improve the imaging capabilities of Compton telescopes and PET detectors. Digitizing the preamplifier waveform yields more information than can be extracted with regular shaping electronics. In addition to the energy, depth of interaction, and which strip was hit, the digitized preamplifier signals can locate the interaction position to less than the strip pitch of the detector by looking at induced signals in neighboring strips. This allows the position of the interaction to be interpolated in three dimensions and improve the imaging capabilities of the system. In a 2 mm thick silicon strip detector with a strip pitch of 0.891 mm, strip interpolation located the interaction of 356 keV gamma rays to 0.3 mm FWHM. In a 2 cm thick germanium detector with a strip pitch of 5 mm, strip interpolation of 356 keV gamma rays yielded a position resolution of 1.5 mm FWHM

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.

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

Science.gov (United States)

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

2016-03-01

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

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

Science.gov (United States)

2011-01-01

Background High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across

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.)

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.

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

methods has not been well characterized. Clinically, cytology is used to establish possible HPV infection. We evaluated the sensitivity and specificity of HPV multiplex PCR assays compared to those of the testing scheme of the Hybrid Capture II (HCII) assay followed by an HPV PCR/line hybridization assay...... (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...... were evaluated for 15 HPV types common in both assays. A slightly higher proportion of samples tested positive by the HPV multiplex PCR than by the HCII-LiPA v2 assay. The sensitivities of the multiplex PCR assay relative to those of the HCII-LiPA v2 assay for HPV types 6, 11, 16, and 18, for example...

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.

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.

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.

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.

Evaluation of the genotypic prediction of HIV-1 coreceptor use versus a phenotypic assay and correlation with the virological response to maraviroc: the ANRS GenoTropism study.

Science.gov (United States)

Recordon-Pinson, Patricia; Soulié, Cathia; Flandre, Philippe; Descamps, Diane; Lazrek, Mouna; Charpentier, Charlotte; Montes, Brigitte; Trabaud, Mary-Anne; Cottalorda, Jacqueline; Schneider, Véronique; Morand-Joubert, Laurence; Tamalet, Catherine; Desbois, Delphine; Macé, Muriel; Ferré, Virginie; Vabret, Astrid; Ruffault, Annick; Pallier, Coralie; Raymond, Stéphanie; Izopet, Jacques; Reynes, Jacques; Marcelin, Anne-Geneviève; Masquelier, Bernard

2010-08-01

Genotypic algorithms for prediction of HIV-1 coreceptor usage need to be evaluated in a clinical setting. We aimed at studying (i) the correlation of genotypic prediction of coreceptor use in comparison with a phenotypic assay and (ii) the relationship between genotypic prediction of coreceptor use at baseline and the virological response (VR) to a therapy including maraviroc (MVC). Antiretroviral-experienced patients were included in the MVC Expanded Access Program if they had an R5 screening result with Trofile (Monogram Biosciences). V3 loop sequences were determined at screening, and coreceptor use was predicted using 13 genotypic algorithms or combinations of algorithms. Genotypic predictions were compared to Trofile; dual or mixed (D/M) variants were considered as X4 variants. Both genotypic and phenotypic results were obtained for 189 patients at screening, with 54 isolates scored as X4 or D/M and 135 scored as R5 with Trofile. The highest sensitivity (59.3%) for detection of X4 was obtained with the Geno2pheno algorithm, with a false-positive rate set up at 10% (Geno2pheno10). In the 112 patients receiving MVC, a plasma viral RNA load of <50 copies/ml was obtained in 68% of cases at month 6. In multivariate analysis, the prediction of the X4 genotype at baseline with the Geno2pheno10 algorithm including baseline viral load and CD4 nadir was independently associated with a worse VR at months 1 and 3. The baseline weighted genotypic sensitivity score was associated with VR at month 6. There were strong arguments in favor of using genotypic coreceptor use assays for determining which patients would respond to CCR5 antagonist.

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.

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

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.

Saccharification Performances of Miscanthus at the Pilot and Miniaturized Assay Scales: Genotype and Year Variabilities According to the Biomass Composition

Directory of Open Access Journals (Sweden)

Nassim Belmokhtar

2017-05-01

Full Text Available HIGHLIGHTSBiomass production and cell wall composition are differentially impacted by harvesting year and genotypes, influencing then cellulose conversion in miniaturized assay.Using a high-throughput miniaturized and semi-automated method for performing the pretreatment and saccharification steps at laboratory scale allows for the assessment of these factors on the biomass potential for producing bioethanol before moving to the industrial scale.The large genetic diversity of the perennial grass miscanthus makes it suitable for producing cellulosic ethanol in biorefineries. The saccharification potential and year variability of five genotypes belonging to Miscanthus × giganteus and Miscanthus sinensis were explored using a miniaturized and semi-automated method, allowing the application of a hot water treatment followed by an enzymatic hydrolysis. The studied genotypes highlighted distinct cellulose conversion yields due to their distinct cell wall compositions. An inter-year comparison revealed significant variations in the biomass productivity and cell wall compositions. Compared to the recalcitrant genotypes, more digestible genotypes contained higher amounts of hemicellulosic carbohydrates and lower amounts of cellulose and lignin. In contrast to hemicellulosic carbohydrates, the relationships analysis between the biomass traits and cellulose conversion clearly showed the same negative effect of cellulose and lignin on cellulose digestion. The miniaturized and semi-automated method we developed was usable at the laboratory scale and was reliable for mimicking the saccharification at the pilot scale using a steam explosion pretreatment and enzymatic hydrolysis. Therefore, this miniaturized method will allow the reliable screening of many genotypes for saccharification potential. These findings provide valuable information and tools for breeders to create genotypes combining high yield, suitable biomass composition, and high saccharification

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

Two-temperature LATE-PCR endpoint genotyping

Directory of Open Access Journals (Sweden)

Reis Arthur H

2006-12-01

Full Text Available Abstract Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of

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.

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

OpenAIRE

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

2015-01-01

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

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.

Prevalence of H63D, S65C and C282Y hereditary hemochromatosis gene mutations in Slovenian population by an improved high-throughput genotyping assay

Directory of Open Access Journals (Sweden)

Rupreht Ruth

2007-11-01

Full Text Available Abstract Background Hereditary hemochromatosis (HH is a common genetic disease characterized by excessive iron overload that leads to multi-organ failure. Although the most prevalent genotype in HH is homozygosity for C282Y mutation of the HFE gene, two additional mutations, H63D and S65C, appear to be associated with a milder form of HH. The aim of this study was to develop a high-throughput assay for HFE mutations screening based on TaqMan technology and to determine the frequencies of HFE mutations in the Slovenian population. Methods Altogether, 1282 randomly selected blood donors from different Slovenian regions and 21 HH patients were analyzed for the presence of HFE mutations by an in-house developed real-time PCR assay based on TaqMan technology using shorter non-interfering fluorescent single nucleotide polymorphism (SNP-specific MGB probes. The assay was validated by RFLP analysis and DNA sequencing. Results The genotyping assay of the H63D, S65C and C282Y mutations in the HFE gene, based on TaqMan technology proved to be fast, reliable, with a high-throughput capability and 100% concordant with genotypes obtained by RFLP and DNA sequencing. The observed frequency of C282Y homozygotes in the group of HH patients was only 48%, others were of the heterogeneous HFE genotype. Among 1282 blood donors tested, the observed H63D, S65C and C282Y allele frequency were 12.8% (95% confidence interval (CI 11.5 – 14.2%, 1.8% (95% CI 1.4 – 2.5% and 3.6% (95% CI 3.0 – 4.5%, respectively. Approximately 33% of the tested subjects had at least one of the three HH mutations, and 1% of them were C282Y homozygotes or compound heterozygotes C282Y/H63D or C282Y/S65C, presenting an increased risk for iron overload disease. A significant variation in H63D allele frequency was observed for one of the Slovenian regions. Conclusion The improved real-time PCR assay for H63D, S65C and C282Y mutations detection is accurate, fast, cost-efficient and ready for

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%,

RHD genotype and zygosity analysis in the Chinese Southern Han D plus , D- and D variant donors using the multiplex ligation-dependent probe amplification assay

NARCIS (Netherlands)

Ji, Y. L.; Luo, H.; Wen, J. Z.; Haer-Wigman, L.; Veldhuisen, B.; Wei, L.; Wang, Z.; Ligthart, P.; Lodén-van Straaten, M.; Fu, Y. S.; van der Schoot, C. E.; Luo, G. P.

2017-01-01

Background and ObjectivesSeveral comprehensive genotyping platforms for determining red blood cell (RBC) antigens have been established and validated for use in the Caucasian and Black populations, but not for the Chinese. The multiplex ligation-dependent probe amplification (MLPA) assay was

High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification

Directory of Open Access Journals (Sweden)

Sun Zhenyu

2001-08-01

Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the foundation of powerful complex trait and pharmacogenomic analyses. The availability of large SNP databases, however, has emphasized a need for inexpensive SNP genotyping methods of commensurate simplicity, robustness, and scalability. We describe a solution-based, microtiter plate method for SNP genotyping of human genomic DNA. The method is based upon allele discrimination by ligation of open circle probes followed by rolling circle amplification of the signal using fluorescent primers. Only the probe with a 3' base complementary to the SNP is circularized by ligation. Results SNP scoring by ligation was optimized to a 100,000 fold discrimination against probe mismatched to the SNP. The assay was used to genotype 10 SNPs from a set of 192 genomic DNA samples in a high-throughput format. Assay directly from genomic DNA eliminates the need to preamplify the target as done for many other genotyping methods. The sensitivity of the assay was demonstrated by genotyping from 1 ng of genomic DNA. We demonstrate that the assay can detect a single molecule of the circularized probe. Conclusions Compatibility with homogeneous formats and the ability to assay small amounts of genomic DNA meets the exacting requirements of automated, high-throughput SNP scoring.

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

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.

A luciferase reporter gene assay and aryl hydrocarbon receptor 1 genotype predict the LD50 of polychlorinated biphenyls in avian species

International Nuclear Information System (INIS)

Manning, Gillian E.; Farmahin, Reza; Crump, Doug; Jones, Stephanie P.; Klein, Jeff; Konstantinov, Alex; Potter, Dave; Kennedy, Sean W.

2012-01-01

Birds differ in sensitivity to the embryotoxic effects of polychlorinated biphenyls (PCBs), which complicates environmental risk assessments for these chemicals. Recent research has shown that the identities of amino acid residues 324 and 380 in the avian aryl hydrocarbon receptor 1 (AHR1) ligand binding domain (LBD) are primarily responsible for differences in avian species sensitivity to selected dibenzo-p-dioxins and furans. A luciferase reporter gene (LRG) assay was developed in our laboratory to measure AHR1-mediated induction of a cytochrome P450 1A5 reporter gene in COS-7 cells transfected with different avian AHR1 constructs. In the present study, the LRG assay was used to measure the concentration-dependent effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and PCBs 126, 77, 105 and 118 on luciferase activity in COS-7 cells transfected with AHR1 constructs representative of 86 avian species in order to predict their sensitivity to PCB-induced embryolethality and the relative potency of PCBs in these species. The results of the LRG assay indicate that the identity of amino acid residues 324 and 380 in the AHR1 LBD are the major determinants of avian species sensitivity to PCBs. The relative potency of PCBs did not differ greatly among AHR1 constructs. Luciferase activity was significantly correlated with embryolethality data obtained from the literature (R 2 ≥ 0.87, p < 0.0001). Thus, the LRG assay in combination with the knowledge of a species' AHR1 LBD sequence can be used to predict PCB-induced embryolethality in potentially any avian species of interest without the use of lethal methods on a large number of individuals. -- Highlights: ► PCB embryolethality in birds can be predicted from a species' AHR1 genotype. ► The reporter gene assay is useful for predicting species sensitivity to PCBs. ► The relative potency of PCBs does not appear to differ between AHR1 genotypes. ► Contamination of PCB 105 and PCB 118 did not affect their relative

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...

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

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

African Journals Online (AJOL)

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 ...

Evaluation of Nobuto filter paper strips for the detection of avian influenza virus antibody in waterfowl

Science.gov (United States)

Dusek, Robert J.; Hall, Jeffrey S.; Nashold, Sean W.; Teslaa, Joshua L.; Ip, Hon S.

2011-01-01

The utility of using Nobuto paper strips for the detection of avian influenza antibodies was examined in mallards (Anas platyrhynchos) experimentally infected with low pathogenic avian influenza viruses. Blood was collected 2 wk after infection and was preserved either as serum or whole blood absorbed onto Nobuto strips. Analysis of samples using a commercially available blocking enzyme-linked immunosorbent assay revealed comparable results (???96% sensitivity for all methods) between sera stored at -30 C and the Nobuto strip preservation method even when the Nobuto strips were stored up to 3 mo at room temperature (RT). Significant differences were detected in the ratio of sample absorbance to negative control absorbance for Nobuto strips stored at RT compared with sera stored at -30 C, although these differences did not affect the ability of the test to reliably detect positive and negative samples. Nobuto strips are a convenient and sensitive alternative to the collection of serum samples when maintaining appropriate storage temperatures is difficult. ?? 2011 American Association of Avian Pathologists.

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.

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

International Nuclear Information System (INIS)

Gao, Hongfei; Han, Jing; Yang, Shijia; Wang, Zhenxing; Wang, Lin; Fu, Zhifeng

2014-01-01

Graphical abstract: A multianalyte immunochromatographic test strip was developed for the rapid detection of two β 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 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 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 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 −1 , with the detection limits of 0.20 and 0.040 ng mL −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 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

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.

Model for prediction of strip temperature in hot strip steel mill

International Nuclear Information System (INIS)

Panjkovic, Vladimir

2007-01-01

Proper functioning of set-up models in a hot strip steel mill requires reliable prediction of strip temperature. Temperature prediction is particularly important for accurate calculation of rolling force because of strong dependence of yield stress and strip microstructure on temperature. A comprehensive model was developed to replace an obsolete model in the Western Port hot strip mill of BlueScope Steel. The new model predicts the strip temperature evolution from the roughing mill exit to the finishing mill exit. It takes into account the radiative and convective heat losses, forced flow boiling and film boiling of water at strip surface, deformation heat in the roll gap, frictional sliding heat, heat of scale formation and the heat transfer between strip and work rolls through an oxide layer. The significance of phase transformation was also investigated. Model was tested with plant measurements and benchmarked against other models in the literature, and its performance was very good

Model for prediction of strip temperature in hot strip steel mill

Energy Technology Data Exchange (ETDEWEB)

Panjkovic, Vladimir [BlueScope Steel, TEOB, 1 Bayview Road, Hastings Vic. 3915 (Australia)]. E-mail: Vladimir.Panjkovic@BlueScopeSteel.com

2007-10-15

Proper functioning of set-up models in a hot strip steel mill requires reliable prediction of strip temperature. Temperature prediction is particularly important for accurate calculation of rolling force because of strong dependence of yield stress and strip microstructure on temperature. A comprehensive model was developed to replace an obsolete model in the Western Port hot strip mill of BlueScope Steel. The new model predicts the strip temperature evolution from the roughing mill exit to the finishing mill exit. It takes into account the radiative and convective heat losses, forced flow boiling and film boiling of water at strip surface, deformation heat in the roll gap, frictional sliding heat, heat of scale formation and the heat transfer between strip and work rolls through an oxide layer. The significance of phase transformation was also investigated. Model was tested with plant measurements and benchmarked against other models in the literature, and its performance was very good.

A luciferase reporter gene assay and aryl hydrocarbon receptor 1 genotype predict the LD{sub 50} of polychlorinated biphenyls in avian species

Energy Technology Data Exchange (ETDEWEB)

Manning, Gillian E., E-mail: gmann017@uottawa.ca [Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5 (Canada); Environment Canada, National Wildlife Research Centre, Ottawa, ON, Canada K1A 0H3 (Canada); Farmahin, Reza, E-mail: mfarm070@uottawa.ca [Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5 (Canada); Environment Canada, National Wildlife Research Centre, Ottawa, ON, Canada K1A 0H3 (Canada); Crump, Doug, E-mail: doug.crump@ec.gc.ca [Environment Canada, National Wildlife Research Centre, Ottawa, ON, Canada K1A 0H3 (Canada); Jones, Stephanie P., E-mail: stephanie.jones@ec.gc.ca [Environment Canada, National Wildlife Research Centre, Ottawa, ON, Canada K1A 0H3 (Canada); Klein, Jeff, E-mail: jeffery@well-labs.com [Wellington Laboratories Inc., Research Division, Guelph, ON, Canada N1G 3M5 (Canada); Konstantinov, Alex, E-mail: alex@well-labs.com [Wellington Laboratories Inc., Research Division, Guelph, ON, Canada N1G 3M5 (Canada); Potter, Dave, E-mail: dpotter@well-labs.com [Wellington Laboratories Inc., Research Division, Guelph, ON, Canada N1G 3M5 (Canada); Kennedy, Sean W., E-mail: sean.kennedy@ec.gc.ca [Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5 (Canada); Environment Canada, National Wildlife Research Centre, Ottawa, ON, Canada K1A 0H3 (Canada)

2012-09-15

Birds differ in sensitivity to the embryotoxic effects of polychlorinated biphenyls (PCBs), which complicates environmental risk assessments for these chemicals. Recent research has shown that the identities of amino acid residues 324 and 380 in the avian aryl hydrocarbon receptor 1 (AHR1) ligand binding domain (LBD) are primarily responsible for differences in avian species sensitivity to selected dibenzo-p-dioxins and furans. A luciferase reporter gene (LRG) assay was developed in our laboratory to measure AHR1-mediated induction of a cytochrome P450 1A5 reporter gene in COS-7 cells transfected with different avian AHR1 constructs. In the present study, the LRG assay was used to measure the concentration-dependent effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and PCBs 126, 77, 105 and 118 on luciferase activity in COS-7 cells transfected with AHR1 constructs representative of 86 avian species in order to predict their sensitivity to PCB-induced embryolethality and the relative potency of PCBs in these species. The results of the LRG assay indicate that the identity of amino acid residues 324 and 380 in the AHR1 LBD are the major determinants of avian species sensitivity to PCBs. The relative potency of PCBs did not differ greatly among AHR1 constructs. Luciferase activity was significantly correlated with embryolethality data obtained from the literature (R{sup 2} ≥ 0.87, p < 0.0001). Thus, the LRG assay in combination with the knowledge of a species' AHR1 LBD sequence can be used to predict PCB-induced embryolethality in potentially any avian species of interest without the use of lethal methods on a large number of individuals. -- Highlights: ► PCB embryolethality in birds can be predicted from a species' AHR1 genotype. ► The reporter gene assay is useful for predicting species sensitivity to PCBs. ► The relative potency of PCBs does not appear to differ between AHR1 genotypes. ► Contamination of PCB 105 and PCB 118 did not affect

Rapid identification of tomato Sw-5 resistance-breaking isolates of Tomato spotted wilt virus using high resolution melting and TaqMan SNP Genotyping assays as allelic discrimination techniques.

Directory of Open Access Journals (Sweden)

Valentina di Rienzo

Full Text Available In tomato, resistance to Tomato spotted wilt virus (TSWV is conferred by the dominant gene, designated Sw-5. Virulent Sw-5 resistance breaking (SRB mutants of TSWV have been reported on Sw-5 tomato cultivars. Two different PCR-based allelic discrimination techniques, namely Custom TaqMan™ SNP Genotyping and high-resolution melting (HRM assays, were developed and compared for their ability to distinguish between avirulent (Sw-5 non-infecting, SNI and SRB biotypes. TaqMan assays proved to be more sensitive (threshold of detection in a range of 50-70 TSWV RNA copies and more reliable than HRM, assigning 25 TSWV isolates to their correct genotype with an accuracy of 100%. Moreover, the TaqMan SNP assays were further improved developing a rapid and simple protocol that included crude leaf extraction for RNA template preparations. On the other hand, HRM assays showed higher levels of sensitivity than TaqMan when used to co-detect both biotypes in different artificial mixtures. These diagnostic assays contributed to gain preliminary information on the epidemiology of TSWV isolates in open field conditions. In fact, the presented data suggest that SRB isolates are present as stable populations established year round, persisting on both winter (globe artichoke and summer (tomato crops, in the same cultivated areas of Southern Italy.

Prototheca zopfii genotypes isolated from cow barns and bovine mastitis in Japan.

Science.gov (United States)

Osumi, Takafumi; Kishimoto, Yuji; Kano, Rui; Maruyama, Haruhiko; Onozaki, Masanobu; Makimura, Koichi; Ito, Takaaki; Matsubara, Kiyoshi; Hasegawa, Atsuhiko

2008-10-15

This study is the first investigation on Japanese isolates of Prototheca zopfii from bovine mastitis and the cow-barn surroundings by molecular characterization to clarify routes of infection for bovine protothecal mastitis. We performed isolation of Prototheca from cow-barn surroundings (drinking water, sewage and feces) and milk samples from cases of bovine mastitis. Genotypes of the 32 isolates of P. zopfii from cow-barn surroundings and 67 isolates from mastitis were analyzed by genotype-specific PCR assays and restriction fragment length polymorphism (RFLP) assays. All mastitis isolates were identified as P. zopfii genotype 2. Conversely, 29 isolates from cow-barn surroundings were identified as P. zopfii genotypes 1 and 3 isolates as genotype 2, respectively. Given these results, both genotypes of P. zopfii could exist in cow-barn surroundings, but no sites were identified as frequent sources of P. zopfii genotype 2. P. zopfii isolates should thus be further explored with regard to genotype to clarify the reservoir of etiological agents in bovine Prototheca mastitis.

Development of a one-step immunochromatographic strip test for the detection of sennosides A and B.

Science.gov (United States)

Putalun, Waraporn; Morinaga, Osamu; Tanaka, Hiroyuki; Shoyama, Yukihiro

2004-01-01

An immunochromatographic strip test was developed to detect sennoside A (1) and sennoside B (2) using anti-1 and anti-2 monoclonal antibodies. The qualitative assay was based on a competitive immunoassay in which the detector reagent consisted of colloidal gold particles coated with the respective sennoside antibodies. The capture reagents were 1- and 2-human serum albumin (HSA) conjugates immobilised on a nitrocellulose membrane on the test strip. The sample containing 1 and 2, together with detector reagent, passed over the zone where the capture reagents had been immobilised. The analytes in the sample competed for binding to the limited amount of antibodies in the detector reagent with the immobilised 1- and 2-HSA conjugates on the membrane and hence positive samples showed no colour in the capture spot zone. Detection limits for the strip test were 125 ng/mL for both sennosides. The assay system is useful as a rapid and simple screening method for the detection of 1 and 2 in plants, drugs and body fluids.

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.

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.

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.

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�

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.

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.

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)

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.

Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application using GoldenGate medium-throughput genotyping assays.

Science.gov (United States)

Bester-Van Der Merwe, Aletta; Blaauw, Sonja; Du Plessis, Jana; Roodt-Wilding, Rouvay

2013-09-23

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 (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.

Rapid diagnosis of drug resistance to fluoroquinolones, amikacin, capreomycin, kanamycin and ethambutol using genotype MTBDRsl assay: a meta-analysis.

Directory of Open Access Journals (Sweden)

Yan Feng

Full Text Available BACKGROUND: There are urgent needs for rapid and accurate drug susceptibility testing of M. tuberculosis. GenoType MTBDRsl is a new molecular kit designed for rapid identification of the resistance to the second-line antituberculosis drugs with a single strip. In recent years, it has been evaluated in many settings, but with varied results. The aim of this meta-analysis was to synthesize the latest data on the diagnostic accuracy of GenoType MTBDRsl in detecting drug resistance to fluoroquinolones, amikacin, capreomycin, kanamycin and ethambutol, in comparison with the phenotypic drug susceptibility test. METHODS: This systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA guideline. The search terms of "MTBDRsl" and "tuberculosis" were used on PubMed, EMBASE, and Web of Science. QUADAS-2 was used to assess the quality of included studies. Data were analyzed by Meta-Disc 1.4. We calculated the sensitivity, specificity, positive likelihood ratio (PLR, negative likelihood ratio (NLR, diagnostic odds ratio (DOR and corresponding 95% confidence interval (CI for each study. From these calculations, forest plots and summary receiver operating characteristic (SROC curves were produced. RESULTS: Patient selection bias as well as flow and timing bias were observed in most studies. The summarized sensitivity (95% CI was 0.874(0.845-0.899, 0.826(0.777-0.869, 0.820(0.772-0.862, 0.444(0.396-0.492, and 0.679(0.652-0.706 for fluoroquinolones, amikacin, capreomycin, kanamycin, and ethambutol, respectively. The specificity (95% CI was 0.971(0.961-0.980, 0.995(0.987-0.998, 0.973(0.963-0.981, 0.993(0.985-0.997, and 0.799(0.773-0.823, respectively. The AUC (standard error were 0.9754(0.0203, 0.9300(0.0598, 0.9885(0.0038, 0.9689(0.0359, and 0.6846(0.0550, respectively. CONCLUSION: Genotype MTBDRsl showed good accuracy for detecting drug resistance to fluoroquinolones, amikacin and capreomycin, but it may not be an

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

Development of an immunochromatographic assay for the rapid detection of bromoxynil in water

International Nuclear Information System (INIS)

Zhu Jiang; Chen Wenchao; Lu Yitong; Cheng Guohua

2008-01-01

A rapid immunochromatographic one-step strip test was developed to specifically determine bromoxynil in surface and drinking water by competitive inhibition with the nano colloidal gold-conjugated monoclonal antibody (mAb). Bromoxynil standard samples of 0.01-10 mg L -1 in water were tested by this method and the visual limit was 0.06 mg L -1 . The assay only required 5 min and one-step by dispensing a drop of sample solution onto a strip. Parallel analysis of water samples with bromoxynil showed comparable results from one-step strip test and ELISA. Therefore, the one-step strip test is very useful as a screening method for qualitative detection of bromoxynil in water. - One-step strip test is a rapid method for qualitative detection of bromoxynil residues in water

Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis.

Science.gov (United States)

Byrne, Allison Q; Rothstein, Andrew P; Poorten, Thomas J; Erens, Jesse; Settles, Matthew L; Rosenblum, Erica Bree

2017-11-01

One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures have advanced our understanding of Bd phylogenetics, genomic architecture and mechanisms of virulence. However, pure cultures are laborious to obtain and whole-genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus, we still know little about the genetic diversity of Bd in natural systems. The most common noninvasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole-genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, noninvasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations. © 2017 John Wiley & Sons Ltd.

Stripping Voltammetry

Science.gov (United States)

Lovrić, Milivoj

Electrochemical stripping means the oxidative or reductive removal of atoms, ions, or compounds from an electrode surface (or from the electrode body, as in the case of liquid mercury electrodes with dissolved metals) [1-5]. In general, these atoms, ions, or compounds have been preliminarily immobilized on the surface of an inert electrode (or within it) as the result of a preconcentration step, while the products of the electrochemical stripping will dissolve in the electrolytic solution. Often the product of the electrochemical stripping is identical to the analyte before the preconcentration. However, there are exemptions to these rules. Electroanalytical stripping methods comprise two steps: first, the accumulation of a dissolved analyte onto, or in, the working electrode, and, second, the subsequent stripping of the accumulated substance by a voltammetric [3, 5], potentiometric [6, 7], or coulometric [8] technique. In stripping voltammetry, the condition is that there are two independent linear relationships: the first one between the activity of accumulated substance and the concentration of analyte in the sample, and the second between the maximum stripping current and the accumulated substance activity. Hence, a cumulative linear relationship between the maximum response and the analyte concentration exists. However, the electrode capacity for the analyte accumulation is limited and the condition of linearity is satisfied only well below the electrode saturation. For this reason, stripping voltammetry is used mainly in trace analysis. The limit of detection depends on the factor of proportionality between the activity of the accumulated substance and the bulk concentration of the analyte. This factor is a constant in the case of a chemical accumulation, but for electrochemical accumulation it depends on the electrode potential. The factor of proportionality between the maximum stripping current and the analyte concentration is rarely known exactly. In fact

Rapid virological response assessment by Abbott RealTime hepatitis C virus assay for predicting sustained virological responses in patients with hepatitis C virus genotype 1 treated with pegylated-interferon and ribavirin

Directory of Open Access Journals (Sweden)

Pei-yuan Su

2016-07-01

Full Text Available The lower limits of virus detection of hepatitis C virus (HCV RNA detection assays are continuously improving. We aimed to assess the utility of more precise definition of 4th week viral load [rapid virological response (RVR] in predicting sustained virological response (SVR in HCV genotype 1 patients treated with pegylated-interferon (PEG-IFN and ribavirin. Clinical data of treatment-naïve HCV genotype 1 patients were retrospectively collected from 2009 to 2014. Patients were grouped according to 4th week viral load as follows: undetectable (n = 90 and detectable but not quantifiable (< 12 IU/mL, n = 27. All patients received PEG-IFNα-2a or -2b and ribavirin for 24 weeks. Serum HCV RNA levels were measured by Abbott RealTime (ART; Abbott Molecular, Abbott Park, IL, USA HCV assay. SVR was 95.5% and 63% in the undetectable group and < 12 IU/mL group of 4th week viral load, respectively. The between-group difference in SVR was significant (p < 0.001. We determined 4th week viral load was independently associated with SVR (odds ratio = 19.28; p = 0.002 and a good predictor of SVR [area under the curve (AUC = 0.775; p = 0.001]. ART HCV assays had a stronger SVR predictive value in HCV genotype 1 patients, indicating that only the undetectable group of 4th week viral load patients measured by ART HCV assay should be considered for shorter treatment time (24 weeks with PEG-IFN and ribavirin.

Aptamer-Based Paper Strip Sensor for Detecting Vibrio fischeri.

Science.gov (United States)

Shin, Woo-Ri; Sekhon, Simranjeet Singh; Rhee, Sung-Keun; Ko, Jung Ho; Ahn, Ji-Young; Min, Jiho; Kim, Yang-Hoon

2018-05-14

Aptamer-based paper strip sensor for detecting Vibrio fischeri was developed. Our method was based on the aptamer sandwich assay between whole live cells, V. fischeri and DNA aptamer probes. Following 9 rounds of Cell-SELEX and one of the negative-SELEX, V. fischeri Cell Aptamer (VFCA)-02 and -03 were isolated, with the former showing approximately 10-fold greater avidity (in the subnanomolar range) for the target cells when arrayed on a surface. The colorimetric response of a paper sensor based on VFCA-02 was linear in the range of 4 × 10 1 to 4 × 10 5 CFU/mL of target cell by using scanning reader. The linear regression correlation coefficient ( R 2 ) was 0.9809. This system shows promise for use in aptamer-conjugated gold nanoparticle probes in paper strip format for in-field detection of marine bioindicating bacteria.

Genotype calling in tetraploid species from bi-allelic marker data using mixture models

NARCIS (Netherlands)

Voorrips, R.E.; Gort, G.; Vosman, B.

2011-01-01

Background: Automated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either

Stripping voltammetric behavior of technetium at various chemically modified electrodes

International Nuclear Information System (INIS)

Dick, R.

1990-09-01

In monitoring of nuclear processing plants and storage facilities the necessity arises of assaying traces of the artificial radioactive element technetium. The oxidation states IV and VII are of particular interest. Stripping voltammetry is among the methods of assay which are suited for this purpose. It allows an enhanced selectivity to be achieved by preconcentration of the analyte and of an oxidation state of the analyte, respectively, at the electrode used. This specific enrichment is successful after appropriate chemical modification of the electrode through immobilization of a Tc-specific reagent. When various approaches of chemical modification of a glassy carbon electrode were examined, the tetraphenylarsonium chloride extractant, which is highly selective with respect to technetium, proved to be the best suited reagent, capable of fixation both by ionic and by covalent bonding on an electrodeposited polymer film. For ionic immobilization the reagent was reacted to m-sulfophenyltriphenyl arsonium and then bound to a copolymer of vinylferrocene and vinylpyridine, which had been provided with cations. It was possible to enrich Tc(VII) at such an electrode and to determine it by stripping voltammetry down to a concentration of 1x10 -8 M after 5 minutes enrichment time. (orig./EF) [de

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.

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.

The redox behaviour of diazepam (Valium®) using a disposable screen-printed sensor and its determination in drinks using a novel adsorptive stripping voltammetric assay.

Science.gov (United States)

Honeychurch, Kevin C; Crew, Adrian; Northall, Hannah; Radbourne, Stuart; Davies, Owian; Newman, Sam; Hart, John P

2013-11-15

In this study we investigated the possibility of applying disposable electrochemical screen-printed carbon sensors for the rapid identification and quantitative determination of diazepam in beverages. This was achieved utilising a previously unreported oxidation peak. The origin of this peak was investigated further by cyclic voltammetry and gas chromatography/mass spectroscopy. At pH 6 the voltammetric behaviour of this oxidation process was found to involve adsorption of the drug allowing for the development of an adsorptive stripping voltammetric assay. Experimental conditions were then optimised for the determination of diazepam in a beverage sample using a medium exchange technique. It was shown that no elaborate extraction procedures were required as the calibration plots obtained in the absence and presence of the beverage were very similar. © 2013 Elsevier B.V. All rights reserved.

Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance

Directory of Open Access Journals (Sweden)

Haque Kashif A

2005-09-01

Full Text Available Abstract Background Whole genome amplification (WGA promises to eliminate practical molecular genetic analysis limitations associated with genomic DNA (gDNA quantity. We evaluated the performance of multiple displacement amplification (MDA WGA using gDNA extracted from lymphoblastoid cell lines (N = 27 with a range of starting gDNA input of 1–200 ng into the WGA reaction. Yield and composition analysis of whole genome amplified DNA (wgaDNA was performed using three DNA quantification methods (OD, PicoGreen® and RT-PCR. Two panels of N = 15 STR (using the AmpFlSTR® Identifiler® panel and N = 49 SNP (TaqMan® genotyping assays were performed on each gDNA and wgaDNA sample in duplicate. gDNA and wgaDNA masses of 1, 4 and 20 ng were used in the SNP assays to evaluate the effects of DNA mass on SNP genotyping assay performance. A total of N = 6,880 STR and N = 56,448 SNP genotype attempts provided adequate power to detect differences in STR and SNP genotyping performance between gDNA and wgaDNA, and among wgaDNA produced from a range of gDNA templates inputs. Results The proportion of double-stranded wgaDNA and human-specific PCR amplifiable wgaDNA increased with increased gDNA input into the WGA reaction. Increased amounts of gDNA input into the WGA reaction improved wgaDNA genotyping performance. Genotype completion or genotype concordance rates of wgaDNA produced from all gDNA input levels were observed to be reduced compared to gDNA, although the reduction was not always statistically significant. Reduced wgaDNA genotyping performance was primarily due to the increased variance of allelic amplification, resulting in loss of heterozygosity or increased undetermined genotypes. MDA WGA produces wgaDNA from no template control samples; such samples exhibited substantial false-positive genotyping rates. Conclusion The amount of gDNA input into the MDA WGA reaction is a critical determinant of genotyping performance of wgaDNA. At least 10 ng of

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.

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/ ...

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...

Assessment of the myostatin Q204X allele using an allelic discrimination assay

OpenAIRE

Sifuentes-Rincón,Ana M.; Puentes-Montiel,Herlinda E.; Moreno-Medina,Víctor R.; Rosa-Reyna,Xóchitl F. de la

2006-01-01

An allelic discrimination assay was designed and used to determine the genotypic and allelic frequencies of the myostatin (MSTN) gene Q204X allele from two Mexican Full-French herds. The assay is a simple high throughput genotyping method that could be applied to investigate the effect of the Q204X allele on the Charolais breed.

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.

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...

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.

Human papillomavirus genotyping using an automated film-based chip array.

Science.gov (United States)

Erali, Maria; Pattison, David C; Wittwer, Carl T; Petti, Cathy A

2009-09-01

The INFINITI HPV-QUAD assay is a commercially available genotyping platform for human papillomavirus (HPV) that uses multiplex PCR, followed by automated processing for primer extension, hybridization, and detection. The analytical performance of the HPV-QUAD assay was evaluated using liquid cervical cytology specimens, and the results were compared with those results obtained using the digene High-Risk HPV hc2 Test (HC2). The specimen types included Surepath and PreservCyt transport media, as well as residual SurePath and HC2 transport media from the HC2 assay. The overall concordance of positive and negative results following the resolution of indeterminate and intermediate results was 83% among the 197 specimens tested. HC2 positive (+) and HPV-QUAD negative (-) results were noted in 24 specimens that were shown by real-time PCR and sequence analysis to contain no HPV, HPV types that were cross-reactive in the HC2 assay, or low virus levels. Conversely, HC2 (-) and HPV-QUAD (+) results were noted in four specimens and were subsequently attributed to cross-contamination. The most common HPV types to be identified in this study were HPV16, HPV18, HPV52/58, and HPV39/56. We show that the HPV-QUAD assay is a user friendly, automated system for the identification of distinct HPV genotypes. Based on its analytical performance, future studies with this platform are warranted to assess its clinical utility for HPV detection and genotyping.

Competitive immunochromatographic assay for the detection of the organophosphorus pesticide chlorpyrifos

Science.gov (United States)

Kim, Young Ah; Lee, Eun-Hye; Kim, Kwang-Ok; Lee, Yong Tae; Hammock, Bruce D.; Lee, Hye-Sung

2014-01-01

An immunochromatographic assay (ICA) based on competitive antigen-coated format using colloidal gold as the label was developed for the detection of the organophosphorus insecticide chlorpyrifos. The ICA test strip consisted of a membrane with a detection zone, a sample pad and an absorbent pad. The membrane was separately coated with chlorpyrifos hapten-OVA conjugate (test line) and anti-mouse IgG (control line). Based on the fact that the competition is between the migrating analyte in the sample and the analyte hapten immobilized on the test strip for the binding sites of the antibody-colloidal gold (Ab-CG) conjugate migrating on the test strip, this study suggests that the relative migration speed between the two migrating substances is a critically important factor for the sensitive detection by competitive ICA. This criterion was utilized for the confirmation of appropriateness of a nitrocellulose (NC) membrane for chlorpyrifos ICA. The detection limit of the ICA for chlorpyrifos standard and chlorpyrifos spiked into agricultural samples were 10 and 50 ng mL−1, respectively. The assay time for the ICA test was less than 10 min, suitable for rapid on-site testing of chlorpyrifos. PMID:21504817

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

Science.gov (United States)

Ramos, Antonio M.; Crooijmans, Richard P. M. A.; Affara, Nabeel A.; Amaral, Andreia J.; Archibald, Alan L.; Beever, Jonathan E.; Bendixen, Christian; Churcher, Carol; Clark, Richard; Dehais, Patrick; Hansen, Mark S.; Hedegaard, Jakob; Hu, Zhi-Liang; Kerstens, Hindrik H.; Law, Andy S.; Megens, Hendrik-Jan; Milan, Denis; Nonneman, Danny J.; Rohrer, Gary A.; Rothschild, Max F.; Smith, Tim P. L.; Schnabel, Robert D.; Van Tassell, Curt P.; Taylor, Jeremy F.; Wiedmann, Ralph T.; Schook, Lawrence B.; Groenen, Martien A. M.

2009-01-01

Background The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next 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 success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs. PMID:19654876

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.

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…

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.

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.

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...... resolved by chemometrics which enabled simultaneous determination of both the copper and the zinc concentrations, thereby eliminating the conventional necessary pretreatment of the sample solution, such as initial addition of Ga(III) or solvent extraction of copper. The brass samples were diluted...... 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....

Neonicotinoid-contaminated pollinator strips adjacent to cropland reduce honey bee nutritional status

OpenAIRE

Christina L. Mogren; Jonathan G. Lundgren

2016-01-01

Worldwide pollinator declines are attributed to a number of factors, including pesticide exposures. Neonicotinoid insecticides specifically have been detected in surface waters, non-target vegetation, and bee products, but the risks posed by environmental exposures are still not well understood. Pollinator strips were tested for clothianidin contamination in plant tissues, and the risks to honey bees assessed. An enzyme-linked immunosorbent assay (ELISA) quantified clothianidin in leaf, necta...

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.…

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...

Nuclear reactor spring strip grid spacer

International Nuclear Information System (INIS)

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

1978-01-01

A bimetallic grid spacer is described comprising a grid structure of zircaloy formed by intersecting striplike members which define fuel element openings for receiving fuel elements and spring strips made of Inconel positioned within the grid structure for cooperating with the fuel elements to maintain them in their desired position. A plurality of these spring strips extend longitudinally between sides of the grid structure, being locked in position by the grid retaining strips. The fuel rods, which are disposed in the fuel openings formed in the grid structure, are positioned by means of the springs associated with the spring strips and a plurality of dimples which extend from the zircaloy grid structure into the openings. In one embodiment the strips are disposed in a plurality of arrays with those spring strip arrays situated in opposing diagonal quadrants of the grid structure extending in the same direction and adjacent spring strip arrays in each half of the spacer extending in relatively perpendicular directions. Other variations of the spring strip arrangements for a particular fuel design are disclosed herein

Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies.

Science.gov (United States)

Fondevila, M; Phillips, C; Santos, C; Freire Aradas, A; Vallone, P M; Butler, J M; Lareu, M V; Carracedo, A

2013-01-01

A revision of an established 34 SNP forensic ancestry test has been made by swapping the under-performing rs727811 component SNP with the highly informative rs3827760 that shows a near-fixed East Asian specific allele. We collated SNP variability data for the revised SNP set in 66 reference populations from 1000 Genomes and HGDP-CEPH panels and used this as reference data to analyse four U.S. populations showing a range of admixture patterns. The U.S. Hispanics sample in particular displayed heterogeneous values of co-ancestry between European, Native American and African contributors, likely to reflect in part, the way this disparate group is defined using cultural as well as population genetic parameters. The genotyping of over 700 U.S. population samples also provided the opportunity to thoroughly gauge peak mobility variation and peak height ratios observed from routine use of the single base extension chemistry of the 34-plex test. Finally, the genotyping of the widely used DNA profiling Standard Reference Material samples plus other control DNAs completes the audit of the 34-plex assay to allow forensic practitioners to apply this test more readily in their own laboratories. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Visual detection of West Nile virus using reverse transcription loop-mediated isothermal amplification combined with a vertical flow visualization strip

Directory of Open Access Journals (Sweden)

Zengguo eCao

2016-04-01

Full Text Available West Nile virus (WNV causes a severe zoonosis, which can lead to a large number of casualties and considerable economic losses. A rapid and accurate identification methodfor WNV for use in field laboratories is urgently needed. Here, a method utilizing reverse transcription loop-mediated isothermal amplification combined with a vertical flow visualization strip (RT-LAMP-VF was developed to detect the envelope (E gene of WNV. The RT-LAMP-VF assay could detect 102 copies/μl ofan WNV RNA standard using a 40 min amplification reaction followed by a 2 min incubationof the amplification product on the visualization strip, and no cross-reaction with other closely related members of theFlavivirus genus was observed. The assay was further evaluated using cells and mouse brain tissues infected with a recombinant rabies virus expressing the E protein of WNV.The assay produced sensitivities of 101.5TCID50/ml and 101.33 TCID50/ml for detection of the recombinant virus in the cells and brain tissues, respectively. Overall, the RT-LAMP-VF assay developed in this study is rapid, simple and effective, and it is therefore suitable for clinical application in the field.

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

Relatedness of Indian flax genotypes (Linum usitatissimum L.): an inter-simple sequence repeat (ISSR) primer assay.

Science.gov (United States)

Rajwade, Ashwini V; Arora, Ritu S; Kadoo, Narendra Y; Harsulkar, Abhay M; Ghorpade, Prakash B; Gupta, Vidya S

2010-06-01

The objective of this study was to analyze the genetic relationships, using PCR-based ISSR markers, among 70 Indian flax (Linum usitatissimum L.) genotypes actively utilized in flax breeding programs. Twelve ISSR primers were used for the analysis yielding 136 loci, of which 87 were polymorphic. The average number of amplified loci and the average number of polymorphic loci per primer were 11.3 and 7.25, respectively, while the percent loci polymorphism ranged from 11.1 to 81.8 with an average of 63.9 across all the genotypes. The range of polymorphism information content scores was 0.03-0.49, with an average of 0.18. A dendrogram was generated based on the similarity matrix by the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), wherein the flax genotypes were grouped in five clusters. The Jaccard's similarity coefficient among the genotypes ranged from 0.60 to 0.97. When the omega-3 alpha linolenic acid (ALA) contents of the individual genotypes were correlated with the clusters in the dendrogram, the high ALA containing genotypes were grouped in two clusters. This study identified SLS 50, Ayogi, and Sheetal to be the most diverse genotypes and suggested their use in breeding programs and for developing mapping populations.

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

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)

Validation of clinical testing for warfarin sensitivity: comparison of CYP2C9-VKORC1 genotyping assays and warfarin-dosing algorithms.

Science.gov (United States)

Langley, Michael R; Booker, Jessica K; Evans, James P; McLeod, Howard L; Weck, Karen E

2009-05-01

Responses to warfarin (Coumadin) anticoagulation therapy are affected by genetic variability in both the CYP2C9 and VKORC1 genes. Validation of pharmacogenetic testing for warfarin responses includes demonstration of analytical validity of testing platforms and of the clinical validity of testing. We compared four platforms for determining the relevant single nucleotide polymorphisms (SNPs) in both CYP2C9 and VKORC1 that are associated with warfarin sensitivity (Third Wave Invader Plus, ParagonDx/Cepheid Smart Cycler, Idaho Technology LightCycler, and AutoGenomics Infiniti). Each method was examined for accuracy, cost, and turnaround time. All genotyping methods demonstrated greater than 95% accuracy for identifying the relevant SNPs (CYP2C9 *2 and *3; VKORC1 -1639 or 1173). The ParagonDx and Idaho Technology assays had the shortest turnaround and hands-on times. The Third Wave assay was readily scalable to higher test volumes but had the longest hands-on time. The AutoGenomics assay interrogated the largest number of SNPs but had the longest turnaround time. Four published warfarin-dosing algorithms (Washington University, UCSF, Louisville, and Newcastle) were compared for accuracy for predicting warfarin dose in a retrospective analysis of a local patient population on long-term, stable warfarin therapy. The predicted doses from both the Washington University and UCSF algorithms demonstrated the best correlation with actual warfarin doses.

Strip casting apparatus and method

Science.gov (United States)

Williams, R.S.; Baker, D.F.

1988-09-20

Strip casting apparatus including a molten-metal-holding container and a nozzle to deposit molten metal onto a moving chill drum to directly cast continuous metallic strip. The nozzle body includes a slot bounded between a back and a front lip. The slot width exceeds about 20 times the gap distance between the nozzle and the chill drum surface. Preferably, the slot width exceeds 0.5 inch. This method of strip casting minimizes pressure drop, insuring better metal-to-chill-drum contact which promotes heat transfer and results in a better quality metallic strip. 6 figs.

HRM and SNaPshot as alternative forensic SNP genotyping methods.

Science.gov (United States)

Mehta, Bhavik; Daniel, Runa; McNevin, Dennis

2017-09-01

Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing. This study compares HRM and SNaPshot®. HRM produced reproducible and concordant genotypes at 500 pg, however, difficulties were encountered when genotyping SNPs with high GC content in flanking regions and differentiating variants of symmetrical SNPs. SNaPshot® was reproducible at 100 pg and is less dependent on SNP choice. HRM has a shorter processing time in comparison to SNaPshot®, avoids post PCR contamination risk and has potential as a screening tool for many forensic applications.

Genotype Diversity and Distribution of Orientia tsutsugamushi Causing Scrub Typhus in Thailand

Science.gov (United States)

2011-07-01

Society for Microbiology. All Rights Reserved. Genotype Diversity and Distribution of Orientia tsutsugamushi Causing Scrub Typhus in Thailand" Toon...2011 Scrub typhus , caused by antigenically disparate isolates of Orientia tsutsugamushi, is a widely distributed mite-borne human disease in the Asia...evaluation of scrub typhus - specific diagnostic assays and vaccines. Using indirect immunoHuorescence assays (IF A) and PCR assays, 0. tsutsugamushi

The Honeycomb Strip Chamber

International Nuclear Information System (INIS)

Graaf, Harry van der; Buskens, Joop; Rewiersma, Paul; Koenig, Adriaan; Wijnen, Thei

1991-06-01

The Honeycomb Strip Chamber (HSC) is a new position sensitive detector. It consists of a stack of folded foils, forming a rigid honeycomb structure. In the centre of each hexagonal cell a wire is strung. Conducting strips on the foils, perpendicular to the wires, pick up the induced avalanche charge. Test results of a prototype show that processing the signals form three adjacent strips nearest to the track gives a spatial resolution better than 64 μm for perpendicular incident tracks. The chamber performance is only slightly affected by a magnetic field. (author). 25 refs.; 21 figs

Use of a Radon Stripping Algorithm for Retrospective Assessment of Air Filter Samples

International Nuclear Information System (INIS)

Hayes, Robert

2009-01-01

An evaluation of a large number of air sample filters was undertaken using a commercial alpha and beta spectroscopy system employing a passive implanted planar silicon (PIPS) detector. Samples were only measured after air flow through the filters had ceased. Use of a commercial radon stripping algorithm was implemented to discriminate anthropogenic alpha and beta activity on the filters from the radon progeny. When uncontaminated air filters were evaluated, the results showed that there was a time-dependent bias in both average estimates and measurement dispersion with the relative bias being small compared to the dispersion. By also measuring environmental air sample filters simultaneously with electroplated alpha and beta sources, use of the radon stripping algorithm demonstrated a number of substantial unexpected deviations. Use of the current algorithm is therefore not recommended for assay applications and so use of the PIPS detector should only be utilized for gross counting without appropriate modifications to the curve fitting algorithm. As a screening method, the radon stripping algorithm might be expected to see elevated alpha and beta activities on air sample filters (not due to radon progeny) around the 200 dpm level

Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing.

Science.gov (United States)

Yamamoto, F; Höglund, B; Fernandez-Vina, M; Tyan, D; Rastrou, M; Williams, T; Moonsamy, P; Goodridge, D; Anderson, M; Erlich, H A; Holcomb, C L

2015-12-01

Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing. Copyright © 2015. Published by Elsevier Inc.

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.

Charge collection in silicon strip detectors

International Nuclear Information System (INIS)

Kraner, H.W.; Beuttenmuller, R.; Ludlam, T.; Hanson, A.L.; Jones, K.W.; Radeka, V.; Heijne, E.H.M.

1982-11-01

The use of position sensitive silicon detectors as very high resolution tracking devices in high energy physics experiments has been a subject of intense development over the past few years. Typical applications call for the detection of minimum ionizing particles with position measurement accuracy of 10 μm in each detector plane. The most straightforward detector geometry is that in which one of the collecting electrodes is subdivided into closely spaced strips, giving a high degree of segmentation in one coordinate. Each strip may be read out as a separate detection element, or, alternatively, resistive and/or capacitive coupling between adjacent strips may be exploited to interpolate the position via charge division measrurements. With readout techniques that couple several strips, the numer of readout channels can, in principle, be reduced by large factors without sacrificing the intrinsic position accuracy. The testing of individual strip properties and charge division between strips has been carried out with minimum ionizing particles or beams for the most part except in one case which used alphs particless scans. This paper describes the use of a highly collimated MeV proton beam for studies of the position sensing properties of representative one dimensional strip detectors

Automation of complex assays: pharmacogenetics of warfarin dosing.

Science.gov (United States)

Wu, Whei-Kuo; Hujsak, Paul G; Kureshy, Fareed

2007-10-01

AutoGenomics, Inc. (Carlsbad, CA, USA) have developed a multiplex microarray assay for genotyping both VKORC1 and CYP2C9 using the INFINITI(™) Analyzer. Multiple alleles in each DNA sample are analyzed by polymerase chain reaction amplification, followed by detection primer extension using the INFINITI Analyzer. The INFINITI Analyzer performs single-nucleotide polymorphism (SNP) analysis using universal oligonucleotides immobilized on the biochip. To genotype broader ethnic groups, genomic DNA from whole blood was tested for nine SNPs for VKORC1 and six for CYP2C9 genotypes. Information related to all 15 SNPs is needed to determine dosing of population of diverse ethnic origin. The INFINITI system provides genotyping information for same day dosing of warfarin.

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.

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)

Comparison of serum HBsAg quantitation by four immunoassays, and relationships of HBsAg level with HBV replication and HBV genotypes.

Directory of Open Access Journals (Sweden)

Edouard Tuaillon

Full Text Available BACKGROUND: The decline in hepatitis B virus surface antigen (HBsAg may be an early predictor of the viral efficacy of Hepatitis B virus (HBV therapy. The HBsAg levels obtained by different immunoassays now need comparing and the relationships between levels of HBsAg and HBV DNA alongside HBsAg and genotype must be evaluated. METHODOLOGY/PRINCIPAL FINDINGS: HBsAg levels were compared among 80 patients using the Abbott Architect assay, a commercial immunoassay approved for HBsAg detection and quantitation, and three other assays derived from immunoassays approved for HBsAg detection (manufactured by Diasorin, Bio-Rad and Roche. Good correlation was found between the Abbot vs. Diasorin, Bio-Rad and Roche assays with narrow 95% limits of agreement and small mean differences: -0.06 to 0.11, -0.09 log(10 IU/mL; -0.57 to 0.64, -0.04 log(10 IU/mL; -0.09 to 0.45, -0.27 log(10 IU/mL, respectively. These agreements were not affected by genotypes A or D. HBsAg was weakly correlated with HBV DNA, whatever the HBsAg assay used: Abbott, ρ = 0.36 p = 0.001, Diasorin ρ = 0.34, p = 0.002; Bio-Rad ρ = 0.37, p<0.001; or Roche ρ = 0.41, p<0.001. This relationship between levels of HBsAg and HBV DNA seemed to depend on genotypes. Whereas HBsAg (Abbott assay tended to correlate with HBV DNA for genotype A (ρ = 0.44, p = 0.02, no such correlation was significant for genotypes D (ρ = 0.29, p = 0.15. CONCLUSION/SIGNIFICANCE: The quantitation of HBsAg in routine clinical samples is comparable between the reference assay and the adapted assays with acceptable accuracy limits, low levels of variability and minimum discrepancy. While HBsAg quantitation is not affected by HBV genotype, the observed association between levels of HBsAg and HBV DNA seems genotype dependent.

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

Science.gov (United States)

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

2017-04-04

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

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.

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.

Using Comic Strips in Language Classes

Science.gov (United States)

Csabay, Noémi

2006-01-01

The author believes that using comic strips in language-learning classes has three main benefits. First, comic strips motivate younger learners. Second, they provide a context and logically connected sentences to help language learning. Third, their visual information is helpful for comprehension. The author argues that comic strips can be used in…

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...

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.

Utility of a rapid immunochromatographic strip test in detecting canine parvovirus infection compared with polymerase chain reaction

Directory of Open Access Journals (Sweden)

Sundaran S. Tinky

2015-04-01

Full Text Available Aim: The present study was undertaken to detect the presence of canine parvovirus (CPV in fecal samples of diarrheic dogs by conventional polymerase chain reaction (PCR and immunochromatographic (IC strip test and to compare the diagnostic potential of these tests. Materials and Methods: A total of 50 fecal samples collected from diarrheic dogs suspected for CPV infection were subjected to PCR using CPV-555 primer amplifying the gene coding for the VP1 protein. These samples were also tested by IC strip test using a commercial rapid Ag test kit. The results were statistically analyzed using McNemar test. Results: A total of 22 samples (44% were detected as positive by PCR, which yielded a specific amplicon of 583 bp. In IC strip test, 18 (36% samples were found to be positive. The sensitivity of the test as compared to PCR was found to be 72.22% and specificity was 92.86%. Positive predictive value and negative predictive value of IC strip test was found to be 88.89% and 81.25%, respectively. Statistical analysis of the results of PCR and IC assay using McNemar test revealed no significant difference (p>0.05. Conclusion: The IC strip test could be employed as a rapid field level diagnostic tool for the diagnosis of canine parvoviral diarrhea.

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

Directory of Open Access Journals (Sweden)

Pavel Tarlykov

2014-12-01

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

An Affymetrix Microarray Design for Microbial Genotyping

Science.gov (United States)

2009-10-01

les échantillons qui ne se prêtent pas aux méthodes culturales de la microbiologie classique. La puce à ADN est une technologie qui permet la... area of microbial genotyping there are multiple platforms that can identify one or a few microbial targets in a single assay iteration. For most

Evaluation of circulating cathodic antigen (CCA strip for diagnosis of urinary schistosomiasis in Hassoba school children, Afar, Ethiopia

Directory of Open Access Journals (Sweden)

Ayele B.

2008-03-01

Full Text Available A total of 206 urine samples collected from Hassoba Elementary schoolchildren, Afar, Ethiopia, a low Schistosoma haematobium endemic setting, was diagnosed to evaluate the performance of CCA strip using double references, urine filtration technique and urinalysis dipstick (Combur 10 Test® that detect schistosome eggs and blood in urine, respectively. The former was used as a gold standard reference method. Sensitivity, specificity, positive and negative predictive values for the CCA were 52%, 63.8%, 56.7% and 59% respectively, with reference to urine filtration technique whereas these parameters were 50.4%, 62.4%, 55.6% and 57.5% respectively, with reference to Combur 10 Test®. 47 S. haematobium egg-positive children were found negative by CCA strip while 38 egg-negative children were found positive by CCA strip. Moreover, among the pre-tests done in duplicate, inconsistent results were also recorded. Assays were also compared with regard to the cost of equipment and reagents, speed and simplicity of use. Though CCA strip was found to be rapid and could be performed with minimal training, it was found to be expensive (US $ 4.95 per test to use it for large-scale field use even if its diagnostic value would have been satisfactory. Further development and standardization of the CCA strip are required for its applicability for field use. It is also recommended that its cost per strip should be substantially cut down if it is to be used in poor schistosomiasis endemic countries.

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.

High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays

Directory of Open Access Journals (Sweden)

Crenshaw Andrew

2009-01-01

Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs have emerged as the genetic marker of choice for mapping disease loci and candidate gene association studies, because of their high density and relatively even distribution in the human genomes. There is a need for systems allowing medium multiplexing (ten to hundreds of SNPs with high throughput, which can efficiently and cost-effectively generate genotypes for a very large sample set (thousands of individuals. Methods that are flexible, fast, accurate and cost-effective are urgently needed. This is also important for those who work on high throughput genotyping in non-model systems where off-the-shelf assays are not available and a flexible platform is needed. Results We demonstrate the use of a nanofluidic Integrated Fluidic Circuit (IFC - based genotyping system for medium-throughput multiplexing known as the Dynamic Array, by genotyping 994 individual human DNA samples on 47 different SNP assays, using nanoliter volumes of reagents. Call rates of greater than 99.5% and call accuracies of greater than 99.8% were achieved from our study, which demonstrates that this is a formidable genotyping platform. The experimental set up is very simple, with a time-to-result for each sample of about 3 hours. Conclusion Our results demonstrate that the Dynamic Array is an excellent genotyping system for medium-throughput multiplexing (30-300 SNPs, which is simple to use and combines rapid throughput with excellent call rates, high concordance and low cost. The exceptional call rates and call accuracy obtained may be of particular interest to those working on validation and replication of genome- wide- association (GWA studies.

Assessment of biochemical mechanisms of tolerance to chlorpyrifos in ancient and contemporary Daphnia pulicaria genotypes.

Science.gov (United States)

Simpson, Adam M; Jeyasingh, Punidan D; Belden, Jason B

2017-12-01

The evolution of tolerance to environmental contaminants in non-target taxa has been largely studied by comparing extant populations experiencing contrasting exposure. Previous research has demonstrated that "resurrected" genotypes from a population of Daphnia pulicaria express temporal variation in sensitivity to the insecticide chlorpyrifos. Ancient genotypes (1301-1646AD.) were on average more sensitive to this chemical compared to the contemporary genotypes (1967-1977AD.). To determine the physiological mechanisms of tolerance, a series of biochemical assays was performed on three ancient and three contemporary genotypes; these six genotypes exhibited the most sensitive and most tolerant phenotypes within the population, respectively. Metabolic tolerance mechanisms were evaluated using acute toxicity testing, while target-site tolerance was assessed via in vitro acetylcholinesterase (AChE) assays. Acute toxicity tests were conducted using i) the toxic metabolite chlorpyrifos-oxon (CPF-oxon) and ii) CPF-oxon co-applied with piperonyl butoxide (PBO), a known Phase-I metabolic inhibitor. Both series of toxicity tests reduced the mean variation in sensitivity between tolerant and sensitive genotypes. Exposure to CPF-O reduced the disparity from a 4.7-fold to 1.6-fold difference in sensitivity. The addition of PBO further reduced the variation to a 1.2-fold difference in sensitivity. In vitro acetylcholinesterase assays yielded no significant differences in constitutive activity or target-site sensitivity. These findings suggest that pathways involving Phase-I detoxification and/or bioactivation of chlorpyrifos play a significant role in dictating the microevolutionary trajectories of tolerance in this population. Copyright © 2017 Elsevier B.V. All rights reserved.

CYP2D7 sequence variation interferes with TaqMan CYP2D6*15 and *35 genotyping

Directory of Open Access Journals (Sweden)

Amanda K Riffel

2016-01-01

Full Text Available TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35 which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696 SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe

Antioxidant capacity of anthocyanins from acerola genotypes

Directory of Open Access Journals (Sweden)

Vera Lúcia Arroxelas Galvão De Lima

2011-03-01

Full Text Available Anthocyanins from 12 acerola genotypes cultivated at the Active Germplasm Bank at Federal Rural University of Pernambuco were isolated for antioxidant potential evaluation. The antioxidant activity and radical scavenging capacity of the anthocyanin isolates were measured according to the β-carotene bleaching method and 1,1-diphenyl-2-picrylhydrazyl (DPPH free radical scavenging assay, respectively. The antioxidant activity varied from 25.58 to 47.04% at 0.2 mg.mL-1, and it was measured using the β-carotene bleaching method. The free radical scavenging capacity increased according to the increase in concentration and reaction time by the DPPH assay. At 16.7 μg.mL-1 concentration and after 5 minutes and 2 hours reaction time, the percentage of scavenged radicals varied from 36.97 to 63.92% and 73.27 to 94.54%, respectively. Therefore, the antioxidant capacity of acerola anthocyanins varied amongst acerola genotypes and methods used. The anthocyanins present in this fruit may supply substantial dietary source of antioxidant which may promote health and produce disease prevention effects.

High-sensitivity immunochromatographic assay for fumonisin B1 based on indirect antibody labeling.

Science.gov (United States)

Urusov, Alexandr E; Petrakova, Alina V; Gubaydullina, Milyausha K; Zherdev, Anatoly V; Eremin, Sergei A; Kong, Dezhao; Liu, Liqiang; Xu, Chuanlai; Dzantiev, Boris B

2017-05-01

To develop a high-sensitivity immunochromatographic test for fumonisin B1 in plant extracts. Unlike conventional immunochromatographic tests, this assay is performed in two stages: competitive reaction with free specific antibodies and identifying immune complexes by their interaction with the anti-species antibody-conjugated gold nanoparticles. The use of a new geometry for the test strip membranes and a novel reagent application method ensures the proper order of these stages without additional manipulations. The contact of the ready-to-use test strip with the liquid sample suffices in initiating all stages of the assay and obtaining test results. The developed test was used on corn extracts; its instrumental limit of fumonisin B1 detection was 0.6 ng ml -1 at 15 min of assay duration. The proposed approach is flexible and can be used for a wide range of low molecular compounds. The use of anti-species antibody-conjugated gold nanoparticles in immunochromatography significantly facilitates the development of test systems by eliminating the need to synthesize and characterize the conjugates with specific antibodies for each new compound to be detected.

Large strip RPCs for the LEPS2 TOF system

Energy Technology Data Exchange (ETDEWEB)

Tomida, N., E-mail: natsuki@scphys.kyoto-u.ac.jp [Department of Physics, Kyoto University, Kyoto 606-8502 (Japan); Niiyama, M. [Department of Physics, Kyoto University, Kyoto 606-8502 (Japan); Ohnishi, H. [RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198 (Japan); Tran, N. [Research Center for Nuclear Physics (RCNP), Osaka University, Ibaraki, Osaka 567-0047 (Japan); Hsieh, C.-Y.; Chu, M.-L.; Chang, W.-C. [Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan (China); Chen, J.-Y. [National Synchrotron Radiation Research Center (NSRRC), Hsinchu 30076, Taiwan (China)

2014-12-01

High time-resolution resistive plate chambers (RPCs) with large-size readout strips are developed for the time-of-flight (TOF) detector system of the LEPS2 experiment at SPring-8. The experimental requirement is a 50-ps time resolution for a strip size larger than 100 cm{sup 2}/channel. We are able to achieve 50-ps time resolutions with 2.5×100 cm{sup 2} strips by directly connecting the amplifiers to strips. With the same time resolution, the number of front-end electronics (FEE) is also reduced by signal addition. - Highlights: • Find a way to achieve a good time resolution with a large strip RPC. • 2.5 cm narrow strips have better resolutions than 5.0 cm ones. • The 0.5 mm narrow strip interval shows flat time resolutions between strips. • FEEs directly connected to strips make the signal reflection at the strip edge small. • A time resolution of 50 ps was achieved with 2.5 cm×100 cm strips.

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.

A multiplex ligation detection assay for the characterization of Salmonella enterica strains

NARCIS (Netherlands)

Aarts, H.J.M.; Vos, P.; Larsson, J.T.; Hoek, van A.H.A.M.; Huehn, S.; Weijers, T.; Gronlund, H.A.; Malorny, B.

2011-01-01

A proof of principle of a multi-target assay for genotyping Salmonella has been developed targeting 62 genomic marker sequences of Salmonella related to pathogenicity. The assay is based on multiplex ligation detection reaction (LDR) followed by customized ArrayTube (R) microarray detection. The

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.

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.

Comparative limnology of strip-mine lakes

Energy Technology Data Exchange (ETDEWEB)

Parsons, J D

1964-01-01

Lakes were classified according to chemical properties. The concentration of the ferric iron oxides was responsible for a reddish-black turbidity which, in turn, played a major role in the thermal stratification of red strip-mine lakes. Owing to the lack of measurable turbidity and as a result of selective absorption of visible solar radiation, other strip-mine lakes appeared blue in color. The annual heat budget and the summer heat budget are essentially equivalent under saline conditions. Regardless of the physical and chemical conditions of the strip-mine lakes, heat income was a function of the circulating water mass. The progressive oxidation and precipitation of the iron oxides is the key to the classification of strip-mine lakes.

Hepatitis C virus (HCV genotype 1 subtype identification in new HCV drug development and future clinical practice.

Directory of Open Access Journals (Sweden)

Stéphane Chevaliez

Full Text Available BACKGROUND: With the development of new specific inhibitors of hepatitis C virus (HCV enzymes and functions that may yield different antiviral responses and resistance profiles according to the HCV subtype, correct HCV genotype 1 subtype identification is mandatory in clinical trials for stratification and interpretation purposes and will likely become necessary in future clinical practice. The goal of this study was to identify the appropriate molecular tool(s for accurate HCV genotype 1 subtype determination. METHODOLOGY/PRINCIPAL FINDINGS: A large cohort of 500 treatment-naïve patients eligible for HCV drug trials and infected with either subtype 1a or 1b was studied. Methods based on the sole analysis of the 5' non-coding region (5'NCR by sequence analysis or reverse hybridization failed to correctly identify HCV subtype 1a in 22.8%-29.5% of cases, and HCV subtype 1b in 9.5%-8.7% of cases. Natural polymorphisms at positions 107, 204 and/or 243 were responsible for mis-subtyping with these methods. A real-time PCR method using genotype- and subtype-specific primers and probes located in both the 5'NCR and the NS5B-coding region failed to correctly identify HCV genotype 1 subtype in approximately 10% of cases. The second-generation line probe assay, a reverse hybridization assay that uses probes targeting both the 5'NCR and core-coding region, correctly identified HCV subtypes 1a and 1b in more than 99% of cases. CONCLUSIONS/SIGNIFICANCE: In the context of new HCV drug development, HCV genotyping methods based on the exclusive analysis of the 5'NCR should be avoided. The second-generation line probe assay is currently the best commercial assay for determination of HCV genotype 1 subtypes 1a and 1b in clinical trials and practice.

Red blood cell and platelet genotyping: from current practice to future high-throughput donor typing

NARCIS (Netherlands)

de Haas, M.; van der Schoot, C. E.; Beiboer, S. H. W.; Feskens, M.; Cheroutre, G.; Maaskant-van Wijkb, P. A.

2006-01-01

The molecular basis of almost all red cell and platelet blood group antigens is known. This enables the prediction of red cell or platelet phenotypes based upon the genotypes. In many laboratories, blood group genotyping assays are routinely used in cases where patient red cells cannot be used for

Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data

Directory of Open Access Journals (Sweden)

Wong Melissa ML

2012-12-01

Full Text Available Abstract Background Next Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP discovery in Acacia auriculiformis and Acacia mangium. Like other non-model species, SNP detection and genotyping in Acacia are challenging due to lack of genome sequences. The main objective of this study is to develop the first high-throughput SNP genotyping assay for linkage map construction of A. auriculiformis x A. mangium hybrids. Results We identified a total of 37,786 putative SNPs by aligning short read transcriptome data from four parents of two Acacia hybrid mapping populations using Bowtie against 7,839 de novo transcriptome contigs. Given a set of 10 validated SNPs from two lignin genes, our in silico SNP detection approach is highly accurate (100% compared to the traditional in vitro approach (44%. Further validation of 96 SNPs using Illumina GoldenGate Assay gave an overall assay success rate of 89.6% and conversion rate of 37.5%. We explored possible factors lowering assay success rate by predicting exon-intron boundaries and paralogous genes of Acacia contigs using Medicago truncatula genome as reference. This assessment revealed that presence of exon-intron boundary is the main cause (50% of assay failure. Subsequent SNPs filtering and improved assay design resulted in assay success and conversion rate of 92.4% and 57.4%, respectively based on 768 SNPs genotyping. Analysis of clustering patterns revealed that 27.6% of the assays were not reproducible and flanking sequence might play a role in determining cluster compression. In addition, we identified a total of 258 and 319 polymorphic SNPs in A. auriculiformis and A. mangium natural germplasms, respectively. Conclusion We have successfully discovered a large number of SNP markers in A. auriculiformis x A. mangium hybrids using next generation transcriptome sequencing. By using a reference genome from the most closely

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)

Detection and genotyping of human papilloma virus in cervical cancer specimens from Saudi patients.

Science.gov (United States)

Al-Badawi, Ismail A; Al-Suwaine, Abdulrahman; Al-Aker, Murad; Asaad, Lina; Alaidan, Alwaleed; Tulbah, Asma; Fe Bohol, Marie; Munkarah, Adnan R

2011-07-01

To determine the rates and types of human papilloma virus (HPV) infection in cervical cancer specimens from Saudi patients. One hundred specimens were randomly selected and retrieved from the achieved samples stored in the pathology department accessioned under the diagnosis of cervical cancer and carcinoma in situ between the years 1997 and 2007. Human papilloma virus in the clinical samples was detected using polymerase chain reaction amplification methods. Two primer systems are commonly used: the MY09-MY11 primers and the GP5+-GP6+ that amplify a wide range of HPV genotypes. Human papilloma virus isolates were genotyped using DNA sequencing and reverse line blot hybridization assay to identify the high-risk HPV genotypes. Ninety cases fulfilled the diagnostic criteria and were analyzed. The rate of HPV genotype detection among cervical cancer samples was 95.5%. The most common HPV genotype detected by both methods was HPV-16 (63.4%), followed by HPV-18 (11.1%), HPV-45 (4.5%), HPV-33 (3.3%), and HPV-31, HPV-52, HPV-53, HPV-58, HPV-59, and HPV-66 with 2.2% prevalence rate each. Prevalence of HPV genotypes among patients with cervical cancer in Saudi Arabia is comparable to the international rates. The use of the reverse line blot hybridization assay genotyping method could be useful for classifying oncogenic HPV-positive women. It is relatively inexpensive and reliable and can be performed in routine practice or epidemiological study compared with the available standard commercial kits.

Simultaneous detection of hepatitis B virus genotypes and mutations associated with resistance to lamivudine, adefovir, and telbivudine by the polymerase chain reaction-ligase detection reaction

Directory of Open Access Journals (Sweden)

Yong-Zhong Wang

Full Text Available OBJECTIVES: Detection of mutations associated to nucleos(tide analogs and hepatitis B virus (HBV genotyping are essential for monitoring treatment of HBV infection. We developed a multiplex polymerase chain reaction-ligase detection reaction (PCR-LDR assay for the rapid detection of HBV genotypes and mutations associated with lamivudine, adefovir, and telbivudine resistance in HBV-infected patients. METHODS: HBV templates were amplified by PCR, followed by LDR and electrophoresis on a sequencer. The assay was evaluated using plasmids that contained wild-type or mutant HBV sequences and 216 clinical samples. RESULTS: The PCR-LDR assay and sequencing gave comparable results for 158 of the 216 samples (73.1% with respect to mutation detection and genotyping. Complete agreement between the two methods was observed for all the samples (100% at codon 180 and codon 204. Concordant results were observed for 99.4% of the 158 samples at codon 181 and 98.7% at codon 236. The genotyping results were completely concordant between the PCR-LDR assay and sequencing. The PCR-LDR assay could detect a proportion of 1% mutant plasmid in a background of wild-type plasmid. CONCLUSION: The PCR-LDR assay is sensitive and specific for detection of HBV genotypes and drug resistance mutations, and could be helpful for decision making in the treatment of HBV infection.

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 ...

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.

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)

An accurate method for quantifying and analyzing copy number variation in porcine KIT by an oligonucleotide ligation assay

Directory of Open Access Journals (Sweden)

Cho In-Cheol

2007-11-01

Full Text Available Abstract Background Aside from single nucleotide polymorphisms, copy number variations (CNVs are the most important factors in susceptibility to genetic disorders because they affect expression levels of genes. In previous studies, pyrosequencing, mini-sequencing, real-time PCR, invader assays and other techniques have been used to detect CNVs. However, the higher the copy number in a genome, the more difficult it is to resolve the copies, so a more accurate method for measuring CNVs and assigning genotype is needed. Results PCR followed by a quantitative oligonucleotide ligation assay (qOLA was developed for quantifying CNVs. The accuracy and precision of the assay were evaluated for porcine KIT, which was selected as a model locus. Overall, the root mean squares of bias and standard deviation of qOLA were 2.09 and 0.45, respectively. These values are less than half of those in the published pyrosequencing assay for analyzing CNV in porcine KIT. Using a combined method of qOLA and another pyrosequencing for quantitative analysis of KIT copies with spliced forms, we confirmed the segregation of KIT alleles in 145 F1 animals with pedigree information and verified the correct assignment of genotypes. In a diagnostic test on 100 randomly sampled commercial pigs, there was perfect agreement between the genotypes obtained by grouping observations on a scatter plot and by clustering using the nearest centroid sorting method implemented in PROC FASTCLUS of the SAS package. In a test on 159 Large White pigs, there were only two discrepancies between genotypes assigned by the two clustering methods (98.7% agreement, confirming that the quantitative ligation assay established here makes genotyping possible through the accurate measurement of high KIT copy numbers (>4 per diploid genome. Moreover, the assay is sensitive enough for use on DNA from hair follicles, indicating that DNA from various sources could be used. Conclusion We have established a high

An efficient genotyping method for genome-modified animals and human cells generated with CRISPR/Cas9 system.

Science.gov (United States)

Zhu, Xiaoxiao; Xu, Yajie; Yu, Shanshan; Lu, Lu; Ding, Mingqin; Cheng, Jing; Song, Guoxu; Gao, Xing; Yao, Liangming; Fan, Dongdong; Meng, Shu; Zhang, Xuewen; Hu, Shengdi; Tian, Yong

2014-09-19

The rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 system, and utilized this approach to genotype mice from F0 to F2 generation, which included single and multiplexed genome-modified mice. We also determined the maximal detection sensitivity for detecting mosaic DNA using PAGE-based assay as 0.5%. We further applied PAGE-based genotyping approach to detect CRISPR/Cas9-mediated on- and off-target effect in human 293T and induced pluripotent stem cells (iPSCs). Thus, PAGE-based genotyping approach meets the rapidly increasing demand for genotyping of the fast-growing number of genome-modified animals and human cell lines created using CRISPR/Cas9 system or other nuclease systems such as TALEN or ZFN.

Depletive stripping chronopotentiometry : a major step forward in electrochemical stripping techniques for metal ion speciation analysis

NARCIS (Netherlands)

Town, R.M.; Leeuwen, van H.P.

2004-01-01

A comparative evaluation of the utility of the various modes of stripping chronopotentiometry (SCP) for trace metal speciation analysis is presented in the broad context of stripping voltammetric techniques. The remarkable fundamental advantages of depletive SCP at scanned deposition potential

Investigation of Parameters that Affect the Success Rate of Microarray-Based Allele-Specific Hybridization Assays

DEFF Research Database (Denmark)

Poulsen, Lena; Søe, Martin Jensen; Moller, Lisbeth Birk

2011-01-01

Background: The development of microarray-based genetic tests for diseases that are caused by known mutations is becoming increasingly important. The key obstacle to developing functional genotyping assays is that such mutations need to be genotyped regardless of their location in genomic regions...

A multiplex ligation detection assay for the characterization of Salmonella enterica strains

DEFF Research Database (Denmark)

Aarts, Henk J.M.; Vos, Pieter; Larsson, Jonas T.

2011-01-01

A proof of principle of a multi-target assay for genotyping Salmonella has been developed targeting 62 genomic marker sequences of Salmonella related to pathogenicity. The assay is based on multiplex ligation detection reaction (LDR) followed by customized ArrayTube® microarray detection. The fea...... assessors that support bio-traceability models....

Cell Line Controls for the Genotyping of a Spectrum of Human Single Nucleotide Polymorphisms in the Clinical Laboratory.

Science.gov (United States)

Kimbacher, Christine; Paar, Christian; Freystetter, Andrea; Berg, Joerg

2018-05-01

Genotyping for clinically important single nucleotide polymorphisms (SNPs) is performed by many clinical routine laboratories. To support testing, quality controls and reference materials are needed. Those may be derived from residual patient samples, left over samples of external quality assurance schemes, plasmid DNA or DNA from cell lines. DNAs from cell lines are commutable and available in large amounts. DNA from 38 cell lines were examined for suitability as controls in 11 SNP assays that are frequently used in a clinical routine laboratory: FV (1691G>A), FII (20210G>A), PAI-1 4G/5G polymorphism, MTHFR (677C>T, 1298A>C), HFE (H63D, S65C, C282Y), APOE (E2, E3, E4), LPH (-13910C>T), UGT1A1 (*28, *36, *37), TPMT (*2, *3A, *3B, *3C), VKORC1 (-1639G>A, 1173C>T), CYP2C9 (*2, *3, *5). Genotyping was performed by real-time PCR with melting curve analysis and confirmed by bi-directional sequencing. We find an almost complete spectrum of genotypic constellations within these 38 cell lines. About 12 cell lines appear sufficient as genotypic controls for the 11 SNP assays by covering almost all of the genotypes. However, hetero- and homozygous genotypes for FII and the alleles TPMT*2, UGT1A1*37 and CYP2C9*5 were not detected in any of the cell lines. DNA from most of the examined cell lines appear suitable as quality controls for these SNP assays in the laboratory routine, as to the implementation of those assays or to prepare samples for quality assurance schemes. Our study may serve as a pilot to further characterize these cell lines to arrive at the status of reference materials.

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...

Rapid detection of drug resistance and mutational patterns of extensively drug-resistant strains by a novel GenoType® MTBDRsl assay

Directory of Open Access Journals (Sweden)

A K Singh

2013-01-01

Full Text Available Background: The emergence of extensively drug-resistant tuberculosis (XDR-TB is a major concern in the India. The burden of XDR-TB is increasing due to inadequate monitoring, lack of proper diagnosis, and treatment. The GenoType ® Mycobacterium tuberculosis drug resistance second line (MTBDRsl assay is a novel line probe assay used for the rapid detection of mutational patterns conferring resistance to XDR-TB. Aim: The aim of this study was to study the rapid detection of drug resistance and mutational patterns of the XDR-TB by a novel GenoType ® MTBDRsl assay. Materials and Methods: We evaluated 98 multidrug-resistant (MDR M. tuberculosis isolates for second line drugs susceptibility testing by 1% proportion method (BacT/ALERT 3D system and GenoType ® MTBDRsl assay for rapid detection of conferring drug resistance to XDR-TB. Results: A total of seven (17.4% were identified as XDR-TB by using standard phenotypic method. The concordance between phenotypic and GenoType ® MTBDRsl assay was 91.7-100% for different antibiotics. The sensitivity and specificity of the MTBDRsl assay were 100% and 100% for aminoglycosides; 100% and 100% for fluoroquinolones; 91.7% and 100% for ethambutol. The most frequent mutations and patterns were gyrA MUT1 (A90V in seven (41.2% and gyrA + WT1-3 + MUT1 in four (23.5%; rrs MUT1 (A1401G in 11 (64.7%, and rrs WT1-2 + MUT1 in eight (47.1%; and embB MUT1B (M306V in 11 (64.7% strains. Conclusions: These data suggest that the GenoType ® MTBDRsl assay is rapid, novel test for detection of resistance to second line anti-tubercular drugs. This assay provides additional information about the frequency and mutational patterns responsible for XDR-TB resistance.

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)

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...

Study on lifetime of C stripping foils

International Nuclear Information System (INIS)

Zhang Hongbin; Lu Ziwei; Zhao Yongtao; Li Zhankui; Xu Hushan; Xiao Guoqing; Wang Yuyu; Zhang Ling; Li Longcai; Fang Yan

2007-01-01

The carbon stripping foils can be prepared with the AC and DC arc discharge methods, or even sandwiched with AC-DC alternative layers. The lifetime of the carbon stripping foils of 19 μg/cm 2 prepared with different methods and/or structures was measured. The factors affecting the bombarding lifetime of the carbon stripping foils, especially the method of the foil preparation and the structure of the carbon stripping foils, were discussed. It is observed that the foils prepared with the DC arc discharge method have a longer bombarding lifetime than those prepared with the AC arc discharge method. (authors)

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

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.

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

A European multicenter study on the analytical performance of the VERIS HBV assay.

Science.gov (United States)

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

Hepatitis B viral load monitoring is an essential part of managing patients with chronic Hepatits B infection. Beckman Coulter has developed the VERIS HBV Assay for use on the fully automated Beckman Coulter DxN VERIS Molecular Diagnostics System. 1 OBJECTIVES: To evaluate the analytical performance of the VERIS HBV Assay at multiple European virology laboratories. Precision, analytical sensitivity, negative sample performance, linearity and performance with major HBV genotypes/subtypes for the VERIS HBV Assay was evaluated. Precision showed an SD of 0.15 log 10 IU/mL or less for each level tested. Analytical sensitivity determined by probit analysis was between 6.8-8.0 IU/mL. Clinical specificity on 90 unique patient samples was 100.0%. Performance with 754 negative samples demonstrated 100.0% not detected results, and a carryover study showed no cross contamination. Linearity using clinical samples was shown from 1.23-8.23 log 10 IU/mL and the assay detected and showed linearity with major HBV genotypes/subtypes. The VERIS HBV Assay demonstrated comparable analytical performance to other currently marketed assays for HBV DNA monitoring. Copyright © 2017 Elsevier B.V. All rights reserved.

Blood group genotyping: the power and limitations of the Hemo ID Panel and MassARRAY platform.

Science.gov (United States)

McBean, Rhiannon S; Hyland, Catherine A; Flower, Robert L

2015-01-01

Matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI-TOF MS), is a sensitive analytical method capable of resolving DNA fragments varying in mass by a single nucleotide. MALDI-TOF MS is applicable to blood group genotyping, as the majority of blood group antigens are encoded by single nucleotide polymorphisms. Blood group genotyping by MALDI-TOF MS can be performed using a panel (Hemo ID Blood Group Genotyping Panel, Agena Bioscience Inc., San Diego, CA) that is a set of genotyping assays that predict the phenotype for 101 antigens from 16 blood group systems. These assays involve three fundamental stages: multiplex target-specific polymerase chain reaction amplification, allele-specific single base primer extension, and MALDI-TOFMS analysis using the MassARRAY system. MALDI-TOF MS-based genotyping has many advantages over alternative methods including high throughput, high multiplex capability, flexibility and adaptability, and the high level of accuracy based on the direct detection method. Currently available platforms for MALDI-TOF MS-based genotyping are not without limitations, including high upfront instrumentation costs and the number of non-automated steps. The Hemo ID Blood Group Genotyping Panel, developed and optimized in a collaboration between the vendor and the Blood Transfusion Service of the Swiss Red Cross in Zurich, Switzerland, is not yet widely utilized, although several laboratories are currently evaluating the MassARRAY system for blood group genotyping. Based on the accuracy and other advantages offered by MALDITOF MS analysis, in the future, this method is likely to become widely adopted for blood group genotyping, in particular, for population screening.

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

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 extensively......)-approximation by two independent research groups [FSTTCS 2016,WALCOM 2017]. This raises a questionwhether strip packing with polynomially bounded input data admits a quasi-polynomial time approximation scheme, as is the case for related twodimensional packing problems like maximum independent set of rectangles or two...

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

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.

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

Science.gov (United States)

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

2017-01-01

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

Transfusion and blood donation in comic strips.

Science.gov (United States)

Lefrère, Jean-Jacques; Danic, Bruno

2013-07-01

The representation of blood transfusion and donation of blood in the comic strip has never been studied. The comic strip, which is a relatively recent art, emerged in the 19th century before becoming a mass medium during the 20th century. We have sought, by calling on collectors and using the resources of Internet, comic strips devoted, wholly or in part, to the themes of transfusion and blood donation. We present some of them here in chronologic order, indicating the title, country of origin, year of publication, and names of authors. The theme of the superhero using transfusion to transmit his virtues or his powers is repeated throughout the 20th century in North American comic strips. More recently, comic strips have been conceived from the outset with a promotional aim. They perpetuate positive images and are directed toward a young readership, wielding humor to reduce the fear of venipuncture. Few comic strips denounce the abuse of the commercialization of products derived from the human body. The image of transfusion and blood donation given by the comic strips is not to be underestimated because their readership is primarily children, some of whom will become blood donors. Furthermore, if some readers are transfused during their lives, the impact of a memory more or less conscious of these childhood readings may resurface, both in hopes and in fears. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

Immunochromatographic lateral flow strip for on-site detection of bisphenol A

International Nuclear Information System (INIS)

Mei, Z.; Deng, Y.; Zhong, Y.; Wu, J.; Yang, H.; Wang, Z.; Zheng, L.; Chen, W.; Chu, H.; Xue, F.

2013-01-01

We have developed a lateral flow assay (LFA) for the detection of bisphenol A (BPA) in water samples. Antibody against BPA was labeled with gold nanoparticles, and these conjugates were used as the recognition probes for the construction of an LFA strip. The diameter of the gold nanoparticles, the amount of antibody, the pH of the buffer, and the categories of the conjugation pad were optimized. The resulting method has a (visual) detection limit of 5 ppb, and of 0.92 ppb if used in combination with professional software. This LFA displays excellent specificity and was applied to spiked water samples with satisfactory results. (author)

Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

Directory of Open Access Journals (Sweden)

Lank Simon M

2012-08-01

Full Text Available Abstract Background High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. Results We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. Conclusions The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.

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

Development of floating strip micromegas detectors

International Nuclear Information System (INIS)

Bortfeldt, Jonathan

2014-01-01

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 34 cm -2 s -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 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 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 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 track inclination in a single

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...

Apparatus for measuring profile thickness of strip material

International Nuclear Information System (INIS)

Hold, A.C.

1982-01-01

Apparatus for measuring the thickness profile of steel strip comprises a radiation source reciprocally movable in a stepwise fashion (by a belt) across the strip width on one side thereof and a single elongated detector on the other side of the strip aligned with the scanning source. This detector may be a fluorescent scintillator detector or an ionisation chamber. Means are provided for sensing the degree of excitation in the detector in synchronism with the scanning source whereby to provide an output representative of the thickness profile of the strip. (author)

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.

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.

Factors affecting hydrocarbon removal by air stripping

International Nuclear Information System (INIS)

McFarland, W.E.

1992-01-01

This paper includes an overview of the theory of air stripping design considerations and the factors affecting stripper performance. Effects of temperature, contaminant characteristics, stripping tower geometry and air/water ratios on removal performance are discussed. The discussion includes treatment of groundwater contaminated with petroleum hydrocarbons and chlorinated solvents such as TCE and PCE. Control of VOC emissions from air strippers has become a major concern in recent years, due to more stringent restrictions on air quality in many areas. This paper includes an overview of available technology to control air emissions (including activated carbon adsorption, catalytic oxidation and steam stripping) and the effects of air emission control on overall efficiency of the treatment process. The paper includes an overview of the relative performance of various packing materials for air strippers and explains the relative advantages and disadvantages of comparative packing materials. Field conditions affecting selection of packing materials are also discussed. Practical guidelines for the design of air stripping systems are presented, as well as actual case studies of full-scale air stripping projects

Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays.

Directory of Open Access Journals (Sweden)

Lena Poulsen

Full Text Available BACKGROUND: The development of microarray-based genetic tests for diseases that are caused by known mutations is becoming increasingly important. The key obstacle to developing functional genotyping assays is that such mutations need to be genotyped regardless of their location in genomic regions. These regions include large variations in G+C content, and structural features like hairpins. METHODS/FINDINGS: We describe a rational, stable method for screening and combining assay conditions for the genetic analysis of 42 Phenylketonuria-associated mutations in the phenylalanine hydroxylase gene. The mutations are located in regions with large variations in G+C content (20-75%. Custom-made microarrays with different lengths of complementary probe sequences and spacers were hybridized with pooled PCR products of 12 exons from each of 38 individual patient DNA samples. The arrays were washed with eight buffers with different stringencies in a custom-made microfluidic system. The data were used to assess which parameters play significant roles in assay development. CONCLUSIONS: Several assay development methods found suitable probes and assay conditions for a functional test for all investigated mutation sites. Probe length, probe spacer length, and assay stringency sufficed as variable parameters in the search for a functional multiplex assay. We discuss the optimal assay development methods for several different scenarios.

Real-time polymerase chain reaction detection of parvovirus B19 DNA in blood donations using a commercial and an in-house assay.

Science.gov (United States)

Koppelman, M H G M; van Swieten, P; Cuijpers, H T M

2011-06-01

European regulations require testing of manufacturing plasma for parvovirus B19 (B19) DNA to limit the load of this virus to a maximum acceptable level of 10 IU/µL. To meet this requirement, most manufacturers introduced a test algorithm to identify and eliminate high-load donations before making large manufacturing pools of plasma units. Sanquin screens all donations using a commercial assay from Roche and an in-house assay. Between 2006 and 2009, 6.2 million donations were screened using two different polymerase chain reaction (PCR) assays targeting B19 DNA. Donations with B19 DNA loads of greater than 1 × 10(6) IU/mL showing significant differences in viral load between the two assays were further analyzed by sequencing analysis. A total of 396 donations with B19 DNA loads of greater than 1 × 10(6) IU/mL were identified. Fifteen samples (3.8%) had discordant test results; 10 samples (2.5%) were underquantified by the Roche assay, two samples (0.5%) were underquantified by the in-house assay, and three samples (0.8%) were not detected by the Roche assay. Sequencing analysis revealed mismatches in primer and probe-binding regions. Phylogenetic analysis showed that 12 samples were B19 Genotype 1. The three samples not detected by the Roche assay were B19 Genotype 2. This study shows that 3.8% of the viremic B19 DNA-positive donations are not quantified correctly by the Roche or in-house B19 DNA assays. B19 Genotype 1 isolates showing incorrect test results are more common than B19 Genotype 2 or 3 isolates. Newly designed B19 PCR assays for blood screening should preferably have multiplexed formats targeting multiple regions of the B19 genome. © 2010 American Association of Blood Banks.

Performance of commercial platforms for rapid genotyping of polymorphisms affecting warfarin dose.

Science.gov (United States)

King, Cristi R; Porche-Sorbet, Rhonda M; Gage, Brian F; Ridker, Paul M; Renaud, Yannick; Phillips, Michael S; Eby, Charles

2008-06-01

Initiation of warfarin therapy is associated with bleeding owing to its narrow therapeutic window and unpredictable therapeutic dose. Pharmacogenetic-based dosing algorithms can improve accuracy of initial warfarin dosing but require rapid genotyping for cytochrome P-450 2C9 (CYP2C9) *2 and *3 single nucleotide polymorphisms (SNPs) and a vitamin K epoxide reductase (VKORC1) SNP. We evaluated 4 commercial systems: INFINITI analyzer (AutoGenomics, Carlsbad, CA), Invader assay (Third Wave Technologies, Madison, WI), Tag-It Mutation Detection assay (Luminex Molecular Diagnostics, formerly Tm Bioscience, Toronto, Canada), and Pyrosequencing (Biotage, Uppsala, Sweden). We genotyped 112 DNA samples and resolved any discrepancies with bidirectional sequencing. The INFINITI analyzer was 100% accurate for all SNPs and required 8 hours. Invader and Tag-It were 100% accurate for CYP2C9 SNPs, 99% accurate for VKORC1 -1639/3673 SNP, and required 3 hours and 8 hours, respectively. Pyrosequencing was 99% accurate for CYP2C9 *2, 100% accurate for CYP2C9 *3, and 100% accurate for VKORC1 and required 4 hours. Current commercial platforms provide accurate and rapid genotypes for pharmacogenetic dosing during initiation of warfarin therapy.

Magnetic stripping studies for SPL

CERN Document Server

Posocco, P; CERN. Geneva. BE Department

2010-01-01

Magnetic stripping of H- can seriously enhance the beam losses along the SPL machine. These losses depend on the beam energy, on the beam transverse distribution and on the intensity of the magnetic field. For radioprotection issues the losses must be limited to 1 W/m. In this paper we will concentrate on the stripping phenomena inside the quadrupole magnets with the aim of defining the quadrupole range for the design phase of SPL.

A fluorometric lateral flow assay for visual detection of nucleic acids using a digital camera readout.

Science.gov (United States)

Magiati, Maria; Sevastou, Areti; Kalogianni, Despina P

2018-06-04

A fluorometric lateral flow assay has been developed for the detection of nucleic acids. The fluorophores phycoerythrin (PE) and fluorescein isothiocyanate (FITC) were used as labels, while a common digital camera and a colored vinyl-sheet, acting as a cut-off optical filter, are used for fluorescence imaging. After DNA amplification by polymerase chain reaction (PCR), the biotinylated PCR product is hybridized to its complementary probe that carries a poly(dA) tail at 3΄ edge and then applied to the lateral flow strip. The hybrids are captured to the test zone of the strip by immobilized poly(dT) sequences and detected by streptavidin-fluorescein and streptavidin-phycoerythrin conjugates, through streptavidin-biotin interaction. The assay is widely applicable, simple, cost-effective, and offers a large multiplexing potential. Its performance is comparable to assays based on the use of streptavidin-gold nanoparticles conjugates. As low as 7.8 fmol of a ssDNA and 12.5 fmol of an amplified dsDNA target were detectable. Graphical abstract Schematic presentation of a fluorometric lateral flow assay based on fluorescein and phycoerythrin fluorescent labels for the detection of single-stranded (ssDNA) and double-stranded DNA (dsDNA) sequences and using a digital camera readout. SA: streptavidin, BSA: Bovine Serum Albumin, B: biotin, FITC: fluorescein isothiocyanate, PE: phycoerythrin, TZ: test zone, CZ: control zone.

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.

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

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

Targeted genotyping-by-sequencing permits cost-effective identification and discrimination of pasture grass species and cultivars.

Science.gov (United States)

Pembleton, Luke W; Drayton, Michelle C; Bain, Melissa; Baillie, Rebecca C; Inch, Courtney; Spangenberg, German C; Wang, Junping; Forster, John W; Cogan, Noel O I

2016-05-01

A targeted amplicon-based genotyping-by-sequencing approach has permitted cost-effective and accurate discrimination between ryegrass species (perennial, Italian and inter-species hybrid), and identification of cultivars based on bulked samples. Perennial ryegrass and Italian ryegrass are the most important temperate forage species for global agriculture, and are represented in the commercial pasture seed market by numerous cultivars each composed of multiple highly heterozygous individuals. Previous studies have identified difficulties in the use of morphophysiological criteria to discriminate between these two closely related taxa. Recently, a highly multiplexed single nucleotide polymorphism (SNP)-based genotyping assay has been developed that permits accurate differentiation between both species and cultivars of ryegrasses at the genetic level. This assay has since been further developed into an amplicon-based genotyping-by-sequencing (GBS) approach implemented on a second-generation sequencing platform, allowing accelerated throughput and ca. sixfold reduction in cost. Using the GBS approach, 63 cultivars of perennial, Italian and interspecific hybrid ryegrasses, as well as intergeneric Festulolium hybrids, were genotyped. The genetic relationships between cultivars were interpreted in terms of known breeding histories and indistinct species boundaries within the Lolium genus, as well as suitability of current cultivar registration methodologies. An example of applicability to quality assurance and control (QA/QC) of seed purity is also described. Rapid, low-cost genotypic assays provide new opportunities for breeders to more fully explore genetic diversity within breeding programs, allowing the combination of novel unique genetic backgrounds. Such tools also offer the potential to more accurately define cultivar identities, allowing protection of varieties in the commercial market and supporting processes of cultivar accreditation and quality assurance.

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

A universal and reliable assay for molecular sex identification of three-spined sticklebacks (Gasterosteus aculeatus).

Science.gov (United States)

Toli, E-A; Calboli, F C F; Shikano, T; Merilä, J

2016-11-01

In heterogametic species, biological differences between the two sexes are ubiquitous, and hence, errors in sex identification can be a significant source of noise and bias in studies where sex-related sources of variation are of interest or need to be controlled for. We developed and validated a universal multimarker assay for reliable sex identification of three-spined sticklebacks (Gasterosteus aculeatus). The assay makes use of genotype scores from three sex-linked loci and utilizes Bayesian probabilistic inference to identify sex of the genotyped individuals. The results, validated with 286 phenotypically sexed individuals from six populations of sticklebacks representing all major genetic lineages (cf. Pacific, Atlantic and Japan Sea), indicate that in contrast to commonly used single-marker-based sex identification assays, the developed multimarker assay should be 100% accurate. As the markers in the assay can be scored from agarose gels, it provides a quick and cost-efficient tool for universal sex identification of three-spined sticklebacks. The general principle of combining information from multiple markers to improve the reliability of sex identification is transferable and can be utilized to develop and validate similar assays for other species. © 2016 John Wiley & Sons Ltd.

Detection and genotyping of enteroviruses in cerebrospinal fluid in patients in Victoria, Australia, 2007-2013.

Science.gov (United States)

Papadakis, Georgina; Chibo, Doris; Druce, Julian; Catton, Michael; Birch, Chris

2014-09-01

Genotyping by VP1 fragment polymerase chain reaction (PCR) and nucleic acid sequencing to detect enterovirus (EV) genotypes was performed directly on 729 EV PCR positive cerebrospinal fluid (CSF) samples collected between 2007 and 2012 from Victorian hospital inpatients. The overall genotype identification rate from CSF-positive material was 43%. The four most common genotypes identified were Echovirus 6 (24%), Echovirus 30 (17%), Echovirus 25 (10%), and Coxsackievirus A9 (10%), together comprising 61% of all EVs typed. The seasonal distribution of all EVs identified followed the recognized pattern of mainly summer epidemics. Three of the four predominant genotypes were present in each of the 6 years in which the study was conducted, with 20 other EV genotypes also detected, often in only a single year. Genotyping of EVs directly in CSF is faster, simpler and more sensitive than traditional virus neutralization assays performed on EV positive samples. © 2014 Wiley Periodicals, Inc.

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.

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.)

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

Micro-strip sensors based on CVD diamond

Energy Technology Data Exchange (ETDEWEB)

Adam, W.; Berdermann, E.; Bergonzo, P.; Bertuccio, G.; Bogani, F.; Borchi, E.; Brambilla, A.; Bruzzi, M.; Colledani, C.; Conway, J.; D' Angelo, P.; Dabrowski, W.; Delpierre, P.; Deneuville, A.; Dulinski, W.; Eijk, B. van; Fallou, A.; Fizzotti, F.; Foulon, F.; Friedl, M.; Gan, K.K.; Gheeraert, E.; Hallewell, G.; Han, S.; Hartjes, F.; Hrubec, J.; Husson, D.; Kagan, H.; Kania, D.; Kaplon, J.; Kass, R.; Koeth, T.; Krammer, M.; Logiudice, A.; Lu, R.; Mac Lynne, L.; Manfredotti, C.; Meier, D. E-mail: dirk.meier@cern.ch; Mishina, M.; Moroni, L.; Oh, A.; Pan, L.S.; Pernicka, M.; Peitz, A.; Perera, L.; Pirollo, S.; Procario, M.; Riester, J.L.; Roe, S.; Rousseau, L.; Rudge, A.; Russ, J.; Sala, S.; Sampietro, M.; Schnetzer, S.; Sciortino, S.; Stelzer, H.; Stone, R.; Suter, B.; Tapper, R.J.; Tesarek, R.; Trischuk, W.; Tromson, D.; Vittone, E.; Walsh, A.M.; Wedenig, R.; Weilhammer, P.; Wetstein, M.; White, C.; Zeuner, W.; Zoeller, M

2000-10-11

In this article we present the performance of recent chemical vapour deposition (CVD) diamond micro-strip sensors in beam tests. In addition, we present the first comparison of a CVD diamond micro-strip sensor before and after proton irradiation.

Micro-strip sensors based on CVD Diamond

CERN Document Server

Adam, W; Bergonzo, P; Bertuccio, G; Bogani, F; Borchi, E; Brambilla, A; Bruzzi, Mara; Colledani, C; Conway, J; D'Angelo, P; Dabrowski, W; Delpierre, P A; Deneuville, A; Dulinski, W; van Eijk, B; Fallou, A; Fizzotti, F; Foulon, F; Friedl, M; Gan, K K; Gheeraert, E; Hallewell, G D; Han, S; Hartjes, F G; Hrubec, Josef; Husson, D; Kagan, H; Kania, D R; Kaplon, J; Kass, R; Koeth, T W; Krammer, Manfred; Lo Giudice, A; Lü, R; MacLynne, L; Manfredotti, C; Meier, D; Mishina, M; Moroni, L; Oh, A; Pan, L S; Pernicka, Manfred; Peitz, A; Perera, L P; Pirollo, S; Procario, M; Riester, J L; Roe, S; Rousseau, L; Rudge, A; Russ, J; Sala, S; Sampietro, M; Schnetzer, S R; Sciortino, S; Stelzer, H; Stone, R; Suter, B; Tapper, R J; Tesarek, R J; Trischuk, W; Tromson, D; Vittone, E; Walsh, A M; Wedenig, R; Weilhammer, Peter; Wetstein, M; White, C; Zeuner, W; Zoeller, M M

2000-01-01

In this article we present the performance of recent chemical vapour deposition (CVD) diamond micro-strip sensors in beam tests. In addition we present the first comparison of a CVD diamond micro-strip sensor before and after proton irradiation.

Micro-strip sensors based on CVD diamond

International Nuclear Information System (INIS)

Adam, W.; Berdermann, E.; Bergonzo, P.; Bertuccio, G.; Bogani, F.; Borchi, E.; Brambilla, A.; Bruzzi, M.; Colledani, C.; Conway, J.; D'Angelo, P.; Dabrowski, W.; Delpierre, P.; Deneuville, A.; Dulinski, W.; Eijk, B. van; Fallou, A.; Fizzotti, F.; Foulon, F.; Friedl, M.; Gan, K.K.; Gheeraert, E.; Hallewell, G.; Han, S.; Hartjes, F.; Hrubec, J.; Husson, D.; Kagan, H.; Kania, D.; Kaplon, J.; Kass, R.; Koeth, T.; Krammer, M.; Logiudice, A.; Lu, R.; Mac Lynne, L.; Manfredotti, C.; Meier, D.; Mishina, M.; Moroni, L.; Oh, A.; Pan, L.S.; Pernicka, M.; Peitz, A.; Perera, L.; Pirollo, S.; Procario, M.; Riester, J.L.; Roe, S.; Rousseau, L.; Rudge, A.; Russ, J.; Sala, S.; Sampietro, M.; Schnetzer, S.; Sciortino, S.; Stelzer, H.; Stone, R.; Suter, B.; Tapper, R.J.; Tesarek, R.; Trischuk, W.; Tromson, D.; Vittone, E.; Walsh, A.M.; Wedenig, R.; Weilhammer, P.; Wetstein, M.; White, C.; Zeuner, W.; Zoeller, M.

2000-01-01

In this article we present the performance of recent chemical vapour deposition (CVD) diamond micro-strip sensors in beam tests. In addition, we present the first comparison of a CVD diamond micro-strip sensor before and after proton irradiation

Micro-strip sensors based on CVD diamond

Science.gov (United States)

Adam, W.; Berdermann, E.; Bergonzo, P.; Bertuccio, G.; Bogani, F.; Borchi, E.; Brambilla, A.; Bruzzi, M.; Colledani, C.; Conway, J.; D'Angelo, P.; Dabrowski, W.; Delpierre, P.; Deneuville, A.; Dulinski, W.; van Eijk, B.; Fallou, A.; Fizzotti, F.; Foulon, F.; Friedl, M.; Gan, K. K.; Gheeraert, E.; Hallewell, G.; Han, S.; Hartjes, F.; Hrubec, J.; Husson, D.; Kagan, H.; Kania, D.; Kaplon, J.; Kass, R.; Koeth, T.; Krammer, M.; Logiudice, A.; Lu, R.; mac Lynne, L.; Manfredotti, C.; Meier, D.; Mishina, M.; Moroni, L.; Oh, A.; Pan, L. S.; Pernicka, M.; Peitz, A.; Perera, L.; Pirollo, S.; Procario, M.; Riester, J. L.; Roe, S.; Rousseau, L.; Rudge, A.; Russ, J.; Sala, S.; Sampietro, M.; Schnetzer, S.; Sciortino, S.; Stelzer, H.; Stone, R.; Suter, B.; Tapper, R. J.; Tesarek, R.; Trischuk, W.; Tromson, D.; Vittone, E.; Walsh, A. M.; Wedenig, R.; Weilhammer, P.; Wetstein, M.; White, C.; Zeuner, W.; Zoeller, M.; RD42 Collaboration

2000-10-01

In this article we present the performance of recent chemical vapour deposition (CVD) diamond micro-strip sensors in beam tests. In addition, we present the first comparison of a CVD diamond micro-strip sensor before and after proton irradiation.

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

Advection endash diffusion past a strip. II. Oblique incidence

International Nuclear Information System (INIS)

Knessl, C.; Keller, J.B.

1997-01-01

Advection and diffusion of particles past an impenetrable strip is considered when the strip is oblique to the advection or drift velocity. The particle concentration p(x,y) is determined asymptotically for large values of vL/D, where v is the drift velocity, D is the diffusion coefficient, and 2L is the width of the strip. The results complement those of Part I, which treated a strip normal to the drift velocity. copyright 1997 American Institute of Physics

Stripping of uranium from Dehpa/kerosene solvents by different aqueous media

International Nuclear Information System (INIS)

Khorfan, S.; Stas, J.; Kassem, M.

1998-01-01

Stripping uranium from Dehpa/kerosene solvent is a crucial step in the recovery of uranium. Stripping was studied using different stripping media mainly ammonium carbonate, phosphoric acid, sulfuric acid, hydrochloric acid and nitric acid. Stripping was measured at different operating conditions such as aqueous concentrations, temperatures, and Dehpa/kerosene concentrations. The results obtained showed that stripping by acid media increases with the acid concentration and follows the order: HF > H 3 PO 4 > H 2 SO 4 > HCl > HNO 3 . To achieve higher stripping by phosphoric acid it was found necessary to increase the temperature to 50 deg C, the acid concentration to 5 mol/l and to reduce the uranium to U 4+ . Stripping by basic media was found to increase with increasing concentration of the stripping media and to follow the order: Na 2 CO 3 > (NH 4 ) 2 CO 3 > NH 4 HCO 3 . Stripping by ammonium carbonate was found to increase with temperature and carbonate concentration. The stripping was optimized at 0.5 mol/l carbonate concentration and at a temperature of 50 deg C. Stripping was decreased by increasing concentration of Dehpa in kerosene and was depressed more by adding the synergant Topo to the Dehpa solvent especially at 1/4 mol/mol ratio. (author)

Recurrent high level parvovirus B19/genotype 2 viremia in a renal transplant recipient analyzed by real-time PCR for simultaneous detection of genotypes 1 to 3.

Science.gov (United States)

Liefeldt, Lutz; Plentz, Annelie; Klempa, Boris; Kershaw, Olivia; Endres, Anne-Sophie; Raab, Ulla; Neumayer, Hans-H; Meisel, Helga; Modrow, Susanne

2005-01-01

Organ transplant recipients infected with parvovirus B19 frequently develop persistent viremia associated with chronic anemia and pure red cell aplasia. In this study, a male renal transplant recipient who had been infected with parvovirus B19/genotype 2 after renal transplantation at the age of 34 years is described. The patient was repeatedly treated with high dose intravenous immunoglobulin (IVIG) that resulted in the resolvement of symptoms but not in virus eradication. During an observation period of 33 months after transplantation three phases associated with high parvovirus B19 viremia were observed. Both the first and the second viremic phases were combined with severe anemia. Parvovirus B19 specific IgM-antibodies were initially detected at the beginning of the second phase in continually rising concentrations. Initially eradication of the virus by immunoglobulin therapy was reported after the first viremic phase [Liefeldt et al. (2002): Nephrol Dial Transplant 17:1840-1842]. Retrospectively this statement has to be corrected. It was based on the use of a qualitative PCR assay specific for parvovirus B19 genotype 1 associated with reduced sensitivity for detection of genotype 2. After sequence analysis of the viral DNA and adjustment of a real-time PCR assay (TaqMan) for quantitative detection of all three B19 virus genotypes analysis of consecutive serum samples allowed the demonstration of long lasting phases with reduced viral loads following IVIG-treatment. These results demonstrate that IVIG treatment of parvovirus B19-triggered anemia in transplant recipients offers an opportunity to resolve symptoms, but does not guarantee eradication of the virus. Since reactivation of parvovirus B19 infection can result in high virus load associated with the recurrence of symptoms repeated screening for viral DNA is recommended using the TaqMan system established for quantitative detection of all three genotypes of parvovirus B19. Copyright 2005 Wiley-Liss, Inc.

Pulse seed germination improves antioxidative activity of phenolic compounds in stripped soybean oil-in-water emulsions.

Science.gov (United States)

Xu, Minwei; Jin, Zhao; Peckrul, Allen; Chen, Bingcan

2018-06-01

The purpose of this study was to investigate antioxidative activity of phenolic compounds extracted from germinated pulse seed including chickpeas, lentils and yellow peas. Phenolic compounds were extracted at different germination time and total phenolic content was examined by Folin Ciocalteu's reaction. Antioxidative activity of extracts was characterized by in vitro assay including 2, 2-diphenyl-1-picrylhydrazyl radical scavenging capacity (DPPH), oxygen radical absorbance capacity (ORAC), iron-binding assay, and in stripped soybean oil-in-water emulsions. The results suggested that germination time is critical for phenolic compounds production. The form variation of phenolic compounds influenced the antioxidative activity of phenolic compounds both in vitro assay and in emulsion systems. Soluble bound phenolic compounds showed higher antioxidative ability in emulsion system with the order of chickpea > yellow pea > lentil. On the basis of these results, soluble bound phenolic compounds may be considered as a promising natural antioxidant to prevent lipid oxidation in foods. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Anal infections with concomitant Chlamydia trachomatis genotypes among men who have sex with men in Amsterdam, the Netherlands

Directory of Open Access Journals (Sweden)

van der Loeff Maarten

2011-03-01

Full Text Available Abstract Background Lymphogranuloma venereum (LGV proctitis is caused by Chlamydia trachomatis (Ct genotype L and is endemic among men who have sex with men (MSM in western society. Genotype L infections need to be distinguished from non-LGV (genotypes A-K Ct infections since they require prolonged antibiotic treatment. For this purpose, an in-house developed pmpH based LGV polymerase chain reaction (PCR test is used at the Amsterdam STI outpatient clinic. We investigated retrospectively the anal Ct genotype distribution, and the frequency of concomitant genotype infections in MSM infected with LGV and non-LGV Ct infections. To detect concomitant Ct genotype infections, the pmpH LGV PCR and genoTyping Reverse Hybridization Assay (Ct-DT RHA were used. Methods A total of 201 Ct positive rectal swabs from MSM were selected, which were previously diagnosed as either LGV (n = 99 or non-LGV Ct infection (n = 102 according to the algorithm of Ct detection by the commercially available Aptima Combo 2 assay followed by an in-house pmpH LGV PCR. The samples were retested with the commercially available Ct-DT RHA, which differentiates between 14 major genotypes and is able to detect concomitant Ct genotypes. Results Excellent genotyping agreement was observed between the Ct-DT RHA and the pmpH LGV PCR (Kappa = 0.900, 95%CI = 0.845-0.955, McNemar's p = 1.000. A concomitant non-LGV genotype was detected in 6/99 (6.1% LGV samples. No additional LGV infections were observed with the Ct-DT RHA among the non-LGV Ct group. In the non-LGV group genotype G/Ga (34.3% was seen most frequent, followed by genotype D/Da (22.5% and genotype J (13.7%. All LGV infections were caused by genotype L2. Conclusions Concomitant non-LGV genotypes do not lead to missed LGV proctitis diagnosis. The pmpH LGV PCR displayed excellent agreement with the commercially available Ct-DT genotyping RHA test. The genotypes G/Ga, D/Da and J were the most frequent non-LGV Ct strains in MSM.

SNP Discovery and Development of a High-Density Genotyping Array for Sunflower

Science.gov (United States)

Bachlava, Eleni; Taylor, Christopher A.; Tang, Shunxue; Bowers, John E.; Mandel, Jennifer R.; Burke, John M.; Knapp, Steven J.

2012-01-01

Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible. PMID:22238659

Blood group genotyping: from patient to high-throughput donor screening.

Science.gov (United States)

Veldhuisen, B; van der Schoot, C E; de Haas, M

2009-10-01

Blood group antigens, present on the cell membrane of red blood cells and platelets, can be defined either serologically or predicted based on the genotypes of genes encoding for blood group antigens. At present, the molecular basis of many antigens of the 30 blood group systems and 17 human platelet antigens is known. In many laboratories, blood group genotyping assays are routinely used for diagnostics in cases where patient red cells cannot be used for serological typing due to the presence of auto-antibodies or after recent transfusions. In addition, DNA genotyping is used to support (un)-expected serological findings. Fetal genotyping is routinely performed when there is a risk of alloimmune-mediated red cell or platelet destruction. In case of patient blood group antigen typing, it is important that a genotyping result is quickly available to support the selection of donor blood, and high-throughput of the genotyping method is not a prerequisite. In addition, genotyping of blood donors will be extremely useful to obtain donor blood with rare phenotypes, for example lacking a high-frequency antigen, and to obtain a fully typed donor database to be used for a better matching between recipient and donor to prevent adverse transfusion reactions. Serological typing of large cohorts of donors is a labour-intensive and expensive exercise and hampered by the lack of sufficient amounts of approved typing reagents for all blood group systems of interest. Currently, high-throughput genotyping based on DNA micro-arrays is a very feasible method to obtain a large pool of well-typed blood donors. Several systems for high-throughput blood group genotyping are developed and will be discussed in this review.

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

Stage- vs. Channel-strip Metaphor

DEFF Research Database (Denmark)

Gelineck, Steven; Korsgaard, Dannie Michael; Büchert, Morten

2015-01-01

This study compares the stage metaphor and the channel strip metaphor in terms of performance. Traditionally, music mixing consoles employ a channels strip control metaphor for adjusting parameters such as volume and panning of each track. An alternative control metaphor, the so-called stage meta...... is surprisingly similar and thus we are not able to detect any significant difference in performance between the two interfaces. Qualitative data however, suggests that the stage metaphor is largely favoured for its intuitive interaction - confirming earlier studies....

Phenotypic and genotypic analysis of anti-tuberculosis drug resistance in Mycobacterium tuberculosis isolates in Myanmar.

Science.gov (United States)

Aung, Wah Wah; Ei, Phyu Win; Nyunt, Wint Wint; Swe, Thyn Lei; Lwin, Thandar; Htwe, Mi Mi; Kim, Kyung Jun; Lee, Jong Seok; Kim, Chang Ki; Cho, Sang Nae; Song, Sun Dae; Chang, Chulhun L

2015-09-01

Tuberculosis (TB) is one of the most serious health problems in Myanmar. Because TB drug resistance is associated with genetic mutation(s) relevant to responses to each drug, genotypic methods for detecting these mutations have been proposed to overcome the limitations of classic phenotypic drug susceptibility testing (DST). We explored the current estimates of drug-resistant TB and evaluated the usefulness of genotypic DST in Myanmar. We determined the drug susceptibility of Mycobacterium tuberculosis isolated from sputum smear-positive patients with newly diagnosed pulmonary TB at two main TB centers in Myanmar during 2013 by using conventional phenotypic DST and the GenoType MTBDRplus assay (Hain Lifescience, Germany). Discrepant results were confirmed by sequencing the genes relevant to each type of resistance (rpoB for rifampicin; katG and inhA for isoniazid). Of 191 isolates, phenotypic DST showed that 27.7% (n=53) were resistant to at least one first-line drug and 20.9% (n=40) were resistant to two or more, including 18.3% (n=35) multidrug-resistant TB (MDR-TB) strains. Monoresistant strains accounted for 6.8% (n=13) of the samples. Genotypic assay of 189 isolates showed 17.5% (n=33) MDR-TB and 5.3% (n=10) isoniazid-monoresistant strains. Genotypic susceptibility results were 99.5% (n=188) concordant and agreed almost perfectly with phenotypic DST (kappa=0.99; 95% confidence interval 0.96-1.01). The results highlight the burden of TB drug resistance and prove the usefulness of the genotypic DST in Myanmar.

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)

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.

Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label.

Science.gov (United States)

Liu, Ke; Pan, Dun; Wen, Yanqin; Zhang, Honglu; Chao, Jie; Wang, Lihua; Song, Shiping; Fan, Chunhai; Shi, Yongyong

2018-02-01

The hepatitis B virus (HBV) genotyping may profoundly affect the accurate diagnosis and antiviral treatment of viral hepatitis. Existing genotyping methods such as serological, immunological, or molecular testing are still suffered from substandard specificity and low sensitivity in laboratory or clinical application. In a previous study, a set of high-efficiency hybridizable DNA origami-based shape ID probes to target the templates through which genetic variation could be determined in an ultrahigh resolution of atomic force microscopy (AFM) nanomechanical imaging are established. Here, as a further confirmatory research to explore the sensitivity and applicability of this assay, differentially predesigned DNA origami shape ID probes are also developed for precisely HBV genotyping. Through the specific identification of visualized DNA origami nanostructure with clinical HBV DNA samples, the genetic variation information of genotypes can be directly identified under AFM. As a proof-of-concept, five genotype B and six genotype C are detected in 11 HBV-infected patients' blood DNA samples of Han Chinese population in the single-blinded test. The AFM image-based DNA origami shape ID genotyping approach shows high specificity and sensitivity, which could be promising for virus infection diagnosis and precision medicine in the future. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stripping of uranium from Dehpa/Kerosene solvents by different aqueous media

International Nuclear Information System (INIS)

Khorfan, S.; Stas, J.; Kassem, M.

2000-01-01

Stripping uranium from Dehpa/kerosene solvent is a crucial step in the recovery of uranium. Stripping was studied using different stripping media mainly ammonium carbonate, phosphoric acid, sulfuric acid, hydrochloric acid and nitric acid. Stripping was measured at different operating conditions such as aqueous concentrations, temperatures, and Dehpa/kerosene concentrations. The results obtained showed that stripping by acid media increases with the acid concentration and follows the order: HF > H sub 3 Po sub 4 > H sub 2 S O sub 4 > HCl > HNO sub 3. To achieve higher stripping by phosphoric acid it was found necessary to increase the temperature to 50 deg C, the acid concentration to 5 mol/l and to reduce the uranium to U sup 4 sup +. Stripping by basic media was found to increase with increasing concentration of the stripping media and to follow the order: Na sub 2 CO sub 3 > (NH sub 4) sub 2 CO sub 3 > NH sub 4 HCO sub 3. Stripping by ammonium carbonate was found to increase with temperature and carbonate concentration. The stripping was optimized at 0.5 mol/l carbonate concentration and at a temperature of 50 deg C. Stripping was decreased by increasing concentration of Dehpa in kerosene and was depressed more by adding the synergant TOPO to the Dehpa solvent especially at 1/4 mol/mol ratio. (author)

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).

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.

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

Stripping voltammetry in environmental and food analysis.

Science.gov (United States)

Brainina, K Z; Malakhova, N A; Stojko, N Y

2000-10-01

The review covers over 230 papers published mostly in the last 5 years. The goal of the review is to attract the attention of researchers and users to stripping voltammetry in particular, its application in environmental monitoring and analysis of foodstuffs. The sensors employed are impregnated graphite, carbon paste, thick film carbon/graphite and thin film metallic electrodes modified in-situ or beforehand. Hanging mercury drop electrodes and mercury coated glassy carbon electrodes are also mentioned. Strip and long-lived sensors for portable instruments and flow through systems are discussed as devices for future development and application of stripping voltammetry.

Prevalence of hepatitis-C virus genotypes and potential transmission risks in Malakand Khyber Pakhtunkhwa, Pakistan.

Science.gov (United States)

Nazir, Nausheen; Jan, Muhammad Rasul; Ali, Amjad; Asif, Muhammad; Idrees, Muhammad; Nisar, Mohammad; Zahoor, Muhammad; Abd El-Salam, Naser M

2017-08-22

Hepatitis C virus (HCV) is a leading cause of chronic liver disease and frequently progresses towards liver cirrhosis and Hepatocellular Carcinoma (HCC). This study aimed to determine the prevalence of HCV genotypes and their association with possible transmission risks in the general population of Malakand Division. Sum of 570 serum samples were collected during March 2011 to January 2012 from suspected patients visited to different hospitals of Malakand. The suspected sera were tested using qualitative PCR and were then subjected to molecular genotype specific assay. Quantitative PCR was also performed for determination of pre-treatment viral load in confirmed positive patients. Out of 570 serum samples 316 sera were seen positive while 254 sera were found negative using qualitative PCR. The positive samples were then subjected to genotyping assay out of 316, type-specific PCR fragments were seen in 271 sera while 45 samples were found untypable genotypes. Genotype 3a was seen as a predominant genotype (63.3%) with a standard error of ±2.7%. Cramer's V statistic and Liklihood-Ratio statistical procedures are used to measure the strength and to test the association, respectively, between the dependent variable, genotype, and explanatory variables (e.g. gender, risk, age and area/districts). The dependent variable, genotype, is observed statistically significant association with variable risk factors. This implies that the genotype is highly dependent on how the patient was infected. In contrast, the other covariates, for example, gender, age, and district (area) no statistical significant association are observed. The association between gender-age indicates that the mean age of female was older by 10.5 ± 2.3 years with 95% confidence level using t-statistic. It was concluded from the present study that the predominant genotype was 3a in the infected population of Malakand. This study also highlights the high prevalence rate of untypable genotypes which an

Utilization of a lateral flow colloidal gold immunoassay strip based on surface-enhanced Raman spectroscopy for ultrasensitive detection of antibiotics in milk

Science.gov (United States)

Shi, Qiaoqiao; Huang, Jie; Sun, Yaning; Yin, Mengqi; Hu, Mei; Hu, Xiaofei; Zhang, Zhijun; Zhang, Gaiping

2018-05-01

An ultrasensitive method for the detection of antibiotics in milk is developed based on inexpensive, simple, rapid and portable lateral flow immunoassay (LFI) strip, in combination with high sensitivity surface-enhanced Raman spectroscopy (SERS). In our strategy, an immunoprobe was prepared from colloidal gold (AuNPs) conjugated with both a monoclonal antibody against neomycin (NEO-mAb) and a Raman probe molecule 4-aminothiophenol (PATP). The competitive interaction with immunoprobe between free NEO and the coated antigen (NEO-OVA) resulted in the change of the amount of the immobilized immunoprobe on the paper substrate. The LFI procedure was completed within 15 min. The Raman intensity of PATP on the test line of the LFI strip was measured for the quantitative determination of NEO. The IC50 and the limit of detection (LOD) of this assay are 0.04 ng/mL and 0.216 pg/mL of NEO, respectively. There is no cross-reactivity (CR) of the assay with other compounds, showing high specificity of the assay. The recoveries for milk samples with added NEO are in the range of 89.7%-105.6% with the relative standard deviations (RSD) of 2.4%-5.3% (n = 3). The result reveals that this method possesses high specificity, sensitivity, reproducibility and stability, and can be used to detect a variety of antibiotic residues in milk samples.

Microfluidic cartridges for DNA purification and genotyping processed in standard laboratory instruments

Science.gov (United States)

Focke, Maximilian; Mark, Daniel; Stumpf, Fabian; Müller, Martina; Roth, Günter; Zengerle, Roland; von Stetten, Felix

2011-06-01

Two microfluidic cartridges intended for upgrading standard laboratory instruments with automated liquid handling capability by use of centrifugal forces are presented. The first microfluidic cartridge enables purification of DNA from human whole blood and is operated in a standard laboratory centrifuge. The second microfluidic catridge enables genotyping of pathogens by geometrically multiplexed real-time PCR. It is operated in a slightly modified off-the-shelf thermal cycler. Both solutions aim at smart and cost-efficient ways to automate work flows in laboratories. The DNA purification cartridge automates all liquid handling steps starting from a lysed blood sample to PCR ready DNA. The cartridge contains two manually crushable glass ampoules with liquid reagents. The DNA yield extracted from a 32 μl blood sample is 192 +/- 30 ng which corresponds to 53 +/- 8% of a reference extraction. The genotyping cartridge is applied to analyse isolates of the multi-resistant Staphyloccus aureus (MRSA) by real-time PCR. The wells contain pre-stored dry reagents such as primers and probes. Evaluation of the system with 44 genotyping assays showed a 100% specificity and agreement with the reference assays in standard tubes. The lower limit of detection was well below 10 copies of DNA per reaction.

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

Reducing Bias of Allele Frequency Estimates by Modeling SNP Genotype Data with Informative Missingness

Directory of Open Access Journals (Sweden)

Wan-Yu eLin

2012-06-01

Full Text Available The presence of missing single-nucleotide polymorphism (SNP genotypes is common in genetic data. For studies with low-density SNPs, the most commonly used approach to deal with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is appropriate only when the missingness is random. However, a given assay often has a different capability in genotyping heterozygotes and homozygotes, causing the phenomenon of ‘differential dropout’ in the sense that the missing rates of heterozygotes and homozygotes are different. In practice, differential dropout among genotypes exists in even carefully designed studies, such as the data from the HapMap project and the Wellcome Trust Case Control Consortium. In this study, we propose a statistical method to model the differential dropout among different genotypes. Compared with the naïve method, our method provides more accurate allele frequency estimates when the differential dropout is present. To demonstrate its practical use, we further apply our method to the HapMap data and a scleroderma data set.

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

eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology

Directory of Open Access Journals (Sweden)

Specht Günther

2009-05-01

Full Text Available Abstract Background High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects. Description We developed a database system for an efficient combination and management of phenotypes and genotypes (eCOMPAGT deriving from genetic epidemiological studies. eCOMPAGT securely stores and manages genotype and phenotype data and enables different user modes with different rights. Special attention was drawn on the import of data deriving from TaqMan and SNPlex genotyping assays. However, the database solution is adjustable to other genotyping systems by programming additional interfaces. Further important features are the scalability of the database and an export interface to statistical software. Conclusion eCOMPAGT can store, administer and connect phenotype data with all kinds of genotype data and is available as a downloadable version at http://dbis-informatik.uibk.ac.at/ecompagt.

Strip specimen tests for pipeline materials and girth welds

Energy Technology Data Exchange (ETDEWEB)

Mohr, William C. [Edison Welding Institute (EWI), Columbus, Ohio (United States)

2009-07-01

Strip specimen testing of pipeline materials has been widely applied as a method of getting data relevant to the performance of pipelines under axial direction loading. Comparisons of strip specimen against smaller standard tests (round tensile bar, fracture toughness specimens, polished round bars) and against full-scale or large-scale testing will be explored. Data from early-generation pipe welds from the 1920's to the 1940's to the most recent materials for offshore reeled pipe will be used for examples. Strip samples can provide full thickness information to take account of varying material properties or imperfection distribution through the thickness. Strip samples can also accommodate measurement of effects of the original surface finish or weld surface shape. Strip samples have more design flexibility than standard tests, but must be designed to limit stress concentrations and effects of local bending. (author)

MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance.

Science.gov (United States)

McGivney, Beatrice A; Browne, John A; Fonseca, Rita G; Katz, Lisa M; Machugh, David E; Whiston, Ronan; Hill, Emmeline W

2012-12-01

Myostatin, encoded by the MSTN gene, is a member of the TGF-β superfamily that regulates skeletal muscle development. A MSTN SNP significantly associated with Thoroughbred horse racing phenotypes has recently been identified as well as significant reductions in Thoroughbred skeletal muscle gene expression for three transcripts 400-1500 base pairs downstream of the MSTN gene following a period of training. Together, these findings indicate that MSTN genotypes may influence MSTN gene expression. To investigate this, MSTN mRNA expression was measured in biopsies from the middle gluteal muscle from 60 untrained yearling Thoroughbreds (C/C, n = 15; C/T, n = 28; T/T, n = 17) using two independent real-time qRT-PCR assays. MSTN gene expression was also evaluated in a subset (N = 33) of these animals using samples collected after a ten-month period of training. A significant association was observed between genotype and mRNA abundance for the untrained horses (assay I, P = 0.0237; assay II, P = 0.003559), with the C/C cohort having the highest MSTN mRNA levels, the T/T group the lowest levels and the C/T group intermediate levels. Following training, there was a significant decrease in MSTN mRNA (-3.35-fold; P = 6.9 × 10(-7) ), which was most apparent for the C/C cohort (-5.88-fold, P = 0.001). These data demonstrate the tight relationship between phenotype, genotype and gene expression at the MSTN gene in Thoroughbred racehorses. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Development of a rapid HRM genotyping method for detection of dog-derived Giardia lamblia.

Science.gov (United States)

Tan, Liping; Yu, Xingang; Abdullahi, Auwalu Yusuf; Wu, Sheng; Zheng, Guochao; Hu, Wei; Song, Meiran; Wang, Zhen; Jiang, Biao; Li, Guoqing

2015-11-01

Giardia lamblia is a zoonotic flagellate protozoan in the intestine of human and many mammals including dogs. To assess a threat of dog-derived G. lamblia to humans, the common dog-derived G. lamblia assemblages A, C, and D were genotyped by high-resolution melting (HRM) technology. According to β-giardin gene sequence, the qPCR-HRM primers BG5 and BG7 were designed. A series of experiments on the stability, sensitivity, and accuracy of the HRM method were also tested. Results showed that the primers BG5 and BG7 could distinguish among three assemblages A, C, and D, which Tm value differences were about 1 °C to each other. The melting curves of intra-assay reproducibility were almost coincided, and those of inter-assay reproducibility were much the same shape. The lowest detection concentration was about 5 × 10(-6)-ng/μL sample. The genotyping results from 21 G. lamblia samples by the HRM method were in complete accordance with sequencing results. It is concluded that the HRM genotyping method is rapid, stable, specific, highly sensitive, and suitable for clinical detection and molecular epidemiological survey of dog-derived G. lamblia.

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.

Fatigue of graphite/epoxy buffer strip panels with center cracks

Science.gov (United States)

Bigelow, C. A.

1985-01-01

The effects of fatigue loading on the behavior of graphite/epoxy panels with either S-Glass or Kevlar-49 buffer strips is studied. Buffer strip panels are fatigued and tested in tension to measure their residual strength with crack-like damage. Panels are made with 45/0/-45/90 sub 2s layup with either S-Glass or Kevlar-49 buffer strip material. The buffer strips are parallel to the loading direction and made by replacing narrow strips of the 0-degree graphite plies with strips of either 0-degree S-Glass/epoxy or Kevlar-49/epoxy on a one-for-one basis. The panels are subjected to a fatigue loading spectrum MINITWIST, the shortened version of the standardized load program for the wing lower surface of a transport aircraft. Two levels of maximum strain are used in the spectrum with three durations of the fatigue spectrum. One group of panels is preloaded prior to the application of the fatigue cycling. The preload consists of statistically loading the spectrum in tension until the crack-tip damage zone reaches the ajacent buffer strips. After fatigue loading, all specimens are statistically loaded in tension to failure to determine their residual strengths.

Detection of knockdown resistance (kdr mutations in Anopheles gambiae: a comparison of two new high-throughput assays with existing methods

Directory of Open Access Journals (Sweden)

Ball Amanda

2007-08-01

Full Text Available Abstract Background Knockdown resistance (kdr is a well-characterized mechanism of resistance to pyrethroid insecticides in many insect species and is caused by point mutations of the pyrethroid target site the para-type sodium channel. The presence of kdr mutations in Anopheles gambiae, the most important malaria vector in Africa, has been monitored using a variety of molecular techniques. However, there are few reports comparing the performance of these different assays. In this study, two new high-throughput assays were developed and compared with four established techniques. Methods Fluorescence-based assays based on 1 TaqMan probes and 2 high resolution melt (HRM analysis were developed to detect kdr alleles in An. gambiae. Four previously reported techniques for kdr detection, Allele Specific Polymerase Chain Reaction (AS-PCR, Heated Oligonucleotide Ligation Assay (HOLA, Sequence Specific Oligonucleotide Probe – Enzyme-Linked ImmunoSorbent Assay (SSOP-ELISA and PCR-Dot Blot were also optimized. The sensitivity and specificity of all six assays was then compared in a blind genotyping trial of 96 single insect samples that included a variety of kdr genotypes and African Anopheline species. The relative merits of each assay was assessed based on the performance in the genotyping trial, the length/difficulty of each protocol, cost (both capital outlay and consumable cost, and safety (requirement for hazardous chemicals. Results The real-time TaqMan assay was both the most sensitive (with the lowest number of failed reactions and the most specific (with the lowest number of incorrect scores. Adapting the TaqMan assay to use a PCR machine and endpoint measurement with a fluorimeter showed a slight reduction in sensitivity and specificity. HRM initially gave promising results but was more sensitive to both DNA quality and quantity and consequently showed a higher rate of failure and incorrect scores. The sensitivity and specificity of AS

Detection of knockdown resistance (kdr) mutations in Anopheles gambiae: a comparison of two new high-throughput assays with existing methods

Science.gov (United States)

Bass, Chris; Nikou, Dimitra; Donnelly, Martin J; Williamson, Martin S; Ranson, Hilary; Ball, Amanda; Vontas, John; Field, Linda M

2007-01-01

Background Knockdown resistance (kdr) is a well-characterized mechanism of resistance to pyrethroid insecticides in many insect species and is caused by point mutations of the pyrethroid target site the para-type sodium channel. The presence of kdr mutations in Anopheles gambiae, the most important malaria vector in Africa, has been monitored using a variety of molecular techniques. However, there are few reports comparing the performance of these different assays. In this study, two new high-throughput assays were developed and compared with four established techniques. Methods Fluorescence-based assays based on 1) TaqMan probes and 2) high resolution melt (HRM) analysis were developed to detect kdr alleles in An. gambiae. Four previously reported techniques for kdr detection, Allele Specific Polymerase Chain Reaction (AS-PCR), Heated Oligonucleotide Ligation Assay (HOLA), Sequence Specific Oligonucleotide Probe – Enzyme-Linked ImmunoSorbent Assay (SSOP-ELISA) and PCR-Dot Blot were also optimized. The sensitivity and specificity of all six assays was then compared in a blind genotyping trial of 96 single insect samples that included a variety of kdr genotypes and African Anopheline species. The relative merits of each assay was assessed based on the performance in the genotyping trial, the length/difficulty of each protocol, cost (both capital outlay and consumable cost), and safety (requirement for hazardous chemicals). Results The real-time TaqMan assay was both the most sensitive (with the lowest number of failed reactions) and the most specific (with the lowest number of incorrect scores). Adapting the TaqMan assay to use a PCR machine and endpoint measurement with a fluorimeter showed a slight reduction in sensitivity and specificity. HRM initially gave promising results but was more sensitive to both DNA quality and quantity and consequently showed a higher rate of failure and incorrect scores. The sensitivity and specificity of AS-PCR, SSOP-ELISA, PCR Dot

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.

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.

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

A simple and inexpensive point-of-care test for hepatitis B surface antigen detection: serological and molecular evaluation.

Science.gov (United States)

Gish, R G; Gutierrez, J A; Navarro-Cazarez, N; Giang, K; Adler, D; Tran, B; Locarnini, S; Hammond, R; Bowden, S

2014-12-01

Early identification of chronic hepatitis B is important for optimal disease management and prevention of transmission. Cost and lack of access to commercial hepatitis B surface antigen (HBsAg) immunoassays can compromise the effectiveness of HBV screening in resource-limited settings and among marginalized populations. High-quality point-of-care (POC) testing may improve HBV diagnosis in these situations. Currently available POC HBsAg assays are often limited in sensitivity. We evaluated the NanoSign(®) HBs POC chromatographic immunoassay for its ability to detect HBsAg of different genotypes and with substitutions in the 'a' determinant. Thirty-seven serum samples from patients with HBV infection, covering HBV genotypes A-G, were assessed for HBsAg titre with the Roche Elecsys HBsAg II quantification assay and with the POC assay. The POC assay reliably detected HBsAg at a concentration of at least 50 IU/mL for all genotypes, and at lower concentrations for some genotypes. Eight samples with substitutions in the HBV 'a' determinant were reliably detected after a 1/100 dilution. The POC strips were used to screen serum samples from 297 individuals at risk for HBV in local clinical settings (health fairs and outreach events) in parallel with commercial laboratory HBsAg testing (Quest Diagnostics EIA). POC testing was 73.7% sensitive and 97.8% specific for detection of HBsAg. Although the POC test demonstrated high sensitivity over a range of genotypes, false negatives were frequent in a clinical setting. Nevertheless, the POC assay offers advantages for testing in both developed and resource-limited countries due to its low cost (0.50$) and immediately available results. © 2014 John Wiley & Sons Ltd.

The development of drift-strip detectors based on CdZnTe

DEFF Research Database (Denmark)

Gostilo, V.; Budtz-Jørgensen, Carl; Kuvvetli, Irfan

2002-01-01

The design and technological development of a CdZnTe drift strip detector is described. The device is based on a monocrystal of dimensions 10 x 10 x 3 mm(3) and has a pitch of 200 mum and a strip width of 100 mum. The strip length is 9.5 mm. The distribution of the leakage currents of the strips...

Eddy current distribution and lift force for finite MAGLEV strips

Energy Technology Data Exchange (ETDEWEB)

Atherton, D L; Eastham, A R; Fombrun, C; Chong, M

1974-07-01

The transverse distribution of induced eddy currents across a flat conducing strip of finite width, due to a rectangular dc magnet moving above it, was modelled experimentally, and was compared with that calculated for an infinite sheet. The electrodynamic suspension was simulated by means of a stationary ac-excited copper magnet suspended above an aluminum strip, and the induced surface current density was measured by a voltage pickup probe connected to a lock-in amplifier. The effect of reducing strip width is examined and shown to produce high current densities close to the edges. These results are related to the variation of lift force with strip width, determined by impedance modelling. A slight enhancement of lift is evident for intermediate strip widths.

Expression of Hepatitis C Virus Core and E2 antigenic recombinant proteins and their use for development of diagnostic assays.

Science.gov (United States)

Ali, Amjad; Nisar, Muhammad; Idrees, Muhammad; Rafique, Shazia; Iqbal, Muhammad

2015-05-01

Early diagnosis of HCV infection is based on detection of antibodies against HCV proteins using recombinant viral antigens. The present study was designed to select, clone and express the antigenic regions of Core and E2 genes from local HCV-3a genotype and to utilize the antigenic recombinant proteins (Core & E2) to develop highly sensitive, specific and economical diagnostic assays for detection of HCV infection. The antigenic sites were determined within Core and E2 genes and were then cloned in pET-28a expression vector. The right orientation of the desired inserted fragments of Core and E2 were confirmed via sequencing prior to expression and were then transformed in BL21 (DE3) pLysS strains of E. coli and induced with 0.5mM Isopropyl-b-D-thiogalactopyranoside (IPTG) for the production of antigenic recombinant proteins. The produced truncated antigens were then purified by Nickel affinity chromatography and were confirmed by western blotting, immunoblotting and enzyme-linked immunosorbent assay (ELISA). The expressed Core and E2 recombinant antigens were used to develop immunoblotting assay for the detection of anti-HCV antibodies in sera. With immunoblotting, a total of 93-HCV infected sera and 35-HCV negative individuals were tested for the presence of anti-HCV antibodies to the Core and E2 antigens. Recombinant antigen showed 100% reactivity against HCV infected sera, with no cross reactivity against HCV-negative sera. The immunoblot assay mixture of recombinant antigens (Core+E2) showed a strong reaction intensity in the test area (TA) as compared to the individual truncated Core and E2 recombinant antigens. In the in-house ELISA assay, mixed Core and E2 recombinant antigens showed 100% reactivity against a standardized panel of 150-HCV-positive sera and non reactivity against a standardized panel of 150 HCV-negative sera while also being non reactive to sera positive for other viral infections. The antigenic recombinant antigens also were tested for the

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.

LYCORIS - A Large Area Strip Telescope

CERN Document Server

Krämer, U; Stanitzki, M; Wu, M

2018-01-01

The LYCORIS Large Area Silicon Strip Telescope for the DESY II Test Beam Facility is presented. The DESY II Test Beam Facility provides elec- tron and positron beams for beam tests of up to 6 GeV. A new telescope with a large 10 × 20 cm2 coverage area based on a 25 μm pitch strip sensor is to be installed within the PCMAG 1 T solenoid. The current state of the system is presented.

Combined effect of bulk and surface damage on strip insulation properties of proton irradiated n$^{+}$-p silicon strip sensors

CERN Document Server

Dalal, R; Ranjan, K; Moll, M; Elliott-Peisert, A

2014-01-01

Silicon sensors in next generation hadron colliders willface a tremendously harsh radiation environment. Requirement tostudy rarest reaction channels with statistical constraints hasresulted in a huge increment in radiation flux, resulting in bothsurface damage and bulk damage. For sensors which are used in acharged hadron environment, both of these degrading processes takeplace simultaneously. Recently it has been observed in protonirradiated n$^{+}$-p Si strip sensors that n$^{+}$ strips had a goodinter-strip insulation with low values of p-spray and p-stop dopingdensities which is contrary to the expected behaviour from thecurrent understanding of radiation damage. In this work a simulationmodel has been devised incorporating radiation damage to understandand provide a possible explanation to the observed behaviour ofirradiated sensors.

Single Nucleotide Polymorphisms in Common Bean: Their Discovery and Genotyping Using a Multiplex Detection System

Directory of Open Access Journals (Sweden)

E. Gaitán-Solís

2008-11-01

Full Text Available Single nucleotide polymorphism (SNP markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean ( L. by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA and to compare sequencing results with those obtained using single base extension (SBE assays on the Luminex-100 system for use in high-throughput germplasm evaluation. We assessed the frequency of SNPs in 47 fragments of common bean DNA, using SBE as the evaluation methodology. We conducted a sequence analysis of 10 genotypes of cultivated and wild beans belonging to the Mesoamerican and Andean genetic pools of . For the 10 genotypes evaluated, a total of 20,964 bp of sequence were analyzed in each genotype and compared, resulting in the discovery of 239 SNPs and 133 InDels, giving an average SNP frequency of one per 88 bp and an InDel frequency of one per 157 bp. This is the equivalent of a nucleotide diversity (θ of 6.27 × 10. Comparisons with the SNP genotypes previously obtained by direct sequencing showed that the SBE assays on the Luminex-100 were accurate, with 2.5% being miscalled and 1% showing no signal. These results indicate that the Luminex-100 provides a high-throughput system that can be used to analyze SNPs in large samples of genotypes both for purposes of assessing diversity and also for mapping studies.

Screening of a Brassica napus bacterial artificial chromosome library using highly parallel single nucleotide polymorphism assays

Science.gov (United States)

2013-01-01

Background Efficient screening of bacterial artificial chromosome (BAC) libraries with polymerase chain reaction (PCR)-based markers is feasible provided that a multidimensional pooling strategy is implemented. Single nucleotide polymorphisms (SNPs) can be screened in multiplexed format, therefore this marker type lends itself particularly well for medium- to high-throughput applications. Combining the power of multiplex-PCR assays with a multidimensional pooling system may prove to be especially challenging in a polyploid genome. In polyploid genomes two classes of SNPs need to be distinguished, polymorphisms between accessions (intragenomic SNPs) and those differentiating between homoeologous genomes (intergenomic SNPs). We have assessed whether the highly parallel Illumina GoldenGate® Genotyping Assay is suitable for the screening of a BAC library of the polyploid Brassica napus genome. Results A multidimensional screening platform was developed for a Brassica napus BAC library which is composed of almost 83,000 clones. Intragenomic and intergenomic SNPs were included in Illumina’s GoldenGate® Genotyping Assay and both SNP classes were used successfully for screening of the multidimensional BAC pools of the Brassica napus library. An optimized scoring method is proposed which is especially valuable for SNP calling of intergenomic SNPs. Validation of the genotyping results by independent methods revealed a success of approximately 80% for the multiplex PCR-based screening regardless of whether intra- or intergenomic SNPs were evaluated. Conclusions Illumina’s GoldenGate® Genotyping Assay can be efficiently used for screening of multidimensional Brassica napus BAC pools. SNP calling was specifically tailored for the evaluation of BAC pool screening data. The developed scoring method can be implemented independently of plant reference samples. It is demonstrated that intergenomic SNPs represent a powerful tool for BAC library screening of a polyploid genome

Induction heating in in-line strip production process

International Nuclear Information System (INIS)

Costa, P.; Santinelli, M.

1995-05-01

ISP (In-line Strip Production), a continuous process for steel strip production, has recently been set in an italian innovative plant, where ecological impact and power requirements are lighter than usual. This report describes the studies performed by ENEA (Italian Agency for New Technologies, Energy and the Environment), while a prototype reheating facility was arranged by Acciaieria ISP in Cremona (Italy). The authors, after a study of the prototype electromagnetic field, calculate the heating rate, with the thermal network method. Then they detect, with a 1-D-FEM, the heat diffusion through the strip cross section. Afterward, since the heat distribution depends on the eddy current density one, which is given by the magnetic field distribution, the authors, with a 3-D-FEM, carry out a coupled, electromagnetic and thermal, analysis in time domain. The strip temperature map is established by the balance between skin depth heating and surface cooling: a thermal analysis, performed with a moving 2-D-FEM, take into account the effects of the different heating and cooling situations, originated by the strip moving at a speed of 6m/min through four consecutive reheating facilities. The temperatures of a strip sample heated by the prototype have been monitored, acquired by a computer and related with the simulation results. The little difference between experiment and simulation assessed the qualitative and quantitative validity of this analysis, that has come out to be a tool, useful to evaluate the effects of possible improvements to the ISP process

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)

Development of a One-Step Multiplex PCR Assay for Differential Detection of Major Mycobacterium Species.

Science.gov (United States)

Chae, Hansong; Han, Seung Jung; Kim, Su-Young; Ki, Chang-Seok; Huh, Hee Jae; Yong, Dongeun; Koh, Won-Jung; Shin, Sung Jae

2017-09-01

The prevalence of tuberculosis continues to be high, and nontuberculous mycobacterial (NTM) infection has also emerged worldwide. Moreover, differential and accurate identification of mycobacteria to the species or subspecies level is an unmet clinical need. Here, we developed a one-step multiplex PCR assay using whole-genome analysis and bioinformatics to identify novel molecular targets. The aims of this assay were to (i) discriminate between the Mycobacterium tuberculosis complex (MTBC) and NTM using rv0577 or RD750, (ii) differentiate M. tuberculosis ( M. tuberculosis ) from MTBC using RD9, (iii) selectively identify the widespread M. tuberculosis Beijing genotype by targeting mtbk_20680 , and (iv) simultaneously detect five clinically important NTM ( M. avium , M. intracellulare , M. abscessus , M. massiliense , and M. kansasii ) by targeting IS 1311 , DT1, mass_3210 , and mkan_rs12360 An initial evaluation of the multiplex PCR assay using reference strains demonstrated 100% specificity for the targeted Mycobacterium species. Analytical sensitivity ranged from 1 to 10 pg for extracted DNA and was 10 3 and 10 4 CFU for pure cultures and nonhomogenized artificial sputum cultures, respectively, of the targeted species. The accuracy of the multiplex PCR assay was further evaluated using 55 reference strains and 94 mycobacterial clinical isolates. Spoligotyping, multilocus sequence analysis, and a commercial real-time PCR assay were employed as standard assays to evaluate the multiplex PCR assay with clinical M. tuberculosis and NTM isolates. The PCR assay displayed 100% identification agreement with the standard assays. Our multiplex PCR assay is a simple, convenient, and reliable technique for differential identification of MTBC, M. tuberculosis , M. tuberculosis Beijing genotype, and major NTM species. Copyright © 2017 American Society for Microbiology.

31 CFR 356.31 - How does the STRIPS program work?

Science.gov (United States)

2010-07-01

... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false How does the STRIPS program work? 356.31 Section 356.31 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued...) Miscellaneous Provisions § 356.31 How does the STRIPS program work? (a) General. Notes or bonds may be “stripped...

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.

Magnetic ring for stripping enhancement

International Nuclear Information System (INIS)

Selph, F.

1992-10-01

A ring designed to recycle ions through a stripping medium offers the possibility for increasing output of the desired charge state by up to 4x. This could be a very important component of a Radioactive Nuclear Beam Facility. In order for such a ring to work effectively it must satisfy certain design conditions. These include achromaticity at the stripper, a dispersed region for an extraction magnet, and a number of first and higher order optics constraints which are necessary to insure that the beam emittance is not degraded unduly by the ring. An example is given of a candidate design of a stripping ring

Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus.

Science.gov (United States)

Rogers, Stephanie M; Payton, Mark; Allen, Robert W; Melcher, Ulrich; Carver, Jesse; Fletcher, Jacqueline

2012-05-17

The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus. This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors. Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA. The molecular typing method presented is one tool that could be incorporated into the forensic science tool box after a thorough

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

Do repeated rumble strip hits improve driver alertness?

NARCIS (Netherlands)

Watling, C.N.; Akerstedt, T.; Kecklund, L.G.; Anund, A.

2016-01-01

Driving while sleepy is associated with increased crash risk. Rumble strips are designed to alert a sleepy or inattentive driver when they deviate outside their driving lane. The current study sought to examine the effects of repeated rumble strip hits on levels of physiological and subjective

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

intraepithelial neoplasia (CIN) in 2.5 years after the baseline testing were determined from the national pathology register. HPV-positive women undergoing primary screening having concordant samples were more likely to harbor high-risk infections and less likely to harbor only low-risk infections than women......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 same HPV infections. Here, we determined the characteristics of the concordant (all four assays returning a positive HPV test result) and discordant samples (all other HPV-positive samples) in primary cervical screening at 30-65 years (n=2859) and in a concurrent referral population from the same...

A displacement assay for the sensing of carbohydrate using zinc oxide biotracers

International Nuclear Information System (INIS)

Yang Chi; Xu Chunxiang; Wang Xuemei; Xiao Zhongdang; Gu Baoxiang

2012-01-01

Due to the high isoelectric point of the ZnO quantum dots (QDs), ZnO QDs were employed as biolabels for carbohydrates to construct a biosensor for determination of the carcinoembryonic antigen (CEA), which act as the carbohydrate. The assay was based on the competition between a quantum dots labeled CEA and analyte CEA using concanavalin A (Con A) as the recognition element. The extent of completion was monitored by the square wave stripping voltammetry. The displacement assay results showed that there are two changes model of the current response to the analyte CEA concentration (0–30 ng/mL and 30–80 ng/mL). The most likely reason for this was also discussed in the paper.

Procedures for identifying S-allele genotypes of Brassica.

Science.gov (United States)

Wallace, D H

1979-11-01

Procedures are described for efficient selection of: (1) homozygous and heterozygous S-allele genotypes; (2) homozygous inbreds with the strong self- and sib-incompatibility required for effective seed production of single-cross F1 hybrids; (3) heterozygous genotypes with the high self- and sib-incompatibility required for effective seed production of 3- and 4-way hybrids.From reciprocal crosses between two first generation inbred (I1) plants there are three potential results: both crosses are incompatible; one is incompatible and the other compatible; and both are compatible. Incompatibility of both crosses is useful information only when combined with data from other reciprocal crosses. Each compatible cross, depending on whether its reciprocal is incompatible or compatible, dictates alternative reasoning and additional reciprocal crosses for efficiently and simultaneously identifying: (A) the S-allele genotype of all individual I1 plants, and (B) the expressions of dominance or codominance in pollen and stigma (sexual organs) of an S-allele heterozygous genotype. Reciprocal crosses provide the only efficient means of identifying S-allele genotypes and also the sexual-organ x S-allele-interaction types.Fluorescent microscope assay of pollen tube penetration into the style facilitates quantitation within 24-48 hours of incompatibility and compatibility of the reciprocal crosses. A procedure for quantitating the reciprocal difference is described that maximizes informational content of the data about interactions between S alleles in pollen and stigma of the S-allele-heterozygous genotype.Use of the non-inbred Io generation parent as a 'known' heterozygous S-allele genotype in crosses with its first generation selfed (I1) progeny usually reduces at least 7 fold the effort required for achieving objectives 1, 2, and 3, compared to the method of making reciprocal crosses only among I1 plants.Identifying the heterozygous and both homozygous S-allele genotypes during

Evaluation of a new test, genotype HelicoDR, for molecular detection of antibiotic resistance in Helicobacter pylori.

Science.gov (United States)

Cambau, Emmanuelle; Allerheiligen, Vera; Coulon, Céline; Corbel, Céline; Lascols, Christine; Deforges, Lionel; Soussy, Claude-James; Delchier, Jean-Charles; Megraud, Francis

2009-11-01

The eradication rate of Helicobacter pylori by standard therapy is decreasing due to antibiotic resistance, mainly to clarithromycin. Our aim was to provide a new molecular test to guide the treatment of new and relapsed cases. We first studied 126 H. pylori strains for phenotypic (MIC) and genotypic resistance to clarithromycin (rrl mutation) and levofloxacin (gyrA mutation) and then developed a DNA strip genotyping test on the basis of the correlation results and literature data. Clinical strains (n = 92) and gastric biopsy specimens containing H. pylori (n = 105) were tested blindly with the new molecular test GenoType HelicoDR. The presence of mutations or the absence of hybridization with wild-type sequences was predictive, in rrl for clarithromycin resistance in 91 cases (mostly the A2147G mutation) and in gyrA for levofloxacin resistance in 58 cases (mutations at codon 87 or 91). Genotyping revealed a mix of genotypes in 33% of the cases, reflecting a coinfection or selection for resistant mutants. The sensitivity and specificity of detecting resistance were 94% and 99% for clarithromycin and 87% and 98.5% for levofloxacin, respectively. The concordance scores were 0.96 for clarithromycin and 0.94 for levofloxacin. With global resistance rates of 46% for clarithromycin and 25% for levofloxacin, which were observed for consecutive positive biopsy specimens from 2007 and 2008, the positive and negative predictive values for detecting resistance were 99% and 94% for clarithromycin and 96% and 96% for fluoroquinolone. GenoType HelicoDR is efficient at detecting mutations predictive of antibiotic resistance in H. pylori when applied to strains or directly to gastric biopsy specimens.

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

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.

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.)

Refuges, flower strips, biodiversity and agronomic interest.

Science.gov (United States)

Roy, Grégory; Wateau, Karine; Legrand, Mickaël; Oste, Sandrine

2008-01-01

Several arthropods are natural predators of pests, and they are able to reduce and control their population development. FREDON Nord Pas-de-Calais (Federation Regionate de Defense contre les Organismes Nuisibles = Regional Federation for Pest Control) has begun for a long time to form farmers to the recognition of beneficial arthropods and to show them their usefulness. These beneficial insects or arachnids are present everywhere, in orchards and even in fields which are areas relatively poor in biodiversity. Adults feed in the flower strips instead larvae and some adults feed on preys such as aphids or caterpillars. Most of the time, beneficial insects can regulate pest but sometimes, in agricultural area, they can't make it early enough and efficiently. Their action begin too late and there biodiversity and number are too low. It's possible to enhance their action by manipulating the ecological infrastructures, like sewing flower strips or installing refuges. Flower strips increase the density of natural enemies and make them be present earlier in the field in order to control pests. Refuges permit beneficial's to spend winter on the spot. So they're able to be active and to grow in number earlier. From 2004 to 2007, on the one hand, FREDON Nord Pas-de-Calais has developed a research program. Its purpose was to inventory practices and also tools and means available and to judge the advisability of using such or such beneficial refuge in orchards. On the second hand, it studied the impact in orchard of refuges on population of beneficial's and the difference there were between manufactured refuges and homemade refuges. Interesting prospects were obtained with some of them. Otherwise, since 2003, FREDON has studied flower strips influence on beneficial population and their impact on pest control. In cabbage fields, results of trials have shown that flower strips lead to a reduction of aphid number under acceptable economic level, up to 50 meters from flower strips

Optimization of the process of steel strip perforation and nickel platting for the purpose of elimination of trichloroethylene from the cleaning process of perforated steel strip

Directory of Open Access Journals (Sweden)

Petrović Aleksandra B.

2009-01-01

Full Text Available In the production of pocket type electrodes for Ni-Cd batteries perforation of proper steel strips and then nickel platting of perforated steel strips were made. In the nickel platting process, the organic solvent, trichloroethylene, has previously been used for cleaning. Due to the carcinogenic nature of trichloroethylene and the many operations previously required during cleaning, it was considered to do cleaning of perforated steel strips without use of the mentioned organic solvent. In the purpose of elimination of trichloroethylene from the cleaning process of perforated steel strips, the tests of perforation of steel strips with use of oils of different viscosity were made. It was shown that there was no dysfunction during the work of the perforation plants, meaning there was no additional heating of the strips, deterring of the steel filings, nor excessive wearing of the perforation apparatus. The perforation percent was the same irrelevant of the viscosity of the used oil. Before being perforated using the oils with different viscosity, the nickel platting steel strips were cleaned in different degreasers (based on NaOH as well as on KOH. It was shown that efficient cleaning without the use of trichloroethylene is possible with the use of oil with smaller viscosity in the perforated steel strips process and the degreaser based on KOH in the cleaning process, before nickel platting. It also appeared that the alkali degreaser based on KOH was more efficient, bath corrections were made less often and the working period of the baths was longer, which all in summary means less quantity of chemicals needed for degreasing of perforated steel strips.

Comparison of three PCR-based assays for SNP genotyping in sugar beet

Science.gov (United States)

Background: PCR allelic discrimination technologies have broad applications in the detection of single nucleotide polymorphisms (SNPs) in genetics and genomics. The use of fluorescence-tagged probes is the leading method for targeted SNP detection, but assay costs and error rates could be improved t...

Content of Phenolic Compounds and Antioxidant Capacity in Fruits of Apricot Genotypes

Directory of Open Access Journals (Sweden)

Helena Skutkova

2010-09-01

Full Text Available Research on natural compounds is increasingly focused on their effects on human health. In this study, we were interested in the evaluation of nutritional value expressed as content of total phenolic compounds and antioxidant capacity of new apricot (Prunus armeniaca L. genotypes resistant against Plum pox virus (PPV cultivated on Department of Fruit Growing of Mendel University in Brno. Fruits of twenty one apricot genotypes were collected at the onset of consumption ripeness. Antioxidant capacities of the genotypes were determined spectrometrically using DPPH• (1,1-diphenyl-2-picryl-hydrazyl free radicals scavenging test, TEAC (Trolox Equivalent Antioxidant Capacity, and FRAP (Ferric Reducing Antioxidant Powermethods. The highest antioxidant capacities were determined in the genotypes LE-3228 and LE-2527, the lowest ones in the LE-985 and LE-994 genotypes. Moreover, close correlation (r = 0.964 was determined between the TEAC and DPPH assays. Based on the antioxidant capacity and total polyphenols content, a clump analysis dendrogram of the monitored apricot genotypes was constructed. In addition, we optimized high performance liquid chromatography coupled with tandem electrochemical and spectrometric detection and determined phenolic profile consisting of the following fifteen phenolic compounds: gallic acid, 4-aminobenzoic acid, chlorogenic acid, ferulic acid, caffeic acid, procatechin, salicylic acid, p-coumaric acid, the flavonols quercetin and quercitrin, the flavonol glycoside rutin, resveratrol, vanillin, and the isomers epicatechin, (–- and (+- catechin.

Joint effect of MCP-1 genotype GG and MMP-1 genotype 2G/2G increases the likelihood of developing pulmonary tuberculosis in BCG-vaccinated individuals.

Directory of Open Access Journals (Sweden)

Malathesha Ganachari

2010-01-01

Full Text Available We previously reported that the -2518 MCP-1 genotype GG increases the likelihood of developing tuberculosis (TB in non-BCG-vaccinated Mexicans and Koreans. Here, we tested the hypothesis that this genotype, alone or together with the -1607 MMP-1 functional polymorphism, increases the likelihood of developing TB in BCG-vaccinated individuals. We conducted population-based case-control studies of BCG-vaccinated individuals in Mexico and Peru that included 193 TB cases and 243 healthy tuberculin-positive controls from Mexico and 701 TB cases and 796 controls from Peru. We also performed immunohistochemistry (IHC analysis of lymph nodes from carriers of relevant two-locus genotypes and in vitro studies to determine how these variants may operate to increase the risk of developing active disease. We report that a joint effect between the -2518 MCP-1 genotype GG and the -1607 MMP-1 genotype 2G/2G consistently increases the odds of developing TB 3.59-fold in Mexicans and 3.9-fold in Peruvians. IHC analysis of lymph nodes indicated that carriers of the two-locus genotype MCP-1 GG MMP-1 2G/2G express the highest levels of both MCP-1 and MMP-1. Carriers of these susceptibility genotypes might be at increased risk of developing TB because they produce high levels of MCP-1, which enhances the induction of MMP-1 production by M. tuberculosis-sonicate antigens to higher levels than in carriers of the other two-locus MCP-1 MMP-1 genotypes studied. This notion was supported by in vitro experiments and luciferase based promoter activity assay. MMP-1 may destabilize granuloma formation and promote tissue damage and disease progression early in the infection. Our findings may foster the development of new and personalized therapeutic approaches targeting MCP-1 and/or MMP-1.

Joint effect of MCP-1 genotype GG and MMP-1 genotype 2G/2G increases the likelihood of developing pulmonary tuberculosis in BCG-vaccinated individuals.

Science.gov (United States)

Ganachari, Malathesha; Ruiz-Morales, Jorge A; Gomez de la Torre Pretell, Juan C; Dinh, Jeffrey; Granados, Julio; Flores-Villanueva, Pedro O

2010-01-25

We previously reported that the -2518 MCP-1 genotype GG increases the likelihood of developing tuberculosis (TB) in non-BCG-vaccinated Mexicans and Koreans. Here, we tested the hypothesis that this genotype, alone or together with the -1607 MMP-1 functional polymorphism, increases the likelihood of developing TB in BCG-vaccinated individuals. We conducted population-based case-control studies of BCG-vaccinated individuals in Mexico and Peru that included 193 TB cases and 243 healthy tuberculin-positive controls from Mexico and 701 TB cases and 796 controls from Peru. We also performed immunohistochemistry (IHC) analysis of lymph nodes from carriers of relevant two-locus genotypes and in vitro studies to determine how these variants may operate to increase the risk of developing active disease. We report that a joint effect between the -2518 MCP-1 genotype GG and the -1607 MMP-1 genotype 2G/2G consistently increases the odds of developing TB 3.59-fold in Mexicans and 3.9-fold in Peruvians. IHC analysis of lymph nodes indicated that carriers of the two-locus genotype MCP-1 GG MMP-1 2G/2G express the highest levels of both MCP-1 and MMP-1. Carriers of these susceptibility genotypes might be at increased risk of developing TB because they produce high levels of MCP-1, which enhances the induction of MMP-1 production by M. tuberculosis-sonicate antigens to higher levels than in carriers of the other two-locus MCP-1 MMP-1 genotypes studied. This notion was supported by in vitro experiments and luciferase based promoter activity assay. MMP-1 may destabilize granuloma formation and promote tissue damage and disease progression early in the infection. Our findings may foster the development of new and personalized therapeutic approaches targeting MCP-1 and/or MMP-1.

Polymer Inclusion Membranes with Strip Dispersion

Directory of Open Access Journals (Sweden)

Yueh-Hsien Li

2017-06-01

Full Text Available The present work investigated the permeation of indium ions through a polymer inclusion membrane (PIM, prepared with cellulose triacetate (CTA as the base polymer, tris(2-butoxyethyl phosphate (TBEP as the plasticizer and di-(2-ethylhexylphosphoric acid (D2EHPA as the extractant. With 5 M HCl aqueous solution as the strip solution, we observed an initial indium permeability of 2.4 × 10−4 m/min. However, the permeability decreases with time, dropping to about 3.4 × 10−5 m/min after 200 min of operation. Evidence was obtained showing that hydrolysis of CTA occurred, causing a dramatic decrease in the feed pH (protons transported from strip to feed solutions and a loss of extractant and plasticizer from the membrane, and then leading to the loss of indium permeability. To alleviate the problem of hydrolysis, we proposed an operation scheme called polymer inclusion membranes with strip dispersion: dispersing the strip solution in extractant-containing oil and then bringing the dispersion to contact with the polymer membrane. Since the strong acid was dispersed in oil, the membrane did not directly contact the strong acid at all times, and membrane hydrolysis was thus alleviated and the loss of indium permeability was effectively prevented. With the proposed scheme, a stable indium permeability of 2.5 × 10−4 m/min was obtained during the whole time period of the permeation experiment.

[Rd7 genotyping of M. tuberculosis strains isolated from patients with lung tuberculosis in different areas of Kazakhstan].

Science.gov (United States)

Demkin, V V; Korneva, I N; Riazanova, Iu A; Muminov, T A; Beĭsembaeva, Sh A; Zhakipbaeva, B T; Shopaeva, G A; Dauletbakova, A M

2008-01-01

A three-primer PCR assay was designed for detection of possible deletions in the RD7 region of the Mycobacterium tuberculosis complex chromosome. The assay produced amplicons of different size depending on the presence or absence of the deletions. The PCR assay was applied to 176 isolates from patients with lung tuberculosis collected in different areas of Kazakhstan in summer 2004. The isolates were initially characterized by culture and biochemical tests. The RD7 genotyping results demonstrated no polymorphism and the absence of deletions in the RD7 genome region. Some strains were additionally characterized using PCR-RFLP analysis of gyrB and hsp64 genes. The RFLP-patterns obtained corresponded to the M. tuberculosis genotypes. The results of this work are consistent with certain previous studies, indicating population stability of the RD7 region in M. tuberculosis strains. Species characterization of the isolates shows that M. tuberculosis sensu stricto is the principal causative agent of human lung tuberculosis in Kazakhstan.

Validity of HydraTrend reagent strips for the assessment of hydration status.

Science.gov (United States)

Abbey, Bryce M; Heelan, Kate A; Brown, Gregory A; Bartee, Rodrick T

2014-09-01

Hydration is used by athletic governing organizations for weight class eligibility. The measurement of urine specific gravity (USG) as a measure of hydration by reagent strips is a controversial issue. The purpose of this study was to determine the validity of HydraTrend reagent strips that facilitate the correction of USG for alkaline urine samples against refractometry for the assessment of USG. Fifty-one participants (33 males, age = 22.3 ± 1.3 years; 18 females, age = 22.4 ± 1.2 years) provided 84 urine samples. The samples were tested for USG using refractometry and reagent strips and for pH using reagent strips and a digital pH meter. Strong correlation coefficients were found between refractometry and reagent strips for USG (rs(82) = 0.812, p refractometry with USG >1.020, pass reagent strips with USG ≤1.020) occurred 39% (33/84) of the time and false negative results for National Federation of State High School Association (NFHS) requirements (fail refractometry with USG >1.025, pass reagent strips with USG ≤1.025) occurred 14% (12/84) of the time. There were no false positives (pass refractometry and fail reagent strips) for NCAA or NFHS requirements. These data show that refractometry and reagent strips have strong positive correlations. However, the risk of a false negative result leading to incorrect certification of euhydration status outweighs the benefits of the HydraTrend reagent strips for the measurement of USG.

Significance of wave form parameters in stripping chronopotentiometric metal speciation analysis

NARCIS (Netherlands)

Town, R.M.; Leeuwen, van H.P.

2002-01-01

An analysis is presented of the significance of stripping chronopotentiometric (SCP) stripping peak parameters (peak potential, Ep, and peak half-width, w1/2) for determination of metal ion speciation. This study focuses on depletive SCP (low stripping current, I¿ constant), and considers the change

Electrode/Dielectric Strip For High-Energy-Density Capacitor

Science.gov (United States)

Yen, Shiao-Ping S.

1994-01-01

Improved unitary electrode/dielectric strip serves as winding in high-energy-density capacitor in pulsed power supply. Offers combination of qualities essential for high energy density: high permittivity of dielectric layers, thinness, and high resistance to breakdown of dielectric at high electric fields. Capacitors with strip material not impregnated with liquid.

Strip reduction testing of lubricants developed during ENFORM project

DEFF Research Database (Denmark)

Gazvoda, S.; Andreasen, Jan Lasson; Olsson, David Dam

Strip reduction testing of lubricants developed during ENFORM project. Experiments were conducted with the strip reduction test [1] in order to classify experimental lubricants, developed during concerned project. One reference lubricant was used during testing....

Micro-strip Metal Foil Detectors for the Beam Profile Monitoring

CERN Document Server

Pugatch, V M; Fedorovitch, O A; Mikhailenko, A V; Prystupa, S V; Pylypchenko, Y

2005-01-01

The Micro-strip Metal Foil Detectors (MMFD) designed and used for the Beam Profile Monitoring (BPM) are discussed. Fast particles hitting a metal strip initiate Secondary Electron Emission (SEE) which occurs at 10 - 50 nm surface layers of a strip. The SEE yield is measured by a sensitive Charge Integrator with built-in current-to-frequency converter (1 Hz per 1 fA). The MMFD (deposited onto the 20 μm thick Si-wafer) with 32 Al strips (10 μm wide, 32 μm pitch) has been used for the BPM of the 32 MeV alpha-particle beam at the MPIfK (Heidelberg) Tandem generator for Single-Event-Upset studies of the BEETLE micro-chip. Similar MMFD (0.5 μm thick Ni-strips) with totally removed Si-wafer (by plasma-chemistry, at the working area of 8 x 10 mm2) has been applied for the on-line X-ray BPM at the HASYLAB (DESY). The number of photons (11.3 GeV, mean X-ray energy 18 keV) producing out of a strip a single SEE was evaluated as (1.5 ±0.5)* 104. MMFD has demonstrated stable...

A novel dNTP-limited PCR and HRM assay to detect Williams-Beuren syndrome.

Science.gov (United States)

Zhang, Lichen; Zhang, Xiaoqing; You, Guoling; Yu, Yongguo; Fu, Qihua

2018-06-01

Williams-Beuren syndrome (WBS) is caused by a microdeletion of chromosome arm 7q11.23. A rapid and inexpensive genotyping method to detect microdeletion on 7q11.23 needs to be developed for the diagnosis of WBS. This study describes the development of a new type of molecular diagnosis method to detect microdeletion on 7q11.23 based upon high-resolution melting (HRM). Four genes on 7q11.23 were selected as the target genes for the deletion genotyping. dNTP-limited duplex PCR was used to amplify the reference gene, CFTR, and one of the four genes respectively on 7q11.23. An HRM assay was performed on the PCR products, and the height ratio of the negative derivative peaks between the target gene and reference gene was employed to analyze the copy number variation of the target region. A new genotyping method for detecting 7q11.23 deletion was developed based upon dNTP-limited PCR and HRM, which cost only 96 min. Samples from 15 WBS patients and 12 healthy individuals were genotyped by this method in a blinded fashion, and the sensitivity and specificity was 100% (95% CI, 0.80-1, and 95% CI, 0.75-1, respectively) which was proved by CytoScan HD array. The HRM assay we developed is an rapid, inexpensive, and highly accurate method for genotyping 7q11.23 deletion. It is potentially useful in the clinical diagnosis of WBS. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Flexible strip supercapacitors for future energy storage

OpenAIRE

Zhang, R-R; Xu, Y-M; Harrison, D; Fyson, J; Qiu, F-L; Southee, D

2015-01-01

Flexible strip supercapacitors are developed and their electrochemical properties are characterized. Activated carbon is used as the electrode material and it is found to have a good porous structure which provides a large surface area for energy storage. Furthermore, this activated carbon performs well. The manufacturing processes for the supercapacitors are described in detail and the preparation process has good reproducibility. The strip supercapacitors are combined in series and parallel...

Comparative characteristics of polystyrene scintillation strips

International Nuclear Information System (INIS)

Gapienko, V.A.; Denisov, A.G.; Mel'nikov, E.A.

1992-01-01

Results are provided for a study of the main characteristics of polystyrene scintillation strips with a cross-section of 200 x 10 mm with two different scintillation-additive compositions: 1.5% p-terphenyl + 0.01% POPOP and 1.5% p-terphenyl + 0.01% DBP. The mean light-attenuation lengths are 180 cm and 260 cm, respectively, for strips with POPOP and DBP. The emittances of the polystyrene scintillators with DBP and POPOP additives have a ratio of 0.8:1.0 as recorded by an FEU-110 photomultiplier. 2 refs., 1 fig., 2 tabs

Evaluation of European Cranberrybush (Viburnum opulus L. genotypes for agro-morphological, biochemical and bioactive characteristics in Turkey

Directory of Open Access Journals (Sweden)

Ersoy Nilda

2017-12-01

Full Text Available The study evaluated some agro-morphological (fruit weight, fruit flesh ratio, fruit skin colour, number of fruits per raceme, number of racemes per bush, biochemical (vitamin C, soluble solids content, organic acids, and bioactive (total phenolics, total anthocyanins, total flavonoids, and antioxidant capacity characteristics of the fruit of a number of selected European Cranberrybush (Viburnum opulus L. genotypes grown in the Sivas province of Turkey. To evaluate the antioxidant capacity, ferric reducing antioxidant power (FRAP assays were performed. The results showed genotype-specific differences in most of the agro-morphological, biochemical and bioactive characteristics. The range of fruit weight, number of fruits per raceme, and number of racemes per bush was between 0.67 and 0.82 g, 40.7 and 57.1, and 470 and 581, respectively. The highest vitamin C and soluble solids contents were found in the fruits of genotypes SIV-9 and SIV-6 as 39 mg per 100 g and 12.6%, respectively. Tartaric acid was the main organic acid in all the genotypes; it ranged from 120 to 144 mg per 100 g of fruit FW. Total phenolic, total anthocyanin and total flavonoid contents ranged from 621 to 987 mg gallic acid equivalents per 100 g, 15 to 51 mg cyanidin-3-rutinoside equivalents per 100 g, and 202 to 318 mg rutin equivalents per 100 g, respectively. Genotype SIV-10 had the highest antioxidant capacity (34.90 μmol Trolox per g, based on FRAP assays. The present study shows the potential of the evaluated European Cranberrybush genotypes for improving the nutritional value through germplasm enhancement programmes.

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.

Genotyping of the 19-bp insertion/deletion polymorphism in the 5' flank of beta-hydroxylase gene by dissociation analysis of allele-specific PCR products

DEFF Research Database (Denmark)

Rasmussen, Henrik Berg; Werge, Thomas

2005-01-01

The 19-bp insertion/deletion polymorphism in the 5' flank of the dopamine beta-hydroxylase (DBH) gene has been associated with psychiatric disorders. We have developed a simple, reliable and inexpensive closed-tube assay for genotyping of this polymorphism based upon T(m) determination of amplified...... and a conventional approach based upon agarose gel electrophoresis of amplified fragments revealed complete concordance between the two procedures. The insights obtained in this study may be utilized to develop assays based upon dissociation analysis of PCR products for genotyping of other insertion...

EurEAs_Gplex--A new SNaPshot assay for continental population discrimination and gender identification.

Science.gov (United States)

Daca-Roszak, P; Pfeifer, A; Żebracka-Gala, J; Jarząb, B; Witt, M; Ziętkiewicz, E

2016-01-01

Assays that allow analysis of the biogeographic origin of biological samples in a standard forensic laboratory have to target a small number of highly differentiating markers. Such markers should be easy to multiplex and the assay must perform well in the degraded and scarce biological material. SNPs localized in the genome regions, which in the past were subjected to differential selective pressure in various populations, are the most widely used markers in the studies of biogeographic affiliation. SNPs reflecting biogeographic differences not related to any phenotypic traits are not sufficiently explored. The goal of our study was to identify a small set of SNPs not related to any known pigmentation/phenotype-specific genes, which would allow efficient discrimination between populations of Europe and East Asia. The selection of SNPs was based on the comparative analysis of representative European and Chinese/Japanese samples (B-lymphocyte cell lines), genotyped using the Infinium HumanOmniExpressExome microarray (Illumina). The classifier, consisting of 24 unlinked SNPs (24-SNP classifier), was selected. The performance of a 14-SNP subset of this classifier (14-SNP subclassifier) was tested using genotype data from several populations. The 14-SNP subclassifier differentiated East Asians, Europeans and Africans with ∼100% accuracy; Palestinians, representative of the Middle East, clustered with Europeans, while Amerindians and Pakistani were placed between East Asian and European populations. Based on these results, we have developed a SNaPshot assay (EurEAs_Gplex) for genotyping SNPs from the 14-SNP subclassifier, combined with an additional marker for gender identification. Forensic utility of the EurEAs_Gplex was verified using degraded and low quantity DNA samples. The performance of the EurEAs_Gplex was satisfactory when using degraded DNA; tests using low quantity DNA samples revealed a previously not described source of genotyping errors, potentially

Study the Z-Plane Strip Capacitance

International Nuclear Information System (INIS)

Parikh, H.; Swain, S.

2005-01-01

The BaBaR detector at the Stanford Linear Accelerator Center is currently undergoing an upgrade to improve its muon and neutral hadron detection system. The Resistive Plate Chambers (RPCs) that had been used till now have deteriorated in performance over the past few years and are being replaced by Limited Streamer Tube (LSTs). Each layer of the system consists of a set of up to 10 streamer tube modules which provide one coordinate (φ coordinate) and a single ''Z-plane'' which provides the Z coordinate of the hit. The large area Z-planes (up to 12m 2 ) are 1mm thick and contain 96 copper strips that detect the induced charge from avalanches created in the streamer tube wires. All the Z-planes needed for the upgrade have already been constructed, but only a third of the planes were installed last summer. After installing the 24 Z-planes last year, it was learned that 0.7% of the strips were dead when put inside the detector. This was mainly due to the delicate solder joint between the read-out cable and the strip, and since it is difficult to access or replace the Z-planes inside the detector, it is very important to perform various tests to make sure that the Z-planes will be efficient and effective in the long term. We measure the capacitance between the copper strips and the ground plane, and compare it to the theoretical value that we expect. Instead of measuring the capacitance channel by channel, which would be a very tedious job, we developed a more effective method of measuring the capacitance. Since all the Z-planes were built at SLAC, we also built a smaller 46 cm by 30 cm Z-plane with 12 strips just to see how they were constructed and to gain a better understanding about the solder joints

Seroprevalence and genotype of Chlamydia in pet parrots in China.

Science.gov (United States)

Zhang, N-Z; Zhang, X-X; Zhou, D-H; Huang, S-Y; Tian, W-P; Yang, Y-C; Zhao, Q; Zhu, X-Q

2015-01-01

Parrots are one of the most popular pet birds in China, and can harbour Chlamydia which has significance for human and animal health. We investigated, by indirect haemagglutination assay, the seroprevalence of Chlamydia infection in four species of parrots, namely budgerigars (Melopsittacus undulatus), lovebirds (Agapornis sp.), cockatiels (Nymphicus hollandicus) and Alexandrine parakeets (Psittacula eupatria) that were collected from Weifang and Beijing cities, North China and explored the association between potential risk factors and chlamydial seropositivity. We further determined the genotype of Chlamydia in 21 fresh faecal samples based on the ompA sequence by reconstruction of phylogenetic relationships. Of the 311 parrots examined, 35·37% (95% confidence interval 30·06-40·68) were seropositive, and species, gender, age, season and geographical location were identified as risk factors. Two PCR-positive samples represented Chlamydia psittaci genotype A. The occurrence of C. psittaci genotype A in the droppings of two pet parrots in China suggests potential environmental contamination with Chlamydiaceae and may raise a public health concern.

Effect of Mahanarva fimbriolata (Hemiptera: Cercopidae) Attack on Photosynthetic Parameters of Sugarcane Genotypes of Contrasting Susceptibility.

Science.gov (United States)

Soares, Bruno Oliveira; Chaves, Vinicius de Vicente; Tomaz, Adriano Cirino; Kuki, Kacilda Naomi; Peternelli, Luiz Alexandre; Barbosa, Márcio Henrique Pereira

2017-12-05

The aim of this study was to compare the effect of spittlebug Mahanarva fimbriolata Stål (Hemiptera: Cercopidae) on photosynthetic parameters of both a susceptible (SP81-3250) and a resistant (H.Kawandang) sugarcane genotype. In the first assay, the susceptibility level of genotypes to spittlebug was confirmed by comparing damage score and chlorophyll content of the plants. In the second assay, the effect of spittlebug nymphs on photosynthetic characteristics was assessed using the following parameters: Net photosynthetic rate (A), carboxylation efficiency (A/Ci), stomata conductance (gS), transpiration (E), electron transport rate (ETR), maximum quantum yield of Photosystem 2 (PSII) (FV/FM), effective quantum yield (Y(II)), photochemical quenching (Y(NPQ)), and nonphotochemical quenching (Y(NO)). Spittlebug nymphs affected the photosynthetic process of the susceptible genotype SP81-3250 by decreasing the Chl content, ETR, FV/FM, and Y(II). However, this genotype was able to maintain A probably due to its ability to maintain stomata aperture, increase the carboxylation efficiency of Rubisco, and dissipate excess energy through the xanthophyll cycle, as Y(NPQ) increased under the spittlebug attack. On the other hand, the spittlebug did not affect Chl content and FV/FM of the H.Kawandang genotype. Furthermore, H.Kawandang increased A to compensate for the sink demand by the spittlebug by increasing stomatal aperture and carboxylation efficiency and increasing efficiency of the photochemical apparatus in converting light energy into chemical products. We can conclude that the feeding habits of spittlebug nymphs have different impacts on photosynthesis of susceptible and resistant sugarcane genotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effects of hydrostatic strain on eigenstates of Möbius strips

DEFF Research Database (Denmark)

Lassen, Benny; Willatzen, Morten; Gravesen, Jens

2011-01-01

In this paper we theoretically investigate the allowed energies and associate wave-functions for Möbius strips with varying thicknesses. We show that the induced strain in fabricating these Möbius strips will have an pronounced impact on the energies and wave-functions for thick strips, while f...... for thin strips the impact of strain is negligible. We furthermore, show that a simpler strain free approximate theory base on differential geometry is in excellent agreement with detailed finite element calculations. © 2011 IEEE....

Low-resistance strip sensors for beam-loss event protection

International Nuclear Information System (INIS)

Ullán, M.; Benítez, V.; Quirion, D.; Zabala, M.; Pellegrini, G.; Lozano, M.; Lacasta, C.; Soldevila, U.; García, C.; Fadeyev, V.; Wortman, J.; DeFilippis, J.; Shumko, M.; Grillo, A.A; Sadrozinski, H.F.-W.

2014-01-01

AC-coupled silicon strip sensors can be damaged in case of a beam loss due to the possibility of a large charge accumulation in the bulk, developing very high voltages across the coupling capacitors which can destroy them. Punch-through structures are currently used to avoid this problem helping to evacuate the accumulated charge as large voltages are developing. Nevertheless, previous experiments, performed with laser pulses, have shown that these structures can become ineffective in relatively long strips. The large value of the implant resistance can effectively isolate the “far” end of the strip from the punch-through structure leading to large voltages. We present here our developments to fabricate low-resistance strip sensors to avoid this problem. The deposition of a conducting material in contact with the implants drastically reduces the strip resistance, assuring the effectiveness of the punch-through structures. First devices have been fabricated with this new technology. Initial results with laser tests show the expected reduction in peak voltages on the low resistivity implants. Other aspects of the sensor performance, including the signal formation, are not affected by the new technology

Development and validation of a genotype 3 recombinant protein-based immunoassay for hepatitis E virus serology in swine

Directory of Open Access Journals (Sweden)

W.H.M. van der Poel

2014-04-01

Full Text Available Hepatitis E virus (HEV is classified within the family Hepeviridae, genus Hepevirus. HEV genotype 3 (Gt3 infections are endemic in pigs in Western Europe and in North and South America and cause zoonotic infections in humans. Several serological assays to detect HEV antibodies in pigs have been developed, at first mainly based on HEV genotype 1 (Gt1 antigens. To develop a sensitive HEV Gt3 ELISA, a recombinant baculovirus expression product of HEV Gt3 open reading frame-2 was produced and coated onto polystyrene ELISA plates. After incubation of porcine sera, bound HEV antibodies were detected with anti-porcine anti-IgG and anti-IgM conjugates. For primary estimation of sensitivity and specificity of the assay, sets of sera were used from pigs experimentally infected with HEV Gt3. For further validation of the assay and to set the cutoff value, a batch of 1100 pig sera was used. All pig sera were tested using the developed HEV Gt3 assay and two other serologic assays based on HEV Gt1 antigens. Since there is no gold standard available for HEV antibody testing, further validation and a definite setting of the cutoff of the developed HEV Gt3 assay were performed using a statistical approach based on Bayes' theorem. The developed and validated HEV antibody assay showed effective detection of HEV-specific antibodies. This assay can contribute to an improved detection of HEV antibodies and enable more reliable estimates of the prevalence of HEV Gt3 in swine in different regions.

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.)

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.)

Metal films with imprinted nanostructures by template stripping

DEFF Research Database (Denmark)

Eriksen, René Lynge; Pors, Anders; Dreier, Jes

We present a novel template stripping procedure for fabricating metal films with imprinted nanostructures. The basic idea is to deposit a gold film onto a nano-structured substrate and subsequently strip the film from the substrate surface thereby revealing imprinted nanostructures in the film...... result is a thin gold film with imprinted nano-cavities....

Liquidity, Reconstitution, and the Value of U.S. Treasury Strips.

OpenAIRE

Daves, Phillip R; Ehrhardt, Michael C

1993-01-01

An apparent pricing anomaly exists in the market for U.S. Treasury strips: zero-coupon strips created from principal payments typically trade at significantly higher prices than otherwi se identical zero-coupon strips created from coupon payments. In additi on to documenting this phenomenon, this study demonstrates that differences in liquidity and differences in reconstitution characteristics explain much of this price variation. Copyright 1993 by American Finance Association.

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

Evaluation of a New Test, GenoType HelicoDR, for Molecular Detection of Antibiotic Resistance in Helicobacter pylori▿

Science.gov (United States)

Cambau, Emmanuelle; Allerheiligen, Vera; Coulon, Céline; Corbel, Céline; Lascols, Christine; Deforges, Lionel; Soussy, Claude-James; Delchier, Jean-Charles; Megraud, Francis

2009-01-01

The eradication rate of Helicobacter pylori by standard therapy is decreasing due to antibiotic resistance, mainly to clarithromycin. Our aim was to provide a new molecular test to guide the treatment of new and relapsed cases. We first studied 126 H. pylori strains for phenotypic (MIC) and genotypic resistance to clarithromycin (rrl mutation) and levofloxacin (gyrA mutation) and then developed a DNA strip genotyping test on the basis of the correlation results and literature data. Clinical strains (n = 92) and gastric biopsy specimens containing H. pylori (n = 105) were tested blindly with the new molecular test GenoType HelicoDR. The presence of mutations or the absence of hybridization with wild-type sequences was predictive, in rrl for clarithromycin resistance in 91 cases (mostly the A2147G mutation) and in gyrA for levofloxacin resistance in 58 cases (mutations at codon 87 or 91). Genotyping revealed a mix of genotypes in 33% of the cases, reflecting a coinfection or selection for resistant mutants. The sensitivity and specificity of detecting resistance were 94% and 99% for clarithromycin and 87% and 98.5% for levofloxacin, respectively. The concordance scores were 0.96 for clarithromycin and 0.94 for levofloxacin. With global resistance rates of 46% for clarithromycin and 25% for levofloxacin, which were observed for consecutive positive biopsy specimens from 2007 and 2008, the positive and negative predictive values for detecting resistance were 99% and 94% for clarithromycin and 96% and 96% for fluoroquinolone. GenoType HelicoDR is efficient at detecting mutations predictive of antibiotic resistance in H. pylori when applied to strains or directly to gastric biopsy specimens. PMID:19759218

Precipitation stripping of neodymium from carboxylate extractant with aqueous oxalic acid solutions

International Nuclear Information System (INIS)

Konishi, Yasuhiro; Asai, Satoru; Murai, Tetuya

1993-01-01

This paper describes a precipitation stripping method in which neodymium ions are stripped from carboxylate extractant in organic solvent and simultaneously precipitated with aqueous oxalic acid solution. For the single-stage process, a quantitative criterion for precipitating oxalate powders was derived theoretically, and stripping experiments were done under the precipitation conditions. The resultant precipitates were neodymium oxalate, which is completely free from contamination by the carboxylate extractant and the organic solvent. The overall rate of stripping was controlled by the transfer of neodymium carboxylate in the organic solution, indicating that the presence of oxalic acid in the aqueous phase has no effect on the stripping rate. These findings demonstrate the feasibility of combining the conventional stripping and precipitation stages in a solvent extraction process for separation and purification of rare earths

Inhibition of Fungal Pathogens across Genotypes and Temperatures by Amphibian Skin Bacteria

Directory of Open Access Journals (Sweden)

Carly R. Muletz-Wolz

2017-08-01

Full Text Available Symbiotic bacteria may dampen the impacts of infectious diseases on hosts by inhibiting pathogen growth. However, our understanding of the generality of pathogen inhibition by different bacterial taxa across pathogen genotypes and environmental conditions is limited. Bacterial inhibitory properties are of particular interest for the amphibian-killing fungal pathogens (Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, for which probiotic applications as conservation strategies have been proposed. We quantified the inhibition strength of five putatively B. dendrobatidis-inhibitory bacteria isolated from woodland salamander skin against six Batrachochytrium genotypes at two temperatures (12 and 18°C. We selected six genotypes from across the Batrachochytrium phylogeny: B. salamandrivorans, B. dendrobatidis-Brazil and four genotypes of the B. dendrobatidis Global Panzootic Lineage (GPL1: JEL647, JEL404; GPL2: SRS810, JEL423. We performed 96-well plate challenge assays in a full factorial design. We detected a Batrachochytrium genotype by temperature interaction on bacterial inhibition score for all bacteria, indicating that bacteria vary in ability to inhibit Batrachochytrium depending on pathogen genotype and temperature. Acinetobacter rhizosphaerae moderately inhibited B. salamandrivorans at both temperatures (μ = 46–53%, but not any B. dendrobatidis genotypes. Chryseobacterium sp. inhibited three Batrachochytrium genotypes at both temperatures (μ = 5–71%. Pseudomonas sp. strain 1 inhibited all Batrachochytrium genotypes at 12°C and four Batrachochytrium genotypes at 18°C (μ = 5–100%. Pseudomonas sp. strain 2 and Stenotrophomonas sp. moderately to strongly inhibited all six Batrachochytrium genotypes at both temperatures (μ = 57–100%. All bacteria consistently inhibited B. salamandrivorans. Using cluster analysis of inhibition scores, we found that more closely related Batrachochytrium genotypes grouped together

An XML-based interchange format for genotype-phenotype data.

Science.gov (United States)

Whirl-Carrillo, M; Woon, M; Thorn, C F; Klein, T E; Altman, R B

2008-02-01

Recent advances in high-throughput genotyping and phenotyping have accelerated the creation of pharmacogenomic data. Consequently, the community requires standard formats to exchange large amounts of diverse information. To facilitate the transfer of pharmacogenomics data between databases and analysis packages, we have created a standard XML (eXtensible Markup Language) schema that describes both genotype and phenotype data as well as associated metadata. The schema accommodates information regarding genes, drugs, diseases, experimental methods, genomic/RNA/protein sequences, subjects, subject groups, and literature. The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB; www.pharmgkb.org) has used this XML schema for more than 5 years to accept and process submissions containing more than 1,814,139 SNPs on 20,797 subjects using 8,975 assays. Although developed in the context of pharmacogenomics, the schema is of general utility for exchange of genotype and phenotype data. We have written syntactic and semantic validators to check documents using this format. The schema and code for validation is available to the community at http://www.pharmgkb.org/schema/index.html (last accessed: 8 October 2007). (c) 2007 Wiley-Liss, Inc.

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.

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.

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.

Evaluation of a portable urinary pH meter and reagent strips.

Science.gov (United States)

De Coninck, Vincent; Keller, Etienne Xavier; Rodríguez-Monsalve, María; Haymann, Jean-Philippe; Doizi, Steeve; Traxer, Olivier

2018-04-27

To evaluate a portable electronic pH meter and to put its accuracy in perspective with reagent strips read by a layperson, a healthcare professional and an electronic reading device. Based on a pre-analysis on 20 patients, a sample size of 77 urine aliquots from healthy volunteers was necessary to obtain sufficient study power. Measurements of urinary pH were obtained by use of reagent strips, a portable pH meter and a laboratory pH meter (gold standard). Reagents strips were read by a professional experienced in interpreting strips, a layperson, and an electronic strip reader. The mean matched pair difference between measurement methods was analyzed by the paired t-test. The degree of correlation and agreement were evaluated by the Pearson's correlation coefficient and Bland-Altman plots, respectively. The mean matched pair difference between the gold standard and all other pH measurement methods was the smallest with the portable electronic pH meter (bias 0.01, 95% CI -0.07 to 0.08; p=0.89), followed by strips read by a professional (bias -0.09, 95% CI -0.21 to 0.02; p=0.10), layperson (bias -0.17, 95% CI -0.31 to -0.04; p=0.015) and electronic strip reader (bias -0.29, 95% CI -0.41 to -0.16; pmeter achieved the highest Pearson's correlation coefficient and narrowest 95% limits of agreement, followed by strip interpretation by a professional, the electronic strip reader and the layperson. In order to quantify the ability of pH measurement methods to correctly classify values within a predefined urinary pH target range, we performed classification tests for several stones. The portable electronic pH meter outperformed all other measurement methods for negative predictive values. Findings of the current study support that the portable electronic pH meter is a reliable pH measuring device. It seems to be more accurate compared to reagent strips readings.

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).

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.

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.

Performance characteristics of the ARCHITECT anti-HCV assay.

Science.gov (United States)

Jonas, Gesa; Pelzer, Claudia; Beckert, Christian; Hausmann, Michael; Kapprell, Hans-Peter

2005-10-01

The ARCHITECT Anti-HCV assay is a fully automated high throughput chemiluminescent microparticle immunoassay (CMIA) for the detection of antibodies to structural and nonstructural proteins of the hepatitis C virus (HCV). To further enhance the performance of this test, the assay was modified to improve the specificity for blood donor specimens. The specificity of the enhanced ARCHITECT Anti-HCV assay was evaluated by screening blood donor samples randomly collected from various German blood banks, as well as hospitalized patient samples derived from Germany and the US. Additionally, antibody sensitivity was determined on commercially available anti-HCV seroconversion panels and on a commercially available worldwide anti-HCV genotype performance panel. Apparent specificity of the modified ARCHITECT Anti-HCV assay in a blood donor population consisting of 3811 specimens was 99.92%, compared to 99.76% for the current on-market assay. Additionally, antibody sensitivity was determined on commercially available anti-HCV seroconversion panels. Seroconversion sensitivity equivalent to or better than the current on-market product was observed by testing 33 seroconversion panels. This study demonstrates that the modified version of the ARCHITECT Anti-HCV assay shows improved specificity for blood donor specimens compared to the current assay on market without compromising sensitivity. With the availability of the improved ARCHITECT Anti-HCV assay and the recent launch of the ARCHITECT HIV Ag/Ab Combo assay, the ARCHITECT system now offers a full hepatitis/retrovirus menu with excellent performance on a high throughput, random access, automated analyzer, ideally suited for blood screening and diagnostic applications.

Genotype I of Japanese Encephalitis Virus Virus-like Particles Elicit Sterilizing Immunity against Genotype I and III Viral Challenge in Swine.

Science.gov (United States)

Fan, Yi-Chin; Chen, Jo-Mei; Lin, Jen-Wei; Chen, Yi-Ying; Wu, Guan-Hong; Su, Kuan-Hsuan; Chiou, Ming-Tang; Wu, Shang-Rung; Yin, Ji-Hang; Liao, Jiunn-Wang; Chang, Gwong-Jen J; Chiou, Shyan-Song

2018-05-10

Swine are a critical amplifying host involved in human Japanese encephalitis (JE) outbreaks. Cross-genotypic immunogenicity and sterile protection are important for the current genotype III (GIII) virus-derived vaccines in swine, especially now that emerging genotype I (GI) JE virus (JEV) has replaced GIII virus as the dominant strain. Herein, we aimed to develop a system to generate GI JEV virus-like particles (VLPs) and evaluate the immunogenicity and protection of the GI vaccine candidate in mice and specific pathogen-free swine. A CHO-heparan sulfate-deficient (CHO-HS(-)) cell clone, named 51-10 clone, stably expressing GI-JEV VLP was selected and continually secreted GI VLPs without signs of cell fusion. 51-10 VLPs formed a homogeneously empty-particle morphology and exhibited similar antigenic activity as GI virus. GI VLP-immunized mice showed balanced cross-neutralizing antibody titers against GI to GIV viruses (50% focus-reduction micro-neutralization assay titers 71 to 240) as well as potent protection against GI or GIII virus infection. GI VLP-immunized swine challenged with GI or GIII viruses showed no fever, viremia, or viral RNA in tonsils, lymph nodes, and brains as compared with phosphate buffered saline-immunized swine. We thus conclude GI VLPs can provide sterile protection against GI and GIII viruses in swine.

Determination of the resistance types to Spodoptera cosmioides (Walker (Lepidoptera: Noctuidae in soybean genotypes

Directory of Open Access Journals (Sweden)

Arlindo Leal Boiça Júnior

2015-04-01

Full Text Available The aim of this work was to evaluate the resistance types in soybean genotypes to Spodoptera cosmioides (Walker in laboratory. Soybean genotypes assessed were as follows: ‘IAC 100’ (resistance standard, ‘BR16’ (susceptible standard, ‘Dowling’, PI 227687, PI 274454, ‘IGRA RA 626 RR’, PI 227682, ‘BRSGO 8360’, ‘IGRA RA 516 RR’ and ‘P 98Y11 RR’. Free-choice and no-choice feeding non-preference tests were done using two newly-hatched larvae per genotype or one third-instar larva per genotype in both tests. Larvae attractiveness was evaluated in different times, and at the end of the experiments the leaf area consumed was quantified. In the antibiosis test, newly-hatched larvae were individualized into Petri dishes, where leaflets of the genotypes were offered over the larval stage, and the following biological parameters were assessed: period and viability of larvae, pupae and overall (larvae + pupae, weight of larvae and pupae, sex ratio and adults longevity. Overall, in the feeding preference tests, significant differences were not found in leaf consumption among the genotypes. In the antibiosis assay, genotypes PI 227687, PI 227682 and ‘IAC 100’ caused 100% larval mortality and the lowest weight of larvae, ranging between 37.65 and 85.56 mg. All soybean genotypes evaluated do not exhibit feeding non-preference type resistance to S. cosmioides, and PI 227687, PI 227682 and ‘IAC 100’ highlighted for possessing antibiosis.

The depletion properties of silicon microstrip detectors with variable strip pitch

International Nuclear Information System (INIS)

Krizmanic, J.F.

1994-01-01

We have investigated the depletion properties of trapezoidal shaped silicon microstrip detectors which have variable strip pitch. Four types of detectors were examined: three detectors have constant strip width and a fourth has a varying strip width. The detectors are single sided with readout performed via p + strips. The depletion properties of the devices were measured using two different methods. The first used capacitance versus voltage measurements, while the second used a 1060 nm wavelength laser coupled to a single mode fiber with a mode field diameter less than 10 μm. The small laser spot size allowed for the depletion depth to be measured in a localized area of the detector. The laser induced charge on an electrode was measured as a function of reverse bias voltage using a sensitive charge preamplifier. The depletion voltages of the detectors demonstrate a strong dependence upon the ratio of strip width to strip pitch. Moreover, these measurements show that a large value of this ratio yields a lower depletion voltage and vice versa. (orig.)

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

Directory of Open Access Journals (Sweden)

Yachun Su

2013-01-01

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

A GEM readout with radial zigzag strips and linear charge-sharing response

Science.gov (United States)

Zhang, Aiwu; Hohlmann, Marcus; Azmoun, Babak; Purschke, Martin L.; Woody, Craig

2018-04-01

We study the position sensitivity of radial zigzag strips intended to read out large GEM detectors for tracking at future experiments. Zigzag strips can cover a readout area with fewer strips than regular straight strips while maintaining good spatial resolution. Consequently, they can reduce the number of required electronic channels and related cost for large-area GEM detector systems. A non-linear relation between incident particle position and hit position measured from charge sharing among zigzag strips was observed in a previous study. We significantly reduce this non-linearity by improving the interleaving of adjacent physical zigzag strips. Zigzag readout structures are implemented on PCBs and on a flexible foil and are tested using a 10 cm × 10 cm triple-GEM detector scanned with a strongly collimated X-ray gun on a 2D motorized stage. Angular resolutions of 60-84 μrad are achieved with a 1.37 mrad angular strip pitch at a radius of 784 mm. On a linear scale this corresponds to resolutions below 100 μm.

Identification of Cryptosporidium Species and Genotypes in Scottish Raw and Drinking Waters during a One-Year Monitoring Period▿

Science.gov (United States)

Nichols, R. A. B.; Connelly, L.; Sullivan, C. B.; Smith, H. V.

2010-01-01

We analyzed 1,042 Cryptosporidium oocyst-positive slides (456 from raw waters and 586 from drinking waters) of which 55.7% contained 1 or 2 oocysts, to determine species/genotypes present in Scottish waters. Two nested PCR-restriction fragment length polymorphism (RFLP) assays targeting different loci (1 and 2) of the hypervariable region of the 18S rRNA gene were used for species identification, and 62.4% of samples were amplified with at least one of the PCR assays. More samples (577 slides; 48.7% from raw water and 51.3% from drinking water) were amplified at locus 1 than at locus 2 (419 slides; 50.1% from raw water and 49.9% from drinking water). PCR at loci 1 and 2 amplified 45.4% and 31.7% of samples containing 1 or 2 oocysts, respectively. We detected both human-infectious and non-human-infectious species/genotype oocysts in Scottish raw and drinking waters. Cryptosporidium andersoni, Cryptosporidium parvum, and the Cryptosporidium cervine genotype (now Cryptosporidium ubiquitum) were most commonly detected in both raw and drinking waters, with C. ubiquitum being most common in drinking waters (12.5%) followed by C. parvum (4.2%) and C. andersoni (4.0%). Numerous samples (16.6% total; 18.9% from drinking water) contained mixtures of two or more species/genotypes, and we describe strategies for unraveling their identity. Repetitive analysis for discriminating mixtures proved useful, but both template concentration and PCR assay influenced outcomes. Five novel Cryptosporidium spp. (SW1 to SW5) were identified by RFLP/sequencing, and Cryptosporidium sp. SW1 was the fourth most common contaminant of Scottish drinking water (3%). PMID:20639357

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)...

Poor Prognosis Associated With Human Papillomavirus α7 Genotypes in Cervical Carcinoma Cannot Be Explained by Intrinsic Radiosensitivity

International Nuclear Information System (INIS)

Hall, John S.; Iype, Rohan; Armenoult, Lucile S.C.; Taylor, Janet; Miller, Crispin J.; Davidson, Susan; Sanjose, Silvia de; Bosch, Xavier; Stern, Peter L.; West, Catharine M.L.

2013-01-01

Purpose: To investigate the relationship between human papillomavirus (HPV) genotype and outcome after radiation therapy and intrinsic radiosensitivity. Methods and Materials: HPV genotyping was performed on cervix biopsies by polymerase chain reaction using SPF-10 broad-spectrum primers, followed by deoxyribonucleic acid enzyme immunoassay and genotyping by reverse hybridization line probe assay (LiPA 25 ) (version 1) (n=202). PapilloCheck and quantitative reverse transcription-polymerase chain reaction were used to genotype cervix cancer cell lines (n=16). Local progression-free survival after radiation therapy alone was assessed using log-rank and Cox proportionate hazard analyses. Intrinsic radiosensitivity was measured as surviving fraction at 2 Gy (SF2) using clonogenic assays. Results: Of the 202 tumors, 107 (53.0%) were positive for HPV16, 29 (14.4%) for HPV18, 9 (4.5%) for HPV45, 23 (11.4%) for other HPV genotypes, and 22 (10.9%) were negative; 11 (5.5%) contained multiple genotypes, and 1 tumor was HPV X (0.5%). In 148 patients with outcome data, those with HPVα9-positive tumors had better local progression-free survival compared with α7 patients in univariate (P<.004) and multivariate (hazard ratio 1.54, 95% confidence interval 1.11-1.76, P=.021) analyses. There was no difference in the median SF2 of α9 and α7 cervical tumors (n=63). In the cell lines, 9 were α7 and 4 α9 positive and 3 negative. There was no difference in SF2 between α9 and α7 cell lines (n=14). Conclusion: The reduced radioresponsiveness of α7 cervical tumors is not related to intrinsic radiosensitivity

Poor Prognosis Associated With Human Papillomavirus α7 Genotypes in Cervical Carcinoma Cannot Be Explained by Intrinsic Radiosensitivity

Energy Technology Data Exchange (ETDEWEB)

Hall, John S.; Iype, Rohan; Armenoult, Lucile S.C. [Translational Radiobiology Group, Institute of Cancer Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester (United Kingdom); Taylor, Janet [Translational Radiobiology Group, Institute of Cancer Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester (United Kingdom); Applied Computational Biology and Bioinformatics Group, Paterson Institute for Cancer Research, Manchester (United Kingdom); Miller, Crispin J. [Applied Computational Biology and Bioinformatics Group, Paterson Institute for Cancer Research, Manchester (United Kingdom); Davidson, Susan [Christie National Health Service Foundation Trust, Manchester (United Kingdom); Sanjose, Silvia de; Bosch, Xavier [Cancer Epidemiology Research Program, Catalan Institute of Oncology, L' Hospitalet de Llobregat (Spain); Stern, Peter L. [Immunology Group, Paterson Institute for Cancer Research, Manchester (United Kingdom); West, Catharine M.L., E-mail: Catharine.West@manchester.ac.uk [Translational Radiobiology Group, Institute of Cancer Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester (United Kingdom)

2013-04-01

Purpose: To investigate the relationship between human papillomavirus (HPV) genotype and outcome after radiation therapy and intrinsic radiosensitivity. Methods and Materials: HPV genotyping was performed on cervix biopsies by polymerase chain reaction using SPF-10 broad-spectrum primers, followed by deoxyribonucleic acid enzyme immunoassay and genotyping by reverse hybridization line probe assay (LiPA{sub 25}) (version 1) (n=202). PapilloCheck and quantitative reverse transcription-polymerase chain reaction were used to genotype cervix cancer cell lines (n=16). Local progression-free survival after radiation therapy alone was assessed using log-rank and Cox proportionate hazard analyses. Intrinsic radiosensitivity was measured as surviving fraction at 2 Gy (SF2) using clonogenic assays. Results: Of the 202 tumors, 107 (53.0%) were positive for HPV16, 29 (14.4%) for HPV18, 9 (4.5%) for HPV45, 23 (11.4%) for other HPV genotypes, and 22 (10.9%) were negative; 11 (5.5%) contained multiple genotypes, and 1 tumor was HPV X (0.5%). In 148 patients with outcome data, those with HPVα9-positive tumors had better local progression-free survival compared with α7 patients in univariate (P<.004) and multivariate (hazard ratio 1.54, 95% confidence interval 1.11-1.76, P=.021) analyses. There was no difference in the median SF2 of α9 and α7 cervical tumors (n=63). In the cell lines, 9 were α7 and 4 α9 positive and 3 negative. There was no difference in SF2 between α9 and α7 cell lines (n=14). Conclusion: The reduced radioresponsiveness of α7 cervical tumors is not related to intrinsic radiosensitivity.

OzPythonPlex: An optimised forensic STR multiplex assay set for the Australasian carpet python (Morelia spilota).

Science.gov (United States)

Ciavaglia, Sherryn; Linacre, Adrian

2018-05-01

Reptile species, and in particular snakes, are protected by national and international agreements yet are commonly handled illegally. To aid in the enforcement of such legislation, we report on the development of three 11-plex assays from the genome of the carpet python to type 24 loci of tetra-nucleotide and penta-nucleotide repeat motifs (pure, compound and complex included). The loci range in size between 70 and 550 bp. Seventeen of the loci are newly characterised with the inclusion of seven previously developed loci to facilitate cross-comparison with previous carpet python genotyping studies. Assays were optimised in accordance with human forensic profiling kits using one nanogram template DNA. Three loci are included in all three of the multiplex reactions as quality assurance markers, to ensure sample identity and genotyping accuracy is maintained across the three profiling assays. Allelic ladders have been developed for the three assays to ensure consistent and precise allele designation. A DNA reference database of allele frequencies is presented based on 249 samples collected from throughout the species native range. A small number of validation tests are conducted to demonstrate the utility of these multiplex assays. We suggest further appropriate validation tests that should be conducted prior to the application of the multiplex assays in criminal investigations involving carpet pythons. Copyright © 2018 Elsevier B.V. All rights reserved.

A novel rapid genotyping technique for Collie eye anomaly: SYBR Green-based real-time polymerase chain reaction method applicable to blood and saliva specimens on Flinders Technology Associates filter paper.

Science.gov (United States)

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

2010-09-01

Collie eye anomaly (CEA) is a canine inherited ocular disease that shows a wide variety of manifestations and severity of clinical lesions. Recently, a CEA-associated mutation was reported, and a DNA test that uses conventional polymerase chain reaction (PCR) has now become available. The objective of the current study was to develop a novel rapid genotyping technique by using SYBR Green-based real-time PCR for future large-scale surveys as a key part in the strategy to eradicate CEA by selective breeding. First, a SYBR Green-based real-time PCR assay for genotyping of CEA was developed and evaluated by using purified DNA samples from normal, carrier, and affected Border Collies in which genotypes had previously been determined by conventional PCR. This real-time PCR assay demonstrated appropriate amplifications in all genotypes, and the results were consistent with those of conventional PCR. Second, the availability of Flinders Technology Associates filter paper (FTA card) as DNA templates for the real-time PCR assay was evaluated by using blood and saliva specimens to determine suitability for CEA screening. DNA-containing solution prepared from a disc of blood- or saliva-spotted FTA cards was available directly as templates for the real-time PCR assay when the volume of solution was 2.5% of the PCR mixture. In conclusion, SYBR Green-based real-time PCR combined with FTA cards is a rapid genotyping technique for CEA that can markedly shorten the overall time required for genotyping as well as simplify the sample preparation. Therefore, this newly developed technique suits large-scale screening in breeding populations of Collie-related breeds.

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.

Haptoglobin genotype and risk markers of cardiovascular disease in patients with chronic kidney disease

DEFF Research Database (Denmark)

Strandhave, Charlotte; Svensson, My; Krarup, Henrik

2013-01-01

-5 were included. Hp genotype was determined by high-performance liquid chromatography. HRV was analysed from the 24 h Holter recordings. Hs-CRP was measured using an immunoturbidimetric assay. The results show that the HRV indices SDNN and SDANN were significantly lower in the Hp 2-2 patients (P = 0...

First results from a silicon-strip detector with VLSI readout

International Nuclear Information System (INIS)

Anzivino, G.; Horisberger, R.; Hubbeling, L.; Hyams, B.; Parker, S.; Breakstone, A.; Litke, A.M.; Walker, J.T.; Bingefors, N.

1986-01-01

A 256-strip silicon detector with 25 μm strip pitch, connected to two 128-channel NMOS VLSI chips (Microplex), has been tested using straight-through tracks from a ruthenium beta source. The readout channels have a pitch of 47.5 μm. A single multiplexed output provides voltages proportional to the integrated charge from each strip. The most probable signal height from the beta traversals is approximately 14 times the rms noise in any single channel. (orig.)

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.

Characterization and Calibration of Large Area Resistive Strip Micromegas Detectors

CERN Document Server

Losel, Philipp Jonathan; The ATLAS collaboration

2015-01-01

Resisitve strip Micromegas detectors behave discharge tolerant. They have been tested extensively as smaller detectors of about 10 x 10 cm$^2$ in size and they work reliably at high rates of 100\\,kHz/cm$^2$ and above. Tracking resolutions well below 100\\,$\\mu$m have been observed for 100 GeV muons and pions. Micromegas detectors are meanwhile proposed as large area muon precision trackers of 2-3\\,m$^2$ in size. To investigate possible differences between small and large detectors, a 1\\,m$^2$ detector with 2048 resistive strips at a pitch of 450 $\\mu$m was studied in the LMU Cosmic Ray Facility (CRF) using two 4 $\\times$ 2.2 m$^2$ large Monitored Drift Tube (MDT) chambers for cosmic muon reference tracking. Segmentation of the resistive strip anode plane in 57.6\\,mm x 95\\,mm large areas has been realized by the readout of 128 strips with one APV25 chip each and by 11 95\\,mm broad trigger scintillators placed along the readout strips.\\\\ This allows for mapping of homogenity in pulse height and efficiency, deter...

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.

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

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......), and Hybrid Capture 2 (HC2) using samples stored in SurePath. METHODS: Residual material from 401 routine samples from women with abnormal cytology was tested by CLART, LA, and HC2 (ClinicalTrial.gov: NCT01671462, Ethical Committee approval: H-2012-070). Histological outcomes were ascertained by linkage...... for high-grade CIN. RESULTS: The κ-coefficient for agreement in detection of genotypes 16, 18, 31, 33, 35, and 51 was ≥0.90 (overall agreement: 98-99%, positive agreement: 84-95%). The values were slightly lower, but still in the "substantial" range for genotypes 39, 45, 52, 56, 58, 59, and several low...

Humor in elementary science: Development and evaluation of comic strips about sound

Directory of Open Access Journals (Sweden)

Ertuğrul Özdemir

2017-06-01

Full Text Available Comic strips on newspapers, magazines and Internet are one of the most accessible materials that may be used in science classroom as instructional tool. However, it is sometimes difficult to find and adapt appropriate comic strips useful for instructional purposes, because most of them are irrelevant. The purpose of this study is to develop and evaluate instructional comic strips aiming to contribute learning about sound related concepts. In this study, a series of instructional comic strips were created and implemented to a group of seventh grade students. Students’ responses to a number of open-ended questions were evaluated through qualitative content analysis. According to results, most of the students believed that comic strips help learning through simplifying science concepts and making retention of them easier. In addition, comic strips seemed to contribute students’ enjoyment toward science and perception of success in science.

Performance of a new test strip for freestyle blood glucose monitoring systems.

Science.gov (United States)

Lock, John Paul; Brazg, Ronald; Bernstein, Robert M; Taylor, Elizabeth; Patel, Mona; Ward, Jeanne; Alva, Shridhara; Chen, Ting; Welsh, Zoë; Amor, Walter; Bhogal, Claire; Ng, Ronald

2011-01-01

a new strip, designed to enhance the ease of use and minimize interference of non-glucose sugars, has been developed to replace the current FreeStyle (Abbott Diabetes Care, Alameda, CA) blood glucose test strip. We evaluated the performance of this new strip. laboratory evaluation included precision, linearity, dynamic range, effects of operating temperature, humidity, altitude, hematocrit, interferents, and blood reapplication. System accuracy, lay user performance, and ease of use for finger capillary blood testing and accuracy for venous blood testing were evaluated at clinics. Lay users also compared the speed and ease of use between the new strip and the current FreeStyle strip. for glucose concentrations blood glucose results obtained by lay users fell within ± 5, 10, and 15 mg/dL, respectively, of the reference. For glucose concentrations ≥75 mg/dL, 68%, 95%, 99%, and 99% of the lay user results fell within  ±  5%, 10%, 15%, and 20%, respectively, of the reference. Comparable accuracy was obtained in the venous blood study. Lay users found the new test strip easy to use and faster and easier to use than the current FreeStyle strip. The new strip maintained accuracy under various challenging conditions, including high concentrations of various interferents, sample reapplication up to 60 s, and extremes in hematocrit, altitude, and operating temperature and humidity. our results demonstrated excellent accuracy of the new FreeStyle test strip and validated the improvements in minimizing interference and enhancing ease of use.

Cross-reactivity profiles of hybrid capture II, cobas, and APTIMA human papillomavirus assays

DEFF Research Database (Denmark)

Preisler, Sarah Nørgaard; Rebolj, Matejka; Ejegod, Ditte Møller

2016-01-01

evaluated to what extent these can be explained by cross-reactivity, i.e. positive test results without evidence of high-risk HPV genotypes. The patterns of cross-reactivity have been thoroughly studied for hybrid capture II (HC2) but not yet for newer HPV assays although the manufacturers claimed...... no or limited frequency of cross-reactivity. In this independent study we evaluated the frequency of cross-reactivity for HC2, cobas, and APTIMA assays. Methods Consecutive routine cervical screening samples from 5022 Danish women, including 2859 from women attending primary screening, were tested...... with normal cytology and positive high-risk HPV test results were invited for repeated testing in 18 months. Results Cross-reactivity to low-risk genotypes was detected in 109 (2.2 %) out of 5022 samples on HC2, 62 (1.2 %) on cobas, and 35 (0.7 %) on APTIMA with only 10 of the samples cross-reacting on all 3...

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...

Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus

Science.gov (United States)

2012-01-01

Background The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus. Method This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors. Result Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA. Conclusion The molecular typing method presented is one tool that could be incorporated into the forensic

[Clinical evaluation of a novel HBsAg quantitative assay].

Science.gov (United States)

Takagi, Kazumi; Tanaka, Yasuhito; Naganuma, Hatsue; Hiramatsu, Kumiko; Iida, Takayasu; Takasaka, Yoshimitsu; Mizokami, Masashi

2007-07-01

The clinical implication of the hepatitis B surface antigen (HBsAg) concentrations in HBV-infected individuals remains unclear. The aim of this study was to evaluate a novel fully automated Chemiluminescence Enzyme Immunoassay (Sysmex HBsAg quantitative assay) by comparative measurements of the reference serum samples versus two independent commercial assays (Lumipulse f or Architect HBsAg QT). Furthermore, clinical usefulness was assessed for monitoring of the serum HBsAg levels during antiviral therapy. A dilution test using 5 reference-serum samples showed linear correlation curve in range from 0.03 to 2,360 IU/ml. The HBsAg was measured in total of 400 serum samples and 99.8% had consistent results between Sysmex and Lumipulse f. Additionally, a positive linear correlation was observed between Sysmex and Architect. To compare the Architect and Sysmex, both methods were applied to quantify the HBsAg in serum samples with different HBV genotypes/subgenotypes, as well as in serum contained HBV vaccine escape mutants (126S, 145R). Correlation between the methods was observed in results for escape mutants and common genotypes (A, B, C) in Japan. Observed during lamivudine therapy, an increase in HBsAg and HBV DNA concentrations preceded the aminotransferase (ALT) elevation associated with drug-resistant HBV variant emergence (breakthrough hepatitis). In conclusion, reliability of the Sysmex HBsAg quantitative assay was confirmed for all HBV genetic variants common in Japan. Monitoring of serum HBsAg concentrations in addition to HBV DNA quantification, is helpful in evaluation of the response to lamivudine treatment and diagnosis of the breakthrough hepatitis.

Science comic-strips on display at Microcosm

CERN Document Server

Alix Marcastel

2011-01-01

To mark the publication of his new comic-strip "Les Vies de Marie Curie", the Genevan artist Fiami will be placing some of his previous creations on the theme "women and science" on display at CERN. The new comic-strip pays tribute to the illustrious Nobel prize-winner by taking a light-hearted look at the history of chemistry and how the role of women scientists in society has evolved through the ages.   It's no easy task,  presenting the history of science to the general public in a light-hearted way. As part of the various events organised in the Fête de la Science and the Europeans Researchers Night, CERN will be hosting an exhibition entirely devoted to the comic-strips created by Fiami. The artist describes his comics as "a relaxed way of looking at serious and apparently highly complex subjects."  Fiami's very latest creation, Les Vies de Marie Curie, published in June 2011, celebrates th...

The Argonne silicon strip-detector array

Energy Technology Data Exchange (ETDEWEB)

Wuosmaa, A H; Back, B B; Betts, R R; Freer, M; Gehring, J; Glagola, B G; Happ, Th; Henderson, D J; Wilt, P [Argonne National Lab., IL (United States); Bearden, I G [Purdue Univ., Lafayette, IN (United States). Dept. of Physics

1992-08-01

Many nuclear physics experiments require the ability to analyze events in which large numbers of charged particles are detected and identified simultaneously, with good resolution and high efficiency, either alone, or in coincidence with gamma rays. The authors have constructed a compact large-area detector array to measure these processes efficiently and with excellent energy resolution. The array consists of four double-sided silicon strip detectors, each 5x5 cm{sup 2} in area, with front and back sides divided into 16 strips. To exploit the capability of the device fully, a system to read each strip-detector segment has been designed and constructed, based around a custom-built multi-channel preamplifier. The remainder of the system consists of high-density CAMAC modules, including multi-channel discriminators, charge-sensing analog-to-digital converters, and time-to-digital converters. The array`s performance has been evaluated using alpha-particle sources, and in a number of experiments conducted at Argonne and elsewhere. Energy resolutions of {Delta}E {approx} 20-30 keV have been observed for 5 to 8 MeV alpha particles, as well as time resolutions {Delta}T {<=} 500 ps. 4 figs.

Determination of residual stresses in roll compacted titanium strips

CSIR Research Space (South Africa)

Mothosi, KL

2017-01-01

Full Text Available residual stresses using x-ray diffraction (XRD) surface probing technique. Preliminary results were obtained for the surface residual stress at the center of the titanium strips for the 100 and 325 mesh strips rolled at 0.1 roll gap for 20 and 50 mm set...

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....

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

OpenAIRE

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

2005-01-01

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

A fast and easy real-time PCR genotyping method for the HLA-G 14-bp insertion/deletion polymorphism in the 3' untranslated region

DEFF Research Database (Denmark)

Djurisic, S; Sørensen, A E; Hviid, T V F

2012-01-01

and reliable method to screen for the HLA-G 14-bp insertion/deletion polymorphism using an optimized real-time polymerase chain reaction protocol. The genotyping assay has been validated by comparison with conventional methods. As results can be obtained within a few hours, the assay will have a potential...

Method of stripping solid particles

International Nuclear Information System (INIS)

1980-01-01

A method of stripping loaded solid particles is specified in which uniform batches of the loaded particles are passed successively upwardly through an elution column in the form of discrete plugs, the particles of which do not intermingle substantially with the particles of the vertically adjacent plug(s), and are contacted therein with eluant liquid flowed downwardly, strong eluate being withdrawn from the lower region of the column, the loaded particles being supplied as a slurry in a carrier liquid, and successive batches of loaded particles being isolated as measured batches and being separated from their carrier liquid before being contacted with strong eluate and slurried with the strong eluate into the lower region of the column. An example describes the stripping of ion exchange resin particles loaded with complex uranium ions. (author)

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.

Epidemiological manifestations of hepatitis C virus genotypes and its association with potential risk factors among Libyan patients.

Science.gov (United States)

Elasifer, Hana A; Agnnyia, Yossif M; Al-Alagi, Basher A; Daw, Mohamed A

2010-11-13

The information on hepatitis C virus genotypes and subtypes among Libyan population and its association with various risk factors is not known. The objectives of this study were to determine the epidemiological manifestations of HCV genotypes among Libyan patients and their association with certain potential risk factors. A total of 1240 of HCV infected patients registered at Tripoli Medical Centre were studied in five years period from January 2005 to October 2009. The information were reviewed and the data were collected. A sample from each patient (785 male; 455 female) was analysed for genotyping and sub-typing using specific genotyping assay. The information was correlated with the risk factors studied and the statistical data were analyzed using SPSS version 11.5. Off the total patients studied, four different genotypes were reported, including genotypes 1, 2, 3, and 4. Genotype4 was the commonest (35.7%), followed by genotype1 (32.6%). According to subtypes 28% were unclassified genotype 4, 14.6% were genotype 1b and some patients infected with more than one subtype (2.3% genotype 4c/d, 1% genotype 2a/c). Genotypes 1 was the commonest among males, while genotype 4 among females. According to the risk factors studied, Genotype1 and genotype 4 were found with most of the risk factors. Though they were particularly evident surgical intervention, dental procedures and blood transfusion while genotype 1 was only followed by genotype 3 mainly which mainly associated with certain risk groups such as intravenous drug abusers. Here in we report on a detailed description of HCV genotype among Libyans. The most common genotype was type 4 followed by genotype 1, other genotypes were also reported at a low rate. The distribution of such genotypes were also variable according to gender and age. The commonly prevalent genotypes found to be attributable to the medical -related transmission of HCV, such as blood, surgery and dental procedures when compared with other risk

Process for recovering uranium using an alkyl pyrophosphoric acid and alkaline stripping solution

International Nuclear Information System (INIS)

Worthington, R.E.; Magdics, A.

1987-01-01

A process is described for stripping uranium for a pregnant organic extractant comprising an alkyl pyrophosphoric acid dissolved in a substantially water-immiscible organic diluent. The organic extractant contains tetravalent uranium and an alcohol or phenol modifier in a quantity sufficient to retain substantially all the unhydrolyzed alkyl pyrophosphoric acid in solution in the diluent during stripping. The process comprises adding an oxidizing agent to the organic extractant and thereby oxidizing the tetravalent uranium to the +6 state in the organic extractant, and contacting the organic extractant containing the uranium in the +6 state with a stripping solution comprising an aqueous solution of an alkali metal or ammonium carbonate or hydroxide thereby stripping uranium from the organic extractant into the stripping solution. The resulting barren organic extractant containing substantially all of the unhydrolyzed alkyl pyrophosphoric acid dissolved in the diluent is separated from the stripping solution containing the stripped uranium, the barren extractant being suitable for recycle

Single electron attachment and stripping cross sections for relativistic heavy ions

International Nuclear Information System (INIS)

Crawford, H.J.

1979-06-01

The results of a Bevalac experiment to measure the single electron attachment and stripping cross sections for relativistic (0.5 1 , and fully stripped, N 0 , ion beams emerging from the targets. Separate counters measured the number of ions in each charge state. The ratios N 1 /N 0 for different target thicknesses were fit to a simple growth curve to yield electron attachment and stripping cross sections. The data are compared to relativistic extrapolations of available theories. Clear evidence for two separate attachment processes, radiative and non-radiative, is found. Data are compared to a recently improved formulation for the stripping cross sections

Genetic and DNA methylation changes in cotton (Gossypium genotypes and tissues.

Directory of Open Access Journals (Sweden)

Kenji Osabe

Full Text Available In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP assays including a methylation insensitive enzyme (BsiSI, and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC. DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.

Genetic and DNA methylation changes in cotton (Gossypium) genotypes and tissues.

Science.gov (United States)

Osabe, Kenji; Clement, Jenny D; Bedon, Frank; Pettolino, Filomena A; Ziolkowski, Lisa; Llewellyn, Danny J; Finnegan, E Jean; Wilson, Iain W

2014-01-01

In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP) assays including a methylation insensitive enzyme (BsiSI), and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC). DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation) in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.

Distribution of Porphyromonas gingivalis fimA genotypes in primary endodontic infections.

Science.gov (United States)

Rôças, Isabela N; Siqueira, José F

2010-03-01

Long fimbriae (FimA) are important virulence factors of Porphyromonas gingivalis. Based on the diversity of the fimA gene, this species is classified into 6 genotypes. This study surveyed samples from primary endodontic infections for the presence of these P. gingivalis fimA variants. Genomic DNA isolated from samples taken from 25 root canals of teeth with chronic apical periodontitis and 25 aspirates from acute apical abscess was used as template in polymerase chain reaction (PCR) assays directed toward the detection of the different P. gingivalis fimA genotypes. Porphyromonas gingivalis was detected by a 16S rRNA gene-based PCR in 36% of the total number of cases sampled (44% of chronic apical periodontitis and 28% of abscess aspirates). In cases of chronic apical periodontitis, P. gingivalis variant type IV was the most prevalent (24%), followed by types I (20%), II (16%), and III (8%). In acute abscess samples, variant type II was the most prevalent (12%), followed by types III and IV (8% of each) and type I (4%). Combinations of up to 3 different genotypes were detected in a few cases. No single fimA genotype variant or combination thereof was significantly associated with symptoms. Overall, fimA types IV (16%), II (14%), and I (12%) were the most prevalent. Findings demonstrated that different P. gingivalis fimA genotypes can be present in primary endodontic infections. Copyright 2010 Mosby, Inc. All rights reserved.

Observational study on the pavement performance effects of shoulder rumble strip on shoulders

Directory of Open Access Journals (Sweden)

Sean Coffey

2016-07-01

Full Text Available Rumble strip implementation has shown a constant increase with its safety benefits. Rumble strips are milled into the roadway shoulder to produce noise and vibrations when driven on. With the milling process, the pavement performance is expected to be negatively impacted by the decreased depth, though not mathematically quantified. Using methods defined by the Long-Term Pavement Performance Program, the severity of the shoulder site’s distresses, with and without shoulder rumble strips, will be quantified. The quantification would permit the design to compensate for the impact. This design compensation allows the implementation of hard shoulder running, the use of shoulder as a travel lane during congestion, and retains the shoulder rumble strip safety instead of removing, as suggested by some proposed projects. While hard shoulder running would not impact specific time periods, the safety benefit of rumble strips could be needed at any time. This study aims to quantify the rumble strip impact to enable the full shoulder strength for hard shoulder running while retaining the safety benefits of rumble strips. Keywords: Rumble strips, Shoulder, Cracking, Pavement performance, Hard shoulder running

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.

Influence for high intensity irradiation on characteristics of silicon strip-detectors

International Nuclear Information System (INIS)

Anokhin, I.E.; Pugatch, V.M.; Zinets, O.S.

1995-01-01

Full text: Silicon strip detectors (SSD) are widely used for the coordinate determination of short-range as well as minimum ionizing particles with high spatial resolution. Submicron position sensitivity of strip-detectors for short-range particles has been studied by means of two dimensional analyses of charges collected by neighboring strips as well as by measurement of charge collection times [1]. Silicon strip detectors was also used for testing high energy electron beam [2]. Under large fluences the radiation defects are stored and such characteristics of strip-detectors as an accuracy of the coordinate determination and the registration efficiency are significantly changed. Radiation defects lead to a decrease of the lifetime and mobility of charge carriers and therefore to changes of conditions for the charge collection in detectors. The inhomogeneity in spatial distribution if defects and electrical field plays an important role in the charge collection. In this report the role of the diffusion and drift in the charge collection in silicon strip-detectors under irradiation up to 10 Mrad has been studied. The electric field distribution and its dependence on the radiation dose in the detector have been calculated. It is shown that for particles incident between adjacent strips the coordinate determination precision depends strongly on the detector geometry and the electric field distribution, particularly in the vicinity of strips. Measuring simultaneously the collected charges and collection times on adjacent strips one can essentially improve reliability of the coordinate determination for short-range particles. Usually SSD are fabricated on n-type wafers. It is well known that under high intensity irradiation n-Si material converts into p-Si as far as p-type silicon is more radiative hard than n-type silicon [3] it is reasonable to fabricate SSD using high resistivity p-Si. Characteristics of SSD in basis n-and P-Si have been compared and higher

Comparisons of boll weevil (Coleoptera: Curculionidae) pheromone traps with and without kill strips.

Science.gov (United States)

Suh, C P C; Armstrong, J S; Spurgeon, D W; Duke, S

2009-02-01

Boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), eradication programs typically equip pheromone traps with an insecticide-impregnated kill strip. These strips are intended to kill captured insects, thereby simplifying trap servicing and reducing the loss of weevils from predation and escape. However, the effectiveness of kill strips has not been extensively evaluated. We examined the influences of kill strips on weevil captures, trap servicing, and the incidences of weevil predation and trap obstruction (e.g., by spider webs). Evaluations were conducted weekly during three different production periods (pre- to early-, late-, and postseason) of cotton, Gossypium hirsutum L., to represent different environmental conditions and weevil population levels. Within each period, mean weekly captures of weevils in traps with and without kill strips were statistically similar. On average, traps with kill strips took 9 s longer to service than traps without kill strips, but statistical differences were only detected during the late-season period. Overall, the mean weekly proportion of traps with evidence of weevil predation or trap obstruction was significantly lower for traps with kill strips (0.25) than for traps without kill strips (0.37). However, this reduction in the frequency of weevil predation or trap obstruction was too small to produce a corresponding increase in the numbers of weevils captured. In light of these findings, the use of kill strips is likely unnecessary in eradication programs, but may be a consideration in situations when the numbers of deployed traps are reduced and chronic problems with weevil predation or trap obstruction exist.

CdSe/ZnS Quantum Dot-Labeled Lateral Flow Strips for Rapid and Quantitative Detection of Gastric Cancer Carbohydrate Antigen 72-4

Science.gov (United States)

Yan, Xinyu; Wang, Kan; Lu, Wenting; Qin, Weijian; Cui, Daxiang; He, Jinghua

2016-03-01

Carbohydrate antigen 72-4 (CA72-4) is an important biomarker associated closely with diagnosis and prognosis of early gastric cancer. How to realize quick, sensitive, specific, and quantitative detection of CA72-4 in clinical specimens has become a great requirement. Herein, we reported a CdSe/ZnS quantum dot-labeled lateral flow test strip combined with a charge-coupled device (CCD)-based reader was developed for rapid, sensitive, and quantitative detection of CA72-4. Two mouse monoclonal antibodies (mAbs) against CA72-4 were employed. One of them was coated as a test line, while another mAb was labeled with quantum dots and coated onto conjugate pad. The goat anti-mouse IgG was immobilized as a control line. After sample was added, a sandwich structure was formed with CA72-4 and these two mAbs. The fluorescent signal from quantum dots (QD)-labeled mAb in sandwich structure was related to the amount of detected CA72-4. A CCD-based reader was used to realize quantitative detection of CA72-4. Results showed that developed QD-labeled lateral flow strips to detect CA72-4 biomarker with the sensitivity of 2 IU/mL and 10 min detection time. One hundred sera samples from clinical patients with gastric cancer and healthy people were used to confirm specificity of this strip method; results showed that established strip method own 100 % reproducibility and 100 % specificity compared with Roche electrochemiluminescence assay results. In conclusion, CdSe/ZnS quantum dot-labeled lateral flow strips for detection of CA72-4 could realize rapid, sensitive, and specific detection of clinical samples and could own great potential in clinical translation in near future.

Performance of strip-based glucose meters and cassette-based blood gas analyzer for monitoring glucose levels in a surgical intensive care setting.

Science.gov (United States)

Claerhout, Helena; De Prins, Martine; Mesotten, Dieter; Van den Berghe, Greet; Mathieu, Chantal; Van Eldere, Johan; Vanstapel, Florent

2016-01-01

We verified the analytical performance of strip-based handheld glucose meters (GM) for prescription use, in a comparative split-sample protocol using blood gas samples from a surgical intensive care unit (ICU). Freestyle Precision Pro (Abbott), StatStrip Connectivity Meter (Nova), ACCU-CHEK Inform II (Roche) were evaluated for recovery/linearity, imprecision/repeatability. The GMs and the ABL90 (Radiometer) blood gas analyzer (BGA) were tested for relative accuracy vs. the comparator hexokinase glucose-6-phosphate-dehydrogenase (HK/G6PDH) assay on a Cobas c702 analyzer (Roche). Recovery of spiked glucose was linear up to 19.3 mmol/L (347 mg/dL) with a slope of 0.91-0.94 for all GMs. Repeatability estimated by pooling duplicate measurements on samples below (n=9), in (n=51) or above (n=80) the 4.2-5.9 mM (74-106 mg/dL) range were for Freestyle Precision Pro: 4.2%, 4.0%, 3.6%; StatStrip Connectivity Meter: 4.0%, 4.3%, 4.5%; and ACCU-CHEK Inform II: 1.4%, 2.5%, 3.5%. GMs were in agreement with the comparator method. The BGA outperformed the GMs, with a MARD of 3.9% compared to 6.5%, 5.8% and 4.4% for the FreeStyle, StatStrip and ACCU-CHEK, respectively. Zero % of the BGA results deviated more than the FDA 10% criterion as compared to 9.4%, 3.7% and 2.2% for the FreeStyle, StatStrip and ACCU-CHEK, respectively. For all GMs, icodextrin did not interfere. Variation in the putative influence factors hematocrit and O2 tension could not explain observed differences with the comparator method. GMs quantified blood glucose in whole blood at about the 10% total error criterion, proposed by the FDA for prescription use.

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.

Numerical analysis of edge effects in side illuminated strip detectors for digital radiology

CERN Document Server

Krizaj, D

2000-01-01

The influence of edge defects on side illuminated X-ray strip detectors for digital radiology is investigated by numerical device modeling. By assuming positive fixed oxide charges on side and top surfaces simulations have shown strong curvature of the equipotential lines in the edge region. A fraction of the edge generated current surpasses the edge guard-ring junction and is collected by the readout strips. As a consequence, strips cannot be placed close to the edge of the structure and collection efficiency is reduced. An n-on-n instead of a p-on-n strip detector is proposed enabling collection of edge generated carriers by a very narrow guard-ring junction and placement of the readout strip close to the edge without increase of the strip leakage current.

Generalized thick strip modelling for vortex-induced vibration of long flexible cylinders

International Nuclear Information System (INIS)

Bao, Y.; Palacios, R.; Graham, M.; Sherwin, S.

2016-01-01

We propose a generalized strip modelling method that is computationally efficient for the VIV prediction of long flexible cylinders in three-dimensional incompressible flow. In order to overcome the shortcomings of conventional strip-theory-based 2D models, the fluid domain is divided into “thick” strips, which are sufficiently thick to locally resolve the small scale turbulence effects and three dimensionality of the flow around the cylinder. An attractive feature of the model is that we independently construct a three-dimensional scale resolving model for individual strips, which have local spanwise scale along the cylinder's axial direction and are only coupled through the structural model of the cylinder. Therefore, this approach is able to cover the full spectrum for fully resolved 3D modelling to 2D strip theory. The connection between these strips is achieved through the calculation of a tensioned beam equation, which is used to represent the dynamics of the flexible body. In the limit, however, a single “thick” strip would fill the full 3D domain. A parallel Fourier spectral/hp element method is employed to solve the 3D flow dynamics in the strip-domain, and then the VIV response prediction is achieved through the strip–structure interactions. Numerical tests on both laminar and turbulent flows as well as the comparison against the fully resolved DNS are presented to demonstrate the applicability of this approach.

Generalized thick strip modelling for vortex-induced vibration of long flexible cylinders

Energy Technology Data Exchange (ETDEWEB)

Bao, Y., E-mail: ybao@sjtu.edu.cn [Department of Civil Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiaotong University, No. 800 Dongchuan Road, Shanghai (China); Department of Aeronautics, Imperial College London, South Kensington Campus, London (United Kingdom); Palacios, R., E-mail: r.palacios@imperial.ac.uk [Department of Aeronautics, Imperial College London, South Kensington Campus, London (United Kingdom); Graham, M., E-mail: m.graham@imperial.ac.uk [Department of Aeronautics, Imperial College London, South Kensington Campus, London (United Kingdom); Sherwin, S., E-mail: s.sherwin@imperial.ac.uk [Department of Aeronautics, Imperial College London, South Kensington Campus, London (United Kingdom)

2016-09-15

We propose a generalized strip modelling method that is computationally efficient for the VIV prediction of long flexible cylinders in three-dimensional incompressible flow. In order to overcome the shortcomings of conventional strip-theory-based 2D models, the fluid domain is divided into “thick” strips, which are sufficiently thick to locally resolve the small scale turbulence effects and three dimensionality of the flow around the cylinder. An attractive feature of the model is that we independently construct a three-dimensional scale resolving model for individual strips, which have local spanwise scale along the cylinder's axial direction and are only coupled through the structural model of the cylinder. Therefore, this approach is able to cover the full spectrum for fully resolved 3D modelling to 2D strip theory. The connection between these strips is achieved through the calculation of a tensioned beam equation, which is used to represent the dynamics of the flexible body. In the limit, however, a single “thick” strip would fill the full 3D domain. A parallel Fourier spectral/hp element method is employed to solve the 3D flow dynamics in the strip-domain, and then the VIV response prediction is achieved through the strip–structure interactions. Numerical tests on both laminar and turbulent flows as well as the comparison against the fully resolved DNS are presented to demonstrate the applicability of this approach.

Design, Analysis, and On-Sun Evaluation of Reflective Strips Under Controlled Buckling

Science.gov (United States)

Jaworske, Donald A.; Sechkar, Edward A.; Colozza, Anthony J.

2014-01-01

Solar concentrators are envisioned for use in a variety of space-based applications, including applications involving in situ resource utilization. Identifying solar concentrators that minimize mass and cost are of great interest, especially since launch cost is driven in part by the mass of the payload. Concentrators must also be able to survive the wide temperature excursions on the lunar surface. Identifying smart structures which compensate for changes in concentrator geometry brought about by temperature extremes are of interest. Some applications may benefit from the ability to change the concentrators focal pattern at will. This paper addresses a method of designing a single reflective strip to produce a desired focal pattern through the use of controlled buckling. Small variations in the cross section over the length of the reflective strip influence the distribution of light in the focal region. A finite element method of analysis is utilized here which calculates the curve produced for a given strip cross section and axial load. Varying axial force and strip cross section over the length of the reflective strip provide a means of optimizing ray convergence in the focal region. Careful selection of a tapered cross section yields a reflective strip that approximates a parabola. An array of reflective strips under controlled buckling produces a light weight concentrator and adjustments in the compression of individual strips provide a means of compensating for temperature excursions or changing the focal pattern at will.

360-degrees profilometry using strip-light projection coupled to Fourier phase-demodulation.

Science.gov (United States)

Servin, Manuel; Padilla, Moises; Garnica, Guillermo

2016-01-11

360 degrees (360°) digitalization of three dimensional (3D) solids using a projected light-strip is a well-established technique in academic and commercial profilometers. These profilometers project a light-strip over the digitizing solid while the solid is rotated a full revolution or 360-degrees. Then, a computer program typically extracts the centroid of this light-strip, and by triangulation one obtains the shape of the solid. Here instead of using intensity-based light-strip centroid estimation, we propose to use Fourier phase-demodulation for 360° solid digitalization. The advantage of Fourier demodulation over strip-centroid estimation is that the accuracy of phase-demodulation linearly-increases with the fringe density, while in strip-light the centroid-estimation errors are independent. Here we proposed first to construct a carrier-frequency fringe-pattern by closely adding the individual light-strip images recorded while the solid is being rotated. Next, this high-density fringe-pattern is phase-demodulated using the standard Fourier technique. To test the feasibility of this Fourier demodulation approach, we have digitized two solids with increasing topographic complexity: a Rubik's cube and a plastic model of a human-skull. According to our results, phase demodulation based on the Fourier technique is less noisy than triangulation based on centroid light-strip estimation. Moreover, Fourier demodulation also provides the amplitude of the analytic signal which is a valuable information for the visualization of surface details.

One-step simultaneous detection of Ureaplasma parvum and genotypes SV1, SV3 and SV6 from clinical samples using PlexPCR technology.

Science.gov (United States)

Payne, M S; Furfaro, L L; Tucker, R; Tan, L Y; Mokany, E

2017-08-01

Ureaplasma spp. are associated with preterm birth. In recent times, it has become apparent that Ureaplasma parvum, but not Ureaplasma urealyticum, is of most relevance. We recently demonstrated this in Australian pregnant women and using high-resolution melt (HRM) PCR, further showed that U. parvum genotype SV6 was of particular significance. However, our assay was unable to identify multiple genotypes in the same sample, required a separate species-level qPCR for low titre samples and was not ideal for diagnostic laboratories due to the nature of HRM PCR result interpretation. Consequently, our current study developed a novel, one-step PlexPCR assay capable of detecting U. parvum and genotypes SV1, SV3 and SV6 in a single reaction directly from clinical samples. We then validated this using vaginal swab DNA from our Australian cohort of pregnant women. The PlexPCR was highly sensitive, detecting all targets to between 0.4 × 10 -5  ng DNA (SV3) and 0.4 × 10 -6  ng DNA (U. parvum, SV1 and SV6). Compared to our HRM PCR, the PlexPCR defined genotype distribution in all seven cases previously reported as 'mixed', and detected another eight cases where multiple genotypes (two) were present in samples previously reported as single genotypes using HRM PCR. Ureaplasma spp. have been associated with prematurity for decades, however, only a minority of studies have examined this beyond the genus level. In those that have, Ureaplasma parvum has been strongly associated with preterm birth. We recently demonstrated this in Australian women and further showed that U. parvum genotype SV6 was of particular significance. Our PlexPCR assay allows rapid detection and concurrent genotyping of U. parvum in clinical samples and may be of particular interest to obstetricians, particularly those caring for women at a high risk of preterm birth, and any other disease phenotypes where U. parvum is of interest. © 2017 The Authors. Letters in Applied Microbiology published by John

Genotypic diversity and clonal structure of Erigeron annuus (Asteraceae in Lithuania

Directory of Open Access Journals (Sweden)

Tunaitienė, Virginija

2014-02-01

Full Text Available This study was conducted to assess the clonal structure and genetic diversity of alien herbaceous plant species Erigeron annuus. The global warming and changes in agriculture practice in the past few decades were favourable for the expansion of this species in Lithuania. We used RAPD and ISSR assays to assess genetic variation within and among 29 populations of E. annuus. A total of 278 molecular markers were revealed. Our study detected reduced level of genetic diversity of invasive populations of E. annuus. Significant differences in DNA polymorphism among populations of E. annuus were also found. Some populations of this species are composed of genetically identical plants, while others were polymorphic. Clonal diversity of study populations ranged from 0.083 to 0.4 for both DNA marker systems. The Simpsons diversity index values ranged from 0.0 to 0.636. The average number of genotypes per population established using both assays was about 1.7. Out of 328 E. annuus individuals only 16 showed unique RAPD and 14 unique ISSR banding patterns. The remaining plants were clones of different size. The most common genotype of E. annuus identified in our study was represented by predominate in nine populations.

[Clinical benefit of HCV core antigen assay in patients receiving interferon and ribavirin combination therapy].

Science.gov (United States)

Higashimoto, Makiko; Takahashi, Masahiko; Jokyu, Ritsuko; Saito, Hidetsugu

2006-02-01

A highly sensitive second generation HCV core antigen assay has recently been developed. We compared viral disappearance and kinetics data between commercially available core antigen assays, Lumipulse Ortho HCV Ag, and a quantitative HCV RNA PCR assay, Cobas Amplicor HCV Monitor Test, Version 2 to estimate the predictive benefit of sustained viral response (SVR) and non-SVR in 59 patients treated with interferon and ribavirin combination therapy. We found a good correlation between HCV core Ag and HCV RNA level regardless of genotype. Although the sensitivity of the core antigen assay was lower than PCR, the dynamic range was broader than that of the PCR assay, so that we did not need to dilute the samples in 59 patients. We detected serial decline of core Ag levels in 24 hrs, 7 days and 14 days after interferon combination therapy. The decline of core antigen levels was significant in SVR patients compared to non-SVR as well as in genotype 2a, 2b patients compared to 1b. Core antigen-negative on day 1 could predict all 10 SVR patients (PPV = 100%), whereas RNA-negative could predict 22 SVR out of 25 on day 14 (PPV = 88.0%). None of the patients who had detectable serum core antigen on day 14 became SVR(NPV = 100%), although NPV was 91.2% on RNA negativity. An easy, simple, low cost new HCV core antigen detecting system seems to be useful for assessing and monitoring IFN treatment for HCV.

Characterization and Calibration of Large Area Resistive Strip Micromegas Detectors

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00389527; The ATLAS collaboration

2016-01-01

Resistive strip Micromegas detectors are discharge tolerant. They have been tested extensively as small detectors of about 10 x 10 cm$^2$ in size and they work reliably at high rates of 100 kHz/cm$^2$ and above. Tracking resolution well below 100 $\\mu$m has been observed for 100 GeV muons and pions. Micromegas detectors are meanwhile proposed as large area muon precision trackers of 2-3 m$^2$ in size. To investigate possible differences between small and large detectors, a 1 m$^2$ detector with 2048 resistive strips at a pitch of 450 $\\mu$m was studied in the LMU Cosmic Ray Measurement Facility (CRMF) using two 4 $\\times$ 2.2 m$^2$ large Monitored Drift Tube (MDT) chambers for cosmic muon reference tracking. A segmentation of the resistive strip anode plane in 57.6 mm x 93 mm large areas has been realized by the readout of 128 strips with one APV25 chip each and by eleven 93 mm broad trigger scintillators placed along the readout strips. This allows for mapping of homogeneity in pulse height and efficiency, d...

Common Genotypes of Hepatitis B virus prevalent in Injecting drug abusers (addicts of North West Frontier Province of Pakistan

Directory of Open Access Journals (Sweden)

Alam Muhammad

2007-06-01

Full Text Available Abstract Background The epidemiological significance of Hepatitis B virus genotypes has been well established and becoming an essential concern day by day however, much little is known about the mixed infection with more than one Hepatitis B virus genotypes and their clinical relevance. Methods Intravenous drug abusers are considered as a major risk group for the acquisition and transmission of blood borne infections like hepatitis B, however, in Pakistan, no such data has ever been reported about the epidemiology of HBV and its genotypes in Injecting Drug Users. 250 individuals were analyzed for hepatitis B virus genotypes after prior screening with serological assay for the detection of HBsAg. Results 56 (22.4% individuals were found positive on ELSIA for HBsAg. The genotype distribution was found to be as: genotype D, 62.5%; genotype A, 8.92% while 28.57% individuals were found to be infected with a mixture of genotype A and D. Conclusion There is an urgent need of the time to develop public health care policies with special emphasis towards the control of HBV transmission through high risk groups especially Injecting Drug Users.

Silicon Strip Detectors for ATLAS at the HL-LHC Upgrade

CERN Document Server

Hara, K; The ATLAS collaboration

2012-01-01

The present ATLAS silicon strip (SCT) and transition radiation (TRT) trackers will be replaced with new silicon strip detectors, as part of the Inner Tracker System (ITK), for the Phase-2 upgrade of the Large Hadron Collider, HL-LHC. We have carried out intensive R&D programs to establish radiation harder strip detectors that can survive in a radiation level up to 3000 fb-1 of integrated luminosity based on n+-on-p microstrip detector. We describe main specifications for this year’s sensor fabrication, followed by a description of possible module integration schema

Wide Strip Casting Technology of Magnesium Alloys

Science.gov (United States)

Park, W.-J.; Kim, J. J.; Kim, I. J.; Choo, D.

Extensive investigations relating to the production of high performance and low cost magnesium sheet by strip casting have been performed for the application to automotive parts and electronic devices. Research on magnesium sheet production technology started in 2004 by Research Institute of Industrial Science and Technology (RIST) with support of Pohang Iron and Steel Company (POSCO). POSCO has completed the world's first plant to manufacture magnesium coil. Another big project in order to develop wide strip casting technology for the automotive applications of magnesium sheets was started in succession.

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...... indicates that asset stripping may take place in mature market economies to the extent that perpetrators are able to circumvent the corporate governance system by giving lawyers, public accountants and banks incentives to act less critically towards dubious business transactions. Research limitations...

Evaluation of tomato genotypes against tomato mosaic virus (ToMV) and its effect on yield contributing parameters

International Nuclear Information System (INIS)

Ullah, N.; Ali, A.; Ahmad, M.; Din, N.; Ahmad, F.; Fahim, M.

2017-01-01

The use of resistant varieties is an effective, economic and environment friendly management of plant diseases particularly those caused by viruses. This paper reports, evaluation of 21 different tomato genotypes to find out resistance sources against Tomato mosaic virus (ToMV) and to study effect of the virus on yield contributing parameters. The virus identity was confirmed both by Direct Antibody Coating Enzyme Linked Immunoassay (DAC-ELISA) and differential host assay. Characteristic necrotic lesions were observed on differential hosts viz., Nicotiana tabacum var. White burly and Chenopodium amaranticolor after 10 and 3-4 days of inoculation, respectively. Upon ToMV inoculation, plants of accession No. 017902 developed no symptoms and were rated as highly resistant. Its resistance was further confirmed by both DAC-ELISA and indicator host assay, while the remaining genotypes displayed a range of symptoms. Plants of accession No. 017883 showed lowest percent disease index (PDI) and were rated as resistant, while plants of cultivar Red jumbo showed maximum PDI (44.97%) and were rated as susceptible. In susceptible genotypes average ELISA absorbance A405 value (2.19) was found higher than resistant one (1.05), while in control healthy plants ELISA absorbance A405 was 0.18. Maximum virus titre 2.73 and 0.91 were found in leaf and root tissues of cultivar Red jumbo, respectively. Among tested genotypes, one was highly resistant, one resistant, four moderately susceptible and 15 were susceptible. The virus significantly (p<=0.05) reduced the yield contributing parameters i.e. plant height, fresh shoot and root weight, dry shoot and root weight in susceptible genotypes. (author)

Apparatus for irradiating a continuous line metallic strip with electron beams

International Nuclear Information System (INIS)

Matsuda, Shozo; Tanaka, Tadashi; Okamoto, Tadaaki; Ueno, Nagaharu.

1970-01-01

The secondary X-rays from an irradiated object are completely shielded by providing direction-change rollers between applicator rollers and irradiation devices. The substrate strip turns its direction of travel by 90 0 through idle rollers and before it enters a front side applicator roller. After the application of coatings, the strip travels over a roller to turn upwardly, so that the applicator is isolated from the following irradiation enclosure. Next, the irradiated strip changes its direction by 90 0 through a roller to enter a bake side coating applicator. After a direction change through a roller, the strip enters the irradiation enclosure. In this way, the applicators can prevent leakage of secondary X-rays. (Iwakiri, K.)

Genotyping of circulating measles strains in Italy in 2010

Directory of Open Access Journals (Sweden)

Melissa Baggieri

2014-12-01

Full Text Available INTRODUCTION: The European Regional Office of the World Health Organization developed a strategic approach to stop the indigenous transmission of measles in its 53 Member States by 2015. In Italy, laboratory surveillance activity is implemented by the National Reference Laboratory for Measles and Rubella at the Italian National Institute of Health (Istituto Superiore di Sanità, Rome. The role of the National Reference Laboratory is to strengthen surveillance systems through rigorous case investigation and laboratory confirmation of suspected sporadic cases and outbreaks. Genetic characterization of wild-type measles virus is an essential component of the laboratory-based surveillance. This study describes the molecular characterization of measles virus strains isolated during 2010. METHODS: Dried blood spots, urine and oral fluid samples were collected from patients with a suspected measles infection. Serological tests were performed on capillary blood, and viral detection was performed on urine and oral fluid samples through molecular assay. Positive samples were sequenced and phylogenetically analysed. RESULTS AND DISCUSSION: The phylogenetic analysis showed a co-circulation of genotypes D4 and D8, and sporadic cases associated to genotypes D9 and B3. Then, molecular epidemiology of measles cases permitted to establish that D4 and D8 were the endemic genotypes in Italy during 2010.

Optimized Use of Low-Depth Genotyping-by-Sequencing for Genomic Prediction Among Multi-Parental Family Pools and Single Plants in Perennial Ryegrass (Lolium perenne L.

Directory of Open Access Journals (Sweden)

Fabio Cericola

2018-03-01

Full Text Available Ryegrass single plants, bi-parental family pools, and multi-parental family pools are often genotyped, based on allele-frequencies using genotyping-by-sequencing (GBS assays. GBS assays can be performed at low-coverage depth to reduce costs. However, reducing the coverage depth leads to a higher proportion of missing data, and leads to a reduction in accuracy when identifying the allele-frequency at each locus. As a consequence of the latter, genomic relationship matrices (GRMs will be biased. This bias in GRMs affects variance estimates and the accuracy of GBLUP for genomic prediction (GBLUP-GP. We derived equations that describe the bias from low-coverage sequencing as an effect of binomial sampling of sequence reads, and allowed for any ploidy level of the sample considered. This allowed us to combine individual and pool genotypes in one GRM, treating pool-genotypes as a polyploid genotype, equal to the total ploidy-level of the parents of the pool. Using simulated data, we verified the magnitude of the GRM bias at different coverage depths for three different kinds of ryegrass breeding material: individual genotypes from single plants, pool-genotypes from F2 families, and pool-genotypes from synthetic varieties. To better handle missing data, we also tested imputation procedures, which are suited for analyzing allele-frequency genomic data. The relative advantages of the bias-correction and the imputation of missing data were evaluated using real data. We examined a large dataset, including single plants, F2 families, and synthetic varieties genotyped in three GBS assays, each with a different coverage depth, and evaluated them for heading date, crown rust resistance, and seed yield. Cross validations were used to test the accuracy using GBLUP approaches, demonstrating the feasibility of predicting among different breeding material. Bias-corrected GRMs proved to increase predictive accuracies when compared with standard approaches to

Relationship Between Genotype Variants Follicle-stimulating Hormone Receptor Gene Polymorphisms (FSHR) and Morphology of Oocytes Prior to ICSI Procedures

OpenAIRE

Gashi, Zafer; Elezaj, Shkelzen; Zeqiraj, Afrim; Grabanica, Driton; Shabani, Isak; Gruda, Bujar; Gashi, Fitore

2016-01-01

Introduction: This study investigated association of Asn680Ser FSHR polymorphism with the ovarian response in 104 women of Albanian ethnic population enrolled in ICSI program. The reason of infertility in all cases has been identified as male factor. Methods: Analysis of the Asn680Ser polymorphism was performed using TaqMan? SNP Genotyping Assay. Clinical and endocrinologic parameters were analyzed based on the genotype, age, BMI, oocyte yield, number of transferred embryos and pregnancy rate...

stripping of uranium from DEHPA/TOPO solvent by ammonium carbonate solutions

International Nuclear Information System (INIS)

Khorfan, S.; Shino, O.; Wahood, A.; Dahdouh, A.

2002-01-01

Uranium is recovered from phosphoric acid by the DEHPA/TOPO process. In this process uranium is stripped from the loaded DEHPA/TOPO solvent in the second cycle by an ammonium carbonate solution. This paper studied stripping of uranium from 0.3 Mol DEHPA/0.075 Mol TOPO in kerosene by different ammonium carbonate solutions. The ammonium carbonate solutions tested were either made locally from ammonia and carbon dioxide gases or commercial and laboratory grades available on the market. A comparison was made between these carbonate solutions in terms of purity, stripping efficiency and phase separation. Both stripping and phase separation were carried out under different conditions of phase ratio and concentrations. The results obtained showed that ammonium carbonate prepared from direct synthesis of ammonia and carbon dioxide gases had a high purity and gave the same stripping yield as the laboratory grade. The phase separation was also slightly improved using a pure synthesized ammonium carbonate solution. the phase separation was found to be best at concentration of 0.5 Mol/L ammonium carbonate solution and at a phase A/O of 1/1 and a temperature of 50 degree centigrade. It was possible to obtain >99% yield by operating 2 stripping stages counter currently under these conditions. (authors)

Genotyping via Sequence Related Amplified Polymorphism Markers in Fusarium culmorum

Directory of Open Access Journals (Sweden)

Işıl Melis Zümrüt

2018-02-01

Full Text Available Fusarium culmorum is predominating causal agent of head blight (HB and root rot (RR in cereals worldwide. Since F. culmorum has a great level of genetic diversity and the parasexual stage is assumed for this phytopathogen, characterization of isolates from different regions is significant step in food safety and controlling the HB. In this study, it was aimed to characterize totally 37 F. culmorum isolates from Turkey via sequence related amplified polymorphism (SRAP marker based genotyping. MAT-1/MAT-2 type assay was also used in order to reveal intraspecific variation in F. culmorum. MAT-1 and MAT-2 specific primer pairs for mating assays resulted in 210 and 260 bp bands, respectively. 11 of isolates were belonged to MAT-1 type whereas 19 samples were of MAT-2. Remaining 7 samples yielded both amplicons. Totally 9 SRAP primer sets yielded amplicons from all isolates. Genetic similarity values were ranged from 39 to 94.7%. Total band number was 127 and PCR product sizes were in the range of 0.1-2.5 kb. Amplicon numbers for individuals were ranged from 1 to 16. According to data obtained from current study, SRAP based genotyping is powerful tool for supporting the data obtained from investigations including phenotypic and agro-ecological characteristics. Findings showed that SRAP-based markers could be useful in F. culmorum characterization.

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

Directory of Open Access Journals (Sweden)

Dawn N Birdsell

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

Compton recoil electron tracking with silicon strip detectors

International Nuclear Information System (INIS)

O'Neill, T.J.; Ait-Ouamer, F.; Schwartz, I.; Tumer, O.T.; White, R.S.; Zych, A.D.

1992-01-01

The application of silicon strip detectors to Compton gamma ray astronomy telescopes is described in this paper. The Silicon Compton Recoil Telescope (SCRT) tracks Compton recoil electrons in silicon strip converters to provide a unique direction for Compton scattered gamma rays above 1 MeV. With strip detectors of modest positional and energy resolutions of 1 mm FWHM and 3% at 662 keV, respectively, 'true imaging' can be achieved to provide an order of magnitude improvement in sensitivity to 1.6 x 10 - 6 γ/cm 2 -s at 2 MeV. The results of extensive Monte Carlo calculations of recoil electrons traversing multiple layers of 200 micron silicon wafers are presented. Multiple Coulomb scattering of the recoil electron in the silicon wafer of the Compton interaction and the next adjacent wafer is the basic limitation to determining the electron's initial direction

Benefit of Hepatitis C Virus Core Antigen Assay in Prediction of Therapeutic Response to Interferon and Ribavirin Combination Therapy

OpenAIRE

Takahashi, Masahiko; Saito, Hidetsugu; Higashimoto, Makiko; Atsukawa, Kazuhiro; Ishii, Hiromasa

2005-01-01

A highly sensitive second-generation hepatitis C virus (HCV) core antigen assay has recently been developed. We compared viral disappearance and first-phase kinetics between commercially available core antigen (Ag) assays, Lumipulse Ortho HCV Ag (Lumipulse-Ag), and a quantitative HCV RNA PCR assay, Cobas Amplicor HCV Monitor test, version 2 (Amplicor M), to estimate the predictive benefit of a sustained viral response (SVR) and non-SVR in 44 genotype 1b patients treated with interferon (IFN) ...

The Analysis of a Wideband Strip-Helical Antenna with 1.1 Turns

Directory of Open Access Journals (Sweden)

Xihui Tang

2016-01-01

Full Text Available A wideband strip-helical antenna with 1.1 turns is analyzed numerically and experimentally. By replacing the traditional wire helix with wide metallic strip, the forward traveling current on the strip helix with about one turn smoothly decays to the minimum value at the open end of the helix. Therefore, the strip helix can excite a wideband circular polarization (CP wave with 50-ohm impedance matching. The proposed antenna is printed on a hollow-cylinder with a substrate relative permittivity of εr=2.2 and a thickness of h=0.5 mm. A 50 Ω coaxial cable is directly connected to excite the strip-helical antenna without any additional impedance matching section. The ground plane is placed below the antenna in order to provide a directional radiation pattern. To demonstrate this method, a prototype of 1.1-turn strip-helical antenna is tested. The test shows that the proposed antenna can reach an overlapped bandwidth of 46% with height of 0.52λ0, where λ0 is the wavelength in free space at the center operation frequency.

Modules and Front-End Electronics Developments for the ATLAS ITk Strips Upgrade

CERN Document Server

Garcia-Argos, Carlos; The ATLAS collaboration

2017-01-01

The ATLAS experiment is currently preparing for an upgrade of the tracking system in the course of the High Luminosity LHC, scheduled for 2024. The existing Inner Detector will be replaced by an all-silicon Inner Tracker (ITk) with a pixel detector surrounded by a strip detector. The ITk strip detector consists of a four layer barrel and a forward region composed of six discs on each side of the barrel. The basic unit of the detector is the silicon-strip module, consisting of a sensor and one or more hybrid circuits that hold the read-out electronics. The geometries of the barrel and end-cap modules take into account the regions that they have to cover. In the central region, the detectors are rectangular with straight strips, whereas on the forward region the modules require wedge shaped sensors with varying strip length and pitch. The current prototyping phase has resulted in the ITk Strip Detector Technical Design Report (TDR), which kicks-off the pre-production readiness phase at the involved institutes. ...

Modules and Front-End Electronics Developments for the ATLAS ITk Strips Upgrade

CERN Document Server

Garcia-Argos, Carlos; The ATLAS collaboration

2017-01-01

The ATLAS experiment is currently preparing for an upgrade of the tracking system in the course of the High Luminosity LHC, scheduled for 2024. The existing Inner Detector will be replaced by an all-silicon Inner Tracker (ITk) with a pixel detector surrounded by a strip detector. The ITk strip detector consists of a four layer barrel and a forward region composed of six discs on each side of the barrel. The basic unit of the detector is the silicon-strip module, consisting of a sensor and one or more hybrid circuits that hold the read-out electronics. The geometries of the barrel and end-cap modules take into account the regions that they have to cover. In the central region, the detectors are rectangular with straight strips, whereas in the forward region the modules require wedge shaped sensors with varying strip length and pitch. The current prototyping phase has resulted in the ITk Strip Detector Technical Design Report (TDR), which kicks-off the pre-production readiness phase at the involved institutes. ...

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.

Clinical and analytical performance of the BD Onclarity™ HPV assay for detection of CIN2+ lesions on SurePath samples

DEFF Research Database (Denmark)

Ejegod, Ditte Møller; Junge, Jette; Franzmann, Maria

2016-01-01

BACKGROUND: The novel BD Onclarity(TM) HPV assay (Onclarity) on the BD Viper™ LT system (BD Diagnostics, Sparks, MD), detects E6/E7 DNA from 13 high-risk HPV genotypes and HPV66. We compared the analytical and clinical performance of the Onclarity Assay to that of Hybrid Capture 2 and LINEAR ARRAY...

First detection of multiple knockdown resistance (kdr)-like mutations in voltage-gated sodium channel using three new genotyping methods in Anopheles sinensis from Guangxi Province, China.

Science.gov (United States)

Tan, Wei L; Li, Chun X; Wang, Zhong M; Liu, Mei D; Dong, Yan D; Feng, Xiang Y; Wu, Zhi M; Guo, Xiao X; Xing, Dan; Zhang, Ying M; Wang, Zhong C; Zhao, Tong Y

2012-09-01

To investigate knockdown resistance (kdr)-like mutations associated with pyrethroid resistance in Anopheles sinensis (Wiedemann, 1828), from Guangxi province, southwest China, a segment of a sodium channel gene was sequenced and genotyped using three new genotyping assays. Direct sequencing revealed the presence of TTG-to-TCG and TG-to-TTT mutations at allele position L1014, which led to L1014S and L1014F substitutions in a few individual and two novel substitutions of N1013S and L1014W in two DNA templates. A low frequency of the kdr allele mostly in the heterozygous state of L1014S and L1014F was observed in this mosquito population. In this study, the genotyping of An. sinensis using three polymerase chain reaction-based methods generated consistent results, which agreed with the results of DNA sequencing. In total, 52 mosquitoes were genotyped using a direct sequencing assay. The number of mosquitoes and their genotypes were as follows: L/L = 24, L/S = 19, L/F = 8, and F/W = 1. The allelic frequency of L1014, 1014S, and 1014F were 72, 18, and 9%, respectively.

PECULIAR FEATURES PERTAINING TO STRIP FORMATION FROM BAR

Directory of Open Access Journals (Sweden)

G. N. Zdor

2010-01-01

Full Text Available The paper describes results of calculations and presents experimental substantiation of the dependence of a strip width being rolled out of a 10-mm diameter bar on its final thickness. It has been shown that the formation technology of thin steel strips out of a round bar makes it possible without any difficulties to obtain rolled products with the given cross-section dimensions due to proper selection of single drafting.

Laser stripping of relativistic H- ions with practical considerations

International Nuclear Information System (INIS)

Tomlin, R.

1995-12-01

This paper describes laser stripping of H - ions. Some applications are suggested for HEP including stripping 2GeV ions circulating in an accelerator with radius 75 meters where laser meets ion head on in a three meter interaction region. The paper describes photoionizaton cross section, laser power calculation, and how to generate the 5 micrometer light

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

Molecular detection of genotype II grass carp reovirus based on nucleic acid sequence-based amplification combined with enzyme-linked immunosorbent assay (NASBA-ELISA).

Science.gov (United States)

Zeng, Weiwei; Yao, Wei; Wang, Yingying; Li, Yingying; Bermann, Sven M; Ren, Yan; Shi, Cunbin; Song, Xinjian; Huang, Qiwen; Zheng, Shuchen; Wang, Qing

2017-05-01

Grass carp reovirus (GCRV) is the causative agent of the grass carp hemorrhagic disease that has resulted in severe economic losses in the grass carp (Ctenopharyngodon idella) farming industry in China. Early diagnosis and vaccine administration are important priorities for GCRV control. In this study, a nucleic acid sequence-based amplification with enzyme-linked immunosorbent assay (NASBA-ELISA) was developed for to detect genotype II GCRV (GCRV- II). Primers specifically targeting viral RNA genome segment 6 were utilized for amplification in an isothermal digoxigenin-labeling NASBA process, resulting in DIG-labeled RNA amplicons. The amplicons were hybridized to specific biotinylated DNA probes and the products were detected colorimetrically using horseradish peroxidase and a microplate reader. The new method is able to detect GCRV at 14 copies/μL within 5h and had a diagnostic sensitivity and a specificity of 100% when GCRV-II and non-target virus were tested. This NASBA-ELISA was evaluated using a panel of clinical samples (n=103) to demonstrate that it is a rapid, effective and sensitive method for GCRV detection in grass carp aquaculture. Copyright © 2017 Elsevier B.V. All rights reserved.

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…

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.

Development of Colloidal Gold-Based Immunochromatographic Assay for Rapid Detection of Goose Parvovirus

Directory of Open Access Journals (Sweden)

Xianglong Yu

2018-05-01

Full Text Available Goose parvovirus (GPV remains as a worldwide problem in goose industry. For this reason, it is necessary to develop a new diagnostic approach that is easier and faster than conventional tests. A rapid immunochromatographic assay based on antibody colloidal gold nanoparticles specific to GPV was developed for the detection of GPV in goose allantoic fluid and supernatant of tissue homogenate. The monoclonal antibodies (Mab was produced by immunizing the BALB/c mice with purified GPV suspension, and the polyclonal antibody (pAb was produced by immunizing the rabbits with recombinant VP3 protein. The colloidal gold was prepared by the reduction of gold salt with sodium citrate coupled with Mab against GPV. The optimal concentrations of the coating antibody and capture antibody were determined to be 1.6 mg/ml and 9 μg/ml. With visual observation, the lower limit was found to be around 1.2 μg/ml. Common diseases of goose were tested to evaluate the specificity of the immune colloidal gold (ICG strip, and no cross-reaction was observed. The clinical detection was examined by carrying out the ICG strip test with 92 samples and comparing the results of these tests with those obtained via agar diffusion test and polymerase chain reaction (PCR test. Therefore, the ICG strip test was a sufficiently sensitive and accurate detection method for a rapid screening of GPV.

Diagnóstico das meningites através de fitas reagentes Diagnosis of meningitis with reagent strips

Directory of Open Access Journals (Sweden)

Roberta M.C. Romanelli

2001-06-01

ção Hospitalar do Estado de Minas Gerais, CGP-FHEMIG during the daytime hours from May of 1997 to May 1999, and who presented with clinical suspicion of meningitis. Patients ranged in age from one month to 12 years (median 12 months. Results from the cytological and biochemical assay (cellularity, cerebrospinal fluid glucose and protein levels were obtained from 154 patients. These results were subsequently compared with the reaction of cerebrospinal fluid in reagent strips. RESULTS: The cytological and biochemical assay identified 43 cases of probable bacterial meningitis, 19 of probable viral meningitis, and 83 with no alterations. According to the reagent strips, there were 41 cases of probable bacterial meningitis, 2 of probable viral meningitis, and 71 with no alterations. By comparing the results of reagent strips and those of the cytological and biochemical assay, we obtained values for sensitivity, specificity, positive and negative predictive values, and accuracy (respectively 90.7; 98.1; 95.1; 96.4; and 96.1. Statistical analysis using McNemer test did not indicate significant differences between the two methods in the diagnosis of bacterial meningitis (P=0.68. Kappa statistics indicated a high level of agreement between the tests (P<0.0001. CONCLUSIONS: Our results suggest that reagent strips may be a useful additional resource in the diagnosis of bacterial meningitis, especially when it is difficult to collect a sufficient amount of cerebrospinal fluid or to indicate the initial treatment.

Transfer printing of graphene strip from the graphene grown on copper wires

International Nuclear Information System (INIS)

Su, Ching-Yuan; Fu Dongliang; Lu, Ang-Yu; Liu, Keng-Ku; Xu Yanping; Juang, Zhen-Yu; Li, Lain-Jong

2011-01-01

A simple, cost-effective and lithography-free fabrication of graphene strips for device applications is demonstrated. The graphene thin layers were directly grown on Cu wires, followed by Cu etching and transfer printing to arbitrary substrates by a PDMS stamp. The Cu wires can be arranged on the PDMS stamp in a desired pattern; hence, the substrates can receive graphene strips with the same pattern. Moreover, the preparation of graphene strips does not involve conventional lithography; therefore, the surface of the graphene strip is free of residual photoresists, which may be useful for studies requiring clean graphene surfaces.

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

Direct Molecular Detection and Genotyping of Borrelia burgdorferi from Whole Blood of Patients with Early Lyme Disease

Science.gov (United States)

Eshoo, Mark W.; Crowder, Christopher C.; Rebman, Alison W.; Rounds, Megan A.; Matthews, Heather E.; Picuri, John M.; Soloski, Mark J.; Ecker, David J.; Schutzer, Steven E.; Aucott, John N.

2012-01-01

Direct molecular tests in blood for early Lyme disease can be insensitive due to low amount of circulating Borrelia burgdorferi DNA. To address this challenge, we have developed a sensitive strategy to both detect and genotype B. burgdorferi directly from whole blood collected during the initial patient visit. This strategy improved sensitivity by employing 1.25 mL of whole blood, a novel pre-enrichment of the entire specimen extract for Borrelia DNA prior to a multi-locus PCR and electrospray ionization mass spectrometry detection assay. We evaluated the assay on blood collected at the initial presentation from 21 endemic area patients who had both physician-diagnosed erythema migrans (EM) and positive two-tiered serology either at the initial visit or at a follow-up visit after three weeks of antibiotic therapy. Results of this DNA analysis showed detection of B. burgdorferi in 13 of 21 patients (62%). In most cases the new assay also provided the B. burgdorferi genotype. The combined results of our direct detection assay with initial physician visit serology resulted in the detection of early Lyme disease in 19 of 21 (90%) of patients at the initial visit. In 5 of 21 cases we demonstrate the ability to detect B. burgdorferi in early Lyme disease directly from whole blood specimens prior to seroconversion. PMID:22590620

Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate.

Science.gov (United States)

Phung, Thi Bich Thuy; Alestig, Erik; Nguyen, Thanh Liem; Hannoun, Charles; Lindh, Magnus

2010-08-01

There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam. (c) 2010 Wiley-Liss, Inc.

Coordinate determination of high energy charged particles by silicon strip detectors

International Nuclear Information System (INIS)

Anokhin, I.E.; Zinets, O.S.

2002-01-01

The coordinate determination accuracy of minimum ionizing and short-range particles by silicon strip detectors has been considered. The charge collection on neighboring strips of the detector is studied and the influence of diffusion and the electric field distribution on the accuracy of the coordinate determination is analyzed. It has been shown that coordinates of both minimum ionizing and short-range particles can be determined with accuracy to a few microns using silicon strip detectors. 11 refs.; 8 figs

Fabrication of silicon strip detectors using a step-and-repeat lithography system

International Nuclear Information System (INIS)

Holland, S.

1991-11-01

In this work we describe the use of a step-and-repeat lithography system (stepper) for the fabrication of silicon strip detectors. Although the field size of the stepper is only 20 mm in diameter, we have fabricated much larger detectors by printing a repetitive strip detector pattern in a step-and-repeat fashion. The basic unit cell is 7 mm in length. The stepper employs a laser interferometer for stage placement, and the resulting high precision allows one to accurately place the repetitive patterns on the wafer. A small overlap between the patterns ensures a continuous strip. A detector consisting of 512 strips on a 50 μm pitch has been fabricated using this technique. The dimensions of the detector are 6.3 cm by 2.56 cm. Yields of over 99% have been achieved, where yield is defined as the percentage of strips with reverse leakage current below 1 nA. In addition to the inherent advantages of a step-and-repeat system, this technique offers great flexibility in the fabrication of large-area strip detectors since the length and width of the detector can be changed by simply reprogramming the stepper computer. Hence various geometry strip detectors can be fabricated with only one set of masks, as opposed to a separate set of masks for each geometry as would be required with a contact or proximity aligner

Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes.

Science.gov (United States)

Jia, Junting; Ma, Yuyuan; Zhao, Xiong; Huangfu, Chaoji; Zhong, Yadi; Fang, Chi; Fan, Rui; Lv, Maomin; Zhang, Jingang

2016-09-17

Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited. One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified. Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified. There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

Moving strip technique of electron beam therapy

Energy Technology Data Exchange (ETDEWEB)

Matsushima, Kishio; Wakasa, Hiroyuki; Oguri, Nobuhiro; Kitayama, Takuichi; Nakagiri, Yoshitada; Mikami, Yasutaka; Hashimoto, Keiji; Hiraki, Yoshio; Aono, Kaname

1984-12-01

The fieldsize in electron beam therapy is determined by the cone size. In case of skin metastasis of a malignant tumor and so on, which need a large field size and whose area is much larger than the size of the cone, a large field size is usually produced by dividing the portals. However, the dose distribution at the border of the field becomes unequal, and hot and cold dose areas are produced according to the distance between portals. We tried the strip field technique in a large field along the long axis of the body in order to flatten the dose of the border employing the moving strip used for whole abdominal irradiation in ovarian cancer. We set the film in Mix-DP and used the strip field technique with 2.5cm steps. We discussed the relationship between the interval (distance between portals) and the flattening of the dose within the field. Skin movement due to breathing and influences on the flattening of the dose were considered. The proper flatness was obtained at depths of 0,1,2, and 3cm by setting the interval at 0.5cm. When skin movement was produced by breathing in +-1.5mm, the proper flaness was obtained also at a 0.5-cm interval. It seems that smoothing is increased by breathing. An ''electron beam moving strip'' with a 2.5-cm step and 0.5-cm interval was clinically effective in the treatment of patients with skin metastasis of colon cancer. (author).

THz Wave Propagation on Strip Lines: Devices, Properties, and Applications

Directory of Open Access Journals (Sweden)

Y. Kadoya

2008-06-01

Full Text Available We report the propagation characteristics of THz pulses on micro-strip-lines and coplanar strip-lines, in which low permittivity polymer materials are used as the dielectric layer or the substrate. As a result of the low attenuation and small dispersion in the devices, the spectral width up to 3 THz can be achieved even after the 1 mm propagation. Spectroscopic characterizations of liquid or powder specimens are demonstrated using the devices. We also show a possibility of realizing a very low attenuation using a quadrupole mode in three strip coplanar lines on the polymer substrate.

Improved dielectric functions in metallic films obtained via template stripping

Science.gov (United States)

Hyuk Park, Jong; Nagpal, Prashant; Oh, Sang-Hyun; Norris, David J.

2012-02-01

We compare the dielectric functions of silver interfaces obtained via thermal evaporation with those obtained with template stripping. Ellipsometry measurements show that the smoother template-stripped surfaces exhibit effective dielectric functions with a more negative real component and a smaller imaginary component, implying higher conductivity and less energy loss, respectively. These results agree with the relation between dielectric function and surface roughness derived from combining the effective-medium model and the Drude-Lorentz model. The improvement in the effective dielectric properties shows that metallic films prepared via template stripping can be favorable for applications in electronics, nanophotonics, and plasmonics.

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.

3D silicon strip detectors

International Nuclear Information System (INIS)