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Sample records for 03-02-1999 amplicor roche

  1. Comparison of the Roche Cobas(®) 4800 HPV assay to Digene Hybrid Capture 2, Roche Linear Array and Roche Amplicor for Detection of High-Risk Human Papillomavirus Genotypes in Women undergoing treatment for cervical dysplasia.

    PubMed

    Phillips, Samuel; Garland, Suzanne M; Tan, Jeffery H; Quinn, Michael A; Tabrizi, Sepehr N

    2015-01-01

    The recently FDA (U.S. food and drug administration) approved Roche Cobas(®) 4800 (Cobas) human papillomavirus (HPV) has limited performance data compared to current HPV detection methods for test of cure in women undergoing treatment for high grade lesions. Evaluation of Cobas HPV assay using historical samples from women undergoing treatment for cervical dysplasia. A selection of 407 samples was tested on the Cobas assay and compared to previous results from Hybrid Capture 2, HPV Amplicor and Roche Linear Array. Overall, a correlation between high-risk HPV positivity and high grade histological diagnosis was 90.6% by the Cobas, 86.1% by Hybrid Capture 2, 92.9% by HPV Amplicor and 91.8% by Roche Linear Array. The Cobas HPV assay is comparative to both the HPV Amplicor and Roche Linear Array assays and better than Hybrid capture 2 assay in the detection of High-Risk HPV in women undergoing treatment for cervical dysplasia. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Diagnostic value of the strand displacement amplification method compared to those of Roche Amplicor PCR and culture for detecting mycobacteria in sputum samples.

    PubMed Central

    Ichiyama, S; Ito, Y; Sugiura, F; Iinuma, Y; Yamori, S; Shimojima, M; Hasegawa, Y; Shimokata, K; Nakashima, N

    1997-01-01

    We compared the ability of the semiautomated BDProbeTec-SDA system, which uses the strand displacement amplification (SDA) method, with that of the Roche Amplicor-PCR system and the Septi-Chek AFB culture system to directly detect Mycobacterium tuberculosis complex (MTB) and other mycobacteria in sputum samples. A total of 530 sputum samples from 299 patients were examined in this study. Of the 530 samples, 129 were culture positive for acid-fast bacilli with the Septi-Chek AFB system; 95 for MTB, 29 for M. avium-M. intracellulare complex (MAC), and 5 for other mycobacteria. The BDProbeTec-SDA system detected 90 of the 95 samples culture positive for MTB (sensitivity, 94.7%), and the Amplicor-PCR system detected 85 of the 95 samples culture positive for MTB (sensitivity, 89.5%). The specificity of each system, based on the clinical diagnosis, was 99.8% for SDA and 100% for PCR, respectively. Among the 29 samples culture positive for MAC, the BDProbeTec-SDA system detected MAC in 24 samples (sensitivity, 82.8%), whereas the Amplicor-PCR system detected MAC in 23 samples (sensitivity, 79.3%). The specificities of the systems were 98.3 and 100%, respectively. The high degrees of sensitivity and specificity of the BDProbeTec-SDA system suggest that it should be very useful in clinical laboratories for the rapid detection of mycobacteria in sputum samples. PMID:9399498

  3. Increased sensitivity of the Roche COBAS AMPLICOR HCV test, version 2.0, using modified extraction techniques.

    PubMed

    Forman, Michael Stuart; Valsamakis, Alexandra

    2004-08-01

    Processing modifications were made to the COBAS AMPLICOR HCV version 2.0 assay to enhance sensitivity. Two methods of specimen concentration, centrifugation ("ultraspin") and cationic detergent plus silica membrane ("ultracolumn"), were compared to the standard method. The effect of these changes on assay sensitivity and specificity was examined using commercial hepatitis C virus (HCV) preparations. The limits of detection (LOD, defined as detection of HCV RNA in >/= 95% of replicates) of genotype 1a were 50, 12, and 6 by standard method, ultraspin and ultracolumn, respectively. For genotype 1b, the LOD was 25 IU/ml, 12 IU/ml, and 3 IU/ml; for 2b, it was 50, 12, and 3; for 3a, it was 25, 12, and 1.5; for 4 it was 18, 4, and 2; for 5a, it was 38, 9, and 2; and for 6a it was 47, 6, and 3. No false positives were detected after ultraspin when controls containing high or low HCV concentrations were alternated with normal human plasma. Plasmas in which HCV RNA was not detected by the standard assay were re-tested with modified methods to assess the effect of altered processing in clinical specimens. Three of 152 specimens with no detectable HCV RNA by the standard method were positive by ultraspin and 2 of 109 were positive by ultracolumn, suggesting that these methods may increase assay sensitivity in clinical specimens.

  4. Comparison of an in-house PCR assay, direct fluorescence assay and the Roche AMPLICOR Chlamydia trachomatis kit for detection of C. trachomatis.

    PubMed

    Sachdeva, Poonam; Patel, Achchhe Lal; Sachdev, Divya; Ali, Mashook; Mittal, Aruna; Saluja, Daman

    2009-07-01

    To improve the control of Chlamydia trachomatis infection in India, a rapid, specific and cost-effective method is much needed. We developed an in-house PCR assay by targeting a unique genomic sequence encoding a protein from the C. trachomatis phospholipase D endonuclease superfamily that produces an amplified fragment of 368 bp. The specificity of the primers was confirmed using genomic DNA from other sexually transmitted disease-causing and related micro-organisms and from humans. The assay was highly sensitive and could detect as low as 10 fg C. trachomatis DNA. Clinical evaluation of the in-house-developed PCR was carried out using 450 endocervical specimens that were divided in two groups. In group I (n=274), in-house PCR was evaluated against the direct fluorescence assay. The resolved sensitivity of the in-house PCR method was 97.22 % compared with 88 % for the direct fluorescent antibody assay. In group II (n=176), the in-house PCR was compared with the commercial Roche AMPLICOR MWP CT detection kit. The resolved sensitivity of the in-house PCR assay reported here was 93.1 % and the specificity was 97.46 %, making it a cost-effective alternative for routine diagnosis of genital infection by C. trachomatis. The method should facilitate early detection leading to better prevention and treatment of genital infection in India.

  5. Comparative performance of the Roche COBAS Amplicor assay and an in-house real-time PCR assay for diagnosis of Chlamydia trachomatis infection.

    PubMed

    Jalal, Hamid; Al-Suwaine, Abdulrahman; Stephen, Hannah; Carne, Christopher; Sonnex, Christopher

    2007-03-01

    This study investigated the comparative performance of the Amplicor assay and an in-house semi-automated, multiplex real-time PCR for the diagnosis of genital chlamydial infection. Four different assays, the COBAS Amplicor CT test (Amplicor PCR), in-house real-time PCR (IHRT-PCR), in-house nested cryptic plasmid PCR and in-house nested major outer membrane protein PCR, were performed on genital swabs from 1000 consecutive patients attending a genitourinary medicine clinic. The samples were designated true positive if Chlamydia trachomatis DNA was detected by at least two of the four above-mentioned assays while a sample was defined as true negative if C. trachomatis DNA was detected in only one or none of the assays. By this criterion, there were 129 true positive and 871 true negative samples for C. trachomatis DNA in this cohort. Amplicor PCR designated 144 samples positive: 128 (89%) of 144 samples were true positive and 16 (11%) were false positive. IHRT-PCR detected 126 of 129 true positive samples and did not generate any false positive results. The sensitivity of IHRT-PCR was comparable with, and specificity was higher than, Amplicor PCR for the diagnosis of genital chlamydial infection.

  6. Evaluation of the NucliSens EasyQ v2.0 assay in comparison with the Roche Amplicor v1.5 and the Roche CAP/CTM HIV-1 Test v2.0 in quantification of C-clade HIV-1 in plasma.

    PubMed

    Muenchhoff, Maximilian; Madurai, Savathee; Hempenstall, Allison Jo; Adland, Emily; Carlqvist, Anna; Moonsamy, Angeline; Jaggernath, Manjeetha; Mlotshwa, Busisiwe; Siboto, Emma; Ndung'u, Thumbi; Goulder, Philip Jeremy Renshaw

    2014-01-01

    Human immunodeficiency virus type 1 (HIV-1) genetic diversity poses a challenge to reliable viral load monitoring. Discrepancies between different testing platforms have been observed, especially for non-clade-B virus. Therefore we compare, in antiretroviral therapy (ART)-naïve South African subjects predominantly infected with HIV-1 clade-C, three commercially available assays: the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test version 2.0 by Roche (CAP/CTM v2.0), the BioMérieux NucliSens Version 2.0 Easy Q/Easy Mag (NucliSens v2.0) and the Roche COBAS Amplicor HIV-1 Monitor Test Version 1.5 (Amplicor v1.5). Strong linear correlation was observed and Bland-Altman analyses showed overall good agreement between the assays with mean viral load differences of 0.078 log cp/ml (NucliSens v2.0 - Amplicor v1.5), 0.260 log cp/ml (CAP/CTM v2.0 - Amplicor v1.5) and 0.164 log cp/ml (CAP/CTM v2.0 - NucliSens v2.0), indicating lower mean viral load results for the Amplicor v1.5 and higher mean readings for the CAP/CTM v2.0. Consistent with observations following previous comparisons of CAP/CTM v2.0 versus Amplicor v1.5, the CAP/CTM v2.0 assay detected low-level viremia (median 65 cp/ml) in more than one-third of those in whom viremia had been undetectable (<20 cp/ml) in assays using the NucliSens platform. These levels of viremia are of uncertain clinical significance but may be of importance in early detection of ART resistance in those on treatment. Overall the three assays showed good comparability of results but with consistent, albeit relatively small, discrepancies for HIV-1 clade-C samples, especially in the low-viremic range that should be taken into account when interpreting viral load data.

  7. Evaluation of the NucliSens EasyQ v2.0 Assay in Comparison with the Roche Amplicor v1.5 and the Roche CAP/CTM HIV-1 Test v2.0 in Quantification of C-Clade HIV-1 in Plasma

    PubMed Central

    Muenchhoff, Maximilian; Madurai, Savathee; Hempenstall, Allison Jo; Adland, Emily; Carlqvist, Anna; Moonsamy, Angeline; Jaggernath, Manjeetha; Mlotshwa, Busisiwe; Siboto, Emma; Ndung'u, Thumbi; Goulder, Philip Jeremy Renshaw

    2014-01-01

    Human immunodeficiency virus type 1 (HIV-1) genetic diversity poses a challenge to reliable viral load monitoring. Discrepancies between different testing platforms have been observed, especially for non-clade-B virus. Therefore we compare, in antiretroviral therapy (ART)-naïve South African subjects predominantly infected with HIV-1 clade-C, three commercially available assays: the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test version 2.0 by Roche (CAP/CTM v2.0), the BioMérieux NucliSens Version 2.0 Easy Q/Easy Mag (NucliSens v2.0) and the Roche COBAS Amplicor HIV-1 Monitor Test Version 1.5 (Amplicor v1.5). Strong linear correlation was observed and Bland-Altman analyses showed overall good agreement between the assays with mean viral load differences of 0.078 log cp/ml (NucliSens v2.0 – Amplicor v1.5), 0.260 log cp/ml (CAP/CTM v2.0 – Amplicor v1.5) and 0.164 log cp/ml (CAP/CTM v2.0 – NucliSens v2.0), indicating lower mean viral load results for the Amplicor v1.5 and higher mean readings for the CAP/CTM v2.0. Consistent with observations following previous comparisons of CAP/CTM v2.0 versus Amplicor v1.5, the CAP/CTM v2.0 assay detected low-level viremia (median 65 cp/ml) in more than one-third of those in whom viremia had been undetectable (<20 cp/ml) in assays using the NucliSens platform. These levels of viremia are of uncertain clinical significance but may be of importance in early detection of ART resistance in those on treatment. Overall the three assays showed good comparability of results but with consistent, albeit relatively small, discrepancies for HIV-1 clade-C samples, especially in the low-viremic range that should be taken into account when interpreting viral load data. PMID:25157919

  8. Pooling Ocular Swab Specimens from Tanzania for testing by Roche Amplicor and Aptima Combo 2 Assays for the detection of Chlamydia trachomatis: Accuracy and Cost Savings

    PubMed Central

    Dize, Laura; West, Sheila; Quinn, Thomas C.; Gaydos, Charlotte A.

    2014-01-01

    Ocular swabs collected in Tanzania were evaluated by Amplicor CT and Aptima Combo2 assays for the detection of Chlamydia trachomatis (CT) to determine if pooling could be used to reduce the cost of detection. Pooling would be an accurate method and so far resulted in a cost-savings of 62.2%. PMID:24079951

  9. Multicenter comparison of Roche COBAS AMPLICOR MONITOR version 1.5, Organon Teknika NucliSens QT with Extractor, and Bayer Quantiplex version 3.0 for quantification of human immunodeficiency virus type 1 RNA in plasma.

    PubMed

    Murphy, D G; Côté, L; Fauvel, M; René, P; Vincelette, J

    2000-11-01

    The performance and characteristics of Roche COBAS AMPLICOR HIV-1 MONITOR version 1.5 (CA MONITOR 1.5) UltraSensitive (usCA MONITOR 1. 5) and Standard (stCA MONITOR 1.5) procedures, Organon Teknika NucliSens HIV-1 RNA QT with Extractor (NucliSens), and Bayer Quantiplex HIV RNA version 3.0 (bDNA 3.0) were compared in a multicenter trial. Samples used in this study included 460 plasma specimens from human immunodeficiency virus (HIV) type 1 (HIV-1)-infected persons, 100 plasma specimens from HIV antibody (anti-HIV)-negative persons, and culture supernatants of HIV-1 subtype A to E isolates diluted in anti-HIV-negative plasma. Overall, bDNA 3.0 showed the least variation in RNA measures upon repeat testing. For the Roche assays, usCA MONITOR 1.5 displayed less variation in RNA measures than stCA MONITOR 1.5. NucliSens, at an input volume of 2 ml, showed the best sensitivity. Deming regression analysis indicated that the results of all three assays were significantly correlated (P < 0.0001). However, the mean difference in values between CA MONITOR 1.5 and bDNA 3.0 (0.274 log(10) RNA copies/ml; 95% confidence interval, 0.192 to 0.356) was significantly different from 0, indicating that CA MONITOR 1.5 values were regularly higher than bDNA 3.0 values. Upon testing of 100 anti-HIV-negative plasma specimens, usCA MONITOR 1.5 and NucliSens displayed 100% specificity, while bDNA 3.0 showed 98% specificity. NucliSens quantified 2 of 10 non-subtype B viral isolates at 1 log(10) lower than both CA MONITOR 1.5 and bDNA 3.0. For NucliSens, testing of specimens with greater than 1,000 RNA copies/ml at input volumes of 0.1, 0.2, and 2.0 ml did not affect the quality of results. Additional factors differing between assays included specimen throughput and volume requirements, limit of detection, ease of execution, instrument work space, and costs of disposal. These characteristics, along with assay performance, should be considered when one is selecting a viral load assay.

  10. Prospective multicenter clinical evaluation of AMPLICOR and COBAS AMPLICOR hepatitis C virus tests.

    PubMed

    Nolte, F S; Fried, M W; Shiffman, M L; Ferreira-Gonzalez, A; Garrett, C T; Schiff, E R; Polyak, S J; Gretch, D R

    2001-11-01

    We conducted a multicenter clinical evaluation of the second versions of the manual AMPLICOR and the semiautomated COBAS AMPLICOR tests for hepatitis C virus (HCV) RNA (Roche Molecular Systems, Inc., Pleasanton, Calif.). The performance characteristics of these HCV RNA tests for diagnosis of active viral infection were determined by comparison to anti-HCV serological test results, alanine aminotransferase levels, and liver biopsy histology results. A total of 878 patients with clinical or biochemical evidence of liver disease were enrolled at four hepatology clinics. A total of 1,089 specimens (901 serum and 188 plasma) were tested with the AMPLICOR test. Sensitivity compared to serology was 93.1% for serum and 90.6% for plasma. The specificity was 97% for serum and 93.1% for plasma. A total of 1,084 specimens (896 serum and 188 plasma) were tested with the COBAS test. Sensitivities for serum and plasma were the same as with the AMPLICOR test. The specificity was 97.8% for serum and 96.6% for plasma. Of the 69 specimens with false-positive and false-negative AMPLICOR test results relative to those of serology, alternative primer set (APS) reverse transcription (RT)-PCR analysis showed that the AMPLICOR test provided the correct result relative to the specimens containing HCV RNA in 64 (92.7%) specimens. Similarly, 66 of 67 (98.5%) false-positive and false-negative COBAS test results were determined to be correct by APS RT-PCR analysis. There were no substantive differences in clinical performances between study sites, patient groups, specimen types, storage conditions (-20 to -80 degrees C versus 2 to 8 degrees C), or anticoagulants (EDTA versus acid citrate dextrose) for either test. Both tests showed >99% reproducibility within runs, within sites, and overall. We conclude that these tests can reliably detect the presence of HCV RNA, as evidence of active infection, in patients with clinical or biochemical evidence of liver disease.

  11. Viral load: Roche applies for marketing approval for ultrasensitive test.

    PubMed

    1998-08-07

    Roche Molecular Systems has applied for FDA permission to market a more sensitive viral load test. The Amplicor HIV-1 Monitor UltraSensitive Method tests viral load as low as 50 copies; current tests are only accurate to 400 copies. There is a widespread consensus among physicians that testing below 400 copies would be a valuable treatment tool.

  12. Overestimation of the Hepatitis C Virus RNA Content of Reference Preparations by the AMPLICOR HCV Monitor Test, Version 2.0

    PubMed Central

    Pisani, Giulio; Cristiano, Karen; Wirz, Maria; Bisso, Guillermo M.; Gentili, Giuliano

    2002-01-01

    An evaluation of the AMPLICOR hepatitis C virus (HCV) monitor test, version 2.0 (Roche Diagnostics), was carried out to investigate whether this test overestimates the HCV RNA content of reference preparations. Satisfactory accuracy was observed when the World Health Organization HCV international standard was included in the assay and a modified formula was used to calculate the viral content. PMID:12454191

  13. Evaluation of AMPLICOR Neisseria gonorrhoeae PCR using cppB nested PCR and 16S rRNA PCR.

    PubMed

    Farrell, D J

    1999-02-01

    Certain strains of Neisseria subflava and Neisseria cinerea are known to produce false-positive results with the AMPLICOR Neisseria gonorrhoeae PCR (Roche Diagnostic Systems, Branchburg, N.J.). The analytical sensitivity and analytical specificity of three PCR tests were assessed with 3 geographically diverse N. gonorrhoeae strains and 30 non-N. gonorrhoeae Neisseria spp. The sensitivities of the in-house nested cppB gene and the 16S rRNA PCR methods were greater than that of the AMPLICOR N. gonorrhoeae PCR with purified DNA from all 3 N. gonorrhoeae strains. Six of 14 clinical strains of N. subflava (1 from a vaginal swab, 5 from respiratory sites) produced false-positive AMPLICOR N. gonorrhoeae PCR results and were negative by the two other PCR methods. When applied to 207 clinical specimens selected from a population with a high prevalence ( approximately 9%) of infection, the results for 15 of 96 (15.6%) AMPLICOR-positive specimens and 14 of 17 (82.3%) AMPLICOR-equivocal specimens were not confirmed by the more sensitive nested cppB PCR method. Only 2 of 94 (2.1%) of AMPLICOR N. gonorrhoeae PCR-negative specimens from the same population tested positive by the nested cppB method. These results suggest that for this population the AMPLICOR N. gonorrhoeae PCR test is suitable as a screening test only and all positive results should be confirmed by a PCR method that is more specific and at least as sensitive. This study also illustrates that caution should be used when introducing commercially available nucleic acid amplification-based diagnostic tests into the regimens of tests used for populations not previously tested with these products.

  14. Preclinical evaluation of AMPLICOR hepatitis C virus test for detection of hepatitis C virus RNA.

    PubMed Central

    Nolte, F S; Thurmond, C; Fried, M W

    1995-01-01

    We compared a single-enzyme, combined reverse transcription-PCR (RT-PCR; AMPLICOR HCV Test; Roche Molecular Systems, Branchburg, N.J.) with an independent, two-enzyme, standard RT-PCR (SRT-PCR) assay for the detection of hepatitis C virus (HCV) RNA in serum and plasma. Test samples included a proficiency testing panel consisting of 10 undiluted plasma samples, three separate dilution series, and sera from 99 patients with chronic liver disease. The quantity of HCV RNA in each patient serum sample was determined by a branched DNA (bDNA) signal amplification assay (Quantiplex HCV-RNA assay; Chiron, Emeryville, Calif.). There was complete concordance between the results of the RT-PCR assays with the 10 undiluted plasma samples used for proficiency testing (3 positive and 7 negative samples). However, the analytical sensitivity of SRT-PCR was 4- to 10-fold greater than that of the AMPLICOR test in the dilution series. HCV RNA was detected in 44, 45, and 40 of the patient serum samples, by SRT-PCR, the AMPLICOR test, and the bDNA assay, respectively. There was 97% agreement between the results of the RT-PCR assays, with only three discrepancies. Review of the patients' medical records resolved all three discrepancies in favor of the AMPLICOR results (two false-negative SRT-PCR results and one false-positive SRT-PCR result). The quantity of HCV RNA in sera from five (11%) patients with viremia detected by AMPLICOR was below the bDNA assay cutoff (< 3.5 x 10(5) RNA equivalents per ml).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7665645

  15. Evaluation of Cobas TaqMan MTB for direct detection of the Mycobacterium tuberculosis complex in comparison with Cobas Amplicor MTB.

    PubMed

    Bloemberg, Guido V; Voit, Antje; Ritter, Claudia; Deggim, Vanessa; Böttger, Erik C

    2013-07-01

    The Roche Cobas Amplicor MTB assay, recently replaced by the Roche Cobas TaqMan MTB assay, was one of the first commercially available assays for detection of the Mycobacterium tuberculosis complex based on nucleic acid amplification. We reported previously on the limited specificity of the Cobas Amplicor MTB assay, in particular for positive samples with an optical density at 660 nm (OD660) of <2.0. Using a selected set of respiratory samples, which were scored as false positive by the Cobas Amplicor test, we demonstrate here that the specificity of the Cobas TaqMan assay is significantly improved. In addition, our study of a set of 133 clinical samples revealed that the Cobas TaqMan MTB assay showed significantly less PCR inhibition than the Cobas Amplicor test. An overall concordance of 98.2% was observed between the two assays. In a subsequent prospective study, we evaluated the performance of the Roche Cobas TaqMan MTB assay on 1,143 clinical specimens, including respiratory (n = 838) and nonrespiratory (n = 305) specimens. Using culture as the gold standard, we found a sensitivity of 88.4% and a specificity of 98.8% for the 838 respiratory specimens, compared to a sensitivity of 63.6% and a specificity of 94.6% for the 305 nonrespiratory specimens. We conclude that the Cobas TaqMan MTB assay is a significantly improved tool for the direct detection of M. tuberculosis DNA in clinical specimens.

  16. RNA versus DNA (NucliSENS EasyQ HIV-1 v1.2 versus Amplicor HIV-1 DNA test v1.5) for early diagnosis of HIV-1 infection in infants in Senegal.

    PubMed

    Kébé, K; Ndiaye, O; Ndiaye, H Diop; Mengue, P Mbakob; Guindo, P M M; Diallo, S; Léye, N; Gueye, S B; Diallo, A Gaye; Kane, C Touré; Mboup, S

    2011-07-01

    The objective of this study was to compare the performance of the NucliSENS EasyQ HIV-1 v1.2 platform (bioMérieux, France) to the Amplicor HIV-1 DNA test v1.5 (Roche Molecular Systems, Switzerland) in detecting HIV-1 infection in infants using venipuncture-derived whole blood in tubes and dried blood spots. A total of 149 dried blood spots and 43 EDTA-anticoagulated peripheral blood samples were collected throughout Dakar and other areas in Senegal from infants and children aged 3 weeks to 24 months who were born to HIV-1-infected mothers. Samples were tested using the NucliSENS and Amplicor technologies. The NucliSENS and Amplicor results were 100% concordant using either EDTA-anticoagulated peripheral blood or dried blood spots. Compared to Amplicor, the sensitivity and specificity of the NucliSENS test were 100%. The NucliSENS EasyQ HIV-1 RNA assay performed as well as the Amplicor HIV-1 DNA test in detecting HIV-1 infection in infants. In addition, this platform can give an indication of the viral load baseline. The NucliSENS EasyQ platform is a good alternative for early infant diagnosis of HIV-1 infection.

  17. Evaluation of automated COBAS AMPLICOR PCR system for detection of several infectious agents and its impact on laboratory management.

    PubMed Central

    Jungkind, D; Direnzo, S; Beavis, K G; Silverman, N S

    1996-01-01

    We evaluated the COBAS AMPLICOR (CA) PCR system (Roche Diagnostic Systems) designed for automated PCR amplification and detection of nucleic acids from infectious agents in clinical samples. The Roche AMPLICOR microwell plate (MWP) PCR was the reference method. CA amplifies target nucleic acid, captures the biotinylated amplification products by using magnetic particles coated with specific oligonucleotide probes, and detects the bound products colorimetrically. For Mycobacterium tuberculosis, the correlation of the results of CA tests with those of MWP tests was 100% with 230 samples, including 20 culture-positive samples. For hepatitis C virus, the correlation was 100% with 214 samples, including 60 positive samples. MultiPlex CA analysis of 199 cervical specimens for Chlamydia trachomatis, Neisseria gonorrhoeae, and the internal control gave 100% concordance. These samples included 19 C. trachomatis and 3 N. gonorrhoeae culture-positive samples. Overall, the agreement between PCR methods for all 842 comparisons was 100%. Compared with culture, the sensitivities of the assays for C. trachomatis and M tuberculosis were > or = 95%. After spiking alternating amplification tubes in the CA system with 10(14) copies of the Chlamydia amplicon per ml, we were unable to demonstrate any carryover cross-contamination of negative samples. Using the criteria of the College of American Pathologists workload recording method, we found that the total hands-on time to produce CA PCR results was 4.4, 7.9, and 3.3 min for M. tuberculosis, hepatis C virus, and the MultiPlexed assay for chlamydia plus gonorrhea and an internal control, respectively. The CA system brings true PCR automation to laboratories. In addition to the accuracy of automated results, the CA system provides labor savings, provides containment of the amplification and detection components of PCR, and supports both MultiPlex amplification and sequential algorithm (ReFlex) detection of analytes. PMID:8897182

  18. Evaluation of automated COBAS AMPLICOR PCR system for detection of several infectious agents and its impact on laboratory management.

    PubMed

    Jungkind, D; Direnzo, S; Beavis, K G; Silverman, N S

    1996-11-01

    We evaluated the COBAS AMPLICOR (CA) PCR system (Roche Diagnostic Systems) designed for automated PCR amplification and detection of nucleic acids from infectious agents in clinical samples. The Roche AMPLICOR microwell plate (MWP) PCR was the reference method. CA amplifies target nucleic acid, captures the biotinylated amplification products by using magnetic particles coated with specific oligonucleotide probes, and detects the bound products colorimetrically. For Mycobacterium tuberculosis, the correlation of the results of CA tests with those of MWP tests was 100% with 230 samples, including 20 culture-positive samples. For hepatitis C virus, the correlation was 100% with 214 samples, including 60 positive samples. MultiPlex CA analysis of 199 cervical specimens for Chlamydia trachomatis, Neisseria gonorrhoeae, and the internal control gave 100% concordance. These samples included 19 C. trachomatis and 3 N. gonorrhoeae culture-positive samples. Overall, the agreement between PCR methods for all 842 comparisons was 100%. Compared with culture, the sensitivities of the assays for C. trachomatis and M tuberculosis were > or = 95%. After spiking alternating amplification tubes in the CA system with 10(14) copies of the Chlamydia amplicon per ml, we were unable to demonstrate any carryover cross-contamination of negative samples. Using the criteria of the College of American Pathologists workload recording method, we found that the total hands-on time to produce CA PCR results was 4.4, 7.9, and 3.3 min for M. tuberculosis, hepatis C virus, and the MultiPlexed assay for chlamydia plus gonorrhea and an internal control, respectively. The CA system brings true PCR automation to laboratories. In addition to the accuracy of automated results, the CA system provides labor savings, provides containment of the amplification and detection components of PCR, and supports both MultiPlex amplification and sequential algorithm (ReFlex) detection of analytes.

  19. Comparison of the Cobas 4800 Human Papillomavirus test against a combination of the Amplicor Human Papillomavirus and the Linear Array tests for detection of HPV types 16 and 18 in cervical samples.

    PubMed

    Martínez, Samuel Bernal; Palomares, José Carlos; Artura, Antonio; Parra, Manuel; Cabezas, Jose Luis; Romo, Jose Ma; Martín-Mazuelos, Estrella

    2012-03-01

    The greater prevalence of human papillomavirus (HPV) types 16 and 18 compared to the other high-risk HPV types of cervical cancer led to the development of clinical tests that detect both types separately from other genotypes. One method is the Roche Cobas 4800 HPV test, which is based on a real-time PCR. The aim of this study was to evaluate the performance of the Cobas 4800 HPV test for detecting genotypes 16 and 18 by comparing the results with those obtained in a combination of the Roche Amplicor HPV assay and the Roche Linear Array (LA) HPV genotyping assay. Excellent concordance was found between both methods (92.7%, kappa value=0.872). The Cobas 4800 HPV test could be used as a single test for identifying HPV types 16 and 18 directly from clinical specimens.

  20. Ranolazine Roche Bioscience.

    PubMed

    Jones, R

    1998-12-01

    Ranolazine is a metabolic modulator developed by Syntex (Roche) and is in phase III clinical trials as an anti-anginal agent and for the treatment of peripheral arterial disease, particularly intermittent claudication. It allows maintenance of energy output by muscle cells under hypoxic conditions. Ranolazine may be especially useful in angina patients in whom other therapies are ineffective. The licensee, CV Therapeutics (CVT), began a pivotal placebo-controlled, phase III clinical trial of ranolazine in October 1997 enrolling 150 angina patients [265551]. CVT plans to begin a second phase III trial in 350 to 400 angina patients receiving other anti-anginal medications during 1998 [279177]. Clinical studies suggest that ranolazine lowers the heart's demand for oxygen by increasing its ability to use carbohydrate, rather than fat, as a fuel. This is thought to be due to activation of pyruvate dehydrogenase and modulation of the activities of L-type calcium channels. This is achieved without reducing heart rate or blood pressure, or impairing pumping ability [253375,247228]. Ranolazine has been tested in more than 1300 US and European patients in phase I and phase II clinical trials, and is now being evaluated in a placebo-controlled, double-blind multicenter study to determine its effectiveness in treating stable angina. Phase II trials, in over 1200 patients with ischemic heart disease, were completed by Syntex. They demonstrated increased exercise times to onset of angina or electrocardiographic change associated with insufficient blood flow to the heart with three times daily dosing of ranolazine [224364]. Roche Bioscience claims that in the US and Western Europe approximately 1.4 million angina patients are not adequately treated with existing therapies and some 5 million patients suffer from intermittent claudication [166817]. In August 1998, CV Therapeutics signed an agreement with Catalytica Pharmaceuticals, which will manufacture specified quantities of

  1. Prospective clinical evaluation of Amplicor Mycobacterium tuberculosis PCR test as a screening method in a low-prevalence population.

    PubMed Central

    Cartuyvels, R; De Ridder, C; Jonckheere, S; Verbist, L; Van Eldere, J

    1996-01-01

    Of 656 respiratory samples analyzed for Mycobacterium tuberculosis by microscopy, culture, and the Amplicor PCR method, 25 were positive by culture, 12 were positive by microscopy, and 17 were positive by the Amplicor PCR method; 16 samples were Amplicor PCR positive and culture negative. No patient except one with culture-negative, Amplicor PCR-positive samples had clinical indications of tuberculosis. The sensitivity and specificity of the Amplicor PCR compared with those of culture were 68 and 97.4%, respectively. For culture-positive, smear-negative samples, the sensitivity of the Amplicor PCR was 46%. PMID:8818898

  2. Neisseria Species Identification Assay for the Confirmation of Neisseria gonorrhoeae-Positive Results of the COBAS Amplicor PCR▿

    PubMed Central

    Mangold, Kathy A.; Regner, MaryAnn; Tajuddin, Mohammed; Tajuddin, Aamair M.; Jennings, Lawrence; Du, Hongyan; Kaul, Karen L.

    2007-01-01

    Screening assays for Neisseria gonorrhoeae exhibit low positive predictive values, particularly in low-prevalence populations. A new real-time PCR assay that detects and identifies individual Neisseria spp. using melt curve analysis was compared to two previously published supplementary assays. NsppID, a 16S rRNA real-time PCR/melt curve assay developed to distinguish N. gonorrhoeae from other Neisseria spp., was compared to real-time PCR assays targeting genes reportedly specific for N. gonorrhoeae, the cppB gene and the porA pseudogene. A total of 408 clinical specimens (324 female endocervical swabs and 84 male urine or urogenital swab specimens) were screened using the COBAS Amplicor assay for Chlamydia trachomatis and N. gonorrhoeae (CT/NG) (Roche Diagnostics, Indianapolis, IN) followed by confirmatory testing via real-time PCR. The NsppID assay detected Neisseria spp. in 150/181 COBAS-positive specimens (82%), including six dual infections, and identified N. gonorrhoeae in 102 (56%) specimens. Sixty-nine of 181 (38%) specimens were positive for N. gonorrhoeae by porA pseudogene, and 115/181 (64%) were positive for cppB. However, cppB was also positive in 15% of COBAS-negative specimens, more than either NsppID (4%) or porA pseudogene (2%) assays. The porA pseudogene assay had the highest specificity for both genders but the lowest sensitivity, especially in female specimens. NsppID had a slightly lower specificity but greater sensitivity and overall accuracy. The least desirable confirmatory assay was cppB, due to poor specificity. The NsppID assay is an accurate confirmatory assay for N. gonorrhoeae detection. In addition, the NsppID assay can identify the non-N. gonorrhoeae species responsible for the majority of false-positive results from the COBAS Amplicor CT/NG assay. PMID:17360838

  3. Pegasys (Hoffmann-La Roche).

    PubMed

    Barnard, D L

    2001-11-01

    Hoffmann-La Roche has developed a PEGylated interferon alpha-2a, Pegasys, for the potential treatment of chronic hepatitis C and hepatitis B virus infection. It was first approved in Switzerland in August 2001 [418260] and was expected to be launched in September/October 2001 [419333]. In May 2000, Roche submitted a BLA to the US FDA, for approval to market Pegasys for the treatment of chronic HCV infection in non-cirrhotic and cirrhotic patients with compensated liver disease [329872], [348368], [367781]. Approval was still pending in December 2000 [387363], [392481]. Roche expects the US launch to take place in the second half of 2001 [400857]. In April 2001, Roche received a complete response letter from the FDA for Pegasys and was working with the FDA to address the questions raised in the letter [407595], [418310]. In August 2001, Roche expected approval for HCV in the US in 2002 and for HBV in 2004 [419333]. At this time, Roche planned to file an sNDA for combination with ribavirin [421285]. By March 2001, EU and Canadian filings had been made [401793]. Roche also planned to launch the product for chronic HBV infection and various malignancies in 2004 and 2005, respectively [400857]. Pegasys was filed for registration in Brazil in the first part of 2000 [418310]. As of December 1999, the drug was in phase II for HCV infection in Japan. It is being developed by Nippon Roche, which intended to extrapolate foreign phase III data for use in an NDA application in Japan [351804]. As a result of a meeting of Japan's PMSB in March 2001, Pegasys may be given priority in the review of its NDA, if submitted [403782]. In August 2001, Schering-Plough entered into a licensing agreement with F Hoffman-La Roche Ltd and Hoffmann-La Roche Inc that settles all patent disputes regarding the two companies' PEGinterferon products. Under the terms of the agreement, Schering-Plough and Roche will cross license to each other all patents applicable to Peg-Intron and Pegasys. The

  4. Ranolazine (Roche Bioscience).

    PubMed

    Jones, R

    1999-12-01

    Ranolazine is a metabolic modulator that is being developed by CV Therapeutics (CVT), under license from Roche (formerly Syntex), as a potential treatment for angina. In August 1999, the first of two pivotal phase III clinical trials in patients with stable angina was completed. In August 1999, CVT announced initial results from this trial, designated the MARISA trial, of ranolazine in patients with stable angina. At each of the three doses studied, ranolazine significantly increased patients' treadmill exercise duration compared to placebo, the primary endpoint for this trial. MARISA (monotherapy assessment of ranolazine in stable angina) was a randomized, double-blind, placebo-controlled trial of a sustained release formulation of ranolazine used in 175 patients who were not receiving other anti-anginal drugs. Compared to placebo, ranolazine taken bid at doses of 500, 1000 or 1500 mg significantly increased exercise duration at trough plasma concentrations, which occur at about 12 h after the previous dose. In addition, two key secondary endpoints, exercise time to onset of angina and exercise time to the electrocardiographic appearance of ischemia were also significantly increased by ranolazine compared to placebo at all three doses. The company plans on presenting additional data at a major medical conference, including safety and tolerability data, which are still under analysis. In July 1999 CVT initiated its second phase III trial. The CARISA trial (combination assessment of ranolazine in stable angina) is a randomized, double-blind, placebo-controlled trial of ranolazine used in combination with other anti-anginal drugs, in approximately 450 patients. The primary endpoint for this trial, duration of exercise on a treadmill, is identical to that used in phase II clinical trials. The CARISA trial, along with the pivotal phase III MARISA trial which completed treatment in June 1999, is expected to form the basis of the company's NDA submission to the FDA. In

  5. [Assessment of the Amplicor PCR for the detection of Mycobacterium tuberculosis in smear negative respiratory and non respiratory specimens: a retrospective analysis].

    PubMed

    Selman, Carolina B; Poggi, Helena M; Román, Juan C; García, Patricia C; Lagos, Marcela L

    2009-12-01

    Commercial polymerase chain reaction (PCR) kits are widely accepted for analysis of smear positive respiratory specimens, but the sensitivity is variable for smear negative ones. To assess the PCR method usefulness in smear negative respiratory and non respiratory specimens. We compared the PCR results (AMPLICOR MTB test, Roche) of 235 specimens subjected to culture in Loewenstein-Jensen agar (as the gold standard). 181 (76%) were respiratory and 54 (24%) extra-respiratory specimens. The sensitivity was 88%) and 50%>, respectively, specificity and PPV was 100%> in both cases. NPV was 99.4%> in respiratory specimens and 96.1% in non-respiratory specimens. The good performance of this PCR in smear negative respiratory specimens allows the clinician to take decisions based on the result of this exam. In extra-respiratory specimens the contribution is important only when the PCR result is positive.

  6. Prospective evaluation of the Hybrid Capture 2 and AMPLICOR human papillomavirus (HPV) tests for detection of 13 high-risk HPV genotypes in atypical squamous cells of uncertain significance.

    PubMed

    Halfon, Philippe; Trepo, Elisabeth; Antoniotti, Gilles; Bernot, Catherine; Cart-Lamy, Philippe; Khiri, Hacène; Thibaud, Didier; Marron, Jean; Martineau, Agnès; Pénaranda, Guillaume; Benmoura, Dominique; Blanc, Bernard

    2007-02-01

    The use of high-risk human papillomavirus (hrHPV) testing as an adjunct to cervical cytology in population-based screening programs is currently based on DNA hybridization and PCR assays. The aim of this study was to prospectively assess the diagnostic performance of the Hybrid Capture 2 test (HC2; Digene Corporation) in comparison with that of the recently developed PCR-based AMPLICOR HPV test (Roche Molecular Systems) for the detection of 13 hrHPV types. A reverse line blot hybridization assay (Innogenetics) was used as an internal reference standard in discordant cases. Two hundred seventy-one patients with atypical squamous cells of uncertain significance (ASCUS) in cervical samples underwent hrHPV testing. The chi-square test was performed to compare respective proportions. Totals of 160/271 (59%) and 156/271 (58%) were found to be positive for hrHPV with HC2 and AMPLICOR, respectively. Concordant results were obtained for 235 (86.7%) of the 271 samples (kappa statistic, 0.73 +/- 0.04). Considering types 26, 53, and 66 as oncogenic types, negative predictive values (NPVs) of HC2 and AMPLICOR were 92.8% and 87.8%, respectively (difference was not significant), and their respective accuracies were 94.8% and 91.9% (difference was not significant). Considering types 26, 53, and 66 as not oncogenic, the respective HC2 and AMPLICOR NPVs were 92.8% and 97.4% (difference was not significant), and accuracy was significantly higher for the AMPLICOR assay (95.9% versus 90.8% for HC2) (P<0.05). For ASCUS samples, the NPV was 92.8% for HC2 testing and might be compromised if the copy number of HPV DNA was low. The NPV was 97.4% for the AMPLICOR assay and might be compromised if HPV types 26, 53, and 66 were considered oncogenic. The accuracy of these two assays is good and is compatible with routine clinical use in the triage of ASCUS cases.

  7. Comparative evaluation of Amplicor HIV-1 DNA test, version 1.5, by manual and automated DNA extraction methods using venous blood and dried blood spots for HIV-1 DNA PCR testing.

    PubMed

    Nsojo, Anthony; Aboud, Said; Lyamuya, Eligius

    2010-10-01

    Human immunodeficiency virus (HIV) DNA polymerase chain reaction (PCR) test using venous blood sample has been used for many years in low resource settings for early infant diagnosis of HIV infection in children less than 18 months. The aim of this study was to evaluate and compare the performance characteristics of Amplicor HIV-1 DNA assay version 1.5 following processing of venous blood and dried blood spot (DBS) samples by Roche manual DNA extraction and automated Roche MagNA Pure LC instrument (MP) for HIV-1 DNA PCR testing in Dar es Salaam, Tanzania, in order to scale up early infant diagnosis of HIV infection in routine practice. Venous blood samples from children under 18 months born to HIV-infected mothers between January and April 2008 were collected. Venous blood was used to prepare cell pellet and DBS samples. DNA extractions by manual procedure and MP were performed each on cell pellet, venous blood and DBS samples and tested by Amplicor HIV-1 DNA assay. Of 325 samples included, 60 (18.5%) were confirmed HIV-infected by manual extraction performed on cell pellets. Sensitivity of the assay following MP processing of venous blood was 95% (95% CI; 86.1-99.0%) and 98.3% (95% CI; 91.1 to 99.9%) for the manual extraction and processing by MP performed on DBS samples. Specificity of the assay with all DNA extraction methods was 99.6% (95% CI; 97.9 to 100%). Performance of the assay with Roche manual extraction and processing by MP on DBS samples compared well with Roche manual extraction performed on cell pellet samples. The choice of DNA extraction method needs to be individualized based on the level of laboratory facility, volume of testing and cost benefit analysis before it is adopted for use.

  8. Performance of Roche CAP/CTM HIV-1 qualitative test version 2.0 using dried blood spots for early infant diagnosis.

    PubMed

    Gueye, Sokhna Bousso; Diop-Ndiaye, Halimatou; Diallo, Mamadou Malick; Ly, Omar; Sow-Ndoye, Aissatou; Diagne-Gueye, Ndèye Diabou; Kébé-Fall, Khady; Diop, Fatou; Gaye-Diallo, Aïssatou; Belec, Laurent; Mboup, Souleymane; Touré-Kane, Coumba

    2016-03-01

    In the context of early infant diagnosis (EID) decentralization in sub-Saharan Africa, dried blood spot (DBS) is now widely used for HIV proviral DNA detection in resource-limited settings. A new version of CAP/CTM (version 2) has been introduced, recently by Roche Diagnosis as a new real-time PCR assay to replace previous technologies on qualitative detection of HIV-1 DNA using whole blood and DBS samples. The objective of this study was to evaluate CAP/CTM version 2 compared to CAP/CTM version 1 and Amplicor on DBS. A total of 261 DBS were collected from children aged 4 weeks to 17 months born from HIV-seropositive mothers and tested by the three techniques. CAP/CTM version 2 showed 100% of agreement with Amplicor including 74 positive results and 187 negative results. CAP/CTM version 2 versus CAP/CTM version 1 as well as CAP/CTM version 1 versus Amplicor showed two discordant results giving a sensitivity of 98.6%, specificity of 99.5%, positive predictive value of 98.6% and negative predictive value of 99.5%. The concordance was 99.12% (95% of confidence interval) giving a Kappa coefficient of 0.97 (p<0.001). These findings confirmed the expected good performance of CAP/CTM version 2 for HIV-1 EID.

  9. Assessment of Chlamydia trachomatis infection by Cobas Amplicor PCR and in-house LightCycler assays using PreservCyt and 2-SP media in voluntary legal abortions.

    PubMed

    Sevestre, Henri; Mention, Jacques; Lefebvre, Jean-François; Eb, François; Hamdad, Farida

    2009-01-01

    Chlamydial infection of the upper genital tract after abortion is well recognized, but routine screening for infection before termination is rare, and few centres are aware of the prevalence of post-abortion complications in their patient population. Knowledge of the patient population is the best guide for developing screening strategies. The aim of this study was to determine the prevalence of chlamydial infection in patients presenting for legal termination of pregnancy, and to assess the presence of Chlamydia trachomatis by PCR on specimens collected in either PreservCyt (ThinPrep) or 2-sucrose phosphate (2-SP) transport medium. Two hundred and eleven single, sexually active women, aged 15-26 years, attending the Gynaecology and Obstetric Hospital, Amiens, France, for surgical termination of pregnancy were enrolled in this study from June 2002 to June 2003. C. trachomatis detection using a Cobas Amplicor PCR test (Roche Diagnostics) targeting a 207 bp segment of the common cryptic plasmid and a quantitative LightCycler real-time PCR (LC-PCR) (Roche Diagnostics) targeting a 123 bp fragment within the highly conserved constant domain 3 of the single-chromosome-copy ompA gene were performed on endocervical swabs in 2-SP, and on specimens collected using a cytobrush and placed in PreservCyt medium. The in-house LC-PCR was used as a chromosomal diagnosis method and to determine the load of C. trachomatis. This method was able to detect the mutant Swedish variant with a deletion of 377 bp in the target area in the cryptic plasmid, which is the region targeted by the Cobas Amplicor PCR test. C. trachomatis was detected in 19/211 patients (9 %) by both PCR methods. Among the 19 infected women, C. trachomatis was detected by the Cobas Amplicor PCR in 16 specimens in PreservCyt (7.6 %) and in 12 endocervical swabs in 2-SP (5.7 %). Specimens from only nine women were PCR-positive in both PreservCyt and 2-SP media by this method. Cobas Amplicor PCR revealed that 10.9 and 2

  10. Evaluation of the AMPLICOR cytomegalovirus test with specimens from human immunodeficiency virus-infected subjects.

    PubMed

    Boivin, G; Handfield, J; Toma, E; Murray, G; Lalonde, R; Tevere, V J; Sun, R; Bergeron, M G

    1998-09-01

    The AMPLICOR cytomegalovirus (CMV) test, a new qualitative assay for the detection of CMV DNA in plasma, was compared to conventional methods and quantitative PCR (Q-PCR) assays by using leukocytes and plasma from 179 blood samples from subjects with AIDS. For the diagnosis of CMV disease, cell-based assays such as a Q-PCR with polymorphonuclear leukocytes (Q-PCR-PMNL) and a pp65 antigenemia assay had the highest sensitivities but suffered from a lack of specificity. The best agreement between the results of the Q-PCR-PMNL assay and those of the AMPLICOR test was found when a threshold diagnostic value of 690 copies per 10(5) cells was selected for the Q-PCR-PMNL assay. In that context, the AMPLICOR CMV test had a sensitivity of 96.4% and a specificity of 95.3% when results were compared to results of the cell-based PCR assay. This threshold was close to the one described as associated with the best sensitivity and specificity for the diagnosis of CMV disease in a recently published study (4). Blood samples that tested positive by the Q-PCR-PMNL assay but negative by the AMPLICOR CMV test were associated with viral loads (mean, 785 copies, median, 96 copies per 10(5) leukocytes) lower than the viral loads of blood samples that tested positive by both assays (mean, 21,452 copies; median, 9,784 copies per 10(5) leukocytes) (P = 0.003). The AMPLICOR CMV test gave positive results at least 48 days before the development of symptomatic CMV disease in a longitudinal analysis of a limited subset of patients (n = 6) from whom sequential specimens were available for testing. In conclusion, the AMPLICOR CMV test is a very convenient assay combining rapidity, simplicity, and the possibility of batch testing. A positive result by this test seems particularly important since this implies, in most instances, the presence or the imminence of CMV disease, although a negative test result does not rule out disease.

  11. Evaluation of the AMPLICOR Cytomegalovirus Test with Specimens from Human Immunodeficiency Virus-Infected Subjects

    PubMed Central

    Boivin, Guy; Handfield, Julie; Toma, Emil; Murray, Gilles; Lalonde, Richard; Tevere, Vincent J.; Sun, Rita; Bergeron, Michel G.

    1998-01-01

    The AMPLICOR cytomegalovirus (CMV) test, a new qualitative assay for the detection of CMV DNA in plasma, was compared to conventional methods and quantitative PCR (Q-PCR) assays by using leukocytes and plasma from 179 blood samples from subjects with AIDS. For the diagnosis of CMV disease, cell-based assays such as a Q-PCR with polymorphonuclear leukocytes (Q-PCR-PMNL) and a pp65 antigenemia assay had the highest sensitivities but suffered from a lack of specificity. The best agreement between the results of the Q-PCR-PMNL assay and those of the AMPLICOR test was found when a threshold diagnostic value of 690 copies per 105 cells was selected for the Q-PCR-PMNL assay. In that context, the AMPLICOR CMV test had a sensitivity of 96.4% and a specificity of 95.3% when results were compared to results of the cell-based PCR assay. This threshold was close to the one described as associated with the best sensitivity and specificity for the diagnosis of CMV disease in a recently published study (4). Blood samples that tested positive by the Q-PCR-PMNL assay but negative by the AMPLICOR CMV test were associated with viral loads (mean, 785 copies, median, 96 copies per 105 leukocytes) lower than the viral loads of blood samples that tested positive by both assays (mean, 21,452 copies; median, 9,784 copies per 105 leukocytes) (P = 0.003). The AMPLICOR CMV test gave positive results at least 48 days before the development of symptomatic CMV disease in a longitudinal analysis of a limited subset of patients (n = 6) from whom sequential specimens were available for testing. In conclusion, the AMPLICOR CMV test is a very convenient assay combining rapidity, simplicity, and the possibility of batch testing. A positive result by this test seems particularly important since this implies, in most instances, the presence or the imminence of CMV disease, although a negative test result does not rule out disease. PMID:9705384

  12. Roch Carrier, Popular Language, and Joual.

    ERIC Educational Resources Information Center

    Walkley, Max

    1997-01-01

    Discusses the language problems in Roch Carrier's French Canadian short stories, as well as his concise, nostalgic writing style. The article gives examples of vocabulary in his characters' dialogue; reviews the evolvement of French in Quebec and the question of "joual," in particular; and focuses on expressions posing difficulty for…

  13. PreservCyt Transport Medium Used for the ThinPrep Pap Test Is a Suitable Medium for Detection of Chlamydia trachomatis by the COBAS Amplicor CT/NG Test: Results of a Preliminary Study and Future Implications

    PubMed Central

    Bianchi, Anne; Moret, François; Desrues, Jean-Marc; Champenois, Thierry; Dervaux, Yves; Desvouas, Orlane; Oursin, André; Quinzat, Dominique; Dachez, Roger; Bathelier, Christian; Ronsin, Christophe

    2002-01-01

    The commercial COBAS Amplicor CT/NG test (Roche Diagnostic Systems, Meylan, France) is a sensitive and specific method for detection of Chlamydia trachomatis infections. This test currently consists of using a nucleic acid amplification method to detect C. trachomatis in first-void urine specimens and in endocervical swabs collected in 2-sucrose-phosphate (2SP) transport medium. We conducted a prospective study to determine whether the automated COBAS Amplicor CT/NG test can detect C. trachomatis in cervical specimens collected in PreservCyt transport medium (ThinPrep Pap Test; Cytyc Corporation, Boxborough, Mass.). PreservCyt medium is used to preserve cervical samples before the preparation of ThinPrep slides. We collected 1,000 cervical specimens from young women (age range, 15 to 25 years) during routine Pap smear tests. Only specimens with normal cytology and in which the gynecologist found no clinical evidence of urogenital infections were selected. The samples were stored in PreservCyt transport medium at 15 to 20°C. C. trachomatis was detected in 22 of the 1,000 cervical specimens that had been stored in PreservCyt. To confirm the positive samples, the test was repeated on new endocervical swab specimens collected in 2SP transport medium. Only 9 of the 22 positive patients agreed to undergo this control, but all 9 retested positive. To evaluate the influence of storage conditions on the sensitivity of the C. trachomatis PCR test, all of the positive samples were stored at 15 to 20°C in PreservCyt transport medium and were retested every 2 weeks for 6 weeks. C. trachomatis was successfully amplified from all 22 specimens for the whole 6-week period. The prevalence of C. trachomatis infection was 2.2% in our study population. These results demonstrate that PreservCyt transport medium is a suitable transport medium for detection of C. trachomatis by the COBAS Amplicor CT/NG test. The ThinPrep Pap Test may enable gynecologists to monitor for both cervical

  14. PreservCyt transport medium used for the ThinPrep Pap test is a suitable medium for detection of Chlamydia trachomatis by the COBAS Amplicor CT/NG test: results of a preliminary study and future implications.

    PubMed

    Bianchi, Anne; Moret, François; Desrues, Jean-Marc; Champenois, Thierry; Dervaux, Yves; Desvouas, Orlane; Oursin, André; Quinzat, Dominique; Dachez, Roger; Bathelier, Christian; Ronsin, Christophe

    2002-05-01

    The commercial COBAS Amplicor CT/NG test (Roche Diagnostic Systems, Meylan, France) is a sensitive and specific method for detection of Chlamydia trachomatis infections. This test currently consists of using a nucleic acid amplification method to detect C. trachomatis in first-void urine specimens and in endocervical swabs collected in 2-sucrose-phosphate (2SP) transport medium. We conducted a prospective study to determine whether the automated COBAS Amplicor CT/NG test can detect C. trachomatis in cervical specimens collected in PreservCyt transport medium (ThinPrep Pap Test; Cytyc Corporation, Boxborough, Mass.). PreservCyt medium is used to preserve cervical samples before the preparation of ThinPrep slides. We collected 1,000 cervical specimens from young women (age range, 15 to 25 years) during routine Pap smear tests. Only specimens with normal cytology and in which the gynecologist found no clinical evidence of urogenital infections were selected. The samples were stored in PreservCyt transport medium at 15 to 20 degrees C. C. trachomatis was detected in 22 of the 1,000 cervical specimens that had been stored in PreservCyt. To confirm the positive samples, the test was repeated on new endocervical swab specimens collected in 2SP transport medium. Only 9 of the 22 positive patients agreed to undergo this control, but all 9 retested positive. To evaluate the influence of storage conditions on the sensitivity of the C. trachomatis PCR test, all of the positive samples were stored at 15 to 20 degrees C in PreservCyt transport medium and were retested every 2 weeks for 6 weeks. C. trachomatis was successfully amplified from all 22 specimens for the whole 6-week period. The prevalence of C. trachomatis infection was 2.2% in our study population. These results demonstrate that PreservCyt transport medium is a suitable transport medium for detection of C. trachomatis by the COBAS Amplicor CT/NG test. The ThinPrep Pap Test may enable gynecologists to monitor for

  15. Are there exoplanets near their Roche limits?

    NASA Astrophysics Data System (ADS)

    Sanders, Timothy; Chatterjee, Sourav; Rasio, Frederic A.; Valsecchi, Francesca

    2016-01-01

    We survey the Kepler catalog for planets that are potentially at or very near the Roche limit separation (a_R) from their host stars. The main challenge is of course that, albeit they have known radii, most candidate planets have unknown masses. We first determine the required mean densities (ρ_R) for the candidate planets if they were truly at a_R. We then compare these $rho_R$ values with the planetary densities previously measured via a combination of transit, TTV, and radial velocity measurements. We identify several planet candidates for which $ρ_R is within the observed range of planetary densities. Detailed study of mass loss via Roche-lobe overflow is potentially interesting for these systems.

  16. Comparison of the Amplicor Chlamydia trachomatis test and cell culture for the detection of urogenital chlamydial infections.

    PubMed Central

    Catry, M A; Borrego, M J; Cardoso, J; Azevedo, J; Santo, I

    1995-01-01

    OBJECTIVE--To compare the polymerase chain reaction (PCR) Amplicor Chlamydia trachomatis test with the cell culture method, in diagnosing urogenital chlamydial infections. SUBJECTS--439 patients (327 women and 112 men) attending one STD clinic and Family Planning and Gynaecological Clinics in Lisbon, Portugal, between November 1993 and March 1994. METHODS--In women, two endocervical swab samples were collected: one for PCR Amplicor and one for standard culture technique. Men were asked to submit 20 ml of urine (first pass urine) for PCR Amplicor and one urethral specimen was taken for culture. The order of collection of the specimens was rotated every 50 patients. Discrepant results were further analysed by a second PCR with primers directed against the C trachomatis major outer membrane protein (MOMP) and by direct fluorescent antibody (DFA). RESULTS--After analysis of discrepancies, the adjusted sensitivity and specificity of PCR on endocervical specimens were 92.9% and 100% and the positive and negative predictive values were 100% and 99.7% respectively; on the urine samples these values were 100%, 99.1%, 100% and 99.1%, respectively. CONCLUSION--These results indicate that the PCR Amplicor test is a rapid sensitive and specific assay for the detection of C trachomatis in urogenital infections and provides a non-invasive technique for screening chlamydia infection in men. PMID:7590718

  17. Géométrie de Roche

    NASA Astrophysics Data System (ADS)

    Hameury, Jean-Marie

    2001-01-01

    I discuss here the geometry of a close binary, described by the Roche potential. The three possible solutions, detached, semi-detached and contact systems, are presented. Ellipsoidal variations found in quiescent soft X-ray transients show that the secondary distortion is indeed quite detectable; they also can be used to constrain the primary mass, and, together with the spectroscopic determination of the mass function, are the only unambiguous evidences for the existence of black holes in LMXBs. Ce chapitre détaille la géométrie d'un système binaire serré, décrite par le potentiel de Roche. Les trois possibilités (système détaché, semi-détaché, en contact) sont présentées. Les variations ellipsoídales observées dans les systèmes transitoires X en quiescence montrent que les déformations de la secondaire sont parfaitement détectables elles permettent surtout de contraindre la masse de l'objet compact, et fournissent, avec la détermination par spectroscopie de la fonction de masse, les seules preuves indiscutables de l'existence de trous noirs dans les systèmes binaires X.

  18. Ice cream and orbifold Riemann-Roch

    NASA Astrophysics Data System (ADS)

    Buckley, Anita; Reid, Miles; Zhou, Shengtian

    2013-06-01

    We give an orbifold Riemann-Roch formula in closed form for the Hilbert series of a quasismooth polarized n-fold (X,D), under the assumption that X is projectively Gorenstein with only isolated orbifold points. Our formula is a sum of parts each of which is integral and Gorenstein symmetric of the same canonical weight; the orbifold parts are called ice cream functions. This form of the Hilbert series is particularly useful for computer algebra, and we illustrate it on examples of {K3} surfaces and Calabi-Yau 3-folds. These results apply also with higher dimensional orbifold strata (see [1] and [2]), although the precise statements are considerably trickier. We expect to return to this in future publications.

  19. Roche volume filling and the dissolution of open star clusters

    NASA Astrophysics Data System (ADS)

    Ernst, A.; Berczik, P.; Just, A.; Noel, T.

    2015-08-01

    From direct N-body simulations we find that the dynamical evolution of star clusters is strongly influenced by the Roche volume filling factor. We present a parameter study of the dissolution of open star clusters with different Roche volume filling factors and different particle numbers. We study both Roche volume underfilling and overfilling models and compare with the Roche volume filling case. We find that in the Roche volume overfilling limit of our simulations two-body relaxation is no longer the dominant dissolution mechanism but the changing cluster potential. We call this mechanism ``mass-loss driven dissolution'' in contrast to ``two-body relaxation driven dissolution'' which occurs in the Roche volume underfilling regime. We have measured scaling exponents of the dissolution time with the two-body relaxation time. In this experimental study we find a decreasing scaling exponent with increasing Roche volume filling factor. The evolution of the escaper number in the Roche volume overfilling limit can be described by a log-logistic differential equation. We report the finding of a resonance condition which may play a role for the evolution of star clusters and may be calibrated by the main periodic orbit in the large island of retrograde quasiperiodic orbits in the Poincaré surfaces of section. We also report on the existence of a stability curve which may be of relevance with respect to the structure of star clusters.

  20. The Roche Cancer Genome Database (RCGDB).

    PubMed

    Küntzer, Jan; Eggle, Daniela; Lenhof, Hans-Peter; Burtscher, Helmut; Klostermann, Stefan

    2010-04-01

    Sequence variations are being studied for a better understanding of the mechanism and development of cancer as a mutation-driven disease. The systematic sequencing of genes in tumors and technological advances in high-throughput techniques combined with efficient data acquisition methods have resulted in an explosion of available cancer genome-related data. Despite the technological progress and increase of data, improvements in the application area, for example, drug target discovery, have failed to keep pace with increased research and development spending. One reason for this discrepancy is the ever increasing number of databases and the absence of a unified access to the mutation data. Currently, researchers typically have to browse several, often highly specialized databases to obtain the required information. A more complete understanding of relations and dependencies between mutations and cancer, however, requires the availability of an efficient integrative cancer genome information system. To facilitate this, we developed the Roche Cancer Genome Database (RCGDB), a freely available biological information system integrating different kinds of mutation data. The database is the first comprehensive integration of disparate cancer genome data like single nucleotide variants, single nucleotide polymorphisms, and chromosomal aberrations (CGH and FISH). RCGDB is freely accessible via a Google-like Web interface at http://rcgdb.bioinf.uni-sb.de/MutomeWeb/. (c) 2010 Wiley-Liss, Inc.

  1. Performance of the COBAS AMPLICOR HCV MONITOR Test, Version 2.0, an Automated Reverse Transcription-PCR Quantitative System for Hepatitis C Virus Load Determination

    PubMed Central

    Gerken, G.; Rothaar, T.; Rumi, M. G.; Soffredini, R.; Trippler, M.; Blunk, M. J.; Butcher, A.; Soviero, S.; Colucci, G.

    2000-01-01

    A clinical evaluation of an automated quantitative PCR assay, the COBAS AMPLICOR HCV MONITOR test, version 2.0 (v2.0), was carried out to assess the performance of this test in comparison with that of the previous, manual version, the AMPLICOR HCV MONITOR test, and with that of nested PCR. Serial dilutions of serum samples infected with genotype 1b, 2a, or 3, as well as synthetic RNA transcripts and serum samples derived from 87 patients with chronic hepatitis C and infected with genotype 1a, 1b, 2a, 2b, 3a, 3b, 4, or 5, were analyzed to determine the ability of the system to efficiently quantify various hepatitis C virus (HCV) genotypes. These experiments showed that the COBAS AMPLICOR HCV MONITOR test, v2.0, has mean intra-assay, interassay, and interoperator coefficients of variation that range from 22 to 34.5% and a 3-logarithm dynamic range, which spans from 103 to 106 copies/ml. Compared to the previous, manual version of the test, the COBAS AMPLICOR HCV MONITOR test, v2.0, showed an improved efficacy for all genotypes, especially genotypes 2, 3, and 4, whose estimated concentrations were on average 1 logarithm higher. When used to monitor patients under treatment, however, both versions showed the same patterns of viremia, indicating that the COBAS AMPLICOR HCV MONITOR test, v2.0, and the AMPLICOR HCV MONITOR test were equally effective at detecting relative viremia changes in serial samples. As expected, the automated test was less sensitive than nested PCR; among specimens from a cohort of patients treated with interferon, nested PCR identified three more viremic specimens, which probably contained very low concentrations of HCV RNA. PMID:10834978

  2. A Riemann-Roch theorem for the noncommutative two torus

    NASA Astrophysics Data System (ADS)

    Khalkhali, Masoud; Moatadelro, Ali

    2014-12-01

    We prove the analogue of the Riemann-Roch formula for the noncommutative two torus Aθ = C(Tθ2)equipped with an arbitrary translation invariant complex structure and a Weyl factor represented by a positive element k ∈C∞(Tθ2). We consider a topologically trivial line bundle equipped with a general holomorphic structure and the corresponding twisted Dolbeault Laplacians. We define a spectral triple (Aθ , H , D) that encodes the twisted Dolbeault complex of Aθ and whose index gives the left hand side of the Riemann-Roch formula. Using Connes' pseudodifferential calculus and heat equation techniques, we explicitly compute the b2 terms of the asymptotic expansion of Tr(e-tD2) . We find that the curvature term on the right hand side of the Riemann-Roch formula coincides with the scalar curvature of the noncommutative torus recently defined and computed in Connes and Moscovici (2014) and independently computed in Fathizadeh and Khalkhali (2014).

  3. SATELLITE FORMATION :spreading of rings beyond the Roche radius

    NASA Astrophysics Data System (ADS)

    Crida, A.; Charnoz, S.

    2013-11-01

    When a disk of solid particles (like Saturn's rings) spreads beyond the Roche radius (inside which planetary tides prevent aggregation), satellites form and migrate away. After a quick derivation of the Roche radius, here we describe analytically this process. When the spreading is fast, only one large satellite forms, as was the case for Pluto and Earth. When the spreading is slow, a retinue of satellites appear with masses increasing with distance to the Roche radius, in excellent agreement with Saturn's, Uranus', and Neptune's satellite systems. This suggests that Uranus and Neptune used to have massive rings that disappeared to give birth to their regular satellites. Thus, we argue in Crida & Charnoz (2012) that most regular satellites in the Solar System probably formed in this way.

  4. Binary Evolution: Roche Lobe Overflow and Blue Stragglers

    NASA Astrophysics Data System (ADS)

    Ivanova, Natalia

    One of the principal mechanisms that is responsible for the origin of blue stragglers is mass transfer that takes place while one of the binary companions overfills its Roche lobe. In this Chapter, we overview the theoretical understanding of mass transfer via Roche lobe overflow: classification, how both the donor and of the accretor respond to the mass transfer on different timescales (adiabatic response, equilibrium response, superadiabatic response, time-dependent response) for different types of their envelopes (convective and radiative). These responses, as well as the assumption on how liberal the process is, are discussed in terms of the stability of the ensuing mass transfer. The predictions of the theory of mass transfer via Roche lobe overflow are then briefly compared with the observed mass-transferring systems with both degenerate and non-degenerate donors. We conclude with the discussion which cases of mass transfer and which primordial binaries could be responsible for blue stragglers formation via Roche lobe overflow, as well as how this can be enhanced for blue stragglers formed in globular clusters

  5. ["Wetlands". Charles Bukowski and Charlotte Roche on hemorrhoids].

    PubMed

    Bahmer, F A; Bahmer, J A

    2010-08-01

    More than 40 years ago Charles Bukowski described his experiences with coloscopy and the ensuing surgery on his hemorrhoids, both performed by a doctor pictured as sadistic. Bukowski not only depicts these procedures but also characterizes his compassionate inpatients as well as the nursing staff. In her bestseller published in 2008 Charlotte Roche's protagonist Helen needs surgical inpatient treatment because of hemorrhoidal bleeding. Her stay in the hospital, prolonged by a postoperative self-inflicted bleeding, provides the basis not only for strategies to bring her divorced parents together but also for thoughts on genitalia, manifold sexual practices, as well as on rules of hygiene. From a psychodynamic viewpoint the protagonists in both stories suffer from a depressive basic conflict, compensated in Bukowski's work by a dependent, self-destructive, philobatic form of coping and in Roche's alter ego Helen by an impulsive, sexualized behaviour.

  6. LUNAR ACCRETION FROM A ROCHE-INTERIOR FLUID DISK

    SciTech Connect

    Salmon, Julien; Canup, Robin M. E-mail: robin@boulder.swri.edu

    2012-11-20

    We use a hybrid numerical approach to simulate the formation of the Moon from an impact-generated disk, consisting of a fluid model for the disk inside the Roche limit and an N-body code to describe accretion outside the Roche limit. As the inner disk spreads due to a thermally regulated viscosity, material is delivered across the Roche limit and accretes into moonlets that are added to the N-body simulation. Contrary to an accretion timescale of a few months obtained with prior pure N-body codes, here the final stage of the Moon's growth is controlled by the slow spreading of the inner disk, resulting in a total lunar accretion timescale of {approx}10{sup 2} years. It has been proposed that the inner disk may compositionally equilibrate with the Earth through diffusive mixing, which offers a potential explanation for the identical oxygen isotope compositions of the Earth and Moon. However, the mass fraction of the final Moon that is derived from the inner disk is limited by resonant torques between the disk and exterior growing moons. For initial disks containing <2.5 lunar masses (M{sub Last-Quarter-Moon }), we find that a final Moon with mass > 0.8 M{sub Last-Quarter-Moon} contains {<=}60% material derived from the inner disk, with this material preferentially delivered to the Moon at the end of its accretion.

  7. Roche-lobe Overflow in Eccentric Planet-Star Systems

    NASA Astrophysics Data System (ADS)

    Dosopoulou, Fani; Naoz, Smadar; Kalogera, Vassiliki

    2017-07-01

    Many giant exoplanets are found near their Roche limit and in mildly eccentric orbits. In this study, we examine the fate of such planets through Roche-lobe overflow as a function of the physical properties of the binary components, including the eccentricity and the asynchronicity of the rotating planet. We use a direct three-body integrator to compute the trajectories of the lost mass in the ballistic limit and investigate the possible outcomes. We find three different outcomes for the mass transferred through the Lagrangian point L 1: (1) self-accretion by the planet, (2) direct impact on the stellar surface, and (3) disk formation around the star. We explore the parameter space of the three different regimes and find that at low eccentricities, e≲ 0.2, mass overflow leads to disk formation for most systems, while, for higher eccentricities or retrograde orbits, self-accretion is the only possible outcome. We conclude that the assumption often made in previous work that when a planet overflows its Roche lobe it is quickly disrupted and accreted by the star is not always valid.

  8. Profile of Roche's cobas® HCV tests.

    PubMed

    Kessler, Harald H; Stelzl, Evelyn

    2017-04-01

    Molecular assays for detection and accurate quantitation of hepatitis C virus (HCV) RNA have been important for identification and management of the hepatitis C. Furthermore, the HCV genotype should be assessed prior to treatment initiation. Recently, Roche developed the cobas® HCV tests for use on the cobas® 6800/8800 Systems and the cobas® 4800 System and the cobas® HCV genotyping (GT) test for use on the cobas® 4800 System. Areas covered: The analytic and clinical performance of the newly-developed tests is described according to the currently existing literature. Both tests for detection and quantitation of HCV RNA have been shown to be sensitive and linear, and correlate well with established Roche tests used in the routine diagnostic laboratory. The cobas® HCV GT test shows a good performance and is suitable for identification of HCV genotypes 1 to 6 and genotype 1 subtypes a and b in clinical specimens from individuals with chronic HCV infection. Expert commentary: The new tests are effective in screening for hepatitis C infection and in the management of patients with chronic HCV infection ensuring full HCV genotype coverage. They will replace the established Roche tests within the next few years.

  9. Roche lobe sizes in deep-MOND gravity

    NASA Astrophysics Data System (ADS)

    Zhao, Hong Sheng

    2005-12-01

    MOdified Newtonian Dynamics survived the test over two decades, fitting the ups and downs of a variety of galaxy velocity curves without fine tuning (Sanders & McGaugh 2002, ARA&A, 40, 263). MOND is also evolving from an empirical to a decent theory respecting fundamental physics after Bekenstein (2004, Phys. Rev. D, 70, 3509) showed that lensing and Hubble expansion can be modeled rigourously in a Modified Relativity. However, many properties of MOND are obscured by its non-linear Poisson's equation. Here we study the effect of tides for a binary stellar system or a baryonic satellite-host galaxy system. We show that the Roche lobe is more squashed than the Newtonian case due to the anisotropic dilation effect in deep-MOND. We prove analytically that the Roche lobe volume scales linearly with the "true" baryonic mass ratio in both Newtonian and deep-MOND regimes, insensitive to the modification to the inertia mass. Hence accurate Roche radii of satellites can break the degeneracy of MOND and dark matter theory. Globular clusters and dwarf galaxies of comparable luminosities and distances show a factor of ten scatter in limiting radii; this is difficult to explain in any "mass-tracing-light" universe.

  10. Rethinking transgression: disgust, affect, and sexuality in Charlotte Roche's Wetlands.

    PubMed

    Hester, Helen

    2013-01-01

    This article explores the critical reaction to Charlotte Roche's novel Wetlands, and considers the ways in which this reaction reflects contemporary thinking on sex and transgression. While reviewers position the text as the site of a subversive politics and a specifically sexualized form of affect, much of the affective power of Wetlands lies less in its treatment of sex than in its largely ignored descriptions of the revolting body. Via an analysis of the different forms of affect in operation within Wetlands, this article will explore whether the association of sex with politically charged subversion may now be subsiding.

  11. Abbott RealTime Hepatitis C Virus (HCV) and Roche Cobas AmpliPrep/Cobas TaqMan HCV Assays for Prediction of Sustained Virological Response to Pegylated Interferon and Ribavirin in Chronic Hepatitis C Patients ▿

    PubMed Central

    Matsuura, Kentaro; Tanaka, Yasuhito; Hasegawa, Izumi; Ohno, Tomoyoshi; Tokuda, Hiroshi; Kurbanov, Fuat; Sugauchi, Fuminaka; Nojiri, Shunsuke; Joh, Takashi; Mizokami, Masashi

    2009-01-01

    Two commercial real-time PCR assays are currently available for sensitive hepatitis C virus (HCV) RNA quantification: the Abbott RealTime HCV assay (ART) and Roche Cobas AmpliPrep/Cobas TaqMan HCV assay (CAP/CTM). We assessed whether the two real-time PCR assays were more effective than Roche Cobas Amplicor HCV Monitor test, v.2.0 (CAM) for prediction of the sustained virological response (SVR) to pegylated interferon (PEG-IFN) plus ribavirin (RBV) in chronic hepatitis C. Sixty patients chronically infected with HCV genotype 1b (37 males and 23 females, 53 ± 12 years of age) were treated with PEG-IFNα2b plus RBV for 48 weeks. Stored specimens at nine time points for each patient (at baseline, on treatment, and 24 weeks after treatment) were tested by the two real-time PCR assays and CAM. Twenty-six (43.3%) patients reached SVR. The positive predictive values (PPVs) for SVR of undetectable HCV RNA at week 12 by CAM, ART, and CAP/CTM were 74.3%, 88.0%, and 95.2%, respectively. An undetectable HCV RNA level by CAM, ART, and CAP/CTM correctly predicted SVR at week 4 in 100%, 100%, and 100% of patients, at weeks 5 to 8 in 91.7%, 100%, and 100% of patients, at weeks 9 to 12 in 55.6%, 75%, and 87.5% of patients, and at weeks 13 to 24 in 0%, 26.7%, and 40% of patients, respectively. Of 16 patients who relapsed after treatment, HCV RNA was detectable in 2 patients at the end of treatment by CAP/CTM but undetectable by ART and CAM. HCV RNA tests using ART and CAP/CTM are considered to be more effective at predicting SVR than CAM, and the PPV for SVR was slightly higher in CAP/CTM than in ART. PMID:19091819

  12. Comparison of Gen-probe transcription-mediated amplification, Abbott PCR, and Roche PCR assays for detection of wild-type and mutant plasmid strains of Chlamydia trachomatis in Sweden.

    PubMed

    Møller, Jens Kjølseth; Pedersen, Lisbeth Nørum; Persson, Kenneth

    2008-12-01

    The clinical performance of two nucleic acid amplification assays targeting the cryptic plasmid and two assays targeting rRNA molecules in Chlamydia trachomatis was examined. First-catch urine samples from Malmoe, Sweden, were tested for C. trachomatis with the Abbott real-time PCR assay m2000 and an in-house PCR for the new variant strain of C. trachomatis with a deletion in the cryptic plasmid. Aliquots of the urine samples were sent to Aarhus, Denmark, and further examined with the Roche COBAS Amplicor CT (RCA) PCR, the Gen-Probe Aptima Combo 2 assay (AC2) targeting the C. trachomatis 23S rRNA, and the Aptima C. trachomatis assay (ACT) targeting the 16S rRNA molecule. A positive prevalence of 9% (163/1,808 urine samples examined) was detected according to the combined reference standard. The clinical sensitivity and specificity of the four assays were as follows: for ACT, 100% (163/163) and 99.9% (1,643/1,645), respectively; for AC2, 100% (163/163) and 99.6% (1,640/1,645); for m2000, 68.7% (112/163) and 99.9% (1,644/1,645); for RCA, 63.8% (104/163) and 99.9% (1,643/1,645). The two Gen-Probe assays detected all mutant strains characterized by the in-house PCR as having the deletion in the cryptic plasmid, whereas the Roche and the Abbott PCRs targeting the plasmid were both unable to detect the plasmid mutant. The difference in clinical sensitivity between the plasmid PCR assays m2000 and RCA, on the one hand, and the rRNA assays AC2 and ACT, on the other, could be attributed almost exclusively to the presence of the plasmid mutant in about one-quarter of the Chlamydia-positive samples examined.

  13. Evolution of Giant Planets Close to the Roche Limit

    NASA Astrophysics Data System (ADS)

    Valsecchi, Francesca

    2015-12-01

    Two formation models have been proposed to explain hot Jupiters’ tight orbits. These could have migrated inward in a disk (disk migration), or they could have formed via tidal circularization of an orbit made highly eccentric following gravitational interactions with a companion (high-eccentricity migration). I will show how current observations coupled with a detailed treatment of tides can be used to constrain both hot Jupiter formation and tidal dissipation theories.Eventually, stellar tides will cause the orbits of many hot Jupiters to decay down to their Roche limit. Using a detailed binary mass transfer model we show how a hot Jupiter undergoing a phase of Roche-lobe overflow (RLO) leads to lower-mass planets in orbits of a few days. The remnant planets have a rocky core and some amount of envelope material, which is slowly removed via photo-evaporation at nearly constant orbital period; these have properties resembling many of the observed super-Earths and sub-Neptunes. For these remnant planets we also predict an anti-correlation between mass and orbital period; very low-mass planets in ultra-short periods cannot be produced through this type of evolution.

  14. Hot-Jupiter core mass from Roche lobe overflow

    NASA Astrophysics Data System (ADS)

    Ginzburg, Sivan; Sari, Re'em

    2017-07-01

    The orbits of many observed hot Jupiters are decaying rapidly due to tidal interaction, eventually reaching the Roche limit. We analytically study the ensuing coupled mass-loss and orbital evolution during the Roche lobe overflow and find two possible scenarios. Planets with light cores Mc ≲ 6 M⊕ (assuming a nominal tidal dissipation factor Q ˜ 106 for the host star) are transformed into Neptune-mass gas planets, orbiting at a separation (relative to the stellar radius) a/R⋆ ≈ 3.5. Planets with heavier cores Mc ≳ 6 M⊕ plunge rapidly until they are destroyed at the stellar surface. Remnant gas Neptunes, which are stable to photoevaporation, are absent from the observations despite their unique transit radius (5-10 R⊕). This result suggests that Mc ≳ 6 M⊕, providing a useful constraint on the poorly known core mass that may distinguish between different formation theories of gas giants. Alternatively, if one assumes a prior of Mc ≈ 6 M⊕ from the core-accretion theory, our results suggest that Q does not lie in the range 106 ≲ Q ≲ 107.

  15. Mycobacterium growth indicator tube testing in conjunction with the AccuProbe or the AMPLICOR-PCR assay for detecting and identifying mycobacteria from sputum samples.

    PubMed Central

    Ichiyama, S; Iinuma, Y; Yamori, S; Hasegawa, Y; Shimokata, K; Nakashima, N

    1997-01-01

    We have compared the ability of the Mycobacterium Growth Indicator Tube (MGIT) system, a new culture method with an oxygen-sensitive fluorescent sensor, to recover mycobacteria from sputum samples with the abilities of egg-based medium and the Septi-Chek AFB system. We have also assessed the clinical utility of the AccuProbe or the AMPLICOR-PCR assay to directly identify Mycobacterium tuberculosis complex and M. avium-M. intracellulare complex (MAC) from positive MGITs. From 382 sputum samples, 99 isolates of M. tuberculosis complex and 20 isolates of MAC were recovered. The MGIT system had the highest recovery rates for M. tuberculosis complex (97.0%) and MAC (100%), compared to recovery rates of 51.5 and 65.0%, respectively, with the egg-based medium and 81.8 and 85.0%, respectively, with the Septi-Chek AFB system. The shortest recovery times were also achieved with the MGIT system: 16.6 days for M. tuberculosis complex and 12.0 days for MAC, compared to 27.1 and 20.1 days, respectively, with the egg-based medium and 21.4 and 13.2 days, respectively, with the Septi-Chek AFB system. The AccuProbe identified 74 (77.1%) of the 96 M. tuberculosis complex-positive MGITs and 17 (85.0%) of the 20 MAC-positive vials. The AMPLICOR system correctly identified 94 (97.9%) of the 96 M. tuberculosis complex-positive MGITs and all 20 MAC-positive vials. Therefore, the MGIT system used in conjunction with the AMPLICOR system is a rapid and sensitive method for detecting and identifying M. tuberculosis complex and MAC isolates from sputum samples. PMID:9230374

  16. Anti-CD18 mAb (Genentech/Roche).

    PubMed

    Brown, W M

    2000-08-01

    Genentech and Roche are collaborating on the development of an anti-CD18 humanized monoclonal antibody (rhuMAb). Inhibition of leukocyte adhesion with antibodies to CD18 is proposed as a therapeutic intervention for indications with an inflammatory component resulting from a reperfusion injury. In June 2000, the company reported that the primary objectives of its phase II trial of the antibody were not met according to preliminary results of the 415-patient trial for the treatment of myocardial infarction [371173], although the company is currently undecided about the implications of the data, and plans to meet with investigators. In 1999, phase II studies for reperfusion injury in patients successfully treated with thrombolytics were planned; enrollment was expected to finish in the third quarter of 1999 [317276]. In February 1999, Lehman Brothers predicted the drug had a 30% probability of reaching market. Assuming a successful launch, Lehman Brothers analysts estimated peak sales would occur in 2009, with sales at that time of 100 million dollars [319225].

  17. The Roche Cancer Genome Database 2.0.

    PubMed

    Küntzer, Jan; Maisel, Daniela; Lenhof, Hans-Peter; Klostermann, Stefan; Burtscher, Helmut

    2011-05-17

    Cancer is a disease of genome alterations that arise through the acquisition of multiple somatic DNA sequence mutations. Some of these mutations can be critical for the development of a tumor and can be useful to characterize tumor types or predict outcome. We have constructed an integrated biological information system termed the Roche Cancer Genome Database (RCGDB) combining different human mutation databases already publicly available. This data is further extended by hand-curated information from publications.The current version of the RCGDB provides a user-friendly graphical interface that gives access to the data in different ways: (1) Single interactive search by genes, samples, cell lines, diseases, as well as pathways, (2) batch searches for genes and cell lines, (3) customized searches for regularly occurring requests, and (4) an advanced query interface enabling the user to query for samples and mutations by various filter criteria. The interfaces of the presented database enable the user to search and view mutations in an intuitive and straight-forward manner. The database is freely accessible at http://rcgdb.bioinf.uni-sb.de/MutomeWeb/.

  18. Unstable Roche-Lobe Overflow of Gaseous Planets

    NASA Astrophysics Data System (ADS)

    Jackson, Brian

    The discoveries of more than 100 roughly Earth-sized bodies with orbital periods less than 1 day, ultra-short-period planets or candidates (USPs), have challenged planet formation theories, and evidence suggests USPs may be the remnants of gaseous planets that shed their atmospheres. Indeed, many hot Jupiters are near Roche-Lobe overflow (RLO), and tidal decay can push them the rest of the way in. Recent work has shown stable RLO (atmospheres lost via a steady outflow and thin accretion disk) probably cannot produce USPs on its own but suggested unstable RLO (atmospheres quickly shed on dynamical timescales) may. In fact, stable RLO may drive overflowing hot Jupiters into unstable RLO, and by analogy with the common-envelope binaries, the core that remains can drive off the gaseous envelope at the cost of its orbital energy. Wellestablished mass-radius relations for gaseous planets, coupled to simple energy and angular momentum considerations, provide a connection between the observed masses and periods for USPs and their putative progenitor gaseous planets, with few free parameters. We propose to investigate the hypothesis that USPs originate through tidal decay and a combination of stable and unstable Roche-lobe overflow of short-period gaseous planets through the following studies: -We will explore the planetary masses, orbital periods, etc. that produce unstable RLO using the Modules for Experiments in Stellar Astrophysics (MESA) suite. -We will relate the observed periods and masses of USPs to their putative progenitor masses and periods to see whether they are consistent with the unstable RLO hypothesis. This proposal is directly relevant to the Exoplanets Research Program since it seeks to "understand the ... physical processes of exoplanets" and "improve understanding of [their] origins" through "theoretical studies ... and modeling'". We also expect that it will have broad impacts on a variety of astrophysical topics: -Ultra-short period planets could

  19. COMPOSITIONS AND ORIGINS OF OUTER PLANET SYSTEMS: INSIGHTS FROM THE ROCHE CRITICAL DENSITY

    SciTech Connect

    Tiscareno, Matthew S.; Hedman, Matthew M.; Burns, Joseph A.; Castillo-Rogez, Julie

    2013-03-10

    We consider the Roche critical density ({rho}{sub Roche}), the minimum density of an orbiting object that, at a given distance from its planet, is able to hold itself together by self-gravity. It is directly related to the more familiar ''Roche limit,'' the distance from a planet at which a strengthless orbiting object of given density is pulled apart by tides. The presence of a substantial ring requires that transient clumps have an internal density less than {rho}{sub Roche}. Conversely, in the presence of abundant material for accretion, an orbiting object with density greater than {rho}{sub Roche} will grow. Comparing the {rho}{sub Roche} values at which the Saturn and Uranus systems transition rapidly from disruption-dominated (rings) to accretion-dominated (moons), we infer that the material composing Uranus' rings is likely more rocky, as well as less porous, than that composing Saturn's rings. From the high values of {rho}{sub Roche} at the innermost ring moons of Jupiter and Neptune, we infer that those moons may be composed of denser material than expected, or more likely that they are interlopers that formed farther from their planets and have since migrated inward, now being held together by internal material strength. Finally, the ''Portia group'' of eight closely packed Uranian moons has an overall surface density similar to that of Saturn's A ring. Thus, it can be seen as an accretion-dominated ring system, of similar character to the standard ring systems except that its material has a characteristic density greater than the local {rho}{sub Roche}.

  20. Evaluation of quantification of HIV-1 RNA viral load in plasma and dried blood spots by use of the semiautomated Cobas Amplicor assay and the fully automated Cobas Ampliprep/TaqMan assay, version 2.0, in Kisumu, Kenya.

    PubMed

    Ouma, Kenneth N; Basavaraju, Sridhar V; Okonji, Jully A; Williamson, John; Thomas, Timothy K; Mills, Lisa A; Nkengasong, John N; Zeh, Clement

    2013-04-01

    In Kenya, HIV-1 viral load monitoring is commonly performed with the Cobas Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the Cobas Ampliprep/Cobas TaqMan (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares the sensitivity, specificity, negative and positive predictive values (NPV and PPV, respectively), concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1-infected pregnant females enrolled in the Kisumu Breastfeeding Study and tested with the Cobas Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity, 100%; 95% confidence interval [CI], 99.1 to 100.0%; NPV, 100%; 95% CI, 59.0 to 100.0%) than the Cobas Amplicor (sensitivity, 96.6%; 95% CI, 94.3 to 98.1%; NPV, 58.8%; 95% CI, 40.7 to 75.4%). The PPVs were comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%; 95% CI, 40.0 to 97.2%) than that of the Cobas Amplicor (95.2%; 95% CI, 76.2 to 99.9%). Good concordance and agreement were observed when paired plasma and DBS specimens were tested with both assays. Lower specificity with the CAP/CTM is likely due to proviral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput than the Cobas Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource-limited settings.

  1. Evaluation of Quantification of HIV-1 RNA Viral Load in Plasma and Dried Blood Spots by Use of the Semiautomated Cobas Amplicor Assay and the Fully Automated Cobas Ampliprep/TaqMan Assay, Version 2.0, in Kisumu, Kenya

    PubMed Central

    Ouma, Kenneth N.; Basavaraju, Sridhar V.; Okonji, Jully A.; Williamson, John; Thomas, Timothy K.; Mills, Lisa A.; Nkengasong, John N.

    2013-01-01

    In Kenya, HIV-1 viral load monitoring is commonly performed with the Cobas Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the Cobas Ampliprep/Cobas TaqMan (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares the sensitivity, specificity, negative and positive predictive values (NPV and PPV, respectively), concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1-infected pregnant females enrolled in the Kisumu Breastfeeding Study and tested with the Cobas Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity, 100%; 95% confidence interval [CI], 99.1 to 100.0%; NPV, 100%; 95% CI, 59.0 to 100.0%) than the Cobas Amplicor (sensitivity, 96.6%; 95% CI, 94.3 to 98.1%; NPV, 58.8%; 95% CI, 40.7 to 75.4%). The PPVs were comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%; 95% CI, 40.0 to 97.2%) than that of the Cobas Amplicor (95.2%; 95% CI, 76.2 to 99.9%). Good concordance and agreement were observed when paired plasma and DBS specimens were tested with both assays. Lower specificity with the CAP/CTM is likely due to proviral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput than the Cobas Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource-limited settings. PMID:23390278

  2. 75 FR 71135 - Hoffmann-La Roche Inc.; Withdrawal of Approval of a New Drug Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-22

    ... Administration (FDA) is withdrawing approval of a new drug application (NDA) for ACCUTANE (isotretinoin) Capsules... INFORMATION: Hoffmann-La Roche Inc. has requested that FDA withdraw approval of NDA 18-662, ACCUTANE... Commissioner of Food and Drugs, approval of NDA 18-662, ACCUTANE (isotretinoin) Capsules, and all...

  3. Toxicologists in public health--Following the path of Louis Roche (based on the Louis Roche lecture "An accidental toxicologist in public health", Bordeaux, 2010).

    PubMed

    Dawson, Andrew H; Buckley, Nicholas A

    2011-02-01

    The global burden of clinical toxicology suggests a natural partnership with public health. This article reflects the content of a Louis Roche lecture given in 2010. HISTORICAL CONTEXT: Our practice and research in clinical toxicology has evolved from clinical cases to toxico-epidemiology to public health. This evolution in practice was initially unplanned but gained momentum and impact as we placed it more formally in a public health framework. This perspective is implicit in Louis Roche's call to "examine all aspects of the poisoning problem" and still provides a valuable starting point for any clinical toxicologist. Clinical toxicology has always had a patient centered focus but its greatest successes have been related to public health interventions. Our early failures and later success in pubic health toxicology correlated with our understanding of the importance of partnerships outside our field. The most rapid dissemination and implementation of information derived from research occur through apriori partnerships with other agencies and international partners. Addressing both local and global need has a number of bilateral synergies. Repositioning clinical toxicology into a public health framework increases access to strategic partnerships, research funds, and policy implementation while still addressing questions that are important to clinical practice.

  4. Life near the Roche limit - Behavior of ejecta from satellites close to planets

    NASA Technical Reports Server (NTRS)

    Dobrovolskis, A. R.; Burns, J. A.

    1980-01-01

    A study of the dynamics of nearby debris from impact craters was made to explain the distinctive features seen on Phobos, Deimis, and Amalthea. The planetary tides and satellite rotation were considered, and the usual pseudo-energy (Jacobi) integral was numerically calculated in the framework of a restricted body problem where satellites are modelled as triaxial ellipsoids rather than point masses. Iso-contours of this integral show that Deimos and Amalthea are entirely closed by Roche lobes, and the surfaces of their model ellipsoids lie nearly along equipotentials. Presently, the surface of Phobos overflows its Roche lobe, except for regions within a few km of the sub-Mars and anti-Mars points. The behavior of crater ejecta from the satellites of Mars were also examined by numerical integration of trajectories for particles leaving their surfaces in the equatorial plane.

  5. Life near the Roche limit - Behavior of ejecta from satellites close to planets

    NASA Technical Reports Server (NTRS)

    Dobrovolskis, A. R.; Burns, J. A.

    1980-01-01

    A study of the dynamics of nearby debris from impact craters was made to explain the distinctive features seen on Phobos, Deimis, and Amalthea. The planetary tides and satellite rotation were considered, and the usual pseudo-energy (Jacobi) integral was numerically calculated in the framework of a restricted body problem where satellites are modelled as triaxial ellipsoids rather than point masses. Iso-contours of this integral show that Deimos and Amalthea are entirely closed by Roche lobes, and the surfaces of their model ellipsoids lie nearly along equipotentials. Presently, the surface of Phobos overflows its Roche lobe, except for regions within a few km of the sub-Mars and anti-Mars points. The behavior of crater ejecta from the satellites of Mars were also examined by numerical integration of trajectories for particles leaving their surfaces in the equatorial plane.

  6. From Hot Jupiters to Super-Earths via Roche Lobe Overflow

    NASA Astrophysics Data System (ADS)

    Valsecchi, Francesca; Rasio, Frederic A.; Steffen, Jason H.

    2014-09-01

    Through tidal dissipation in a slowly spinning host star, the orbits of many hot Jupiters may decay down to the Roche limit. We expect that the ensuing mass transfer will be stable in most cases. Using detailed numerical calculations, we find that this evolution is quite rapid, potentially leading to the complete removal of the gaseous envelope in a few gigayears, and leaving behind an exposed rocky core (a "hot super-Earth"). Final orbital periods are quite sensitive to the details of the planet's mass-radius relation and to the effects of irradiation and photo-evaporation, but could be as short as a few hours or as long as several days. Our scenario predicts the existence of planets with intermediate masses ("hot Neptunes") that should be found precisely at their Roche limit and in the process of losing mass through Roche lobe overflow. The observed excess of small single-planet candidate systems observed by Kepler may also be the result of this process. If so, the properties of their host stars should track those of the hot Jupiters. Moreover, the number of systems that produced hot Jupiters could be two to three times larger than one would infer from contemporary observations.

  7. Roche DAT immunoassay: sensitivity and specificity testing for amphetamines, cocaine, and opiates in oral fluid.

    PubMed

    Crooks, C Richard; Brown, Sue

    2010-03-01

    Laboratory testing of oral fluid for drugs of abuse continues to expand in the workplace, legal, treatment, and health settings. In this study, we assessed recently developed homogeneous Roche DAT screening assays for amphetamines, cocaine metabolite [benzoylecgonine (BZE)], methamphetamines, and opiates in oral fluid. Precision and accuracy were assessed using control samples at +/-25% of cutoff. Sensitivity, specificity, and agreement compared to liquid chromatography-tandem mass spectrometry (LC-MS-MS) was assessed by analysis of oral fluid specimens collected from 994 subjects enrolled in a drug treatment or probation and parole drug-testing program. An additional 180 research specimens from Kroll Laboratories were analyzed for amphetamine and methamphetamine. Screening cutoff concentrations (ng/mL) were as follows: amphetamines, 40; cocaine metabolite, 3; methamphetamines, 40; and opiates, 10. LC-MS-MS analyses were performed with the following cutoff concentrations (ng/mL): amphetamine, 40; BZE, 2.0; methamphetamine, 40; and codeine or morphine, 10. The percent coefficient of variation ranged from 3.4% to 7.3%. Sensitivity and specificity of the Roche DAT assays compared to LC-MS-MS were > 94%, and agreement was > 96% for the four assays. The performance of the Roche DAT assays suggests these new homogeneous screening assays will be an attractive alternative to existing more labor-intensive enzyme immunoassays.

  8. FROM HOT JUPITERS TO SUPER-EARTHS VIA ROCHE LOBE OVERFLOW

    SciTech Connect

    Valsecchi, Francesca; Rasio, Frederic A.; Steffen, Jason H.

    2014-09-20

    Through tidal dissipation in a slowly spinning host star, the orbits of many hot Jupiters may decay down to the Roche limit. We expect that the ensuing mass transfer will be stable in most cases. Using detailed numerical calculations, we find that this evolution is quite rapid, potentially leading to the complete removal of the gaseous envelope in a few gigayears, and leaving behind an exposed rocky core (a {sup h}ot super-Earth{sup )}. Final orbital periods are quite sensitive to the details of the planet's mass-radius relation and to the effects of irradiation and photo-evaporation, but could be as short as a few hours or as long as several days. Our scenario predicts the existence of planets with intermediate masses ({sup h}ot Neptunes{sup )} that should be found precisely at their Roche limit and in the process of losing mass through Roche lobe overflow. The observed excess of small single-planet candidate systems observed by Kepler may also be the result of this process. If so, the properties of their host stars should track those of the hot Jupiters. Moreover, the number of systems that produced hot Jupiters could be two to three times larger than one would infer from contemporary observations.

  9. The significance of low-level plasma HIV viral load on COBAS TaqMan HIV-1 assays for patients with undetectable plasma viral load on COBAS Amplicor monitor version 1.5.

    PubMed

    Manavi, Kaveh

    2008-01-01

    COBAS TaqMan assay is a new HIV assay for measuring plasma viral load (VL). A significant number of patients with undetectable plasma VL on Amplicor assay were reported to have detectable VL with TaqMan in the study centre. The aim of the present study was to investigate the significance of detectable VL counts with TaqMan assay amongst patients who have had undetectable plasma VL with COBAS Amplicor assay. Observational study on patients who have had undetectable (Amplicor version 1.5 assay but detectable plasma VL with COBAS TaqMan assay between June 1, 2006 and April 30, 2007. All patients were on highly active antiretroviral therapy (HAART) for longer than 6 months before use of COBAS TaqMan assay. Patients with detectable VL were followed up on a monthly basis until their VL was <40 copes/mL or there was confirmed new resistance to HAART using genotypic and Virco resistance assay. Plasma VL was detectable (>40 copies/mL) in 113 (14%) patients on 126 episodes using TaqMan assay. VL was less than 500 copies/mL in 90% of those episodes. All episodes ended with VL <40 copies/mL after a median of 117 (94-143) days without change in HAART regimes. The duration of those episodes was longer than 150 days in 75% of cases. No new mutation was detected amongst specimens with detectable VL. Short-term detectable VL may be common with using TaqMan assay. This phenomenon did not result in new mutations or failure of HAART in study patients in the short term.

  10. Evaluation of clinical usefulness of second-generation HCV core antigen assay: comparison with COBAS AMPLICOR HCV MONITOR assay version 2.0.

    PubMed

    Yokosuka, Osamu; Kawai, Shigenobu; Suzuki, Yoichi; Fukai, Kenichi; Imazeki, Fumio; Kanda, Tatsuo; Tada, Motohisa; Mikata, Rintarou; Hata, Akira; Saisho, Hiromitsu

    2005-12-01

    Hepatitis C virus (HCV) is an important etiologic agent for chronic liver diseases. The aim of this study was to evaluate the clinical usefulness of second-generation HCV core antigen assay by comparing the results of the assay with those of the COBAS AMPLICOR HCV MONITOR version 2.0 (COBAS v2.0). HCV core antigen was detectable by this assay in 142/149 (95.3%) of serotype 1 (3821+/-322 fmol/l; mean+/-SD), in 56/58 (96.6%) of serotype 2 (2589+/-449 fmol/l), and in 6/6 (100%) of serotypes 1+2 (1240+/-548 fmol/l). The HCV core antigen levels measured by this assay correlated well with the HCV RNA levels by COBAS v2.0 (r=0.848, P<0.0001). In relation to the outcome of interferon monotherapy, the pretreatment HCV core antigen levels of sustained and non-sustained virological responders were 659+/-189 and 4904+/-376 fmol/l in serotype 1, 1993+/-740 and 3145+/-519 fmol/l in serotype 2. The cutoff values with the best accuracy for HCV core Ag levels to discriminate between sustained and non-sustained virological response were 699 fmol/l for serotype 1 and 292 fmol/l for serotype 2, respectively, by receiver operating characteristic curve analysis. This new assay was considered to be useful in evaluating the HCV levels in patients with chronic hepatitis C.

  11. Amplicor HIV monitor, NASBA HIV-1 RNA QT and quantiplex HIV RNA version 2.0 viral load assays: a Canadian evaluation.

    PubMed

    Prud'homme, I T; Kim, J E; Pilon, R G; Minkus, T; Hawley-Foss, N; Cameron, W; Rud, E W

    1998-12-01

    HIV-1 viral load quantitation is now recognized as a useful tool to monitor the efficiency of antiviral treatment and a powerful predictor of disease outcome. Three HIV-1 viral load quantitation methods have been currently available as commercial kits in Canada since 1996. To evaluate the ability to quantify HIV-1 RNA in plasma of the Amplicor HIV Monitor Test, the NASBA HIV-1 RNA QT Assay and the Quantiplex HIV RNA Assay, version 2.0, at comparable lower detection limits. Blood was collected from 50 HIV-1-infected patients at various stages of infection and therapy. CD4+ cell count were estimated by flow cytometry. Plasma was isolated and tested in duplicate on four occasions using viral load kits from a single lot. HIV RNA data, performance, sensitivity and intra- and inter-assay variability were compared. RNA could be quantified in 33 patients by each technique. An inverse correlation was observed between viral load level and CD4+ cell counts in patients with counts below 200. Monitor could detect RNA in 94% of patients, but it showed the greatest variability and failure rate. Quantiplex 2.0 could detect HIV-1 RNA in 78%, and NASBA in 88% of the patients at theoretically equivalent lower detection limits, suggesting that the detection limit of Quantiplex 2.0 may be higher than 500 HIV-1 RNA copies per ml. NASBA had the fewest invalid tests and good reproducibility, comparable to that of Quantiplex 2.0. The mean values from NASBA and Monitor were the most similar but the best correlation was observed between Monitor and Quantiplex 2.0 results. Monitor, NASBA and Quantiplex results were comparable, although those obtained by Quantiplex were significantly lower. Performing this study at comparable detection limits showed that the detection limit of Quantiplex 2.0 may be higher than stated by the manufacturer.

  12. Exo-Mercury Analogues and the Roche Limit for Close-Orbiting Rocky Planets

    NASA Astrophysics Data System (ADS)

    Rogers, Leslie A.; Price, Ellen

    2015-12-01

    The origin of Mercury's enhanced iron content is a matter of ongoing debate. The characterization of rocky exoplanets promises to provide new independent insights on this topic, by constraining the occurrence rate and physical and orbital properties of iron-enhanced planets orbiting distant stars. The ultra-short-period transiting planet candidate KOI-1843.03 (0.6 Earth-radius, 4.245 hour orbital period, 0.46 Solar-mass host star) represents the first exo-Mercury planet candidate ever identified. For KOI-1843.03 to have avoided tidal disruption on such a short orbit, Rappaport et al. (2013) estimate that it must have a mean density of at least 7g/cc and be at least as iron rich as Mercury. This density lower-limit, however, relies upon interpolating the Roche limits of single-component polytrope models, which do not accurately capture the density profiles of >1000 km differentiated rocky bodies. A more exact calculation of the Roche limit for the case of rocky planets of arbitrary composition and central concentration is needed. We present 3D interior structure simulations of ultra-short-period tidally distorted rocky exoplanets, calculated using a modified version of Hachisu’s self-consistent field method and realistic equations of state for silicates and iron. We derive the Roche limits of rocky planets as a function of mass and composition, and refine the composition constraints on KOI-1843.03. We conclude by discussing the implications of our simulations for the eventual characterization of short-period transiting planets discovered by K2, TESS, CHEOPS and PLATO.

  13. TIDALLY DRIVEN ROCHE-LOBE OVERFLOW OF HOT JUPITERS WITH MESA

    SciTech Connect

    Valsecchi, Francesca; Rasio, Frederic A.; Rappaport, Saul; Marchant, Pablo; Rogers, Leslie A. E-mail: rasio@northwestern.edu E-mail: pablo@astro.uni-bonn.de

    2015-11-10

    Many exoplanets have now been detected in orbits with ultra-short periods very close to the Roche limit. Building upon our previous work, we study the possibility that mass loss through Roche lobe overflow (RLO) may affect the evolution of these planets, and could possibly transform a hot Jupiter into a lower-mass planet (hot Neptune or super-Earth). We focus here on systems in which the mass loss occurs slowly (“stable mass transfer” in the language of binary star evolution) and we compute their evolution in detail with the binary evolution code Modules for Experiments in Stellar Astrophysics. We include the effects of tides, RLO, irradiation, and photo-evaporation (PE) of the planet, as well as the stellar wind and magnetic braking. Our calculations all start with a hot Jupiter close to its Roche limit, in orbit around a Sun-like star. The initial orbital decay and onset of RLO are driven by tidal dissipation in the star. We confirm that such a system can indeed evolve to produce lower-mass planets in orbits of a few days. The RLO phase eventually ends and, depending on the details of the mass transfer and on the planetary core mass, the orbital period can remain around a few days for several Gyr. The remnant planets have rocky cores and some amount of envelope material, which is slowly removed via PE at a nearly constant orbital period; these have properties resembling many of the observed super-Earths and sub-Neptunes. For these remnant planets, we also predict an anti-correlation between mass and orbital period; very low-mass planets (M{sub pl} ≲ 5 M{sub ⊕}) in ultra-short periods (P{sub orb} < 1 day) cannot be produced through this type of evolution.

  14. Tidally-driven Roche-lobe Overflow of Hot Jupiters with MESA

    NASA Astrophysics Data System (ADS)

    Valsecchi, Francesca; Rappaport, Saul; Rasio, Frederic A.; Marchant, Pablo; Rogers, Leslie A.

    2015-11-01

    Many exoplanets have now been detected in orbits with ultra-short periods very close to the Roche limit. Building upon our previous work, we study the possibility that mass loss through Roche lobe overflow (RLO) may affect the evolution of these planets, and could possibly transform a hot Jupiter into a lower-mass planet (hot Neptune or super-Earth). We focus here on systems in which the mass loss occurs slowly (“stable mass transfer” in the language of binary star evolution) and we compute their evolution in detail with the binary evolution code Modules for Experiments in Stellar Astrophysics. We include the effects of tides, RLO, irradiation, and photo-evaporation (PE) of the planet, as well as the stellar wind and magnetic braking. Our calculations all start with a hot Jupiter close to its Roche limit, in orbit around a Sun-like star. The initial orbital decay and onset of RLO are driven by tidal dissipation in the star. We confirm that such a system can indeed evolve to produce lower-mass planets in orbits of a few days. The RLO phase eventually ends and, depending on the details of the mass transfer and on the planetary core mass, the orbital period can remain around a few days for several Gyr. The remnant planets have rocky cores and some amount of envelope material, which is slowly removed via PE at a nearly constant orbital period; these have properties resembling many of the observed super-Earths and sub-Neptunes. For these remnant planets, we also predict an anti-correlation between mass and orbital period; very low-mass planets (Mpl ≲ 5 M⊕) in ultra-short periods (Porb < 1 day) cannot be produced through this type of evolution.

  15. Accretion in the Roche zone: Coexistence of rings and ring moons.

    NASA Astrophysics Data System (ADS)

    Canup, Robin M.; Esposito, Larry W.

    1995-02-01

    Traditional accretion simulations predict rapid accumulation of ring debris into single satellites, while most theories of ring formation dismiss any accretion within the classical Roche limit. The former contradicts the continued presence of planetary rings, while the latter fails to adequately account for the many small satellites observed within ring systems. The coexistence of rings and small satellites thus challenges the premise of a strict boundary between accreting and nonaccreting regions. We have developed an accretion model designed to better examine accumulation processes in the dynamically transitional regime of outer planetary rings. We utilize "three-body" capture criteria, motivated by the work of Ohtsuki (1993 Icarus 106, 228-246), to account for the effects of strong tidal forces on accretion. Our findings indicate that tidally modified accretion occurs in a relatively broad range of orbital radii surrounding the classical Roche limit. Tidally modified accretion has a very unique character: for a given particle density, only bodies which differ greatly in mass can remain gravitationally bound, as like-sized bodies overflow their mutual Hill sphere. We find that this constraint greatly limits the degree of accretional growth and prevents runaway accretion near the Roche limit. Numerical simulations show that through the course of tidally modified accretion, a fragmentation-produced debris distribution evolves into a bimodal population, with one element consisting of a swarm of small, high-velocity bodies and the other composed of a small number of large "moonlets" on fairly circular orbits. The latter are precluded from accreting with one another due to the tidal influences of the planet. Tidally modified accretion thus offers a natural explanation for the formation of systems of coexisting rings and ringmoons from disrupted parent bodies.

  16. Self-sustained strong mass transfer without Roche lobe overflow - Cygnus X-3

    NASA Technical Reports Server (NTRS)

    Tavani, Marco; Ruderman, Malvin; Shaham, Jacob

    1989-01-01

    It is proposed that the binary evolution of Cyg X-3 is driven by a self-excited wind from a solar composition companion star sustained by radiation from a neutron star primary. Observations would then imply that the companion is a white dwarf underfilling its Roche lobe, with mass between 0.01 and 0.03 solar masses. Cyg X-3 could then be in the late stage of very low mass X-ray binary evolution expected to result in a millisecond pulsar binary similar to the eclipsing system PSR 1957 + 20.

  17. Self-sustained strong mass transfer without Roche lobe overflow - Cygnus X-3

    NASA Astrophysics Data System (ADS)

    Tavani, Marco; Ruderman, Malvin; Shaham, Jacob

    1989-07-01

    It is proposed that the binary evolution of Cyg X-3 is driven by a self-excited wind from a solar composition companion star sustained by radiation from a neutron star primary. Observations would then imply that the companion is a white dwarf underfilling its Roche lobe, with mass between 0.01 and 0.03 solar masses. Cyg X-3 could then be in the late stage of very low mass X-ray binary evolution expected to result in a millisecond pulsar binary similar to the eclipsing system PSR 1957 + 20.

  18. Thermal waters as cosmeceuticals: La Roche-Posay thermal spring water example

    PubMed Central

    Seite, Sophie

    2013-01-01

    The curative use of thermal spring water is well known, but further investigation of its biological properties and therapeutic benefits is necessary. This present article reports all available scientific data concerning La Roche-Posay Thermal Spring Water and provides a better understanding of the biological mechanism of action of this water in regard to its composition and physicochemical properties and its clinical benefits for patients. These data justify the use of this selenium-rich water as an active or “cosmeceutical” ingredient in topical formulations to increase quality of life and compliance in patients with chronic disease. PMID:23345985

  19. Performance evaluation of the Sysmex Cystatin C assay on the Roche Modular P Analyzer.

    PubMed

    He, Min; Ke, Pei-Feng; Xu, Jian-Hua; Chen, Wei-Ye; Lin, Hai-Biao; Zhang, Cheng; Wang, Yun-Xiu; Zhuang, Jun-Hua; Huang, Xian-Zhang

    2016-08-01

    Serum Cystatin C (CysC) is a promising endogenous marker for estimation of glomerular filtration rate. This study evaluated the analytical performance of the Sysmex CysC assay on the Roche Modular P Chemistry Analyzer (Modular P). The evaluation of imprecision, linearity, recovery, and interference were performed in accordance with the relevant Clinical and Laboratory Standards Institute guidelines protocols, using quality controls and patient samples. Comparison studies were conducted against the Siemens and Roche assay for CysC. At CysC concentrations of 0.45 and 1.80mg/L, the within-run coefficient of variations (CVs) were 2.81% and 2.04%, respectively, and the between-run CVs were 3.14% and 3.26%. The CysC assay was proven throughout the measuring range from 0.10 to 8.00mg/L. Good correlations were achieved among the 3 CysC assays. The Sysmex assay appeared to report higher results than the Siemens assay. No interference was detected from hemoglobin 5g/L, bilirubin (free or conjugated) 200mg/L, or chyle 1500 formazin turbidity units. The Sysmex CysC assay performed well with regard to basic performance, including precision, dilution linearity, and effects of interfering substances, and is an acceptable assay for the determination of CysC on the Modular P. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  20. [THE CULT OF ST. ROCH IN CASTELLI (ABRUZZO) AND THE EARTHENWARE ANATOMICAL EX VOTO].

    PubMed

    Bencivenga, Alessandro; Di Luigi, Gianluca

    2015-01-01

    Ex voto are devotional objects, widely used in Italy as a form of prayer or wish, or as thanksgiving for a grace received. In a broader historical perspective, votive offerings are hung in Greek, Etruscan, Roman shrines and later in churches or to show gratitude for miracles obtained, healing from illness or infirmity, or as a simple supplication and prayer. The ex voto here presented seem to be unique in the world: made of majolica, they come from the church of St. Roch in Castelli (Abruzzo). They depict breast benign and malignant lesions (mastitis, abscess, fat necrosis, inflammatory cancer, infiltrating carcinoma) in three dimensions, performing an accurate and personalized portrait of breast diseases (in some cases with the depicted name of the sick woman), showing fine details of each disease, and demonstrating accurate knowledge of the female anatomy and pathology.

  1. Roche tomography of cataclysmic variables - V. A high-latitude starspot on RU Pegasi

    NASA Astrophysics Data System (ADS)

    Dunford, A.; Watson, C. A.; Smith, Robert Connon

    2012-06-01

    We present Roche tomograms of the secondary star in the dwarf nova system RU Pegasi derived from blue- and red-arm ISIS data taken on the 4.2-m William Herschel Telescope. We have applied the entropy landscape technique to determine the system parameters and obtained component masses of M1= 1.06 M⊙, M2= 0.96 M⊙, an orbital inclination angle of i= 43° and an optimal systemic velocity of γ= 7 km s-1. These are in good agreement with previously published values. Our Roche tomograms of the secondary star show prominent irradiation of the inner Lagrangian point due to illumination by the disc and/or bright spot, which may have been enhanced as RU Peg was in outburst at the time of our observations. We find that this irradiation pattern is axisymmetric and confined to regions of the star which have a direct view of the accretion regions. This is in contrast to previous attempts to map RU Peg which suggested that the irradiation pattern was non-symmetric and extended beyond the terminator. We also detect additional inhomogeneities in the surface distribution of stellar atomic absorption that we ascribe to the presence of a large starspot. This spot is centred at a latitude of ˜82° and covers approximately 4 per cent of the total surface area of the secondary. In keeping with the high-latitude spots mapped on the cataclysmic variables (CVs) AE Aqr and BV Cen, the spot on RU Peg also appears slightly shifted towards the trailing hemisphere of the star. Finally, we speculate that early mapping attempts which indicated non-symmetric irradiation patterns which extended beyond the terminator of CV donors could possibly be explained by a superposition of symmetric heating and a large spot.

  2. A New Model of Roche Lobe Overflow for Short-period Gaseous Planets and Binary Stars

    NASA Astrophysics Data System (ADS)

    Jackson, Brian; Arras, Phil; Penev, Kaloyan; Peacock, Sarah; Marchant, Pablo

    2017-02-01

    Some close-in gaseous exoplanets are nearly in Roche lobe contact, and previous studies show that tidal decay can drive hot Jupiters into contact during the main sequence of their host stars. Improving on a previous model, we present a revised model for mass transfer in a semidetached binary system that incorporates an extended atmosphere around the donor and allows for an arbitrary mass ratio. We apply this new formalism to hypothetical, confirmed, and candidate planetary systems to estimate mass-loss rates and compare with models of evaporative mass loss. Overflow may be significant for hot Neptunes out to periods of ˜2 days, while for hot Jupiters, it may only be important inward of 0.5 days. We find that CoRoT-24 b may be losing mass at a rate of more than an Earth mass in a gigayear. The hot Jupiter WASP-12 b may lose an Earth mass in a megayear, while the putative planet PTFO8-8695 orbiting a T Tauri star might shed its atmosphere in a few megayears. We point out that the orbital expansion that can accompany mass transfer may be less effective than previously considered because the gas accreted by the host star removes some of the angular momentum from the orbit, but simple scaling arguments suggest that the Roche lobe overflow might remain stable. Consequently, the recently discovered small planets in ultrashort periods (<1 day) may not be the remnants of hot Jupiters/Neptunes. The new model presented here has been incorporated into Modules for Experiments in Stellar Astrophysics (MESA).

  3. Racialized Spaces in Teacher Discourse: A Critical Discourse Analysis of Place-Based Identities in Roche Bois, Mauritius

    ERIC Educational Resources Information Center

    Wiehe, Elsa M.

    2013-01-01

    This eleven-month ethnographic study puts critical discourse analysis in dialogue with postmodern conceptualizations of space and place to explore how eight educators talk about space and in the process, produce racialized spaces in Roche Bois, Mauritius. The macro-historical context of racialization of this urban marginalized community informs…

  4. Racialized Spaces in Teacher Discourse: A Critical Discourse Analysis of Place-Based Identities in Roche Bois, Mauritius

    ERIC Educational Resources Information Center

    Wiehe, Elsa M.

    2013-01-01

    This eleven-month ethnographic study puts critical discourse analysis in dialogue with postmodern conceptualizations of space and place to explore how eight educators talk about space and in the process, produce racialized spaces in Roche Bois, Mauritius. The macro-historical context of racialization of this urban marginalized community informs…

  5. Numerical Simulations of Collisional Cascades at the Roche Limits of White Dwarf Stars

    NASA Astrophysics Data System (ADS)

    Kenyon, Scott J.; Bromley, Benjamin C.

    2017-08-01

    We consider the long-term collisional and dynamical evolution of solid material orbiting in a narrow annulus near the Roche limit of a white dwarf. With orbital velocities of 300 {km} {{{s}}}-1, systems of solids with initial eccentricity e≳ {10}-3 generate a collisional cascade where objects with radii r ≲ 100{--}300 {km} are ground to dust. This process converts 1-100 km asteroids into 1 μm particles in 102-106 yr. Throughout this evolution, the swarm maintains an initially large vertical scale height H. Adding solids at a rate \\dot{M} enables the system to find an equilibrium where the mass in solids is roughly constant. This equilibrium depends on \\dot{M} and {r}0, the radius of the largest solid added to the swarm. When {r}0 ≲ 10 km, this equilibrium is stable. For larger {r}0, the mass oscillates between high and low states; the fraction of time spent in high states ranges from 100% for large \\dot{M} to much less than 1% for small \\dot{M}. During high states, the stellar luminosity reprocessed by the solids is comparable to the excess infrared emission observed in many metallic line white dwarfs.

  6. Environmental risk assessment for the galenical formulation of solid medicinal products at Roche Basle, Switzerland.

    PubMed

    Hoerger, Corinne C; Dörr, Benno; Schlienger, Claude; Straubt, Jürg O

    2009-04-01

    An environmental risk assessment for losses to wastewater from galenical manufacturing at solid medicinal products at F. Hoffmann-La Roche in Basle, Switzerland, was performed based on an annual total materials balance. This balance resulted in a loss factor of 0.2% relative to the sum of all starting materials, which was later confirmed as valid by analysis for 1 specific active pharmaceutical ingredient (API). The initial risk assessment for all 25 different APIs formulated resulted in no evident risk for the wastewater treatment plant, based on biodegradation no-effect data. However, based on acute ecotoxicity data, potential risk to the local receiving water, the River Rhine, was identified from 1 single API, the antibiotic sulfamethoxazole (SMX). A refinement of the risk assessment for SMX, based on chronic ecotoxicity data, or the predicted no-effect concentration (PNEC), and documented sewage works degradability, or the predicted environmental concentration (PEC), led to a significant decrease of the initial PEC/PNEC ratio to well below 1. In view of this refinement, the final conclusion is that the galenical production investigated poses no significant risk to the environment.

  7. Roche tomography of cataclysmic variables - VII. The long-term magnetic activity of AE Aqr

    NASA Astrophysics Data System (ADS)

    Hill, C. A.; Watson, C. A.; Steeghs, D.; Dhillon, V. S.; Shahbaz, T.

    2016-06-01

    We present a long-term study of the secondary star in the cataclysmic variable AE Aqr, using Roche tomography to indirectly image starspots on the stellar surface spanning 8 years of observations. The seven maps show an abundance of spot features at both high and low latitudes. We find that all maps have at least one large high-latitude spot region, and we discuss its complex evolution between maps, as well as its compatibility with current dynamo theories. Furthermore, we see the apparent growth in fractional spot coverage, fs, around 45° latitude over the duration of observations, with a persistently high fs near latitudes of 20°. These bands of spots may form as part of a magnetic activity cycle, with magnetic flux tubes emerging at different latitudes, similar to the `butterfly' diagram for the Sun. We discuss the nature of flux tube emergence in close binaries, as well as the activity of AE Aqr in the context of other stars.

  8. Structures in the D ring and Roche division tied to asymmetries in Saturn's magnetosphere

    NASA Astrophysics Data System (ADS)

    Chancia, Robert O.; Hedman, Matthew M.; Carter, Brian

    2016-10-01

    Saturn's dusty rings contain multiple patterns that appear to be rotating around the planet at about the same rate as Saturn itself, and so are probably generated by resonances with asymmetries in the planet's gravitational or magnetic fields. These structures are found in the D ring (which lies interior to the main rings) and in the Roche Division (which is located just outside the main rings, between the A and F rings). In 2007 the strongest patterns in both of these regions appeared to track magnetospheric anomalies associated with the Saturn Kilometric Radiation (SKR). This implied that these rings were responding to structures in the planet's magnetosphere, which is not unreasonable since the particles in both these ring regions are very small and therefore sensitive to non-gravitational forces. Over the last few years, the frequencies of the SKR and related magnetospheric asymmetries have shifted, and we have observed some changes in the ring patterns that might be connected with these shifts. However, there are also patterns in these rings that appear to have more stable rotation rates and so could reflect more persistent asymmetries in Saturn's magnetosphere. These patterns can therefore provide novel insights into the structure and evolution of Saturn's magnetosphere.

  9. Robotic Enrichment Processing of Roche 454 Titanium Emlusion PCR at the DOE Joint Genome Institute

    SciTech Connect

    Hamilton, Matthew; Wilson, Steven; Bauer, Diane; Miller, Don; Duffy-Wei, Kecia; Hammon, Nancy; Lucas, Susan; Pollard, Martin; Cheng, Jan-Fang

    2010-05-28

    Enrichment of emulsion PCR product is the most laborious and pipette-intensive step in the 454 Titanium process, posing the biggest obstacle for production-oriented scale up. The Joint Genome Institute has developed a pair of custom-made robots based on the Microlab Star liquid handling deck manufactured by Hamilton to mediate the complexity and ergonomic demands of the 454 enrichment process. The robot includes a custom built centrifuge, magnetic deck positions, as well as heating and cooling elements. At present processing eight emulsion cup samples in a single 2.5 hour run, these robots are capable of processing up to 24 emulsion cup samples. Sample emulsions are broken using the standard 454 breaking process and transferred from a pair of 50ml conical tubes to a single 2ml tube and loaded on the robot. The robot performs the enrichment protocol and produces beads in 2ml tubes ready for counting. The robot follows the Roche 454 enrichment protocol with slight exceptions to the manner in which it resuspends beads via pipette mixing rather than vortexing and a set number of null bead removal washes. The robotic process is broken down in similar discrete steps: First Melt and Neutralization, Enrichment Primer Annealing, Enrichment Bead Incubation, Null Bead Removal, Second Melt and Neutralization and Sequencing Primer Annealing. Data indicating our improvements in enrichment efficiency and total number of bases per run will also be shown.

  10. Spurious hemolysis does not influence the reliability of digoxin testing on Siemens RXL MAX and Roche Cobas e601.

    PubMed

    Lippi, Giuseppe; Mercadanti, Mariella; Romero, Araelsis; Lipreri, Graziella; Salvagno, Gian Luca; Guidi, Gian Cesare

    2012-01-01

    Little information is available on the influence of spurious hemolysis on digoxin immunoassays. Seventeen consecutive, non-hemolyzed, sodium-heparin samples were divided in three aliquots. The first was immediately centrifuged and tested for hemolysis index (HI), as well as plasma digoxin on Siemens RXL MAX using the Siemens Dimension Flex and Roche Cobas e601 by electrochemiluminescent (ECLIA) technique. The second and third aliquots were subjected to mechanical hemolysis by aspirating the blood one and two times through a thin needle. The concentration of digoxin measured on Siemens RXL MAX was significantly decreased from aliquot #A, to aliquot #B (-4%), and aliquot #C (-6%), but in none of the hemolyzed specimens the 10% bias was exceeded. No significant variation was observed by measuring plasma digoxin on Roche Cobas.

  11. Analytical performance evaluation of a particle-enhanced turbidimetric cystatin C assay on the Roche COBAS 6000 analyzer.

    PubMed

    Conde-Sánchez, Manuel; Roldán-Fontana, Esther; Chueca-Porcuna, Natalia; Pardo, Susana; Porras-Gracia, Juan

    2010-07-01

    Cystatin C is a low molecular protein that has been proposed to estimate the glomerular filtration rate. Here we investigated the performance of the Roche cystatin C assay on the COBAS 6000 analyzer. We studied the imprecision, recovery, limit of detection and quantification, linearity and interferences. For method comparison, split sample aliquots were assayed using the described method and a Siemens cystatin C assay. The assay displayed a low total imprecision and a good linearity over the entire range tested. Bilirubin and triglycerides did not interfere with the assay, and only a haemoglobin concentration higher than 6g/dl interfered with the assay. The assay agreed well with the Siemens assay. The Roche cystatin C assay is an acceptable method for determining the cystatin C and the glomerular filtration rate estimate. On a COBAS 6000, the assay improves and simplifies the laboratory's workload. Copyright 2010 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  12. Elevated ethyl methanesulfonate (EMS) in nelfinavir mesylate (Viracept®, Roche): overview

    PubMed Central

    Pozniak, Anton; Müller, Lutz; Salgo, Miklos; Jones, Judith K; Larson, Peter; Tweats, David

    2009-01-01

    Roche's protease inhibitor nelfinavir mesylate (Viracept®) produced between March 2007-June 2007 was found to contain elevated levels of ethyl methanesulfonate (EMS), a known mutagen (alkylator) – leading to a global recall of the drug. EMS levels in a daily dose (2,500 mg Viracept/day) were predicted not to exceed a dose of ~2.75 mg/day (~0.055 mg/kg/day based on 50 kg patient). As existing toxicology data on EMS did not permit an adequate patient risk assessment, a comprehensive animal toxicology evaluation of EMS was conducted. General toxicity of EMS was investigated in rats over 28 days. Two studies for DNA damage were performed in mice; chromosomal damage was assessed using a micronucleus assay and gene mutations were detected using the MutaMouse transgenic model. In addition, experiments designed to extrapolate animal exposure to humans were undertaken. A general toxicity study showed that the toxicity of EMS occurred only at doses ≥ 60 mg/kg/day, which is far above that received by patients. Studies for chromosomal damage and mutations in mice demonstrated a clear threshold effect with EMS at 25 mg/kg/day, under chronic dosing conditions. Exposure analysis (Cmax) demonstrated that ~370-fold higher levels of EMS than that ingested by patients, are needed to saturate known, highly conserved, error-free, mammalian DNA repair mechanisms for alkylation. In summary, animal studies suggested that patients who took nelfinavir mesylate with elevated levels of EMS are at no increased risk for carcinogenicity or teratogenicity over their background risk, since mutations are prerequisites for such downstream events. These findings are potentially relevant to >40 marketed drugs that are mesylate salts. PMID:19660105

  13. Roche tomography of cataclysmic variables - VI. Differential rotation of AE Aqr - not tidally locked!

    NASA Astrophysics Data System (ADS)

    Hill, C. A.; Watson, C. A.; Shahbaz, T.; Steeghs, D.; Dhillon, V. S.

    2014-10-01

    We present Roche tomograms of the K4V secondary star in the cataclysmic variable AE Aqr, reconstructed from two data sets taken 9 d apart, and measure the differential rotation of the stellar surface. The tomograms show many large, cool starspots, including a large high-latitude spot and a prominent appendage down the trailing hemisphere. We find two distinct bands of spots around 22° and 43° latitude, and estimate a spot coverage of 15.4-17 per cent on the Northern hemisphere. Assuming a solar-like differential rotation law, the differential rotation of AE Aqr was measured using two different techniques. The first method yields an equator-pole lap time of 269 d and the second yields a lap time of 262 d. This shows that the star is not fully tidally locked, as was previously assumed for CVs, but has a co-rotation latitude of ˜40°. We discuss the implications that these observations have on stellar dynamo theory, as well as the impact that spot traversal across the L1 point may have on accretion rates in CVs as well as some of their other observed properties. The entropy landscape technique was applied to determine the system parameters of AE Aqr. For the two independent data sets, we find M1 = 1.20 and 1.17 M⊙, M2 = 0.81 and 0.78 M⊙, and orbital inclinations of 50° to 51° at optimal systemic velocities of γ = -64.7 and -62.9 km s-1.

  14. Roche tomography of cataclysmic variables - IV. Star-spots and slingshot prominences on BV Cen

    NASA Astrophysics Data System (ADS)

    Watson, C. A.; Steeghs, D.; Shahbaz, T.; Dhillon, V. S.

    2007-12-01

    We present Roche tomograms of the G5-G8 IV/V secondary star in the long-period cataclysmic variable BV Cen reconstructed from Magellan Inamori Kyocera Echelle spectrograph echelle data taken on the Magellan Clay 6.5-m telescope. The tomograms show the presence of a number of large, cool star-spots on BV Cen for the first time. In particular, we find a large high-latitude spot which is deflected from the rotational axis in the same direction as seen on the K3-K5 IV/V secondary star in the cataclysmic variable AE Aqr. BV Cen also shows a similar relative paucity of spots at latitudes between 40° and 50° when compared with AE Aqr. Furthermore, we find evidence for an increased spot coverage around longitudes facing the white dwarf which supports models invoking star-spots at the L1 point to explain the low states observed in some cataclysmic variables. In total, we estimate that some 25 per cent of the Northern hemisphere of BV Cen is spotted. We also find evidence for a faint, narrow, transient emission line with characteristics reminiscent of the peculiar low-velocity emission features observed in some outbursting dwarf novae. We interpret this feature as a slingshot prominence from the secondary star and derive a maximum source size of 75000 km and a minimum altitude of 160000 km above the orbital plane for the prominence. The entropy landscape technique was applied to determine the system parameters of BV Cen. We find M1 = 1.18 +/-0.280.16Msolar and M2 = 1.05 +/-0.230.14Msolar and an orbital inclination of i = 53° +/- 4° at an optimal systemic velocity of γ = -22.3 km s-1. Finally, we also report on the previously unknown binarity of the G5IV star HD 220492.

  15. Tidal decay and stable Roche-lobe overflow of short-period gaseous exoplanets

    NASA Astrophysics Data System (ADS)

    Jackson, Brian; Jensen, Emily; Peacock, Sarah; Arras, Phil; Penev, Kaloyan

    2016-11-01

    Many gaseous exoplanets in short-period orbits are on the verge or are in the process of Roche-lobe overflow (RLO). Moreover, orbital stability analysis shows tides can drive many hot Jupiters to spiral inevitably toward their host stars. Thus, the coupled processes of orbital evolution and RLO likely shape the observed distribution of close-in exoplanets and may even be responsible for producing some of the short-period rocky planets. However, the exact outcome for an overflowing planet depends on its internal response to mass loss, and the accompanying orbital evolution can act to enhance or inhibit RLO. In this study, we apply the fully-featured and robust Modules for Experiments in Stellar Astrophysics suite to model RLO of short-period gaseous planets. We show that, although the detailed evolution may depend on several properties of the planetary system, it is largely determined by the core mass of the overflowing gas giant. In particular, we find that the orbital expansion that accompanies RLO often stops and reverses at a specific maximum period that depends on the core mass. We suggest that RLO may often strand the remnant of a gas giant near this orbital period, which provides an observational prediction that can corroborate the hypothesis that short-period gas giants undergo RLO. We conduct a preliminary comparison of this prediction to the observed population of small, short-period planets and find some planets in orbits that may be consistent with this picture. To the extent that we can establish some short-period planets are indeed the remnants of gas giants, that population can elucidate the properties of gas giant cores, the properties of which remain largely unconstrained.

  16. Assessment of viral loads in patients with chronic hepatitis C with AMPLICOR HCV MONITOR version 1.0, COBAS HCV MONITOR version 2.0, and QUANTIPLEX HCV RNA version 2.0 assays.

    PubMed

    Martinot-Peignoux, M; Le Breton, V; Fritsch, S; Le Guludec, G; Labouret, N; Keller, F; Marcellin, P

    2000-07-01

    The correlation between response to antiviral therapy and pretreatment viral load in patients with chronic hepatitis C has prompted the development of quantitative assays to measure viral load. The aim of our study was to assess the clinical relevance of the newly developed semiautomated PCR system COBAS HCV MONITOR version 2.0 in comparison with (i) the AMPLICOR HCV MONITOR version 1.0 assay, which underestimates RNA concentration of hepatitis C virus (HCV) genotypes 2 to 6, and (ii) the QUANTIPLEX HCV RNA version 2.0 assay, which achieves equivalent quantification for each HCV genotype, with samples from 174 patients diagnosed with chronic hepatitis C before therapy. The level and range of quantification measured with AMPLICOR HCV MONITOR version 1.0 were 1 log lower than when measured with the COBAS HCV MONITOR version 2.0, at 0.261 x 10(6) RNA copies/ml (range, 0.001 x 10(6) to 2.50 x 10(6) RNA copies/ml) and 4.032 x 10(6) RNA copies/ml (range, 0.026 x 10(6) to 72.6 x 10(6) RNA copies/ml), respectively. The two assays showed a poor correlation (r(2) = 0.175). The level and range of quantification were similar when measured with the COBAS HCV MONITOR version 2.0 and QUANTIPLEX HCV RNA version 2.0 assays, at 3.03 x 10(6) RNA copies/ml (range, 0.023 x 10(6) to 72.6 x 10(6) RNA copies/ml) and 4.91 Meq/ml (range, 0.200 to 49.5 Meq/ml), respectively. The two assays showed a strong correlation (r(2) = 0. 686) for each HCV genotype. The duration of treatment (6 or 12 months) is modulated according to HCV genotype and viral load. Our results indicate that COBAS HCV MONITOR version 2.0 and QUANTIPLEX HCV RNA version 2.0 assays showing an equal dynamic range for each HCV genotype are suitable tools to assess patients before therapy.

  17. An in-house real-time polymerase chain reaction: standardisation and comparison with the Cobas Amplicor HBV monitor and Cobas AmpliPrep/Cobas TaqMan HBV tests for the quantification of hepatitis B virus DNA

    PubMed Central

    Santos, Ana Paula de Torres; Levi, José Eduardo; Lemos, Marcilio Figueiredo; Calux, Samira Julien; Oba, Isabel Takano; Moreira, Regina Célia

    2016-01-01

    This study aimed to standardise an in-house real-time polymerase chain reaction (rtPCR) to allow quantification of hepatitis B virus (HBV) DNA in serum or plasma samples, and to compare this method with two commercial assays, the Cobas Amplicor HBV monitor and the Cobas AmpliPrep/Cobas TaqMan HBV test. Samples from 397 patients from the state of São Paulo were analysed by all three methods. Fifty-two samples were from patients who were human immunodeficiency virus and hepatitis C virus positive, but HBV negative. Genotypes were characterised, and the viral load was measure in each sample. The in-house rtPCR showed an excellent success rate compared with commercial tests; inter-assay and intra-assay coefficients correlated with commercial tests (r = 0.96 and r = 0.913, p < 0.001) and the in-house test showed no genotype-dependent differences in detection and quantification rates. The in-house assay tested in this study could be used for screening and quantifying HBV DNA in order to monitor patients during therapy. PMID:26872342

  18. Selected performance characteristics of the Roche Elecsys testosterone II assay on the Modular analytics E 170 analyzer.

    PubMed

    Owen, William E; Rawlins, Mindy L; Roberts, William L

    2010-08-05

    Serum testosterone measurements have utility in diagnosis of clinical conditions characterized by both increased and decreased testosterone concentrations. Studies have indicated that testosterone immunoassays may give inaccurate results for women and children. We evaluated the performance of a second generation testosterone immunoassay from Roche Diagnostics. Testo II performed on a Modular Analytics E 170 analyzer is an automated random access electrochemiluminometric assay. We evaluated limit of blank (LoB), imprecision, linearity, interference, and method comparison with liquid chromatography-tandem mass spectrometry assay (LC-MS/MS). Method comparison included the current generation Roche testosterone assay (Testo I) and the Access 2 testosterone chemiluminometric assay (Beckman Coulter). Results for men and women were analyzed for analytic concordance. The relative % differences of immunoassay compared to LC-MS/MS results were evaluated. The LoB was 0.07nmol/l. Total imprecision was <6%. The assay was linear from 0.2 to 46.6nmol/l. Negative interference was observed for lipemia at concentrations >22.5g/l. Analytic concordance showed improved specificity for women. Comparison of results to LC-MS/MS indicated comparable performance with other immunoassays for men and improved performance for women, boys, and girls with mean differences of 0.5%, -0.7%, and 24.4%, respectively. The Roche Testo II assay demonstrated excellent precision. Comparison to 2 other automated immunoassays showed comparable performance for men and improved performance for women and children. However, challenges still exist for quantifying testosterone concentrations <10.4nmol/l for men and <1.7nmol/l for women and children by immunoassay. Copyright 2010 Elsevier B.V. All rights reserved.

  19. Glucose meters: evaluation of the new formulation measuring strips from Roche (Accu-Chek) and Abbott (MediSense).

    PubMed

    Dimeski, G; Jones, B W; Tilley, V; Greenslade, M N; Russell, A W

    2010-07-01

    Both Roche and Abbott have released new glucose meter strips. They supply the entire Australian hospital market. The present study compared the performance of the new strips utilizing various specimen types (capillary, venous lithium heparin whole blood, venous lithium heparin plasma and serum) and evaluated how well they comply with the International Standards Organization (ISO) 15197 criteria. The study included imprecision, patient comparison and interference studies. Participants with and without diabetes were recruited to evaluate the performance of various specimen types against the Beckman DxC800 glucose method. The strips were tested for different interferences: galactose, maltose, lactose, Icodextrin, Intragam, paracetamol, sodium, ascorbic acid, variable strip storage temperature, haematocrit, haemolysis and lipaemia. The imprecision of the two strips was approximately 5% or less, except for the Abbott strip at very low values (1.4 mmol/L), approximately 7%. In total, 78% and 84%, respectively, of the results from the finger prick capillary specimens with the Roche (Accu-Chek Performa meter) and Abbott (Optium Xceed meter) strips, not 95% or greater as recommended by the ISO guideline, were within the recommended limits compared with reference plasma estimation on laboratory analysers. Galactose, ascorbic acid, haematocrit and sodium on the Roche and ascorbic acid and haematocrit on the Abbott strip continue to interfere to a variable degree with the glucose measurement. Analytically small differences exist between the glucose meter strips. The most significant analytical difference with the strips was at low glucose levels when compared with laboratory analyses and this may be of clinical importance. The impact of some of the interferences is variable between the two strips. Individuals, health-care professionals and health-care institutions should consider these data when selecting glucose meters for the management of people with diabetes mellitus.

  20. A Comparison of the Roche Cobas HPV Test With the Hybrid Capture 2 Test for the Detection of High-Risk Human Papillomavirus Genotypes.

    PubMed

    Levi, Angelique W; Bernstein, Jane I; Hui, Pei; Duch, Kara; Schofield, Kevin; Chhieng, David C

    2016-02-01

    All Food and Drug Administration-approved methods in the United States for human papillomavirus testing including the Hybrid Capture 2 human papillomavirus assay and the Roche cobas human papillomavirus test are approved for cytology specimens collected into ThinPrep media but not for specimens collected into SurePath solution. To compare the performance of the Roche cobas and Hybrid Capture 2 tests for the detection of high-risk human papillomavirus using both ThinPrep and SurePath preparations as part of a validation study. One thousand three hundred seventy-one liquid-based cytology samples, including 1122 SurePath and 249 ThinPrep specimens, were tested for high-risk human papillomavirus DNA using the Roche cobas human papillomavirus test and the Hybrid Capture 2 human papillomavirus assay. For cases with discrepant results, confirmatory testing was performed using Linear Array human papillomavirus testing. One hundred and fifty-six (11.38%) and 184 (13.42%) of the 1371 specimens tested positive for high-risk human papillomavirus DNA using the Hybrid Capture 2 human papillomavirus assay and Roche cobas human papillomavirus assay, respectively. In addition, 1289 (94.0%) of 1371 specimens demonstrated concordant high-risk human papillomavirus results with a κ value of 0.72 (95% confidence interval, 065-0.78). There was no statistically significant difference in the percentage of positive high-risk human papillomavirus results between the 2 liquid-based preparations with either assay. Discordant results between the 2 assays were noted in 82 of 1371 cases (6%). Twenty-seven of 82 cases (32.9%) were Hybrid Capture 2 positive/Roche cobas negative and 55 of 82 cases (67.1%) were Roche cobas positive/Hybrid Capture 2 negative. Two of 20 Hybrid Capture 2-positive/Roche cobas-negative cases (10%) and 26 of 37 Roche cobas-positive/Hybrid Capture 2-negative cases (70%) tested positive for high-risk human papillomavirus by Linear Array. Both assays showed good agreement

  1. CCD Photometry and Roche Modeling of the Eclipsing Overcontact Binary Star System TYC 01963-0488-1

    NASA Astrophysics Data System (ADS)

    Alton, K. B.

    2016-12-01

    TYC 01963-0488-1 (ASAS J094440+2632.1) is a W UMa binary system (P=0.427036 d) which has been largely overlooked since first being detected nearly 15 years ago by the ROTSE-I telescope. Other than the monochromatic ROTSE-I survey data, no multi-colored light curves (LC) have been published. Photometric data collected in three bandpasses (B, V and Ic) at UnderOak Observatory (UO) produced 5 new times-of-minimum for TYC 01963-0488-1 which were used to establish a linear ephemeris from the first Min I epoch (HJD0). No published radial velocity data are available for this system; however, since this W UMa binary undergoes very obvious total eclipses, Roche modeling yielded a well-constrained photometric value for q ( 0.25). There is a suggestion from the ROTSE-I data and new results herein that Max II is more variable than Max I. Therefore, Roche model fits for the TYC 01963-0488-1 LCs collected in 2015 were assessed with and without spots.

  2. Effect of specimen type on free immunoglobulin light chains analysis on the Roche Diagnostics cobas 8000 analyzer.

    PubMed

    Nelson, Louis S; Steussy, Bryan; Morris, Cory S; Krasowski, Matthew D

    2015-01-01

    The measurement of free immunoglobulin light chains is typically performed on serum; however, the use of alternative specimen types has potential benefits. Using the Freelite™ kappa and lambda free light chains assay on a Roche Diagnostics cobas 8000 c502 analyzer, we compared three specimen types (serum, EDTA-plasma and lithium heparin plasma separator gel-plasma) on 100 patients. Using Deming regression and eliminating outliers (limiting data to light chain concentrations below 400 mg/L), the three specimen types showed comparable results for kappa light chain concentration, lambda light chain concentration, and kappa/lambda ratio with slopes close to 1.0 and y-intercepts close to zero. EDTA-plasma showed slightly more positive bias relative to serum than lithium heparin. Analysis using EDTA-plasma and lithium heparin plasma showed comparable linearity, precision, and temperature stability. A single sample showing hook effect (not in the comparison set) gave comparable results using either plasma specimen type. For the Freelite™ kappa and lambda free light chains assay, both EDTA-plasma or lithium heparin-plasma can serve as acceptable substitutes for serum, at least for the Roche cobas 8000 analyzer.

  3. Profile of the Roche cobas® EGFR mutation test v2 for non-small cell lung cancer.

    PubMed

    Malapelle, Umberto; Sirera, Rafael; Jantus-Lewintre, Eloísa; Reclusa, Pablo; Calabuig-Fariñas, Silvia; Blasco, Ana; Pisapia, Pasquale; Rolfo, Christian; Camps, Carlos

    2017-03-01

    The discovery of driver mutations in non-small cell lung cancer (NSCLC) has led to the development of genome-based personalized medicine. Fifteen to 20% of adenocarcinomas harbor an epidermal growth factor receptor (EGFR) activating mutation associated with responses to EGFR tyrosine kinase inhibitors (TKIs). Individual laboratories' expertise and the availability of appropriate equipment are valuable assets in predictive molecular pathology, although the choice of methods should be determined by the nature of the samples to be tested and whether the detection of only well-characterized EGFR mutations or rather, of all detectable mutations, is required. Areas covered: The EGFR mutation testing landscape is manifold and includes both screening and targeted methods, each with their own pros and cons. Here we review one of these companion tests, the Roche cobas® EGFR mutation test v2, from a methodological point of view, also exploring its liquid-biopsy applications. Expert commentary: The Roche cobas® EGFR mutation test v2, based on real time RT-PCR, is a reliable option for testing EGFR mutations in clinical practice, either using tissue-derived DNA or plasma-derived cfDNA. This application will be valuable for laboratories with whose purpose is purely diagnostic and lacking high-throughput technologies.

  4. Comparison of clinical performances among Roche Cobas HPV, RFMP HPV PapilloTyper and Hybrid Capture 2 assays for detection of high-risk types of human papillomavirus.

    PubMed

    Yu, Shinae; Kwon, Min-Jung; Lee, Eun Hee; Park, Hyosoon; Woo, Hee-Yeon

    2015-09-01

    The cervical cancer screening guidelines suggest that early detection of HPV16 and HPV18 is helpful for identifying women with cervical intraepithelial neoplasia (CIN) grade two or higher. We comparatively evaluated three HPV DNA assays, Roche Cobas HPV, RFMP HPV PapilloTyper, and Hybrid Capture 2 (HC2). A total of 861 cervical swab samples from women over 30 years of age were classified into two groups, that is, high grade squamous intraepithelial lesion (HSIL) and non-HSIL, according to cervical cytology results and analyzed by three assays. The results of direct sequencing or Linear array HPV genotyping test were considered true when the three assays presented discrepancies. The concordance rates between Roche Cobas HPV versus RFMP HPV PapilloTyper, RFMP HPV PapilloTyper versus HC2, and Roche Cobas versus HC2 were 94.5%, 94.3%, and 95.9%, respectively. For detection of HPV16 and HPV18, Roche Cobas HPV showed the concordance rates of 98.3% (κ = 0.73) and 99.4% (κ = 0.40) with the confirmation tests, respectively; and RFMP HPV PapilloTyper showed the concordance rates of 99.5% (κ = 0.92) and 100.0% (κ = 1.00), respectively. In conclusion, Roche Cobas HPV, RFMP HPV PapilloTyper, and HC2 showed high agreement rates. Roche Cobas HPV and RFMP HPV PapilloTyper are particularly useful, since both provide HPV specific genotypes, HPV16 and HPV18. © 2015 Wiley Periodicals, Inc.

  5. On a model for the evolution of a mass-conservative circular binary system by Roche lobe overflow and by emission of gravitational waves

    NASA Astrophysics Data System (ADS)

    Chia, T. T.

    1999-11-01

    In some ranges of mass ratio and mass-radius exponent, it is shown that there are inconsistencies in Faulkner's (1971) analytic model of a mass-conservative circular binary system that is evolving via the combined processes of mass exchange through Roche lobe overflow and emission of gravitational waves. These inconsistencies occur because of the use of an assumption that the time derivative of the Roche lobe radius is equal to that of the stellar radius. Consequently, his equations for the rate of mass exchange and orbital period variations are generally invalid.

  6. Skin Microbiome in Patients With Psoriasis Before and After Balneotherapy at the Thermal Care Center of La Roche-Posay.

    PubMed

    Martin, Richard; Henley, Jessica B; Sarrazin, Patrick; Seité, Sophie

    2015-12-01

    Changes in the composition of microbial communities that colonize skin have been linked to several diseases including psoriasis. Nevertheless, the intra-individual dynamics and how these communities respond to balneotherapy remain poorly understood. This open label study was conducted between July and September 2012. Microbial communities of patients with psoriasis vulgaris were characterized prior and post a 3-week selenium-rich water balneotherapy treatment at the thermal care center La Roche-Posay (La Roche-Posay, France). Balneotherapy consisted of high-pressure filiform showers, baths, facial, and body spray treatments as well as La Roche-Posay thermal spring water (LRP-TSW) consumption. Swabs were taken from affected and proximal unaffected skin and the 16S rRNA bacterial gene was used to analyze the composition of bacterial communities. Using the same 16S rRNA gene tool, we tried to describe the LRP-TSW bacterial landscape. This study included 54 patients diagnosed with moderate to severe forms of psoriasis vulgaris. After eliminating individuals lacking paired samples from both visits, 29 individuals were analyzed for their microbiome profile. Shannon Diversity Index and global bacterial landscape indicate similar microbial communities on both unaffected and adjacent affected skin. PASI values decreased post-balneotherapy implying improvement of disease severity. No significant change in the Shannon Diversity Index was noticed at the end of the third week. The average taxonomic composition of skin microbial communities associated with unaffected and affected skin of psoriatic patients post-balneotherapy shows that treatment with LRP-TSW significantly increased the level of Xanthomonas genus and, to a lesser extent, Corynebacterium genus. The Xanthomonas genus belongs to the main Xanthomonadaceae family found in LRP-TSW and also on healthy skin. In psoriatic patients, a poor bacterial biodiversity was noticed and the bacterial communities were similar on

  7. High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform.

    PubMed

    Fordyce, Sarah L; Ávila-Arcos, Maria C; Rockenbauer, Eszter; Børsting, Claus; Frank-Hansen, Rune; Petersen, Frederik Torp; Willerslev, Eske; Hansen, Anders J; Morling, Niels; Gilbert, M Thomas P

    2011-08-01

    The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method in combination with a bioinformatic tool designed specifically to analyze sequence lengths and frequencies, we found that GS FLX STR sequence data are comparable to conventional capillary electrophoresis-based STR typing. Furthermore, we found DNA base substitutions and repeat sequence variations that would not have been identified using conventional STR typing.

  8. THE QUASI-ROCHE LOBE OVERFLOW STATE IN THE EVOLUTION OF CLOSE BINARY SYSTEMS CONTAINING A RADIO PULSAR

    SciTech Connect

    Benvenuto, O. G.; De Vito, M. A.

    2015-01-01

    We study the evolution of close binary systems formed by a normal (solar composition), intermediate-mass-donor star together with a neutron star. We consider models including irradiation feedback and evaporation. These nonstandard ingredients deeply modify the mass-transfer stages of these binaries. While models that neglect irradiation feedback undergo continuous, long-standing mass-transfer episodes, models including these effects suffer a number of cycles of mass transfer and detachment. During mass transfer, the systems should reveal themselves as low-mass X-ray binaries (LMXBs), whereas when they are detached they behave as binary radio pulsars. We show that at these stages irradiated models are in a Roche lobe overflow (RLOF) state or in a quasi-RLOF state. Quasi-RLOF stars have radii slightly smaller than their Roche lobes. Remarkably, these conditions are attained for an orbital period as well as donor mass values in the range corresponding to a family of binary radio pulsars known as ''redbacks''. Thus, redback companions should be quasi-RLOF stars. We show that the characteristics of the redback system PSR J1723-2837 are accounted for by these models. In each mass-transfer cycle these systems should switch from LMXB to binary radio pulsar states with a timescale of approximately one million years. However, there is recent and fast growing evidence of systems switching on far shorter, human timescales. This should be related to instabilities in the accretion disk surrounding the neutron star and/or radio ejection, still to be included in the model having the quasi-RLOF state as a general condition.

  9. Comparison of Roche MONITOR and Organon Teknika NucliSens assays to quantify human immunodeficiency virus type 1 RNA in cerebrospinal fluid.

    PubMed

    Spearman, P; Fiscus, S A; Smith, R M; Shepard, R; Johnson, B; Nicotera, J; Harris, V L; Clough, L A; McKinsey, J; Haas, D W

    2001-04-01

    We compared Roche MONITOR and Organon Teknika NucliSens assays for human immunodeficiency virus type 1 (HIV-1) RNA in cerebrospinal fluid (CSF). Results of 282 assays were highly correlated (r = 0.826), with MONITOR values being 0.29 +/- 0.4 log(10) copies/ml (mean +/- standard deviation) values. Both assays can reliably quantify HIV-1 RNA in CSF.

  10. Utility of the Roche Cobas 4800 for detection of high-risk human papillomavirus in formalin-fixed paraffin-embedded oropharyngeal squamous cell carcinoma.

    PubMed

    Pettus, Jason R; Wilson, Terri L; Steinmetz, Heather B; Lefferts, Joel A; Tafe, Laura J

    2017-02-01

    Clinical laboratories are expected to reliably identify human papilloma virus (HPV) associated oropharyngeal squamous cell carcinoma (OPSCC) for prognostic and potential therapeutic applications. In addition to surrogate p16 immunohistochemistry (IHC) testing, DNA-based HPV-specific testing strategies are widely utilized. Recognizing the efficiency of the Roche Cobas 4800 platform for testing gynecological cytology specimens for high-risk HPV, we elected to evaluate the potential utility of this platform for testing formalin-fixed paraffin-embedded (FFPE) OPSCC tissue. Using the Roche Linear Array assay for comparison, we tested twenty-eight samples (16 primary OPSCC, 2 lymph node metastases from primary OPSCC, 1 oral tongue carcinoma, 3 benign squamous papillomas, and 3 non-oropharyngeal carcinoma tissues). Excluding two invalid results, the Roche Cobas 4800 testing resulted in excellent inter-assay concordance (25/26, 96.2%) and 100% concordance for HPV-16/HPV-18 positive samples. This data suggests that the Roche Cobas 4800 platform may be a cost-effective method for testing OPSCC FFPE tissues in a clinical molecular pathology laboratory setting. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Performance of the Roche second generation hemoglobin A1c immunoassay in the presence of HB-S or HB-C traits.

    PubMed

    Abadie, Jude M; Koelsch, Angela A

    2008-01-01

    Blood HbA1c determination is a powerful tool for the evaluation and management of patients with diabetes mellitus. Many HbA1c analytical methods demonstrate bias in samples from patients with hemoglobinopathies. This study evaluated the analytical performance of Roche Diagnostics' 1st and 2nd generation HbA1c assays in patients with or without hemoglobinopathies whose HbA1c levels were elevated or normal, respectively. Boronate-affinity high performance liquid chromatography (HPLC) served as the reference method. Whole blood samples were collected from 80 patients with HbS or HbC whose group mean HbA1c value was elevated and also from 80 patients without hemoglobinopathy whose HbA1c values were in the well-controlled range. Each sample was assayed for HbA1c by the Primus boronate-affinity HPLC technique and by Roche's 1st and 2nd generation immunoassays using a Cobas Integra 800 analytical system. Results by the HPLC technique were compared with the results of both Roche assays by linear regression and Bland-Altman analysis. The 1st and 2nd generation assays yielded regression lines and correlation values vs HPLC assay of y = 1.43x - 1.59; R(2) = 0.83, and y = 0.94x + 0.10; R(2) = 0.92, respectively, in the 80 patients with hemoglobinopathies. The mean difference and the +/-2SD range were greater in the 1st than in the 2nd generation assay (2.68, +/-2.07 vs -0.54, +/-0.86, respectively). The 2nd generation assay also showed better performance than the 1st generation assay in samples from the 80 patients without hemoglobinopathy. In conclusion, this study validates the accuracy of Roche's 2nd generation assay, which is substantially improved over Roche's 1st generation HbA1c assay.

  12. Detection of genetically diverse human immunodeficiency virus type 1 group M and O isolates by PCR.

    PubMed Central

    Respess, R A; Butcher, A; Wang, H; Chaowanachan, T; Young, N; Shaffer, N; Mastro, T D; Biryahwaho, B; Downing, R; Tanuri, A; Schechter, M; Pascu, R; Zekeng, L; Kaptué, L; Gürtler, L; Eberle, J; Ellenberger, D; Fridlund, C; Rayfield, M; Kwok, S

    1997-01-01

    A panel of 136 genetically diverse group M and 5 group O adult isolates from outside the United States and Europe were evaluated by PCR with the Roche AMPLICOR HIV-1 test, a modified version of the AMPLICOR HIV-1 test, and a new primer pair/probe system. Detection of some of these isolates was less efficient with the AMPLICOR HIV-1 test; however, the assay was significantly improved by reducing the sample input and lowering the annealing temperature. The new primer pair/probe set detected 140 of 141 isolates, including the 5 group O isolates that were not detected with either of the AMPLICOR HIV-1 test formats. PMID:9114428

  13. [Cytological and virological medium performance and stability assessment using the Cobas 4800 HPV test (Roche Diagnostics) used in France].

    PubMed

    Khiri, Hacène; Camus, Claire; Portugal, Mireille; Pénaranda, Guillaume; Boyer, Stéphane; Halfon, Philippe

    2014-01-01

    Analytical and stability performances of ten media were compared to PreservCyt medium using the Cobas 4800 HPV test: Easyfix (Labonord SAS, France), Qualicyt (Qualicyt, France), NovaPrep HQ+ (NovaCyt, France), CMDH (SARL Alphapath France), Cyt-All (Cytomega, France), Digene Cervical Sampler (Qiagen, USA), Aptima (Gen-Probe, USA), Multi-Collect (Abbott, Allemagne), M4RT Micro Test (Remel, USA), et PCR-Media (Roche, Suisse). Most of media show a good correlation for all the performance characteristics studied. Cyt-All and NovaPrep HQ+ media are perfectly concordant with PreservCyt all parameters and genotypes considered. CMDH and M4RT have a reduced stability at +25°C (3 and 2 days respectively) and would not be conformed to current shipping practices. Most of media tested show analytical and stability performances equivalent with the reference medium. The prospects of such study are interesting because in the near future, providers would make available media adapted to the problem of cervical smear but also to the conservation, transport of virus or bacteria for performing simultaneous searches of HPV, Chlamydia trachomatis or Neisseria gonorrhea.

  14. Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes

    PubMed Central

    Becker, Ericka A.; Burns, Charles M.; León, Enrique J.; Rajabojan, Saravanan; Friedman, Robert; Friedrich, Thomas C.; O'Connor, Shelby L.; Hughes, Austin L.

    2012-01-01

    Factors affecting the reliability of Roche/454 pyrosequencing for analyzing sequence polymorphism in within-host viral populations were assessed by two experiments: 1) sequencing four clonal simian immunodeficiency virus (SIV) stocks and 2) sequencing mixtures in different proportions of two SIV strains with known fixed nucleotide differences. Observed nucleotide diversity and frequency of undetermined nucleotides were increased at sites in homopolymer runs of four or more identical nucleotides, particularly at AT sites. However, in the mixed-strain experiments, the effects on estimated nucleotide diversity of such errors were small in comparison to known strain differences. The results suggest that biologically meaningful variants present at a frequency of around 10% and possibly much lower are easily distinguished from artifacts of the sequencing process. Analysis of the clonal stocks revealed numerous rare variants that showed the signature of purifying selection and that elimination of variants at frequencies of less than 1% reduced estimates of nucleotide diversity by about an order of magnitude. Thus, using a 1% frequency cutoff for accepting a variant as real represents a conservative standard, which may be useful in studies that are focused on the discovery of specific mutations (such as those conferring immune escape or drug resistance). On the other hand, if the goal is to estimate nucleotide diversity, an optimal strategy might be to include all observed variants (even those at less than 1% frequency), while masking out homopolymer runs of four or more nucleotides. PMID:22436995

  15. Comparison of NucliSens and Roche Monitor Assays for Quantitation of Levels of Human Immunodeficiency Virus Type 1 RNA in Plasma

    PubMed Central

    Dyer, John R.; Pilcher, Christopher D.; Shepard, Robin; Schock, Jody; Eron, Joseph J.; Fiscus, Susan A.

    1999-01-01

    We compared the performance of Organon Teknika’s NucliSens and Roche Diagnostic Systems’ Monitor quantitative human immunodeficiency type 1 RNA assays. Both had similar linearity and sensitivity over most of the dynamic range of the assays, although the Monitor assay was superior at the low range of RNA values while the NucliSens assay was more consistent at higher RNA values. NucliSens generally showed less interassay variability. PMID:9889240

  16. Comparison of Roche MONITOR and Organon Teknika NucliSens Assays To Quantify Human Immunodeficiency Virus Type 1 RNA in Cerebrospinal Fluid

    PubMed Central

    Spearman, Paul; Fiscus, Susan A.; Smith, Rita M.; Shepard, Robin; Johnson, Benjamin; Nicotera, Janet; Harris, Victoria L.; Clough, Lisa A.; McKinsey, Joel; Haas, David W.

    2001-01-01

    We compared Roche MONITOR and Organon Teknika NucliSens assays for human immunodeficiency virus type 1 (HIV-1) RNA in cerebrospinal fluid (CSF). Results of 282 assays were highly correlated (r = 0.826), with MONITOR values being 0.29 ± 0.4 log10 copies/ml (mean ± standard deviation) values. Both assays can reliably quantify HIV-1 RNA in CSF. PMID:11283098

  17. Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach.

    PubMed

    Le Cam, Aurélie; Bobe, Julien; Bouchez, Olivier; Cabau, Cédric; Kah, Olivier; Klopp, Christophe; Lareyre, Jean-Jacques; Le Guen, Isabelle; Lluch, Jérôme; Montfort, Jérôme; Moreews, Francois; Nicol, Barbara; Prunet, Patrick; Rescan, Pierre-Yves; Servili, Arianna; Guiguen, Yann

    2012-05-25

    Rainbow trout, Oncorhynchus mykiss, is an important aquaculture species worldwide and, in addition to being of commercial interest, it is also a research model organism of considerable scientific importance. Because of the lack of a whole genome sequence in that species, transcriptomic analyses of this species have often been hindered. Using next-generation sequencing (NGS) technologies, we sought to fill these informational gaps. Here, using Roche 454-Titanium technology, we provide new tissue-specific cDNA repertoires from several rainbow trout tissues. Non-normalized cDNA libraries were constructed from testis, ovary, brain and gill rainbow trout tissue samples, and these different libraries were sequenced in 10 separate half-runs of 454-Titanium. Overall, we produced a total of 3million quality sequences with an average size of 328bp, representing more than 1Gb of expressed sequence information. These sequences have been combined with all publicly available rainbow trout sequences, resulting in a total of 242,187 clusters of putative transcript groups and 22,373 singletons. To identify the predominantly expressed genes in different tissues of interest, we developed a Digital Differential Display (DDD) approach. This approach allowed us to characterize the genes that are predominantly expressed within each tissue of interest. Of these genes, some were already known to be tissue-specific, thereby validating our approach. Many others, however, were novel candidates, demonstrating the usefulness of our strategy and of such tissue-specific resources. This new sequence information, acquired using NGS 454-Titanium technology, deeply enriched our current knowledge of the expressed genes in rainbow trout through the identification of an increased number of tissue-specific sequences. This identification allowed a precise cDNA tissue repertoire to be characterized in several important rainbow trout tissues. The rainbow trout contig browser can be accessed at the following

  18. Standardization of DiaSorin and Roche automated third generation PTH assays with an International Standard: impact on clinical populations.

    PubMed

    Cavalier, Etienne; Delanaye, Pierre; Lukas, Pierre; Carlisi, Agnes; Gadisseur, Romy; Souberbielle, Jean-Claude

    2014-08-01

    Standardization of parathyroid hormone (PTH) assays is a major issue, especially in hemodialyzed (HD) patients. Two automated third generation PTH assays (Roche Elecsys and DiaSorin Liaison) are now available. These assays are specific for the (1-84) PTH and do not cross-react with the (7-84) fragment, contrary to second generation (intact) assays. We aimed to calibrate the two methods against the WHO International PTH Standard (IS) 95/646 to see if the two assays could provide comparable results in a population of healthy subjects, HD patients and patients suffering from primary hyperparathyroidism (PHP). We selected 79 healthy subjects and two populations of patients presenting PTH disorders: 56 HD and 27 PHP patients. We reconstituted the IS in a pool of human serum containing undetectable levels of 1-84 PTH and prepared 13 serum standards ranging from 0 to 2000 pg/mL. The standards were run on the two instruments to calibrate the assays on the IS. The different populations were run before and after restandardization. As these kits were differently calibrated, the results obtained after restandarization were significantly different. Restandardization process improved concordance between assays and, taking the analytical variability of the two kits into account, the results could be considered to be similar. Restandardization of automated third generation PTH assays with the WHO 1-84 PTH Standard significantly reduces inter-method variability. Reference ranges and raw values are totally transposable from one method to the other in healthy subjects, but also in diseased patients, e.g., with HD or those suffering from PHP.

  19. Comparison of Hybribio GenoArray and Roche human papillomavirus (HPV) linear array for HPV genotyping in anal swab samples.

    PubMed

    Low, Huey Chi; Silver, Michelle I; Brown, Brandon J; Leng, Chan Yoon; Blas, Magaly M; Gravitt, Patti E; Woo, Yin Ling

    2015-02-01

    Human papillomavirus (HPV) is causally associated with anal cancer, as HPV DNA is detected in up to 90% of anal intraepithelial neoplasias and anal cancers. With the gradual increase of anal cancer rates, there is a growing need to establish reliable and clinically relevant methods to detect anal cancer precursors. In resource-limited settings, HPV DNA detection is a potentially relevant tool for anal cancer screening. Here, we evaluated the performance of the Hybribio GenoArray (GA) for genotyping HPV in anal samples, against the reference standard Roche Linear Array (LA). Anal swab samples were obtained from sexually active men who have sex with men. Following DNA extraction, each sample was genotyped using GA and LA. The overall interassay agreement, type-specific, and single and multiple genotype agreements were evaluated by kappa statistics and McNemar's χ(2) tests. Using GA and LA, 68% and 76% of samples were HPV DNA positive, respectively. There was substantial interassay agreements for the detection of all HPV genotypes (κ = 0.70, 86% agreement). Although LA was able to detect more genotypes per sample, the interassay agreement was acceptable (κ = 0.53, 63% agreement). GA had poorer specific detection of HPV genotypes 35, 42, and 51 (κ < 0.60). In conclusion, GA and LA showed good interassay agreement for the detection of most HPV genotypes in anal samples. However, the detection of HPV DNA in up to 76% of anal samples warrants further evaluation of its clinical significance. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  20. Techniques used in high-scoring and low-scoring 'Roche' vaults performed by elite male gymnasts.

    PubMed

    Takei, Yoshiaki; Dunn, J Hubert; Blucker, Erik

    2003-07-01

    The 16 highest-scored Roche vaults (G1) performed during the 2000 Olympic Games were compared with those receiving the 16 lowest-scores (G2). A 16-mm motion picture camera operating at 100 Hz recorded the vaults during the competition. The results of t tests (p < .05) indicated G1, compared to G2, had (a) shorter time of board support, greater normalised average upward vertical force and backward horizontal force exerted by the board, greater change in the vertical velocity while on the board, and greater vertical velocity at board take-off, (b) comparable linear and angular motions in pre-flight, (c) smaller backward horizontal impulse exerted by the horse, smaller loss of the horizontal velocity while on the horse, and greater horizontal and vertical velocities at horse take-off, (d) greater height and larger horizontal distance of post-flight, (e) higher body mass centre at knee release, and (f) higher mass centre, greater normalised moment of inertia, and smaller vertical velocity at mat touchdown. Therefore, gymnasts and coaches should focus on sprinting the approach; blocking and pushing-off the take-off board rapidly and vigorously; departing the board with a large vertical velocity; exerting large downward vertical force and small forward horizontal force from the hand-stand position while on the horse; departing the horse with large horizontal and vertical velocities; and completing the majority of the double salto forward near the peak of trajectory and releasing the knees above the top of the horse to prepare for a controlled landing.

  1. Multicenter Comparison Study of both Analytical and Clinical Performance across Four Roche Hepatitis C Virus RNA Assays Utilizing Different Platforms.

    PubMed

    Vermehren, Johannes; Stelzl, Evelyn; Maasoumy, Benjamin; Michel-Treil, Veronique; Berkowski, Caterina; Marins, Ed G; Paxinos, Ellen E; Marino, Enrique; Wedemeyer, Heiner; Sarrazin, Christoph; Kessler, Harald H

    2017-04-01

    The efficacy of antiviral treatment for chronic hepatitis C virus (HCV) infection is determined by measuring HCV RNA at specific time points throughout therapy using highly sensitive and accurate HCV RNA assays. This study compared the performances of two recently developed real-time PCR HCV RNA assays, cobas HCV for use on the cobas 6800/8800 systems (cobas 6800/8800 HCV) and cobas HCV for use on the cobas 4800 system (cobas 4800 HCV), with those of two established assays, the Cobas AmpliPrep/Cobas TaqMan HCV quantitative test, version 2 (CAP/CTM v2) and the Cobas TaqMan HCV test, version 2 for use with the High Pure system (HPS/CTM v2). The limits of detection (LODs) and linearity at lower concentrations (5 to 1000 IU/ml) were assessed for cobas 6800/8800 HCV and cobas 4800 HCV using WHO standard traceable panels representing HCV genotypes (GT) 1 to 4. Pairwise assay comparisons were also performed using 245 clinical samples representing HCV GT 1 to GT 4. Results from cobas 6800/8800 HCV and cobas 4800 HCV were linear at low HCV RNA concentrations (<0.3 log10 IU/ml difference between expected and observed results) with LODs of 8.2 IU/ml and 11.7 IU/ml, respectively, for GT 1. The new assays showed excellent agreement with results from CAP/CTM v2 and HPS/CTM v2 in samples with quantifiable viral loads. The concordances using the 6 million IU/ml cutoff were high among all four assays (90 to 94%). In conclusion, the cobas 6800/8800 HCV and cobas 4800 HCV tests are sensitive and linear and correlate well with the established Roche assays used in clinical practice. Copyright © 2017 Vermehren et al.

  2. Multicenter Comparison Study of both Analytical and Clinical Performance across Four Roche Hepatitis C Virus RNA Assays Utilizing Different Platforms

    PubMed Central

    Vermehren, Johannes; Stelzl, Evelyn; Maasoumy, Benjamin; Michel-Treil, Veronique; Berkowski, Caterina; Marins, Ed G.; Paxinos, Ellen E.; Marino, Enrique; Wedemeyer, Heiner; Sarrazin, Christoph

    2017-01-01

    ABSTRACT The efficacy of antiviral treatment for chronic hepatitis C virus (HCV) infection is determined by measuring HCV RNA at specific time points throughout therapy using highly sensitive and accurate HCV RNA assays. This study compared the performances of two recently developed real-time PCR HCV RNA assays, cobas HCV for use on the cobas 6800/8800 systems (cobas 6800/8800 HCV) and cobas HCV for use on the cobas 4800 system (cobas 4800 HCV), with those of two established assays, the Cobas AmpliPrep/Cobas TaqMan HCV quantitative test, version 2 (CAP/CTM v2) and the Cobas TaqMan HCV test, version 2 for use with the High Pure system (HPS/CTM v2). The limits of detection (LODs) and linearity at lower concentrations (5 to 1000 IU/ml) were assessed for cobas 6800/8800 HCV and cobas 4800 HCV using WHO standard traceable panels representing HCV genotypes (GT) 1 to 4. Pairwise assay comparisons were also performed using 245 clinical samples representing HCV GT 1 to GT 4. Results from cobas 6800/8800 HCV and cobas 4800 HCV were linear at low HCV RNA concentrations (<0.3 log10 IU/ml difference between expected and observed results) with LODs of 8.2 IU/ml and 11.7 IU/ml, respectively, for GT 1. The new assays showed excellent agreement with results from CAP/CTM v2 and HPS/CTM v2 in samples with quantifiable viral loads. The concordances using the 6 million IU/ml cutoff were high among all four assays (90 to 94%). In conclusion, the cobas 6800/8800 HCV and cobas 4800 HCV tests are sensitive and linear and correlate well with the established Roche assays used in clinical practice. PMID:28122870

  3. Roche-lobe overflow systems powered by black holes in young star clusters: the importance of dynamical exchanges

    SciTech Connect

    Mapelli, Michela; Zampieri, Luca

    2014-10-10

    We have run 600 N-body simulations of intermediate-mass (∼3500 M {sub ☉}) young star clusters (SCs; with three different metallicities (Z = 0.01, 0.1, and 1 Z {sub ☉}). The simulations include the dependence of stellar properties and stellar winds on metallicity. Massive stellar black holes (MSBHs) with mass >25 M {sub ☉} are allowed to form through direct collapse of very massive metal-poor stars (Z < 0.3 Z {sub ☉}). We focus on the demographics of black hole (BH) binaries that undergo mass transfer via Roche lobe overflow (RLO). We find that 44% of all binaries that undergo an RLO phase (RLO binaries) formed through dynamical exchange. RLO binaries that formed via exchange (RLO-EBs) are powered by more massive BHs than RLO primordial binaries (RLO-PBs). Furthermore, the RLO-EBs tend to start the RLO phase later than the RLO-PBs. In metal-poor SCs (0.01-0.1 Z {sub ☉}), >20% of all RLO binaries are powered by MSBHs. The vast majority of RLO binaries powered by MSBHs are RLO-EBs. We have produced optical color-magnitude diagrams of the simulated RLO binaries, accounting for the emission of both the donor star and the irradiated accretion disk. We find that RLO-PBs are generally associated with bluer counterparts than RLO-EBs. We compare the simulated counterparts with the observed counterparts of nine ultraluminous X-ray sources. We discuss the possibility that IC 342 X-1, Ho IX X-1, NGC 1313 X-2, and NGC 5204 X-1 are powered by an MSBH.

  4. On the evolution of binary components which first fill their Roche lobes after the exhaustion of central helium

    NASA Astrophysics Data System (ADS)

    Iben, I., Jr.

    1986-05-01

    The evolution of model close binary components of initial mass 3-7 Msun and of Population I composition is followed from the beginning of the core helium-burning phase. For one set of models, mass loss is initiated at an arbitrary point during the early AGB phase (early case C events) and evolution is followed to the degenerate dwarf stage. For another set of models, mass loss is initiated when hydrogen is reignited and thermal pulses begin (late case C events). It is found that the inclusion of overshoot and semiconvection during the core helium-burning phase has little effect on the relationship between progenitor mass and final degenerate dwarf mass. A new channel for producing both oxygen-neon (ONe) degenerate dwarfs and neutron stars is identified. Involved are stars of initial mass 7. 8.5 Msun which undergo early case C events. For such stars, mass loss from the surface proceeds sufficiently more rapidly than the mass of the hydrogen-exhausted core can be decreased by convective dredge-up that carbon ignition at the center occurs before degeneracy sets in; the remnant of the mass transfer event can evolve into either an ONe degenerate dwarf or a neutron star at a combined frequency that is comparable to the observed rate of supernova formation in the Galaxy. In binary systems in which the primary becomes a neutron star or an ONe degenerate dwarf, the secondary will normally evolve into a CO degenerate dwarf, and common envelope action will lead in some instances to small enough orbital separations that orbital shrinkage due to gravitational wave radiation will again lead to Roche-lobe filling by the CO dwarf. If before the merging and explosion process begins, the heavier compact component is an ONe degenerate dwarf, a supernova-like explosion fueled by the conversion of carbon and oxygen into iron peak nuclei may result, and the light curve and spectrum may be of the Type I "peculiar" variety. The compact remnant remaining after the explosion may be either

  5. CCD Photometry, Roche Modeling and Evolutionary History of the WUMa-type Eclipsing Binary TYC01664-0110-1

    NASA Astrophysics Data System (ADS)

    Alton, K. B.; Stępień, K.

    2016-09-01

    TYC 01664-0110-1 (ASAS J212915+1604.9), a W UMa-type variable system (P=0.282962 d), was first detected over 17 years ago by the ROTSE-I telescope. Photometric data (B, V and Ic) collected at UnderOak Observatory (UO) resulted in five new times-of-minima for this variable star which were used to establish a revised linear ephemeris. No published radial velocity (RV) data are available for this system. However, since this W UMa binary undergoes a total eclipse, Roche modeling based on the Wilson-Devinney (W-D) code yielded a well-constrained photometric value for M2/M1 (q=0.356±0.001). There is a suggestion from ROTSE-I (1999) and ASAS survey data (2003, 2005, and 2008) that the secondary maximum is more variable than the primary one probably due to the so-called O'Connell effect. However, peak asymmetry in light curves (LC) from 2015 was barely evident during quadrature. Therefore, W-D model fits of these most recent data did not yield any substantive improvement with the addition of spot(s). Using the evolutionary model of cool close binaries we searched for a possible progenitor of TYC 01664-0110-1. The best fit is obtained if the initial binary has an orbital period between 3.3-3.8 d and component masses between 1.0-1.1 M⊙ and 0.30-0.35 M⊙. The model progenitor needs about 10 Gyr to attain the presently observed parameters of the variable. Its period slowly increases and the mass ratio decreases. According to the model predictions TYC 01664-0110-1 will go through the common envelope (CE) phase in the future, followed by merging of both components or formation of a double degenerate. Due to its apparent brightness (mV,max≍10.9 mag) and unique properties, the star is an excellent target for spectroscopic investigation of any possible deviations from a simple static model of a contact binary.

  6. The equilibrium of rubble-pile satellites: The Darwin and Roche ellipsoids for gravitationally held granular aggregates

    NASA Astrophysics Data System (ADS)

    Sharma, Ishan

    2009-04-01

    Many new small moons of the giant planets have been discovered recently. In parallel, satellites of several asteroids, e.g., Ida, have been found. Strikingly, a majority of these new-found planetary moons are estimated to have very low densities, which, along with their hypothesized accretionary origins, suggests a rubble internal structure. This, coupled to the fact that many asteroids are also thought to be particle aggregates held together principally by self-gravity, motivates the present investigation into the possible ellipsoidal shapes that a rubble-pile satellite may achieve as it orbits an aspherical primary. Conversely, knowledge of the shape will constrain the granular aggregate's orbit—the closer it gets to a primary, both primary's tidal effect and the satellite's spin are greater. We will assume that the primary body is sufficiently massive so as not to be influenced by the satellite. However, we will incorporate the primary's possible ellipsoidal shape, e.g., flattening at its poles in the case of a planet, and the proloidal shape of asteroids. In this, the present investigation is an extension of the first classical Darwin problem to granular aggregates. General equations defining an ellipsoidal rubble pile's equilibrium about an ellipsoidal primary are developed. They are then utilized to scrutinize the possible granular nature of small inner moons of the giant planets. It is found that most satellites satisfy constraints necessary to exist as equilibrated granular aggregates. Objects like Naiad, Metis and Adrastea appear to violate these limits, but in doing so, provide clues to their internal density and/or structure. We also recover the Roche limit for a granular satellite of a spherical primary, and employ it to study the martian satellites, Phobos and Deimos, as well as to make contact with earlier work of Davidsson [Davidsson, B., 2001. Icarus 149, 375-383]. The satellite's interior will be modeled as a rigid-plastic, cohesion-less material

  7. Evaluation of the Upgraded Version 2.0 of the Roche COBAS® AmpliPrep/COBAS® TaqMan HIV-1 Qualitative Assay in Central African Children

    PubMed Central

    Mossoro-Kpinde, CD; Jenabian, MA; Gody, JC; Robin, L; Talla, P; Longo, JDD; Grésenguet, G; Belec, L

    2016-01-01

    Background: Several commercially available molecular techniques were developed based on subtype B of HIV-1, which represents only 10% of HIV strains worldwide. Indeed, in sub-Saharan Africa, non-B subtypes of HIV-1 are predominant. The aim of this study was to evaluate the performances of the COBAS® AmpliPrep/COBAS® (CAP/CTM) HIV-1 Qualitative assays to detect the broad range of HIV-1 variants circulating in Central Africa and compare to the outgoing CAP/CTM HIV-1 Quantitative test v2.0 (Roche Molecular Systems), chosen as reference gold standard molecular assay. Methods: The CAP/CTM HIV-1 Qualitative tests versions 1.0 and 2.0 (Roche Molecular Systems, Inc., Branchburg, NJ, USA) were evaluated compared to CAP/CTM TaqMan HIV-1 Quantitative test v2.0 (Roche Molecular Systems) on 239 dried plasma spot (DPS) from 133 HIV-1-infected (with detectable plasma HIV RNA load) and 106 uninfected children, followed-up at Complexe Pédiatrique, Bangui, Central African Republic. Results: The version 1.0 showed low sensitivity (93.2%), with 9 (6.8%) false negative results, demonstrating under-detection of non-B HIV-1 subtypes. In contrast, the upgraded version 2.0 showed 100%-sensitivity, 100%-specificity and perfect agreement (κ coefficient, 1.0). Conclusion: Our evaluation in the Central African Republic demonstrates the clinical implications of the accuracy and reliability of the CAP/CTM HIV-1 Qualitative assay for early diagnosis of HIV-1 in Central African children. PMID:27857825

  8. Clinical evaluation of the new Roche platform of serological and molecular cytomegalovirus-specific assays in the diagnosis and prognosis of congenital cytomegalovirus infection.

    PubMed

    Chiereghin, Angela; Pavia, Claudia; Gabrielli, Liliana; Piccirilli, Giulia; Squarzoni, Diego; Turello, Gabriele; Gibertoni, Dino; Simonazzi, Giuliana; Capretti, Maria Grazia; Lanari, Marcello; Lazzarotto, Tiziana

    2017-08-08

    Clinical evaluation of the Elecsys(®) CMV IgM, IgG, IgG Avidity and COBAS AmpliPrep/COBAS TaqMan CMV (COBAS CMV) assays (Roche Diagnostics AG) in the diagnosis and prognosis of congenital CMV infection was performed. In this study, 150 preselected clinical samples (50 primary infection sera, 50 amniotic fluid [AF] and 50 newborn urine) were processed using Roche serological/molecular CMV-specific tests. Results were compared with those obtained by routine assays (comparator assays). The Elecsys(®) CMV IgM and IgG assays showed a perfect agreement (100%) with the comparator assays. Using the combination of the Elecsys(®) CMV IgM and IgG Avidity assays results, a primary infection was identified in 100% of cases. Inappropriate avidity CMV IgG values in two samples with very low IgG values (<6 AU/mL) were observed. COBAS CMV assay showed an agreement equal to 98% and 100% with comparator assays by processing AF and urine samples, respectively. Among AF with quantitative results, Lin's concordance correlation was 0.933 and comparator-COBAS CMV assays gave CMV-DNA loads differing by <0.5 log10 DNA. Finally, higher CMV-DNA levels in AF samples were associated with a symptomatic outcome (p=0.003). The Roche CMV-specific assays compared well with the comparator assays, thus providing to be suitable for clinical use. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Beyond Skinner? A review of relational frame theory: A post-skinnerian account of human language and cognition by Hayes, Barnes-Holmes, and Roche.

    PubMed

    Osborne, J Grayson

    2003-01-01

    In their book, Relational Frame Theory: A Post-Skinnerian Account of Human Language and Cognition (2001), Hayes, Barnes-Holmes and Roche challenge behavior analysts to put aside Skinner and Verbal Behavior in favor of relational frame theory's approach to human language and cognition. However, when viewed from the contexts of behavior analysis, the principles of behavior analysis, and the principles of the founder of behavior analysis, Relational Frame Theory fits squarely in the Skinnerian, behavior analytic tradition. As with Verbal Behavior, Relational Frame Theory and its theses may be thought of as logical and empirical extensions of that which precedes them.

  10. Performance Characteristics of the Cavidi ExaVir Viral Load Assay and the Ultra-Sensitive P24 Assay Relative to the Roche Monitor HIV-1 RNA Assay

    PubMed Central

    Stewart, Paul; Cachafeiro, Ada; Napravnik, Sonia; Eron, Joseph J.; Frank, Ian; van der Horst, Charles; Bosch, Ronald J.; Bettendorf, Daniel; Bohlin, Peter; Fiscus, Susan A.

    2010-01-01

    Background The Cavidi viral load assay and the ultra-sensitive p24 antigen assay (Up24 Ag) have been suggested as more feasible alternatives to PCR-based HIV viral load assays for use in monitoring patients infected with HIV-1 in resource-limited settings. Objectives To describe the performance of the Cavidi ExaVir Load™ assay (version 2.0) and two versions of the Up24 antigen assay and to characterize their agreement with the Roche Monitor HIV-1 RNA assay (version 1.5). Study Design Observational study using a convenience sample of 342 plasma specimens from 108 patients enrolled in two ACTG clinical trials to evaluate the performance characteristics of the Up24 Ag assay using two different lysis buffers and the Cavidi ExaVir Load™ assay. Results In analysis of agreement with the Roche assay, the Cavidi assay demonstrated superiority to the Up24 Ag assays in accuracy and precision, as well as sensitivity, specificity, and positive and negative predictive values for HIV-1 RNA ≥400, ≥1000 and ≥5000 copies/mL. Logistic performance curves indicated that the Cavidi assay was superior to the Up24 assays for viral loads greater than 650 copies/mL. Conclusions The results suggest that the Cavidi ExaVir Load assay could be used for monitoring HIV-1 viral load in resource-limited settings. PMID:20832356

  11. Method comparison of the Ortho Vitros Fusion 5,1 chemistry analyzer and the Roche COBAS Integra 400 for urine drug screen testing in the emergency department.

    PubMed

    Johnson-Davis, Kamisha L; Thompson, Catherine D; Clark, Chantry J; McMillin, Gwen A; Lehman, Christopher M

    2012-06-01

    Exposure to drugs and toxins is a major cause for the rising number of emergency department visits each year. Immunoassays are commonly used in the emergency department to provide rapid turnaround time for acute care. The purpose of this study was to compare two automated immunoassay chemistry analyzers to determine which platform produced the fewest number of false positive/negative results. Residual patient urine samples were were collected for each of the following drugs/drug classes: cocaine (n = 40), opiates (n = 45), and amphetamines (n = 54) and confirmed either positive or negative by mass spectrometry. Split sample analyses of these specimens were performed on both the Roche COBAS INTEGRA 400 plus and Ortho Vitros 5,1 FS instruments. The results from the two chemistry analyzers were compared to confirmed results. Both immunoassays were prone to false positive results for cocaine and false negative results for opiates and amphetamines. The Vitros Fusion analyzer generated fewer false positive and false negative results for opiate and amphetamine testing than the Roche Integra, but the platforms performed comparably for cocaine.

  12. Establishing and evaluating pediatric thyroid reference intervals on the Roche Modular Analytics E 170 using computational statistics and data-mining techniques.

    PubMed

    Henderson, M P A; Grey, V

    2011-07-01

    This study determined age specific, free thyroxine and thyroid stimulating hormone reference intervals for a pediatric population. The data set was partitioned into age groups and the Tukey method was used to identify outliers for removal. The Harris and Boyd algorithm was used to determine if groups could be merged. Reference intervals were calculated using both non-parametric and robust methods. Boot-strapping was used to determine the 90% confidence intervals surrounding the upper and lower limits of each reference interval. These population based reference intervals were then compared to the manufactures suggested reference intervals. This study provides non-parametric and robust reference intervals with associated 90% confidence intervals for free thyroxine and thyroid stimulating hormone as measured on the Roche Modular Analytics E 170. The results emphasize the importance of establishing population-based reference intervals for the clinical laboratory. Copyright © 2011. Published by Elsevier Inc.

  13. Evaluation of the Roche cobas s 201 system and cobas TaqScreen multiplex test for blood screening: a European multicenter study.

    PubMed

    Jarvis, Lisa; Becker, Janine; Tender, Alzira; Cleland, Alexander; Queiros, Lucinda; Aquiar, Ana; Azevedo, Joana; Aprili, Giuseppe; Bressan, Fausto; Torres, Pilar; Nieto, Serafin; Ursitti, Antonella; Montoro, Jose; Vila, Enrique; Ramada, Concha; Saldanha, John

    2008-09-01

    The Roche cobas TaqScreen test, an automated, multiplex nucleic acid test for blood screening for hepatitis B virus (HBV) DNA, hepatitis C virus (HCV) RNA, human immunodeficiency virus type 1 (HIV-1) groups M and O, and HIV-2 RNA, on the cobas s 201 platform, was evaluated by six European blood screening laboratories. The 95 percent limit of detection (LOD) of the cobas TaqScreen test for HBV, HCV, and HIV-1, using dilutions of the WHO International Standards, were evaluated. The clinical performance was determined by testing between 2000 to 6000 routine donor samples. Some laboratories evaluated the robustness, cross-contamination, and workflow. The mean 95 percent LOD (95% lower and upper confidence intervals) for HBV, HCV, and HIV-1 across all the laboratories were 3.8 (range, 3.0-5.2), 10.8 (range, 8.4-14.4), and 56.7 (range, 43.0-79.2) IU/mL, respectively. A total of 23,716 donors were tested in pools of 6. Fourteen initially reactive pools were detected, of which 6 contained a reactive donation, giving a positive predictive value of the pool results of 43 percent. One of the reactive donations was a HBV yield case (hepatitis B surface antigen-negative/anti-HBc-positive). Evaluation of the workflow for the system showed that an optimized batch loading in which a pipettor (Hamilton Microlab Star IVD) was utilized to half capacity was better than a full batch loading. The 95 percent LOD for the three viruses were comparable to those obtained by Roche. The test and platform were shown to be sensitive, specific, flexible, and robust.

  14. Field evaluation of Abbott Real Time HIV-1 Qualitative test for early infant diagnosis using dried blood spots samples in comparison to Roche COBAS Ampliprep/COBAS TaqMan HIV-1 Qual test in Kenya.

    PubMed

    Chang, Joy; Omuomo, Kenneth; Anyango, Emily; Kingwara, Leonard; Basiye, Frank; Morwabe, Alex; Shanmugam, Vedapuri; Nguyen, Shon; Sabatier, Jennifer; Zeh, Clement; Ellenberger, Dennis

    2014-08-01

    Timely diagnosis and treatment of infants infected with HIV are critical for reducing infant mortality. High-throughput automated diagnostic tests like Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 Qual Test (Roche CAPCTM Qual) and the Abbott Real Time HIV-1 Qualitative (Abbott Qualitative) can be used to rapidly expand early infant diagnosis testing services. In this study, the performance characteristics of the Abbott Qualitative were evaluated using two hundred dried blood spots (DBS) samples (100 HIV-1 positive and 100 HIV-1 negative) collected from infants attending the antenatal facilities in Kisumu, Kenya. The Abbott Qualitative results were compared to the diagnostic testing completed using the Roche CAPCTM Qual in Kenya. The sensitivity and specificity of the Abbott Qualitative were 99.0% (95% CI: 95.0-100.0) and 100.0% (95% CI: 96.0-100.0), respectively, and the overall reproducibility was 98.0% (95% CI: 86.0-100.0). The limits of detection for the Abbott Qualitative and Roche CAPCTM Qual were 56.5 and 6.9copies/mL at 95% CIs (p=0.005), respectively. The study findings demonstrate that the Abbott Qualitative test is a practical option for timely diagnosis of HIV in infants.

  15. Field evaluation of Abbott Real Time HIV-1 Qualitative test for early infant diagnosis using dried blood spots samples in comparison to Roche COBAS Ampliprep/COBAS TaqMan HIV-1 Qual Test in Kenya

    PubMed Central

    Chang, Joy; Omuomo, Kenneth; Anyango, Emily; Kingwara, Leonard; Basiye, Frank; Morwabe, Alex; Shanmugam, Vedapuri; Nguyen, Shon; Sabatier, Jennifer; Zeh, Clement; Ellenberger, Dennis

    2016-01-01

    Timely diagnosis and treatment of infants infected with HIV are critical for reducing infant mortality. High-throughput automated diagnostic tests like Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 Qual Test (Roche CAPCTM Qual) and the Abbott Real Time HIV-1 Qualitative (Abbott Qualitative) can be used to rapidly expand early infant diagnosis testing services. In this study, the performance characteristics of the Abbott Qualitative were evaluated using two hundred dried blood spots (DBS) samples (100 HIV-1 positive and 100 HIV-1 negative) collected from infants attending the antenatal facilities in Kisumu, Kenya. The Abbott Qualitative results were compared to the diagnostic testing completed using the Roche CAPCTM Qual in Kenya. The sensitivity and specificity of the Abbott Qualitative were 99.0% (95% CI: 95.0–100.0) and 100.0% (95% CI: 96.0–100.0), respectively, and the overall reproducibility was 98.0% (95% CI: 86.0–100.0). The limits of detection for the Abbott Qualitative and Roche CAPCTM Qual were 56.5 and 6.9 copies/mL at 95% CIs (p = 0.005), respectively. The study findings demonstrate that the Abbott Qualitative test is a practical option for timely diagnosis of HIV in infants. PMID:24726703

  16. A comparative evaluation of the analytical performances of Capillarys 2 Flex Piercing, Tosoh HLC-723 G8, Premier Hb9210, and Roche Cobas c501 Tina-quant Gen 2 analyzers for HbA1c determination

    PubMed Central

    Wu, Xiaobin; Chao, Yan; Wan, Zemin; Wang, Yunxiu; Ma, Yan; Ke, Peifeng; Wu, Xinzhong; Xu, Jianhua; Zhuang, Junhua; Huang, Xianzhang

    2016-01-01

    Introduction Haemoglobin A1c (HbA1c) is widely used in the management of diabetes. Therefore, the reliability and comparability among different analytical methods for its detection have become very important. Materials and methods A comparative evaluation of the analytical performances (precision, linearity, accuracy, method comparison, and interferences including bilirubin, triglyceride, cholesterol, labile HbA1c (LA1c), vitamin C, aspirin, fetal haemoglobin (HbF), and haemoglobin E (Hb E)) were performed on Capillarys 2 Flex Piercing (Capillarys 2FP) (Sebia, France), Tosoh HLC-723 G8 (Tosoh G8) (Tosoh, Japan), Premier Hb9210 (Trinity Biotech, Ireland) and Roche Cobas c501 (Roche c501) (Roche Diagnostics, Germany). Results A good precision was shown at both low and high HbA1c levels on all four systems, with all individual CVs below 2% (IFCC units) or 1.5% (NGSP units). Linearity analysis for each analyzer had achieved a good correlation coefficient (R2 > 0.99) over the entire range tested. The analytical bias of the four systems against the IFCC targets was less than ± 6% (NGSP units), indicating a good accuracy. Method comparison showed a great correlation and agreement between methods. Very high levels of triglycerides and cholesterol (≥ 15.28 and ≥ 8.72 mmol/L, respectively) led to falsely low HbA1c concentrations on Roche c501. Elevated HbF induced false HbA1c detection on Capillarys 2FP (> 10%), Tosoh G8 (> 30%), Premier Hb9210 (> 15%), and Roche c501 (> 5%). On Tosoh G8, HbE induced an extra peak on chromatogram, and significantly lower results were reported. Conclusions The four HbA1c methods commonly used with commercial analyzers showed a good reliability and comparability, although some interference may falsely alter the result. PMID:27812304

  17. Comparison of the Microgenics CEDIA heroin metabolite (6-AM) and the Roche Abuscreen ONLINE opiate immunoassays for the detection of heroin use in forensic urine samples.

    PubMed

    Holler, Justin M; Bosy, Thomas Z; Klette, Kevin L; Wiegand, Russel; Jemionek, John; Jacobs, Aaron

    2004-09-01

    Current Department of Defense (DoD) and Department of Health and Human Services (HHS) procedures for the detection of heroin abuse by testing urine utilize an initial opiate (codeine/morphine) immunoassay (IA) screen followed by gas chromatography-mass spectrometry (GC-MS) confirmation of 6-acetylmorphine (6-AM), if the morphine concentration is above established cutoff. An alternative to the current opiates screen for heroin abuse is the direct IA for the metabolite of heroin, 6-acetylmorphine. In this regard, the performance of the Microgenics CEDIA heroin metabolite (6-AM) screening reagent was assessed. This evaluation was conducted on the P module of a Hitachi Modular automated IA analyzer calibrated using 6-AM at 10 ng/mL. Reproducibility, linearity, accuracy, sensitivity, and interferences associated with use of the 6-AM IA reagent were evaluated. The IA reagent precision (percent coefficient of variation (%CV)) around each of seven standards was less than 0.63%, with a linearity (r(2)) value of 0.9951. A total of 37,713 active duty service members' urine samples were analyzed simultaneously using the CEDIA heroin metabolite (6-AM) reagent and the Roche Abuscreen ONLINE opiate reagent to evaluate both the prevalence rate of 6-AM in the demographic group and the sensitivity and specificity of the reagents for the detection of heroin use. Of the 37,713 samples tested using the CEDIA heroin metabolite (6-AM) reagent, three samples screened positive at the DoD and HHS cutoff of 10 ng/mL. One of the three samples confirmed positive for 6-AM by GC-MS above the cutoff of 10 ng/mL, the two remaining samples confirmed negative for 6-AM at a GC-MS limit of detection (LOD) of 2.1 ng/mL. In contrast, the Roche Abuscreen ONLINE opiate IA produced 74 opiate-positive results for codeine/morphine, with 6 of the 74 specimens confirming positive for morphine above the DoD cutoff concentration of 4000 ng/mL (8% DoD morphine confirmation rate), only one of the 74 opiate

  18. 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.

    PubMed

    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

  19. Evaluation of performance across the dynamic range of the Abbott RealTime HIV-1 assay as compared to VERSANT HIV-1 RNA 3.0 and AMPLICOR HIV-1 MONITOR v1.5 using serial dilutions of 39 group M and O viruses.

    PubMed

    Swanson, Priscilla; Huang, Shihai; Abravaya, Klara; de Mendoza, Carmen; Soriano, Vincent; Devare, Sushil G; Hackett, John

    2007-04-01

    Performance of the Abbott m2000 instrument system and the Abbott RealTime HIV-1 assay was evaluated using a panel of 37 group M (subtypes A-D, F, G, CRF01_AE, CRF02_AG and unique recombinant forms) and 2 group O virus isolates. Testing was performed on 273 sample dilutions and compared to VERSANT HIV-1 RNA 3.0 (bDNA) and AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) test results. RealTime HIV-1, bDNA, and Monitor v1.5 tests quantified 87%, 78%, and 81% of samples, respectively. RealTime HIV-1 detected an additional 31 samples at < 40 copies/mL. For group M, RealTime HIV-1 dilution profiles and viral loads were highly correlated with bDNA and Monitor v1.5 values; 87% and 89% of values were within 0.5 log(10) copies/mL. In contrast, the group O viruses were not detected by Monitor v1.5 and were substantially underquantified by approximately 2 log(10) copies/mL in bDNA relative to the RealTime HIV-1 assay. Sequence analysis revealed that RealTime HIV-1 primer/probe binding sites are highly conserved and exhibit fewer nucleotide mismatches relative to Monitor v1.5. The automated m2000 system and RealTime HIV-1 assay offer the advantages of efficient sample processing and throughput with reduced "hands-on" time while providing improved sensitivity, expanded dynamic range and reliable quantification of genetically diverse HIV-1 strains.

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

    PubMed

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

    2007-05-01

    One of the most interesting aspects of real-time PCR based on the detection of fluorophoric labeled oligonucleotides is the possibility of being able to detect conveniently multiple targets in the same PCR reaction. Recently, Roche Diagnostics launched a real-time PCR platform, the LightCycler480 (LC480), which should be well suited for multiplex real-time PCR analysis. In this paper the performance of the LC480 and accompanying software for the detection of five different targets was analyzed. Target DNAs mixed at equimolar concentrations were detected reproducibly and quantitatively. In addition, mixing different concentrations of the five targets demonstrated that the LC480 is capable of providing quantitative results for a mixture of DNA sequences without losing sensitivity. When applied to the practice of molecular diagnosis of four respiratory viral infections the multiplex assay showed almost complete concordance with corresponding single-target PCRs. The application of multiplex PCR for the detection of multiple pathogens within the same sample will provide a major contribution to the efficiency, logistics and cost-effectiveness of molecular diagnostics.

  1. Comparison of the performance of carcinogenic HPV typing of the Roche Linear Array and Qiagen LiquiChip® HPV assays.

    PubMed

    Halfon, Philippe; Sandri, Maria Teresa; Raimondo, Audrey; Ravet, Sophie; Khiri, Hacène; Sideri, Mario; Penaranda, Guillaume; Camus, Claire; Mateos Lindemann, Maria Luisa

    2013-10-24

    Cervical cancer is caused by high-risk types of human papillomavirus (HPV). DNA testing of such high-risk types of HPV could improve cervical screening.The aim of the study was to compare the sensitivities and positive predictive values of two commercially available typing assays (Qiagen LQ and Roche LA) and to comparatively assess the distribution of HPV types with these two assays. The study population comprised 311 ASCUS + women with abnormal pap tests who were HCII positive and who were admitted to three European referral gynecology clinics between 2007 and 2010 (Madrid, Marseille and Milan). All patients underwent LQ and LA tests. The sensitivity of the two assays for HPV typing was 94% for LQ and 99% for LA (compared with HCII). The overall concordance between LQ and LA was 93%. The three prevalent genotypes, HPV16, HPV18, and HPV31, were identified with a high concordance using the two assays: kappa 0.93, 0.83, and 0.91, respectively. Mixed genotypes were more frequently detected by LA than by LQ: 52% vs. 18%, respectively (p < .0001). These assays have a good clinical sensitivity for detecting HPV types in CIN2+ patients and allow the virus type to be detected in the same experiment. Our study revealed no significant difference between LQ and LA for CIN2+ or CIN3+ diagnosis, indicating similar distributions of HPV types and a mixed genotype detection that is higher for LA than for LQ.

  2. THE ROCHE LIMIT FOR CLOSE-ORBITING PLANETS: MINIMUM DENSITY, COMPOSITION CONSTRAINTS, AND APPLICATION TO THE 4.2 hr PLANET KOI 1843.03

    SciTech Connect

    Rappaport, Saul; Sanchis-Ojeda, Roberto; Winn, Joshua N.; Rogers, Leslie A.; Levine, Alan E-mail: sar@mit.edu E-mail: larogers@caltech.edu

    2013-08-10

    The requirement that a planet must orbit outside of its Roche limit gives a lower limit on the planet's mean density. The minimum density depends almost entirely on the orbital period and is immune to systematic errors in the stellar properties. We consider the implications of this density constraint for the newly identified class of small planets with periods shorter than half a day. When the planet's radius is accurately known, this lower limit to the density can be used to restrict the possible combinations of iron and rock within the planet. Applied to KOI 1843.03, a 0.6 R{sub Circled-Plus} planet with the shortest known orbital period of 4.245 hr, the planet's mean density must be {approx}> 7 g cm{sup -3}. By modeling the planetary interior subject to this constraint, we find that the composition of the planet must be mostly iron, with at most a modest fraction of silicates ({approx}< 30% by mass)

  3. Universal human papillomavirus genotyping by the digene HPV Genotyping RH and LQ Tests.

    PubMed

    Geraets, D T; Lenselink, C H; Bekkers, R L M; van Doorn, L J; Quint, W G V; Melchers, W J G

    2011-04-01

    High-risk (hr)HPV testing plays an important role in primary cervical cancer screening. Subsequent hrHPV genotyping might contribute to better risk stratification. The majority of hrHPV tests do not include identification of individual hrHPV genotypes. The digene HPV Genotyping RH Test (strip-based) and LQ Test (xMAP-based) allow genotyping of GP5+/6+ amplimers, but their probes target a region in the L1 ORF, which is also amplified by other broad-spectrum hrHPV assays, e.g., the Roche Amplicor HPV Test (Amplicor) and the Roche Linear Array. The goal was to test whether the RH Test and LQ Test can be used as an universal hrHPV genotyping test. Self-collected cervico-vaginal specimens (n=416) from an epidemiologic study were analyzed with Amplicor. The amplimers obtained were also tested with the RH Test and LQ Test for identification of 18 HPV types, including the 13 hrHPVs targeted by Amplicor. 197 specimens were positive by Amplicor, in which the RH Test and LQ Test identified one of the 13 hrHPVs in 94.4% and 98.0%, respectively. In 219 specimens remaining negative by Amplicor, the RH Test and LQ Test, performed on the Amplicor amplification products, still detected one of the 13 hrHPVs in 3.7% and 5.5%, respectively, and include identification of HPV53, 66, and 82. Overall, the RH and LQ Tests demonstrated high concordance with Amplicor for hrHPV detection (κ=0.908 and κ=0.923, respectively). The digene HPV Genotyping RH and LQ Tests can be directly used for amplimers generated by the Amplicor HPV Test. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Comparative evaluation of the Abbott HIV-1 RealTime™ assay with the Standard Roche COBAS® Amplicor™ HIV-1 Monitor® Test, v1.5 for determining HIV-1 RNA levels in plasma specimens from Pune, India.

    PubMed

    Khopkar, Priyanka; Mallav, Vikas; Chidrawar, Shweta; Kulkarni, Smita

    2013-07-01

    The implementation of cost effective HIV-1 viral load assays in resource-limited settings have been an impediment for monitoring HIV-1 therapy. A study involving the comparative analytical performance of two HIV-1 viral load assays - Standard Roche COBAS(®) Amplicor™ HIV-1 Monitor(®) Test, version 1.5 (Roche Diagnostics, Basel, Switzerland) and Abbott HIV-1 RealTime™ assay (Abbott Molecular, Wiesbaden, Germany) was performed using 125 specimens in Pune, India. A strong correlation was observed between the manual endpoint reverse transcriptase polymerase chain reaction assay and the recent real time polymerase chain reaction assay (r=0.989, p value<0.0001) and agreement was 94.4%. Results of the study indicate a higher sensitivity of the Abbott HIV-1 RealTime™ assay for HIV-1 Virology Quality Assurance copy controls as compared to the Standard Roche COBAS(®) Amplicor™ HIV-1 Monitor(®) Test, version 1.5. Furthermore, features of the Abbott m2000rt RealTime™ PCR assay platform such as higher analytical sensitivity, automated/manual extraction platforms for high/low sample throughputs and ability to quantify a variety of infectious agents (Hepatitis B virus, Hepatitis C virus, Human Papillomavirus and Neisseria gonorrhoeae/Chlamydia trachomatis) justify its suitability in resource-limited Indian settings. Besides, the study also highlights utility of the precise Virology Quality Assurance validation template in performance evaluation of various quantitative viral load assays.

  5. Lithostratigraphic position and petrographic characteristics of R.A.T. (“Roches Argilo-Talqueuses”) Subgroup, Neoproterozoic Katangan Belt (Congo)

    NASA Astrophysics Data System (ADS)

    Cailteux, J. L. H.; Kampunzu, A. B. H.; Batumike, M. J.

    2005-07-01

    The Neoproterozoic Katangan R.A.T. ("Roches Argilo-Talqueuses") Subgroup is a sedimentary sequence composed of red massive to irregularly bedded terrigenous-dolomitic rocks occurring at the base of the Katangan succession in Congo. Red R.A.T. is rarely exposed in a continuous section because it was affected by a major layer-parallel décollement during the Lufilian thrusting. However, in a number of thrust sheets, Red R.A.T. is in conformable sedimentary contact with Grey R.A.T which forms the base of the Mines Subgroup. Apart from the colour difference reflecting distinct depositional redox conditions, lithological, petrographical and geochemical features of Red and Grey R.A.T. are similar. A continuous sedimentary transition between these two lithological units is shown by the occurrence of variegated to yellowish R.A.T. The D. Strat. "Dolomies Stratifiées" formation of the Mines Subgroup conformably overlies the Grey R.A.T. In addition, a transitional gradation between Grey R.A.T. and D. Strat. occurs in most Cu-Co mines in Katanga and is marked by interbedding of Grey R.A.T.-type and D. Strat.-type layers or by a progressive petrographic and lithologic transition from R.A.T. to D. Strat. Thus, there is an unquestionable sedimentary transition between Grey R.A.T. and D. Strat. and between Grey R.A.T. and Red R.A.T. The R.A.T. Subgroup stratigraphically underlies the Mines Subgroup and therefore R.A.T. cannot be comprised of syn-orogenic sediments deposited upon the Kundelungu (formerly "Upper Kundelungu") Group as suggested by Wendorff (2000). As a consequence, the Grey R.A.T. Cu-Co mineralisation definitely is part of the Mines Subgroup Lower Orebody, and does not represent a distinct generation of stratiform Cu-Co sulphide mineralisation younger than the Roan orebodies.

  6. Laboratory blood analysis in Strigiformes-Part II: plasma biochemistry reference intervals and agreement between the Abaxis Vetscan V2 and the Roche Cobas c501.

    PubMed

    Ammersbach, Mélanie; Beaufrère, Hugues; Gionet Rollick, Annick; Tully, Thomas

    2015-03-01

    Limited plasma biochemical information is available in Strigiformes. Only one study investigated the agreement between a point-of-care with a reference laboratory analyzer for biochemistry variables in birds. The objective was to report reference intervals (RI) for plasma biochemistry variables in Strigiformes, and to assess agreement between the Abaxis Vetscan V2 and Roche Cobas c501. A prospective study was designed to assess plasma biochemistry RI for concentration of calcium, phosphorus, total protein, albumin, globulin, glucose, bilirubin, uric acid, bile acids, sodium, potassium, and chloride, and activities of AST, GGT, CK, amylase, lipase, LDH, and GLDH. In addition, the agreement between the Vetscan and the Cobas in owl species was assessed. A total of 190 individuals were sampled belonging to 12 Strigiformes species including Barn Owls, Barred Owls, Great Horned Owls, Eurasian Eagle Owls, Spectacled Owls, Eastern Screech Owls, Long-Eared Owls, Short-Eared Owls, Great Gray Owls, Snowy Owls, Northern Saw-Whet Owls, and Northern Hawk-Owls. Order-, species-, and method-specific RI were determined on both analyzers. Although Vetscan data were not equivalent to the Cobas, 4 analytes (glucose, AST, CK, and total protein, with correction for bias) were within acceptable agreement, 3 analytes (uric acid, calcium, and phosphorus) were within close agreement, and the remaining analytes were in strong disagreement. Species-specific differences were observed notably for the concentration of glucose in Barn Owls and electrolytes in Northern Saw-Whet Owls. Overall, this study suggests that the Vetscan has acceptable clinical performance in Strigiformes for some analytes and highlights discrepancies for several analytes. © 2015 American Society for Veterinary Clinical Pathology.

  7. GLM-based optimization of NGS data analysis: A case study of Roche 454, Ion Torrent PGM and Illumina NextSeq sequencing data

    PubMed Central

    de Graaf, Aniek O.; van der Reijden, Bert A.; Jansen, Joop H.

    2017-01-01

    Background There are various next-generation sequencing techniques, all of them striving to replace Sanger sequencing as the gold standard. However, false positive calls of single nucleotide variants and especially indels are a widely known problem of basically all sequencing platforms. Methods We considered three common next-generation sequencers—Roche 454, Ion Torrent PGM and Illumina NextSeq—and applied standard as well as optimized variant calling pipelines. Optimization was achieved by combining information of 23 diverse parameters characterizing the reported variants and generating individually calibrated generalized linear models. Models were calibrated using amplicon-based targeted sequencing data (19 genes, 28,775 bp) from seven to 12 myelodysplastic syndrome patients. Evaluation of the optimized pipelines and platforms was performed using sequencing data from three additional myelodysplastic syndrome patients. Results Using standard analysis methods, true mutations were missed and the obtained results contained many artifacts—no matter which platform was considered. Analysis of the parameters characterizing the true and false positive calls revealed significant platform- and variant specific differences. Application of optimized variant calling pipelines considerably improved results. 76% of all false positive single nucleotide variants and 97% of all false positive indels could be filtered out. Positive predictive values could be increased by factors of 1.07 to 1.27 in case of single nucleotide variant calling and by factors of 3.33 to 53.87 in case of indel calling. Application of the optimized variant calling pipelines leads to comparable results for all next-generation sequencing platforms analyzed. However, regarding clinical diagnostics it needs to be considered that even the optimized results still contained false positive as well as false negative calls. PMID:28222155

  8. Comparison of GMT presto assay and Roche cobas® 4800 CT/NG assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in dry swabs.

    PubMed

    de Waaij, Dewi J; Dubbink, Jan Henk; Peters, Remco P H; Ouburg, Sander; Morré, Servaas A

    2015-11-01

    Urogenital Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the most prevalent bacterial STIs worldwide. Molecular tests are the standard for the detection of CT and NG, as these are difficult to culture. The recently introduced CE-IVD marked GMT Presto assay promises to be a valuable addition in CT and NG diagnostics. The advantage of the Presto assay is that it works on many PCR systems and the DNA can be isolated by any system.We compared the Presto assay to the widely used Roche cobas® 4800 CT/NG test for the detection of CT and NG in 612 vaginal and rectal dry collected swabs. Discrepant samples were tested by the TIB MOLBIOL Lightmix Kit 480 HT CT/NG assay. The alloyed gold standard was defined as two concurring Presto and cobas® 4800 results, or, with discrepant Presto and cobas® results, two concurring results of either test together with the Lightmix Kit 480 HT CT/NG assay. For the Presto assay,we observed 77 CT positive (13%) and 22 NG positive (3,6%) vaginal samples, and 41 CT positive (6,7%) and 11 NG positive (1,8%) rectal samples. For the cobas® 4800 assay,we observed 77 CT positive (13%) and 21NG positive (3,4%) vaginal samples, and 39 CT positive (6,4%) and 11 NG positive (1,8%) rectal samples. Ten CT samples were discrepant between Presto and cobas® 4800 CT/NG assays, while two NG samples were discrepant. CT sensitivity in both assays was 100% compared to the alloyed gold standard. The sensitivity was 100% for both vaginal and rectal dry swabs, underlining the suitability of these sample types for detection of CT and NG. The Presto assay is therefore valuable for molecular detection of CT and NG in dry vaginal and rectal swabs.

  9. Performance of the Roche cobas 4800 high-risk human papillomavirus test in cytologic preparations of squamous cell carcinoma of the head and neck.

    PubMed

    Kerr, Darcy A; Pitman, Martha B; Sweeney, Brenda; Arpin, Ronald N; Wilbur, David C; Faquin, William C

    2014-03-01

    Determining high-risk human papillomavirus (HR-HPV) status of head and neck squamous cell carcinoma (HNSCC) defines a tumor subset with important clinical implications. Cytologic sampling often provides the sentinel or sole diagnostic specimen. The authors assessed the performance characteristics for the Roche cobas 4800 HPV real-time polymerase chain reaction (PCR)-based system (cobas) on cytologic specimens of HNSCC compared with standard methods of in situ hybridization (ISH) for HR-HPV and immunohistochemistry (IHC) for p16 on formalin-fixed, paraffin-embedded (FFPE) tissue. Samples of HNSCC were collected by fine-needle aspiration and from surgical biopsies or resections, fixed, and processed with the cobas system. Available corresponding FFPE samples were synchronously evaluated for HR-HPV using ISH and IHC. Discrepant cases underwent additional PCR studies for adjudication. Thirty-six samples from 33 patients were analyzed. Forty-two percent (n = 15) of tumors were positive for HR-HPV according to cobas. Corresponding histology with ISH (n = 30) was concordant in 91% of samples. Compared with the adjudication PCR standard, there were 3 false-positive cases according to cobas. Ninety-two percent (n = 12) of cases were the HPV16 subtype. The overall sensitivity for the cobas system was 100%, and the specificity was 86%. Concordance in HNSCC HR-HPV status between cobas and ISH/IHC was > 90%, and cobas demonstrated a sensitivity of 100% and a specificity of 86%, broadening options for HR-HPV testing of fine-needle aspiration samples. Advantages for this system include subtyping of HR-HPV and the ability to discern HR-HPV status earlier in a patient's treatment course. © 2013 American Cancer Society.

  10. Comparison of the clinical performance of restriction fragment mass polymorphism (RFMP) and Roche linear array HPV test assays for HPV detection and genotyping.

    PubMed

    Lee, Hyo-Pyo; Cho, Woojae; Bae, Jae-Man; Shin, Ji Young; Shin, Soo-Kyung; Hwang, Sun Young; Min, Kyung Tae; Kim, Soo Nyung; Lee, Sun Joo; Kim, Soo-Ok; Yoo, Wang Don; Hong, Sun Pyo

    2013-06-01

    The need for accurate genotyping of human papillomavirus (HPV) infections is becoming increasingly important as HPV is the primary cause of cervical cancer worldwide. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry-based restriction fragment mass polymorphism (RFMP) assay provides accurate, broad-spectrum, high-throughput genotyping of HPV. We evaluated the clinical performance of the RFMP assay compared to a commercially available Roche linear array HPV genotyping test (LA) for detecting and genotyping of HPV. The RFMP assay and the LA were compared for detecting and genotyping HPV among a cohort of 244 liquid-based cytology samples. Overall, 216 specimens (93.1%, κ = 0.86) generated concordant results for the presence or absence of high-risk HPV (HR-HPV) by the two assays. The RFMP assay and the LA assay generated concordant, compatible, and discordant genotyping results for 79.3, 9.9, and 10.8%, respectively. The diagnostic sensitivity and specificity of RFMP and LA for the cervical lesions of squamous cell carcinoma (SCC) were similar, at 92.9 and 85.0% (RFMP) and 92.9 and 83.8% (LA), respectively. In addition, the odds ratio for SCC with HR-HPV positivity estimated by the RFMP assay (73.7, 95% CI: 8.9-3173.3) was higher than the LA assay (67.0, 95% CI: 8.2-2887.0). The RFMP and the LA assays were highly comparable with regard to detection and genotyping analysis of HPV. The sensitivity and specificity of RFMP assay for the detection of HR-HPV in various levels of cervical lesions seems to be valuable in the monitoring of HPV-associated cervical cancer. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Roche/BIOTECON Diagnostics LightCycler foodproof L. monocytogenes detection kit in combination with ShortPrep foodproof II Kit. Performance-Tested Method 070401.

    PubMed

    Junge, Benjamin; Berghof-Jäger, Kornelia

    2006-01-01

    A method was developed for the detection of L. monocytogenes in food based on real-time polymerase chain reaction (PCR). This advanced PCR method was designed to reduce the time needed to achieve results from PCR reactions and to enable the user to monitor the amplification of the PCR product simultaneously, in real-time. After DNA isolation using the Roche/BIOTECON Diagnostics ShortPrep foodproof II Kit (formerly called Listeria ShortPrep Kit) designed for the rapid preparation of L. monocytogenes DNA for direct use in PCR, the real-time detection of L. monocytogenes DNA is performed by using the Roche/BIOTECON Diagnostics LightCycler foodproof L. monocytogenes Detection Kit. This kit provides primers and hybridization probes for sequence-specific detection, convenient premixed reagents, and different controls for reliable interpretation of results. For repeatability studies, 20 different foods, covering the 15 food groups recommended from the AOAC Research Institute (AOAC RI) for L. monocytogenes detection were analyzed: raw meats, fresh produce/vegetables, processed meats, seafood, egg and egg products, dairy (cultured/noncultured), spices, dry foods, fruit/juices, uncooked pasta, nuts, confectionery, pet food, food dyes and colorings, and miscellaneous. From each food 20, samples were inoculated with a low level (1-10 colony-forming units (CFU)/25 g) and 20 samples with a high level (10-50 CFU/25 g) of L. monocytogenes. Additionally, 5 uninoculated samples were prepared from each food. The food samples were examined with the test kits and in correlation with the cultural methods according to U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) or U.S. Department of Agriculture (USDA)/Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook. After 48 h of incubation, the PCR method in all cases showed equal or better results than the reference cultural FDA/BAM or USDA/FSIS methods. Fifteen out of 20 tested food types

  12. Comparison of the Roche cobas® 4800 and Digene Hybrid Capture® 2 HPV tests for primary cervical cancer screening in the HPV FOCAL trial.

    PubMed

    Cook, Darrel A; Mei, Wendy; Smith, Laurie W; van Niekerk, Dirk J; Ceballos, Kathy; Franco, Eduardo L; Coldman, Andrew J; Ogilvie, Gina S; Krajden, Mel

    2015-12-16

    HPV FOCAL is a randomized trial (ISRCTN79347302, registered 20 Apr 2007) comparing high-risk (hr) HPV testing vs. liquid-based cytology (LBC) for cervical cancer screening of women aged 25-65. We compared the Digene Hybrid Capture® 2 High-Risk HPV DNA Test® (HC2) and the Roche cobas® 4800 HPV Test (COBAS) for primary screening. Women (n=6,172) were screened at baseline by HC2 and COBAS and by LBC 24 months later. We assessed HPV genotyping and reflex LBC for colposcopy triage of baseline HPV positive women. Overall HC2/COBAS agreement was 96.1% (kappa 0.75) and positive agreement was 77.5%. Baseline CIN2 and CIN3+ rates based on HPV screening were 8.6/1,000 and 6.6/1,000 respectively; 24 month rates were 0.7/1,000 and 0.4/1,000 (LBC screening). HC2 and COBAS were concordant positive for 91% of round 1 CIN2 and 98% of CIN3+. CIN3+ was significantly associated with HPV 16 (Odds Ratio [OR] 5.11; 95% confidence interval [CI] 2.30, 11.37), but not HPV 18 (OR 2.62; 95% CI 0.73, 9.49), vs. non-HPV 16/18 HPV at baseline. There was no significant association between HPV genotype and CIN2. CIN3+ was significantly more likely for high-grade (OR 5.99; 95% CI 2.53, 14.18), but not low-grade (OR 0.54; 95% CI 0.20, 1.49), vs. negative LBC. No significant association was observed between LBC grade and CIN2. HPV 16 and 18 were associated with 33% of CIN2 and 68% of CIN3+ identified at baseline. For hrHPV positive women, abnormal reflex LBC is appropriate for colposcopy triage. In addition, immediate referral of women with HPV 16/18 and normal cytology may allow for earlier detection of CIN2+ lesions which would not be detected until after follow-up testing.

  13. An analysis of human papillomavirus testing and endocervical component on pap tests: A pilot study using the Roche Cobas(®) assay.

    PubMed

    Pierce, Kirsten J; Currens, Heather S; Tafe, Laura J; Tsongalis, Gregory J; Padmanabhan, Vijayalakshmi

    2016-04-01

    HPV is known to have a predilection for infecting the transformation zone (TZ). Endocervical cells (EC) on a Pap test (PT) indicate that the cervical TZ has been sampled. Earlier repeat testing of women lacking EC is of little value in further detecting disease, thus a sample without EC is not necessarily inadequate. Both HPV testing and PT can be performed using a single sample; however, few studies have investigated the relationship between HPV results and TZ sampling. Specimens were collected following the ThinPrep(®) liquid-based PT protocol. The Roche Cobas(®) HPV test was performed on post-aliquot samples. Data was collected retrospectively on 500 patients: 250 consecutive cases of EC- and 250 of EC+ on PT. To maintain uniformity, we included only cases diagnosed as negative (NILM). We compared HPV test results within each category. As a positive control, five consecutive cases each of LSIL and HSIL were also reviewed. Of NILM cases, 11 of 250 EC+ cases and 14 of 250 EC- cases were positive for hrHPV. HPV 16 was present in 5 of 11 EC + cases and in 1 of 14 EC- cases. Of LSIL cases, 1 of 5 EC+ cases was positive for hrHPV, and 2 of 5 EC- cases were positive for hrHPV. Of HSIL cases, 5 of 5 EC+ cases were hrHPV+. In the time period studied, only one case of EC- HSIL was found, which was positive for hrHPV. Although our study did not prove a significant correlation between HPV testing results and EC on PT, more EC+ PTs were positive for HPV16 compared to EC- PTs. The absence of EC on PT does not appear to warrant re-testing for HPV infection, though larger studies are required to determine the significance of low HPV 16 in PT without EC. Diagn. Cytopathol. 2016;44:280-282. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

    PubMed

    Pas, S; Molenkamp, R; Schinkel, J; Rebers, S; Copra, C; Seven-Deniz, S; Thamke, D; de Knegt, R J; Haagmans, B L; Schutten, M

    2013-01-01

    To evaluate the analytical performance and explore the clinical applicability of the new Roche cobas AmpliPrep/cobas TaqMan HCV test, v2.0 (CAP/CTM v2.0), a platform comparison was performed on panels and diagnostic samples with the Roche cobas AmpliPrep/cobas TaqMan HCV test (CAP/CTM v1.0), the Siemens Versant HCV RNA 3.0 branched DNA (bDNA) test, the Abbott m2000 RealTime HCV assay (Realtime assay), and the Siemens Versant HCV transcription-mediated amplification (TMA) test (TMA assay). The analytical performance of the CAP/CTM v2.0 on WHO and Acrometrix panels and clinical specimens of patients infected with HCV genotype 1, 2, 3, 4, 5, or 6 relative to that of the CAP/CTM v1.0 was significantly improved. In a qualitative comparison of the CAP/CTM v2.0 relative to the TMA assay on genotype 1 to 4 samples, the two tests proved to be almost equally sensitive. Response-guided therapy in one of five HCV genotype 4-infected patients previously tested with the CAP/CTM v1.0 would have significantly changed if tested with the CAP/CTM v2.0. In conclusion, the Roche CAP/CTM v2.0 has significantly better performance characteristics than the former CAP/CTM HCV v1.0 and the bDNA assay and performance characteristics comparable to those of the Realtime assay.

  15. Total vitamin D assay comparison of the Roche Diagnostics "Vitamin D total" electrochemiluminescence protein binding assay with the Chromsystems HPLC method in a population with both D2 and D3 forms of vitamin D.

    PubMed

    Abdel-Wareth, Laila; Haq, Afrozul; Turner, Andrew; Khan, Shoukat; Salem, Arwa; Mustafa, Faten; Hussein, Nafiz; Pallinalakam, Fasila; Grundy, Louisa; Patras, Gemma; Rajah, Jaishen

    2013-03-22

    This study compared two methods of assaying the 25-hydroxylated metabolites of cholecalciferol (vitamin D3) and ergocalciferol (vitamin D2). A fully automated electrochemiluminescence assay from Roche Diagnostics and an HPLC based method from Chromsystems were used to measure vitamin D levels in surplus sera from 96 individuals, where the majority has the D2 form of the vitamin. Deming regression, concordance rate, correlation and Altman Bland agreement were performed. Seventy two subjects (75%) had a D2 concentration >10 nmol/L while the remaining twenty four subjects had vitamin D2 concentration of less than 10 nmol/L by HPLC. Overall, the Roche Diagnostics method showed a negative bias of -2.59 ± 4.11 nmol/L on the e602 as compared to the HPLC with a concordance rate of 84%. The concordance rate was 91% in samples with D2 of less than 10 nmol/L and 82% in those with D2 concentration >10 nmol/L. The overall correlation had an r value of 0.77. The r value was higher in samples with D2 levels of less than 10 nmol/L, r = 0.96, as compared to those with D2 values of greater than 10 nmol/L, r = 0.74. The observed bias had little impact on clinical decision and therefore is clinically acceptable.

  16. Total Vitamin D Assay Comparison of the Roche Diagnostics “Vitamin D Total” Electrochemiluminescence Protein Binding Assay with the Chromsystems HPLC Method in a Population with both D2 and D3 forms of Vitamin D

    PubMed Central

    Abdel-Wareth, Laila; Haq, Afrozul; Turner, Andrew; Khan, Shoukat; Salem, Arwa; Mustafa, Faten; Hussein, Nafiz; Pallinalakam, Fasila; Grundy, Louisa; Patras, Gemma; Rajah, Jaishen

    2013-01-01

    This study compared two methods of assaying the 25-hydroxylated metabolites of cholecalciferol (vitamin D3) and ergocalciferol (vitamin D2). A fully automated electrochemiluminescence assay from Roche Diagnostics and an HPLC based method from Chromsystems were used to measure vitamin D levels in surplus sera from 96 individuals, where the majority has the D2 form of the vitamin. Deming regression, concordance rate, correlation and Altman Bland agreement were performed. Seventy two subjects (75%) had a D2 concentration >10 nmol/L while the remaining twenty four subjects had vitamin D2 concentration of less than 10 nmol/L by HPLC. Overall, the Roche Diagnostics method showed a negative bias of −2.59 ± 4.11 nmol/L on the e602 as compared to the HPLC with a concordance rate of 84%. The concordance rate was 91% in samples with D2 of less than 10 nmol/L and 82% in those with D2 concentration >10 nmol/L. The overall correlation had an r value of 0.77. The r value was higher in samples with D2 levels of less than 10 nmol/L, r = 0.96, as compared to those with D2 values of greater than 10 nmol/L, r = 0.74. The observed bias had little impact on clinical decision and therefore is clinically acceptable. PMID:23525081

  17. Comparison of nested and ELISA based polymerase chain reaction assays for detecting Chlamydia trachomatis in pregnant women with preterm complications.

    PubMed

    Sulaiman, S; Chong, P P; Mokhtarudin, R; Lye, M S; Wan Hassan, W H

    2014-03-01

    Identification of pregnant women infected with Chlamydia trachomatis is essential to allow early antibiotic treatment in order to prevent adverse pregnancy outcomes. In this study, two nucleic acid amplification tests (NAAT) namely nested PCR (BioSewoom, Korea) and Amplicor CT/NG (Roche Diagnostic, USA) were evaluated in terms of sensitivity and specificity for the detection of C. trachomatis DNA in pregnant women with preterm complications. A cross-sectional study was carried out in two public hospitals in Southern Selangor, Malaysia. Endocervical swabs obtained were subjected to DNA amplification using nested PCR (BioSewoom, Korea) and Amplicor CT/NG (Roche Diagnostic, USA). A total of 83 endocervical swabs obtained from pregnant women of less than 37 weeks gestation and presented with preterm complications were subjected to chlamydial DNA detection using both assays. The study shows that Amplicor CT/NG assay is more effective in the detection of C. trachomatis DNA from endocervical swabs compared to Biosewoom nested PCR kit. Agreement between the two assays were poor (kappa=0.094) with nested PCR showing a low sensitivity of 10.81% and a 97.83% specificity when compared to Amplicor CT/NG. The results obtained indicated that BioSewoom nested PCR was less sensitive than Amplicor CT/ NG for detecting C. trachomatis in endocervical specimens and that another more reliable test is required for confirmatory result.

  18. Comparison of the Digene Hybrid Capture System Cytomegalovirus (CMV) DNA (version 2.0), Roche CMV UL54 analyte-specific reagent, and QIAGEN RealArt CMV LightCycler PCR reagent tests using AcroMetrix OptiQuant CMV DNA quantification panels and specimens from allogeneic-stem-cell transplant recipients.

    PubMed

    Hanson, Kimberly E; Reller, L Barth; Kurtzberg, Joanne; Horwitz, Mitchell; Long, Gwynn; Alexander, Barbara D

    2007-06-01

    The Digene Hybrid Capture system cytomegalovirus (CMV) DNA (version 2.0), Roche CMV UL54 analyte-specific reagent, and QIAGEN RealArt CMV LightCycler PCR reagent tests were compared using whole-virus standards and plasma specimens collected from allogeneic-stem-cell transplant recipients. PCR assays showed better speed, sensitivity, and specificity.

  19. Relationship between cyclosporine concentrations obtained using the Roche Cobas Integra and Abbott TDx monoclonal immunoassays in pre-dose and two hour post-dose blood samples from kidney transplant recipients.

    PubMed

    Garrido, Manuel J; Hermida, Jesús; Tutor, J Carlos

    2002-12-01

    Current evidence suggests that cyclosporine (CsA) concentration in blood samples taken 2 hours after Neoral microemulsion (Novartis Pharmaceuticals; East Hanover, NJ) administration (C2) predicts clinical events in transplant patients better than the pre-dose (trough) concentration (C0). Similarly, previous findings have shown that the metabolites/CsA ratio is substantially lower in C2 than in C0 samples; however the between-monoclonal immunoassay differences for C2 samples have received little attention in the literature. In 56 C samples and 60 C samples from renal transplant patients, CsA levels were determined using the monoclonal fluorescence polarization immunoassay (mFPIA) from Abbott (Abbott Park, IL) and the homogeneous enzyme immunoassay technique (HEIT) from Roche Diagnostics (Basel, Switzerland). In both cases a high correlation coefficient between the results was obtained (r > or = 0.971), with a linear regression for C0 samples: mFPIA = 1.47 HEIT + 22.0 and for C2 samples: mFPIA = 1.11 HEIT + 71.96. The difference between the linear regression slopes was statistically significant (P < 0.001), and the mFPIA/HEIT ratio was significantly higher for C than for C samples (P < 0.001).

  20. Comparative evaluation of the Aptima HIV-1 Quant Dx assay and COBAS TaqMan HIV-1 v2.0 assay using the Roche High Pure System for the quantification of HIV-1 RNA in plasma.

    PubMed

    Schalasta, Gunnar; Börner, Anna; Speicher, Andrea; Enders, Martin

    2016-03-01

    Quantification of human immunodeficiency virus type 1 (HIV-1) RNA in plasma has become the standard of care in the management of HIV-infected patients. There are several commercially available assays that have been implemented for the detection of HIV-1 RNA in plasma. Here, the new Hologic Aptima® HIV-1 Quant Dx assay (Aptima HIV) was compared to the Roche COBAS® TaqMan® HIV-1 Test v2.0 for use with the High Pure System (HPS/CTM). The performance characteristics of the assays were assessed using commercially available HIV reference panels, dilution of the WHO 3rd International HIV-1 RNA International Standard (WHO-IS) and plasma from clinical specimens. Assay performance was determined by linear regression, Deming correlation analysis and Bland-Altman analysis. Testing of HIV-1 reference panels revealed excellent agreement. The 61 clinical specimens quantified in both assays were linearly associated and strongly correlated. The Aptima HIV assay offers performance comparable to that of the HPS/CTM assay and, as it is run on a fully automated platform, a significantly improved workflow.

  1. Diagnostic single nucleotide polymorphism analysis of factor V Leiden and prothrombin 20210G > A. A comparison of the Nanogen Eelectronic Microarray with restriction enzyme digestion and the Roche LightCycler.

    PubMed

    Schrijver, Iris; Lay, Marla J; Zehnder, James L

    2003-04-01

    Genetic thrombosis risk factors include a sequence variant in the prothrombin gene (20210G > A) and factor V Leiden (1691G > A). These single nucleotide polymorphisms can be diagnosed with restriction fragment length polymorphism (RFLP) analysis, fluorescent genotyping on the LightCycler (Roche Diagnostics, Indianapolis, IN), and microarray-based testing on the novel NanoChip electronic microarray (NanoChip Molecular Biology Workstation, Nanogen, San Diego, CA). We compared these methods for accuracy, time to results, throughput, and interpretation. Results from 789 of 800 individual amplicons analyzed on the NanoChip were in complete agreement with the other assays. Eleven were "no calls" (uninterpreted by the NanoChip system) resulting from failed polymerase chain reaction amplifications. Although the NanoChip System, when used in a low-throughput setting, requires more overall time than the LightCycler, it is nearly equivalent per genotyping call. Owing to minimal sample handling, assay results are more reliable on the NanoChip platform and on the LightCycler than with RFLP. The NanoChip assay is reliable and may be especially valuable to laboratories with a large volume of thrombophilia test requests.

  2. [Detection of Staphylococcus aureus resistant to methicillin (MRSA) by molecular biology (Cepheid GeneXpert IL, GeneOhm BD, Roche LightCycler, Hyplex Evigene I2A) versus screening by culture: Economic and practical strategy for the laboratory].

    PubMed

    Laudat, P; Demondion, E; Jouannet, C; Charron, J; Chillou, C; Salaun, V; Mankikian, B

    2012-06-01

    Patients admitted in cardiac surgery and cardiac ICU at the Clinic Saint-Gatien (Tours) are screened for MRSA at the entrance by nasal swab and culture on blood agar and selective chromogenic medium made by addition of cefoxitin: BBL CHROMagar MRSA-II BD (result obtained at Day +1). We wanted to assess the molecular biology techniques available to obtain a result at day 0 for the majority of patients and to define an economic and practical strategy for the laboratory. We studied four molecular biology techniques: Cepheid GeneXpert (Cepheid) GeneOhm (BD), LightCycler (Roche) and Hyplex (I2A). Upon reception, nasal swabs were treated by culture, considered as reference, and one of the techniques of molecular biology, according to the manufacturer's notice. We conducted four studies between April 2008 and February 2009 to obtain a significant sample for each of them. By screening we mean a method that allows us to exclude MRSA carriage for patients waiting for surgery, and not to change patient management: for example, lack of isolation measures specific to entrance, no modification of antibiotic prophylaxis during surgery and no isolation measures in the immediate postoperative period. The criteria we considered for this evaluation were: (1) technician time: time to perform one or a series of sample(s) n=10 or more (about 2h for all techniques except GeneXpert 75min), level of skilled competences (no specific training for GeneXpert); (2) results: turnaround time (all molecular biology techniques), ease of reading and results interpretations (no specialized training required for GeneXpert), failure or not (12% of failure of internal controls for GeneOhm); (3) economic: cost for one or a series of sample(s) (n=10 or more), if we considered X as the reference culture cost (10 X Hyplex and LightCycler, 20 X and 40 X for GeneXpert GeneOhm); (4) NPV: 100% for GeneXpert and LightCycler. At same sensitivity, no technique, including culture, can solve alone our problem, which

  3. [Evaluation of COBAS TaqMan: a real-time PCR-based diagnostic kit for mycobacteria].

    PubMed

    Yonemaru, Makoto; Horiba, Masahide; Tada, Atsuhiko; Nagai, Takayuki

    2009-12-01

    The real-time PCR-based diagnostic kits, COBAS TaqMan MTB and COBAS TaqMan MAI (Roche Diagnostics, Tokyo, Japan), were developed to detect Mycobacterium tuberculosis (MTB) and M. avium (MAV)/M. intracellulare (MIN), respectively. The TaqMan kits simultaneously perform amplification and detection of mycobacterial DNA to reduce assay time. We evaluated the diagnostic accuracy of both TaqMan kits in 781 clinical specimens, and compared the results with those obtained from the AMPLICOR MTB and MAI kits. With smear-positive specimens, the TaqMan kits showed 100% concordance with AMPLICOR in MTB, MAV and MIN. With all specimens, the concordances of TaqMan with AMPLICOR were 99.1%, 99.0%, and 99.7% in MTB, MAV and MIN, respectively. Four specimens for MTB and one for MAV were AMPLICOR positive/TaqMan negative. Among them, two specimens were culture-positive for MTB and one for MAV. Three specimens for MTB, seven for MAV, and two for MIN were AMPLICOR negative/TaqMan positive. Among them, two specimens were culture-positive for MTB, seven for MAV, and one for MIN. In twelve out of 21 specimens in which AMPLICOR failed to activate PCR, TaqMan successfully determined the results which were in concordance with those of mycobacterial culture. Thus, our data suggest that the accuracy of TaqMan in detecting mycobacterial DNA is superior to that of AMPLICOR. We conclude that TaqMan, which is an easy and rapid DNA amplification test, is useful for detecting MTB, MAV and MIN.

  4. Comparison of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 test v1.0 with v2.0 in HIV-1 viral load quantification.

    PubMed

    Tung, Yi-Ching; Ke, Liang-Yin; Lu, Po-Liang; Lin, Kuei-Hsiang; Lee, Su-Chen; Lin, Yi-Ying; Chou, Li-Chiu; Tsai, Wen-Chan

    2015-04-01

    Roche modified the COBAS AmpliPrep/COBAS TaqMan human immunodeficiency virus type 1 (HIV-1) test version 1.0 (CAP/CTM v1.0), resulting in the COBAS AmpliPrep/COBAS TaqMan HIV-1 test version 2.0 (CAP/CTM v2.0). The aim of this study was to evaluate the performance of the CAP/CTM v2.0 and to compare this performance with that of the CAP/CTM v1.0. The study was conducted in a small local study group in Kaohsiung Medical University Hospital, Kaohsiung, Taiwan. A total of 86 plasma samples from HIV-1-seropositive patients were tested using the two assays. The correlation and concordance of results between the two assays were calculated. The CAP/CTM v2.0 generated higher values than did the CAP/CTM v1.0, and five samples (5.8%) yielded a difference of > 1 log10 copies/mL. In addition, our data show that CAP/CTM v1.0 and CAP/CTM v2.0 yielded relatively consistent values for 23 samples with low viral loads (< 200 copies/mL). Furthermore, when viral loads were in a medium range (2-5 log10 copies/mL), the results of the two assays were more compatible. This study shows a good correlation between CAP/CTM v1.0 and v2.0 in HIV-1 viral load measurement. Further attention must be paid to those cases in which measured viral loads present larger differences between the two assays.

  5. Comparison of the Abbott RealTime High-Risk Human Papillomavirus (HPV), Roche Cobas HPV, and Hybrid Capture 2 assays to direct sequencing and genotyping of HPV DNA.

    PubMed

    Park, Yongjung; Lee, Eunhee; Choi, Jonghyeon; Jeong, Seri; Kim, Hyon-Suk

    2012-07-01

    Infection with high-risk (HR) human papillomavirus (HPV) genotypes is an important risk factor for cervical cancers. We evaluated the clinical performances of two new real-time PCR assays for detecting HR HPVs compared to that of the Hybrid Capture 2 test (HC2). A total of 356 cervical swab specimens, which had been examined for cervical cytology, were assayed by Abbott RealTime HR and Roche Cobas HPV as well as HC2. Sensitivities and specificities of these assays were determined based on the criteria that concordant results among the three assays were regarded as true-positive or -negative and that the results of genotyping and sequencing were considered true findings when the HPV assays presented discrepant results. The overall concordance rate among the results for the three assays was 82.6%, and RealTime HR and Cobas HPV assays agreed with HC2 in 86.1% and 89.9% of cases, respectively. The two real-time PCR assays agreed with each other for 89.6% of the samples, and the concordance rate between them was equal to or greater than 98.0% for detecting HPV type 16 or 18. HC2 demonstrated a sensitivity of 96.6% with a specificity of 89.1% for detecting HR HPVs, while RealTime HR presented a sensitivity of 78.3% with a specificity of 99.2%. The sensitivity and specificity of Cobas HPV for detecting HR HPVs were 91.7% and 97.0%. The new real-time PCR assays exhibited lower sensitivities for detecting HR HPVs than that of HC2. Nevertheless, the newly introduced assays have an advantage of simultaneously identifying HPV types 16 and 18 from clinical samples.

  6. CLSI-based transference of the CALIPER database of pediatric reference intervals from Abbott to Beckman, Ortho, Roche and Siemens Clinical Chemistry Assays: direct validation using reference samples from the CALIPER cohort.

    PubMed

    Estey, Mathew P; Cohen, Ashley H; Colantonio, David A; Chan, Man Khun; Marvasti, Tina Binesh; Randell, Edward; Delvin, Edgard; Cousineau, Jocelyne; Grey, Vijaylaxmi; Greenway, Donald; Meng, Qing H; Jung, Benjamin; Bhuiyan, Jalaluddin; Seccombe, David; Adeli, Khosrow

    2013-09-01

    The CALIPER program recently established a comprehensive database of age- and sex-stratified pediatric reference intervals for 40 biochemical markers. However, this database was only directly applicable for Abbott ARCHITECT assays. We therefore sought to expand the scope of this database to biochemical assays from other major manufacturers, allowing for a much wider application of the CALIPER database. Based on CLSI C28-A3 and EP9-A2 guidelines, CALIPER reference intervals were transferred (using specific statistical criteria) to assays performed on four other commonly used clinical chemistry platforms including Beckman Coulter DxC800, Ortho Vitros 5600, Roche Cobas 6000, and Siemens Vista 1500. The resulting reference intervals were subjected to a thorough validation using 100 reference specimens (healthy community children and adolescents) from the CALIPER bio-bank, and all testing centers participated in an external quality assessment (EQA) evaluation. In general, the transferred pediatric reference intervals were similar to those established in our previous study. However, assay-specific differences in reference limits were observed for many analytes, and in some instances were considerable. The results of the EQA evaluation generally mimicked the similarities and differences in reference limits among the five manufacturers' assays. In addition, the majority of transferred reference intervals were validated through the analysis of CALIPER reference samples. This study greatly extends the utility of the CALIPER reference interval database which is now directly applicable for assays performed on five major analytical platforms in clinical use, and should permit the worldwide application of CALIPER pediatric reference intervals. Copyright © 2013 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  7. Grouped frequent sequential patterns derived from terrestrial image time series to monitor landslide behaviour - Application to the dynamics of the Sanières/Roche Plombée rockslide.

    NASA Astrophysics Data System (ADS)

    Péricault, Youen; Pothier, Catherine; Méger, Nicolas; Trouvé, Emmanuel; Vernier, Flavien; Rigotti, Christophe; Malet, Jean-Philippe

    2016-04-01

    Image time series acquired with remote sensing methods based on optical terrestrial photogrammetry have great potential for understanding and monitoring the Earth surface dynamics at local scale, and are particularly interesting for landslide monitoring. Image correlation techniques can be applied to calculate the displacement fields, in either the image geometry or the terrain geometry if orthorectification procedures are applied. The resulting products are times series of displacement vectors for each epoch in which knowledge extraction techniques can be applied to discover relevant movement patterns in space and time. We used an unsupervised method (Grouped Frequent Sequential patterns / GFS-patterns) based on the mining of the displacement field. The method was originally developed for the analysis of time series of satellite images. It involves the extraction of trends / sub-trends affecting each pixel covering at least a minimum surface area and sufficiently connected to each other. The results of the mining are presented in spatio-temporal location maps (STL-map) of each GFS-pattern. In these maps, the spatial information is given by the pixel locations and the time information is displayed using a color ramp. The method is tested on a time series of 36 optical terrestrial images of the Sanières/Roche Plombée rockslide (South East French Alps) from 28 of July to 1 September 2014. From this series 35 2D displacement fields were calculated for epochs of three days, and the time series of vector magnitude and direction were analysed with GFS-patterns / STL-map. The method allowed identifying several patterns corresponding to different kinematical behaviour of the rockslide (long-term creep at the top of the slope, surficial movement of the debris at the base of the slope). The unsupervised knowledge extraction method GFS-pattern / STL-map, originally developed to analyse time series of satellite images showed in this study real possibilities of use for

  8. Automated Extraction of Formalin-Fixed, Paraffin-Embedded Tissue for High-Risk Human Papillomavirus Testing of Head and Neck Squamous Cell Carcinomas Using the Roche Cobas 4800 System.

    PubMed

    Kerr, Darcy A; Sweeney, Brenda; Arpin, Ronald N; Ring, Melissa; Pitman, Martha B; Wilbur, David C; Faquin, William C

    2016-08-01

    -Testing for high-risk human papillomavirus (HR-HPV) in head and neck squamous cell carcinomas (HNSCCs) is important for both prognostication and clinical management. Several testing platforms are available for HR-HPV; however, effective alternative automated approaches are needed. -To assess the performance of the automated Roche cobas 4800 HPV real-time polymerase chain reaction-based system on formalin-fixed, paraffin-embedded HNSCC specimens and compare results with standard methods of in situ hybridization (ISH) and p16 immunohistochemistry. -Formalin-fixed, paraffin-embedded samples of HNSCC were collected from archival specimens in the Department of Pathology, Massachusetts General Hospital (Boston), and prepared using the automated system by deparaffinization and dehydration followed by tissue lysis. Samples were integrated into routine cervical cytology testing runs by cobas. Corresponding formalin-fixed, paraffin-embedded samples were evaluated for HR-HPV by ISH and p16 by immunohistochemistry. Discrepant cases were adjudicated by polymerase chain reaction. -Sixty-two HNSCC samples were analyzed using the automated cobas system, ISH, and immunohistochemistry. Fifty-two percent (n = 32 of 62) of formalin-fixed, paraffin-embedded tumors were positive for HR-HPV by cobas. Eighty-eight percent (n = 28 of 32) of cases were the HPV 16 subtype and 12% (n = 4 of 32) were other HR-HPV subtypes. Corresponding testing with ISH was concordant in 92% (n = 57 of 62) of cases. Compared with the adjudication polymerase chain reaction standard, there were 3 false-positive cases by cobas. -Concordance in HNSCC HR-HPV status between cobas and ISH was more than 90%. The cobas demonstrated a sensitivity of 100% and a specificity of 91% for detection of HR-HPV. Advantages favoring cobas include its automation, cost efficiency, objective results, and ease of performance.

  9. Use of Sno Strip Filter-Paper Wicks for Collection of Genital-Tract Samples Allows Reproducible Determination of Human Immunodeficiency Virus Type 1 (HIV-1) RNA Viral Load with a Commercial HIV-1 Viral Load Assay

    PubMed Central

    Sherlock, Christopher H.; Lott, Paula M.; Money, Deborah M.; Merrick, Linda; Arikan, Yasemin; Remple, Valencia P.; Craib, Kevin; Burdge, David R.

    2006-01-01

    To assess the reproducibility of measurements of cervical and vaginal human immunodeficiency virus (HIV) viral load, 92 duplicate cervical and 88 duplicate vaginal samples were collected from 13 HIV-infected women using Sno Strip filter-paper wicks. RNA was eluted from the strips, extracted, and assayed using a modified protocol for the Roche Cobas Amplicor HIV-1 Monitor assay. Pearson's correlation coefficient (R), coefficient of determination (D), and Bland-Altman plots (BA) were used to compare paired log10-transformed viral loads. Analysis of duplicate same-site samples showed good reproducibility (cervix: R = 0.72, D = 52%, BA = 89% within range; vagina: R = 0.72, D = 51%, BA = 87% within range); paired cervix/vagina measurements showed moderate correlation only (R = 0.56; D = 31.3%). Standardized sample collection and simple modification of the Roche Cobas Amplicor HIV-1 Monitor assay allows reproducible measurement of genital viral load. PMID:16517908

  10. Peer Group Learning in Roche Pharma Development

    ERIC Educational Resources Information Center

    Boulden, George P.; De Laat, Richard

    2005-01-01

    Pharma Development has used action learning to help participants in their 360[degrees] feedback programme develop their leadership competencies. The article describes how the programme was designed, supported and run across four sites over a period of 2 years. The programme was systematically evaluated and found to be successful in meeting its…

  11. Peer Group Learning in Roche Pharma Development

    ERIC Educational Resources Information Center

    Boulden, George P.; De Laat, Richard

    2005-01-01

    Pharma Development has used action learning to help participants in their 360[degrees] feedback programme develop their leadership competencies. The article describes how the programme was designed, supported and run across four sites over a period of 2 years. The programme was systematically evaluated and found to be successful in meeting its…

  12. Les roches extraterrestres d'Atacama

    NASA Astrophysics Data System (ADS)

    Gattacceca, Jerome

    2017-07-01

    With hyperarid conditions for the last several million years, the Atacama desert in Chile possesses the oldest pristine surfaces on the Earth. As a consequence, meteorites accumulate with time and can survive for several hundreds thousands years at the surface (longer than anywhere else in the world including Antarctica), until wind abrasion and chemical weathering eventually turn them into dust. We describe here our field work for meteorite recovery in the Atacama desert (Chile). Systematic search by foot conducted for the last ten years allowed recovery of more than 1000 meteorites, with up to 200 unpaired meteorites per km^2 in the best areas. This meteorite collection, besides providing its share of rare meteorites, allows studying the flux of meteorite to the Earth over the last million of years.

  13. Sex-specific 99th percentiles derived from the AACC Universal Sample Bank for the Roche Gen 5 cTnT assay: Comorbidities and statistical methods influence derivation of reference limits.

    PubMed

    Gunsolus, Ian L; Jaffe, Allan S; Sexter, Anne; Schulz, Karen; Ler, Ranka; Lindgren, Brittany; Saenger, Amy K; Love, Sara A; Apple, Fred S

    2017-09-13

    Our purpose was to determine a) overall and sex-specific 99th percentile upper reference limits (URL) and b) influences of statistical methods and comorbidities on the URLs. Heparin plasma from 838 normal subjects (423 men, 415 women) were obtained from the AACC (Universal Sample Bank). The cobas e602 measured cTnT (Roche Gen 5 assay); limit of detection (LoD), 3ng/L. Hemoglobin A1c (URL 6.5%), NT-proBNP (URL 125ng/L) and eGFR (60mL/min/1.73m(2)) were measured, along with identification of statin use, to better define normality. 99th percentile URLs were determined by the non-parametric (NP), Harrell-Davis Estimator (HDE) and Robust (R) methods. 355 men and 339 women remained after exclusions. Overall<50% of subjects had measureable concentrations ≥ LoD: 45.6% no exclusion, 43.5% after exclusion; compared to men: 68.1% no exclusion, 65.1% post exclusion; women: 22.7% no exclusion, 20.9% post exclusion. The statistical method used influenced URLs as follows: pre/post exclusion overall, NP 16/16ng/L, HDE 17/17ng/L, R not available; men NP 18/16ng/L, HDE 21/19ng/L, R 16/11ng/L; women NP 13/10ng/L, HDE 14/14ng/L, R not available. We demonstrated that a) the Gen 5 cTnT assay does not meet the IFCC guideline for high-sensitivity assays, b) surrogate biomarkers significantly lowers the URLs and c) statistical methods used impact URLs. Our data suggest lower sex-specific cTnT 99th percentiles than reported in the FDA approved package insert. We emphasize the importance of detailing the criteria used to include and exclude subjects for defining a healthy population and the statistical method used to calculate 99th percentiles and identify outliers. Copyright © 2017. Published by Elsevier Inc.

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

    PubMed

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

    2004-02-01

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

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

    PubMed Central

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

    2004-01-01

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

  16. Ability of two commercially available assays (Abbott RealTime HIV-1 and Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Version 2.0) to quantify low HIV-1 RNA Levels (<1,000 copies/milliliter): comparison with clinical samples and NIBSC working reagent for nucleic acid testing assays.

    PubMed

    Amendola, Alessandra; Marsella, Patrizia; Bloisi, Maria; Forbici, Federica; Angeletti, Claudio; Capobianchi, Maria R

    2014-06-01

    Concordance between molecular assays may be suboptimal at low HIV-1 viremia levels (<1,000 copies/ml); therefore, it may be difficult to define and compare virologic endpoints for successful and failed therapy. We compared two commercial assays (the Abbott RealTime HIV-1 and the Roche Cobas AmpliPrep/TaqMan HIV-1 version 2.0) for their ability to detect and quantify low viral loads. A comparison was performed using 167 residual clinical samples (with values ranging from "not detected" to 1,000 copies/ml, as measured by the Abbott assay) and the National Institute and Biological Standards and Control (NIBSC) HIV-1 RNA working reagent 1 for nucleic acid amplification techniques (NAT) assays (serially diluted to a range from 1 to 1,000 copies/ml). Quantitative results were compared using Lin's concordance correlation coefficient and a Bland-Altman plot. Concordance with the qualitative results was measured by Cohen's kappa statistic. With clinical samples, the degree of interassay concordance of the qualitative results at a 40-copies/ml HIV-1 RNA threshold was substantial (κ = 0.762); the correlation among the quantified samples was suboptimal (concordance correlation coefficient, 0.728; P < 0.0001); the mean difference of the values between the Roche and Abbott assays was 0.193 log10 copies/ml. Using the HIV-1 RNA working reagent 1 for NAT assays, the results provided by the Roche assay were, on average, 3 times higher than expected, while the Abbott assay showed high accuracy. The Roche assay was highly sensitive, being able to detect a level as low as 3.5 copies/ml HIV-1 RNA with 95% probability. The performance characteristics of each molecular assay should be taken into account when HIV-1 RNA threshold values for "virologic suppression," "virologic failure," "persistent low viral loads," etc., are defined and indicated in the support of clinical decisions. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  17. Evaluation of the performance of Abbott m2000 and Roche COBAS Ampliprep/COBAS Taqman assays for HIV-1 viral load determination using dried blood spots and dried plasma spots in Kenya

    PubMed Central

    Ndiege, Kenneth; Inzaule, Seth; Achieng, Rebecca; Williamson, John; Chih-Wei Chang, Joy; Ellenberger, Dennis; Nkengasong, John

    2017-01-01

    Background Routine HIV viral load testing is not widely accessible in most resource-limited settings, including Kenya. To increase access to viral load testing, alternative sample types like dried blood spots (DBS), which overcome the logistic barriers associated with plasma separation and cold chain shipment need to be considered and evaluated. The current study evaluated matched dried blood spots (DBS) and dried plasma spots (DPS) against plasma using the Abbott M 2000 (Abbott) and Roche Cobas Ampliprep/Cobas TaqMan (CAP/CTM) quantitative viral load assays in western Kenya. Methods Matched plasma DBS and DPS were obtained from 200 HIV-1 infected antiretroviral treatment (ART)-experienced patients attending patient support centers in Western Kenya. Standard quantitative assay performance parameters with accompanying 95% confidence intervals (CI) were assessed at the assays lower detection limit (400cps/ml for CAP/CTM and 550cps/ml for Abbott) using SAS version 9.2. Receiver operating curves (ROC) were further used to assess viral-load thresholds with best assay performance (reference assay CAP/CTM plasma). Results Using the Abbott test, the sensitivity and specificity, respectively, for DPS were (97.3%, [95%CI: 93.2–99.2] and 98.1% [95%CI: 89.7–100]) and those for DBS (93.9% [95%CI: 88.8–97.2] and 88.0% [95%CI: 82.2–92.4]). The correlation and agreement using paired plasma and DPS/DBS were strong, with r2 = 90.5 and rc = 68.1. The Bland-Altman relative percent change was 95.3 for DPS, (95%CI: 90.4–97.7) and 73.6 (95%CI: 51.6–86.5) for DBS. Using the CAP/CTM assay, the sensitivity for DBS was significantly higher compared to DPS (100.0% [95% CI: 97.6–100.0] vs. 94.7% [95%CI: 89.8–97.7]), while the specificity for DBS was lower: 4%, [95% CI: 0.4–13.7] compared to DPS: 94.0%, [95% CI: 83.5–98.7]. When compared under different clinical relevant thresholds, the accuracy for the Abbott assay was 95% at the 1000cps/ml cut-off with a sensitivity and

  18. Comparison of Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 (CAP/CTM v2.0) with other real-time PCR assays in HIV-1 monitoring and follow-up of low-level viral loads.

    PubMed

    Wojewoda, Christina M; Spahlinger, Timothy; Harmon, Marlene Louise; Schnellinger, Brian; Li, Qing; Dejelo, Corazon; Schmotzer, Christine; Zhou, Lan

    2013-01-01

    Viral load monitoring of HIV-1 has become standard of care in HIV-1 positive patients. In this study, we evaluated the performance characteristics of the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 (CAP/CTM v2.0) in comparison with Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 1.0 (CAP/CTM v1.0) and Abbott RealTime HIV-1 assay (m2000), with special emphasis on the quantitation of clinically controversial low-level viral loads. The performance characteristics of CAP/CTM v2.0 were confirmed by the validation study. All three assays performed comparably, with Abbott m2000 showing slightly decreased sensitivity for detection of viral loads close to the lower limit of quantitation. Follow-up of patients with low-level viral loads revealed that some of those represent single viral blips; however, a significant portion of these patients have intermittent or persistent low-positive viremia. We conclude that CAP/CTM v2.0 is an accurate and reliable assay for HIV-1 viral load monitoring.

  19. Comparison of Two Amplification Technologies for Detection and Quantitation of Human Immunodeficiency Virus Type 1 RNA in the Female Genital Tract

    PubMed Central

    Bremer, James; Nowicki, Marek; Beckner, Suzanne; Brambilla, Donald; Cronin, Mike; Herman, Steven; Kovacs, Andrea; Reichelderfer, Patricia

    2000-01-01

    Human immunodeficiency virus type 1 (HIV-1) RNA levels in female genital tract and peripheral blood samples were compared using two commercial amplification technologies: the Roche AMPLICOR HIV-1 MONITOR test and either the Organon Teknika nucleic acid sequence-based amplification (NASBA-QT) assay or the NucliSens assay. Estimates of HIV-1 RNA copy number were derived from internal kit standards and analyzed unadjusted and adjusted to a common set of external standards. We found a discordance rate of approximately 18% between the two technologies for the detection of HIV-1 in either the genital tract or peripheral blood samples. Detection discordance was not consistent among specimens or among women. There were no significant differences in adjusted or unadjusted estimates of HIV-1 RNA copy number in the genital tract samples using the AMPLICOR HIV-1 MONITOR test and either the NASBA-QT assay or the NucliSens assay. In addition, the estimated HIV-1 RNA copy number in peripheral blood samples did not differ when tested with the NucliSens assay and the AMPLICOR HIV-1 MONITOR test using kit standards. However, there was a significant difference in estimated RNA copy number between the NASBA-QT assay and the AMPLICOR HIV-1 MONITOR test for internal kit standards, which, as we have previously shown, was eliminated after adjustment with the external standards. Our results suggest that the Roche and Organon Teknika assays are equivalent for quantifying HIV-1 RNA in female genital tract specimens, although variation in detection does exist. PMID:10878061

  20. Evaluation of Six Commercial Nucleic Acid Amplification Tests for Detection of Neisseria gonorrhoeae and Other Neisseria Species▿

    PubMed Central

    Tabrizi, Sepehr N.; Unemo, Magnus; Limnios, Athena E.; Hogan, Tiffany R.; Hjelmevoll, Stig-Ove; Garland, Susanne M.; Tapsall, John

    2011-01-01

    Molecular detection of Neisseria gonorrhoeae in extragenital samples may result in false-positive results due to cross-reaction with commensal Neisseria species or Neisseria meningitidis. This study examined 450 characterized clinical culture isolates, comprising 216 N. gonorrhoeae isolates and 234 isolates of nongonococcal Neisseria species (n = 218) and 16 isolates of other closely related bacteria, with six commercial nucleic acid amplification tests (NAATs). The six NAATs tested were Gen-Probe APTIMA COMBO 2 and APTIMA GC, Roche COBAS Amplicor CT/NG and COBAS 4800 CT/NG tests, BD ProbeTec GC Qx amplified DNA assay, and Abbott RealTime CT/NG test. All assays except COBAS Amplicor CT/NG test where four (1.9%) isolates were not detected showed a positive result with all N. gonorrhoeae isolates (n = 216). Among the 234 nongonococcal isolates examined, initial results from all assays displayed some false-positive results due to cross-reactions. Specifically, the COBAS Amplicor and ProbeTec tests showed the highest number of false-positive results, detecting 33 (14.1%) and 26 (11%) nongonococcal Neisseria isolates, respectively. On the first testing, APTIMA COMBO 2, APTIMA GC, Abbott RealTime, and Roche COBAS 4800 showed lower level of cross-reactions with five (2.1%), four (1.7%), two (1%), and two (1%) of the isolates showing low-level positivity, respectively. Upon retesting of these nine nongonococcal isolates using freshly cultured colonies, none were positive by the APTIMA COMBO 2, Abbott RealTime, or COBAS 4800 test. In conclusion, the COBAS Amplicor and ProbeTec tests displayed high number of false-positive results, while the remaining NAATs showed only sporadic low-level false-positive results. Supplementary testing for confirmation of N. gonorrhoeae NAATs remains recommended with all samples tested, in particular those from extragenital sites. PMID:21813721

  1. Evaluation of Cobas TaqMan MTB PCR for detection of Mycobacterium tuberculosis.

    PubMed

    Kim, Jeong Hyun; Kim, Young Jae; Ki, Chang-Seok; Kim, Ji-Youn; Lee, Nam Yong

    2011-01-01

    Nucleic acid-based amplification tests allow the rapid detection of Mycobacterium tuberculosis. Recently, a real-time PCR assay for M. tuberculosis complex, the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), was introduced. We performed a prospective study to evaluate the diagnostic performance of the Cobas TaqMan MTB test system. A total of 406 specimens collected from 247 patients were simultaneously tested by conventional culture, Cobas Amplicor MTB PCR, and TaqMan MTB PCR. The cross-reactivity with other Mycobacterium species and the detection limit were also evaluated. Among 406 specimens, a total of 24 specimens (5.9%) were culture positive: 14 specimens were positive by both TaqMan and Amplicor MTB PCRs, while 5 specimens were positive by only TaqMan PCR. The remaining five specimens were negative by both PCR methods. Seven specimens with negative culture results were positive by TaqMan PCR, but five of these were negative by Amplicor MTB PCR. The sensitivity, specificity, and positive (PPV) and negative (NPV) predictive values were 79.1%, 98.2%, 73.1%, and 98.7% for TaqMan and 58.3%, 99.5%, 87.5%, and 97.4% for the Amplicor MTB PCR test, respectively. There was no cross-reactivity with M. tuberculosis and nontuberculous mycobacterial species. The detection limit for the Cobas TaqMan MTB PCR test was 4.0 copies/μl. The Cobas TaqMan MTB PCR test showed higher sensitivity for detection of the M. tuberculosis complex without disturbing the specificity and NPV than the Amplicor MTB PCR test.

  2. Comparison of the Roche RealTime ready Influenza A/H1N1 Detection Set with CDC A/H1N1pdm09 RT-PCR on samples from three hospitals in Ho Chi Minh City, Vietnam

    PubMed Central

    Tham, Nguyen thi; Hang, Vu thi Ty; Khanh, Trong Huu; Viet, Do Chau; Hien, Tran Tinh; Farrar, Jeremy; van Vinh Chau, Nguyen; van Doorn, H. Rogier

    2012-01-01

    Background Real-time PCR can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influenza A/H1N1 Detection Set, consisting of a generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the HA of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009 H1N1 in clinical samples. Methods We evaluated this kit against the USCDC/WHO real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh city, Vietnam. Results In the per patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8 and 97.6%, respectively; the sensitivity and specificity of HA PCR were 88.2 and 100%, respectively. In the per sample analysis, the sensitivity and specificity in nose swabs were higher than in throat swabs for both M2 and HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Conclusion Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of Influenza A virus and A/H1N1-pdm09. However, given the current status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable. PMID:22785431

  3. A Riemann-Roch Theoremfor One-Dimensional Complex Groupoids

    NASA Astrophysics Data System (ADS)

    Perrot, Denis

    We consider a smooth groupoid of the form Σ⋊Γ, where Σ is a Riemann surface and Γ a discrete pseudogroup acting on Σ by local conformal diffeomorphisms. After defining a K-cycle on the crossed product C0(Σ)⋊Γ generalising the classical Dolbeault complex, we compute its Chern character in cyclic cohomology, using the index theorem of Connes and Moscovici. This involves in particular a generalisation of the Euler class constructed from the modular automorphism group of the von Neumann algebra L∞(Σ)⋊Γ.

  4. Clinical Performance of Roche Cobas 4800 HPV Test

    PubMed Central

    Cui, Miao; Chan, Nicholas; Liu, Momo; Thai, Khanh; Malaczynska, Joanna; Singh, Ila; Zhang, David

    2014-01-01

    Evaluation of the Cobas 4800 test demonstrated that Cobas had a low rate of cross-reactivity with low-risk human papillomavirus (lrHPV), a 3.74% disconcordance rate between prealiquots and postaliquots, and failure rates of 4.57% and 1.16%, respectively, after vortexing and swirling. This study demonstrated that the Cobas test has good sensitivity, accuracy, and reproducibility for detecting 14 high-risk HPV (hrHPV) genotypes. PMID:24719443

  5. Quantitation of HIV-1 RNA in breast milk by real time PCR.

    PubMed

    Becquart, Pierre; Foulongne, Vincent; Willumsen, Juana; Rouzioux, Christine; Segondy, Michel; Van de Perre, Philippe

    2006-04-01

    HIV-1 RNA in breast milk is a strong predictor of HIV-1 transmission through breastfeeding. In the present report, breast milk samples from HIV-1 uninfected donors were spiked with dilution of quantified culture supernatant from HIV-1(NDK) infected PBMC. Two RNA extraction techniques based on silica extraction, Nuclisens (BioMerieux) and Triazol (Qiagen), two techniques based on guanidine thiocynanate/chloroforme extraction, TRIzol (Life Technologie) and Amplicor HIV-1 Monitor (Roche Diagnostic Systems), and one technique based on electrostatic adsorption on iron oxide micro beads (Promega) were compared. HIV-1 RNA was quantitated by real time PCR (LTR gene) and Amplicor HIV-1 Monitor. Combining magnetic micro beads extraction and real time PCR quantitation allowed to correctly quantify breast milk HIV-1 RNA, with a difference between the expected and measured HIV-1 RNA levels always lower than 0.3 log copies/ml. The same combination was confirmed on 25 breast milk samples from HIV-1 infected women collected in Kwazulu-Natal, South Africa, by comparing measurements with those obtained by the Amplicor HIV-1 Monitor (r(2)=0.88). Nucleic acid extraction by magnetic micro beads followed by real time PCR is a reliable, sensitive, rapid and simple procedure to quantify HIV-1 RNA in breast milk and allows for PCR inhibitors found frequently in these samples.

  6. Comparison of performance characteristics of three real-time reverse transcription-PCR test systems for detection and quantification of hepatitis C virus.

    PubMed

    Sábato, M Fernanda; Shiffman, Mitchell L; Langley, Michael R; Wilkinson, David S; Ferreira-Gonzalez, Andrea

    2007-08-01

    We evaluated the performance characteristics of three real-time reverse transcription-PCR test systems for detection and quantification of hepatitis C virus (HCV) and performed a direct comparison of the systems on the same clinical specimens. Commercial HCV panels (genotype 1b) were used to evaluate linear range, sensitivity, and precision. The Roche COBAS TaqMan HCV test for research use only (RUO) with samples processed on the MagNA Pure LC instrument (Roche RUO-MPLC) and Abbott analyte-specific reagents (ASR) with QIAGEN sample processing (Abbott ASR-Q) showed a sensitivity of 1.0 log(10) IU/ml with a linear dynamic range of 1.0 to 7.0 log(10) IU/ml. The Roche ASR in combination with the High Pure system (Roche ASR-HP) showed a sensitivity of 1.4 log(10) IU/ml with a linear dynamic range of 2.0 to 7.0 log(10) IU/ml. All of the systems showed acceptable reproducibility, the Abbott ASR-Q being the most reproducible of the three systems. Seventy-six clinical specimens (50 with detectable levels of HCV RNA and various titers and genotypes) were tested, and results were compared to those of the COBAS Amplicor HCV Monitor v2.0. Good correlation was obtained for the Roche RUO-MPLC and Abbott ASR-Q (R(2) = 0.84 and R(2) = 0.93, respectively), with better agreement for the Abbott ASR-Q. However, correlation (R(2) = 0.79) and agreement were poor for Roche ASR-HP, with bias relative to concentration and genotype. Roche ASR-HP underestimated HCV RNA for genotypes 3 and 4 as much as 2.19 log(10) IU/ml. Our study demonstrates that Roche RUO-MPLC and Abbott ASR-Q provided acceptable results and agreed sufficiently with the COBAS Amplicor HCV Monitor v2.0.

  7. Duplex detection of the Mycobacterium tuberculosis complex and medically important non-tuberculosis mycobacteria by real-time PCR based on the rnpB gene.

    PubMed

    Abdeldaim, Guma; Svensson, Erik; Blomberg, Jonas; Herrmann, Björn

    2016-11-01

    A duplex real-time PCR based on the rnpB gene was developed for Mycobacterium spp. The assay was specific for the Mycobacterium tuberculosis complex (MTB) and also detected all 19 tested species of non-tuberculous mycobacteria (NTM). The assay was evaluated on 404 clinical samples: 290 respiratory samples and 114 from tissue and other non-respiratory body sites. M. tuberculosis was detected by culture in 40 samples and in 30 samples by the assay. The MTB assay showed a sensitivity similar to Roche Cobas Amplicor MTB-PCR (Roche Molecular Systems, Pleasanton, CA, USA). There were only nine samples with non-tuberculous mycobacteria detected by culture. Six of them were detected by the PCR assay.

  8. Reliability of nucleic acid amplification methods for detection of Chlamydia trachomatis in urine: results of the first international collaborative quality control study among 96 laboratories.

    PubMed

    Verkooyen, Roel P; Noordhoek, Gerda T; Klapper, Paul E; Reid, Jim; Schirm, Jurjen; Cleator, Graham M; Ieven, Margareta; Hoddevik, Gunnar

    2003-07-01

    The first European Quality Control Concerted Action study was organized to assess the ability of laboratories to detect Chlamydia trachomatis in a panel of urine samples by nucleic acid amplification tests (NATs). The panel consisted of lyophilized urine samples, including three negative, two strongly positive, and five weakly positive samples. Ninety-six laboratories in 22 countries participated with a total of 102 data sets. Of 204 strongly positive samples 199 (97.5%) were correctly reported, and of 506 weakly positive samples 466 (92.1%) were correctly reported. In 74 (72.5%) data sets correct results were reported on all samples, and 17 data sets (16.7%) showed either one false-negative or one false-positive result. In another 11 data sets, two or more incorrect results were reported, and two data sets reported a false-positive result on one negative sample. The Roche COBAS Amplicor test was performed in 44 (43%) data sets, the Abbott LCx assay was performed in 31 (30%) data sets, the Roche Amplicor manual assay was performed in 9 (9%) data sets, an in-house PCR was performed in 9 (9%) data sets, the Becton Dickinson ProbeTec ET assay was performed in 5 (4.9%) data sets, and the GenProbe TMA assay was performed in 4 (3.9%) data sets. The results of the Roche Amplicor manual (95.6% correct), COBAS Amplicor (97.0%), and Abbott LCx (94.8%) tests were comparable (P = 0.48). The results with the in-house PCR, BD ProbeTec ET, and GenProbe TMA tests were reported correctly in 88.6, 98, and 92.5% of the tests, respectively. Freeze-drying of clinical urine specimens proved to be a successful method for generating standardized, stable, and easy-to-transport samples for the detection of C. trachomatis by using NATs. Although the results, especially the specificity, for this proficiency panel were better than most quality control studies, sensitivity problems occurred frequently, underlining the need for good laboratory practice and reference reagents to monitor the

  9. Prevalence of Chlamydia infection among women visiting a gynaecology outpatient department: evaluation of an in-house PCR assay for detection of Chlamydia trachomatis.

    PubMed

    Patel, Achchhe L; Sachdev, Divya; Nagpal, Poonam; Chaudhry, Uma; Sonkar, Subash C; Mendiratta, Suman L; Saluja, Daman

    2010-09-08

    Screening women for Chlamydia trachomatis infection in developing countries is highly desirable because of asymptomatic infection. The existing diagnostic methods in developing countries are not effective and their sensitivity fall below 45.0% which leads to further spread of infection. There is an urgent need for improved and cost effective diagnostic tests that will reduce the burden of sexually transmitted infections in the developing world. Prevalence of C. trachomatis infection among women visiting gynaecology department of Hindu Rao hospital in Delhi, India was determined using Roche Amplicor Multi Well Plate kit (MWP) as well as using in-house PCR assay. We used 593 endocervical swabs for clinical evaluation of the in-house developed assay against Direct Fluorescence Assay (DFA; Group I n = 274) and Roche Amplicor MWP kit (Group II, n = 319 samples) and determined the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) of the in-house developed assay. We detected 23.0% positive cases and there was a higher representation of women aged 18-33 in this group. An in-house PCR assay was developed and evaluated by targeting unique sequence within the gyrA gene of C. trachomatis. Specificity of the reaction was confirmed by using genomic DNA of human and other STI related microorganisms as template. Assay is highly sensitive and can detect as low as 10 fg of C. trachomatis DNA. The resolved sensitivity of in-house PCR was 94.5% compared with 88.0% of DFA assay. The high specificity (98.4%) and sensitivity (97.1%) of the in-house assay against Roche kit and availability of test results within 3 hours allowed for immediate treatment and reduced the risk of potential onward transmission. The in-house PCR method is cost effective (~ 20.0% of Roche assay) and hence could be a better alternative for routine diagnosis of genital infection by C. trachomatis to facilitate improved screening and treatment management.

  10. Potential applications of oral brush cytology with liquid-based technology: results from a cohort of normal oral mucosa.

    PubMed

    Kujan, Omar; Desai, Mina; Sargent, Alexandra; Bailey, Andrew; Turner, Andrew; Sloan, Philip

    2006-09-01

    Fifty healthy volunteers were studied to assess the potential applications of oral brush sampling using liquid-based cytology. Three specimens from the buccal mucosa and lateral border of tongue were collected from each subject by using cervical brushes and brooms. The brush was immersed in a preservative fluid. The sample in the preservative fluid was processed according to the manufacturer's directions (SurePath, UK). Slides were stained by the Papanicolaou method and assessed for squamous cell adequacy by the same criteria used for cervical cytology screening. Immunocytochemical staining for FHIT (Fragile Histidine Triad) was applied in liquid-based preparations following the streptavidin-biotin-peroxidase method. Human papillomavirus (HPV) detection was performed using the Hybrid Capture 2 assay (Digene) and the PCR-based Roche AMPLICOR HPV Test. LBC preparation slides showed good sample preservation, specimen adequacy and visualization of cell morphology. Interestingly, nine cases showed borderline cytological abnormalities from apparently normal oral mucosa. All cases showed good quality positive FHIT immunoreactivity staining. All studied cases were high-risk HPV negative using HC2 assay method. However, the AMPLICOR Roche Test detected four samples with positive results for high-risk HPVs. Liquid-based cytology has potential as a screening tool for oral cancer and precancer. The method may also have applications for research and practice in the field of oral cancer and precancer. However a special custom-designed oral cytobrush is required.

  11. Impact of HIV-1 genetic diversity on plasma HIV-1 RNA Quantification: usefulness of the Agence Nationale de Recherches sur le SIDA second-generation long terminal repeat-based real-time reverse transcriptase polymerase chain reaction test.

    PubMed

    Rouet, François; Chaix, Marie-Laure; Nerrienet, Eric; Ngo-Giang-Huong, Nicole; Plantier, Jean-Christophe; Burgard, Marianne; Peeters, Martine; Damond, Florence; Ekouevi, Didier Koumavi; Msellati, Philippe; Ferradini, Laurent; Rukobo, Sandra; Maréchal, Valérie; Schvachsa, Nilda; Wakrim, Lahcen; Rafalimanana, Christian; Rakotoambinina, Benjamin; Viard, Jean-Paul; Seigneurin, Jean-Marie; Rouzioux, Christine

    2007-08-01

    The high genetic diversity of HIV-1 has a major impact on the quantification of plasma HIV-1 RNA, representing an increasingly difficult challenge. A total of 898 plasma specimens positive for HIV-1 RNA by commercial assays (Amplicor v1.5; Roche Diagnostic Systems, Alameda, CA or Versant v3.0; Bayer Diagnostics, Emeryville, CA) were tested using the Agence Nationale de Recherches sur le SIDA second-generation (G2) real-time reverse transcriptase polymerase chain reaction (RT-PCR) test: 518 samples containing HIV-1 of known subtype, including 88 from 2 subtype panels and 430 harboring B (n = 266) and non-B (n = 164) group M HIV-1 subtypes from patients followed up in 2002 through 2005 at Necker Hospital (Paris, France), and 380 samples from 10 different countries (Argentina, Cambodia, Cameroon, Central African Republic, France, Ivory Coast, Madagascar, Morocco, Thailand, and Zimbabwe). HIV-1 RNA values obtained by G2 real-time PCR were highly correlated with those obtained by the Amplicor v1.5 for B and non-B subtypes (R = 0.892 and 0.892, respectively) and for samples from diverse countries (R = 0.867 and 0.893 for real-time PCR vs. Amplicor v1.5 and real-time PCR vs. Versant v3.0, respectively). Approximately 30% of specimens harboring non-B subtypes were underquantified by at least -0.51 log10 in Amplicor v1.5 versus 5% underquantified in G2 real-time PCR. Discrepant results were also obtained with subtype B samples (14% underquantified by Amplicor v1.5 vs. 7% by G2 real-time PCR). Similar percentages were observed when comparing results obtained with the G2 real-time PCR assay with those obtained using the Versant assay. Addressing HIV-1 diversity, continual monitoring of HIV-1 RNA assays, together with molecular epidemiology studies, is required to improve the accuracy of all HIV RNA assays.

  12. Comparative effectiveness study on human papillomavirus detection methods used in the cervical cancer screening programme

    PubMed Central

    Nygård, Mari; Røysland, Kjetil; Campbell, Suzanne; Dillner, Joakim

    2014-01-01

    Objectives To compare the short-term and long-term effectiveness of human papillomavirus (HPV) tests in Norwegian Cervical Cancer Screening Programme (NCCSP). Design Nationwide register-based prospective follow-up study. Setting In 2005, the NCCSP implemented HPV testing in follow-up of unsatisfactory, atypical squamous cells of undetermined significance (ASC-US) and low-grade squamous intraepithelial lesion (LSIL) cytology. Participants 19 065 women with repeat cytology and HPV test after unsatisfactory ASC-US or LSIL screening result in 2005–2009. Interventions Through individual registry linkages we observed how women were treated in the regular medical care. Main outcome measures We estimated cumulative incidence of cervical intraepithelial neoplasia grade 2 or worse (CIN2+) in 6 months and 3 years after repeat cytology and HPV test. Patients diagnosed with CIN2+ in 6 months and 3 years were assessed for initial HPV positivity. Results 5392 had ASC-US/LSIL and 13 673 had normal/unsatisfactory repeat cytology; for HPV detection 4715 used AMPLICOR HPV Test (Roche Diagnostics, Basel, Switzerland), 9162 Hybrid Capture 2 (HC2) High-Risk HPV DNA Test (QIAGEN, Gaithersburg, Maryland, USA) and 5188 PreTect HPV-Proofer (NorChip, Klokkarstua, Norway). Among those with ASC-US/LSIL repeat cytology, 3-year risk of CIN2+ was 15-fold in Amplicor/HC2-positives compared with Amplicor/HC2-negatives and sevenfold in Proofer-positives compared with Proofer-negatives; a 3-year risk of CIN2+ was 2.1% (95% CI 0.7% to 3.4%) in Amplicor-negatives and 7.2% (95% CI 5.4% to 8.9%) in Proofer-negatives. Close to 100% of patients with CIN2+ diagnosed within 6 months tested positive to HPV (all methods). Considering all patients diagnosed with CIN2+ in 3-year follow-up, 97% were initially positive in the Amplicor group and more than 94% in the HC2 group, compared with less than 80% in the Proofer group. Conclusions While the long-term evaluation of new screening routines

  13. Cobas ampliprep/cobas TaqMan HIV-1 v2.0 assay: consequences at the cohort level.

    PubMed

    Taylor, Ninon; Grabmeier-Pfistershammer, Katharina; Egle, Alexander; Greil, Richard; Rieger, Armin; Ledergerber, Bruno; Oberkofler, Hannes

    2013-01-01

    High-sensitive real-time PCR assays are routinely used to monitor HIV-1 infected subjects. Inter-assay discrepancies have been described at the low viral load (VL) end, where clinical decisions regarding possible virological rebound are based. A retrospective study was performed to analyze frequencies of viral blips after transition to the COBAS Ampliprep/COBAS TaqMan v2.0 HIV-1 assay (Taqman v2.0) in patients with prior undetectable VLs as measured with the Roche Cobas Ampliprep Amplicor HIV-1 Monitor Test, v1.5 (Amplicor) and was evaluated in comparison to a group of patients monitored with the Abbott Real-time HIV-1 assay (Abbott RT) during the same period of time. 85 of 373 patients with VLs below the limit of quantification with Amplicor had VLs >50 copies/mL after transition to the TaqMan v2.0 assay. Among these 74.1% had VLs ranging from 50-499 copies/mL, 22.9% had VLs >500 copies/mL. From 22 patients with initial Taqman v2.0 based VLs exceeding 500 copies/mL, 6 patients had VLs <20 copies/mL after novel VL measurement on a next visit. In our control group with VL quantification using the Abbott RT assay, only 1 patient became detectable and showed a VL of <40 copies/mL after new measurement. Transition to the Taqman v2.0 assay was accompanied by an increase of quantifiable HIV-1 VLs in patients with long term viral suppression under antiretroviral therapy that might be attributed to technical shortcomings of the Taqman v2.0 assay. A high test variability at the low VL end but also beyond was observed, making meaningful clinical interpretation of viral blips derived from different assays difficult.

  14. Multicenter Quality Control for the Detection of Hepatitis C Virus RNA in Seminal Plasma Specimens

    PubMed Central

    Bourlet, Thomas; Levy, Rachel; Laporte, Silvy; Blachier, Stéphane; Bocket, Laurence; Cassuto, Guy; Chollet, Lionel; Leruez-Ville, Marianne; Maertens, Anne; Mousnier, Fabienne; Pasquier, Christophe; Payan, Christopher; Pellegrin, Bertrand; Schvoerer, Evelyne; Zavadzki, Patricia; Chouteau, Jacques; Duverlie, Gilles; Izopet, Jacques; Lunel-Fabiani, Françoise; Pawlotsky, Jean-Michel; Profizi, Nerina; Rouzioux, Christine; Stoll-Keller, Françoise; Thibault, Vincent; Wattré, Pierre; Pozzetto, Bruno

    2003-01-01

    The discrepant results available in the literature about the presence of hepatitis C virus (HCV) RNA in seminal plasma of men chronically infected by this agent are related, at least in part, to the molecular techniques used and particularly to the wide range of protocols dedicated to RNA extraction. In order to evaluate these protocols and to standardize the method of detection of HCV RNA in this fluid, a panel of coded specimens was tested blindly in 12 French laboratories; it included 14 seminal plasma specimens and four water controls spiked with HCV RNA ranging from 10 to 20,000 IU/ml and two HCV-negative seminal plasma specimens. The extraction step was performed according to methods using either silica beads (NucliSens [Organon Teknika S.A., Fresnes, France]; RNA viral kit [Qiagen, Courtaboeuf, France]) or guanidinium thiocyanate (Amplicor HCV assay; Roche Diagnostics, Meylan, France), preceded or not by a centrifugation of the seminal plasma. For the amplification step, all the laboratories performed the same reverse transcription-PCR technique (Amplicor HCV Cobas assay). The percentage of correct results ranged from 53.3 to 100, the poorest results being obtained when no centrifugation step preceded the Amplicor extraction protocol. The rate of correct results was significantly higher in laboratories using a preliminary centrifugation of the specimen (P = 0.034 by chi-square test). By contrast, the overall number of correct results was not correlated to the initial volume of sample used for the test. These results allowed us to validate standardized techniques adapted to the performance of this test on a routine basis, especially in men infected with HCV and involved in programs of medically assisted reproduction. PMID:12574284

  15. Development and evaluation of a next-generation digital PCR diagnostic assay for ocular Chlamydia trachomatis infections.

    PubMed

    Roberts, Chrissy H; Last, Anna; Molina-Gonzalez, Sandra; Cassama, Eunice; Butcher, Robert; Nabicassa, Meno; McCarthy, Elizabeth; Burr, Sarah E; Mabey, David C; Bailey, Robin L; Holland, Martin J

    2013-07-01

    Droplet digital PCR (ddPCR) is an emulsion PCR process that performs absolute quantitation of nucleic acids. We developed a ddPCR assay for Chlamydia trachomatis infections and found it to be accurate and precise. Using PCR mixtures containing plasmids engineered to include the PCR target sequences, we were able to quantify with a dynamic range between 0.07 and 3,160 targets/μl (r(2) = 0.9927) with >95% confidence. Using 1,509 clinical conjunctival swab samples from a population in which trachoma is endemic in Guinea Bissau, we evaluated the specificity and sensitivity of the quantitative ddPCR assay in diagnosing ocular C. trachomatis infections by comparing the performances of ddPCR and the Roche Amplicor CT/NG test. We defined ddPCR tests as positive when we had ≥95% confidence in a nonzero estimate of target load. The sensitivity of ddPCR against Amplicor was 73.3% (95% confidence interval [CI], 67.9 to 78.7%), and specificity was 99.1% (95% CI, 98.6 to 99.6%). Negative and positive predictive values were 94.6% (95% CI, 93.4 to 95.8%) and 94.5% (95% CI, 91.3 to 97.7%), respectively. Based on Amplicor CT/NG testing, the estimated population prevalence of C. trachomatis ocular infection was ∼17.5%. Receiver-operator curve analysis was used to select critical cutoff values for use in clinical settings in which a balance between higher sensitivity and specificity is required. We concluded that ddPCR is an effective diagnostic technology suitable for both research and clinical use in diagnosing ocular C. trachomatis infections.

  16. Evaluation of the Gen-Probe Chlamydia trachomatis transcription-mediated amplification assay with urine specimens from women.

    PubMed Central

    Pasternack, R; Vuorinen, P; Miettinen, A

    1997-01-01

    We evaluated the Gen-Probe Chlamydia trachomatis transcription-mediated amplification (TMA) assay with urine specimens for the detection of C. trachomatis infections in women. The novel test, based on the isothermal amplification of chlamydial RNA, was compared with the Roche Amplicor PCR with urine and cell culture with endocervical specimens. First-catch urine and endocervical swab specimens were collected from a total of 561 patients, of whom 70 (12.3%) were confirmed to have chlamydial infection. The diagnostic sensitivity and specificity of TMA with urine were 91.4 and 99.6%, respectively, and those of Amplicor PCR were 97.1 and 99.8%, respectively. By repeated analysis of the specimens with discrepant results, the sensitivity of TMA could be increased to 99%, indicating that some methodological improvements in the assay are still to be expected. The sensitivity of PCR could be increased to 100% by the elimination of DNA polymerase inhibitors in a repeated analysis. The sensitivity and specificity of cell culture with cervical specimens were 85.7 and 100%, respectively. The results indicate that TMA with urine specimens from women is a sensitive and specific assay for the detection of C. trachomatis, providing a new noninvasive technique for the screening of chlamydial infections in women. PMID:9041411

  17. Impact of occult HBV infection in HIV/HCV co-infected patients: HBV-DNA detection in liver specimens and in serum samples.

    PubMed

    Fabris, Paolo; Biasin, Maria R; Giordani, Maria T; Berardo, Laura; Menini, Vania; Carlotto, Antonio; Miotti, Maria G; Manfrin, Vinicio; Baldo, Vincenzo; Nebbia, Gaia; Infantolino, Domenico

    2008-03-01

    Prevalence and impact of occult HBV infection in HIV positive patients is controversial. The aims of this study were to determine the prevalence of occult HBV infection and its impact on histological and virological parameters. 52 HIV/HCV (but HBsAg-negative) co-infected patients, 29 HBsAg and anti-HCV negative chronic hepatitis, and 20 HBsAg positive chronic hepatitis controls were studied. DNA was extracted from frozen biopsies and amplified with primers for S, C and X regions, and for (ccc) HBV-DNA. Sera were tested for HBV-DNA with two quantitative assays (Cobas Amplicor HBV Monitor, and the real-time COBAS (r) Taqman HBV Test, Roche Diagnostics, UK). Occult HBV infection was detected in 7 (13.4%) liver biopsies of the study group, and in none case of the non viral chronic hepatitis group (p=0.04). All serum samples were HBV-DNA negative with Cobas Amplicor HBV monitor assay, while 3 cases were found positive with real time PCR. Statistical analysis didn't show any impact of occult HBV infection on liver histology, CD4+ cells count, HIV and HCV load, and ALT levels. Occult B infection is relatively frequent in HIV/HCV co-infected patients, and is underestimated by common HBV-DNA serological assays. However, it doesn't seem to exert a relevant impact.

  18. Global cost modeling analysis of HIV-1 and HCV viral load assays.

    PubMed

    Elbeik, Tarek; Chen, Yi-Ming Arthur; Soutchkov, Serguei V; Loftus, Richard A; Beringer, Scott

    2003-08-01

    This review addresses hidden costs associated with the Bayer VERSANT assay, Roche AMPLICOR MONITOR test and COBAS AMPLICOR MONITOR test and how these influence the final per reportable cost to a testing laboratory in resource-rich and -poor countries. An in-depth evaluation and recommendation of the most cost-effective approach for these tests is presented. The analyses demonstrate the need for manufacturers to consider labor and supply costs when marketing a kit in resource-poor countries, noting that marketing strategies need to change. In the absence of any proven monitoring alternative, emphasis is placed on increasing market share to promote significant reduction in kit prices to suit the demands of markets in resource-poor countries. Finally, recommendations are made to improve the overall cost structure of viral load testing. This review is intended as a tool to optimize assay usage in attaining the lowest performance costs by assay and is not to endorse any test, as will become apparent.

  19. Diff-Quik stain as a simplified alternative to Papanicolaou stain for determination of quality of endocervical specimens submitted for PCR detection of Chlamydia trachomatis.

    PubMed

    Kellogg, J A; Seiple, J W; Klinedinst, J L; Stroll, E

    1996-10-01

    The simple, rapid, two-step Diff-Quik stain procedure (Baxter Diagnostics) was compared with the Papanicolaou stain for microscopic determination of endocervical specimen quality. Results from 230 (98.7%) of 233 specimens stained by both methods indicated agreement between the two staining methods for detection of the endocervical cells or erythrocytes indicating specimen adequacy. By using the Amplicor Chlamydia trachomatis Test (Roche Diagnostic Systems) to detect C.trachomatis and the Diff-Quik stain to assess specimen adequacy, PCR-positive results were obtained from 147 (9.1%) of 1,615 microscopically adequate specimens but from only 13 (2.2%) of the 583 inadequate specimens (P < 0.001).

  20. Diff-Quik stain as a simplified alternative to Papanicolaou stain for determination of quality of endocervical specimens submitted for PCR detection of Chlamydia trachomatis.

    PubMed Central

    Kellogg, J A; Seiple, J W; Klinedinst, J L; Stroll, E

    1996-01-01

    The simple, rapid, two-step Diff-Quik stain procedure (Baxter Diagnostics) was compared with the Papanicolaou stain for microscopic determination of endocervical specimen quality. Results from 230 (98.7%) of 233 specimens stained by both methods indicated agreement between the two staining methods for detection of the endocervical cells or erythrocytes indicating specimen adequacy. By using the Amplicor Chlamydia trachomatis Test (Roche Diagnostic Systems) to detect C.trachomatis and the Diff-Quik stain to assess specimen adequacy, PCR-positive results were obtained from 147 (9.1%) of 1,615 microscopically adequate specimens but from only 13 (2.2%) of the 583 inadequate specimens (P < 0.001). PMID:8880526

  1. Evaluation of Performance of the Gen-Probe Human Immunodeficiency Virus Type 1 Viral Load Assay Using Primary Subtype A, C, and D Isolates from Kenya

    PubMed Central

    Emery, Sandra; Bodrug, Sharon; Richardson, Barbra A.; Giachetti, Cristina; Bott, Martha A.; Panteleeff, Dana; Jagodzinski, Linda L.; Michael, Nelson L.; Nduati, Ruth; Bwayo, Job; Kreiss, Joan K.; Overbaugh, Julie

    2000-01-01

    Accurate and sensitive quantification of human immunodeficiency virus type 1 (HIV-1) RNA has been invaluable as a marker for disease prognosis and for clinical monitoring of HIV-1 disease. The first generation of commercially available HIV-1 RNA tests were optimized to detect the predominant HIV-1 subtype found in North America and Europe, subtype B. However, these tests are frequently suboptimal in detecting HIV-1 genetic forms or subtypes found in other parts of the world. The goal of the present study was to evaluate the performance of a new viral load assay with non-subtype B viruses. A transcription-mediated amplification method for detection and quantitation of diverse HIV-1 subtypes, called the Gen-Probe HIV-1 viral load assay, is under development. In this study we examined the performance of the Gen-Probe HIV-1 viral load assay relative to that of the commonly used commercial HIV-1 RNA assays using a panel of primary isolates from Kenya. For comparison, we included several subtype B cloned viruses, and we quantified each virus using an in-house quantitative-competitive reverse transcriptase PCR (QC-RT-PCR) method and gagp24 antigen capture. The Gen-Probe HIV-1 viral load assay and a version of the Roche AMPLICOR HIV-1 MONITOR test (version 1.5) that was designed to detect a broader range of subtypes were both sensitive for the quantification of Kenyan primary isolates, which represented subtype A, C, and D viruses. The Gen-Probe HIV-1 viral load assay was more sensitive for the majority of viruses than the Roche AMPLICOR HIV-1 MONITOR test version 1.0, the Bayer Quantiplex HIV RNA 3.0 assay, or a QC-RT-PCR method in use in our laboratory, suggesting that it provides a useful method for quantifying HIV-1 RNAs from diverse parts of the world, including Africa. PMID:10878065

  2. Defending the Freedom to Innovate: Faculty Intellectual Property Rights after "Stanford v. Roche"

    ERIC Educational Resources Information Center

    American Association of University Professors, 2014

    2014-01-01

    Tensions over faculty control of the fruits of their scholarship have been slowly building since the 1980s, but they have also intensified since late 2011. There have long been differences of opinion over ownership of patentable inventions, but over the last two years a number of universities have categorically asserted that they own these…

  3. Integrating molecular design resources within modern drug discovery research: the Roche experience.

    PubMed

    Stahl, Martin; Guba, Wolfgang; Kansy, Manfred

    2006-04-01

    Various computational disciplines, such as cheminformatics, ADME modeling, virtual screening, chemogenomics search strategies and classic structure-based design, should be seen as one multifaceted discipline contributing to the early drug discovery process. Although significant resources enabling these activities have been established, their true integration into daily research should not be taken for granted. This article reviews value-adding activities from target assessment to lead optimization, and highlights the technical and process-related aspects that can be considered essential for performance and alignment within the research organization.

  4. "Der Bleistift roch nach Rosmarin": the art of foraging in Stifter, Handke, and Beuys.

    PubMed

    Brady, Martin

    2012-01-01

    Taking as its starting point the notion of ‘reading’ as ‘gathering’, implied by the word Lesen, this essay examines some correspondences between foraging, naming, writing, drawing, and reading to establish a clear distinction between foraging and collecting more generally. By way of example, three kinds of foraging are addressed: berry picking, in Adalbert Stifter's short story Der Waldsteig; mushroom collecting, in Peter Handke's fairy-tale Lucie im Wald mit den Dingsda; gathering medicinal herbs, in particular rosemary, in the drawings, performances, and social sculptures of Joseph Beuys (including Manresa, Barraque D’dull Odde, Geruchsplastik, Blitzschlag mit Lichtschein auf Hirsch). In the literary and visual works discussed here, foraging and its products are therapeutic both physically and spiritually, what Handke terms ‘traumerweiternd’. Moreover, in the case of Beuys in particular this healing process has explicitly social and political implications. The essay also examines foraging as an analogy for the construction of meaning and concludes with a discussion of the clearing as a privileged space in which foraging and gathering, both literally and figuratively, can take place.

  5. Clinical evaluation of the Roche Elecsys CMV IgG Avidity assay.

    PubMed

    Vauloup-Fellous, C; Lazzarotto, T; Revello, M G; Grangeot-Keros, L

    2014-08-01

    Congenital cytomegalovirus (CMV) infection has potentially severe consequences in newborns. The testing of pregnant women for CMV-specific antibodies may be useful for the identification of women at risk of transmitting the infection to the fetus. The determination of CMV IgG avidity helps to establish the timing of infection as IgG avidity matures during the course of infection. This study examines the performance of the Elecsys CMV IgG Avidity assay using preselected samples from patients at different phases of CMV infection. The Elecsys CMV IgG Avidity assay was tested at three sites using sequential samples from patients with recent primary CMV infection, as well as single samples from patients with recent primary or past CMV infection. The Elecsys assay discriminated well between early (low avidity) and late (high avidity) phases of infection in sequential serum samples. Overall, 98.8% of low-avidity samples corresponded to infection onset <180 days before sampling and 77.8% of all high-avidity results corresponded to infection onset >90 days before sampling. The assay's sensitivity was 90-97%, with specificity ranging from 89 to 100%, depending on the consideration of gray-zone avidity values. Single samples from recent primary or past infection showed similar distributions of avidity results. The Elecsys CMV IgG Avidity assay results are in agreement with preselected samples from patients with primary or past CMV infection, showing that the test is an adequate predictor of the phase of infection.

  6. Cross-reactivity of amphetamine analogues with Roche Abuscreen radioimmunoassay reagents

    SciTech Connect

    Cody, J.T. )

    1990-01-01

    Cross-reactivity of amphetamine analogues with the Abuscreen amphetamine radioimmunoassay reagents was determined for both the standard and high specificity antibody systems. Compounds tested included 2-methoxyamphetamine, 4-hydroxymethamphetamine, 2,5-dimethoxyamphetamine (DMA), 4-bromo-2,5-dimethoxyamphetamine (DOB), 4-bromo-2,5-dimethoxy-beta-phenethylamine (BDMPEA), 3,4,5-trimethoxyamphetamine (TMA), 3,4-methylenedioxyamphetamine (MDA), N,N-dimethyl-3,4-methylenedioxyamphetamine and N-hydroxy-3,4-methylenedioxyamphetamine (N-OH MDA), 3,4-methylenedioxymethamphetamine (MDMA), 3,4-methylenedioxyethylamphetamine (MDEA), 2,5-dimethoxy-4-ethylamphetamine, 2,5-dimethoxy-4-methylamphetamine (DOM), and 3,4,5-trimethoxyphenethylamine (mescaline). Blank negative reference material was spiked with 1,000 to 100,000 ng/mL of the amphetamine analogue and used as sample in the assays. MDA was the only analogue that showed cross reactivity equal to or greater than that of amphetamine. None of the other analogue compounds demonstrated a positive result at even the highest concentration; however several showed depressed counts at various concentration levels.

  7. Defending the Freedom to Innovate: Faculty Intellectual Property Rights after "Stanford v. Roche"

    ERIC Educational Resources Information Center

    American Association of University Professors, 2014

    2014-01-01

    Tensions over faculty control of the fruits of their scholarship have been slowly building since the 1980s, but they have also intensified since late 2011. There have long been differences of opinion over ownership of patentable inventions, but over the last two years a number of universities have categorically asserted that they own these…

  8. Distribution of HCV Genotypes in the Populations of Inmates in Polish Prison Potulice and Patients Hospitalised in Bydgoszcz

    PubMed Central

    Tyczyno, Malgorzata; Halota, Waldemar; Nowak, Wojciech; Pawlowska, Małgorzata

    2014-01-01

    Background: According to many studies, one of the social groups with high rate of HCV infections are prisoners. Objectives: The aim of the study was to determine and compare the genotypes distribution among prisoners and patients of hospital. Patients and Methods: HCV genotypes among prisoners (281 inmates) and patients of hospital (1415 patients) were determined in years 2002-2012. HCV genotypes were determined in 2002-2005 with INNO-LiPA HCV II test (Innogenetics, Gent, Belgium) and since 2006 with LINEAR ARRAY assay (Roche, Mannheim, Germany), after isolation and amplification of the material with COBAS AMPLICOR v 2.0 (Roche, Mannheim, Germany). Results: The most frequent HCV genotype among inmates was genotype 3, which was detected in169 of 281 patients (60.1%). Most frequent genotype among hospitalized was genotype 1, which was found in 1127 cases (79.6%). Comparing the results of prisoners with a group of patients with HIV/HCV co-infection gave similar results. In both groups most frequent was genotype 3 (respectively 60.1 and 45.5%). However, most prisoners in this study (96%) were HIV-negative. Conclusions: The current study shows that the predominant HCV genotype among inmates from prison in Potulice is genotype 3. PMID:24910703

  9. Multilaboratory Comparison of Hepatitis C Virus Viral Load Assays

    PubMed Central

    Caliendo, A. M.; Valsamakis, A.; Zhou, Y.; Yen-Lieberman, B.; Andersen, J.; Young, S.; Ferreira-Gonzalez, A.; Tsongalis, G. J.; Pyles, R.; Bremer, J. W.; Lurain, N. S.

    2006-01-01

    We report a multilaboratory evaluation of hepatitis C virus (HCV) viral load assays to determine their linear range, reproducibility, subtype detection, and agreement. A panel of HCV RNA samples ranging in nominal concentration from 1.0 to 7.0 log10 IU/ml was constructed by diluting a clinical specimen (genotype 1b). Replicates of the panel were tested in multiple laboratories using the Abbott TaqMan analyte-specific reagent (Abbott reverse transcription-PCR [RT-PCR]), Roche TaqMan RUO (Roche RT-PCR), Roche Amplicor Monitor HCV 2.0 (Roche Monitor), and Bayer VERSANT HCV RNA 3.0 (Bayer bDNA) assays. Bayer bDNA-negative specimens were tested reflexively using the Bayer VERSANT HCV RNA qualitative assay (Bayer TMA). Abbott RT-PCR and Roche RT-PCR detected all 28 replicates with a concentration of 1.0 log10 IU/ml and were linear to 7.0 log10 IU/ml. Roche Monitor and Bayer bDNA detected 27 out of 28 and 13 out of 28 replicates, respectively, of 3.0 log10 IU/ml. Bayer TMA detected all seven replicates with 1.0 log10 IU/ml. Bayer bDNA was the most reproducible of the four assays. The mean viral load values for panel members in the linear ranges of the assays were within 0.5 log10 for the different tests. Eighty-nine clinical specimens of various genotypes (1 through 4) were tested in the Bayer bDNA, Abbott RT-PCR, and Roche RT-PCR assays. For Abbott RT-PCR, mean viral load values were 0.61 to 0.96 log10 greater than the values for Bayer bDNA assay for samples with genotype 1, 2, or 3 samples and 0.08 log10 greater for genotype 4 specimens. The Roche RT-PCR assay gave mean viral load values that were 0.28 to 0.82 log10 greater than those obtained with the Bayer bDNA assay for genotype 1, 2, and 3 samples. However, for genotype 4 samples the mean viral load value obtained with the Roche RT-PCR assay was, on average, 0.15 log10 lower than that of the Bayer bDNA. Based on these data, we conclude that the sensitivity and linear range of the Abbott and Roche RT-PCR assays

  10. Clinic‐based evaluation of Clearview Chlamydia MF for detection of Chlamydia trachomatis in vaginal and cervical specimens from women at high risk in China

    PubMed Central

    Yin, Y‐P; Peeling, R W; Chen, X‐S; Gong, K‐L; Zhou, H; Gu, W‐M; Zheng, H‐P; Wang, Z‐S; Yong, G; Cao, W‐L; Shi, M‐Q; Wei, W‐H; Dai, X‐Q; Gao, X; Chen, Q; Mabey, D

    2006-01-01

    Objectives To determine the performance of a rapid Chlamydia trachomatis (CT) test (Clearview Chlamydia MF) compared to the current “gold standard” (Roche Amplicor CT assay) test, and to assess acceptability of the tests to patients. Methods A total of 1497 women at sexually transmitted diseases (STD) clinics or re‐education centres in six urban cities (Shanghai, Nanjing, Shenzhen, Guangzhou, Chengdu and Fuzhou) in China participated in the study. Three vaginal and three cervical swabs were collected from each participant. Rapid CT tests were performed locally on the first vaginal and cervical swabs and the results were read independently by two staff members. The second and third swabs were randomised for performing the Roche CT assay at the National STD Reference Laboratory. Acceptability of the rapid tests to patients was determined by asking patients in clinics about their willingness to wait for the results. Results The prevalence of CT was 13.2% (197/1497), as determined by the Roche assay with cervical specimens. CT was detected in 78 vaginal and 127 cervical specimens by the rapid test and the positive rates determined with cervical specimens were significantly higher than those with vaginal specimens (p<0.001). There was good agreement between the results read by two independent staff for either vaginal or cervical specimens (both κ = 0.98, p<0.001). Sensitivities for vaginal and cervical specimens were 32.8% and 49.7%, respectively, and specificities were 99.2% and 97.9%, respectively. The positive predictive value was 85.7% for vaginal and 78.4% for cervical specimens. The vast majority of the patients (99.1%) were willing to wait up to two hours for the results. Conclusion Clearview Chlamydia MF, while yielding a rapid result and requiring minimal laboratory facilities, had unacceptably low sensitivity compared to a nucleic acid amplification test. Rapid tests yielding results within one hour are generally accepted by the clients. PMID

  11. Analytical Performance of the Roche LightCycler® Mycobacterium Detection Kit for the Diagnosis of Clinically Important Mycobacterial Species

    PubMed Central

    Omar, Shaheed V.; Roth, Andreas; Ismail, Nazir A.; Erasmus, Linda; Ehlers, Marthie; Kock, Marleen; Paulse, Nuraan; Said, Halima M.; Hoosen, Anwar A.; Reischl, Udo

    2011-01-01

    Background The LightCycler® Mycobacterium Detection Kit based on real-time PCR technology for the detection of Mycobacterium tuberculosis, Mycobacterium avium and Mycobacterium kansasii was recently developed. This study evaluated its analytical sensitivity, specificity and reproducibility. Methodology/Principal Findings Plasmid standards were prepared and used to determine the limit of detection. The assay was also performed against organisms other than mycobacteria, other mycobacterial strains and interfering substances to exclude cross-reactivity and interference. Reference standards were prepared and tested to assess the assay's reproducibility. All PCR assays were performed using the LightCycler® 2.0 Instrument. The detection limit for M. tuberculosis was 28 copies per microlitre. Neither cross-reactivity nor interference occurred with non-mycobacterial organisms and substances tested. Overall reproducibility for consecutive measurements, run-to-run, lot-to-lot, day-to-day and laboratory-to-laboratory achieved a coefficient of variance of less than two percent. Significance The LightCycler® Mycobacterium Detection kit has shown to be a robust and accurate assay with the potential to be used as a rapid TB diagnostic test. PMID:21961045

  12. Clinical Comparative Bioavailability Study of ICN- and Roche-Manufactured 30 mg Pyridostigmine Bromide Tablets in Healthy Volunteers

    DTIC Science & Technology

    2001-09-01

    concenrations were used to determine bioequivalence . The products were found to be bioequivalen based upon the 90% confidence intervals of the...i80 to 1.25 bioequivalence limits. 14. SUBJECT TERMS 15. NUMBER OF PAGES11 16. PRICE CODE 17. SECURITY CLASSIFICATION 18. SECURITY CLASSIFICATION 19...test and reference means and geometric means were reported using least squares means from the ANOVAs. Bioequivalence was determined using the two one

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

    PubMed

    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.

  14. Rapid screening for early detection of mother-to-child transmission of human immunodeficiency virus type 1.

    PubMed

    Cassol, S; Butcher, A; Kinard, S; Spadoro, J; Sy, T; Lapointe, N; Read, S; Gomez, P; Fauvel, M; Major, C

    1994-11-01

    The testing of dried blood spots (DBSs) for the presence of human immunodeficiency type 1 (HIV-1) proviral DNA by PCR was first described in 1991. The technology has proven to be particularly valuable for resolving the infection status in HIV-1-indeterminate infants born to HIV-1-seropositive mothers. To broaden the applicability of DBS PCR, we adapted it to a standardized, commercially available microwell plate amplification and detection kit, Amplicor HIV-1, produced by Roche Diagnostic Systems. The microwell assay is rapid and easy to perform and uses equipment that is readily available in routine diagnostic laboratories. The high level of performance of the assay was demonstrated in 1,168 duplicate tests performed on 584 DBSs from 178 uninfected and 100 HIV-1-infected individuals, including 56 children with perinatally acquired HIV-1. Of 12 infants who were followed prospectively from birth, 3 (25%) were infected in utero (PCR positive at birth) and 9 (75%) were infected intrapartum (PCR negative, culture negative at birth). Overall, HIV-1 DNA was identified in 3 of 11 (27.3%) DBSs collected from infected infants during the first 4 days of life, 8 of 9 (88.9%) DBSs collected between 10 and 15 days postpartum, and 166 of 167 (99.4%) DBSs collected after 15 days of age. All 320 DBSs from uninfected children were PCR DNA negative. These findings indicate that use of the Roche microwell DBS PCR assay provides a powerful new approach for large-scale perinatal screening programs and population-based studies of vertical transmission.

  15. Efficient Methodologies for Sensitive HIV-1 RNA Quantitation from Plasma and Vaginal Secretions

    PubMed Central

    Randolph, Tara C.; Lacour, Nedra; Amedee, Angela Martin

    2014-01-01

    Background Quantifying HIV levels in mucosal secretions is essential to study compartmentalized expression of HIV and facilitate development of intervention strategies to prevent disease progression and transmission. Objectives To develop a sensitive, reliable, and cost-effective technique to quantify HIV from blood and vaginal secretions that is compatible with efficient implementation in clinical research environments. Study Design A sensitive, reliable, internally-controlled real-time reverse transcriptase (RT) PCR assay, which uses the HIV-1 pol gene as a target (Hpol assay) was developed to quantify HIV levels in plasma and genital secretions, and compared to the widely-used Roche Amplicor HIV-1 Monitor assay. In addition, a simplified method of sample collection and processing of genital secretions (self-collection and use of RNAlater with batch processing) was compared to provider collection of samples and immediate processing. Results The sensitivity and reliability of HIV levels detected by the assay described herein correlate well with measurements from Roche Amplicor™ HIV-1 Monitor assay for both plasma and vaginal secretions (R2= 0.9179 and R2=0.942, respectively). The Hpol assay reproducibly quantifies a lower limit of 5 HIV-1 RNA copies per reaction, with low-levels of inter-assay and intra-assay variation. Additionally, vaginal viral levels and detection frequency did not differ significantly between the two the collection and processing methods. Conclusions The methodologies developed here provide sensitive, reliable, and cost-effective quantification of HIV levels in plasma and mucosal secretions, and are compatible with efficient use in clinical research studies. PMID:19783472

  16. Validation of the Gen-Probe Aptima qualitative HIV-1 RNA assay for diagnosis of human immunodeficiency virus infection in infants.

    PubMed

    Fiscus, Susan A; McMillion, Takesha; Nelson, Julie A E; Miller, William C

    2013-12-01

    The qualitative Roche HIV-1 DNA Amplicor assay has been used for the past 20 years to diagnose HIV infection in infants and young children but is being phased out; hence, alternative assays must be found. The Gen-Probe Aptima qualitative HIV-1 RNA assay is currently the only FDA-cleared HIV-1 nucleic acid assay approved for diagnosis, but data on the use of this assay with infant plasma are limited. We assessed Aptima's performance using control material for reproducibility and limit of detection and 394 plasma samples (0.2 to 0.5 ml) from HIV-exposed infected and uninfected infants and children for analytical sensitivity and specificity. Assays to assess within-run repeatability and between-run reproducibility indicated that the controls with 10,000 (5 of 5), 200 (5 of 5), 100 (16 of 16), 50 (12 of 12), and 25 (20 of 20) HIV-1 RNA copies/ml (cp/ml) were always positive, and negatives were always negative (20 of 20). The limit of detection was 14 cp/ml, as determined by probit analysis. The analytic sensitivity of the assay was 99.5% (189/190 samples; 95% confidence interval [CI], 97.1 to 99.9%) and specificity was 99.5% (199/200 samples; 95% CI, 97.2 to 99.9%). These results suggest that the assay is suitable for early infant diagnosis of HIV-1.

  17. Evaluation of the Siemens VERSANT® CT/GC DNA 1.0 assay (kPCR) for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

    PubMed

    Bongaerts, Maarten; van de Bovenkamp, Jeroen H B; Morré, Servaas A; Manders, Monique E L M; Heddema, Edou R

    2011-11-01

    The Siemens VERSANT kPCR system is an automated system which combines extraction of nucleic acids from 96 samples with subsequent real-time PCR. The VERSANT CT/GC DNA 1.0 (kPCR) assay detects Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) in a multiplex real-time PCR on this system. We compared this assay with the BD ProbeTe™ ET System (PT) and the Roche Cobas Amplicor (CA). Three different sets of samples were tested in the kPCR: PT pre-treated samples, prospectively collected urine samples during routine CT/GC testing and urine samples obtained in a blinded fashion by an external lab facility. Agreement of kPCR with the comparator tests was >0.99 for sample set I and complete agreement was observed for sample set II and III. The kPCR assay demonstrated to be an easy to use robust diagnostic platform. A few modifications to the manufacturer's instructions are recommended to intercept false positivity. We advise to retest samples with Cq values above 35 cycles at least one time and we suggest checking the amplification curves.

  18. Assessment of the low cost Cavidi ExaVir™ Load assay for monitoring HIV viral load in pediatric and adult patients

    PubMed Central

    Greengrass, Vicki; Lohman, Barbera; Morris, Lisa; Plate, Megan; Steele, Pauline M; Walson, Judd L; Crowe, Suzanne M

    2009-01-01

    Background Viral load (VL) is a critical marker for monitoring HIV disease progression and response to antiretroviral therapy. In resource-constrained settings, there is a need for a simple and inexpensive assay to monitor infected adults and children. Methods We compared versions 2 and 3 of the ExaVir™ Load assay, Cavidi AB (HIV RT) with the Roche, COBAS® Amplicor® HIV-1 Monitor assay (HIV RNA) for quantifying HIV VL. Results The HIV RT version 2 assay showed good sensitivity with detection in 94% of samples with HIV RNA >1000 copies/ml. Adult samples were tested using HIV RT version 2 (n=35) and version 3 (n=23) assays with plasma volumes of 1ml (recommended), 0.5ml and 0.25ml in comparison with HIV RNA. The HIV RT and HIV RNA assay results were comparable when tested using different volumes. Comparison of results from pediatric samples (n=27), tested using 1ml and a smaller volume by HIV RT version 2 were not significantly different. Conclusion The HIV RT assay was comparable to the HIV RNA assay with sensitivity approaching that of RT-PCR. Smaller volumes than the recommended 1ml can be used, improving utility of this assay for pediatric monitoring. PMID:19617845

  19. Chronic hepatitis B in children in Gothenburg, Sweden.

    PubMed

    Söderström, A; Lindh, M; Eriksson, K; Horal, P; Krantz, M; Kristiansson, B; Lindberg, J; Norkrans, G

    1999-01-01

    Sweden is a low prevalence area for hepatitis B, but the number of chronic carriers has increased during the last decade due to immigration. Out of a total of 120 children with identified chronic hepatitis B in Gothenburg, Sweden, 93 were investigated during the 2-year period 1994-95. The children had a mean age of 10.9 years and originated from 21 different countries. Most infections were discovered during various screening programmes after arrival in Sweden. A total of 90 of the 93 children were HBV-DNA positive by Amplicor HBV Monitor (Roche Diagnostics) and 58% (54/93) were HBeAg positive. All children either originated from areas with a high or medium prevalence of HBV infection (81/93, 87%) or were born in Sweden to mothers originating from high or medium prevalence countries (12/93, 13%). Three of these 12 children were vertically infected in spite of adequate immunoprophylaxis and 8 were born to mothers with undiscovered chronic HBV infection. In all, 34 children had mothers who were HBsAg positive. No overt case of transmission was notified in day-care centres or schools, or from a child to a non-immune parent. None of the children reported any symptoms of liver disease, but 38% (35/93) had elevated aminotransferases. Therefore, screening programmes are essential to identify chronic HBV infection in children in order to prevent transmission and to find individuals at risk of progressive liver damage who should be considered for treatment.

  20. Diagnosis of Neisseria gonorrhoeae Using Molecular Beacon

    PubMed Central

    Patel, Achchhe Lal; Sonkar, Subash Chandra; Kumari, Indu; Saluja, Daman

    2015-01-01

    Neisseria gonorrhoeae is an important sexually transmitted diseases (STD) causing pathogen worldwide. Due to absence of an affordable diagnostic assay, routine screening of gonococcal infection becomes impossible in developing countries where infection rates are maximum. Treatment is given on the basis of symptoms alone which leads to spread of infection. Thus, development of a rapid, sensitive, specific, and PCR based visual diagnostic assay suitable for developing countries, required for better disease management, is aimed at in present study. Endocervical swabs were collected from patients visiting gynecology department of various hospitals in Delhi. In-house PCR based assay was developed and modified to visual assay using molecular beacon for end-point detection. It was evaluated against Roche AMPLICOR NG kit and rmp gene. Specificity of beacon was confirmed by competition experiments. Diagnostic test was 98.21% specific and 99.59% sensitive whereas negative and positive predicted value were 99.40% and 98.78%, respectively. We also observed that twice the concentration (2X) of premix was stable at 4°C for 4 months and dry swab samples gave concordant results with that of wet swabs. These features make the test best suitable for routine diagnosis of genital infections in developing countries. PMID:25802857

  1. Low risk of contamination with automated and manual excision of dried blood spots for HIV DNA PCR testing in the routine laboratory.

    PubMed

    Driver, Glenn A; Patton, Janet C; Moloi, Jackie; Stevens, Wendy S; Sherman, Gayle G

    2007-12-01

    In low resource settings the inability to diagnose HIV in infants early presents a major obstacle to providing care for HIV-infected children. Dried blood spot samples offer a solution to the scarcity of skills available for venesecting young infants but pose challenges to laboratories because their processing requirements are distinct from that of the liquid blood samples widely used for viral detection assays. Different methods of excising 287 paired HIV-positive and HIV-negative dried blood spot samples (n=574) for testing by the Roche Amplicor HIV-1 DNA assay version 1.5 were assessed. A manual punch in conjunction with three different cleaning protocols (n=372) and an automated punch (BSD 1000 GenePunch) using a single cleaning protocol (n=202) was assessed for the risk of cross contamination between samples. A single false positive result obtained using the automated punch may have been attributable to contamination during the excision step of the assay. Excision of dried blood spot samples is associated with a very low risk of cross contamination regardless of the instrument or cleaning intervention used. The process of excising dried blood spot samples should not compromise the results of HIV viral detection assays performed on dried blood spots in routine laboratories which is encouraging for increasing access to an accurate diagnosis of HIV in infants.

  2. Detection of human papillomavirus in intraepithelial lesions and carcinoma of the cervix uteri in southern Thai women.

    PubMed

    Tungsinmunkong, Kobkul; Suwiwat, Supaporn; Sriplung, Hutcha

    2006-01-01

    To evaluate the prevalence of high-risk type human papillomavirus (HR-HPV) in preneoplastic lesions and invasive squamous cell carcinoma (SCC) of the cervix uteri in southern Thai women. A total of 148 formalin-fixed, paraffin-embedded blocks of cervix tissue were retrieved from the files of the Department of Pathology, Prince of Songkla University Hospital. They were classified as negative for intraepithelial lesion (NIL) in 37 cases, low grade lesion (LGL) in 58 cases, high grade lesion (HGL) in 39 cases and SCC in 14 cases. HR-HPV DNA was tested with an Amplicor HPV (Roche Diagnostics) detection kit. Of the 111 cases, 42 of 58 LGLs (72.4%), 34 of 39 HGLs (87.2%) and 13 of 14 SCCs (92.9%) were positive for HR-HPV DNA. In 37 cases of histologically normal cervix, there were 15 cases that showed the presence of HR-HPV DNA. Applying the HR-HPV results for NILs to the general population, the age standardized incidence rate of HR-HPV infection in the normal Thai population was 12.8%. HR-HPV DNA can be found in all grades of intraepithelial lesions and carcinoma of the cervix uteri, even in the histologically "normal" looking cervix. These results provide strong evidence for a role in carcinogenesis of the cervix uteri and the existence of a non-productive or latent period of HPV infection.

  3. Single-step PCR in molecular diagnosis of hepatitis C virus infection.

    PubMed Central

    Farma, E; Boeri, E; Bettini, P; Repetto, C M; McDermott, J; Lillo, F B; Varnier, O E

    1996-01-01

    The diagnostic utility of two PCR systems and three PCR detection methods for hepatitis C virus (HCV) RNA was evaluated in serum samples. A nested PCR was considered the reference assay and was compared with two single-step PCR methods: the first is based on the detection of PCR products by liquid hybridization with a 32P-end-labeled probe, and the second is the Roche Amplicor colorimetric assay using microwell plate hybridization with a specific nucleic acid probe. Using the Pelicheck HCV RNA Eurohep genotype 1 proficiency panel, our laboratory achieved medium-high levels of performance with all three methods. The highest sensitivity was, however, observed with the isotopic single-step PCR (ss-PCR) method. The analytical sensitivity of ss-PCR with isotopic detection and ss-PCR with colorimetric detection was identical to that of nested PCR, with a 100% result concordance. Comparison of ss-PCR with enzyme-linked immunosorbent and RIBA assays in the analysis of clinical samples showed a high concordance. ss-PCR methods appear more suitable for diagnostic application. Nevertheless, HCV RNA PCR cannot be considered a screening assay; it should be requested in the presence of reactive serology or specific clinical symptomatology with altered liver parameters, and it is a potential tool for the follow-up of patients with HCV infection. PMID:8940466

  4. Ultra-high-throughput, automated nucleic acid detection of human immunodeficiency virus (HIV) for infant infection diagnosis using the Gen-Probe Aptima HIV-1 screening assay.

    PubMed

    Stevens, Wendy S; Noble, Lara; Berrie, Leigh; Sarang, Somaya; Scott, Lesley E

    2009-08-01

    The early diagnosis of human immunodeficiency virus (HIV) infection in infants is critical to ensure the initiation of treatment before significant immunological compromise. Each year an estimated 300,000 HIV-exposed infants in South Africa require access to tests for the diagnosis of HIV infection. Currently, testing is performed at several facilities by using PCR amplification of HIV DNA at 6 weeks of age by the use of dried blood spots (DBSs) and whole blood (WB). The Gen-Probe Aptima HIV type 1 (HIV-1) screening assay (the Aptima assay) is a qualitative nucleic acid test based on transcription-mediated amplification (TMA), a technology routinely used in blood banks in South Africa. The performance characteristics of Gen-Probe's TMA technology compared well to those of the Roche Amplicor HIV-1 DNA (version 1.5) assay. The sensitivity of the assay with WB and DBS samples was 100%, and the specificities were 99.4% and 99.5% for DBSs and WB, respectively. The detection of HIV by the Aptima assay at greater levels of dilution in samples negative by the comparator assay indicates an improvement in sensitivity by the use of the TMA technology. The ability to process 1,900 samples in a 24-h period on the Tigris instrument makes the Aptima assay an attractive option for high-volume, centralized laboratories.

  5. Single genome amplification of proviral HIV-1 DNA from dried blood spot specimens collected during early infant screening programs in Lusaka, Zambia.

    PubMed

    Seu, Lillian; Mwape, Innocent; Guffey, M Bradford

    2014-07-01

    The ability to evaluate individual HIV-1 virions from the quasispecies of vertically infected infants was evaluated in a field setting at the Centre for Infectious Disease Research in Zambia. Infant heel-prick blood specimens were spotted onto dried blood spot (DBS) filter paper cards at government health clinics. Nucleic acid was extracted and used as a template for HIV-1 proviral DNA detection by a commercial Amplicor HIV-1 PCR test (Roche, version 1.5). On samples that tested positive by commercial diagnostic assay, amplification of DNA was performed using an in-house assay of the 5' and 3' region of the HIV-1 genome. Additionally, fragments covering 1200 nucleotides within pol (full length protease and partial reverse transcriptase) and 1400 nucleotides within env (variable 1-variable 5 region) were further analyzed by single genome amplification (SGA). In summary, we have demonstrated an in-house assay for amplifying the 5' and 3' proviral HIV-1 DNA as well as pol and env proviral DNA fragments from DBS cards collected and analyzed entirely in Zambia. In conclusion, this study shows the feasibility of utilizing DBS cards to amplify the whole proviral HIV-1 genome as well as perform SGA on key HIV-1 genes.

  6. Will droplet digital PCR become the test of choice for detecting and quantifying ocular Chlamydia trachomatis infection? Maybe not.

    PubMed

    Schachter, Julius

    2013-11-01

    Evaluation of: Roberts CH, Last A, Molina-Gonzalez S et al. Development and evaluation of a next-generation digital PCR diagnostic assay for ocular chlamydia trachomatis infections. J. Clin. Microbiol. 51(7), 2195-2203 (2013). Trachoma is the leading infectious cause of blindness in developing countries. Currently, there is no program to eliminate blinding trachoma as a public health problem. We need better diagnostic tests for research and to assess progress in control programs. Roberts et al. adapted droplet digital PCR (ddPCR), an emulsion PCR process that performs absolute quantitation of nucleic acids, to detect and quantify Chlamydia trachomatis infections. They compared the results with ddPCR on conjunctival swab specimens collected in trachoma-endemic area to results using Roche's Amplicor® C. trachomatis/Neisseria gonorrhoeae (CT/NG) PCR and found that ddPCR sensitivity was 73.3%. The authors concluded that 'ddPCR is an effective diagnostic technology suitable for both research and clinical use in diagnosing ocular C. trachomatis infections'. This reviewer disagrees, feeling that if the stated sensitivity is accurate, it is too low, and suggests there may be good reasons to adapt commercially available tests for this purpose.

  7. Cytology and Human Papillomavirus Testing 6 to 12 Months after ASCUS or LSIL Cytology in Organized Screening To Predict High-Grade Cervical Neoplasia between Screening Rounds

    PubMed Central

    Sjøborg, Katrine D.; Nygård, Mari; Røysland, Kjetil; Campbell, Suzanne; Alfsen, G. Cecilie; Jonassen, Christine M.

    2012-01-01

    We carried out a prospective study comparing the performance of human papillomavirus (HPV) E6/E7 mRNA (PreTect HPV-Proofer; NorChip, Klokkarstua, Norway) and DNA (Amplicor HPV test; Roche Diagnostics, Basel, Switzerland) triage testing of women 6 to 12 months after atypical-squamous-cells-of-undetermined-significance (ASCUS) or low-grade-squamous-intraepithelial-lesion (LSIL) cytology in organized screening to predict high-grade cervical intraepithelial neoplasia of grade 2 or worse (CIN2+) between screening rounds. Between January 2005 and April 2008, 692 study women with screening-detected ASCUS/LSIL cytology 6 to 12 months earlier returned for HPV mRNA and DNA testing and repeat cytology. The median follow-up time was 3 years, using existing health care facilities. Follow-up test results were available for 625 women. Of the 145 CIN2+ cases detected during the study period, 95 (65.5%) were HPV mRNA positive 6 to 12 months after screening-detected ASCUS/LSIL, 44 (30.4%) were HPV mRNA negative, and 6 (4.1%) were invalid. The corresponding HPV DNA results were 139 (95.9%), 5 (3.4%), and 1 (0.7%), respectively. The cumulative incidences of CIN2+ 3 years after a negative HPV mRNA and DNA test were 10.3% (95% confidence interval [CI], 7.2 to 13.3%) and 1.8% (95% CI, 0.0 to 3.6%), respectively. The cumulative incidences of CIN2+ 3 years after positive HPV mRNA and DNA tests were 52.8% (95% CI, 40.1 to 60.1%) and 41.3% (95% CI, 35.5 to 46.6%), respectively. In conclusion, both positive HPV mRNA and DNA test results have a high enough long-term prediction of CIN2+ risk to consider referral to colposcopy as good practice when performed in delayed triage of women with ASCUS/LSIL cytology. In addition, the low CIN2+ risk among women with a negative Amplicor HPV test in our study confirms its safe use in a clinical setting. PMID:22518869

  8. Loop-Mediated Isothermal Amplification for Direct Detection of Mycobacterium tuberculosis Complex, M. avium, and M. intracellulare in Sputum Samples

    PubMed Central

    Iwamoto, Tomotada; Sonobe, Toshiaki; Hayashi, Kozaburo

    2003-01-01

    Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method in which reagents react under isothermal conditions with high specificity, efficiency, and rapidity. We used LAMP for detection of Mycobacterium tuberculosis complex, Mycobacterium avium, and Mycobacterium intracellulare directly from sputum specimens as well as for detection of culture isolates grown in a liquid medium (MGIT; Nippon Becton Dickinson Co., Ltd., Tokyo, Japan) or on a solid medium (Ogawa's medium). Species-specific primers were designed by targeting the gyrB gene, and their specificities were validated on 24 mycobacterial species and 7 nonmycobacterial species. The whole procedure is quite simple, starting with the mixing of all reagents in a single tube, followed by an isothermal reaction during which the reaction mixture is held at 63°C. The resulting amplicons are visualized by adding SYBR Green I to the reaction tube. The only equipment needed for the amplification reaction is a regular laboratory water bath or heat block that furnishes a constant temperature of 63°C. The assay had a detection limit of 5 to 50 copies of purified DNA with a 60-min incubation time. The reaction time could be shortened to 35 min for the species identification of M. tuberculosis complex, M. avium, and M. intracellulare from a solid-medium culture. Residual DNA lysates prepared for the Amplicor assay (Roche Diagnostics GmbH) from 66 sputum specimens were tested in the LAMP assay. Although the sample size used for the latter assay was small, 2.75 μl of the DNA lysates, it showed a performance comparable with that of the Amplicor assay, which required 50 μl of the lysates. This LAMP-based assay is simple, rapid, and sensitive; a result is available in 35 min for a solid-medium culture and in 60 min for a liquid-medium culture or for a sputum specimen that contains a corresponding amount of DNA available for testing. PMID:12791888

  9. Rapid and sensitive detection of enteroviruses in specimens from patients with aseptic meningitis.

    PubMed

    Yerly, S; Gervaix, A; Simonet, V; Caflisch, M; Perrin, L; Wunderli, W

    1996-01-01

    A 5-h PCR assay (Amplicor enterovirus test) was compared with viral culture for the detection of enteroviruses in cerebrospinal fluid. Of the cerebrospinal fluid specimens collected during a summer outbreak of aseptic meningitis, 34% were positive by viral culture whereas 66% were positive by the Amplicor PCR, suggesting that this technique improves the diagnosis of enteroviral meningitis.

  10. Stratigraphic and technological evidence from the Middle Palaeolithic-Châtelperronian-Aurignacian record at the Bordes-Fitte rockshelter (Roches d'Abilly site, Central France).

    PubMed

    Aubry, Thierry; Dimuccio, Luca Antonio; Almeida, Miguel; Buylaert, Jan-Pieter; Fontana, Laure; Higham, Thomas; Liard, Morgane; Murray, Andrew S; Neves, Maria João; Peyrouse, Jean-Baptiste; Walter, Bertrand

    2012-01-01

    This paper presents a geoarchaeological study of Middle and Upper Palaeolithic (Châtelperronian, Aurignacian and Solutrean) occupations preserved at the Bordes-Fitte rockshelter in Central France. The lithostratigraphic sequence is composed of near-surface sedimentary facies with vertical and lateral variations, in a context dominated by run-off and gravitational sedimentary processes. Field description and micromorphological analysis permit us to reconstruct several episodes of sediment slope-wash and endokarst dynamics, with hiatuses and erosional phases. The archaeostratigraphic succession includes Châtelperronian artefacts, inter-stratified between Middle Palaeolithic and Aurignacian occupations. Systematic refitting and spatial analysis reveal that the Châtelperronian point production and flake blanks retouched into denticulates, all recovered in the same stratigraphic unit, result from distinct and successive occupations and are not a 'transitional' Middle to Upper Palaeolithic assemblage. The ages obtained by (14)C place the Châtelperronian occupation in the 41-48 ka cal BP (calibrated thousands of years before present) interval and are consistent with the quartz optically stimulated luminescence age of 39 ± 2 ka and feldspar infra-red stimulated luminescence age of 45 ± 2 ka of the sediments. The Bordes-Fitte rockshelter sequence represents an important contribution to the debate about the characterization and timing of the Châtelperronian, as well as its affinities to earlier and later industries.

  11. [A comparison of manual methods and enterotube II (Roche) for the identification of gram-negative enteric bacteria isolated from feces].

    PubMed

    Hasçelik, G

    1987-10-01

    The Enterotube II and classic manual methods were used in parallel to identify 100 members of the enteric bacteria isolated from feces culture. Among these isolated bacteria Shigella, Salmonella and E. coli were found 34%, 25%, 22% respectively. The Enterotube II and classic manual methods gave the same results for identification of Salmonella and Shigella. The Enterotube II correctly identified 98% of all gram negative enteric bacteria. Other advantages and disadvantages of these methods are discussed in our study.

  12. Geochemical characterisation, provenance, source and depositional environment of ‘Roches Argilo-Talqueuses’ (RAT) and Mines Subgroups sedimentary rocks in the Neoproterozoic Katangan Belt (Congo): Lithostratigraphic implications

    NASA Astrophysics Data System (ADS)

    Kampunzu, A. B.; Cailteux, J. L. H.; Moine, B.; Loris, H. N. B. T.

    2005-07-01

    The chemical characteristics of sedimentary rocks provide important clues to their provenance and depositional environments. Chemical analyses of 192 samples of Katangan sedimentary rocks from Kolwezi, Kambove-Kabolela and Luiswishi in the central African Copperbelt (Katanga, Congo) are used to constrain (1) the source and depositional environment of RAT and Mines Subgroup sedimentary rocks and (2) the geochemical relations between the rocks from these units and the debate on the lithostratigraphic position of the RAT Subgroup within the Katangan sedimentary succession. The geochemical data indicate that RAT, D. Strat., RSF and RSC are extremely poor in alkalis and very rich in MgO. SD are richer in alkalis, especially K 2O. Geochemical characteristics of RAT and Mines Subgroups sedimentary rocks indicate deposition under an evaporitic environment that evolved from oxidizing (Red RAT) to reducing (Grey RAT and Mines Subgroup) conditions. There is no chemical difference between RAT and fine-grained clastic rocks from the lower part of the Mines Subgroup. The geochemical data preclude the genetic model that RAT are syn-orogenic sedimentary rocks originating from Mines Group rocks by erosion and gravity-induced fragmentation in front of advancing nappes.

  13. Propriétés mécaniques des roches argileuses carbonatées: Importance de la relation calcite-argile

    NASA Astrophysics Data System (ADS)

    Bauer-Plaindoux, Corinne; Tessier, Daniel; Ghoreychi, Mehdi

    1998-02-01

    Mechanical properties and swelling of a clayey rock do not depend only on the quantity and the nature of the clay. Different experiments showed that the properties are a function of the material structure and texture. Clay properties can be more or less expressed and means that a carbonated phase may prevent clay hydration and swelling.

  14. Prevalence of human papillomavirus in 5,072 consecutive cervical SurePath samples evaluated with the Roche cobas HPV real-time PCR assay.

    PubMed

    Preisler, Sarah; Rebolj, Matejka; Untermann, Anette; Ejegod, Ditte Møller; Lynge, Elsebeth; Rygaard, Carsten; Bonde, Jesper

    2013-01-01

    New commercially available Human Papillomavirus (HPV) assays need to be evaluated in a variety of cervical screening settings. Cobas HPV Test (cobas) is a real-time PCR-based assay allowing for separate detection of HPV genotypes 16 and 18 and a bulk of 12 other high-risk genotypes. The aim of the present study, Horizon, was to assess the prevalence of high-risk HPV infections in an area with a high background risk of cervical cancer, where women aged 23-65 years are targeted for cervical screening. We collected 6,258 consecutive cervical samples from the largest cervical screening laboratory in Denmark serving the whole of Copenhagen. All samples were stored in SurePath media. In total, 5,072 samples were tested with cobas, Hybrid Capture 2 High Risk HPV DNA test (HC2) and liquid-based cytology. Of these, 27% tested positive on cobas. This proportion decreased by age, being 43% in women aged 23-29 years and 10% in women aged 60-65 years. HC2 assay was positive in 20% of samples, and cytology was abnormal (≥ atypical squamous cells of undetermined significance) for 7% samples. When only samples without recent abnormalities were taken into account, 24% tested positive on cobas, 19% on HC2, and 5% had abnormal cytology. The proportion of positive cobas samples was higher than in the ATHENA trial. The age-standardized cobas positivity vs. cytology abnormality was 3.9 in our study and 1.7 in ATHENA. If in Copenhagen the presently used cytology would be replaced by cobas in women above age 30 years, an extra 11% of women would based on historical data be expected to have a positive cobas test without an underlying cervical intraepithelial lesion grade 3 or worse. Countries with a high prevalence of HPV infections should therefore proceed to primary HPV-based cervical screening with caution.

  15. Analytical and clinical comparison of Elecsys syphilis (Roche(®)) - Architect syphilis TP and reformulated Architect syphilis TP (Abbott(®)) assay.

    PubMed

    De Keukeleire, Steven; Desmet, Stefanie; Lagrou, Katrien; Oosterlynck, Julie; Verhulst, Manon; Van Besien, Jessica; Saegeman, Veroniek; Reynders, Marijke

    2017-03-01

    The performance of Elecsys Syphilis was compared to Architect Syphilis TP and Reformulated Architect Syphilis TP. The overall sensitivity and specificity were 98.4% and 99.5%, 97.7% and 97.1%, and 99.2% and 99.7% respectively. The assays are comparable and considered adequate for syphilis screening.

  16. [The saliva cortisol level test using the automatic immunochemical analyzer Cobas e601 (Roche) to diagnose endogenous hypercorticalism in patients with obesity].

    PubMed

    Belaia, Zh E; Il'in, A V; Mel'nichenko, G A; Rozhinskaia, L Ia; Dragunova, N V; Dzeranova, L K; Ogneva, N A; Butrova, S A; Troshina, E A; Kolesnikova, G S; Dedov, I I

    2011-12-01

    The saliva cortisol level test applies to diagnose endogenous hypercorticalism. However the methods of die format immunoassay traditionally used do not make it possible to get the study results on-the-fly. Also, reference interval and optimal takeoffs differ under implementing various techniques of cortisol tests. The purpose of actual study is to investigate the possibilities of electrochemiluminescent technique of testing free cortisol in saliva. The device Cobas e601 was applied to diagnose endogenous hypercorticalism in patients with obesity. The saliva samples were collected at 11 PM from 98 healthy volunteers and 123 patients with obesity (in 45 cases endogenous hypercorticalism was diagnosed). In total, 205 persons donated saliva at 11 PM two days running to evaluate the technique reproducibility. The samples of 197 individuals were frozen to implement the immune-enzyme assay. The minor test with dexamethasone was applied to patients with suspected endogenous hypercorticalism. The diagnosis of endogenous hypercorticalism was finally confirmed after the results of histological analysis of post-operative material or autopsy. Among healthy volunteers, the reference interval on indicators consisted 0.5-9.4 nMol/l. The correlation coefficient under free cortisol measuring at the same time two days running was -0.785. The optimal takeoff to diagnose endogenous hypercorticalism in patients with obesity consisted 9.4 nMol/l, sensitivity--84.4% (95% confidence band 71.2-92.2%), specificity--92.3% (95% confidence band 84.2-96.4%), predictive value of positive result--11.0 (95% confidence band 5.0-23.9), predictive value of negative result--0.17 (95% confidence band 0.08-0.33) and likelihood ratio for positive result--65.1 (95% confidence band 20.4-207.6). The two-fold cortisol test in saliva using immune-enzyme assay and minor test with dexamethasone with their diagnostic capabilities corresponded to one-fold saliva free cortisol test using electrochemiluminescent technique. The one-fold free cortisol test in saliva collected in 11 PM using the analyzer Cobas e601 for electrochemiluminescent immunoanalysis is a convenient and informative endogenous hypercorticalism screening technique in patients with obesity.

  17. Âges K sbnd Ar des roches magmatiques du fossé de Garoua (Cameroun) : leur place dans le cadre de la « Ligne du Cameroun »

    NASA Astrophysics Data System (ADS)

    Montigny, Raymond; Ngounouno, Ismaïla; Déruelle, Bernard

    2004-12-01

    K sbnd Ar analyses on whole rock and minerals are reported for the Kokoumi anorogenic pluton and alkaline volcanics of the Benue valley, west of Garoua (northern Cameroon), which belong to the northern part of the 'Cameroon Line'. The two formations yield similar ages of 39 and 37 Ma, respectively. These values likely correspond to the time of emplacement. They are in agreement with the interpretation considering the 'Cameroon Line' as a huge lithospheric crack tapping a hot deep asthenospheric zone. To cite this article: R. Montigny et al., C. R. Geoscience 336 (2004).

  18. Le massif tertiaire du Nkogam (Ouest Cameroun): caractéristiques principales et géochronologie Rb/Sr sur roches totales

    NASA Astrophysics Data System (ADS)

    Caen-Vachette, M.; Tempier, P.; Kamgang, P.

    The Nkogam massif is exposed over an area of about 140 km 2. It is located on the 'Cameroun Line' and is one of the tertiary massives along this structure. It is composed of three units: (1) basalts; (2) ignimbrites; and (3) acid plutonic rocks. The first two are alkalic, the third one is peraluminous. Rb/Sr radiometric analysis on whole rocks yields an age of 67 Ma for the granites. The fact that two parallel isochrons are obtained shows possible slightly different origins.

  19. Découverte des roches à affinité ophiolitique dans la chaîne panafricaine au Cameroun : les talcschistes de Ngoung, Lamal Pougue et Bibodi Lamal

    NASA Astrophysics Data System (ADS)

    Nkoumbou, Charles; Goune, Clément Yonta; Villiéras, Frédéric; Njopwouo, Daniel; Yvon, Jacques; Ekodeck, Georges Emmanuel; Tchoua, Félix

    2006-12-01

    Outcrops of talc schists extending over >1 km have been discovered within the garnet- and muscovite-bearing mica schist of the Pan-African belt near Yaoundé (Cameroon). Mineralogical studies show that a metamorphism of the upper greenschist facies was prolonged by hydrothermal reactions. This latter led to the transformation of hornblendites into talc schists. Chemically, talc schists and relicts of hornblendite remind ultrabasic rocks, and REE patterns point to E-MORB and peridotite. It is thus suggested that the talc schists and relicts of hornblendite may correspond to slices of a dismembered Pan-African ophiolite set. To cite this article: C. Nkoumbou et al., C. R. Geoscience 338 (2006).

  20. Meaningful application of the new 454 large scale pyrosequencing technology (Roche GS-FLX 454) to the identification of microsatellites for small-scale research projects

    USDA-ARS?s Scientific Manuscript database

    Technical abstract: Microsatellites or simple sequence repeats are DNA sequences that consist of tandem repeats of 1-6 nucleotides. Because of high levels of polymorphism, ease to use and co-dominance, they are generally seen as the most pertinent markers to study at a fine scale level the genetic s...

  1. Monkeypox detection in rodents using real-time 3’minor groove binder Taqman assays on the Roche LightCycler, Laboratory Investigation 84:1200 - 1208

    DTIC Science & Technology

    2007-11-02

    reaction (PCR) assays, an antigen-detection immunoassay, and virus culture. We designed and extensively tested two specific real - time PCR assays for...monkeypox virus strain Zaire-96-I-16 (a human isolate from the Congo). These real - time PCR and ECL assays represent a significant addition to the battery of tests for the detection of various orthopoxviruses.

  2. [Results transferability on RXL, ARX, X-Pand, BN2 (Dade Behring) and modular DP (Roche Diagnostics) analysers: application to component assays of fibrotest and Actitest].

    PubMed

    Imbert-Bismut, F; Messous, D; Raoult, A; Poynard, T; Bertrand, J J; Marie, P A; Louis, V; Audy, C; Thouy, J M; Hainque, B; Piton, A

    2005-01-01

    The follow up of patients with chronic liver diseases and the data from multicentric clinical studies are affected by the variability of assay results for the same parameter between the different laboratories. Today, the main objective in clinical chemistry throughout the world is to harmonise the assay results between the laboratories after the confirmation of their traceability, in relation to defined reference systems. In this context, the purpose of our study was to verify the homogeneity of haptoglobin, apolipoprotein A1, total bilirubin, GGT activity, ALAT activity results, which are combined in Fibrotest and Actitest, between Dimension Analysers RXL, ARX and X-PAND (Dade Behring Society). Moreover, we verified the transferability of Fibrotest and Actitest results between the RXL, and either the BN2 (haptoglobin and apolipoprotein A1) or the Modular DP (total bilirubin, GGT and ALAT activity concentrations). The serum samples from 150 hospitalised patients were analysed on the different analysers. Specific protein assays were calibrated using solutions standardised against reference material on Dimension and BN2 analysers. Total bilirubin assays were performed by a diazoreaction on Dimension and Modular DP analysers. The GGT and ALAT activity measurements on the Dimension analysers were performed in accordance with the reference methods defined by the International Federation of Clinical Chemisty and Laboratory Medicine (IFCC). On the Modular, enzyme activity measurements were performed according to the Szasz method (L-gamma- glutamyl-4-nitroanilide as substrate) modified by Persijn and van der Slik (L-gamma- glutamyl-3-carboxy- 4-nitroanilide as substrat) for GGT and according to the IFCC specifications for ALAT. The methods of enzymatic activity measurement were calibrated on the Modular only. Liver fibrosis and necroinflammatory activity indices were determined using calculation algorithms, after having adjusted each component's result of Fibrotest and Actitest for gender and age. Our study has shown, for each parameter, harmonious results between the Dimension analysers and between RXL and BN2- Modular DP. Disregarding alpha-2 macroglobulin which cannot be assayed on RXL, the results of Fibrotest and Actitest were similar as performed on BN2- Modular DP and RXL.

  3. Prevalence of Sexually Transmitted Infection in Teenage Pregnancy in Rajavithi Hospital, Thailand.

    PubMed

    Asavapiriyanont, Suvanna; Chaovarindr, Udom; Kaoien, Surasak; Chotigeat, Uraiwan; Kovavisarach, Ekachai

    2016-02-01

    Behavioral and social changes in the modern era have triggered an increase in the incidence of early sexual contact and teenage pregnancy. Since there is no routine Gonococcal & Chlamydial (GC & CT) screening in teens in antenatal clinics in Thailand, the present study was performed to find the prevalence of STI, especially Chlamydial infection, in teenage pregnancy. To evaluate the prevalence of sexually transmitted infections (STIs), especially Chlamydial infection (CT), in teenage pregnancy and its related factors. One hundred and twenty-one teenage pregnancies were recruited at the ANC in Rajavithi Hospital from October 2006 to May 2007. After signing informed consent forms, they were asked to answer questionnaires about baseline data, sexual information and risk factors, after which urine specimens were collected for screening for GC and CT using the PCR technique (AMPLICOR by Roche). Later, pelvic examination was per formed by the gynecologist at the STD (sexually transmitted disease) clinic. All the data and LAB results were recorded and analyzed by the SPSS program. Numbers, percentages, means with SD, Chi-squared test, Fisher's exact test and odds ratio were used. Potential risk factors were analyzed using binary logistic regression. The prevalence of STI in pregnant teenagers was 28.1% (CT = 19.8%, GC = 1.7%, hepatitis B = 3.3%, trichomoniasis 1.7%, Herpes simplex = 0.8% and condyloma acuminata = 0.8%). No Syphilis, chancroid or HIV were found in the present study Other non-STI like candidiasis and bacterial vaginosis were found in 45.5% of participants (candidiasis and bacterial vaginosis at 19.0% and 24.8%, respectively). The risk of CT infection was significantly related (6.9 times higher) to having previous sexual contact before the current partner (95% CI, 1.8-27.0). STI, especially Chlamydial infection, was found in a significant number of teenage pregnancies. Measures should be taken to prevent this resulting in complicated outcomes in the future.

  4. Variables that influence HIV-1 cerebrospinal fluid viral load in cryptococcal meningitis: a linear regression analysis

    PubMed Central

    2009-01-01

    Background The central nervous system is considered a sanctuary site for HIV-1 replication. Variables associated with HIV cerebrospinal fluid (CSF) viral load in the context of opportunistic CNS infections are poorly understood. Our objective was to evaluate the relation between: (1) CSF HIV-1 viral load and CSF cytological and biochemical characteristics (leukocyte count, protein concentration, cryptococcal antigen titer); (2) CSF HIV-1 viral load and HIV-1 plasma viral load; and (3) CSF leukocyte count and the peripheral blood CD4+ T lymphocyte count. Methods Our approach was to use a prospective collection and analysis of pre-treatment, paired CSF and plasma samples from antiretroviral-naive HIV-positive patients with cryptococcal meningitis and assisted at the Francisco J Muñiz Hospital, Buenos Aires, Argentina (period: 2004 to 2006). We measured HIV CSF and plasma levels by polymerase chain reaction using the Cobas Amplicor HIV-1 Monitor Test version 1.5 (Roche). Data were processed with Statistix 7.0 software (linear regression analysis). Results Samples from 34 patients were analyzed. CSF leukocyte count showed statistically significant correlation with CSF HIV-1 viral load (r = 0.4, 95% CI = 0.13-0.63, p = 0.01). No correlation was found with the plasma viral load, CSF protein concentration and cryptococcal antigen titer. A positive correlation was found between peripheral blood CD4+ T lymphocyte count and the CSF leukocyte count (r = 0.44, 95% CI = 0.125-0.674, p = 0.0123). Conclusion Our study suggests that CSF leukocyte count influences CSF HIV-1 viral load in patients with meningitis caused by Cryptococcus neoformans.

  5. Evaluation of three commercial detection systems for Mycobacterium tuberculosis where clinical diagnosis is difficult.

    PubMed Central

    Brown, T J; Power, E G; French, G L

    1999-01-01

    AIMS: To assess the performance of three commercially available Mycobacterium tuberculosis detection systems employing nucleic acid amplification, when applied directly to respiratory and non-respiratory specimens from patients where the diagnosis of tuberculosis is difficult using clinical and traditional bacteriological methods. METHODS: 42 respiratory and 21 non-respiratory specimens were concentrated, examined with auramine staining, and cultured on Lowenstein-Jensen slopes. These specimens were also assayed using the Amplicor Mycobacterium tuberculosis test (AM) (Roche Diagnostic Systems), the Amplified Mycobacterium tuberculosis direct test (AMD) (Gen-Probe), and the LCx Mycobacterium tuberculosis assay (LMA) (Abbott Laboratories). RESULTS: All three amplification systems used in this study gave specificities of 100% when used on respiratory specimens. When used on non-respiratory specimens, AM and LMA gave specificities of 100% and AMD 75%. With respiratory specimens the AM, AMD, and LMA systems gave sensitivities of 75%, 65.2%, and 79.2%, respectively. With non-respiratory specimens the sensitivities were 50%, 66.7%, and 60%, while with smear negative, culture positive specimens they were 33.3%, 66.7%, and 55.6%. Positive predictive values of 100% were seen with all specimens except non-respiratory specimens assayed using AMD where the value was 66.7%. CONCLUSIONS: The manufacturers of these systems recommend that they should only be used for the direct analysis of respiratory specimens, and the US Food and Drug Administration has approved them for use only with smear positive specimens. This study confirms that sensitivities are lower for non-respiratory and smear negative specimens, but positive predictive values are high. Provided they are interpreted with caution, positive results with these tests in respiratory and non-respiratory specimens are useful in tuberculous patients who are otherwise difficult to diagnose. Each amplification has advantages and

  6. Evaluation of a modified sanitary napkin as a sample self-collection device for the detection of genital chlamydial infection in women.

    PubMed

    Alary, M; Poulin, C; Bouchard, C; Fortier, M; Murray, G; Gingras, S; Aubé, M; Morin, C

    2001-07-01

    A modified sanitary napkin was compared with endocervical swab and urine specimens for the detection of urogenital Chlamydia trachomatis infection. Endocervical swabs and/or first-catch urine were collected from 510 women at medical or community settings in Quebec City. Participants were also asked to wear a modified sanitary napkin (Ezy-Detek) during 4 consecutive hours and to bring it back to the clinic or mail it to the laboratory. Endocervical and urine specimens were tested using the Cobas Amplicor CT/NG assay (Roche Diagnostic Systems) according to the manufacturer's instructions, as were specimens collected with the napkin after adequate preparation. If the PCR test result was positive on the endocervical sample or on any two samples, a woman was considered to be infected. PCR testing results on paired samples were identical for 493 (96.6%) of 510 women. According to the definition given above, 58 (11.3%; 95% confidence interval [CI], 8.7 to 14.5%) women were infected with C. trachomatis. The sensitivity and specificity of PCR testing on modified sanitary napkin specimens were, respectively, 93.1% (54 of 58; 95% CI, 83.3 to 98.1%) and 98.9% (447 of 452; 95% CI, 97.4 to 99.6%) compared to 81.0% (47 of 58; 95% CI, 68.6 to 90.1%) and 100% (451 of 451; 95% CI, 99.2 to 100%) for urine specimens. The positive and negative predictive values were, respectively, 91.5% (54 of 59) and 99.1% (447 of 451) for the sanitary napkin specimens compared to 100% (47 of 47) and 97.6% (451 of 462) for urine samples. These results suggest that a modified sanitary napkin represents an effective noninvasive device for self-collection of specimens to detect urogenital C. trachomatis infection.

  7. Prevalence of oral lesions in HIV patients related to CD4 cell count and viral load in a Venezuelan population.

    PubMed

    Bravo, Inés María; Correnti, María; Escalona, Laura; Perrone, Marianella; Brito, Aubert; Tovar, Vilma; Rivera, Helen

    2006-01-01

    To determine the prevalence of oral lesions in a HIV+ group of patients, related to CD4 cell count and viral load in a Venezuelan population. In the present study, we evaluated 75 HIV+ adult patients, attended at the Center of Infectious Diseases, at the Faculty of Dentistry, Central University of Venezuela. Each patient was clinically examined for detection of oral mucosal lesions. In addition, CD4 cell count was determined by flow cytometry, as well as viral load by RT-PCR (Amplicor HIV-RNA, TM test 1.5, Roche). 85% (64/75) of HIV/AIDS patients showed associated HIV lesions. Oral Candidiasis constituted the most common lesion representing a 61% (39/64), followed by Oral Hairy Leukoplakia 53% (34/64); Oral Leukoplakia 34% (22/64), Melanic Hyperpigmentation 38% (18/64); Papilloma 13 (6/64), Lineal Gingival Erythema 8% (5/64); Aphtous Recurrent Stomatitis 5% (4/64) and Kaposi's Sarcoma 5% (3/64). Only one case of the following lesions were represented by Non Hodgkin Lymphoma, Multifocal Epithelial Hyperplasia, Recurrent Herpes, Histoplasmosis and Molluscum Contagiosum. The patients with a viral load of 30.000 copies/mm3 exhibited oral lesions related with HIV, independent of CD4 cell count, although patients with CD4+ levels of 200 cel/mm3 were more susceptible to develop these lesions. The most common oral lesion was Oral Candidiasis followed by Oral Hairy Leukoplakia, Oral Leukoplakia and Melanic Hyperpigmentation. A high viral load was strongly associated to the oral lesions occurrence independently of CD4+ cell count.

  8. Quantitation of Human Immunodeficiency Virus Type 1 RNA in Different Biological Compartments

    PubMed Central

    Shepard, Robin N.; Schock, Jody; Robertson, Kevin; Shugars, Diane C.; Dyer, John; Vernazza, Pietro; Hall, Colin; Cohen, Myron S.; Fiscus, Susan A.

    2000-01-01

    Little information is available describing viral loads in body fluids other than blood. In addition, the suitability of commercially available assays for human immunodeficiency virus type 1 (HIV-1) RNA quantitation has not been evaluated in most nonblood fluids. We compared Organon Teknika's nucleic acid sequence-based amplification method (NASBA) and Roche's Amplicor HIV-1 Monitor (reverse transcriptase PCR [RT-PCR]) for quantitating HIV-1 RNA in cerebrospinal fluid (CSF), saliva, breast milk, seminal plasma, and cervical-vaginal lavage fluid (CVL). Saliva and breast milk frequently demonstrated some inhibition in the RT-PCR assay, similar to the inhibition previously described in seminal plasma. Inhibition of the RT-PCR assay was not observed with CSF or CVL, nor in any of the NASBA assays. When fluids from HIV-infected individuals were tested by RT-PCR and NASBA, 73 and 27% of CSF samples and 60 and 40% of breast milk specimens had detectable RNA, respectively. These differences were not statistically significant. In cross-sectional studies using RT-PCR to measure viral RNA in paired blood plasma and CSF samples, 71% of blood plasma samples and 42% of CSF samples were positive. A similar analysis using NASBA with paired blood plasma and CVL, saliva, or seminal plasma samples revealed 91% were blood plasma positive and 55% were CVL positive, 76% were blood plasma positive and 46% were saliva positive, and 83% were blood plasma positive and 63% were seminal plasma positive. NASBA worked fairly well to quantitate HIV-1 RNA from all fluids without apparent inhibition. RT-PCR performed well on CVL and CSF, frequently with greater sensitivity, although its use in other fluids appears limited due to the presence of inhibitors. These studies demonstrate that viral loads in nonblood fluids were generally lower than in blood. PMID:10747117

  9. Estimation of the rate of mother to child transmission of HIV in Nigeria.

    PubMed

    Audu, R A; Salu, O B; Musa, A Z; Onyewuche, J; Funso-Adebayo, E O; Iroha, E O; Ezeaka, V C; Adetifa, I M O; Okoeguale, B; Idigbe, E O

    2006-06-01

    Definitive diagnosis of HIV infection in infants < 18 months of age who were born to HIV-infected mothers is still posing some difficulty in Nigeria and other developing countries. Within this age definitive diagnosis can only be carried out by antigen based techniques which are indeed not available in these developing countries. This has resulted in the absence of authoritative data on the rate of mother-to-child transmission in these countries. Nigeria inclusive. The present pilot study was therefore carried out to generate some information on the rate of mother to child transmission in Nigeria using the PCR technique. Plasma samples were obtained from 68 children of both sexes less than 18 months of age and who were born to HIV infected mothers. The samples were collected from two pediatric departments. in Lagos and in Benin. The presence of HIV 1 RNA in each of the samples. was determined using the Amplicor Monitor V 1.5 technique (Roche Diagnostics). Data showed that HIV-1 RNA was detected in 15 of the 68 samples tested. This gave an HIV-1 RNA detection rate of 22%. Among women who had some intervention, the rate of transmission of infection was 11% while the rate among those without intervention was 30%. The 22% transmission rate recorded in this study is close to the range of 25 to 35% that has been reported in several developed and a few developing countries. A multicenter nationwide study will still be needed to determine the national mother to child transmission rate in Nigeria.

  10. Diagnosis and follow-up of genital chlamydial infection by direct methods and by detection of serum IgG, IgA and secretory IgA.

    PubMed

    Fresse, A S; Sueur, J M; Hamdad, F

    2010-01-01

    To determine the prevalence of Chlamydia trachomatis infection in a high-risk population by direct and indirect methods and to evaluate the diagnosis of secretory immunoglobulin A (sIgA). Urethral or endocervical specimens from 78 patients (48 females and 30 males) were examined by cell culture, direct fluorescence assay, PCR Cobas Amplicor (Roche Molecular Diagnostics), and sIgA was detected by the recombinant lipopolysaccharide (LPS)-enzyme-linked immunoassay (rELISA). Serum from each patient was also obtained and analysed for the presence of IgG and IgA antibody by in-house microimmunofluorescence (MIF) and by the rELISA method (Medac, Hamburg, Germany). The overall C. trachomatis prevalence determined by direct methods was 28%. The detection of sIgA antibodies was significantly higher in the group of patients with a positive direct detection (50%) than in the group of negative direct detection (10.7%). The Chlamydia-specific IgA antibodies were detected by the rELISA in 40.9 and 53.6% of group I (positive direct detection) and group II patients (negative direct detection), respectively. The species-specific IgA antibodies were detected by the MIF method in 18.2 and 16.1% of group I and II patients, respectively. Chlamydia genus-specific IgG antibodies were detected by the rELISA in 86.4 and 83.9% of group I and group II patients and, C. trachomatis specific IgG were present in 81.8 and 73.2% of group I and group II patients, respectively, as assessed by the MIF test. Combining the positive direct methods and/or positive sIgA antibody results from cervical or urethral specimens had an indication of current C. trachomatis infection.

  11. Characteristics of the m2000 Automated Sample Preparation and Multiplex Real-Time PCR System for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae▿

    PubMed Central

    Marshall, R.; Chernesky, M.; Jang, D.; Hook, E. W.; Cartwright, C. P.; Howell-Adams, B.; Ho, S.; Welk, J.; Lai-Zhang, J.; Brashear, J.; Diedrich, B.; Otis, K.; Webb, E.; Robinson, J.; Yu, H.

    2007-01-01

    We evaluated a new real-time PCR-based prototype assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae developed by Abbott Molecular Inc. This assay is designed to be performed on an Abbott m2000 real-time instrument system, which consists of an m2000sp instrument for sample preparation and an m2000rt instrument for real-time PCR amplification and detection. The limit of detection of this prototype assay was determined to be 20 copies of target DNA for both C. trachomatis and N. gonorrhoeae, using serially diluted linearized plasmids. No cross-reactivity could be detected when 55 nongonococcal Neisseria isolates and 3 non-C. trachomatis Chlamydia isolates were tested at 1 million genome equivalents per reaction. Concordance with the Roche Amplicor, BDProbeTec ET, and Gen-Probe APTIMA Combo 2 tests was assessed using unlinked/deidentified surplus clinical specimens previously analyzed with these tests. For C. trachomatis, concordance for positive results ranged from 93.7% to 100%, while concordance for negative results ranged from 98.2% to 100%. For N. gonorrhoeae, concordance for positive and negative results ranged from 91.4% to 100% and 99.3% to 100%, respectively. A workflow analysis of the prototype assay was conducted to obtain information on throughput under laboratory conditions. At 48 samples/run, the time to first result for both C. trachomatis and N. gonorrhoeae was 4.5 h. A total of 135 patient specimens could be analyzed in 8.9 h, with 75 min of hands-on time. This study demonstrated the technical and clinical feasibility of the new Abbott real-time PCR C. trachomatis/N. gonorrhoeae assay. PMID:17202273

  12. Comparison of transcription mediated amplification (TMA) and reverse transcription polymerase chain reaction (RT-PCR) for detection of hepatitis C virus RNA in liver tissue.

    PubMed

    Hofmann, Wolf Peter; Dries, Volker; Herrmann, Eva; Gärtner, Barbara; Zeuzem, Stefan; Sarrazin, Christoph

    2005-04-01

    Transcription mediated amplification (TMA) is known to be one of the most sensitive detection assays for hepatitis C virus (HCV) RNA in serum but has not yet been evaluated in liver tissue. It is unknown whether the higher sensitivity of TMA in comparison with polymerase chain reaction (PCR)-based assays is related to a higher efficiency of the extraction and/or amplification step. The sensitivity of a TMA-based assay (Versant HCV RNA Qualitative assay, Bayer Diagnostics) and a standard RT-PCR-based assay (Cobas Amplicor HCV 2.0, Roche Diagnostics) was compared in formalin-fixed paraffin-embedded liver biopsy specimens of patients with chronic hepatitis C. After deparaffinization of 7.5 microm liver sections HCV RNA was extracted by standard phenol/chloroform. HCV RNA dilution panels were transferred in parallel to cDNA synthesis and amplification steps of PCR and TMA. Furthermore, TMA amplification from stepwise diluted HCV sera was performed following RNA extraction by either microcentrifuge colums (QIAmp Viral RNA spin Kit, Qiagen, Hilden, Germany) or magnetic microparticles (VERSANT HCV RNA Qualitative assay). The total number of HCV RNA positive liver specimens detected by TMA was higher compared with those detected by RT-PCR (P=0.032). The total number of TMA positive serum samples was higher when HCV RNA was extracted using magnetic microparticles in comparison with multicentrifuge column extraction (P=0.019). Our results suggest that both the extraction and amplification step of the TMA-based assay contribute to the higher sensitivity compared with standard RT-PCR.

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

    PubMed

    Dalgard, Olav; Martinot-Peignoux, Michelle; Verbaan, Hans; Bjøro, Kristian; Ring-Larsen, Helmer; Marcellin, Patrick

    2015-01-01

    The aim of this study was to determine in patients with HCV genotype 2 or 3 the performance at week 4 of two assays with different sensitivities for HCV RNA detection, for the prediction of SVR and stratification for treatment duration (14 and 24 weeks). Recruitment was from two trials comparing 14 and 24 weeks treatment to patients with rapid virological response (RVR) (n = 550). RVR was originally defined as HCV RNA <50 IU/ml at week 4. Patients with an available frozen plasma sample drawn at week 4 and with follow-up data week 24 post-treatment were included (n = 429). HCV-RNA was prospectively measured with COBAS Amplicor V2, Roche (CA) (lower detection limit 50 IU/ml) and retrospectively assessed with VERSANT HCV-RNA Qualitative Assay, Siemens (TMA) (lower limit detection 10 IU/ml). Genotype 3 was present in 80% and genotype 2 in 20%. A SVR was achieved in 82%. At week 4 HCV-RNA was undetectable in 74.8% and 63% of serum samples tested with CA and TMA, respectively. CA undetectable/TMA positive was observed in 61/341 (18%) of the samples. In genotype 3 patients a relapse was seen in 9% of the patients with both CA and TMA undetectable and in 25% of the patients who were CA undetectable/TMA positive (p = 0.006). In patients allocated to 14 weeks treatment a relapse was observed in 11% of TMA undetectable patients and 26% of TMA positive (p = 0.031). In genotype 2 patients treated for 14 weeks relapse was observed in 6% of the patients with both CA and TMA undetectable week 4. Assays with high sensitivity for HCV RNA identifies patients at week 4 with high risk of virological relapse. We recommend that patients with genotype 3 and detectable HCV RNA at levels below 50 IU/ml do not receive truncated therapy with pegIFN and ribavirin.

  14. HCV RNA detection by TMA during the hepatitis C antiviral long-term treatment against cirrhosis (Halt-C) trial.

    PubMed

    Morishima, Chihiro; Morgan, Timothy R; Everhart, James E; Wright, Elizabeth C; Shiffman, Mitchell L; Everson, Gregory T; Lindsay, Karen L; Lok, Anna S F; Bonkovsky, Herbert L; Di Bisceglie, Adrian M; Lee, William M; Dienstag, Jules L; Ghany, Marc G; Gretch, David R

    2006-08-01

    For making treatment decisions related to chronic hepatitis C, the utility of HCV RNA tests with increased sensitivity has not been defined. Prior interferon nonresponders with advanced fibrosis (n = 1,145) were retreated with peginterferon alpha-2a and ribavirin. Patients who were HCV RNA-negative by a polymerase chain reaction (PCR)-based assay (Roche COBAS Amplicor HCV Test, v. 2.0; lower limit of detection [LOD] 100 IU/mL) at week 20 (W20) received treatment for 48 weeks. Stored specimens were tested using the Bayer VERSANT HCV RNA Qualitative (TMA) Assay (LOD 9.6 IU/mL) and compared to PCR results for the ability to predict sustained virological response (SVR; defined as undetectable HCV RNA by PCR at W72). Nearly all PCR-positive samples (1006/1007, 99.9%) were positive as assessed by TMA. Among 1,294 PCR-negative samples, 22% were TMA-positive. Negative TMA results were more predictive of SVR than were negative PCR results at W12 (82% vs. 64%, P < .001) and at W20 (66% vs. 52%, P = 0.001). SVR was more likely the earlier TMA had become negative during treatment (82% at W12, 44% at W20, 20% at W24). Among 45 patients who were TMA-positive but were PCR-negative at W20 and W24, none achieved SVR (95% CI: 0%-8%). Approximately 10% of patients with a single positive TMA result at the end of treatment still achieved SVR. In conclusion, negative TMA results at or after W12 were superior to negative PCR results for predicting SVR. In patients with negative PCR results during treatment, a single positive TMA test did not exclude SVR, although persistently positive tests did.

  15. Evaluation of a Modified Sanitary Napkin as a Sample Self-Collection Device for the Detection of Genital Chlamydial Infection in Women

    PubMed Central

    Alary, Michel; Poulin, Céline; Bouchard, Céline; Fortier, Michel; Murray, Gilles; Gingras, Suzanne; Aubé, Michel; Morin, Carol

    2001-01-01

    A modified sanitary napkin was compared with endocervical swab and urine specimens for the detection of urogenital Chlamydia trachomatis infection. Endocervical swabs and/or first-catch urine were collected from 510 women at medical or community settings in Quebec City. Participants were also asked to wear a modified sanitary napkin (Ezy-Detek) during 4 consecutive hours and to bring it back to the clinic or mail it to the laboratory. Endocervical and urine specimens were tested using the Cobas Amplicor CT/NG assay (Roche Diagnostic Systems) according to the manufacturer's instructions, as were specimens collected with the napkin after adequate preparation. If the PCR test result was positive on the endocervical sample or on any two samples, a woman was considered to be infected. PCR testing results on paired samples were identical for 493 (96.6%) of 510 women. According to the definition given above, 58 (11.3%; 95% confidence interval [CI], 8.7 to 14.5%) women were infected with C. trachomatis. The sensitivity and specificity of PCR testing on modified sanitary napkin specimens were, respectively, 93.1% (54 of 58; 95% CI, 83.3 to 98.1%) and 98.9% (447 of 452; 95% CI, 97.4 to 99.6%) compared to 81.0% (47 of 58; 95% CI, 68.6 to 90.1%) and 100% (451 of 451; 95% CI, 99.2 to 100%) for urine specimens. The positive and negative predictive values were, respectively, 91.5% (54 of 59) and 99.1% (447 of 451) for the sanitary napkin specimens compared to 100% (47 of 47) and 97.6% (451 of 462) for urine samples. These results suggest that a modified sanitary napkin represents an effective noninvasive device for self-collection of specimens to detect urogenital C. trachomatis infection. PMID:11427561

  16. Comparison of Three Different FDA-Approved Plasma HIV-1 RNA Assay Platforms Confirms the Virologic Failure Endpoint of 200 Copies per Milliliter Despite Improved Assay Sensitivity

    PubMed Central

    Jennings, Cheryl; Johnson, Victoria A.; Coombs, Robert W.; McKinnon, John E.; Bremer, James W.; Cobb, Bryan R.; Cloherty, Gavin A.; Mellors, John W.; Ribaudo, Heather J.

    2015-01-01

    Discrepancies between HIV-1 RNA results assayed by different FDA-approved platforms have been reported. Plasma samples collected from 332 randomly selected clinical trial participants during the second year of antiretroviral treatment were assayed with three FDA-approved platforms: UltraSensitive Roche Amplicor Monitor, v1.5 (Monitor), the Abbott RealTime HIV-1 test on the m2000 system (Abbott), and the Roche TaqMan HIV-1 test, v2.0 (TaqMan). Samples from 61 additional participants with confirmed HIV-1 RNA levels of >50 copies/ml during trial follow-up were also included. Endpoints were HIV-1 RNA quantification of ≤50 copies/ml versus >50 copies/ml at an individual-sample level (primary) and determination of confirmed virologic failure (VF) from longitudinal samples. A total of 389 participants had results obtained from all assays on at least one sample (median = 6). Proportions of results of >50 copies/ml were 19% (Monitor), 22% (TaqMan), and 25% (Abbott). Despite indication of strong agreement (Cohen's kappa, 0.76 to 0.82), Abbott was more likely to detect HIV-1 RNA levels of >50 copies/ml than Monitor (matched-pair odds ratio [mOR] = 4.2; modified Obuchowski P < 0.001) and TaqMan (mOR = 2.1; P < 0.001); TaqMan was more likely than Monitor (mOR = 2.6; P < 0.001). Despite strong agreement in classifying VF across assay comparisons (kappa, 0.75 to 0.92), at a 50-copies/ml threshold, differences in the probability of VF classification (in the same direction as primary) were apparent (all McNemar's P < 0.007). At a 200-copies/ml VF threshold, no differences between assays were apparent (all P > 0.13). Despite strong agreement among assays, significant differences were observed with respect to detecting HIV-1 RNA levels of >50 copies/ml and identifying VF at the 50-copies/ml threshold. This has important implications for the definition of VF in clinical trials and clinical practice. PMID:26063861

  17. Genital human papillomavirus infection in women from the Zagreb region.

    PubMed

    Marijan, Tatjana; Vranes, Jasmina; Mlinarić-Dzepina, Ana; Leskovar, Vladimira; Knezević, Jasna; Kvaternik, Matea

    2007-04-01

    Human papillomavirus (HPV) infection is the most common sexually transmitted infection, especially among young, sexually active individuals. As persistent infection with oncogenic types may lead to cervical cancer, HPV testing is a useful tool to screen for women at risk for subsequent development of cervical cancer. The aim of the study was to determine the prevalence of high-risk HPV (hrHPV) infection in different age groups of cytologically selected women from the Zagreb region, and to evaluate the frequency and results of repeat hrHPV testing. During a one-year study period (November 2005 to November 2006), a total of 3,440 cervical samples from women attending gynecological services of public and private health care systems were received. They were tested for 13 hrHPV genotypes by the polymerase chain reaction based AMPLICOR HPV test (Roche Molecular Systems). The overall prevalence of hrHPV was 34.6%. Most samples were obtained from women aged 21-30 years (44.2%), followed by the 31-40 (27.6%), 41-50 (15.7%), 51-60 (5.3%) and 261 (2.4%) age groups. Out of 3,227 cervical samples obtained from women of known age, 4.9% were obtained from the group of girls younger than 21, in which the highest prevalence of hrHPV (49.4%) was found. A similar prevalence was observed in women aged 21-30 (45.1%). The prevalence gradually decreased with age. During the study period, repeat hrHPV testing was performed in samples from 66 women at different intervals. Out of 28 women that were hrHPV negative on initial testing, only five women turned positive on repeat testing. Out of 38 women that were positive on initial testing, in one-third hrHPV could not be detected on repeat testing. As expected, hrHPV infection was highly prevalent in female adolescents and young women. Further investigation on repeat hrHPV testing is needed to assess virus clearance and rate of newly acquired infection.

  18. Hepatitis B virus activity in patients with anti-hepatitis C virus antibody positivity and hepatitis B antigen positivity.

    PubMed

    Haushofer, Alexander C; Hauer, René; Brunner, Harald; Köller, Ursula; Trubert-Exinger, Doris; Halbmayer, Walter Michael; Haas, Josef; Kessler, Harald H

    2002-12-01

    Co-infection with hepatitis B virus (HBV) and HCV seems to be relatively frequent. There might be a mutual influence on replication activity of HBV and HCV. To determine the HBV activity in patients with serum HCV RNA and HBsAg positivity and in those with confirmed anti-HCV antibody and HBsAg positivity but serum HCV RNA negativity. A total of 1,200 anti-HCV antibody positive samples were investigated. Samples of HCV RNA and HBsAg positive patients were compared with those of confirmed anti-HCV and HBsAg positive but serum HCV RNA negative patients. HBV activity was tested with the quantitative Cobas Amplicor HBV Monitor Test (Roche Diagnostic Systems, Pleasanton, CA). Of all studied patients with chronic hepatitis C (serum HCV RNA positivity) only 1.0% were found to be HBsAg positive. In contrast, of all patients with confirmed anti-HCV positivity but serum HCV RNA negativity, 11.9% tested HBsAg positive. The median of HBV DNA levels of patients with serum HCV RNA positivity and HBeAg seroconversion (4.0 x 10(2) HBV DNA copies per ml) was found to be slightly lower than that of patients with serum HCV RNA negativity and HBeAg seroconversion (2.5 x 10(3) HBV DNA copies per ml; P>0.05). The median of HBV DNA levels of patients with serum HCV RNA positivity but without HBeAg seroconversion (1.1 x 10(4) HBV DNA copies per ml) was found to be significantly lower than that of patients with serum HCV RNA negativity but without HBeAg seroconversion (2.6 x 10(7) HBV DNA copies per ml; P<0.05). A mutual effect on HBV and HCV replication could be observed. The molecular assay for quantification of serum HBV DNA was found to be useful for the routine diagnostic laboratory.

  19. Development and implementation challenges of a quality assured HIV infant diagnosis program in Nigeria using dried blood spots and DNA polymerase chain reaction.

    PubMed

    Audu, Rosemary; Onwuamah, Chika; Salu, Olumuyiwa; Okwuraiwe, Azuka; Ou, Chin-Yih; Bolu, Omotayo; Bond, Kyle B; Diallo, Karidia; Lu, Lydia; Jelpe, Tapdiyel; Okoye, McPaul; Ngige, Evelyn; Vertefeuille, John

    2015-04-01

    Nigeria has one of the highest HIV burdens as well as mother-to-infant transmission rates in the world. A pilot program using polymerase chain reaction (PCR)-based testing of dried blood spot (DBS) specimens was implemented to enable early identification of HIV-infected infants and timely referral and linkage to care. From February 2007 to October 2008, whole blood was collected by finger prick to prepare DBS from infants <18 months presenting in six public mother-and-child health facilities in Lagos, Nigeria. The DBS were tested using the Roche Amplicor HIV-1 DNA Test, v1.5. To monitor laboratory testing quality, all of the PCR-positive and 10% of the PCR-negative DBS were retested by the same method at another reference laboratory. Three hundred and sixty-five randomly selected infants were screened using HIV rapid tests (RT) according to the national algorithm and RT-negative and PCR-positive specimens were also tested using Genscreen enzyme-linked immunosorbent assay (EIA) (Bio-Rad, France). The turnaround time (TAT) from sample collection, testing, and dispatching of results from each health facility was monitored. A total of 1,273 infants with a median age of 12.6 weeks (1 day to 71.6 weeks) participated in the program and 280 (22.0%) were PCR positive. HIV transmission levels varied greatly in the different health facilities ranging from 7.1% to 38.4%. Infants aged 48 to 72 weeks had the highest level of PCR positivity (41.1%). All PCR-positive specimens were confirmed by retesting. The mean turnaround time from DBS collection to returning of the laboratory result to the health facilities was 25 days. Three infants were found to be HIV antibody negative by rapid tests but were positive by both PCR and the fourth generation EIA. The DBS-based PCR program accurately identified all of the HIV-infected infants. However, many programmatic challenges related to the laboratory and TAT were identified.

  20. Development and Implementation Challenges of a Quality Assured HIV Infant Diagnosis Program in Nigeria Using Dried Blood Spots and DNA Polymerase Chain Reaction

    PubMed Central

    Audu, Rosemary; Onwuamah, Chika; Salu, Olumuyiwa; Okwuraiwe, Azuka; Ou, Chin-Yih; Bolu, Omotayo; Bond, Kyle B.; Diallo, Karidia; Lu, Lydia; Jelpe, Tapdiyel; Okoye, McPaul; Ngige, Evelyn; Vertefeuille, John

    2015-01-01

    Nigeria has one of the highest HIV burdens as well as mother-to-infant transmission rates in the world. A pilot program using polymerase chain reaction (PCR)-based testing of dried blood spot (DBS) specimens was implemented to enable early identification of HIV-infected infants and timely referral and linkage to care. From February 2007 to October 2008, whole blood was collected by finger prick to prepare DBS from infants < 18 months presenting in six public mother-and-child health facilities in Lagos, Nigeria. The DBS were tested using the Roche Amplicor HIV-1 DNA Test, v1.5. To monitor laboratory testing quality, all of the PCR-positive and 10% of the PCR-negative DBS were retested by the same method at another reference laboratory. Three hundred and sixty-five randomly selected infants were screened using HIV rapid tests (RT) according to the national algorithm and RT-negative and PCR-positive specimens were also tested using Genscreen enzyme-linked immunosorbent assay (EIA) (Bio-Rad, France). The turnaround time (TAT) from sample collection, testing, and dispatching of results from each health facility was monitored. A total of 1,273 infants with a median age of 12.6 weeks (1 day to 71.6 weeks) participated in the program and 280 (22.0%) were PCR positive. HIV transmission levels varied greatly in the different health facilities ranging from 7.1% to 38.4%. Infants aged 48 to 72 weeks had the highest level of PCR positivity (41.1%). All PCR-positive specimens were confirmed by retesting. The mean turnaround time from DBS collection to returning of the laboratory result to the health facilities was 25 days. Three infants were found to be HIV antibody negative by rapid tests but were positive by both PCR and the fourth generation EIA. The DBS-based PCR program accurately identified all of the HIV-infected infants. However, many programmatic challenges related to the laboratory and TAT were identified. PMID:25381805

  1. [Comparison of two commercial molecular assays for quantitative measurement of hepatitis B viral DNA].

    PubMed

    Zalewska, Małgorzata; Domagała, Małgorzata; Gładysz, Andrzej

    2003-12-01

    The detection and quantification of hepatitis B virus (HBV) genomes appear to be the most reliable method for monitoring HBV infection and assessing responses to antiviral treatment. For quantitative determination of HBV viremia molecular biology-based assays are used. The aim of this study was to compare and evaluate the performance of two HBV DNA detection and quantification commercial assays: hybrid-capture Digene Hybrid Capture HBV DNA assays and based on competitive polymerase chain reaction (PCR) Cobas Amplicor HBV Monitor Roche Diagnostics. Reproducibility, linearity, sensitivity were determined with 2-fold dilution series of high-titers samples and with 113 sera samples from patients with chronic HBV infection. Within-run and between-run coefficients of variation ranged from 2.4-9.7% for hybrid-capture and from 3.7-15% for PCR-based Monitor. The hybrid-capture and PCR Monitor assays appeared to be linear throughout their range of quantification: 5-2000 pg/ml and 2 x 10(2)-2 x 10(5) copies/ml respectively. The HBV DNA units used in the two assays were not comparable. Hybrid-capture and Monitor gave concordant results with 87 (82.1%) of 106 samples. The assays were both positive with 79 (74.5%) samples and were negative in 7 (7.5%) cases. Hybrid-capture and Monitor gave discordant results in 17 (17.9%) cases. The Monitor Assay was positive in 13 (61.9%) of the 21 samples negative in hybrid-capture. The competitive PCR-based Monitor assay appear to be significantly more sensitive but slightly less reproducible than the hybrid-capture. In the group of patients with seroconversion to anti-HBe PCR method should be used for measurement of viral load. In the presence of HBe antigen concentration of HBV DNA may be tested by hybrid-capture assay. Also these two assays may be used in complementary fashion in the management of HBV infected patients. It seems reasonable to use a hybrid-capture assay first, because its linear range of quantification is extended to high

  2. Evaluation of a rapid point‐of‐care test for the detection of gonococcal infection among female sex workers in Benin

    PubMed Central

    Alary, M; Gbenafa‐Agossa, C; Aïna, G; Ndour, M; Labbé, A C; Fortin, D; Steele, M; Peeling, R W

    2006-01-01

    Objectives To assess the validity of the PATH (Seattle, Washington, USA) GC‐Check rapid test, a point‐of‐care immunochromatographic strip test, in the detection of gonococcal infection among female sex workers (FSWs) in Benin. Methods Women consulting consecutively at two FSW‐dedicated clinics in Cotonou and Porto Novo (Benin) were recruited over three, 1‐month periods between October 2003 and July 2004. After written informed consent, participants were administered a short interview and underwent a speculum examination where two cervical swabs were collected (in a subset of women, a vaginal swab was also collected). One cervical swab and the vaginal swab were immediately tested with the rapid test. The other cervical swab was frozen at –20°C for at most four weeks and then transported to Québec (Canada), where it was tested with the Roche Amplicor CT/NG PCR assay. Samples positive for gonococcal infection were confirmed using a 16SrRNA PCR assay. Results 1084 FSWs (median age 29 years) participated in the study, of whom 50 (4.6%) had a confirmed gonococcal infection. The sensitivity, specificity, positive and negative predictive values of the rapid test on cervical samples were 70.0% (95% confidence interval (CI) 55.4% to 82.1%), 97.2% (95% CI 96.0% to 98.1%), 54.7% and 98.5%, respectively. The sensitivity of the rapid test on vaginal swabs among 759 women (37 positives for gonococcal infection) was significantly lower than with the cervical swab (54.1%, p = 0.008), whereas the specificity was comparable (98.2%, p = 0.13). Conclusions The PATH GC‐Check test may be as efficient as a gold standard polymerase chain reaction (PCR) test for treating gonococcal infection when taking into account the proportion of women who do not return for their test results. In clinics serving populations with moderate prevalence of this infection, it could significantly reduce over‐treatment compared to the syndromic approach. PMID:17215275

  3. Comparison of molecular tests for detection and quantification of cell-associated cytomegalovirus DNA.

    PubMed

    Caliendo, Angela M; Yen-Lieberman, Belinda; Baptista, Jovana; Andersen, Janet; Crumpacker, Clyde; Schuurman, Rob; Spector, Stephen A; Bremer, James; Lurain, Nell S

    2003-08-01

    A cell-based standard was developed to compare the COBAS Amplicor CMV Monitor test, the Hybrid Capture System CMV DNA test, and the NucliSens CMV test. The standard was prepared by infecting human foreskin fibroblasts (HFFs) with cytomegalovirus (CMV) strain AD169 at low multiplicity of infection (0.03) and harvesting the cells at 6 h postinfection. Buffy coat cells were added to produce concentrations of from 0 to 10(5) HFFs per 10(6) total cells. Five laboratories performed the Amplicor PCR test and two laboratories performed the NucliSens and Hybrid Capture tests. The Amplicor PCR test was 1.5 to 2.0 log(10) more sensitive than the Hybrid Capture test. The specificities of the Amplicor PCR and Hybrid Capture tests were 100 and 93.8%, respectively. The linear range of the Amplicor PCR and Hybrid Capture tests were 2 to 4.48 log(10) and 3.48 to at least 5.0 log(10) CMV target cells, respectively. The standard deviations of the Amplicor PCR and Hybrid Capture tests varied throughout their linear range, and for both tests the variability was greater for lower concentrations of input CMV DNA. These data allow the direct comparison of viral load values between the Amplicor and Hybrid Capture tests. The analytical sensitivity of the NucliSens test could not be determined by using the 6-h standard, because the low multiplicity of infection and short culture time did not allow for adequate transcription of pp67 late mRNA measured in the test. Extending the incubation time of the standard to 24 h increased the analytical sensitivity of the NucliSens test to 3.0 log(10) target cells.

  4. Smallpox and pan-Orthodox Virus Detection by Real-Time 3’-Minor Groove Binder TaqMan Assays Oil the Roche LightCycler and the Cepheid Smart Cycler Platforms

    DTIC Science & Technology

    2003-11-08

    virus , herpes simplex virus, monkeypox virus, vac- cinia virus, and varicella-zoster virus. The origin, propagation, and harvest pro- cedures for...M. J., J. R. Uhl, L. M. Sloan, J. E. Rosenblatt, F. R. Cockerill III, and T. F. Smith. 2002. Detection of vaccinia virus , herpes simplex virus

  5. Evaluation of performances of VERSANT HCV RNA 1.0 assay (kPCR) and Roche COBAS AmpliPrep/COBAS TaqMan HCV test v2.0 at low level viremia.

    PubMed

    Mazzuti, Laura; Lozzi, Maria Antonietta; Riva, Elisabetta; Maida, Paola; Falasca, Francesca; Antonelli, Guido; Turriziani, Ombretta

    2016-07-01

    We assess the concordance between low level HCV values obtained using the VERSANT HCV RNA 1.0 Assay (kPCR) and COBAS AmpliPrep/COBAS TaqMan HCV Quantitative Test v2.0. The correlation between the values obtained by the two RT-PCR assays for samples with quantifiable HCV RNA levels revealed that viral load measured by kPCR significantly correlated with that of the CAP/CTM (R=0.644, P<0.0001). The results show a good concordance (n=126/144, 87%); discordant results were mainly observed in the assessment of values below the lower limit of detection of the assays. These variations may have an impact on clinical decisions for patients on HCV triple therapy or interferon- free regimens. It is therefore recommended to monitor individual patients with the same test throughout treatment.

  6. Les syénites du castillet (massif de l'agly, pyrénées orientales, France): une roche exceptionnelle dans les pyrénées

    NASA Astrophysics Data System (ADS)

    Demange, Michel; Lia-Aragnouet, Florence; Pouliguen, Marcel; Perrot, Xavier; Sauvage, Hubert

    1999-09-01

    Le Castillet syenites (Agly massif) are unusual rocks in the eastern Pyrenees made up of more than 95 % of potash feldspar and albite. These rocks are hosted in the Variscan Saint-Arnac granite and form small domes, the shape of which suggests an emplacement by magmatic stopping. Syenites and their closest host rocks suffered various hydrothermal alterations, the most obvious being transformation of biotite into muscovite + rutile. Discussion of the origin of these syenites is difficult because of those alterations: many magmatic features are well preserved but metasomatic transformation may have very much modified the primary rocks.

  7. POCT PT INR - Is it adequate for patient care? A comparison of the Roche Coaguchek XS vs. Stago Star vs. Siemens BCS in patients routinely seen in an anticoagulation clinic.

    PubMed

    Baker, Wendy S; Albright, Kathleen J; Berman, Megan; Spratt, Heidi; Mann, Peggy A; Unabia, Jaime; Petersen, John R

    2017-09-01

    In this study we examined the difference in patient INR values as measured by the POCT CoaguChek XS device and central laboratory Stago Evolution and Siemens BCS XP analyzers. This study composed of 100 warfarin therapy patients and 20 coagulation normal subjects, showed that the difference between the POCT and clinical laboratory values increased with increasing INR and was exacerbated by the use of different thromboplastin reagents by the POCT and central lab. The CoaguChek XS and on-site Stago analyzers which used human recombinant (ISI=1.01) and rabbit brain thromboplastin (ISI=1.25), respectively, showed reasonable agreement for INR<3.0 (k=0.62) but significant difference for INR≥3.0 (k=0.10). In contrast, the CoaguChek XS and Siemens BCS XP, which both employed human recombinant thromboplastin (BCS ISI=1.02), showed greater agreement for the complete range INR values (INR<3.0 k=0.84; INR≥3.0 k=0.70). ECAA Poller calibrant data showed the automated instruments were performing as expected, indicating that ISI calibrations were correct but insufficient to standardize the INR values for the different thromboplastin methods across the full range of measured INRs. Central lab verification of POCT INR>5.0 with the Stago Evolution prevented adverse treatment events for the warfarin therapy patients in the six months preceding and following this investigation. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Post-Skinnerian, Post-Skinner, or Neo-Skinnerian? Hayes, Barnes-Holmes, and Roche's Relational Frame Theory: A Post-Skinnerian Account of Human Language and Cognition

    ERIC Educational Resources Information Center

    Ingvarsson, Einar T.; Morris, Edward K.

    2004-01-01

    The perceived inability of behaviorism to deal with complex human behavior has been a recurrent theme among its critics. Although ingenious and subtle, even Skinner's Verbal Behavior (1957) is widely faulted on these grounds, in particular, for failing to explain linguistic generativity (Chomsky, 1959). In Relational Frame Theory: A…

  9. Post-Skinnerian, Post-Skinner, or Neo-Skinnerian? Hayes, Barnes-Holmes, and Roche's Relational Frame Theory: A Post-Skinnerian Account of Human Language and Cognition

    ERIC Educational Resources Information Center

    Ingvarsson, Einar T.; Morris, Edward K.

    2004-01-01

    The perceived inability of behaviorism to deal with complex human behavior has been a recurrent theme among its critics. Although ingenious and subtle, even Skinner's Verbal Behavior (1957) is widely faulted on these grounds, in particular, for failing to explain linguistic generativity (Chomsky, 1959). In Relational Frame Theory: A…

  10. Umbrella structure and channel-wall stoping in the Cambrian St. Roch Formation, Quebec Appalachians: significance for particle support mechanisms and turbulence development in hyper-concentrated sediment gravity flows

    NASA Astrophysics Data System (ADS)

    Hesse, Reinhard; Fong, Christopher

    2014-03-01

    Umbrella structure is a newly recognized sedimentary structure associated with large platy clasts in resedimented boulder-bearing pebble conglomerate with a sandy matrix. It consists of a sand rim that lacks pebbles on parts or the entire underside of platy boulders, whereas on the upper side, pebbles are in direct contact with the boulders. The depositing processes were high- to hyper-concentrated sediment gravity flows in a submarine channel or canyon on the Cambrian continental slope of North America bordering the Iapetus Ocean. The structure occurs predominantly where clasts dip moderately in the down-current direction. Based on the association of the structure with slightly forward dipping slabs, it is proposed that these down-current dipping slabs may have been in the process of counter-clockwise rotation that was aborted and may have generated a pressure shadow on the underside enabling the inrush of fluid and the infiltration of sand into the anomalous low-pressure zone. The structure has implications for particle support mechanisms in high- to hyper-concentrated sedimentary gravity flows, in that it redirects attention to the much debated mechanism of dispersive pressure and alternatives. It provides an observable sediment structure that supports dispersive pressure which so far depended on experimental evidence and theoretical arguments alone. Vrolijk and Southard's (1997) concept of a `laminar sheared layer' is here for the first time interpreted as having an upward-moving `free-surface' layer effect during deposition from hyper-concentrated flows. Channel-wall stoping involves unlithified turbiditic spillover sand in the levee sediment of the canyon wall that was washed out by the upper diluted parts of the high-concentration flows coming down the channel and leaving a niche in the wall that was filled with coarser channel-axis facies by the same flow (or later flows) when its aggradation reached the level of the niche. The contact between turbidite and pebble conglomerate occurs now more than 2 m laterally into the exposed channel wall. Channel-wall stoping tracks turbulence development in hyper-concentrated gravity flows.

  11. [Evolution of residual risk for HIV, HCV and HBV, from 1999 to 2010, in blood donations of the Centro Hospitalar S. João, EPE, Porto, Portugal].

    PubMed

    Koch, Carmo; Araújo, Fernando

    2013-01-01

    Introdução/Objectivo: A monitorização do risco residual infeccioso pela transfusão, é importante pois permite avaliar a melhoria alcançada na segurança das dádivas de sangue e adoptar políticas adequadas de redução dos riscos. Este estudo calcula as estimativas da taxa de incidência e do risco residual infeccioso para as infecções pelo vírus da imunodeficiência humana (VIH), vírus da hepatite B (VHB) e vírus da hepatite C (VHC), entre 1999 e 2010. Os dados foram analisados em períodos de quatro anos (1999-2002, 2003-2006 e 2007-2010) e as estimativas foram comparadas com as obtidas previamente, para dádivas ocorridas entre 1991 e 1998.Material e Métodos: O estudo incluiu 209 640 colheitas de sangue, provenientes de 42 634 dadores regulares, voluntários e não remunerados. Para o cálculo do risco residual infeccioso, utilizamos o modelo matemático taxa de incidência-período de janela, descrito por Schreiber et al. Todas as dádivas foram rastreadas de acordo com a legislação portuguesa. Em Janeiro de 2001 foi implementado, em todas as dádivas de sangue, o teste de ácidos nucleicos em minipool, para o rastreio simultâneo de ácido ribonucleico (ARN) VIH-1 e VHC (Cobas Amplicor Ampliscreen-Roche©) o qual foi substituído, em Janeiro de 2007, pelo rastreio simultâneo de ácido desoxirribonucleico VHB e de ácido ribonucleico VHC e VIH-1/VIH-2, em minipool (Cobas TaqScreen MPX Test-Roche©).Resultados: O risco residual infeccioso de uma dádiva em período de janela é muito reduzido e tem diminuído ao longo dos anos. Após a implementação de teste de ácidos nucleicos em minipool para os três vírus, a probabilidade de colhermos uma dádiva infecciosa e não detectada pelos testes de rastreio foi de 1/1,67 milhões de dádivas para o vírus da imunodeficiência humana, de 1/3,33 milhões para o vírus da hepatite C e de 1/526 000 para o vírus da hepatite B.Conclusões: Durante os 12 anos em estudo verificamos uma diminuição do

  12. Comparative evaluation of two commercial amplification assays for direct detection of Mycobacterium tuberculosis complex in respiratory specimens.

    PubMed Central

    Piersimoni, C; Callegaro, A; Nista, D; Bornigia, S; De Conti, F; Santini, G; De Sio, G

    1997-01-01

    Two commercial assays detecting the presence of Mycobacterium tuberculosis complex in clinical specimens by rRNA target amplification (Gen-Probe Amplified M. tuberculosis Direct Test [AMTD]) and PCR (Amplicor) were evaluated. The tests were applied to 327 digested, decontaminated respiratory specimens collected from 236 patients. Results were compared with those of acid-fast staining and culture. The combination of culture and clinical diagnosis was considered the "gold standard." A total of 60 specimens were collected from 27 patients with a diagnosis of pulmonary tuberculosis. Thirteen of these specimens were from patients receiving standard antituberculosis therapy and therefore were not included in the comparison. Of the remaining 47 specimens, 33 were smear positive, 40 were culture positive, 45 were AMTD positive, and 39 were Amplicor positive. After resolution of discrepant results, the overall sensitivities, specificities, and positive and negative predictive values were 77, 100, 100, and 95 for staining; 87, 100, 100, and 97.4 for culture; 95.9, 98.9, 94, and 99.2 for AMTD; and 85.4, 99.6, 97.9, and 97.1 for Amplicor, respectively. Agreement between AMTD and Amplicor assay results was 96.8%. It is concluded that although both nucleic acid amplification methods are rapid and specific for the detection of M. tuberculosis complex in respiratory specimens, AMTD appeared to be more sensitive than Amplicor. PMID:8968906

  13. Trachoma Prevalence and Associated Risk Factors in The Gambia and Tanzania: Baseline Results of a Cluster Randomised Controlled Trial

    PubMed Central

    Harding-Esch, Emma M.; Edwards, Tansy; Mkocha, Harran; Munoz, Beatriz; Holland, Martin J.; Burr, Sarah E.; Sillah, Ansumana; Gaydos, Charlotte A.; Stare, Dianne; Mabey, David C. W.; Bailey, Robin L.; West, Sheila K.

    2010-01-01

    Background Blinding trachoma, caused by ocular infection with Chlamydia trachomatis, is targeted for global elimination by 2020. Knowledge of risk factors can help target control interventions. Methodology/Principal Findings As part of a cluster randomised controlled trial, we assessed the baseline prevalence of, and risk factors for, active trachoma and ocular C. trachomatis infection in randomly selected children aged 0–5 years from 48 Gambian and 36 Tanzanian communities. Both children's eyes were examined according to the World Health Organization (WHO) simplified grading system, and an ocular swab was taken from each child's right eye and processed by Amplicor polymerase chain reaction to test for the presence of C. trachomatis DNA. Prevalence of active trachoma was 6.7% (335/5033) in The Gambia and 32.3% (1008/3122) in Tanzania. The countries' corresponding Amplicor positive prevalences were 0.8% and 21.9%. After adjustment, risk factors for follicular trachoma (TF) in both countries were ocular or nasal discharge, a low level of household head education, and being aged ≥1 year. Additional risk factors in Tanzania were flies on the child's face, being Amplicor positive, and crowding (the number of children per household). The risk factors for being Amplicor positive in Tanzania were similar to those for TF, with the exclusion of flies and crowding. In The Gambia, only ocular discharge was associated with being Amplicor positive. Conclusions/Significance These results indicate that although the prevalence of active trachoma and Amplicor positives were very different between the two countries, the risk factors for active trachoma were similar but those for being Amplicor positive were different. The lack of an association between being Amplicor positive and TF in The Gambia highlights the poor correlation between the presence of trachoma clinical signs and evidence of C. trachomatis infection in this setting. Only ocular discharge was associated with

  14. Development and validation of a rotor-gene real-time PCR assay for detection, identification, and quantification of Chlamydia trachomatis in a single reaction.

    PubMed

    Jalal, Hamid; Stephen, Hannah; Curran, Martin D; Burton, Janet; Bradley, Michelle; Carne, Christopher

    2006-01-01

    A multitarget real-time PCR (MRT-PCR) for detection of Chlamydia trachomatis DNA was developed and validated. There were three targets for amplification in a single reaction: the cryptic plasmid (CP), the major outer membrane protein (MOMP) gene, and an internal control. The assay had the following characteristics: (i) detection and confirmation of the presence of C. trachomatis DNA in a single reaction, (ii) detection of all genovars of C. trachomatis without any cross-reactivity with pathogenic bacteria or commensal organisms of the oropharynx and genital tract, (iii) a 95% probability of detection with three copies of MOMP and one copy of CP per reaction mixture, (iv) identification of the inhibition of amplification, (v) a quantitative dynamic range of 25 to 250,000 genome copies per reaction mixture, (vi) high intra- and interassay reproducibilities, and (vii) correct identification of all samples in the validation panel. There were 146 COBAS Amplicor PCR (Amplicor PCR)-positive samples and 122 Amplicor PCR-negative samples in the panel. MRT-PCR detected CP DNA alone in 6 (4%) Amplicor PCR-positive samples and both CP and MOMP DNAs in 140 (96%) of 146 Amplicor PCR-positive samples. The quantity of MOMP DNA in 95 (68%) of 140 samples was within the dynamic range of the assay. The median C. trachomatis load in these samples was 321 genome copies per reaction mixture (range, 26 to 40,137 genome copies per reaction mixture). Due to the inclusion of two different C. trachomatis-specific targets, the assay confirmed 259 (97%) of 268 results in a single reaction. This assay could be used in the qualitative format for the routine detection of C. trachomatis and in the quantitative format for study of the pathogenesis of C. trachomatis-associated diseases. The assay demonstrated the potential to eliminate the need for confirmatory testing in almost all samples, thus reducing the turnaround time and the workload.

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

    PubMed

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

    2017-10-01

    Hepatitis B viral load testing is essential to treatment and monitoring decisions in patients with chronic Hepatitis B. Beckman Coulter has developed the VERIS HBV Assay (Veris) for use on the fully automated DxN VERIS Molecular Diagnostics System.(1) OBJECTIVES: To evaluate the clinical performance of the Veris HBV Assay at multiple EU laboratories STUDY DESIGN: Method comparison was performed with a total of 344 plasma specimens from HBV infected patients tested with Veris and COBAS(®) TaqMan(®) HBV Test (Cobas), 207 specimens tested with Veris and RealTime HBV Assay (RealTime), 86 specimens tested with Veris and VERSANT(®) HBV Assay (Versant), and 74 specimens tested with Veris and artus(®) HBV RG PCR kit (artus). Bland-Altman analysis showed average bias of -0.46 log10 IU/mL between Veris and Cobas, -0.46 log10IU/mL between Veris and RealTime, -0.36 log10IU/mL between Veris and Versant, and -0.12 log10IU/mL between Veris and artus. Bias was consistent across the assay range. Patient monitoring results using Veris demonstrated similar viral load trends over time to Cobas, RealTime, and artus. The VERIS HBV Assay demonstrated comparable clinical performance, with varying degrees of negative bias, compared to other currently marketed assays for HBV DNA monitoring. This negative bias should be taken into consideration if switching monitoring methods to Veris. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. The Cobas® EGFR Mutation Test v2 assay.

    PubMed

    Brown, Paul

    2016-02-01

    Paul Brown speaks to Gemma Westcott, Commissioning Editor: Paul Brown has served as the Head of Roche Molecular Diagnostics at Roche Diagnostics Corporation since February 2010 having previously held a variety of positions within Roche Pharma. After completing his doctorate in organic chemistry he was awarded a post-doctoral fellowship at the California Institute of Technology in Pasadena, CA, USA, but soon returned to his native UK to join Roche Pharma Research. Paul's first post within Roche was as group leader, doing drug discovery and making new small molecule drugs, but later moved into the business part of the company. Since then, he has enjoyed roles such as lifecycle leader for brands such as Tamiflu(®) and Xenical, vice president of sales and marketing of the pharmaceutical division and most recently general manager of Roche Pharma, Sweden.

  17. The Smart/Empire Tipster IR System

    DTIC Science & Technology

    1998-10-01

    State Transducer for Extracting Information from Natural-Language Text. In E. Roche andY. Schabes , editor, Finite-State Language Processing, pages 383...Fran- cisco, CA, 1997. Morgan Kaufmann. [ 16] Roche, E. and Schabes , Y., editor. Finite State De- vices for Natural Language Processing. MIT Press

  18. 75 FR 54154 - Medical Devices; Availability of Safety and Effectiveness Summaries for Premarket Approval...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-03

    ... BRONCHIAL THERMOPLASTY April 27, 2010 FDA-2010-0242 P090007 Roche Diagnostics ELECSYS ANTI-HCV IMMUNOASSAY AND April 29, 2010 FDA-2010-M-0261 Corp. ELECSYS PRECICONTROL ANTI-HCV FOR USE ON THE COBAS E411 IMMUNOASSAY ANALYZER P090008 Roche Diagnostics ELECSYS ANTI-HCV IMMUNOASSAY AND April 29, 2010...

  19. 78 FR 314 - Current List of Laboratories and Instrumented Initial Testing Facilities Which Meet Minimum...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-03

    ... 19044, 800- 235-4890 ElSohly Laboratories, Inc., 5 Industrial Park Drive, Oxford, MS 38655, 662-236-2609...; Roche CompuChem Laboratories, Inc., a Member of the Roche Group) Laboratory Corporation of America... Monitoring Laboratory, University of Missouri Hospital & Clinics, 301 Business Loop 70 West, Suite...

  20. An Interlingual-based Approach to Reference Resolution

    DTIC Science & Technology

    2000-01-01

    miilones de francos o el 14 por eiento de las ventas del grupo. Las inversiones en investigaci6n y desarrollo (I+D) fueron de 1.210 millones de francos... inversiones realizadas totalizaron 223 millones de pesetas. English Translation of Text 93-1 Roche Buys Docteur Andreu The Roche Group acquired the

  1. Before You Search that Locker.

    ERIC Educational Resources Information Center

    Dowling-Sendor, Benjamin

    1998-01-01

    In DesRoches v Caprio, federal district court ruled in favor of Jim DesRoches who had decided not to consent to a search of his backpack for a pair of allegedly stolen sneakers. Judge Robert G. Doumar decided the need to find the stolen sneakers did not outweigh the students' privacy interest and offered guidelines about school searches for stolen…

  2. Survival in Idiopathic Pulmonary Fibrosis: Perspectives from Pulmonary Arterial Hypertension.

    PubMed

    Maher, Toby M; Dejonckheere, Fred; Nathan, Steven D

    2017-03-01

    Maher has received grants, consulting fees, and speaker fees from GlaxoSmithKline and UCB and grants from Novartis. He has also received consulting fees and speaker fees from AstraZeneca, Bayer, Biogen Idec, Boehringer Ingelheim, Cipla, Lanthio, InterMune International AG (a wholly owned Roche subsidiary since 2014), F. Hoffmann-La Roche, Sanofi-Aventis, and Takeda. Maher is supported by a National Institute for Health Research Clinician Scientist Fellowship (NIHR Ref: CS:-2013-13-017). Dejonckheere is an employee of F. Hoffmann-La Roche. Nathan has received consulting fees from Roche-Genentech and Boehringer Ingelheim. He is also on the speakers bureau for Roche-Genentech and Boehringer Ingelheim and has received research funding from both companies. All authors contributed equally to study concept and design, data collection and analysis, and manuscript preparation.

  3. Use of the polymerase chain reaction for the detection of Chlamydia trachomatis from endocervical and urine specimens in an asymptomatic low-prevalence population of women.

    PubMed

    Skulnick, M; Chua, R; Simor, A E; Low, D E; Khosid, H E; Fraser, S; Lyons, E; Legere, E A; Kitching, D A

    1994-12-01

    The Amplicor Chlamydia trachomatis test is a polymerase chain reaction (PCR)-based methodology used for the detection of a cryptic plasmid found in C. trachomatis. It was evaluated in comparison with cell culture and the Microtrak II Chlamydia enzyme immunoassay (EIA) for the detection of C. trachomatis in urogenital specimens from women. Endocervical swabs were collected from 993 women attending the women's unit at the Mount Sinai Hospital in Toronto. In addition, concomitant first void urine specimens were collected from 394 of these women for PCR testing only. As compared with culture of the endocervical specimens, PCR and EIA had a sensitivity, specificity, positive predictive value and negative predictive value of 84.6%, 99.2%, 57.9%, and 99.8% and 61.5%, 99.7%, 72.7%, and 99.5%, respectively. As compared with the secondary gold standard of a positive culture and/or a positive PCR using a primer to the major outer membrane protein the sensitivity, specificity, positive, and negative predictive values for culture were 72.2%, 100%, 100%, and 99.5%, respectively. For the Amplicor PCR and EIA the results were 88.9%, 99.7%, 84.2%, and 99.9% and 61.1%, 99.9%, 91.7%, and 99.6%, respectively. When the urine PCR was compared with the same standard, the test had a sensitivity of 91.7% and a specificity of 99.5%. Based on this study the Amplicor C. trachomatis test was found to be sensitive and specific for the detection of C. trachomatis in both endocervical and urine specimens.

  4. Presidential Green Chemistry Challenge: 2000 Greener Synthetic Pathways Award

    EPA Pesticide Factsheets

    Presidential Green Chemistry Challenge 2000 award winner, Roche Colorado, developed a greener synthesis for gancyclovir (Cytovene, a potent antiviral drug) that uses a second-generation Guanine Triester (GTE) process.

  5. Someone You Know Has MS: A Book for Families

    MedlinePlus

    ... Ba rba ra LaRoche, and Patr ici a Dick Illustr ations by: Cl aude Martinot Martha King ... Chuck, John, and Nancy Delgreco; Jennifer and John Dick; Judy and Pamela DiPalma; Mary Hooley; Nicole Klabunde; ...

  6. Passive Acoustic Monitoring for the Detection and Identification of Marine Mammals

    DTIC Science & Technology

    2010-09-30

    detection task,” Intl. Workshop on the Detection and Classification of Marine Mammals Using Passive Acoustics, Pavia , Italy, September 2009. M. A. Roch...Classification of Marine Mammals Using Passive Acoustics, Pavia , Italy, September 2009.

  7. A family of zero-velocity curves in the restricted three-body problem

    NASA Astrophysics Data System (ADS)

    Roman, R.; Szücs-Csillik, I.

    2014-08-01

    The equilibrium points and the curves of zero-velocity (Roche varieties) are analyzed in the frame of the regularized circular restricted three-body problem. The coordinate transformation is done with Levi-Civita generalized method, using polynomial functions of n degree. In the parametric plane, five families of equilibrium points are identified: , . These families of points correspond to the five equilibrium points in the physical plane L 1, L 2,…, L 5. The zero-velocity curves from the physical plane are transformed in Roche varieties in the parametric plane. The properties of these varieties are analyzed and the Roche varieties for n∈{1,2,…,6} are plotted. The equation of the asymptotic variety is obtained and its shape is analyzed. The slope of the Roche variety in point is obtained. For n=1 the slope obtained by Plavec and Kratochvil (1964) in the physical plane was found.

  8. Studies in matter antimatter separation and in the origin of lunar magnetism

    NASA Technical Reports Server (NTRS)

    Barker, W. A.; Greeley, R.; Parkin, C.; Aggarwal, H.

    1974-01-01

    Antimatter experiments of the University of Santa Clara are investigated. Topics reported include: (1) planetary geology, (2) lunar Apollo magnetometer experiments, and (3) Roche limit of a solid body.

  9. Teachers Holding Back from Telling: A Key to Student Persistence on Challenging Tasks

    ERIC Educational Resources Information Center

    Roche, Anne; Clarke, Doug

    2014-01-01

    Anne Roche and Doug Clarke discuss the importance of developing students' persistence in relation to problem solving during the use of challenging tasks. They provide a useful list of strategies that teachers can use to encourage persistence amongst their students.

  10. Little Tuber Moon

    NASA Image and Video Library

    2010-01-05

    Saturn small moon Prometheus, slightly overexposed in this image taken by NASA Cassini spacecraft, shows off its potato-like shape as it orbits in the Roche Division between the A ring and thin F ring.

  11. 78 FR 3967 - Notice of Application for Special Permits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-17

    ...--Motor vehicle, 2--Rail freight, 3--Cargo vessel, 4--Cargo aircraft only, 5--Passenger-carrying aircraft... PERMITS 15773-N Roche Molecular 49 CFR To authorize the Systems, Inc. 173.242(e)(1). transportation in...

  12. 75 FR 36694 - Importer of Controlled Substances; Notice of Registration

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-28

    ... manufacture of diagnostic products for distribution to its customers. No comments or objections have been..., conventions, or protocols in effect on May 1, 1971, at this time. DEA has investigated Roche...

  13. The Darleen Druyun Debacle: Procurement, Power, and Corruption

    DTIC Science & Technology

    2005-08-01

    196 The resignation of Boeing’s CEO, Phil Condit, was also, at least partially, due to the events surrounding Ms. Druyun’s hiring. 197 Press...Ralph Crosby .268 The “blame the system/institution” set may point to an e-mail exchange between Secretary Roche and Ms. Druyun that occurred...268 Secretary Roche had worked with Crosby at Northrop Grumman. Id at 3. 66 not have been surprised at the slime…his day of reckoning will

  14. Acoustic Moorings for Integrated Cetacean-Prey Studies

    DTIC Science & Technology

    2015-09-30

    Wiggins SM, Roch MA (2015) Seven years of blue and fin whale call abundance in southern California. Endangered Species Research 28:61-76. Širović A...Chou E, Roch MA (in prep) Habitat use of calling blue and fin whales in Southern California Bight. Marine Ecology Progress Series. Wiggins SM...passive acoustic component for monitoring of cetaceans, active acoustic echosounders at two depths to monitor both baleen whale and beaked whale prey

  15. Effects of Sarin on the Operant Behavior of Guinea Pigs

    DTIC Science & Technology

    2005-07-19

    chemistry analyzer (Roche Diagnostics, Nutley, NJ). After 10 left lever presses, the schedule converted to a fixed- The analytical procedure was based... chemistry analyzer (Roche Diagnostics, Nutley, NJ). After 10 left lever presses, the schedule converted to a fixed- The analytical procedure was based on...Erythrocyte Acetylcholinesterase in the Primate, Brown, W. Slikker Jr., Chronic marijuana smoke exposure in Battelle Laboratories, Columbus, OH, 1988

  16. Adaptive Statistical Language Modeling; A Maximum Entropy Approach

    DTIC Science & Technology

    1994-04-19

    ACCUSE] ACCUSE, ACCUSED, ACCUSES, ACCUSING [ACCUSTOM] : ACCUSTOMED [ ACCUTANE ] ACCUTANE [ACE] :ACE [ACHIEVE] : ACHIEVE, ACHIEVED, ACHIEVES, ACHIEVING...Appendix C. Best Triggers by the MI-3g Measure ACCUSING 4= FILED COURT ACCUTANE 4- ACCUTANE ACNE DEFECTS HOFFMANN ROCHE BIRTH DRUG’S DRUG PREG- NANT...TOP GOING INDUSTRY PRESIDENT WANT OFTEN LOT OWN TOO WHERE ACME = ACME STEEL ACNE = ACNE RETIN DRUG ACCUTANE HOFFMANN ROCHE PRESCRIPTION DRUG’S SKIN

  17. Performance of Bordetella pertussis IS481 real-time PCR in a vaccine trial setting.

    PubMed

    Gullsby, Karolina; Hallander, Hans O; Bondeson, Kåre

    2007-12-01

    A real-time PCR method targeting the Bordetella pertussis IS481 gene fragment was evaluated in a vaccine trial setting in which real-time PCR results could be validated against culture and serology results. Two commonly used DNA extraction methods, Amplicor Respiratory Preparation kit and the QIAamp DNA Mini Kit, were compared. An approximately 50-fold higher sensitivity was achieved using the Amplicor kit. 89 of 276 aspirates analysed with the IS481 real-time PCR were positive. Interestingly, six of these were culture negative and came from serology-negative patients. Defining true positive cases either as culture-positive or as PCR-positive cases that had been confirmed with a serology-positive result or verified with a newly constructed recA PCR, the sensitivity and specificity of the IS481 real-time PCR were 89% and 98%, respectively. This study confirms the specificity and high diagnostic sensitivity of IS481-based PCR methods for diagnosis of B. pertussis.

  18. Clinical Evaluation of COBAS TaqMan PCR for the Detection of Mycobacterium tuberculosis and M. avium Complex

    PubMed Central

    Ikegame, Satoshi; Sakoda, Yoritake; Fujino, Nao; Taguchi, Kazuhito; Kawasaki, Masayuki; Kajiki, Akira

    2012-01-01

    A retrospective observational study was performed to determine the sensitivity and limitation of PCR test for the detection of Mycobacterium tuberculosis and M. avium complex. We obtained clinical specimens collected from the respiratory tract, cultured M. tuberculosis or M. avium complex, and performed PCR analysis. A total of 299 samples (M. tuberculosis, 177; M. avium, 35; M. intracellulare, 87) were analyzed by COBAS TaqMan PCR from April 2007 to March 2011. The PCR positivity rates were 50–55%, 70–100%, 88–98%, and 100% in smear-negative, smear 1+, 2+, and 3+ groups, respectively. The PCR positivity of tuberculosis in smear 1+ was 80.6%, which was statistically significantly (P < 0.001) lower than that of smear 2+ (97.3%). From January 2005 to March 2007, we collected an additional 138 samples (M. tuberculosis, 74; M. avium, 21; M. intracellulare, 43), which were analyzed by COBAS Amplicor PCR. The PCR positivity rates obtained using COBAS TaqMan PCR and COBAS Amplicor PCR were not significantly different. The sensitivity of PCR test for mycobacteria is not sufficient in case of smear 1+. Careful consideration must be given to the interpretation of negative PCR test results in smear 1+, because smear-positive tuberculosis is the criterion for isolation. PMID:23029612

  19. Dried blood spots for the diagnosis and quantitation of HIV-1: stability studies and evaluation of sensitivity and specificity for the diagnosis of infant HIV-1 infection in Thailand.

    PubMed

    Leelawiwat, W; Young, N L; Chaowanachan, T; Ou, C Y; Culnane, M; Vanprapa, N; Waranawat, N; Wasinrapee, P; Mock, P A; Tappero, J; McNicholl, J M

    2009-02-01

    Molecular methods for HIV-1 infection using dried blood-spot (DBS) for HIV-1 CRF01_AE subtypes have not been fully optimized. In this study assays for HIV-1 diagnosis or quantitation were evaluated using infant DBS from Thailand. Paired DBS and whole blood samples from 56 HIV-1 CRF01_AE or B'-infected infants were tested for infant diagnosis using modified Amplicor DNA PCR and NucliSens RNA NASBA and an in-house real-time PCR assay. The Amplicor Monitor viral load (VL) assay, with modifications for DBS, was also evaluated. DBS VL were hematocrit corrected. Stability studies were done on DBS stored at -70 degrees C to 37 degrees C for up to 1 year. The DBS diagnostic assays were 96-100% sensitive and 100% specific for HIV-1 diagnosis. DBS HIV-1 VL were highly correlated with plasma VL when corrected using the actual or an assumed hematocrit factor (r(c)=0.88 or 0.93, respectively). HIV-1 DNA in DBS appeared to be more stable than RNA and could be detected after up to 9 months at most temperatures. DBS VL could be consistently determined when stored frozen. These results show that DBS can be used accurately instead of whole blood for the diagnosis of HIV-1 infection and VL quantitation, particularly if samples are appropriately stored.

  20. Comparison of molecular assays for detection and typing of human papillomavirus.

    PubMed

    Koidl, Christoph; Bozic, Michael; Hadzisejdic, Ita; Grahovac, Maja; Grahovac, Blazenka; Kranewitter, Wolfgang; Marth, Egon; Kessler, Harald H

    2008-08-01

    The objective of the study was to compare the performance of 3 different extraction instruments in conjunction with 4 different amplification and detection kits for detection and typing of human papillomavirus (HPV) deoxyribonucleic acid (DNA). A total of 42 cervical swabs were investigated. HPV DNA was extracted on the 3 different instruments. Each of the extracts was then amplified, and HPV DNA amplification products were detected with 4 different kits. In 31 samples, HPV DNA was detected by both the Amplicor HPV test and the LINEAR ARRAY HPV genotyping test in conjunction with DNA extraction on the easyMAG instrument. In another 6 samples, only low-risk types were detected with the linear array HPV genotyping test. After extraction on the easyMAG instrument, 32 samples tested positive when the PapilloCheck with the HotStarTaq DNA polymerase was used. Together with extraction on the easyMAG instrument, the Amplicor HPV test, the linear array HPV genotyping test, and the new PapilloCheck with the HotStarTaq DNA polymerase provide comparable results allowing reliable and safe HPV diagnostics in the routine laboratory. Use of alternative assays may lead to an increase of invalid and divergent HPV typing results.

  1. Intramolecular Oxidative O-Demethylation of an Oxoferryl Porphyrin Complexed with a Per-O-methylated β-Cyclodextrin Dimer.

    PubMed

    Kitagishi, Hiroaki; Kurosawa, Shun; Kano, Koji

    2016-11-22

    The intramolecular oxidation of ROCH3 to ROCH2 OH, where the latter compound spontaneously decomposed to ROH and HCHO, was observed during the reaction of the supramolecular complex (met-hemoCD3) with cumene hydroperoxide in aqueous solution. Met-hemoCD3 is composed of meso-tetrakis(4-sulfonatophenyl)porphinatoiron(III) (Fe(III) TPPS) and a per-O-methylated β-cyclodextrin dimer having an -OCH2 PyCH2 O- linker (Py=pyridine-3,5-diyl). The O=Fe(IV) TPPS complex was formed by the reaction of met-hemoCD3 with cumene hydroperoxide, and isolated by gel-filtration chromatography. Although the isolated O=Fe(IV) TPPS complex in the cyclodextrin cage was stable in aqueous solution at 25 °C, it was gradually converted to Fe(II) TPPS (t1/2 =7.6 h). This conversion was accompanied by oxidative O-demethylation of an OCH3 group in the cyclodextrin dimer. The results indicated that hydrogen abstraction by O=Fe(IV) TPPS from ROCH3 yields HO-Fe(III) TPPS and ROCH2(.) . This was followed by radical coupling to afford Fe(II) TPPS and ROCH2 OH. The hemiacetal (ROCH2 OH) immediately decomposed to ROH and HCHO. This study revealed the ability of oxoferryl porphyrin to induce two-electron oxidation. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Formation of Saturn's F ring by collision between rubble-pile satellites

    NASA Astrophysics Data System (ADS)

    Hyodo, Ryuki; Ohtsuki, Keiji

    2014-11-01

    Saturn’s F ring is located just outside the Roche limit. This pure icy ring is radially narrow and is thought to be dynamically young. Two shepherding satellites, inner Pandora and outer Prometheus, confine and regulate its current dynamical evolution. The bulk density of these satellites is lower than that of rigid water ice, thus they are likely to be rubble-pile bodies. Crida & Charnoz (2012) showed that Saturn’s inner major satellites are formed by spreading of ancient massive rings through the Roche limit using one-dimensional analytical model. Recently, we have performed N-body simulations of the evolution of circumplanetary particle disks initially confined within a planet’s Roche limit, and showed that rubble-pile co-orbital satellites are often formed just outside the Roche limit (Hyodo et al, submitted). However, these co-orbital satellites are not always stable but can experience collisions between them. In addition, at radial locations barely outside the Roche limit, accretion efficiency is not 100%, and collision between aggregates can lead to complete or partial disruption (Karjalainen 2007, Hyodo & Ohtsuki 2014).In the present work, we perform local N-body simulations in the Hill coordinate system and investigate collisional disruption of rubble-pule satellites just outside the Roche limit corresponding to the location of Saturn’s F ring. We find that in some cases, collision between two aggregates results in partial disruption such that the dispersed particles are distributed between the two remnant satellites with small radial extent. Our results suggest that the F ring is a relic of collisional disruption between rubble-pile satellites formed at the last stage of the formation of inner major satellites as the rings spread across the Roche limit.

  3. Systematic review of the performance of HIV viral load technologies on plasma samples.

    PubMed

    Sollis, Kimberly A; Smit, Pieter W; Fiscus, Susan; Ford, Nathan; Vitoria, Marco; Essajee, Shaffiq; Barnett, David; Cheng, Ben; Crowe, Suzanne M; Denny, Thomas; Landay, Alan; Stevens, Wendy; Habiyambere, Vincent; Perrins, Jos; Peeling, Rosanna W

    2014-01-01

    Viral load (VL) monitoring is the standard of care in developing country settings for detecting HIV treatment failure. Since 2010 the World Health Organization has recommended a phase-in approach to VL monitoring in resource-limited settings. We conducted a systematic review of the accuracy and precision of HIV VL technologies for treatment monitoring. A search of Medline and Embase was conducted for studies evaluating the accuracy or reproducibility of commercially available HIV VL assays. 37 studies were included for review including evaluations of the Amplicor Monitor HIV-1 v1.5 (n = 25), Cobas TaqMan v2.0 (n = 11), Abbott RealTime HIV-1 (n = 23), Versant HIV-1 RNA bDNA 3.0 (n = 15), Versant HIV-1 RNA kPCR 1.0 (n = 2), ExaVir Load v3 (n = 2), and NucliSens EasyQ v2.0 (n = 1). All currently available HIV VL assays are of sufficient sensitivity to detect plasma virus levels at a lower detection limit of 1,000 copies/mL. Bias data comparing the Abbott RealTime HIV-1, TaqMan v2.0 to the Amplicor Monitor v1.5 showed a tendency of the Abbott RealTime HIV-1 to under-estimate results while the TaqMan v2.0 overestimated VL counts. Compared to the Amplicor Monitor v1.5, 2-26% and 9-70% of results from the Versant bDNA 3.0 and Abbott RealTime HIV-1 differed by greater than 0.5log10. The average intra and inter-assay variation of the Abbott RealTime HIV-1 were 2.95% (range 2.0-5.1%) and 5.44% (range 1.17-30.00%) across the range of VL counts (2log10-7log10). This review found that all currently available HIV VL assays are of sufficient sensitivity to detect plasma VL of 1,000 copies/mL as a threshold to initiate investigations of treatment adherence or possible treatment failure. Sources of variability between VL assays include differences in technology platform, plasma input volume, and ability to detect HIV-1 subtypes. Monitoring of individual patients should be performed on the same technology platform to ensure appropriate interpretation of

  4. Systematic Review of the Performance of HIV Viral Load Technologies on Plasma Samples

    PubMed Central

    Sollis, Kimberly A.; Smit, Pieter W.; Fiscus, Susan; Ford, Nathan; Vitoria, Marco; Essajee, Shaffiq; Barnett, David; Cheng, Ben; Crowe, Suzanne M.; Denny, Thomas; Landay, Alan; Stevens, Wendy; Habiyambere, Vincent; Perrins, Jos; Peeling, Rosanna W.

    2014-01-01

    Background Viral load (VL) monitoring is the standard of care in developing country settings for detecting HIV treatment failure. Since 2010 the World Health Organization has recommended a phase-in approach to VL monitoring in resource-limited settings. We conducted a systematic review of the accuracy and precision of HIV VL technologies for treatment monitoring. Methods and Findings A search of Medline and Embase was conducted for studies evaluating the accuracy or reproducibility of commercially available HIV VL assays. 37 studies were included for review including evaluations of the Amplicor Monitor HIV-1 v1.5 (n = 25), Cobas TaqMan v2.0 (n = 11), Abbott RealTime HIV-1 (n = 23), Versant HIV-1 RNA bDNA 3.0 (n = 15), Versant HIV-1 RNA kPCR 1.0 (n = 2), ExaVir Load v3 (n = 2), and NucliSens EasyQ v2.0 (n = 1). All currently available HIV VL assays are of sufficient sensitivity to detect plasma virus levels at a lower detection limit of 1,000 copies/mL. Bias data comparing the Abbott RealTime HIV-1, TaqMan v2.0 to the Amplicor Monitor v1.5 showed a tendency of the Abbott RealTime HIV-1 to under-estimate results while the TaqMan v2.0 overestimated VL counts. Compared to the Amplicor Monitor v1.5, 2–26% and 9–70% of results from the Versant bDNA 3.0 and Abbott RealTime HIV-1 differed by greater than 0.5log10. The average intra and inter-assay variation of the Abbott RealTime HIV-1 were 2.95% (range 2.0–5.1%) and 5.44% (range 1.17–30.00%) across the range of VL counts (2log10–7log10). Conclusions This review found that all currently available HIV VL assays are of sufficient sensitivity to detect plasma VL of 1,000 copies/mL as a threshold to initiate investigations of treatment adherence or possible treatment failure. Sources of variability between VL assays include differences in technology platform, plasma input volume, and ability to detect HIV-1 subtypes. Monitoring of individual patients should be performed on the same

  5. [Low rate of oropharyngeal human papillomavirus infection among women with cervical lesion. Preliminary results from the South-Eastern Hungarian population].

    PubMed

    Vanya, Melinda; Jakó, Mária; Terhes, Gabriella; Szakács, László; Kaiser, László; Deák, Judit; Bártfai, György

    2016-01-10

    Although the natural history of cervical and oral human papillomavirus infection has been intensively investigated in the past years, the ability of this virus to infect oral and genital mucosae in the same individual and its potential to co-infect both cervical and oral mucosa are still unclear. The aim of the authors was to assess the presence of oropharyngeal human papillomavirus infection in women with cervical lesions in the South-Eastern Hungarian population. The total of 103 women have been included in the study between March 1, 2013 and January 1, 2015. Brushing was used to collect cells from the oropharyngeal mucosa. Human papillomavirus DNA was detected using polymerase chain reaction, and Amplicor line blot test was used for genotyping. Oropharyngeal human papillomavirus infection was detected in 2 cases (3%). The detected genotypes were 31, 40/61 and 73 in the oropharyngeal region. The results indicate that in women with cervical lesions oropharyngeal human papillomavirus infection rarely occurs.

  6. [Viral loads in pediatric HIV patients with antiretroviral treatment].

    PubMed

    Porto-Espinoza, Leticia; Moronta, Reyna; Cuadra-Sánchez, César; Callejas-Valero, Diana; Costa-León, Luciana; Monsalve-Castillo, Francisca; Bernardoni, Cecilia; Estévez, Jesús

    2008-08-01

    Viral load in pediatric patients with HIV infections can help to make therapeutic decisions to modify the evolution of the disease. To evaluate viral load in positive HIV children with antiretroviral treatment. Viral load was measured every six months during three years in fifty pediatric patients chosen randomly in aged 1 to 12 years, using the Test Monitor HIV-1 AMPLICOR, version 1.5. During the three years follow up, there was an increase in CD4 and CD8 lymphocyte count and decrease in the viral load. However, there was no significant relationship between lymphocyte subpopulation counts and viral loads. Viral load demonstrated to be an appropriate method to quantify plasma HIV-RNA. This tool can help to define the condition of a particular patient to predict clinical course of the disease and to assess the response to the treatment.

  7. Tidal disruption of inviscid protoplanets

    NASA Technical Reports Server (NTRS)

    Boss, Alan P.; Cameron, A. G. W.; Benz, W.

    1991-01-01

    Roche showed that equilibrium is impossible for a small fluid body synchronously orbiting a primary within a critical radius now termed the Roche limit. Tidal disruption of orbitally unbound bodies is a potentially important process for planetary formation through collisional accumulation, because the area of the Roche limit is considerably larger then the physical cross section of a protoplanet. Several previous studies were made of dynamical tidal disruption and different models of disruption were proposed. Because of the limitation of these analytical models, we have used a smoothed particle hydrodynamics (SPH) code to model the tidal disruption process. The code is basically the same as the one used to model giant impacts; we simply choose impact parameters large enough to avoid collisions. The primary and secondary both have iron cores and silicate mantles, and are initially isothermal at a molten temperature. The conclusions based on the analytical and numerical models are summarized.

  8. Rheumatoid factor measurement--continuing problems 70 years after discovery.

    PubMed

    Ameratunga, Rohan; Musaad, Samarina; Sugrue, Claudia; Kyle, Campbell

    2011-09-01

    There have been long-standing unpublished differences in rheumatoid factor (RF) results, based on the Royal College of Pathologists of Australasia external quality assurance program. This study compared RF results between two commonly used commercial instruments. Serum samples were exchanged between a laboratory using a Beckman Immage immunonephelometer and another using a Roche Modular immunoturbidimeter. The World Health Organization (WHO) reference standard for RF (W1066) was then used to compare the two methods. The Roche immunoturbidimeter appears to have superior sensitivity. Furthermore, there is significant bias between the two instruments as levels of RF increase. Results from the WHO RF reference preparation correlated most closely with the results from the Roche immunoturbidimeter. Standardization for RF measurement is not optimal and has not been achieved between these two commonly used instruments. This may have clinical implications for patient management.

  9. Evaluating HPV-negative CIN2+ in the ATHENA trial.

    PubMed

    Petry, Karl Ulrich; Cox, J Thomas; Johnson, Kristin; Quint, Wim; Ridder, Ruediger; Sideri, Mario; Wright, Thomas C; Behrens, Catherine M

    2016-06-15

    A post hoc analysis of the ATHENA study was performed to determine whether true HPV-negative cervical lesions occur and whether they have clinical relevance. The ATHENA database was searched for all CIN2 or worse (CIN2+) cases with cobas HPV-negative results and comparison was made with Linear Array (LA) and Amplicor to detect true false-negative HPV results. Immunostaining with p16 was performed on these cases to identify false-positive histology results. H&E slides were re-reviewed by the study pathologists with knowledge of patient age, HPV test results and p16 immunostaining. Those with positive p16 immunostaining and/or a positive histopathology review underwent whole tissue section HPV PCR by the SPF10/LiPA/RHA system. Among 46,887 eligible women, 497 cases of CIN2+ were detected, 55 of which tested negative by the cobas(®) HPV Test (32 CIN2, 23 CIN3/ACIS). By LA and/or Amplicor, 32 CIN2+ (20 CIN2, 12 CIN3/ACIS) were HPV positive and categorized as false-negatives by cobas HPV; nine of 12 false-negative CIN3/ACIS cases were p16+. There were 23 cases (12 CIN2, 11 CIN3/ACIS) negative by all HPV tests; seven of 11 CIN3/ACIS cases were p16+. H&E slides were available for six cases for re-review and all were confirmed as CIN3/ACIS. Tissue PCR was performed on the six confirmed CIN3/ACIS cases (and one without confirmation): four were positive for HPV types not considered oncogenic, two were positive for oncogenic genotypes and one was indeterminate. In summary, subanalysis of a large cervical cancer screening study did not identify any true CIN3/ACIS not attributable to HPV.

  10. Effect of Antiviral Therapy on Serum Activity of Angiotensin Converting Enzyme in Patients with Chronic Hepatitis C

    PubMed Central

    Husic-Selimovic, Azra; Sofic, Amela; Huskic, Jasminko; Bulja, Deniz

    2016-01-01

    Introduction: Renin-angiotenzin system (RAS) is frequently activated in patients with chronic liver disease. Angiotenzin - II (AT-II), produced by angiotenzin converting enzyme (ACE), has many physiological effects, including an important role in liver fibrogenesis. Combined antiviral therapy with PEG-IFN and ribavirin besides its antiviral effect also leads to a reduction in liver parenchyma fibrosis. Aim of the study: Determining the value of ACE in serum of patients with chronic hepatitis C before and after combined antiviral therapy, as well as the value of ACE activities in sera of the control group. Materials and methods: We studied 50 patients treated at Gastroenterohepatology Department, in the time-period of four years. Value of ACE in serum was determined by Olympus AU 400 device, with application of kit “Infinity TN ACE Liquid Stable Reagent”. HCV RNA levels in sera were measured by real time PCR. HCV RNA test was performed with modular analysis of AMPLICOR and COBAS AMPLICOR HCV MONITOR test v2.0, which has proved infection and was used for quantification of the viruses and monitoring of the patients’ response to therapy. Liver histology was evaluated in accordance with the level of necroinflammation activity and stage of fibrosis. Results: Serum activities of ACE in chronic hepatitis C patients is statistically higher than the values in the control group (p=0.02). Antiviral therapy in chronic hepatitis C patients statistically decreases serum activities of ACE (p= 0.02) and indirectly affects fibrogenesis of the liver parenchyma. Correlation between ACE and ALT activity after the therapy was proved (0.3934). Conclusion: Our findings suggest that the activity of ACE in serum is a good indirect parameter of the liver damage, and could be used as an indirect prognostic factor of the level of liver parenchyma damage. Serum activity of ACE can be used as a parameter for non-invasive assessment of intensity of liver damage. PMID:27147779

  11. Numerical Modeling of Lunar Accretion Using a New Hydrocode Coupled to an N-Body Code

    NASA Astrophysics Data System (ADS)

    Salmon, J.; Canup, R. M.

    2016-12-01

    We perform numerical simulations of accretion of the Moon from an impact-generated circumterrestrial disk using a newly developed numerical model. This unique code couples 1) a 1-dimensional (in the radial direction) hydrocode (Salmon et al. 2010, Charnoz et al. 2010) to model the evolution of the protolunar disk's material located inside the Roche limit, with 2) the symplectic integrator SyMBA (Duncan et al. 1998) to model the orbital evolution of moonlets located outside the Roche limit and their mutual interactions as they collide to grow the Moon. This model represents an improvement over prior work that assumed a uniform surface density Roche-interior disk (Salmon and Canup 2012). Compared to the prior model, we evolve the surface density of the Roche-interior disk by: 1) computing the local viscous torque throughout the disk, and 2) applying the resonant torque due to interactions with outer bodies at the actual position of the resonance in the disk. This allows us to model the disk's radial structure, which allows us to better track the transport of mass and angular momentum in the disk and more accurately compute how disk material is delivered through the Roche limit. This will affect the efficiency of incorporation of disk's material onto the growing Moon, and thus constrains the disk's properties (initial mass and surface density profile) required to form a lunar-size satellite. We will present results from a suite of simulations in which we vary the total mass of the disk, the fraction of the mass located inside and outside the Roche limit, and the disk's surface density profile. We track the dynamics of the Moon's accretion from the disk (e.g. its mass as a function of time, accretion timescales, post-accretion orbital parameters of the Moon), and discuss implications and constraints for the Giant Impact scenario.

  12. The future of discovery chemistry: quo vadis? Academic to industrial--the maturation of medicinal chemistry to chemical biology.

    PubMed

    Hoffmann, Torsten; Bishop, Cheryl

    2010-04-01

    At Roche, we set out to think about the future role of medicinal chemistry in drug discovery in a project involving both Roche internal stakeholders and external experts in drug discovery chemistry. To derive a coherent strategy, selected scientists were asked to take extreme positions and to derive two orthogonal strategic options: chemistry as the traditional mainstream science and chemistry as the central entrepreneurial science. We believe today's role of medicinal chemistry in industry has remained too narrow. To provide the innovation that industry requires, medicinal chemistry must play its part and diversify at pace with our increasing understanding of chemical biology and network pharmacology.

  13. FDA review of viral load test kits. Food and Drug Administration.

    PubMed

    1996-03-01

    Viral load testing, which quantifies the amount of HIV in the blood plasma of infected individuals, may dramatically shorten the time necessary to test drugs prior to approval and marketing. Two manufacturers have applied for approval of their test kits. Hoffman-LaRoche (Roche Molecular Systems) developed a test kit called quantitative competitive polymerase chain reaction (quantitative PCR). Chiron Corporation's product is called branched chain DNA, or bDNA. Both tests give similar results. Viral load is an indicator of the effectiveness of drug therapy, and high viral load is an indicator of disease progression and clinical decline.

  14. Analysis of Proton Transport Experiments.

    DTIC Science & Technology

    1980-09-05

    AGENCY NAME & ADDRESS(if different from Controlling Office) IS. SECURITY CLASS. (of this report) Sandia Laboratories Albuquerque, New Mexico 87115...B. 14 21120 Is-sur-Tille France Attn: C. Patou 1 copy C. Peugnet 1 copy M. Roche 1 copy N. Camarcat 1 copy C. Bruno 1 copy J. Barbaro 1 copy Ecole

  15. Salivary cortisol and cortisone responses to tetracosactrin (synacthen).

    PubMed

    Cornes, Michael P; Ashby, Helen L; Khalid, Yasmeen; Buch, Harit N; Ford, Clare; Gama, Rousseau

    2015-09-01

    To establish cutoff values for salivary liquid chromatography tandem mass spectroscopy cortisol and cortisone in defining adequate adrenocortical function during a standard synacthen test. We compared salivary liquid chromatography tandem mass spectroscopy cortisol and cortisone responses to those of serum cortisol measured on the Roche E170 immunoassay analyser and the Abbott Architect i2000 before and 30 min and 60 min following 0.25 mg of intravenous synacthen. Correlations of salivary cortisol and cortisone were bimodal and linear, respectively. Based on these correlations, adequate salivary cortisol and cortisone responses to synacthen were extrapolated from a serum cortisol (Roche) cut-off of 550 nmol/L and defined as 15 nmol/L and 45 nmol/L, respectively. The Abbott method correlated well with the Roche but gave results that were about 20% lower than the Roche method. Measurement of salivary cortisol and cortisone responses offers an alternative to those of serum cortisol during a synacthen test in the investigation of adrenal hypofunction. © The Author(s) 2015.

  16. Draft Genome Sequences of Two Strains of Salmonella enterica Serovar Typhimurium Displaying Different Virulence in an Experimental Chicken Model

    PubMed Central

    Blais, Burton; Huang, Hongsheng; Wang, Linru; Elmufti, Mohamed; Allain, Ray; Hazelwood, Jennifer; Grenier, Chris; Amoako, Kingsley; Savic, Mirjana; Fattahi Ghazi, Nashmil

    2017-01-01

    ABSTRACT Salmonella enterica serovar Typhimurium strains 22495 and 22792, obtained from wild birds, were found to display different virulence attributes in an experimental chicken model. Closed genome sequences were assembled after sequencing with the Roche 454 and Illumina MiSeq platforms. An additional plasmid was present in the more virulent strain 22495. PMID:28183752

  17. Roughness-Induced Resonance for Molecular Fluorescence Near a Corrugated Metallic Surface

    DTIC Science & Technology

    1988-07-01

    Chemistry University of hester Pennsylvania State University Roches , ew York 14627 University Park, Pennsylvania 16802 r. G. Rubloff Dr. Roald ... Hoffmann IBM Department of Chemistry Thomas J. Watson Research Ceiter Cornell University P.O. Box 218 Ithaca, New York 14853 Yorktown Heights, New York

  18. Correlations between Photons in Resonance Fluorescence Emitted by an Atom Near a Metal Surface.

    DTIC Science & Technology

    1987-10-01

    Department of Chemistry University of chester Pennsylvania Stte University Roches -,ew York 14627 University Park, Pennsylvania 16802 ,_r. G. Rubloff Dr. Roald ... Hoffmann IBM Department of Chemistry Thomas J. Watson Research Center Cornell University P.O. Box 218 Ithaca, New York 14853 Yorktown Heights, New

  19. Squeezing of Atomic Variables in the One-Photon and Two-Photon Jaynes-Cummings Model

    DTIC Science & Technology

    1989-06-01

    of Chemistry University of hester Pennsylvania State University Roches ew York 14627 University Park, Pennsylvania 16802 r. G. Rubloff Dr. Roald ... Hoffmann IBM Department of Chemistry Thomas J. Watson Research Center Cornell University P.O. Box 218 Ithaca, New York 14853 Yorktown Heights, New York

  20. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    USDA-ARS?s Scientific Manuscript database

    An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions fr...

  1. The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants

    USDA-ARS?s Scientific Manuscript database

    The American cranberry (Vaccinium macrocarpon Ait.) mitochondrial genome was assembled and reconstructed from whole genome 454 Roche GS-FLX and Illumina shotgun sequences. Compared with other Asterids, the reconstruction of the genome revealed an average size mitochondrion (459,678 nt) with comparat...

  2. Comparison of Intraosseous and Intravenous Delivery of Hypertonic Saline/Dextran (HSD) in Anesthetized, Euvolemic Pigs

    DTIC Science & Technology

    1991-04-01

    Biochemical Assays Total carbohydrate concentrations in plasma were determined by the anthrone reaction (16) following precipitation of serum protein with 10...concentrations of total carbohydrate. Assays for sodium, potassium, chloride and protein were also performed by the Analytical Chemistry Branch, LAIR...concentrations were determined by a commercial kit (Roche Diagnostic Systems, Nutley, NJ) and the Biuret method, respectively, both adapted for

  3. Waiting for 4.1

    ERIC Educational Resources Information Center

    Bernd, Karen

    2003-01-01

    What better way to clarify a topic and allow it to come alive than to provide students with a way to actually see it? Images, diagrams, and flowcharts can draw students in. In this article, the author reviews "Roche Genetics: Education Program" CD-ROM version 4.0. The program is organized using a theme park analogy. An information booth leads to a…

  4. Stabilization of Pyridostigmine as Preventive Antidote

    DTIC Science & Technology

    2001-09-01

    inhibiting the destruction of acetylcholine by cholinesterase. In current therapy pyridostigmine tablets are useful in the treatment of myasthenia ... gravis being put on the market by Roche with the name Mestinon). In the form of manganese bromide salt, Arzneimittelwerk Dresden produced pyridostigmine

  5. Waiting for 4.1

    ERIC Educational Resources Information Center

    Bernd, Karen

    2003-01-01

    What better way to clarify a topic and allow it to come alive than to provide students with a way to actually see it? Images, diagrams, and flowcharts can draw students in. In this article, the author reviews "Roche Genetics: Education Program" CD-ROM version 4.0. The program is organized using a theme park analogy. An information booth leads to a…

  6. Characteristics of Periodical Use in the Small College Library.

    ERIC Educational Resources Information Center

    Puvogel, Cole

    Characteristics of periodical use at a small liberal arts college were studied using a methodology aimed at providing a more accurate system for data collection by recording all the periodicals used in an entire semester. In the John J. Wright Library at La Roche College (Pennsylvania), circulation records were consulted, and one person while…

  7. Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content and rearrangements revealed by next generation sequencing

    USDA-ARS?s Scientific Manuscript database

    The complete plastid genome sequence of the American cranberry was reconstructed using next-generation sequencing data by in silico procedures. We used Roche 454 shotgun sequence data to isolate cranberry plastid-specific sequences of the cultivar ‘HyRed’ via homology comparisons with complete seque...

  8. 454-pyrosequencing: A tool for discovery and biomarker development

    USDA-ARS?s Scientific Manuscript database

    The Roche GS-FLX (454) sequencer has made possible what was thought impossible just a few years ago: sequence >1 million high-quality nucleotide reads (mean 400 bp) in less than 12 h. This technology provides valuable species-specific sequence information, and is a valuable tool to discover and und...

  9. Sharing Cookies: A Case Study

    ERIC Educational Resources Information Center

    Salls, Jenny

    2014-01-01

    Rational number interpretations can include part-whole, measure, ratio, quotient, and operator. These are all subconstructs of partitioning (Barnett-Clarke et al. 2010; Behr et al. 1980; Clarke, Roche, and Mitchell 2008; Flores, Samson, and Yanik 2006). Each of these subconstructs uses different cognitive skills (Driscoll 1984), so it is important…

  10. Identification and initial characterization of a novel turkey-origin picobirnavirus using a metagenomic approach

    USDA-ARS?s Scientific Manuscript database

    Using the Genome Sequencer FLX Titanium technology (Roche, 454 Life Sciences), a ribonucleic acid (RNA) virus-specific metagenome was prepared using the pooled intestinal contents collected from North Carolina turkey flocks experiencing enteric disease signs. This analysis produced 6526 contigs rang...

  11. Genome Wide Characterization of Simple Sequence Repeats in Cucumber

    USDA-ARS?s Scientific Manuscript database

    The whole genome sequence of the cucumber cultivar Gy14 was recently sequenced at 15× coverage with the Roche 454 Titanium technology. The microsatellite DNA sequences (simple sequence repeats, SSRs) in the assembled scaffolds were computationally explored and characterized. A total of 112,073 SSRs ...

  12. Digital Vasculitis Associated With Interferon Therapy

    DTIC Science & Technology

    1992-06-01

    Rheumatoid fac- rheumatoid arthritis [5], and with increasing fre- tor, antinuclear antibody , VDRL, antibody to the quency in hematologic...Goldsweig (Hoffmann-La Roche) nia. In addition, numbness, paresthesias, and sen- and Ms. D. Davis (Genentecn) in the interferon antibody assays. sory

  13. Listening Walks and Singing Maps

    ERIC Educational Resources Information Center

    Cardany, Audrey Berger

    2011-01-01

    The Listening Walk by Paul Showers and illustrated by Aliki, and "It's My City: A Singing Map" by April Pulley Sayre with pictures by Denis Roche, provide two examples of texts that aid in building children's phonological awareness for reading and music. The author describes each narrative and discusses its function as a springboard to composition…

  14. The determination of the parameters of the W Ser type-eclipsing binary system V367 Cyg.

    NASA Astrophysics Data System (ADS)

    Antokhina, Eh. A.; Menchenkova, E. V.

    Fresa's blue light curve of V367 Cyg was analyzed by the synthesis method in the Roche model and in the model with a geometrically thick disk. The new spectroscopic mass ratio q = M2/M1 = 1.57 was used. The basic parameters and the absolute dimensions of the system were obtained.

  15. Determination of the parameters of the eclipsing binary system V367 CYG by the light-curve synthesis method

    NASA Astrophysics Data System (ADS)

    Antokhina, E. A.; Menchenkova, E. V.

    1990-06-01

    Fresa's (1966) blue light curve of V367 Cyg is analyzed by the synthesis method in the framework of the Roche model and a model with a geometrically thick disk. The new spectroscopic mass ratio q = M2//M1 = 1.57 was used. The fundamental parameters and the absolute dimensions of the system were determined.

  16. Caspase Inhibitors Attenuate Superantigen-Induced Inflammatory Cytokines, Chemokines, and T-Cell Proliferation

    DTIC Science & Technology

    2004-05-01

    of caspases, groups 2 and 3, function mostly in apotosis and in other cellular proteolytic cascades resulting in DNA fragmentation and degradation of...instructions. DNA fragmentation was detected by the presence of oligonucleosomes by using a cell death detec- tion ELISA PLUS kit (Roche) according to the

  17. ACS chemical neuroscience molecule spotlight on RG1678.

    PubMed

    Hopkins, Corey R

    2011-12-21

    RG1678 is a glycine transporter-1 inhibitor currently in Phase III trials for the treatment of the negative symptoms of schizophrenia and is being developed by Roche (in combination with Chugai). Recent Phase II data shows that RG1678 is effective in reducing the negative symptoms when given in combination with second generation antipsychotics.

  18. Nonlinear Time Series Analysis via Neural Networks

    NASA Astrophysics Data System (ADS)

    Volná, Eva; Janošek, Michal; Kocian, Václav; Kotyrba, Martin

    This article deals with a time series analysis based on neural networks in order to make an effective forex market [Moore and Roche, J. Int. Econ. 58, 387-411 (2002)] pattern recognition. Our goal is to find and recognize important patterns which repeatedly appear in the market history to adapt our trading system behaviour based on them.

  19. Characterization of Marine Mammal Recordings from the Hawaii Range Complex

    DTIC Science & Technology

    2010-11-01

    Germany. 100 pp. Baumann-Pickering, S., S. M. Wiggins, E. Roth , M. A. Roch, H.-U. Schnitzler, and J. A. Hildebrand. (2010). “Echolocation...Institution Woods Hole, MA Ian Boyd University of St. Andrews St. Andrews, Scotland , UK 1 1 1 1 1

  20. [Comparison of efficiency and cytotoxicity of different transfection reagents in transfecting RIP140-siRNA into Kupffer cells].

    PubMed

    Li, Ji; Liu, Zuojin

    2015-12-01

    To compare the efficiency and cytotoxicity of different transfection reagents used in transfection of RIP140-siRNA into Kupffer cells to optimize the transfection conditions. Kupffer cells were transfected with RIP140-siRNA labeled with GFP as the reporter gene using lipofectamine 2000, Roche reagent (X-treme GENE siRNA Transfection Reagent) and puro screening lentivirus (1.0×10(8) TU/mL) as the transfection reagents. The transfection effect was observed under a fluorescent inverted microscope, and laser scanning confocal microscopy was used to analyze RIP140 expression in trasnfected Kupffer cells. Flow cytometry was performed to detect cell apoptosis, and CCK-8 test was used to evaluate the cell proliferation inhibition. RT-RCR and Western blotting were performed to detect the expressions of RIP140 mRNA and protein in the trasnfected cells. Puro screening lentivirus yielded the highest cell transfection efficiency, which exceeded 90%, followed by Roche reagent and then by lipofectamine 2000. Flow cytometry and CCK-8 test showed that the cytotoxicity was the mildest with Roche reagent, moderate with lentivirus, and severe with lipofectamine 2000. The cells trasnfected with lentivirus showed a significantly lower RIP140 expression than cells trasnfected with lipofectamine 2000 and Roche reagent (P<0.05). In Kupffer cells, lentivirus-mediated transfection, as compared with the other two trasnfection reagents, can achieve good transfection efficiency with a relativelty low cytotoxicity, and allows for better controllability and stability of the trasnfectiion conditions.

  1. Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads

    USDA-ARS?s Scientific Manuscript database

    A de novo genome assembly of Bos taurus indicus sub-species, specifically a Nelore bull, has been developed using a multi-platform sequencing strategy. Genome sequence data for assembly (>120 Gb) was produced from Roche FLX454 and Illumina GAIIx platforms using paired-end reads from long (5 and 20 ...

  2. Global Analysis of Transcript and Protein Levels Across the Plasmodium falciparum Life Cycle

    DTIC Science & Technology

    2004-01-01

    presence of 500 ng·mL1 pyrimethamine and gametocytogenesis was induced (Ifediba and Vanderberg 1981). N-acetyl-D- glucosamine (50 mM) was added to the...in 5 mM Tris(2-Carboxyethyl)phosphine hydrochloride (TCEP, Roche); (3) alkylated by 20 mM iodoacetamide (IAM); and (4) digested with proteinase K

  3. Forging a Combat Mobility Culture

    DTIC Science & Technology

    2006-04-01

    and SECAF James Roche promoted the concept of a culture change within the air mobility community in their November 2003 USAF Transformation Flight...United Kingdom Austria Libya Venezuela Bahrain Malawi Yugoslavia Belgium Malaysia Yugoslavia Benin Mali Zambia Bosnia Mauritius Zimbabwe Botswana

  4. Sharing Cookies: A Case Study

    ERIC Educational Resources Information Center

    Salls, Jenny

    2014-01-01

    Rational number interpretations can include part-whole, measure, ratio, quotient, and operator. These are all subconstructs of partitioning (Barnett-Clarke et al. 2010; Behr et al. 1980; Clarke, Roche, and Mitchell 2008; Flores, Samson, and Yanik 2006). Each of these subconstructs uses different cognitive skills (Driscoll 1984), so it is important…

  5. Feasibility Analysis For Heating Tribal Buildings with Biomass

    SciTech Connect

    Steve Clairmont; Micky Bourdon; Tom Roche; Colene Frye

    2009-03-03

    This report provides a feasibility study for the heating of Tribal buildings using woody biomass. The study was conducted for the Confederated Salish and Kootenai Tribes of the Flathead Reservation in western Montana. S&K Holding Company and TP Roche Company completed the study and worked together to provide the final report. This project was funded by the DOE's Tribal Energy Program.

  6. Piperidine and pyrrolidine analogs as glycogen synthase activators; a patent evaluation (WO2011058122).

    PubMed

    Uto, Yoshikazu

    2012-01-01

    A small series of piperidine analogs that effectively activate glycogen synthase (GS) was prepared in WO2011058122. The treatment or prophylaxis of metabolic disease and disorders by these novel GS activators is claimed. These compounds represent further variations around a structural motif explored in the prior patent publications by Roche.

  7. Infrared Radiation Transmittance and Pilot Vision Through Civilian Aircraft Windscreens

    DTIC Science & Technology

    2008-06-01

    consequences. Examples of these sources nclude lasers, mercury -vapor and xenon halogen lamps, weldng devces, and nfrared and germcdal lamps. These...how best to mtgate ther mpact on avaton safety. REFERENCES 1. West SK, Duncan DD, Munoz B, Rub n GS, Fred LP, Bandeen-Roche K, et al. Sunlght

  8. Ultra high-throughput nucleic acid sequencing as a tool for virus discovery in the turkey gut.

    USDA-ARS?s Scientific Manuscript database

    Recently, the use of the next generation of nucleic acid sequencing technology (i.e., 454 pyrosequencing, as developed by Roche/454 Life Sciences) has allowed an in-depth look at the uncultivated microorganisms present in complex environmental samples, including samples with agricultural importance....

  9. Application of Cydia pomonella expressed sequence tags: identification and expression of three general odorant binding proteins in codling moth

    USDA-ARS?s Scientific Manuscript database

    The codling moth, Cydia pomonella, is one of the most important pests of pome fruits in the world, yet the molecular genetics and physiology of this insect remains poorly understood. A combined assembly of 8340 expressed sequence tags (ESTs) was generated from Roche 454 GS-FLX sequencing of 8 tissu...

  10. A Relational Frame Theory Account of Empathy

    ERIC Educational Resources Information Center

    Vilardaga, Roger

    2009-01-01

    The current paper proposes a Relational Frame Theory (RFT, Hayes, Barnes-Holmes, & Roche, 2001a) conceptualization of empathy and perspective taking that follows previous literature outlining a relationship between those phenomena and general functioning. Deictic framing, a relational operant investigated by RFT researchers, constitutes the…

  11. Derived Relational Responding and Performance on Verbal Subtests of the WAIS-III

    ERIC Educational Resources Information Center

    O'Hora, Denis; Pelaez, Martha; Barnes-Holmes, Dermot

    2005-01-01

    Twenty-six monolingual and 46 bilingual college students were assigned to 2 groups on the basis of their performance on a complex relational task, an empirical model of instructional control (O'Hora, Barnes-Holmes, Roche, & Smeets, 2004). The subjects were then exposed to the vocabulary, arithmetic, and digit-symbol encoding subtests of the…

  12. The Advantage of Reading over Listening Text Comprehension in Down Syndrome: What Is the Role of Verbal Memory?

    ERIC Educational Resources Information Center

    Roch, Maja; Florit, Elena; Levorato, M. Chiara

    2012-01-01

    The current study was designed to investigate the role played by verbal memory in the advantage shown by individuals with Down syndrome in reading over listening text comprehension (Roch & Levorato, 2009). Two different aspects of verbal memory were analyzed: processing load and coding modality. Participants were 20 individuals with Down syndrome,…

  13. Suitability of Commercial Transport Media for Biological Pathogens under Nonideal Conditions

    DTIC Science & Technology

    2011-01-01

    Real - time PCR was utilized for nucleic acid detection. B. anthracis Sterne and Y. pestis A1122 were assayed on the Roche LightCycler 2.0 using the Idaho...assay. B. anthracis Sterne, Y. pestis A1122, ricin, and VEE extracts were all assayed using ECL MINItubes available from the CRP. 2.5. Real-Time PCR

  14. Sequencing Technologies Panel at SFAF

    SciTech Connect

    Turner, Steve; Fiske, Haley; Knight, Jim; Rhodes, Michael; Vander Horn, Peter

    2010-06-02

    From left to right: Steve Turner of Pacific Biosciences, Haley Fiske of Illumina, Jim Knight of Roche, Michael Rhodes of Life Technologies and Peter Vander Horn of Life Technologies' Single Molecule Sequencing group discuss new sequencing technologies and applications on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  15. New Generation Sequencing Technology Panel at SFAF-Part I

    SciTech Connect

    Fiske, Haley; Turner, Steve; Rhodes, Michael; Milos, Patrice; Harkins, Tim

    2009-05-27

    From left to right: Haley Fiske of Illumina Inc., Steve Turner of Pacific Biosciences, Michael Rhodes of Applied Biosystems, Patrice Milos of Helicos Biosciences and Tim Harkins of Roche Diagnostics answer questions in a forum moderated by Bob Fulton at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  16. New Generation Sequencing Technology Panel at SFAF-Part II

    SciTech Connect

    Fiske, Haley; Turner, Steve; Rhodes, Michael; Milos, Patrice; Harkins, Tim

    2009-05-27

    From left to right: Haley Fiske of Illumina Inc., Steve Turner of Pacific Biosciences, Michael Rhodes of Applied Biosystems, Patrice Milos of Helicos Biosciences and Tim Harkins of Roche Diagnostics answer questions in a forum moderated by Bob Fulton at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  17. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    USDA-ARS?s Scientific Manuscript database

    Next generation sequencing is helping to solve the data insufficiency problem hindering well-resolved dominant gene phylogenies. We used Roche 454 technology to obtain DNA sequences from 93 nuclear orthologs, dispersed throughout all linkage groups of Daucus. Of these 93 orthologs, ten were designed...

  18. Next generation sequencing of crown and rhizome transcriptome from an upland, tetraploid switchgrass

    USDA-ARS?s Scientific Manuscript database

    The crown and rhizome transcriptome of a winter-adapted, upland tetraploid switchgrass cultivar Summer, was investigated using the Roche 454-FLX pyrosequencing platform. In all approximately 1 million reads consisting of 216 million bases were assembled into 27,687 contigs and 43,094 singletons. A...

  19. Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.)

    USDA-ARS?s Scientific Manuscript database

    This study reports generation of large-scale genomic resources for pigeonpea, a so-called ‘orphan crop species’ of the semi-arid tropic regions. Roche FLX/454 sequencing was carried out on a normalized cDNA pool prepared from 31 tissues produced 494,353 short transcript reads (STRs). Cluster analysi...

  20. 75 FR 29253 - Proposed Flood Elevation Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-25

    ... 925 6th Street, Del Norte, CO 81132. Washington County, Florida, and Incorporated Areas Alligator... confluence with Holmes Creek. Helms Branch At the confluence with None +78 City of Chipley, Alligator Creek... Alligator Creek. Johnson Branch At Roche Avenue........ None +37 City of Vernon, Unincorporated Areas of...

  1. National Program for Inspection of Non-Federal Dams. Chase Pond Dam (NH 00255), NHWRB Number 253.02, Merrimack River Basin, Wilmot, New Hampshire. Phase I Inspection Report.

    DTIC Science & Technology

    1980-03-01

    ROCH.ESTER.* N.M. 2 4- CLIENT (4vx Co.-QDc Joe______________ -: PROJECT 5 9 .c, ’~- Compiro. By _______ Alre.. DETAIL L-~.~ CSCbao. By DATE ______ 3.1 ~de. 3.Cys1 o .e., -5,u ect-, CA rorm-i goot k-- -~..-. N c -- FILMED 8-- D I7.

  2. miRNA Involved in Six1-Induced Breast Cancer

    DTIC Science & Technology

    2013-05-01

    Tween, 50mg/ml Heparin, 500mg/ml yeast tRNA) at hybridization temperatures 30 degrees below the RNA Tm. Detection was achieved with BM purple (Roche...Breast Carcinoma Cells. Cancer Res 2006; 66: 11370 - 11380. 36 Jørgensen S, Baker A, Møller S, Nielsen BS. Robust one-day in situ hybridization protocol

  3. Theory of the Tetragonal-to-Orthorhombic Structural Phase Transition in La2CuO4.

    DTIC Science & Technology

    1987-11-01

    J. G. Bednorz and K. A. Muller, Z. Phys. B j4, 189 (1986). 2. C. W. Chu, P. H. Hor, R. L. Meng, L. Gao, Z. J. Huang and Y. Q. Wang , Phys. Rev. Lett...Chemistry University of2 chester Pennsylvania State University Roches ew York 14627 University Park, Pennsylvania 16802 r. G. Rubloff Dr. Roald

  4. BCS (Bardeen-Cooper-Schrieffer) Primer: a Guide to Computational Methods in Superconductivity Theory

    DTIC Science & Technology

    1989-12-01

    Ed. Superconductivity; Dekker: New York, 1969; vols. I and II. 16. Rice, M. J.; Wang , Y. R. Phys. Rev. B 1988, 37, 5893-5896. 17. Ott, H. R.; Rudigier...Pennsylvania State University Roches . ew York 14627 University Park, Pennsylvania 16802 r. G. Rubloff Dr. Roald Hoffmann IBM Department of Chemistry

  5. N-body simulations of star clusters

    NASA Astrophysics Data System (ADS)

    Engle, Kimberly Anne

    1999-10-01

    We investigate the structure and evolution of underfilling (i.e. non-Roche-lobe-filling) King model globular star clusters using N-body simulations. We model clusters with various underfilling factors and mass distributions to determine their evolutionary tracks and lifetimes. These models include a self-consistent galactic tidal field, mass loss due to stellar evolution, ejection, and evaporation, and binary evolution. We find that a star cluster that initially does not fill its Roche lobe can live many times longer than one that does initially fill its Roche lobe. After a few relaxation times, the cluster expands to fill its Roche lobe. We also find that the choice of initial mass function significantly affects the lifetime of the cluster. These simulations were performed on the GRAPE-4 (GRAvity PipE) special-purpose hardware with the stellar dynamics package ``Starlab.'' The GRAPE-4 system is a massively-parallel computer designed to calculate the force (and its first time derivative) due to N particles. Starlab's integrator ``kira'' employs a 4th- order Hermite scheme with hierarchical (block) time steps to evolve the stellar system. We discuss, in some detail, the design of the GRAPE-4 system and the manner in which the Hermite integration scheme with block time steps is implemented in the hardware.

  6. 75 FR 39024 - Determination That ACCUTANE (Isotretinoin) Capsules, 10 Milligrams, 20 Milligrams, and 40...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-07

    ... Administration (FDA) is announcing its determination that ACCUTANE (isotretinoin) Capsules, 10 milligrams (mg), 20 mg, and 40 mg, were not withdrawn from sale for reasons of safety or effectiveness. This...) Capsules, 10 mg, 20 mg, and 40 mg, are the subject of NDA 18-662, held by Hoffman-La Roche, Inc....

  7. Sandy Point Fun Run: A Context for Understanding and Using Scale

    ERIC Educational Resources Information Center

    Roche, Anne

    2013-01-01

    In the middle years of school, it is important that mathematics is challenging, engaging and focuses on worthwhile mathematics. In this article, Anne Roche describes a lesson that seemed to have all three of these characteristics, as students grappled with issues of scale to create a fun run, given a range of challenging mathematical constraints.…

  8. A Year after a Degrading Scandal, Hillsdale Moves On.

    ERIC Educational Resources Information Center

    Van der Werf, Martin

    2000-01-01

    Describes the new atmosphere at Hillsdale College, Michigan, a conservative institution distinguished by its refusal to accept federal funds, in the wake of a scandal involving the previous president George C. Roche, III. Discusses the role of the new president and the attitudes of the faculty following the change of administration. (SLD)

  9. Cystatin C standardization decreases assay variation and improves assessment of glomerular filtration rate.

    PubMed

    Ebert, Natalie; Delanaye, Pierre; Shlipak, Michael; Jakob, Olga; Martus, Peter; Bartel, Jan; Gaedeke, Jens; van der Giet, Markus; Schuchardt, Mirjam; Cavalier, Etienne; Schaeffner, Elke

    2016-05-01

    Cystatin C is increasingly used in glomerular filtration rate (GFR) estimation equations. The dependence of cystatin C results upon the analytical method has been a major source of controversy. Cystatin C was measured with non-standardized turbidimetric Roche Generation 1 and standardized nephelometric Siemens assays in 3666 and additionally with standardized Roche Generation 2 and Siemens in 567 blood samples of the Berlin Initiative Study. Cystatin C-based GFR was assessed with CKD-EPIcys (Chronic Kidney Disease Epidemiology) and CAPA (Caucasian, Asian, Pediatric, Adult) equations and the impact of the assays on GFR estimation was determined. Equation performance compared to measured GFR was evaluated. Concordance of Roche Gen2 and Siemens was high with median difference of 0.003 ± 0.13 mg/L (limits of agreement: -0.12 to 0.12) and Passing Bablok correlation was essentially perfect. Roche Gen1 assay showed worse concordance with Siemens: median difference was 0.08 ± 0.13 mg/L (limits of agreement: -0.18 to 0.34) and correlation was inferior. Mean difference (± SD) of estimated GFRCKD-EPIcys was 0 ± 4 mL/min/1.73 m(2) for Gen2 and Siemens compared to -5 ± 8 with Gen1. Performance of GFR estimating equations was not influenced by the choice of Siemens or Gen2 assays. Standardization of Roche Gen2 assay improved accuracy of cystatin C measurement compared to Siemens. It suggests only negligible method bias and results in equal performance of both assays when estimating GFR indicating that successful calibration has led to major progress in cystatin C analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Baseline morning cortisol level as a predictor of pituitary-adrenal reserve: a comparison across three assays.

    PubMed

    Sbardella, Emilia; Isidori, Andrea M; Woods, Conor P; Argese, Nicola; Tomlinson, Jeremy W; Shine, Brian; Jafar-Mohammadi, Bahram; Grossman, Ashley B

    2017-02-01

    The short ACTH stimulation test (250 μg) is the dynamic test most frequently used to assess adrenal function. It is possible that a single basal cortisol could be used to predict the dynamic response, but research has been hampered by the use of different assays and thresholds. To propose a morning baseline cortisol criterion of three of the most commonly used modern cortisol immunoassays - Advia Centaur (Siemens), Architect (Abbott) and the Roche Modular System (Roche) - that could predict adrenal sufficiency. Observational, retrospective cross-sectional study at two centres. Retrospective analysis of the results of 1019 Short Synacthen tests (SSTs) with the Advia Centaur, 449 SSTs with the Architect and 2050 SSTs with the Roche Modular System assay. Serum cortisol levels were measured prior to injection of 250 μg Synacthen and after 30 min. Overall, we were able to collate data from a total of 3518 SSTs in 3571 patients. Using receiver-operator curve analysis, baseline cortisol levels for predicting passing the SST with 100% specificity were 358 nmol/l for Siemens, 336 nmol/l for Abbott and 506 nmol/l for Roche. Utilizing these criteria, 589, 158 and 578 SSTs, respectively, for Siemens, Abbott and Roche immunoassays could have been avoided. We have defined assay-specific morning cortisol levels that are able to predict the integrity of the hypothalamo-pituitary-adrenal axis. We propose that this represents a valid tool for the initial assessment of adrenal function and has the potential to obviate the need for dynamic testing in a significant number of patients. © 2016 John Wiley & Sons Ltd.

  11. EQUILIBRIUM CONFIGURATIONS OF SYNCHRONOUS BINARIES: NUMERICAL SOLUTIONS AND APPLICATION TO KUIPER BELT BINARY 2001 QG{sub 298}

    SciTech Connect

    Gnat, Orly; Sari, Re'em

    2010-08-20

    We present numerical computations of the equilibrium configurations of tidally locked homogeneous binaries rotating in circular orbits. Unlike the classical Roche approximations, we self-consistently account for the tidal and rotational deformations of both components, and relax the assumptions of ellipsoidal configurations and Keplerian rotation. We find numerical solutions for mass ratios q between 10{sup -3} and 1, starting at a small angular velocity for which tidal and rotational deformations are small, and following a sequence of increasing angular velocities. Each series terminates at an appropriate 'Roche limit', above which no equilibrium solution can be found. Even though the Roche limit is crossed before the 'Roche lobe' is filled, any further increase in the angular velocity will result in mass-loss. For close, comparable-mass binaries, we find that local deviations from ellipsoidal forms may be as large as 10%-20%, and departures from Keplerian rotation are significant. We compute the light curves that arise from our equilibrium configurations, assuming their distance is >>1 AU (e.g., in the Kuiper Belt). We consider both backscatter (proportional to the projected area) and diffuse (Lambert) reflections. Backscatter reflection always yields two minima of equal depths. Diffuse reflection, which is sensitive to the surface curvature, generally gives rise to unequal minima. We find detectable intensity differences of up to 10% between our light curves and those arising from the Roche approximations. Finally, we apply our models to Kuiper Belt binary 2001 QG{sub 298}, and find a nearly edge-on binary with a mass ratio q = 0.93{sup +0.07}{sub -0.03}, angular velocity {omega}{sup 2}/G{rho} = 0.333 {+-} 0.001 (statistical errors only), and pure diffuse reflection. For the observed period of 2001 QG{sub 298}, these parameters imply a bulk density {rho} = 0.72 {+-} 0.04 g cm{sup -3}.

  12. Estimation of measurement error in plasma HIV-1 RNA assays near their limit of quantification

    PubMed Central

    Wang, Lu; Brumme, Chanson; Wu, Lang; Montaner, Julio S. G.; Harrigan, P. Richard

    2017-01-01

    Background Plasma HIV-1 RNA levels (pVLs), routinely used for clinical management, are influenced by measurement error (ME) due to physiologic and assay variation. Objective To assess the ME of the COBAS HIV-1 Ampliprep AMPLICOR MONITOR ultrasensitive assay version 1.5 and the COBAS Ampliprep Taqman HIV-1 assay versions 1.0 and 2.0 close to their lower limit of detection. Secondly to examine whether there was any evidence that pVL measurements closest to the lower limit of quantification, where clinical decisions are made, were susceptible to a higher degree of random noise than the remaining range. Methods We analysed longitudinal pVL of treatment-naïve patients from British Columbia, Canada, during their first six months on treatment, for time periods when each assay was uniquely available: Period 1 (Amplicor): 08/03/2000–01/02/2008; Period 2 (Taqman v1.0): 07/01/2010–07/03/2012; Period 3 (Taqman v2.0): 08/03/2012–30/06/2014. ME was estimated via generalized additive mixed effects models, adjusting for several clinical and demographic variables and follow-up time. Results The ME associated with each assay was approximately 0.5 log10 copies/mL. The number of pVL measurements, at a given pVL value, was not randomly distributed; values ≤250 copies/mL were strongly systematically overrepresented in all assays, with the prevalence decreasing monotonically as the pVL increased. Model residuals for pVL ≤250 copies/mL were approximately three times higher than that for the higher range, and pVL measurements in this range could not be modelled effectively due to considerable random noise of the data. Conclusions Although the ME was stable across assays, there is substantial increase in random noise in measuring pVL close to the lower level of detection. These findings have important clinical significance, especially in the range where key clinical decisions are made. Thus, pVL values ≤250 copies/mL should not be taken as the “truth” and repeat p

  13. Ranibizumab (Lucentis) versus Bevacizumab (Avastin) for the Treatment of Age-Related Macular Degeneration: An Economic Disparity of Eye Health.

    PubMed

    Moreno, Tomas A; Kim, Stephen J

    2016-01-01

    Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, and the advent of anti-vascular endothelial growth factor agents (VEGF) has revolutionized treatment for neovascular AMD. Two of the most popular anti-VEGF agents, ranibizumab (Lucentis; Genentech/Roche) and bevacizumab (Avastin; Genentech/Roche), effectively treat neovascular AMD but have a substantial difference in price. Multiple level 1 trials have demonstrated that bevacizumab is noninferior to ranibizumab in the treatment of neovascular AMD and that both have similar safety profiles. The decision to use one drug over the other is multifactorial with influences from industry as well as individual physician biases. However, the additional billions spent on ranibizumab result in a large economic disparity that is not rationalized by cost effectiveness models.

  14. The Fraction of KBO Contact Binaries

    NASA Astrophysics Data System (ADS)

    Lacerda, Pedro

    2007-05-01

    We use Roche binary models to improve previous estimates of the contact binariy fraction within the Kuiper Belt object (KBO) population (Sheppard & Jewitt 2004). Our simulations can be used to determine the lightcurve range of Roche binaries at arbitrary observing geometries, and for different surface types. This allows us to better correct the apparent fraction for observing geometry effects. We find that at least 9% of KBOs are contact binaries. Such high incidence of KBOs contact binaries has important implications to binary formation and collisional evolution scenarios. PL is grateful to the Portuguese Fundacao para a Ciencia e a Tecnologia (BPD/SPFH/18828/2004) for financial support. This work was supported, in part, by a grant from the NSF to David C. Jewitt.

  15. Infrared photometry of the intermediate polar XYArietis (H0253+193)

    NASA Astrophysics Data System (ADS)

    Allan, Alasdair; Hellier, Coel; Ramseyer, Tod F.

    1996-09-01

    Near-infrared H-band photometry of the eclipsing intermediate polar XYAri shows an ellipsoidal variation from the Roche-lobe-filling secondary star, and a marginally significant spin pulse. We model the light curve, finding that the mass ratio of the system lies in the range 0.43<q<0.71, and the system inclination in the range 80 deg<i<87 deg. We show that IR-emitting material circles around the white dwarf, consistent with an accretion disc extending to more than 0.3 of the primary's Roche lobe. The H-band light of this material cannot be asymmetric about the white dwarf by more than a factor of 2.

  16. Masses and radii for thirteen chromospherically active ellipsoidal variables

    NASA Technical Reports Server (NTRS)

    Hall, Douglas S.

    1990-01-01

    The amplitude of the ellipticity effect, the mass function, and the V sin i in ten long-period RS CVn SB1 binaries are used to compute limits on the masses of the two stars and the radius of the primary: zeta And, UV CrB, V1764 Cyg, V826 Her, V350 Lac, GX Lib, V1197 Ori, AP Psc, 33 Psc, and EE UMa. Explicit masses and radii are computed for three SB2 systems: BL CVn, V1817 Cyg, and TZ Tri. The primary in several is found to fill 95 percent or more of its Roche lobe. The two minima produced by the ellipticity effect are unequal in depth, with the effect largest when i is near 90 deg and the primary nearly fills its Roche lobe. The greatest inequality found, in UV CrB, was 0.08 mag.

  17. Fiber-optic-echelle-CCD spectral monitoring of UX Arietis

    SciTech Connect

    Huenemoerder, D.P.; Buzasi, D.L.; Ramsey, L.W. )

    1989-10-01

    Results are presented on 30 fiber-optic-echelle-CCD spectra for the UX Ari system, covering one orbit in the spring and two orbits in the fall of 1987. The spectra obtained have a resolution of about 12,000 over the range of the Ca II H lines in the near UV to the Ca II triplet in the near IR, covering several activity sensitive lines. The most striking features observed were strong H-alpha and H-beta absorption near phase 0.8, which were present at epochs eight months apart. The geometry of the system, as determined from the mass ratio, rotational velocities, and the assumption of synchronous rotation, gives a radius for the K star that is approximately filling its Roche lobe. It is suggested that the excess absorption seen is due to mass-transfer activity resulting from Roche lobe overflow of the K star and accretion onto the G star. 30 refs.

  18. Formation of regular satellites from ancient massive rings in the solar system.

    PubMed

    Crida, A; Charnoz, S

    2012-11-30

    When a planetary tidal disk--like Saturn's rings--spreads beyond the Roche radius (inside which planetary tides prevent aggregation), satellites form and migrate away. Here, we show that most regular satellites in the solar system probably formed in this way. According to our analytical model, when the spreading is slow, a retinue of satellites appear with masses increasing with distance to the Roche radius, in excellent agreement with Saturn's, Uranus', and Neptune's satellite systems. This suggests that Uranus and Neptune used to have massive rings that disappeared to give birth to most of their regular satellites. When the spreading is fast, only one large satellite forms, as was the case for Pluto and Earth. This conceptually bridges the gap between terrestrial and giant planet systems.

  19. X-ray orbital modulation of a white dwarf accreting from an L dwarf. The system SDSS J121209.31+013627.7

    NASA Astrophysics Data System (ADS)

    Stelzer, B.; de Martino, D.; Casewell, S. L.; Wynn, G. A.; Roy, M.

    2017-01-01

    In an XMM-Newton observation of the binary SDSS J121209.31+013627.7, consisting of a white dwarf and an L dwarf, we detect X-ray orbital modulation as proof of accretion from the substellar companion onto the magnetic white dwarf. We constrain the system geometry (inclination as well as magnetic and pole-cap angle) through modelling of the X-ray light curve, and we derive a mass accretion rate of 3.2 × 10-14M⊙/ yr from the X-ray luminosity ( 3 × 1029 erg/s). From X-ray studies of L dwarfs, a possible wind driven from a hypothesized corona on the substellar donor is orders of magnitude too weak to explain the observed accretion rate, while the radius of the L dwarf is comparable to its Roche lobe (0.1 R⊙), making Roche-lobe overflow the likely accretion mechanism in this system.

  20. On the behavior of double degenerate binaries associated with Type I supernovae

    NASA Technical Reports Server (NTRS)

    Cameron, A. G. W.; Iben, I., Jr.

    1986-01-01

    An analytical investigation is performed of the evolution of double degenerate dwarf binary systems into Type I supernovae. The discussion is limited to systems consisting of carbon-oxygen and oxygen-neon-magnesium dwarfs and those composed of two carbon-oxygen dwarfs. The companions spiral together and the secondary, with a mass more than about 0.6 solar mass, fills its Roche lobe. The radius of the secondary increases faster than the Roche lobe due to mass overflow, which becomes unstable. The instability can lead to a Type I explosion and may or may not cause the formation of a neutron star. If a neutron star forms, the secondary, reduced to below 0.6 solar mass, will spiral inward to the primary and eventually be absorbed by the neutron star. If a white dwarf remnant remains after the supernova explosion of the overflow radius, then a second supernova explosion can occur.

  1. Introduction to the application of QbD principles for the development of monoclonal antibodies.

    PubMed

    Finkler, Christof; Krummen, Lynne

    2016-09-01

    Quality by Design (QbD) is a global regulatory initiative with the goal of enhancing pharmaceutical development through the proactive design of pharmaceutical manufacturing process and controls to consistently deliver the intended performance of the product. The principles of pharmaceutical development relevant to QbD are described in the ICH guidance documents (ICHQ8-11). An integrated set of risk assessments and their related elements developed at Roche/Genentech were designed to provide an overview of product and process knowledge for the production of a recombinant monoclonal antibody. This chapter introduces a publication series on the application of Quality by Design for biopharmaceuticals, with a focus on the development of recombinant monoclonal antibodies. The development of and overview on the QbD concept applied by Roche and Genentech is described and essential QbD elements are presented. Copyright © 2016 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

  2. Predicting Life Expectancy for Pirfenidone in Idiopathic Pulmonary Fibrosis.

    PubMed

    Fisher, Mark; Nathan, Steven D; Hill, Christian; Marshall, Jade; Dejonckheere, Fred; Thuresson, Per-Olof; Maher, Toby M

    2017-03-01

    Conducting an adequately powered survival study in idiopathic pulmonary fibrosis (IPF) is challenging due to the rare nature of the disease and the need for extended follow-up. Consequently, registration trials of IPF treatments have not been designed to estimate long-term survival. To predict life expectancy for patients with IPF receiving pirfenidone versus best supportive care (BSC) in a population that met the inclusion criteria of patients enrolled in the ASCEND and CAPACITY trials. Kaplan-Meier survival data for pirfenidone and BSC were obtained from randomized controlled clinical studies (CAPACITY, ASCEND), an open-label extension study (RECAP), and the Inova Fairfax Hospital database. Data from the Inova registry were matched to the inclusion criteria of the CAPACITY and ASCEND trials. Life expectancy was estimated by the area under the curve of parametric survival distributions fit to the Kaplan-Meier data. Mean (95% confidence interval) life expectancy was calculated as 8.72 (7.65-10.15) years with pirfenidone and 6.24 (5.38-7.18) years with BSC. Therefore, pirfenidone improved life expectancy by 2.47 (1.26-4.17) years compared with BSC. In addition, treatment with pirfenidone recuperated 25% of the expected years of life lost due to IPF. Sensitivity analyses found that results were sensitive to the choice of parametric survival distribution, and alternative piecewise and parametric approaches. This analysis suggests that this population of patients with IPF has an improved life expectancy if treated with pirfenidone compared with BSC. This study was funded by InterMune International AG, a wholly owned Roche subsidiary since 2014. Fisher was previously employed by InterMune UK, a wholly owned Roche subsidiary, until July 2015. He is currently employed by FIECON, which has received funding from F. Hoffmann-La Roche for consulting services. Nathan has received consulting fees from Roche-Genentech and Boehringer Ingelheim. He is also on the speakers' bureau

  3. GSC3658-0076: A Binary System at the Beginning of Mass Transfer

    NASA Astrophysics Data System (ADS)

    Zhu, L.-Y.; Qian, S.-B.; Xiang, F.-Y.; González-Rojas, D. J.

    2005-10-01

    Photometric data of the new discovered binary GSC3658-0076 observed by [González-Rojas et al.: 2003, IBVS, No. 5437.] were analyzed using the latest Wilson-Devinney code. The system turns out to be a detached binary system with the primary component almost filling its Roche lobe, while the secondary one is detached from the critical Roche lobe. According to the mass-radius relation of unevolved (ZAMS) detached binaries given by [Demircan and Kahraman: 1991, Ap&SS 181, 313.], the primary component is more evolved. These properties reveal that GSC3658-0076 may be at the beginning of the mass transfer phase and may evolve from the present detached system into a contact binary or be in the broken-contact phase predicted by TRO theory.

  4. SATELLITE FORMATION from ancient massive rings

    NASA Astrophysics Data System (ADS)

    Crida, Aurélien; Charnoz, Sébastien

    2013-07-01

    When a planetary tidal disk - like Saturn's rings - spreads beyond the Roche radius (inside which planetary tides prevent aggregation), satellites form and migrate away. Here, we show that most regular satellites in the solar system probably formed in this way. According to our analytical model, when the spreading is slow, a retinue of satellites appear with masses increasing with distance to the Roche radius, in excellent agreement with Saturn's, Uranus', and Neptune's satellite systems. This suggests that Uranus and Neptune used to have massive rings that disappeared to give birth to most of their regular satellites. In contrast, when the spreading is fast, only one large satellite forms, as was the case for Pluto and Earth. This conceptually bridges the gap between terrestrial and giant planet systems. (Ref: Crida & Charnoz 2012, Science, 338, 1196-1199)

  5. Formation of Regular Satellites from Ancient Massive Rings in the Solar System

    NASA Astrophysics Data System (ADS)

    Crida, A.; Charnoz, S.

    2012-11-01

    When a planetary tidal disk—like Saturn’s rings—spreads beyond the Roche radius (inside which planetary tides prevent aggregation), satellites form and migrate away. Here, we show that most regular satellites in the solar system probably formed in this way. According to our analytical model, when the spreading is slow, a retinue of satellites appear with masses increasing with distance to the Roche radius, in excellent agreement with Saturn’s, Uranus’, and Neptune’s satellite systems. This suggests that Uranus and Neptune used to have massive rings that disappeared to give birth to most of their regular satellites. When the spreading is fast, only one large satellite forms, as was the case for Pluto and Earth. This conceptually bridges the gap between terrestrial and giant planet systems.

  6. Biosimilars lining up to compete with Herceptin--opportunity knocks.

    PubMed

    Nelson, Kevin M; Gallagher, Patrick C

    2014-11-01

    Trastuzumab is a monoclonal antibody developed by Genentech as a treatment for breast cancer and gastric cancer when the cancer cells overexpress HER2, a membrane-bound receptor activated by epidermal growth factor. Now marketed by Roche under the trade name Herceptin, trastuzumab has been readily adopted as treatment for some of the most invasive types of breast cancer. The cost for Herceptin is over $50,000 for a full course of treatment. With the development of regulatory pathways for biosimilar products, and the imminent expiry of patents covering Herceptin, several companies have developed biosimilar trastuzumab products. As biosimilar manufacturers look for opportunities to market biosimilar trastuzumab products, Roche has positioned itself to protect its market by developing additional anti-HER2 products complementary to Herceptin. The advent of competition from biosimilars should bring some opportunity for cost savings for patients, as well as incentive for continued advancement in development of better treatments to fight breast cancer.

  7. VizieR Online Data Catalog: Simulations of hot gas planets atmospheres (Salz+, 2016)

    NASA Astrophysics Data System (ADS)

    Salz, M.; Czesla, S.; Schneider, P. C.; Schmitt, J. H. M. M.

    2015-11-01

    The following tables contain the simulation results from the publication. Each table contains a 1D spherically symmetric, hydrodynamically escaping thermosphere of a hot gas planet. The atmospheres contain hydrogen and helium, and no molecules. The simulations were performed with the PLUTO-CLOUDY interface (Salz et al., Cat. J/A+A/576/A21). Each table contains a header, which specifies the system parameters, that where used for the simulations. The simulation region extends to 12/15 planetary radii, but the atmospheres are only approximately valid up to the Roche-lobe height, above which the spherical approximation is invalid. The Roche-lobe height is also given in the header. In the cases of WASP-10 b and WASP-8 b the atmospheres are hydrodynamically stable and the atmospheres extend only up to the exobase defined for proton-proton scattering as given in the publication. (17 data files).

  8. Identification of novel viruses using VirusHunter--an automated data analysis pipeline.

    PubMed

    Zhao, Guoyan; Krishnamurthy, Siddharth; Cai, Zhengqiu; Popov, Vsevolod L; Travassos da Rosa, Amelia P; Guzman, Hilda; Cao, Song; Virgin, Herbert W; Tesh, Robert B; Wang, David

    2013-01-01

    Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens.

  9. Ellipsoidal figures of equilibrium - Compressible models. [for self-gravitating Newtonian fluids in rotating polytropes

    NASA Technical Reports Server (NTRS)

    Lai, Dong; Rasio, Frederic A.; Shapiro, Stuart L.

    1993-01-01

    The results of Chandrasekhar (1969) are generalized to polytropes, using a formalism based on ellipsoidal energy variational principle to construct approximate stellar equilibrium solutions and study their stability. After reviewing the energy variational method and describing the approach, several equivalent stability conditions are established and secular vs. dynamical instabilities are discussed. Then, the equilibrium structure equations are derived for isolated, rotating polytropes, and axisymmetric configurations (compressible Maclaurin spheroids) are considered. Particular attention is given to triaxial configurations, either in a state of uniform rotation (generalizing the classical Jacobi ellipsoids) or with internal fluid motions of uniform vorticity (the compressible analogues of Riemann-S ellipsoids) and to the stability of these single star configurations. The compressible generalizations of the Roche and Roche-Riemann problems for a polytrope in orbit about a point-mass companion are solved, and the generalized Darwin problem for two identical polytropes in a binary is considered.

  10. A PIONIER and Incisive Look at the Interacting Binary SS Lep

    NASA Astrophysics Data System (ADS)

    Blind, N.; Boffin, H. M. J.; Berger, J.-P.; Lebouquin, J.-B.; Mérand, A.

    2011-09-01

    Symbiotic stars are excellent laboratories to study a broad range of poorly understood physical processes, such as mass loss of red giants, accretion onto compact objects, and evolution of nova-like outbursts. As their evolution is strongly influenced by the mass transfer episodes, understanding the history of these systems requires foremost to determine which process is at play: Roche lobe overflow, stellar wind accretion, or some more complex mixture of both. We report here an interferometric study of the symbiotic system SS Leporis, performed with the unique PIONIER instrument. By determining the binary orbit and revisiting the parameters of the two stars, we show that the giant does not fill its Roche lobe, and that the mass transfer most likely occurs via the accretion of an important part of the giant's wind.

  11. Further considerations on contracting solar nebula

    NASA Astrophysics Data System (ADS)

    Rawal, J. J.

    1986-01-01

    Kepler's third law of the planetary system is analyzed in terms of Prentice's (1978a) modern Laplacian theory and Rawal's (1984) Roche limit concept. Prentice has determined, based on laws of conservation of mass and angular momentum and the concept of supersonic turbulent convection, that the ratio of orbital radii of successively disposed gaseous rings is a constant of approximately 1.69. Rawal studied the relationship between the supersonic turbulent convection concept and Roche limit and established a limit of 1.442. It is concluded that Kepler's law determines the rotation period of the sun at the time of its formation at the present radius to be equal to 0.1216 d. The correlation between orbital periods of the radii and resonant structure is investigated.

  12. Contraction of the solar nebula

    NASA Astrophysics Data System (ADS)

    Rawal, J. J.

    1984-10-01

    The concept of Roche limit is applied to the Laplacian theory of the origin of the solar system to study the contraction of a spherical gas cloud (solar nebula). In the process of contraction of the solar nebula, it is assumed that the phenomenon of supersonic turbulent convection described by Prentice (1978) is operative. It is found that the radius of the contracting solar nebula follows Titius-Bode law Rp = R_sun; ap, where R_sun; is the radius of the present Sun and a = 1.442. The consequences of the relation are also discussed. The aim, here, is an attempt to explain, on the basis of the concept of Roche limit, the distribution of planets in the solar system and try to understand the physics underlying it.

  13. Haemolysis in neonatal blood samples: a survey of practice.

    PubMed

    Joshi, S; Vaitkute, R; Jeffery, J; Ayling, R M

    2007-03-01

    To survey how laboratories report, and neonatologists perceive them to report, the presence of haemolysis in neonatal blood samples. A questionnaire was sent to clinical biochemists and neonatologists in 88 hospitals believed to be using Roche methodology. A 49% response rate was obtained. Seventeen hospitals were excluded from analysis owing to incomplete questionnaires or altered methodology. Of the remaining 71 hospitals, 30 (42%) laboratories and 18 (25%) neonatologists responded - where both responded, none gave identical replies. Eighteen laboratories admitted the use of serum indices to make decisions on haemolysed samples. Although recommended interference limits are available from Roche, there was little consensus between laboratories. Laboratories should have clear guidelines on the processing of haemolysed samples from neonates and these should be adequately communicated to those responsible for their direct care.

  14. Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline

    PubMed Central

    Zhao, Guoyan; Krishnamurthy, Siddharth; Cai, Zhengqiu; Popov, Vsevolod L.; Travassos da Rosa, Amelia P.; Guzman, Hilda; Cao, Song; Virgin, Herbert W.; Tesh, Robert B.; Wang, David

    2013-01-01

    Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens. PMID:24167629

  15. Aspects of computer vision in surgical endoscopy

    NASA Astrophysics Data System (ADS)

    Rodin, Vincent; Ayache, Alain; Berreni, N.

    1993-09-01

    This work is related to a project of medical robotics applied to surgical endoscopy, led in collaboration with Doctor Berreni from the Saint Roch nursing-home in Perpignan, France). After taking what Doctor Berreni advises, two aspects of endoscopic color image processing have been brought out: (1) The help to the diagnosis by the automatic detection of the sick areas after a learning phase. (2) The 3D reconstruction of the analyzed cavity by using a zoom.

  16. Innovative Microsystems: Novel Nanostructures to Capture Circulating Breast Cancer Cells

    DTIC Science & Technology

    2009-05-01

    cells are already captured around the inlet location prior to entering the microchannel. Downstream of the inlet, the number of captured cells...was linearized and transfected into MDA- MB-231 cells (ATCC) using Fugene6 (Roche). Following selec- tion with Neomycin (Invitrogen) at 800 mg ml1...13,14]. A plasmid was transfected into MDA-MB-231 cells and selected with neomycin . N– cadherin positive clones (Ncdh+MDA-MB-231) are characterized

  17. Bibliography of Battle Fatigue Literature

    DTIC Science & Technology

    1986-01-16

    Traumatic Stress Disorder (PTSD) as a diagnostic category in the Diagnostic and Statistical Manual of Mental Disorders (DSM-III). This bibliography of battle...Roche Medical Image & Commentary, 12, 27-29. American Psychiatric Association. 1980). Diagnostic and statistical manual of mental disorders (3rd ed...P., & Gerardi, R. J. (1982). A psychophysiological study of post traumatic stress disorder in Vietnam veterans. Psychiatric Quarterly, 54(4), 220-229

  18. Multidimensional Time Dependent Structure and Mechanisms for Non-LTE CO2 Infrared Emissions and 4.3 Micrometers Aurora.

    DTIC Science & Technology

    1979-08-31

    over the previous conceptual design which is given in the 1975 Kumer and Roche technical brief in that the detector and all of the optics including the...surveillance systems to perform a variety of missions are currently under consideration. An important consideration of the design of such a system is the...signal/noise of approximately 30 in the spatial wing region of the nominal arc. The optimum design NBFTR uses liquid Nitrogen (LN2 ) cooled optics

  19. The Role of BRCA1 Domains and Motifs in Tumor Suppression

    DTIC Science & Technology

    2011-08-01

    media was supplemented with penicillin and streptomycin. Transfections were performed using Fugene 6 (Roche) according to the manufacturer’s... hypersensitive to ionizing radiation (IR) and develop *Correspondence to: Alvaro N.A. Monteiro; H. Lee Moffitt Cancer Center; 12902 Magnolia Drive; Tampa, FL...media supplemented with 7.5% FBS, 100 units/mL penicillin /streptomycin and 1.25 μg/ mL amphotericin B (Sigma, St. Louis MO). HCT116 wild-type and Chk2

  20. Boston, Galveston, Jackson County, Jefferson County, New York City, Portland--new saquinavir trial.

    PubMed

    1995-09-29

    A 90-patient trial comparing different doses of saquinavir, Hoffmann-LaRoche's new protease inhibitor, is enrolling patients in Boston, Galveston, Jackson County MO, Jefferson County AL, New York City, and Portland OR. Subjects, who will be randomized to one of four dose levels, must be eighteen or older, have a CD4 count between 100 and 500, have a viral load of more than 20,000 copies, and not have been previously treated with a protease inhibitor.

  1. Evidence for Two Hot-Jupiter Formation Paths

    NASA Astrophysics Data System (ADS)

    Nelson, Benjamin E.; Ford, Eric B.; Rasio, Frederic A.

    2017-09-01

    Disk migration and high-eccentricity migration are two well-studied theories to explain the formation of hot Jupiters. The former predicts that these planets can migrate up until the planet-star Roche separation ({a}{Roche}) and the latter predicts they will tidally circularize at a minimum distance of 2 {a}{Roche}. Considering long-running radial velocity and transit surveys have identified a couple hundred hot Jupiters to date, we can revisit the classic question of hot-Jupiter formation in a data-driven manner. We approach this problem using data from several exoplanet surveys (radial velocity, Kepler, HAT, and WASP) allowing for either a single population or a mixture of populations associated with these formation channels, and applying a hierarchical Bayesian mixture model of truncated power laws of the form {x}γ -1 to constrain the population-level parameters of interest (e.g., location of inner edges, γ, mixture fractions). Within the limitations of our chosen models, we find that the current radial velocity and Kepler sample of hot Jupiters can be well explained with a single truncated power-law distribution with a lower cutoff near 2 {a}{Roche}, a result that still holds after a decade, and γ =-0.51{+/- }0.200.19. However, the HAT and WASP data show evidence for multiple populations (Bayes factor ≈ {10}21). We find that 15{+/- }69 % reside in a component consistent with disk migration (γ =-0.04{+/- }1.270.53) and 85{+/- }96 % in one consistent with high-eccentricity migration (γ =-1.38{+/- }0.470.32). We find no immediately strong connections with some observed host star properties and speculate on how future exoplanet surveys could improve upon hot-Jupiter population inference.

  2. MOVPE Growth of LWIR AlInAs/GaInAs/InP Quantum Cascade Lasers: Impact of Growth and Material Quality on Laser Performance

    DTIC Science & Technology

    2017-02-01

    Bulaev, I. V. Budkin, and I. D. Zalevsky, "Investigation of indium segregation in InGaAs/(Al)GaAs quantum wells grown by MOCVD ," Journal of Crystal...Roch, C. Pflügl, A. M. Andrews, W. Schrenk, and G. Strasser, "X-ray investigation of quantum well intermixing after postgrowth rapid thermal processing...conduction band of a coupled quantum - well structure. These structures are designed using band structure engineering to optimize optical transitions and

  3. Acoustic Metadata Management and Transparent Access to Networked Oceanographic Data Sets

    DTIC Science & Technology

    2015-09-30

    call abundance in Southern California," Endang . Species Res. 28, 61-75. [published] Roch, M. A., Batchelor, H., Baumann-Pickering, S., Berchock, C...context. One might need to know what kind of call was made by which species , where and when it was made, what effort was made in making, detecting...and Time Species Call Detection Date and Time Species Call DetectionsInstrumentDeployment Location or Trackline Recording parameters Effort Species

  4. Annual Historical Report - AMEDD Activities, Calendar Year 1987

    DTIC Science & Technology

    1987-01-01

    loaded breathing during submaximal exercise. Fed. Proc. 46:501, 1987. Neufer , P.D., A.J. Young, M.N. Sawka and J. Buchbinder. Influence of skeletal...P.D. Neufer , J. Bogart and K.B. Pandolf. Muscle metabolism during prolonged shivering. Med. Sci. Sports Exerc. 19:S8, 1987. PRESENTATIONS: Gonzalez...Hodgess, E. Roche, M. Rose, E. Askew, A. Young, D. Neufer . Manipulation of muscle glycogen concentrations using high and low carbohydrate diets and

  5. Thermoregulation during Cold Water Immersion is Unimpaired by Low Muscle Glycogen Levels

    DTIC Science & Technology

    1989-01-01

    DARRELL NEUFER , 3 H STEPHEN R. MUZA, ELDON W. ASKEW, AND KENT B. PANDOLF US Army Research Institute of Environmental Medicine, Natick, Massacausetts...01760-5007 YOUNG, ANDREW J., MICHAEL N. SAWKA, P. DARRELL energy substrates. Although the principal substrate has NEUFER , STEPHEN R. MUZA, ELDON W...T. ROCHE, M. compared with moderate-intensity exercise. Vo 2 during S. ROSE, E. W. ASKEW, A. J. YOUNG, AND P. D. NEUFER . Manip- ulation of Muscle

  6. Targeted Upregulation of FMRP Expression as an Approach to the Treatment of Fragile X Syndrome

    DTIC Science & Technology

    2016-10-01

    secondary screens initially tended to bear out the initial observations, we noted more recently that the degree of induction – measured by parallel...Western blot of the primary hit compounds – did not manifest the same degree of induction . This result, which resulted in some primary hits being...HRSA, Pharmaceutical companies (Neuren, Curemark, Novartis, Hoffman-LaRoche) Name: Glenda Espinal Project Role: Staff research assistant Researcher

  7. Complete genome sequence of Clostridium pasteurianum NRRL B-598, a non-type strain producing butanol.

    PubMed

    Sedlar, Karel; Kolek, Jan; Skutkova, Helena; Branska, Barbora; Provaznik, Ivo; Patakova, Petra

    2015-11-20

    The strain Clostridium pasteurianum NRRL B-598 is non-type, oxygen tolerant, spore-forming, mesophilic and heterofermentative strain with high hydrogen production and ability of acetone-butanol fermentation (ethanol production being negligible). Here, we present the annotated complete genome sequence of this bacterium, replacing the previous draft genome assembly. The genome consisting of a single circular 6,186,879 bp chromosome with no plasmid was determined using PacBio RSII and Roche 454 sequencing.

  8. Prevention of Trauma/Hemorrhagic Shock-Induced Mortality, Apoptosis, Inflammation and Mitochondrial Dysfunction Using IL-6 as a Resuscitation Adjuvant

    DTIC Science & Technology

    2011-12-01

    cryotome into 5-micron sections and resuspended in cell lysis buffer for pStat3 detection (Cell Death Detection ELISAplus Kit , Roche Diagnostics , Manheim...adjuvant. They have developed a panel of sensitive urine analyte assays to test for kidney injury, which they wanted to use to establish if kidney...lung and liver injury in rat T/HS? 2) What is the most sensitive and robust urine test to monitor for kidney injury in this setting? 3) Can IL-6

  9. Approaching Resistance to Targeted Inhibition of PI3K in Breast Cancer

    DTIC Science & Technology

    2011-10-01

    to numerous ligands including insulin (InsR), EGF (EGFR), and PDGF (PDGFR) (Roche et al. 1998; Hooshmand-Rad et al. 2000; Park et al. 2003). Notably...2000; Park et al. 2003). Several possible explanations present themselves for this apparent paradox, perhaps the simplest being that in the absence of...HER2-amplification) in combination with PI3K-mutation could lead to oncogene-dependence (tumor cell- addiction ) whereby pharmacological inhibition would

  10. Strategic Attack: Defined and Refined

    DTIC Science & Technology

    2002-12-01

    writer, Edmund H. North, screenwriter, and Franklin J. Schaffner . General George S. Patton Jr. (George C. Scott), in Patton (film), opening speech in...24, and JP 3-0, Doctrine for Joint Operations, 10 September 2001, I-3 3 Panel consisted of SECAF James Roche, CSAF Gen John Jumper and four star...the Nuclear Age, Princeton, New Jersey: Princeton University Press, 1986. Paul, James and Spirit, Martin. “The Inchon Invasion” 2002, on-line

  11. Strategy, Requirements, and Forces The Rising Imperative of Air and Space Power

    DTIC Science & Technology

    2003-02-01

    Operations,” Inside the Air Force, Nov. 1, 2002. 195 Donald Rumsfeld and Paul Wolfowitz , Pentagon news briefing, May 8, 2002. 196James G. Roche, Defense...Air Force Magazine, February 2002. 208 Lt. Gen. Charles Wald , USAF Deputy Chief of Staff for Air & Space Operations, interview with John Tirpak...2002. _______ and Deputy Secretary of Defense Paul Wolfowitz , Pentagon news briefing, May 8, 2002. RYAN, Gen. Michael E., Statement to the Senate Armed

  12. Therapeutic Evaluation of Mesenchymal Stem Cells in Chronic Gut Inflammation

    DTIC Science & Technology

    2014-09-01

    disease; ulcerative colitis) are chronic inflammatory disorders of the small bowel and/or colon that affects approximately 1.5 million people in the US...Affairs database from 1975-2006 reports that although rates of hospitalization for ulcerative colitis (UC) and Crohn’s disease (CD) have begun to...using standard protocols and 16S rRNA sequencing was performed using the Roche 454 platform. For some studies, mice were colonized (via gastric gavage

  13. Advanced Methods for Passive Acoustic Detection, Classification, and Localization of Marine Mammals

    DTIC Science & Technology

    2013-09-30

    whistles (Kershenbaum and Roch, submitted). By looking at a spectrogram as a topological map , it is possible to examine the direction in gradient vectors...shows one of these kernels and its corresponding feature map (Fig. 3(d)), which is the result of cross- correlating it with the normalized...using relative amplitude. Baleen whale call detection Figure 5 shows the Islands of Kauai and Niihau, approximate locations of 41 of the 47

  14. Hair Follicle Bulb as a Biodosimeter for Low-Level VX Vapor Exposure: Initial Studies Validating the Presence of Potential Protein Biomarkers of Exposure in the Sprague-Dawley Rat Whisker Follicle

    DTIC Science & Technology

    2006-10-01

    were dialyzed against 0.2 M Tris- HC1, pH 8.0 containing Complete Protease Inhibitor Cocktail tablets (Roche, Indianapolis, IN) at room temperature for 4...Dependent Expression of Hepatocyte-Growth Factor (HGF) Activator, Other Proteinases, AND Proteinase Inhibitors Correlates with the Expression of HGF in Rat...Premelanosomal Antigens but Not a Melanosomal Antigen or the Melanosome- Associated Glycoproteins Tyrosinase , TRP-1, and TRP-2. The Journal of

  15. Clinical implications for biochemical diagnostic thresholds of adrenal sufficiency using a highly specific cortisol immunoassay.

    PubMed

    Kline, G A; Buse, J; Krause, R D

    2017-06-01

    Recent guidelines recommend a diagnosis of adrenal insufficiency when a stimulated peak cortisol level falls below 500nmol/L. This may not be valid using a highly specific cortisol immunoassay or liquid chromatography-mass spectroscopy (LCMS/MS). We sought to determine the diagnostic threshold for adrenal insufficiency using a new and widely available, highly specific cortisol immunoassay. All patients having a dynamic test of adrenal reserve had results measured using the historical cortisol assay (Roche Cortisol) and the newer assay (Roche Cortisol II). Subjects were categorized according to the traditional assay (normal>500nmol/L) with clinical case adjudication where necessary. Results from Cortisol II assay were concomitantly measured along with cortisol levels measured by LCMS/MS. ROC curve analysis was performed to generate new diagnostic thresholds. The Roche Cortisol II compared favourably with measures by LCMS/MS, generating cortisol levels approximately 30% lower than the older immunoassay. Many normal subjects had peak cortisols as low as 300nmol/L with Cortisol II. The optimized diagnostic threshold for adrenal insufficiency was 350nmol/L with a sensitivity of 91% and specificity 97%. Use of the old diagnostic threshold with the Cortisol II assay would have inappropriately doubled the rate of patient-classification as adrenal insufficient. Transition to a more specific cortisol assay requires revision of diagnostic thresholds for dynamic tests of adrenal insufficiency. With the Roche Cortisol II assay, a cut-off of 350nmol/L should replace the traditional 500nmol/L although some healthy subjects may be very close to this level. Copyright © 2017 The Canadian Society of Clinical Chemists. All rights reserved.

  16. Evaluating of the Anticonvulsant Gabapentin against Nerve Agent-Induced Seizures in a Guinea Pig Model

    DTIC Science & Technology

    2010-07-01

    from Cutter Labs, Inc. (Berkeley, CA). Pyridostigmine bromide was obtained from Hoffmann- La Roche, Inc. (Nutley, NJ), and pyridine-2-aldoxime... Pyridostigmine bromide was prepared in sterile water to a concentration of 0.052 mg/ml. Atropine sulfate (4 mg/ml) and 2-PAM (50 mg/ml) were prepared in...activity. After a week recovery, animals were pretreated with pyridostigmine 30 min prior to subcutaneous soman challenge (56 ug/kg; 2 X LD50

  17. SS433 Trek 2: light curve analysis.

    NASA Astrophysics Data System (ADS)

    Fukue, J.; Obana, Y.; Okugami, M.

    The authors have calculated theoretical light curves of SS433 during eclipse and precession, using a model in which SS433 consists of a geometrically thick torus around a compact star and a companion star filling the Roche lobe. The favorite combination is that the mass ratio is about 2 (a compact star is a black hole) and the surface temperature of the companion is around 17000K.

  18. Geldanamycin Prevents Hemorrhage-Induced ATP Loss by Overexpressing Inducible HSP70 and Activating Pyruvate Dehydrogenase

    DTIC Science & Technology

    2006-03-24

    levels were determined using the ATP Bioluminescence Assay Kit HS II (Roche; Mannheim, Germany). Luminescence was measured with a TD-20/20...Geldanamycin prevents hemorrhage-induced ATP loss by overexpressing inducible HSP70 and activating pyruvate dehydrogenase Juliann G. Kiang,1,2,3...Geldanamycin prevents hemorrhage-induced ATP loss by overexpressing inducible HSP70 and activating pyruvate dehy- drogenase. Am J Physiol Gastrointest

  19. Discordance with 3 Cardiac Troponin I and T Assays: Implications for the 99th Percentile Cutoff.

    PubMed

    Ungerer, Jacobus Petrus Johannes; Tate, Jillian Russyll; Pretorius, Carel Jacobus

    2016-08-01

    We compared the 99th percentile reference intervals with 3 modern cardiac troponin assays in a single cohort and tested the hypothesis that the same individuals will be identified as above the cutoff and that differences will be explained by analytical imprecision. Blood was collected from 2005 apparently healthy blood donors. Cardiac troponin was measured with Abbott Architect STAT high sensitive troponin I, Beckman Coulter Access AccuTnI+3, and Roche Elecsys troponin T highly sensitive assays. The 99th percentile cutoff limits were as follows: Abbott cardiac troponin I (cTnI) 28.9 ng/L; Beckman Coulter cTnI 31.3 ng/L; and Roche cardiac troponin T (cTnT) 15.9 ng/L. Correlation among the assays was poor: Abbott cTnI vs Beckman Coulter cTnI, R(2) = 0.18; Abbott cTnI vs Roche cTnT, R(2) = 0.04; and Beckman Coulter cTnI vs Roche cTnT R(2) = 0.01. Of the results above the cutoff 50% to 70% were unique to individual assays, with only 4 out of 20 individuals above the cutoff for all 3 assays. The observed differences among assays were larger than predicted from analytical imprecision. The 99th percentile cutoff values were in agreement with those reported elsewhere. The poor correlation and concordance amongst the assays were notable. The differences found could not be explained by analytical imprecision and indicate the presence of inaccuracy (bias) that is unique to sample and assay combinations. Based on these findings we recommend less emphasis on the cutoff value and greater emphasis on δ values in the diagnosis of myocardial infarction. © 2016 American Association for Clinical Chemistry.

  20. Next generation sequence analysis of the transcriptome of Sydney rock oysters (Saccostrea glomerata) exposed to a range of environmental stressors.

    PubMed

    Hook, Sharon E; Johnston, Emma L; Nair, Sham; Roach, Anthony C; Moncuquet, Philippe; Twine, Natalie A; Raftos, David A

    2014-12-01

    Sydney rock oysters (Saccostrea glomerata) were exposed to environmental stressors at contaminated field sites or in a controlled laboratory setting. RNA seq transcriptome data were generated for the gill and digestive gland using Roche's 454 pyrosequencing technology. 28,685 contigs were de novo assembled which encoded 11,671 different protein products. The data will act as a reference for future studies in ecology, immunology and environmental toxicology.

  1. Erlotinib hydrochloride.

    PubMed

    Minna, John D; Dowell, Jonathan

    2005-05-01

    Erlotinib hydrochloride (Tarceva; OSI Pharmaceuticals/Genentech/Roche), a member of a class of targeted anticancer drugs that inhibit the activity of the epidermal growth factor receptor, was approved by the US FDA in November 2004 for the treatment of advanced non-small-cell lung cancer after failure of at least one prior chemotherapy regimen. It is the first such drug to demonstrate an increase in survival in Phase III trials in patients with advanced non-small-cell lung cancer.

  2. Routine screening of blood donations at Qingdao central blood bank, China, for hepatitis B virus (HBV) DNA with a real-time, multiplex nucleic acid test for HBV, hepatitis C virus, and human immunodeficiency virus Types 1 and 2.

    PubMed

    Yang, Zhongsi; Xu, Lei; Liu, Li; Feng, Qiuxia; Zhang, Longmu; Ma, Weijuan; Saldanha, John; Wang, Mingmin; Zhao, Lin

    2013-10-01

    The Roche cobas TaqScreen MPX test was used to evaluate the rate of hepatitis B surface antigen (HBsAg)-negative donations that were hepatitis B virus (HBV) DNA reactive from June 2010 to January 2011 in Qingdao, China. HBsAg-negative samples from 65,800 voluntary blood donors were tested with the cobas TaqScreen MPX test in pools of 6 on the Roche cobas s 201 blood screening platform. Samples positive for HBV DNA and negative for HBsAg were quantitated with the Roche COBAS AmpliPrep/COBAS TaqMan HBV test. In addition, serologic tests for HBsAg, hepatitis B surface antibody, anti-hepatitis B core antigen (anti-HBc), anti-hepatitis B e antigen (anti-HBe), and hepatitis B e antigen (HBe) were done using the Roche electrochemiluminescence immunoassay. A total of 80 nucleic acid amplification technology (NAT) test-reactive pools were identified and 59 pools (74%) resolved to a reactive sample. All samples were HBV DNA reactive and the viral load in each sample was quantitated. The viral loads of the samples ranged from less than 20 to 34,600 IU/mL; 13 samples (22%) had viral loads of more than 20 IU/mL, 27 samples (45.8%) had viral loads of less than 20 IU/mL, and 19 samples (32.2%) had undetectable viral loads. Of the 59 NAT-reactive samples, 40 (67.8%) were anti-HBc positive. Fifteen of the 59 samples could not be confirmed as NAT reactive either by an alternative NAT test or by serology. The HBV NAT yield in blood donors in Qingdao is 0.06% (38/65,800). This study confirmed the value of NAT for interdicting HBV-positive donations and preventing transfusion-transmitted HBV infections. © 2013 American Association of Blood Banks.

  3. Influence of the immunoassay used in measurement of serum vitamin D levels.

    PubMed

    Górriz Pintado, Silvia; Estela Burriel, Pedro Luis

    2014-03-01

    Serum 25-hydroxyvitamin D [25(OH)D] levels are the best indicator of vitamin D levels in the body. Precision, reproducibility, and lack of standardization are the main problems in such measurements. The aim of this study was to compare the 25(OH)D levels measured using Elecsys Vitamin D Total (Roche) and ADVIA Centaur Vitamin D Total (Siemens). 25(OH)D levels were tested in 166 patients using both methods. Patients were subsequently divided into two groups: a «supplemented group» consisting of patients receiving vitamin D supplements, and an «untreated group» consisting of the rest of patients. 25(OH)D mean levels measured by the Roche and Siemens methods in the overall group were 33.6±16.0 and 19.8±12.4 ng/mL respectively. 54.2% of patients were receiving vitamin D supplements. In this group, mean 25(OH)D levels measured by the Roche and Siemens methods were 40.6±14.5 and 25.4±13.1 ng/mL respectively. In the untreated group, the respective values were 24.9±13.2 and 12.8±6.6 ng/mL. Prevalence of vitamin D deficiency (serum 25(OH)D levels less than 20 ng/mL) was higher in samples analyzed using the Siemens method (60.2%) as compared to those tested using the Roche method (23.5%). The assays evaluated are not comparable to each other. Laboratory specialists should inform clinicians of the features of the method used for measuring 25(OH)D because this will have a direct impact on interpretation of the results and medical decisions. Copyright © 2013 SEEN. Published by Elsevier Espana. All rights reserved.

  4. DETECTION OF ACCRETION X-RAYS FROM QS Vir: CATACLYSMIC OR A LOT OF HOT AIR?

    SciTech Connect

    Matranga, Marco; Drake, Jeremy J.; Kashyap, Vinay; Steeghs, Danny

    2012-03-10

    An XMM-Newton observation of the nearby 'pre-cataclysmic' short-period (P{sub orb} = 3.62 hr) binary QS Vir (EC 13471-1258) revealed regular narrow X-ray eclipses when the white dwarf passed behind its M2-4 dwarf companion. The X-ray emission provides a clear signature of mass transfer and accretion onto the white dwarf. The low-resolution XMM-Newton EPIC spectra are consistent with a cooling flow model and indicate an accretion rate of M-dot = 1.7 Multiplication-Sign 10{sup -13} M{sub sun} yr{sup -1}. At 48 pc distant, QS Vir is then the second nearest accreting cataclysmic variable known, with one of the lowest accretion rates found to date for a non-magnetic system. To feed this accretion through a wind would require a wind mass-loss rate of M-dot {approx}2 Multiplication-Sign 10{sup -12} M{sub sun} yr{sup -1} if the accretion efficiency is of the order of 10%. Consideration of likely mass-loss rates for M dwarfs suggests this is improbably high and pure wind accretion unlikely. A lack of accretion disk signatures also presents some difficulties for direct Roche lobe overflow. We speculate that QS Vir is on the verge of Roche lobe overflow, and that the observed mass transfer could be supplemented by upward chromospheric flows on the M dwarf, analogous to spicules and mottles on the Sun, that escape the Roche surface to be subsequently swept up into the white dwarf Roche lobe. If so, QS Vir would be in a rare evolutionary phase lasting only a million years. The X-ray luminosity of the M dwarf estimated during primary eclipse is L{sub X} = 3 Multiplication-Sign 10{sup 28} erg s{sup -1}, which is consistent with that of rapidly rotating 'saturated' K and M dwarfs.

  5. Biocatalytic Synthesis of Pikromycin, Methymycin, Neomethymycin, Novamethymycin, and Ketomethymycin

    PubMed Central

    Hansen, Douglas A.; Rath, Christopher M.; Eisman, Eli B.; Narayan, Alison R. H.; Kittendorf, Jeffrey D.; Mortison, Jonathan D.; Yoon°, Yeo Joon; Sherman, David H.

    2013-01-01

    A biocatalytic platform that employs the final two monomodular type I polyketide synthases (PKS) of the pikromycin pathway in vitro followed by direct appendage of D-desosamine and final C-H oxidation(s) in vivo was developed and applied toward the synthesis of a suite of 12-and 14-membered ring macrolide natural products. This methodology delivered both compound classes in thirteen steps (longest linear sequence) from commercially available (R)-Roche ester in >10% overall yields. PMID:23866020

  6. Particle simulation for accretion sheets in narrow double stars

    NASA Astrophysics Data System (ADS)

    Geyer, F.; Herold, H.; Ruder, H.

    1988-11-01

    Development and behavior of accretion sheets in double stars systems are studied by particle simulation calculations. Numerical analysis considers the following parameters in the binary system: primary and secondary components, path period of the system, and mass flow rates. Mass behavior is described by Roche-potential. The particle motion equation in the double star system is solved by the Leap-Frog procedure. Velocity friction simulation is obtained by viscous interaction considerations.

  7. Systemic and Pulmonary Hypertension After Resuscitation with Cell-Free Hemoglobin

    DTIC Science & Technology

    1992-07-01

    according to published standards (24). Inorganic phosphate was measured on a blood chemistry analyzer (Cobas-Fara; Roche Diagnostic Systems, Nutley, NJ...alanine aminotransferase (ALT), and lactate dehydrogenase (LDH) on the blood chemistry analyzer . The final 4 ml of blood was heparinized, centrifuged...milliliter of blood was placed in 2 ml of ice-cold perchioric acid (70% wt/vol), which was used to determine whole blood lactate in the blood chemistry

  8. Saddam Hussein and the Uses of Political Power. An Examination of the Relative Power of the Cult of Personality and the Nationalist Myth

    DTIC Science & Technology

    1990-09-01

    Lieutenant David B. Des Roches ’, ’" r:: U.S. Army Dissertation submitted as partial fulfillment of the requirements for the degree: Master of Arts...military men to rise to undue prominence: the frequent command shuffles and rotations prevented one man from grabbing the spotlight for long, and all of...officer is able to stay in one place long enough to build up a loyal company of fellow conspirators, although granted with a loss of organization

  9. Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.

    PubMed

    Ahmad, Riaz; Parfitt, Dan E; Fass, Joseph; Ogundiwin, Ebenezer; Dhingra, Amit; Gradziel, Thomas M; Lin, Dawei; Joshi, Nikhil A; Martinez-Garcia, Pedro J; Crisosto, Carlos H

    2011-11-22

    The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced using Roche 454 and Illumina/Solexa technologies to obtain long contigs for alignment to the draft 'Lovell' peach sequence as well as sufficient depth of coverage for 'in silico' SNP discovery. The sequences were aligned to the 'Lovell' peach genome released April 01, 2010 by the International Peach Genome Initiative (IPGI). 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle' were sequenced to add SNPs segregating in two breeding populations, Pop DF ('Dr. Davis' × 'F8, 1-42') and Pop DG ('Dr. Davis' × 'Georgia Belle'). Roche 454 sequencing produced 980,000 total reads with 236 Mb sequence for 'Dr. Davis' and 735,000 total reads with 172 Mb sequence for 'F8, 1-42'. 84 bp × 84 bp paired end Illumina/Solexa sequences yielded 25.5, 21.4, 25.5 million sequences for 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle', respectively. BWA/SAMtools were used for alignment of raw reads and SNP detection, with custom PERL scripts for SNP filtering. Velvet's Columbus module was used for sequence assembly. Comparison of aligned and overlapping sequences from both Roche 454 and Illumina/Solexa resulted in the selection of 6654 high quality SNPs for 'Dr. Davis' vs. 'F8, 1-42' and 'Georgia Belle', distributed on eight major peach genome scaffolds as defined from the 'Lovell' assembly. The eight scaffolds contained about 215-225 Mb of peach genomic sequences with one SNP/~ 40,000 bases. All sequences from Roche 454 and Illumina/Solexa have been submitted to NCBI for public use in the Short Read Archive database. SNPs have been deposited in the NCBI SNP database.

  10. Transcriptome analysis of gill tissue of Atlantic cod Gadus morhua L. from the Baltic Sea.

    PubMed

    Małachowicz, Magdalena; Kijewska, Agnieszka; Wenne, Roman

    2015-10-01

    The Atlantic cod (Gadus morhua L.) is one of the most ecologically and economically important marine fish species in the North Atlantic Ocean. Using Roche GS-FLX 454 pyrosequencing technique 962,516 reads, representing 379Mbp of the Baltic cod transcriptome, were obtained. Data was assembled into 14,029 contigs of which 100% displayed homology to the Atlantic cod transcriptome. Despite a high similarity between transcripts, evidence for significant differences between Baltic and Atlantic cod was found.

  11. Studies of an x ray selected sample of cataclysmic variables. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Silber, Andrew D.

    1986-01-01

    Just prior to the thesis research, an all-sky survey in hard x rays with the HEAO-1 satellite and further observations in the optical resulted in a catalog of about 700 x-ray sources with known optical counterparts. This sample includes 43 cataclysmic variables, which are binaries consisting of a detached white-dwarf and a Roche lobe filling companion star. This thesis consists of studies of the x-ray selected sample of catalcysmic variables.

  12. Glider-Based Passive Acoustic Monitoring Techniques in the Southern California Region

    DTIC Science & Technology

    2009-09-30

    Southern California Region John A. Hildebrand Scripps Institution of Oceanography University of California San Diego, La Jolla, CA 92093-0205...6746 email: marie.roch@sdsu.edu Michael B. Porter Heat Light and Sound Research 3366 North Torrey Pines Court, Suite 310, La Jolla, CA 92037...Iridium data communications, allows for real-time notification of marine mammal presence. John Hildebrand and Sean Wiggins are responsible for

  13. Structure Optimization of 21,23-Core-Modified Porphyrins Absorbing Long-Wavelength Light as Potential Photosensitizers Against Breast Cancer Cells

    DTIC Science & Technology

    2007-04-01

    4518. 8. You Y, Gibson SL, Hilf R, Davies SR, Oseroff AR, Roy I, Ohulchanskyy TY, Bergey EJ and Detty MR. J. Med. Chem. 2003; 46: 3734- 3747. 9. You...kit and the details followed the instruc- tional manual (Roche Diagnostics, Cat. No. 11 920 685 001) [14]. Cell numbers were determined with the... Bergey , M.R. Detty, Water soluble, core-modi- fied porphyrins. 3. Synthesis, photophysical properties, and in vitro studies of photosensitization

  14. Bacterial community composition of three candidate insect vectors of palm phytoplasma (Texas Phoenix Palm Decline and Lethal Yellowing).

    PubMed

    Powell, Christopher M; Hail, Daymon; Potocnjak, Julia; Hanson, J Delton; Halbert, Susan H; Bextine, Blake R

    2015-02-01

    Texas Phoenix Palm Decline (TPPD) and Lethal Yellowing are two phytoplasma-linked diseases in palms. The phytoplasma causing TPPD is thought to be transmitted by three putative planthopper vectors, Ormenaria rufifascia, Omolicna joi, and Haplaxius crudus. These insects have been morphologically and molecularly described, and have screened positive for Candidatus Phytoplasma palmae. Individuals from each species were subjected to 16S bacterial community sequencing using the Roche 454 platform, providing new information regarding the previously unexplored bacterial communities present in putative vectors.

  15. Exoplanet recycling in massive white-dwarf debris discs

    NASA Astrophysics Data System (ADS)

    Van Lieshout, Rik

    2017-06-01

    When a star evolves into a white dwarf, the planetary system it hosts can become unstable. Planets in such systems may then be scattered onto star-grazing orbits, leading to their tidal disruption as they pass within the white dwarf’s Roche limit. We study the massive, compact debris discs that may arrise from this process using a combination of analytical estimates and numerical modelling. The discs are gravitationally unstable, resulting in an enhanced effective viscosity due to angular momentum transport associated with self-gravity wakes. For disc masses greater than ~1026 g (corresponding to progenitor objects comparable to the Galilean moons), viscous spreading dominates over Poynting-Robertson drag in the outer parts of the disc. In such massive discs, mass is transported both in- and outwards. When the outward-flowing material spreads beyond the Roche limit, it coagulates into new (minor) planets in a process analogous to the ongoing formation of Saturn’s innermost moonlets. This process recycles a substantial fraction of the original disc mass (tens of percents), with the bulk of the mass locked in a single large body orbitting in a 2:1 mean-motion resonance with the Roche limit. As such, the recycling of a tidally disrupted super-Earth could yield an Earth-mass planet on a 10--20 hr orbit. For white dwarfs with a temperature below 6000-7000 K (corresponding to a cooling age of >1--2 Gyr), this orbit is located in the white dwarf’s habitable zone. The recycling process also creates a string of smaller bodies just outside the Roche limit. These may account for the collection of minor planets postulated to orbit white dwarf WD 1145+017.

  16. Genome Sequence of Rheinheimera salexigens sp. nov. Isolated from a Fishing Hook off O‘ahu, Hawai‘i

    PubMed Central

    Hayashi, Kazukuni; Anderson, James

    2016-01-01

    Rheinheimera salexigens KH87T is an obligately halophilic gammaproteobacterium. The strain’s draft genome sequence, generated by the Roche 454 GS FLX+ platform, comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding sequences and 58 tRNA coding regions. The G+C content is 42 mol%. PMID:27979942

  17. Spectroscopic Transit of Exoplanet WASP-32 b

    NASA Astrophysics Data System (ADS)

    Grauzhanina, A. O.; Gadelshin, D. R.; Baklanova, D. N.; Plachinda, S. I.; Antonyuk, K. A.; Pit, N. V.; Valyavin, G. G.; Galazutdinov, G. A.; Valeev, A. F.; Burlakova, T. E.; Kholtygin, A. F.

    2017-06-01

    Observations of the exoplanet WASP-32 b with the Main Stellar Spectrograph at the 6-m BTA telescope have revealed the presence of a significant change in the intensity and the equivalent width of the Hα spectral line in the spectrum of the parent star of WASP-32 at the time of planet's transit. These observations are discussed in the context of the presence of a hydrogen shell at WASP-32 b filling the Roche lobe of the planet.

  18. Wolf-Rayet stars with relativistic companions

    NASA Astrophysics Data System (ADS)

    Tutukov, A. V.; Fedorova, A. V.; Cherepashchuk, A. M.

    2013-09-01

    The evolution of close binary systems containing Wolf-Rayet (WR) stars and black holes (BHs) is analyzed numerically. Both the stellar wind from the donor star itself and the induced stellar wind due to irradiation of the donor with hard radiation arising during accretion onto the relativistic component are considered. The mass and angular momentum losses due to the stellar wind are also taken into account at phases when the WR star fills its Roche lobe. It is shown that, if a WR star with a mass higher than ˜10 M ⊙ fills its Roche lobe in an initial evolutionary phase, the donor star will eventually lose contact with the Roche lobe as the binary loses mass and angular momentum via the stellar wind, suggesting that the semi-detached binary will become detached. The star will remain a bright X-ray source, since the stellar wind that is captured by the black hole ensures a near-Eddington accretion rate. If the initial mass of the helium donor is below ˜5 M ⊙, the donor may only temporarily detach from its Roche lobe. Induced stellar wind plays a significant role in the evolution of binaries containing helium donors with initial masses of ˜2 M ⊙. We compute the evolution of three observed WR-BH binaries: Cyg X-3, IC 10 X-1, and NGC 300 X-1, as well as the evolution of the SS 433 binary system, which is a progenitor of such systems, under the assumption that this binary will avoid a common-envelope stage in its further evolution, as it does in its current evolutionary phase.

  19. Analysis of HCV genotypes from blood donors shows three new HCV type 6 subgroups exist in Myanmar.

    PubMed

    Shinji, Toshiyuki; Kyaw, Yi Yi; Gokan, Katsunori; Tanaka, Yasuhito; Ochi, Koji; Kusano, Nobuchika; Mizushima, Takaaki; Fujioka, Shin-ichi; Shiraha, Hidenori; Lwin, Aye Aye; Shiratori, Yasushi; Mizokami, Masashi; Khin, Myo; Miyahara, Masayuki; Okada, Shigeru; Koide, Norio

    2004-06-01

    The prevalence of hepatitis C virus (HCV) genotypes in Myanmar in comparison with the rest of Southeast Asia is not well known. Serum samples were obtained from 201 HCV antibody-positive volunteer blood donors in and around the Myanmar city of Yangon. Of these, the antibody titers of 101 samples were checked by serial dilution using HCV antibody PA test II and Terasaki microplate as a low-cost method. To compare antibody titers by this method and RNA identification, we also checked HCV-RNA using the Amplicor 2.0 test. Most high-titer groups were positive for HCV-RNA. Of the 201 samples, 110 were successfully polymerase chain reaction (PCR) amplified. Among them, 35 (31.8%) were of genotype 1, 52 (47.3%) were of genotype 3, and 23 (20.9%) were of type 6 variants, and phylogenetic analysis of these type 6 variants revealed that 3 new type 6 subgroups exist in Myanmar. We named the subgroups M6-1, M6-2, and M6-3. M6-1 and M6-2 were relatively close to types 8 and 9, respectively. M6-3, though only found in one sample, was a brand-new subgroup. These subtypes were not seen in Vietnam, where type 6 group variants are widely spread. These findings may be useful for analyzing how and when these subgroups were formed.

  20. Evaluation of in-house polymerase chain reaction assay sensitivity, can it be utilized in limited-resources settings?

    PubMed

    Dorudinia, Atosa; Shamaei, Masoud; Karimi, Shirin; Javadi, Alireza; Mohammadi Ziazi, Leila; Pourabdollah, Mihan

    2014-01-01

    Polymerase chain reaction (PCR) assay has widely used for the detection of tuberculosis (TB). This study tried to compare in-house PCR with some well-known commercial PCR kits for detection of TB agent. Clinical samples obtained from 620 TB suspected patients were analyzed for the diagnosis of Mycobacterium tuberculosis complex (MTC) by in-house PCR. All samples were obtained through pulmonary specimens consisted of 384 sputum, 148 bronchial aspirates and 88 pleural effusions. Considering culture as a golden criterion, in which its diagnostic sensitivity and specificity of PCR assay were 87.7% and 85.6%, respectively. The findings of this study also indicate 22.1% (137/620) of the specimens were detected as MTC by PCR. Both PCR and culture confirmed presence of MTC in 57 of the samples. In comparison to culture, the diagnostic sensitivity of PCR for sputum was 87.5% (42/48), bronchial aspirates 100% (12/12), and 60% (3/5) for pleural effusions. The sensitivity of in-house PCR method is comparable with the sensitivity of Amplicor and Cobas TaqMan for MTC. The study illustrates the in-house PCR assay for detection of MTC has high sensitivity and specificity versus approved commercial kits. This could be reliable test in the diagnosis of MTC in resource-limited countries.

  1. Prevalence of Mycoplasma genitalium among female students in vocational schools in Japan.

    PubMed

    Hamasuna, R; Imai, H; Tsukino, H; Jensen, J S; Osada, Y

    2008-08-01

    In Japan it was reported that about 9% of sexually active female teenagers had Chlamydia trachomatis. Most of them were asymptomatic, which may lead to continuing spread of the infection. Like C trachomatis, Mycoplasma genitalium is a pathogen in male non-gonococcal urethritis. However, few studies of the prevalence of M genitalium in the general population have been reported. The objective of this study was to determine the prevalence of M genitalium infection among younger females and to determine risk factors for this infection. The study was conducted between October 2005 and January 2006 using first voided urine specimens and questionnaires from female students of three vocational schools in the Miyazaki prefecture, Japan. C trachomatis was detected with Amplicor PCR. M genitalium was detected with inhibitor controlled real-time TaqMan PCR detecting the MgPa adhesion gene and with a PCR detecting the 16S rRNA. Risk factors associated with infection of M genitalium or C trachomatis were analysed with Fisher's exact test. Among 298 female, 249 (84%) had had experience of sexual intercourse. The prevalence of M genitalium was 2.8% (95% CI 0.76% to 4.86%) and the prevalence of C trachomatis was 8.8% (95% CI 5.31% to 12.36%). The risk factors of infection with M genitalium were more than five lifetime sexual partners and co-infection with C trachomatis.

  2. [Prevalence of hepatitis C virus and excessive consumption of alcohol in a nonhospital worker population].

    PubMed

    Prieto Domingo, J J; Carrión Bolaños, J A; Bandrés Moya, F

    1997-12-01

    The aim of the study was to know the prevalence of the hepatitis C virus (HCV) in a non hospital work population by ELISA 3.0 and PCR-Amplicor, as well as its relationship with excessive alcohol intake (more than 280 g/week in men and 168 g/week in women). A transversal seroepidemiologic study was carried out in 1,109 workers of the Empresa Nacional de Electricidad, S.A. (ENDESA). During the annual medical examinations (April 1993-October 1994) the amount of alcoholic beverages each worker had consumed over the 7 days prior to the medical examination was obtained by anamnesis together with a blood sample for different laboratory tests. Sixteen percent of the workers had had excessive alcohol intake. The prevalence of anti HCV antibodies in the study population was 2.4% being up to 4.6% in the workers declaring excessive alcohol consumption and 10.4% if they also presented an elevation in any of the transaminases. The prevalence of the potentially ineffective workers was 1.46%. The prevalence of anti C antibodies by ELISA 3.0 was greater than expected (2.4%) significantly increasing in the population group which declared excessive alcohol intake, thereby demonstrating the relationship between alcohol and hepatitis C.

  3. Frequency and significance of antibodies against hepatitis B core (anti-HBc) antigen as the only serological marker for hepatitis B infection in Lebanese blood donors.

    PubMed

    Ramia, S; Ramlawi, F; Kanaan, M; Klayme, S; Naman, R

    2005-08-01

    During a 2-year period, blood samples from 2505 Lebanese blood donors were chosen at random, at various periods of time at one blood donation centre (Hotel Dieu de France, Beirut, Lebanon) and were screened for markers of HBV infection (HBsAg, anti-HBc and anti-HBs). The study showed HBsAg positivity of 0.6% and an overall exposure rate to HBV of 10.0%. Out of the 2505 blood donors screened, 56 (22%) were found to be 'anti-HBc alone' positive which is almost four times the HBsAg positivity. The 56 'anti-HBc alone' samples were retested by another ELISA kit commercially available and 54 samples were 'anti-HBc alone' positive by both assays. The 54 samples had no serological markers as evidence of infection with human immunodeficiency virus (HIV) or hepatitis C virus (HCV). Only seven (13%) out of the 54 samples were HBV DNA positive by PCR and all were HBV genotype D. All seven HBV DNA-positive samples had HBV DNA levels below 400 copies/ml. Although any circulating HBV DNA among our 'anti-HBc alone' blood donors was below the detection limit of our Amplicor Monitor assay, some of these samples had circulating virus. A national study, where a larger number of blood donors from different blood donation centres across the country will perhaps determine whether screening for anti-HBc in addition to HBsAg detection is needed in Lebanese blood donors.

  4. [Simple and rapid detection of HLA-DRB polymorphism from forensic samples].

    PubMed

    Kimura, T; Nata, M; Hashiyada, M; Funayama, M; Sagisaka, K

    1998-08-01

    Simple and rapid detection of HLA-DRB polymorphism has been performed using AMPLICOR HLA-DRB Typing Kit. We tried to apply this kit to various forensic samples. When DNA was extracted from the forensic samples using conventional phenol-chloroform method, addition of 7.5 mM MgCl2 was required to PCR amplification. HLA-DRB types were detected from DNA more than 0.1 ng by PCR amplification. Typing of unrelated 50 Japanese showed 38 different patterns, of which 30 patterns occurred once in the group. A total of 16 serotypes were deduced from the HLA-DRB DNA types. Out of them, high frequency serotypes were DR4 (24%), DR9 (18%) and DR15/16 (14%). This kit was very useful in forensic cases such as rape and in paternity cases. When we tried to detect HLA-DRB types from a single hair shaft of 3 cm in length, we were successful in detection from only one of five persons.

  5. Occult hepatitis B in HIV-HCV coinfected patients.

    PubMed

    Piroth, Lionel; Lafon, Marie-Edith; Binquet, Christine; Bertillon, Pascale; Gervais, Anne; Lootvoet, Enguerrand; Lang, Jean-Marie; De Jaureguiberry, Jean Pierre; Chene, Geneviève; Leport, Catherine

    2008-01-01

    The prevalence of occult hepatitis B infection in HIV infected patients is controversial, varying from less than 1% to 62% in different studies. Blood samples of 111 HIV-infected patients, HCV-positive, HBs antigen negative, followed in the APROCO-ANRS EP11 cohort, were used to detect HBV DNA by using 2 different validated assays (Cobas Amplicor HBV Monitor Test and INSERM U271 qualitative ultra-sensitive PCR), completed when positive by HBV real-time PCR. HBV DNA was found in 6 (5.4%, 95% CI 1.2%-9.6%) patients by at least 1 of these assays, but none tested positive in all 3 assays. All 6 patients had anti-HBc without anti-HBs antibodies; 5 were not on lamivudine. Their median CD4 and CD8 counts were significantly lower and their HIV viral load higher than in the other 105 patients. In conclusion, the prevalence of occult hepatitis B may vary significantly according to the molecular assay used, even though these assays are validated with high specificity and quite high sensitivity. Occult hepatitis B may be encountered in HIV-HCV coinfected patients without anti-HBV treatment, with anti-HBc but without anti-HBs antibodies, and relatively low immunity, suggesting a potential risk of further reactivation, as already sporadically reported.

  6. Magnitude of virologic blips is associated with a higher risk for virologic rebound in HIV-infected individuals: a recurrent events analysis.

    PubMed

    Grennan, J Troy; Loutfy, Mona R; Su, DeSheng; Harrigan, P Richard; Cooper, Curtis; Klein, Marina; Machouf, Nima; Montaner, Julio S G; Rourke, Sean; Tsoukas, Christos; Hogg, Bob; Raboud, Janet

    2012-04-15

    The importance of human immunodeficiency virus (HIV) blip magnitude on virologic rebound has been raised in clinical guidelines relating to viral load assays. Antiretroviral-naive individuals initiating combination antiretroviral therapy (cART) after 1 January 2000 and achieving virologic suppression were studied. Negative binomial models were used to identify blip correlates. Recurrent event models were used to determine the association between blips and rebound by incorporating multiple periods of virologic suppression per individual. 3550 participants (82% male; median age, 40 years) were included. In a multivariable negative binomial regression model, the Amplicor assay was associated with a lower blip rate than branched DNA (rate ratio, 0.69; P < .01), controlling for age, sex, region, baseline HIV-1 RNA and CD4 count, AIDS-defining illnesses, year of cART initiation, cART type, and HIV-1 RNA testing frequency. In a multivariable recurrent event model controlling for age, sex, intravenous drug use, cART start year, cART type, assay type, and HIV-1 RNA testing frequency, blips of 500-999 copies/mL were associated with virologic rebound (hazard ratio, 2.70; P = .002), whereas blips of 50-499 were not. HIV-1 RNA assay was an important determinant of blip rates and should be considered in clinical guidelines. Blips ≥500 copies/mL were associated with increased rebound risk.

  7. Sensitivity evaluation of the Gen-Probe AMP-CT assay by pooling urine samples for the screening of Chlamydia trachomatis urogenital infection.

    PubMed

    Gomes, J P; Viegas, S; Paulino, A; Catry, M A

    2002-08-01

    The sensitivity of two urine pool sizes versus individual testing, to detect Chlamydia trachomatis urogenital infection, was evaluated using the Gen-Probe AMP-CT assay. Thirty-three (33) known polymerase chain reaction (PCR) positive urine specimens were combined with 231 fresh first-catch urine (FCU) samples in 33 groups of four and 33 groups of eight, to make up 4X and 8X pooled samples, respectively. Gen-Probe AMP-CT assay was performed on pools as well as on individual samples at the same time. For the discrepant cases, the known positive samples were diluted 1:4 and 1:8 using the manufacturer's dilution buffer and were retested. Additional positive specimens found among fresh FCU samples were also tested by the Amplicor-PCR assay to confirm their positivity. The sensitivities of 8X pooling, 4X pooling and individual testing were 86.5%, 94.3% and 91.9%, respectively. The Gen-Probe AMP-CT assay applied to a 4X urine pooling model was highly sensitive and may be useful for a population based screening programme.

  8. Formation of Janus and Epimetheus from Saturn's rings as coorbitals, thanks to Mimas' 2:3 inner Mean Motion Resonances

    NASA Astrophysics Data System (ADS)

    Crida, Aurelien; El Moutamid, Maryame

    2016-10-01

    Janus and Epimetheus orbit Saturn at 151461 km on average, on mutual horseshoe orbits with orbital separation 50 km, exchanging position every 4 years. This configuration is unique and intriguing : Lissauer et al. (1985) have shown that their orbital separation should converge to zero in about 20 Myrs only, and no satisfactory model for the origin of this co-orbital resonance exists yet.Charnoz et al. (2010) have shown that Janus and Epimetheus probably formed from the spreading of the rings beyond the Roche radius. Here, we show that this happened when Mimas' 2:3 Lindblad Resonance, which used to confine the rings, receded past the Roche radius. This first explains the gap in mass and distance between Janus and Mimas, which is unexpected in the pyramidal regime of the ring spreading model (Crida & Charnoz 2012). Furthermore, at this time, the two capture sites of Mimas's 2:3 Corotation Resonance were full of ring material. We suggest that as the two capture sites were brought beyond the Roche radius, the captured material agglomerated into two bodies of ~1015 kg on the exact same orbit. These bodies then migrated outwards together due to their interaction with the rings, in mutual horseshoe orbits. The rings then spawn new small satellites, eventually accreted by the proto-Janus and the proto-Epimetheus. This excites their orbital separation, leading to today's configuration.

  9. The history of benzodiazepines.

    PubMed

    Wick, Jeannette Y

    2013-09-01

    After more than 50 years of experience with benzodiazepines, the American health care system has a love-hate relationship with them. In 1955, Hoffmann-La Roche chemist Leo Sternbach serendipitously identified the first benzodiazepine, chlordiazepoxide (Librium). By 1960, Hoffmann-La Roche marketed it as Librium, and it pursued molecular modifications for enhanced activity. Valium (diazepam) followed in 1963. Hoffmann-La Roche's competitors also began looking for analogues. Initially, benzodiazepines appeared to be less toxic and less likely to cause dependence than older drugs. A specific improvement was their lack of respiratory depression, a safety concern with barbiturates. Medical professionals greeted benzodiazepines enthusiastically at first, skyrocketing their popularity and patient demand. In the mid-to-late 1970s, benzodiazepines topped all "most frequently prescribed" lists. It took 15 years for researchers to associate benzodiazepines and their effect on gamma-aminobutyric acid as a mechanism of action. By the 1980s, clinicians' earlier enthusiasm and propensity to prescribe created a new concern: the specter of abuse and dependence. As information about benzodiazepines, both raising and damning, accumulated, medical leaders and legislators began to take action. The result: individual benzodiazepines and the entire class began to appear on guidelines and in legislation giving guidance on their use. Concurrently, clinicians began to raise concerns about benzodiazepine use by elderly patients, indicating that elders'lesser therapeutic response and heightened sensitivity to side effects demanded prescriber caution. The benzodiazepine story continues to evolve and includes modern-day issues and concerns beyond those ever anticipated.

  10. Mass-loss evolution of close-in exoplanets: Evaporation of hot Jupiters and the effect on population

    SciTech Connect

    Kurokawa, H.; Nakamoto, T.

    2014-03-01

    During their evolution, short-period exoplanets may lose envelope mass through atmospheric escape owing to intense X-ray and extreme ultraviolet (XUV) radiation from their host stars. Roche-lobe overflow induced by orbital evolution or intense atmospheric escape can also contribute to mass loss. To study the effects of mass loss on inner planet populations, we calculate the evolution of hot Jupiters considering mass loss of their envelopes and thermal contraction. Mass loss is assumed to occur through XUV-driven atmospheric escape and the following Roche-lobe overflow. The runaway effect of mass loss results in a dichotomy of populations: hot Jupiters that retain their envelopes and super Earths whose envelopes are completely lost. Evolution primarily depends on the core masses of planets and only slightly on migration history. In hot Jupiters with small cores (≅ 10 Earth masses), runaway atmospheric escape followed by Roche-lobe overflow may create sub-Jupiter deserts, as observed in both mass and radius distributions of planetary populations. Comparing our results with formation scenarios and observed exoplanets populations, we propose that populations of closely orbiting exoplanets are formed by capturing planets at/inside the inner edges of protoplanetary disks and subsequent evaporation of sub-Jupiters.

  11. Heat Redistribution and Misaligned Orbit Models in PHOEBE

    NASA Astrophysics Data System (ADS)

    Horvat, Martin; Prsa, Andrej; Conroy, Kyle E.

    2017-01-01

    Reflection and aligned Roche geometry have been long supported in modeling codes that synthesize light and radial velocity curves of eclipsing binary stars. However, recent advances in observational data, mostly in terms of precision and temporal baseline, demonstrated that the assumptions of these two effects are frequently violated. Reflection treatment neglected the energy absorbed by the irradiated star, and Roche geometry assumed aligned vectors of spin and orbital angular momentum. Observations of night- and day-side brightness variation of cooler stellar and substellar companions point to a clear deficiency in treating heat redistribution, and the break in symmetry of the Rossiter-McLaughlin effect points to misaligned stellar spins w.r.t. orbital plane. The framework of existing codes did not allow for revising these effects while keeping the rest of the logic intact, which prompted a complete rewrite of the modeling code PHOEBE (PHysics Of Eclipsing BinariEs). Here we present the basic considerations and proof-of-concept examples of the revised reflection effect and misaligned spin-orbit support. Reflection has been extended with heat absorption and consequent redistribution, which can be local, longitudinal or global. Misaligned spin-orbit vectors are supported by deriving the equation of the Roche potential that allows misaligned rotational axes and are provided by the corresponding Euler angles. This research is supported by the NSF grant #1517474.

  12. Instability of mass transfer in a planet-star system

    NASA Astrophysics Data System (ADS)

    Jia, Shi; Spruit, H. C.

    2017-02-01

    We show that the angular momentum exchange mechanism governing the evolution of mass-transferring binary stars does not apply to Roche lobe filling planets, because most of the angular momentum of the mass-transferring stream is absorbed by the host star. Apart from a correction for the difference in specific angular momentum of the stream and the centre of mass of the planet, the orbit does not expand much on Roche lobe overflow. We explore the conditions for dynamically unstable Roche lobe overflow as a function of planetary mass and mass and radius (age) of host star and equation of state of planet. For a Sun-like host, gas giant planets in a range of mass and entropy can undergo dynamical mass transfer. Examples of the evolution of the mass transfer process are given. Dynamic mass transfer of rocky planets depends somewhat sensitively on equation of state used. Silicate planets in the range 1 < Mp < 10 M⊕ typically go through a phase of dynamical mass transfer before settling to slow overflow when their mass drops to less than 1 M⊕.

  13. Evaluation of six commercial amphetamine and methamphetamine immunoassays for cross-reactivity to phenylpropanolamine and ephedrine in urine.

    PubMed

    D'Nicuola, J; Jones, R; Levine, B; Smith, M L

    1992-01-01

    We evaluated six commercially available amphetamine (A) and methamphetamine (MA) immunoassays for their relative cross-reactivities to isomers of phenylpropanolamine (PPA) and ephedrine (E) in urine: Syva EMIT, Abbott fluorescence polarization (FPIA), Roche, and Diagnostic Products Corporation (DPC) radioimmunoassays for A and MA. Two stereoisomers of PPA and four stereoisomers of E were tested using (1) drug-free urine spiked at 1,000 mg/L or 100 mg/L of each compound and (2) 60 clinical urine specimens not containing A or MA but having varying amounts of PPA and/or E. Specimens responding greater than the 1-mg/L A or MA cutoff were defined as positive. All specimens spiked at 100 mg/L were negative by all immunoassays. All specimens spiked at 1,000 mg/L were positive by EMIT and negative by FPIA, Roche A, and DPC A; 1,000 mg/L/-E and d-pseudoephedrine were also positive by Roche MA and DPC MA. Three of the 60 clinical specimens tested positive by EMIT and one specimen tested positive by DPC A and DPC MA.

  14. LUT observations of the mass-transferring binary AI Dra

    NASA Astrophysics Data System (ADS)

    Liao, Wenping; Qian, Shengbang; Li, Linjia; Zhou, Xiao; Zhao, Ergang; Liu, Nianping

    2016-06-01

    Complete UV band light curve of the eclipsing binary AI Dra was observed with the Lunar-based Ultraviolet Telescope (LUT) in October 2014. It is very useful to adopt this continuous and uninterrupted light curve to determine physical and orbital parameters of the binary system. Photometric solutions of the spot model are obtained by using the W-D (Wilson and Devinney) method. It is confirmed that AI Dra is a semi-detached binary with secondary component filling its critical Roche lobe, which indicates that a mass transfer from the secondary component to the primary one should happen. Orbital period analysis based on all available eclipse times suggests a secular period increase and two cyclic variations. The secular period increase was interpreted by mass transfer from the secondary component to the primary one at a rate of 4.12 ×10^{-8}M_{⊙}/yr, which is in agreement with the photometric solutions. Two cyclic oscillations were due to light travel-time effect (LTTE) via the presence of two cool stellar companions in a near 2:1 mean-motion resonance. Both photometric solutions and orbital period analysis confirm that AI Dra is a mass-transferring binary, the massive primary is filling 69 % of its critical Roche lobe. After the primary evolves to fill the critical Roche lobe, the mass transfer will be reversed and the binary will evolve into a contact configuration.

  15. Wind-driven angular momentum loss in binary systems. I - Ballistic case

    NASA Technical Reports Server (NTRS)

    Brookshaw, Leigh; Tavani, Marco

    1993-01-01

    We study numerically the average loss of specific angular momentum from binary systems due to mass outflow from one of the two stars for a variety of initial injection geometries and wind velocities. We present results of ballistic calculations in three dimensions for initial mass ratios q of the mass-losing star to primary star in the range q between 10 exp -5 and 10. We consider injection surfaces close to the Roche lobe equipotential surface of the mass-losing star, and also cases with the mass-losing star underfilling its Roche lobe. We obtain that the orbital period is expected to have a negative time derivative for wind-driven secular evolution of binaries with q greater than about 3 and with the mass-losing star near filling its Roche lobe. We also study the effect of the presence of an absorbing surface approximating an accretion disk on the average final value of the specific angular momentum loss. We find that the effect of an accretion disk is to increase the wind-driven angular momentum loss. Our results are relevant for evolutionary models of high-mass binaries and low-mass X-ray binaries.

  16. Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples.

    PubMed

    Mosher, Jennifer J; Bernberg, Erin L; Shevchenko, Olga; Kan, Jinjun; Kaplan, Louis A

    2013-11-01

    Longer sequences of the bacterial 16S rRNA gene could provide greater phylogenetic and taxonomic resolutions and advance knowledge of population dynamics within complex natural communities. We assessed the accuracy of a Pacific Biosciences (PacBio) single molecule, real time (SMRT) sequencing based on DNA polymerization, a promising 3rd generation high-throughput technique, and compared this to the 2nd generation Roche 454 pyrosequencing platform. Amplicons of the 16S rRNA gene from a known isolate, Shewanella oneidensis MR1, and environmental samples from two streambed habitats, rocks and sediments, and a riparian zone soil, were analyzed. On the PacBio we analyzed ~500 bp amplicons that covered the V1-V3 regions and the full 1500 bp amplicons of the V1-V9 regions. On the Roche 454 we analyzed the ~500 bp amplicons. Error rates associated with the isolate were lowest with the Roche 454 method (2%), increased by more than 2-fold for the 500 bp amplicons with the PacBio SMRT chip (4-5%), and by more than 8-fold for the full gene with the PacBio SMRT chip (17-18%). Higher error rates with the PacBio SMRT chip artificially inflated estimates of richness and lowered estimates of coverage for environmental samples. The 3rd generation sequencing technology we evaluated does not provide greater phylogenetic and taxonomic resolutions for studies of microbial ecology. © 2013.

  17. Evaluation of in-house and commercial genotyping assays for molecular typing of hepatitis C virus in Hong Kong.

    PubMed

    Lam, T H J; Cheng, R S; Lai, S T; Tsang, T Y; Cheng, V C C; Ho, S L; Yam, W C

    2010-01-01

    This study aims to evaluate genotyping assays for hepatitis C virus (HCV). An in-house nucleic acid sequencing method is performed in parallel with the Roche Linear Array HCV genotyping test on 73 HCV-positive (66 clinical samples and seven proficiency testing quality control samples) and 12 HCV-negative samples (11 clinical samples and one proficiency testing sample). The performance of the in-house method was comparable with that of the Roche assay (concordance rate: 89.4%). Discordant results included four mixed infections missed by the in-house method, two false-negatives with the Roche assay, and three discrepant results. The in-house method exhibited a higher resolution (subtype vs. genotype level) at a lower running cost (25% of the commercial assay). The in-house method was also used to genotype 375 HCV clinical isolates to determine the genotypic distribution of HCV in Hong Kong between 2005 and 2008. A total of 441 (52.8%) clinical isolates proved to be genotype 1, which shows a poorer response to interferon therapy. Genotype 6 was the next most common (32.0%). Prevalence of genotypes 2 and 3 was 7.7% and 6.6%, respectively, and prevalence of genotypes 4 and 5 was 0.9% and 0%, respectively. Although the in-house nucleic acid sequencing method failed to detect a few cases of mixed HCV infection, its high resolution and low running cost make it suitable for surveillance and outbreak investigation.

  18. Accretion disks around black holes

    NASA Technical Reports Server (NTRS)

    Abramowicz, M. A.

    1994-01-01

    The physics of accretion flow very close to a black hole is dominated by several general relativistic effects. It cannot be described by the standard Shakura Sunyaev model or by its relativistic version developed by Novikov and Thome. The most important of these effects is a dynamical mass loss from the inner edge of the disk (Roche lobe overflow). The relativistic Roche lobe overflow induces a strong advective cooling, which is sufficient to stabilize local, axially symmetric thermal and viscous modes. It also stabilizes the non-axially-symmetric global modes discovered by Papaloizou and Pringle. The Roche lobe overflow, however, destabilizes sufficiently self-gravitating accretion disks with respect to a catastrophic runaway of mass due to minute changes of the gravitational field induced by the changes in the mass and angular momentum of the central black hole. One of the two acoustic modes may become trapped near the inner edge of the disk. All these effects, absent in the standard model, have dramatic implications for time-dependent behavior of the accretion disks around black holes.

  19. Black hole tidal problem in the Fermi normal coordinates

    SciTech Connect

    Ishii, Masaki; Shibata, Masaru; Mino, Yasushi

    2005-02-15

    We derive a tidal potential for a self-gravitating fluid star orbiting a Kerr black hole along a timelike geodesic, extending previous works by Fishbone and Marck. In this paper, the tidal potential is calculated up to the third- and fourth-order terms in R/r, where R is the stellar radius and r the orbital separation, in the Fermi normal coordinate system following the framework developed by Manasse and Misner. The new formulation is applied for determining the tidal disruption limit (Roche limit) of corotating Newtonian stars in circular orbits moving on the equatorial plane of Kerr black holes. It is demonstrated that the third- and fourth-order terms quantitatively play an important role in the Roche limit for close orbits with R/r > or approx. 0.1. It is also indicated that the Roche limit of neutron stars orbiting a stellar-mass black hole near the innermost stable circular orbit may depend sensitively on the equation of state of the neutron star.

  20. Overview of existing research and information linking isotretinoin (accutane), depression, psychosis, and suicide.

    PubMed

    O'Donnell, James

    2003-01-01

    Isotretinoin (Accutane; Hoffmann-La Roche, Nutley, NJ) is a drug closely related to the chemical structure of vitamin A. The pharmacology and toxicology of these two retinoids are similar enough to warrant comparison. Accutane is a powerful drug that its manufacturer, Roche, indicates is limited for severe recalcitrant nodular acne. This potency is also reflected in Accutane's well-known ability to produce severe birth defects if taken during pregnancy. Less well known is the risk of this lipid-soluble chemical to affect the central nervous system. Reports of intracranial hypertension, depression, and suicidal ideation with Accutane use have prompted an examination of its serious and life-threatening potential. Although Roche has added a warning to its product label for signs of depression, and suicidal ideation, this product is overprescribed for all forms of acne, including mild and moderate cases that have not been treated with alternative medications with less risk of depression and suicide. There is no contesting that this drug is effective at clearing up the most severe forms of acne, but the public must be informed of the proper limited indication for its use, because depression and suicide can follow in patients with no prior history of psychiatric symptoms or suicide attempts.

  1. A hybrid fluid - N-body model for the formation of the Moon

    NASA Astrophysics Data System (ADS)

    Salmon, J.; Canup, R. M.

    2011-12-01

    We perform numerical simulations of the formation of the Moon from an impact-generated disk, with a new hybrid model: material within the Roche-limit is represented by a fluid inner disk with a vapor atmosphere, and we track outer solid bodies with an N-body code. We include: (1) viscous spreading of the inner disk, with either an instability driven viscosity (Ward & Cameron 1978), or a radiation-limited viscosity (Thompson & Stevenson 1988); (2) accretion of moonlets when material crosses the Roche limit; (3) tidal accretion criteria (Canup & Esposito 1995) to determine whether collisions rebound or merge; and (4) interactions of orbiting bodies with the inner disk at 0-th order resonances. While pure N-body simulations show accretion timescales of less than a year (e.g., Ida et al. 1997), the slow spreading of the inner disk due to its radiation-limited viscosity can delay the final accretion of the Moon by up to hundreds of years. Such long timescales might allow the disk to compositionally equilibrate with the Earth (Pahlevan & Stevenson 2007), providing an explanation for, e.g., the identical O-isotope compositions of the Earth and Moon. Our typical simulation shows a three-step accretion process: (1) bodies outside the Roche limit collide, accrete and scatter until only a few massive objects remain; (2) the inner disk is confined below the Roche limit by the outer bodies, which in turn recede away, eventually allowing the inner disk to spread outward; and (3) as the inner disk reaches the Roche limit, new moonlets are spawned and collide with the outer bodies. This process continues until the inner disk is depleted (see Figure). Resonant confinement of the inner disk is very efficient, so that most of its mass is lost onto the planet: a ~2 lunar mass disk with 70% of the mass initially in the inner disk leads to the formation of a 0.8 lunar mass Moon, with ~25% of its mass originating from the inner disk, where material may have compositionally equilibrated

  2. Reference intervals for common thyroid function tests, during different stages of pregnancy in Chinese women.

    PubMed

    Fan, Jian-xia; Han, Mi; Tao, Jun; Luo, Jun; Song, Meng-fan; Yang, Shuai; Khor, Shu-zin

    2013-07-01

    The importance of diagnosis of thyroid dysfunction during pregnancy has been widely recognized. Our study was designed to compare two different detection reagents between Abbott and Roche and to establish the gestational related reference intervals for thyroid function tests (TFT) in Chinese women and to assay the reference ranges with the American Thyroid Association recommended standard. Serum samples were collected from 693 normal pregnant Chinese women and divided into five groups according to their gestational age: 9-13, 16-20, 24-28, 32-34 and 37-40 weeks. Thyroid stimulating hormone (TSH) and free thyroxine (FT4) levels were determined by two different detection reagents: Abbott Architect I 2000 and Roche Cobas Elecsys 600. The reference ranges of the TFT indexes were calculated according to the National Academy of Clinical Biochemistry (NACB). The 2.5th and 97.5th percentiles of each stage were calculated, and the results were analyzed by one-way analysis of variances, t-test, and Spearman correlation analysis. Thyroid hormone levels varied greatly among different gestational stages. TSH levels, as assessed via two different TSH ELISA kits showed consistent changing pattern during pregnancy and displayed linear correlation (P < 0.001). In 9-13 gestational weeks, TSH levels were significantly lower than that of other groups; and in 37-40 gestational weeks, it was higher than that of other groups (all P < 0.001). TSH reference ranges determined by Roche detection reagent in each group were higher than those by Abbott detection reagent (P < 0.01 respectively). FT4 levels were higher in 9-13 gestational weeks than that of other groups (P < 0.001). FT4 levels determined by Roche reagent were higher than Abbott reagent in 9-13 weeks, (P < 0.001), and lower in 24-28 and 37-40 weeks (P < 0.001 and P = 0.016, respectively). The TSH level was correlated with FT4 levels in 9-13 gestational weeks by detection reagents (for Abbott reagent, r=-0.319 for FT4 P < 0

  3. Evaluation of a modified direct agar proportion method for testing susceptibility of Mycobacterium tuberculosis from MGIT samples.

    PubMed

    Yu, Fang-Lan; Lee, Jau-Ching; Wang, Mei-Shiang; Hsu, Han-Lin; Chen, Tzu-Ting; Cheng, Chia-Ling; Yang, Yi-Yuan; Wang, Giueng-Chueng; Yu, Ming-Chih

    2016-02-01

    The emergence of resistance to anti-tuberculosis (TB) drugs has become an obstacle to effective TB control. Thus, there is an urgent need to identify patients and initiate adequate treatment for drug-resistant cases in a timely manner. The BACTEC MGIT 960 system is well known for its rapid culturing time, and is in widespread use in Taiwan. In this study, we evaluated the possibility of replacing the traditional indirect agar proportion method with a modified direct agar proportion method (MDAPM), as a technique for rapid testing the drug susceptibility of Mycobacterium tuberculosis without additional cost. In this study, 432 positive MGIT 960 samples that were identified as M. tuberculosis complex using the MeDiPro M. tuberculosis Antigen Rapid Test or the Cobas Amplicor MTB test were evaluated. Each sample was tested separately by the MDAPM and indirect agar proportion method, between July 2008 and December 2008, to compare the consistency and total turnaround time. Four first-line anti-TB drugs-rifampin, isoniazid, ethambutol, and streptomycin-were tested. For the MDAPM and indirect agar proportion method, the respective consistencies for each drug were 99.31%, 98.38%, 98.38%, and 97.22%. Our results also indicated that the MDAPM leads to an average saving in working time of 2 weeks, compared with the traditional indirect agar proportion method. In addition to having the potential to shorten turnaround time without compromising diagnostic quality, the MDAPM also provides a more efficient and cost-effective procedure. This modified procedure presents potential benefits for TB diagnosis in laboratories already equipped with the MGIT 960 system. Copyright © 2014. Published by Elsevier B.V.

  4. Early diagnosis of in utero and intrapartum HIV infection in infants prior to 6 weeks of age.

    PubMed

    Lilian, Rivka R; Kalk, Emma; Bhowan, Kapila; Berrie, Leigh; Carmona, Sergio; Technau, Karl; Sherman, Gayle G

    2012-07-01

    Early initiation of antiretroviral therapy reduces HIV-related infant mortality. The early peak of pediatric HIV-related deaths in South Africa occurs at 3 months of age, coinciding with the earliest age at which treatment is initiated following PCR testing at 6 weeks of age. Earlier diagnosis is necessary to reduce infant mortality. The performances of the Amplicor DNA PCR, COBAS AmpliPrep/COBAS TaqMan (CAP/CTM), and Aptima assays for detecting early HIV infection (acquired in utero and intrapartum) up to 6 weeks of age were compared. Dried blood spots (DBS) were collected at birth and at 2, 4, and 6 weeks from HIV-exposed infants enrolled in an observational cohort study in Johannesburg, South Africa. HIV status was determined at 6 weeks by DNA PCR on whole blood. Serial DBS samples from all HIV-infected infants and two HIV-uninfected, age-matched controls were tested with the 3 assays. Of 710 infants of known HIV status, 38 (5.4%) had in utero (n = 29) or intrapartum (n = 9) infections. By 14 weeks, when treatment should have been initiated, 13 (45%) in utero-infected and 2 (22%) intrapartum-infected infants had died or were lost to follow-up. The CAP/CTM and Aptima assays identified 76.3% of all infants with early HIV infections at birth and by 4 weeks were 96% sensitive. DNA PCR demonstrated lower sensitivities at birth and 4 weeks of 68.4% and 87.5%, respectively. All assays had the lowest sensitivity at 2 weeks of age. CAP/CTM was the only assay with 100% specificity at all ages. Testing at birth versus 6 weeks of age identifies a higher total number of HIV-infected infants, irrespective of the assay.

  5. HIV/AIDS in older adults: a case report and literature review.

    PubMed

    Inelman, Emine Meral; Gasparini, Giulia; Enzi, Giuliano

    2005-09-01

    A 75-year-old man presented in May 2003 with suspected drop attack (atonic seizure). He reported falling over and losing consciousness. He was a retired, single ex-smoker, who lived alone in an apartment that was in a poor state of repair with precarious hygienic conditions. Over the course of 2 years he had unintentionally lost more than 10 kg (22 lbs) in weight. He had been diagnosed with diabetes approximately 10 years prior, and was receiving treatment with oral hypoglycemic therapy (fenformin/ glibenclamide, 25/2.5 mg, bid). He had been hospitalized for pneumonia in 2000. In recent months, he had gone to the emergency department several times (about once every 2 weeks) due to his weight loss and asthenia, without obtaining a definite diagnosis. On physical examination, his cognitive status was normal, but his nutritional status was deteriorated. Other clinical findings were negative. Blood chemistry tests revealed hypoalbuminemia (26.00 g/L). His personal hygiene was precarious and the apartment was completely neglected despite assistance by social support networks. In conversation with the social support worker, it was revealed that the patient was homosexual; with the patient's informed consent, he was tested and found positive for HIV. He was consequently transferred to the Infectious Diseases Department where further biochemical tests revealed: HIV-RNA Quantitative > 100.000 copies/ML COBAS Amplicor, antibodies anti-HIV 1-2 reactive sample (Enzygnost HIV Integral and Axsym HIV 1/2 GO [Abbott] EIA method, antibodies anti-HIV 1 positive (Western Blot). The patient's serum also tested positive for syphilis (TPHA positive 1:320). The patient refused any specific treatment, left the hospital, and was lost to follow-up.

  6. Improved COBAS TaqMan hepatitis C virus test (Version 2.0) for use with the High Pure system: enhanced genotype inclusivity and performance characteristics in a multisite study.

    PubMed

    Colucci, G; Ferguson, J; Harkleroad, C; Lee, S; Romo, D; Soviero, S; Thompson, J; Velez, M; Wang, A; Miyahara, Y; Young, S; Sarrazin, C

    2007-11-01

    We have evaluated the COBAS TaqMan hepatitis C virus (HCV) test (version 2.0) for use with the High Pure system (HCVHPS V2), a new, revised real-time reverse transcription-PCR assay developed to improve the genotype quantitation of version 1.0 (HCVHPS V1). Revisions were made in the wash buffer and in the reverse transcription temperature. The genotype inclusivity of HCVHPS V2 was evaluated at three different sites, using HCVHPS V2, HCVHPS V1, and the COBAS AMPLICOR HCV MONITOR test (version 2.0) (CAHCM). The fully automated COBAS Ampliprep/COBAS TaqMan HCV test was also used in one of the participating laboratories. The mean differences in HCV RNA values between HCVHPS V2 and CAHCM and between HCVHPS V2 and HCVHPS V1 ranged from -0.21 to 0.13 log and from 0.24 to 1.27 log, respectively, with >0.5-log differences for genotypes 2, 3, 4, and 5. With a NIBSC panel of HCV genotypes 1 through 6, the measured HCVHPS V2 values were within 0.25 log of the nominal values for all 6 genotypes. When serial dilutions of genotype-specific clinical HCV specimens were tested, the assay showed a limit of detection between 10 and 20 IU/ml and a linear range of 25 IU/ml to 3.91 x 10(8) IU/ml. Clinical and analytical specificities of 100% were demonstrated with 100 HCV-seronegative specimens as well as with 12 non-HCV members of Flaviviridae and 22 additional microorganisms. These data indicate that HCVHPS V2 is a robust and accurate test for the quantitation of all six HCV genotypes and useful in monitoring viral load in all clinical HCV specimens.

  7. HIV-1 Viral Load and Phenotypic Antiretroviral Drug Resistance Assays Based on Reverse Transcriptase Activity in Comparison to Amplification Based HIV-1 RNA and Genotypic Assays

    PubMed Central

    Napravnik, Sonia; Cachafeiro, Ada; Stewart, Paul; Eron, Joseph J.; Fiscus, Susan A.

    2009-01-01

    Background Amplification based HIV-1 viral load and genotypic resistance assays are expensive, technologically complex and may be difficult to implement in resource limited settings. Inexpensive, simpler assays are urgently needed. Objectives To determine the suitability of the ExaVir™ Load and ExaVir™ Drug assays for use in patient monitoring. Study Design Specimens from 108 adults were used to compare ExaVir™ Load HIV-1 RT to Amplicor HIV-1 Monitor® HIV-1 RNA, and ExaVir™ Drug phenotype to HIV GenoSure™ genotype. Results HIV-1 RT and HIV-1 RNA levels were comparable (Pearson correlation coefficient 0.83). Most (94%) had detectable results in both assays. The mean difference (HIV-1 RT minus HIV-1 RNA) was -0.21 log10 cps/mL equivalents. Relationship between HIV-1 RT and HIV-1 RNA was not affected by RT mutations, CD4 cell count, or efavirenz (EFV) or nevirapine (NVP) use. Phenotypes were generally consistent with genotype findings for EFV, but not for NVP. Most patients (93.9%) with phenotypic EFV resistance had at least one EFV mutation, while 78.0% of patients with phenotypic NVP resistance had at least one NVP mutation. Eleven of 49 samples tested for EFV susceptibility were found resistant (n=2) or with reduced susceptibility (n=9) despite the absence of genotypic resistance. Eleven of 45 samples tested for NVP susceptibility were found resistant (n=9) or with reduced susceptibility (n=2) with no evidence of genotypic mutations. Conclusions The ExaVir™ Load assay performed well and may be an alternative to amplification based techniques for HIV-1 RNA quantification. The ExaVir™ Drug assay for phenotypic resistance testing requires further evaluation, especially for NVP. PMID:19896416

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

    PubMed

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

    2003-08-01

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

  9. Trichomonas Vaginalis Treatment Reduces Vaginal HIV-1 Shedding

    PubMed Central

    KISSINGER, PATRICIA; AMEDEE, ANGELA; CLARK, REBECCA A.; DUMESTRE, JEANNE; THEALL, KATHERINE P.; MYERS, LEANN; HAGENSEE, MICHAEL E.; FARLEY, THOMAS A.; MARTIN, DAVID H.

    2013-01-01

    Background: Vaginal HIV-1 shedding has been associated with Trichomonas vaginalis (TV) infection and could play a role in HIV transmission. The purpose of the study was to examine if effective TV treatment reduces the presence of vaginal HIV-1 RNA. Methods: TV+ women attending an HIV outpatient clinic in New Orleans, LA, who resolved infection (n = 58) and TV-negative controls (n = 92), matched on antiretroviral therapy (ART) were examined and interviewed at baseline, 1, and 3 months. TV status was tested by culture and the amount of cell free HIV-1 RNA in the vaginal fluids was determined by the Amplicor HIV-1 Monitor ultrasensitive assay. Results: Most women (81.3%) were black and the mean age was 37.5 (SD 8.7). At baseline, 46.0% had plasma HIV-1 RNA ≥10,000 copies/mL, 26.4% had CD4<200 cells/μL, 54.7% were taking ART, and only 26.0% had detectable HIV-1 RNA in their vaginal fluids. TV-positive women who were effectively treated for TV were less likely to shed HIV vaginally at 3-months post-treatment compared to baseline (R.R. 0.34, 95% CI: 0.12–0.92, P = 0.03), whereas there was no change for TV-negative women. Conclusion: This study provides additional support that reducing TV infection among HIV-positive women may have an impact on the prevention of HIV transmission. Reasons for the delayed treatment effect and the effect on cervical shedding need further investigation. PMID:19008776

  10. Performance characteristics of the TRUGENE HIV-1 Genotyping Kit and the Opengene DNA Sequencing System.

    PubMed

    Kuritzkes, Daniel R; Grant, Robert M; Feorino, Paul; Griswold, Marshal; Hoover, Marie; Young, Russell; Day, Stephen; Lloyd Jr, Robert M; Reid, Caroline; Morgan, Gillian F; Winslow, Dean L

    2003-04-01

    The TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System are designed to sequence the protease (PR)- and reverse transcriptase (RT)-coding regions of human immunodeficiency virus type 1 (HIV-1) pol. Studies were undertaken to determine the accuracy of this assay system in detecting resistance-associated mutations and to determine the effects of RNA extraction methods, anticoagulants, specimen handling, and potentially interfering substances. Samples were plasma obtained from HIV-infected subjects or seronegative plasma to which viruses derived from wild-type and mutant infectious molecular clones (IMC) of HIV-1 were added. Extraction methods tested included standard and UltraSensitive AMPLICOR HIV-1 MONITOR, QIAGEN viral RNA extraction mini kit, and QIAGEN Ultra HIV extraction kit, and NASBA manual HIV-1 quantitative NucliSens. Sequence data from test sites were compared to a "gold standard" reference sequence to determine the percent agreement. Comparisons between test and reference sequences at the nucleotide level showed 97.5 to 100% agreement. Similar results were obtained regardless of extraction method, regardless of use of EDTA or acid citrate dextrose as anticoagulant, and despite the presence of triglycerides, bilirubin, hemoglobin, antiretroviral drugs, HIV-2, hepatitis C virus (HCV), HBV, cytomegalovirus, human T-cell leukemia virus type 1 (HTLV-1), or HTLV-2. Samples with HIV-1 RNA titers of >or=1,000 copies/ml gave consistent results. The TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System consistently generate highly accurate sequence data when tested with IMC-derived HIV and patient samples.

  11. HCV clearance patterns in saliva and serum of patients with chronic HCV infection under interferon plus ribavirin therapy.

    PubMed

    Diz Dios, P; Castro, A; Rodríguez, I; Reforma, N G; Castro, M; Eirea, M; Hermida, M

    2005-05-01

    Hepatitis C virus (HCV)-RNA is often present in saliva of HCV-infected patients, with plasma viral load being the only known predictable factor. Interferon plus ribavirin therapy yields a sustained reduction in HCV viremia. This study aimed to assess the presence of HCV in saliva and serum specimens from patients undergoing this combination therapy (CT). Paired serum and saliva specimens were collected from 44 chronic HCV-infected patients at basal time, 4 and 12 weeks after CT onset, at the end of treatment and 6 months latter. Serum HCV-RNA levels were determined by the polymerase chain reaction (PCR) Amplicor system. Presence of HCV-RNA in saliva was tested by a highly sensitive non-commercialized nested-PCR. The HCV-RNA was detected in 26 saliva specimens at basal time (59.1%). In 34.1% of cases, a concordance viral clearance pattern in serum and saliva was observed in both responders (pattern 1a) and non-responders (pattern 1b). In pattern 2 (13.6% of cases), HCV was detected longer during CT in serum than in saliva (pattern 2a) or in saliva than in serum (pattern 2b). In 11.3% of patients, viral clearance was corroborated either in their serum (pattern 3a) or in their saliva (pattern 3b), but not in both fluids. Of the eight primary responders with 1a clearance pattern, seven were sustained responders. None of the patients with 2a clearance pattern was a sustained responder. Of the two primary responders showing the 3b salivary pattern, one had already relapsed in the first 6 months of follow up. The present results suggest that the monitoring of salivary levels of HCV would be a helpful means of determining sustained antiviral effects of interferon and ribavirin in the treatment of HCV disease.

  12. Development of a Second Version of the Cobas AmpliPrep/Cobas TaqMan Hepatitis C Virus Quantitative Test with Improved Genotype Inclusivity▿

    PubMed Central

    Vermehren, Johannes; Colucci, Giuseppe; Gohl, Peter; Hamdi, Nabila; Abdelaziz, Ahmed Ihab; Karey, Ursula; Thamke, Diana; Zitzer, Heike; Zeuzem, Stefan; Sarrazin, Christoph

    2011-01-01

    Hepatitis C virus (HCV) RNA measurement has been facilitated by the introduction of real-time PCR-based assays with low limits of detection and broad dynamic ranges for quantification. In the present study, the performance of two second-version prototypes of the Cobas AmpliPrep/Cobas TaqMan HCV Quantitative Test (CAP/CTM v2) with decreased sample input volume and improved genotype inclusivity was investigated. A total of 232 serum and plasma samples derived from patients with chronic hepatitis C (genotype 1 [GT1], n = 108; GT2, n = 8; GT3, n = 24; GT4, n = 87; GT5, n = 3; and GT6, n = 2) were processed in parallel with the Cobas AmpliPrep/Cobas TaqMan HCV Test (CAP/CTM), Cobas Amplicor HCV Monitor Test v2.0 (CAM), and two second-version prototype formulations of CAP/CTM, Mastermix 1 (MMx1) and MMx2. In addition, three GT4 transcripts containing rare variant sequences were tested. The mean log10 HCV RNA differences for the best-performing CAP/CTM v2/MMx2 formulation in comparison to CAM were −0.05, 0.05, −0.12, −0.10, −0.44, and −0.29 for patients with GT1, GT2, GT3, GT4, GT5, and GT6 infections, respectively. GT1, GT2, and GT4 samples including isolates with known variants within the 5′ untranslated region (G145A, A165T) that were underquantified with CAP/CTM were correctly quantified with the second-version prototype. In addition, CAP/CTM v2 was able to accurately quantify the three transcripts with rare variant sequences. In conclusion, CAP/CTM v2 accurately quantifies HCV RNA across all HCV genotypes, including specimens with rare polymorphisms previously associated with underquantification. PMID:21752967

  13. Development of a second version of the Cobas AmpliPrep/Cobas TaqMan hepatitis C virus quantitative test with improved genotype inclusivity.

    PubMed

    Vermehren, Johannes; Colucci, Giuseppe; Gohl, Peter; Hamdi, Nabila; Abdelaziz, Ahmed Ihab; Karey, Ursula; Thamke, Diana; Zitzer, Heike; Zeuzem, Stefan; Sarrazin, Christoph

    2011-09-01

    Hepatitis C virus (HCV) RNA measurement has been facilitated by the introduction of real-time PCR-based assays with low limits of detection and broad dynamic ranges for quantification. In the present study, the performance of two second-version prototypes of the Cobas AmpliPrep/Cobas TaqMan HCV Quantitative Test (CAP/CTM v2) with decreased sample input volume and improved genotype inclusivity was investigated. A total of 232 serum and plasma samples derived from patients with chronic hepatitis C (genotype 1 [GT1], n = 108; GT2, n = 8; GT3, n = 24; GT4, n = 87; GT5, n = 3; and GT6, n = 2) were processed in parallel with the Cobas AmpliPrep/Cobas TaqMan HCV Test (CAP/CTM), Cobas Amplicor HCV Monitor Test v2.0 (CAM), and two second-version prototype formulations of CAP/CTM, Mastermix 1 (MMx1) and MMx2. In addition, three GT4 transcripts containing rare variant sequences were tested. The mean log(10) HCV RNA differences for the best-performing CAP/CTM v2/MMx2 formulation in comparison to CAM were -0.05, 0.05, -0.12, -0.10, -0.44, and -0.29 for patients with GT1, GT2, GT3, GT4, GT5, and GT6 infections, respectively. GT1, GT2, and GT4 samples including isolates with known variants within the 5' untranslated region (G145A, A165T) that were underquantified with CAP/CTM were correctly quantified with the second-version prototype. In addition, CAP/CTM v2 was able to accurately quantify the three transcripts with rare variant sequences. In conclusion, CAP/CTM v2 accurately quantifies HCV RNA across all HCV genotypes, including specimens with rare polymorphisms previously associated with underquantification.

  14. Improved COBAS TaqMan Hepatitis C Virus Test (Version 2.0) for Use with the High Pure System: Enhanced Genotype Inclusivity and Performance Characteristics in a Multisite Study▿

    PubMed Central

    Colucci, G.; Ferguson, J.; Harkleroad, C.; Lee, S.; Romo, D.; Soviero, S.; Thompson, J.; Velez, M.; Wang, A.; Miyahara, Y.; Young, S.; Sarrazin, C.

    2007-01-01

    We have evaluated the COBAS TaqMan hepatitis C virus (HCV) test (version 2.0) for use with the High Pure system (HCVHPS V2), a new, revised real-time reverse transcription-PCR assay developed to improve the genotype quantitation of version 1.0 (HCVHPS V1). Revisions were made in the wash buffer and in the reverse transcription temperature. The genotype inclusivity of HCVHPS V2 was evaluated at three different sites, using HCVHPS V2, HCVHPS V1, and the COBAS AMPLICOR HCV MONITOR test (version 2.0) (CAHCM). The fully automated COBAS Ampliprep/COBAS TaqMan HCV test was also used in one of the participating laboratories. The mean differences in HCV RNA values between HCVHPS V2 and CAHCM and between HCVHPS V2 and HCVHPS V1 ranged from −0.21 to 0.13 log and from 0.24 to 1.27 log, respectively, with >0.5-log differences for genotypes 2, 3, 4, and 5. With a NIBSC panel of HCV genotypes 1 through 6, the measured HCVHPS V2 values were within 0.25 log of the nominal values for all 6 genotypes. When serial dilutions of genotype-specific clinical HCV specimens were tested, the assay showed a limit of detection between 10 and 20 IU/ml and a linear range of 25 IU/ml to 3.91 × 108 IU/ml. Clinical and analytical specificities of 100% were demonstrated with 100 HCV-seronegative specimens as well as with 12 non-HCV members of Flaviviridae and 22 additional microorganisms. These data indicate that HCVHPS V2 is a robust and accurate test for the quantitation of all six HCV genotypes and useful in monitoring viral load in all clinical HCV specimens. PMID:17898157

  15. Rapid and early virological response to chronic hepatitis C treatment with IFN α2b or PEG‐IFN α2b plus ribavirin in HIV/HCV co‐infected patients

    PubMed Central

    Payan, Christopher; Pivert, Adeline; Morand, Patrice; Fafi‐Kremer, Samira; Carrat, Fabrice; Pol, Stanislas; Cacoub, Patrice; Perronne, Christian; Lunel, Françoise

    2007-01-01

    Background and aims An algorithm based on a 2 log10 decline in hepatitis C virus (HCV) RNA at week (W) 12 has been proposed in US and European recommendations for the management of patients with chronic hepatitis C treated with pegylated‐interferon and ribavirin. Methods We examined rapid virological response (RVR; at W2 and W4 after the initiation of therapy) in HIV/HCV co‐infected patients. Using HCV RNA measurements (Versant HCV RNA 3.0, Cobas Amplicor HCV 2.0), RVR was studied in 323 patients from the ANRS HC02 RIBAVIC trial, comparing interferon α2b 3 MU ×3/week with pegylated interferon α2b 1.5 μg/kg/week, each combined with ribavirin 800 mg/day over 48 weeks. Results The best positive and negative predictive values of sustained virological response (SVR) were obtained with an undetectable HCV RNA at W4 (97%) and with more than a 2 log10 decrease at W12 (99%), respectively. Prediction of non‐SVR was obtained in all patients by using HCV RNA cut‐off levels above 460 000 IU/ml at W4 and above 39 000 UI/ml at W12 irrespective of the HCV genotype and arm of treatment. Conclusion We propose a new algorithm based on RVR thresholds using HCV RNA that allows for excellent prediction of non‐SVR as early as W4. PMID:17363475

  16. Magnitude of Virologic Blips Is Associated With a Higher Risk for Virologic Rebound in HIV-Infected Individuals: A Recurrent Events Analysis

    PubMed Central

    Grennan, J. Troy; Loutfy, Mona R.; Su, DeSheng; Harrigan, P. Richard; Cooper, Curtis; Klein, Marina; Machouf, Nima; Montaner, Julio S. G.; Rourke, Sean; Tsoukas, Christos; Hogg, Bob

    2012-01-01

    (See the editorial commentary by Taiwo and Bosch, on pages 1189–91.) Background. The importance of human immunodeficiency virus (HIV) blip magnitude on virologic rebound has been raised in clinical guidelines relating to viral load assays. Methods. Antiretroviral-naive individuals initiating combination antiretroviral therapy (cART) after 1 January 2000 and achieving virologic suppression were studied. Negative binomial models were used to identify blip correlates. Recurrent event models were used to determine the association between blips and rebound by incorporating multiple periods of virologic suppression per individual. Results. 3550 participants (82% male; median age, 40 years) were included. In a multivariable negative binomial regression model, the Amplicor assay was associated with a lower blip rate than branched DNA (rate ratio, 0.69; P < .01), controlling for age, sex, region, baseline HIV-1 RNA and CD4 count, AIDS-defining illnesses, year of cART initiation, cART type, and HIV-1 RNA testing frequency. In a multivariable recurrent event model controlling for age, sex, intravenous drug use, cART start year, cART type, assay type, and HIV-1 RNA testing frequency, blips of 500–999 copies/mL were associated with virologic rebound (hazard ratio, 2.70; P = .002), whereas blips of 50–499 were not. Conclusions. HIV-1 RNA assay was an important determinant of blip rates and should be considered in clinical guidelines. Blips ≥500 copies/mL were associated with increased rebound risk. PMID:22438396

  17. New Real-Time Reverse Transcriptase-Initiated PCR Assay with Single-Copy Sensitivity for Human Immunodeficiency Virus Type 1 RNA in Plasma

    PubMed Central

    Palmer, Sarah; Wiegand, Ann P.; Maldarelli, Frank; Bazmi, Holly; Mican, JoAnn M.; Polis, Michael; Dewar, Robin L.; Planta, Angeline; Liu, Shuying; Metcalf, Julia A.; Mellors, John W.; Coffin, John M.

    2003-01-01

    More sensitive assays for human immunodeficiency virus type 1 (HIV-1) RNA are needed to detect, quantify, and characterize persistent viremia in patients who are receiving antiretroviral therapy and whose plasma HIV-1 RNA levels are suppressed to less than 50 to 75 copies/ml. We therefore developed an internally controlled real-time reverse transcriptase-initiated PCR assay that quantifies HIV-1 RNA concentrations down to 1 copy per ml of plasma. This assay with single-copy sensitivity (the single-copy assay) generates a reproducible linear regression plot of input copy number versus threshold cycle by using HIV-1 RNA transcripts at copy numbers ranging from 1 to 106 per reaction mixture. The single-copy assay was compared to the ultrasensitive AMPLICOR HIV-1 MONITOR assay and a more sensitive modification of the ultrasensitive assay by repeatedly testing a low-copy-number panel containing 200 to 0.781 copies of HIV-1 RNA per ml of plasma. This comparison showed that the single-copy assay had a greater sensitivity than the other assays and was the only assay that detected HIV-1 RNA at levels as low as 0.781 copies/ml. Testing of plasma samples from 15 patients who were receiving antiretroviral therapy and who had <75 HIV-1 RNA copies/ml revealed persistent viremia in all 15 patients, with HIV-1 RNA levels ranging from 1 to 32 copies/ml (median, 13 copies/ml). The greater sensitivity of the single-copy assay should allow better characterization of persistent viremia in patients who are receiving antiretroviral therapy and whose HIV-1 RNA levels are suppressed to below the detection limits of present assays. PMID:14532178

  18. Polymerase chain reaction for diagnosis of human immunodeficiency virus infection in infancy in low resource settings.

    PubMed

    Sherman, Gayle G; Cooper, Peter A; Coovadia, Ashraf H; Puren, Adrian J; Jones, Stephanie A; Mokhachane, Mantoa; Bolton, Keith D

    2005-11-01

    Diagnosis of human immunodeficiency virus (HIV) is essential for accessing treatment. Current HIV diagnostic protocols for infants require adaptation and validation before they can be implemented in the developing world. The timing and type of HIV assays will be dictated by country-specific circumstances and experience from similar settings. The performance of an HIV-1 DNA polymerase chain reaction (PCR) test, and in particular a single test at 6 weeks of age, in diagnosing HIV subtype C infection acquired in utero or peripartum was assessed. A retrospective review of 1825 Amplicor HIV-1 DNA PCR version 1.5 tests performed between 2000 and 2004 in 2 laboratories in Johannesburg, South Africa on 769 effectively non-breast-fed infants from 3 clinically well characterized cohorts was undertaken. The HIV status of each infant was used as the standard against which the HIV PCR results were compared. The overall sensitivity and specificity of the HIV PCR test were 99.3 and 99.5% respectively. A single test was 98.8% sensitive and 99.4% specific in the 627 infants tested at 6 weeks of age (58 HIV-infected and 569 HIV-uninfected). Repeat testing of all positive HIV PCR tests minimized false positive results. In resource-poor settings where HIV PCR testing in an environment of good laboratory practice is feasible, a single 6-week HIV DNA PCR test can increase identification of HIV-infected children substantially from current levels. Further operational research on how best to implement and monitor such a diagnostic protocol in specific local settings, especially in breast-fed infants, is necessary.

  19. Chronological constraints on the Holocene glacier dynamics of the Argentière Glacier (Mont Blanc massif, France) based on cosmogenic nuclide dating

    NASA Astrophysics Data System (ADS)

    Protin, Marie; Schimmelpfennig, Irene; Mugnier, Jean-Louis; Ravanel, Ludovic; Deline, Philip; Le Roy, Melaine; Moreau, Luc; Aster Team

    2017-04-01

    While reconstruction of glacier fluctuations during the Holocene provides important information about the glacier response to natural climate change, it is still a challenge to accurately constrain chronologies of past glacier advances and retreats. Moraine deposits and roches moutonnées represent valuable geomorphic markers of advanced glacier extensions, while the currently ongoing glacier melt uncovers proglacial bedrock that can be used as a new archive to investigate the durations when a glacier was in retreated position during the Holocene. Our study focuses on the Mont-Blanc massif (MBM), located in the Western Alps and hosting some of the largest glaciers of Europe. Chronologies of Holocene glacier fluctuations in this area are still sparse, even if recent studies considerably improved the temporal reconstruction of Holocene advances of some glaciers in the MBM and locations near-by (e.g. Le Roy et al., 2015). Here we present preliminary 10Be exposure ages obtained from moraine boulders, roches moutonnées and pro- and subglacial bedrock in the area of the Argentière Glacier, located on the north-western flank of the MBM. The ages of moraine boulders and roche moutonnée surfaces outboard of the investigated moraines suggest that the Early Holocene deglaciation of this area started around 11 ka ago. Also, 10Be measurements of recently deglaciated bedrock surfaces indicate that the glacier was at a position at least as retracted as today for a minimum duration of 7 ka throughout the Holocene. The 10Be measurement of one sample from a surface that is currently still covered by 60 m of ice suggests that the glacier was shorter than today for at least a duration of 3 ka. These first results will soon be completed with in situ 14C measurements, which will allow us to quantify and take into account subglacial erosion rates and thus to more accurately determine the cumulative duration of pro- and subglacial bedrock exposure during the Holocene.

  20. Comparative evaluation of three automated systems for DNA extraction in conjunction with three commercially available real-time PCR assays for quantitation of plasma Cytomegalovirus DNAemia in allogeneic stem cell transplant recipients.

    PubMed

    Bravo, Dayana; Clari, María Ángeles; Costa, Elisa; Muñoz-Cobo, Beatriz; Solano, Carlos; José Remigia, María; Navarro, David

    2011-08-01

    Limited data are available on the performance of different automated extraction platforms and commercially available quantitative real-time PCR (QRT-PCR) methods for the quantitation of cytomegalovirus (CMV) DNA in plasma. We compared the performance characteristics of the Abbott mSample preparation system DNA kit on the m24 SP instrument (Abbott), the High Pure viral nucleic acid kit on the COBAS AmpliPrep system (Roche), and the EZ1 Virus 2.0 kit on the BioRobot EZ1 extraction platform (Qiagen) coupled with the Abbott CMV PCR kit, the LightCycler CMV Quant kit (Roche), and the Q-CMV complete kit (Nanogen), for both plasma specimens from allogeneic stem cell transplant (Allo-SCT) recipients (n = 42) and the OptiQuant CMV DNA panel (AcroMetrix). The EZ1 system displayed the highest extraction efficiency over a wide range of CMV plasma DNA loads, followed by the m24 and the AmpliPrep methods. The Nanogen PCR assay yielded higher mean CMV plasma DNA values than the Abbott and the Roche PCR assays, regardless of the platform used for DNA extraction. Overall, the effects of the extraction method and the QRT-PCR used on CMV plasma DNA load measurements were less pronounced for specimens with high CMV DNA content (>10,000 copies/ml). The performance characteristics of the extraction methods and QRT-PCR assays evaluated herein for clinical samples were extensible at cell-based standards from AcroMetrix. In conclusion, different automated systems are not equally efficient for CMV DNA extraction from plasma specimens, and the plasma CMV DNA loads measured by commercially available QRT-PCRs can differ significantly. The above findings should be taken into consideration for the establishment of cutoff values for the initiation or cessation of preemptive antiviral therapies and for the interpretation of data from clinical studies in the Allo-SCT setting.

  1. Accretion of Saturn’s Inner Mid-sized Moons from a Massive Primordial Ice Ring

    NASA Astrophysics Data System (ADS)

    Salmon, J.; Canup, R. M.

    2017-02-01

    Saturn’s rings are rock-poor, containing 90%–95% ice by mass. As a group, Saturn’s moons interior to and including Tethys are also about 90% ice. Tethys itself contains < 6 % rock by mass, in contrast to its similar-mass outer neighbor Dione, which contains > 40 % rock. Here we simulate the evolution of a massive primordial ice-rich ring and the production of satellites as ring material spreads beyond the Roche limit. We describe the Roche-interior ring with an analytic model, and use an N-body code to describe material beyond the Roche limit. We track the accretion and interactions of spawned satellites, including tidal interaction with the planet, assuming a tidal dissipation factor for Saturn of Q∼ {10}4. We find that ring torques and capture of moons into mutual resonances produce a system of ice-rich inner moons that extends outward to approximately Tethys’s orbit in 109 years, even with relatively slow orbital expansion due to tides. The resulting mass and semimajor axis distribution of spawned moons resembles that of Mimas, Enceladus, and Tethys. We estimate the mass of rock delivered to the moons by external cometary impactors during a late heavy bombardment. We find that the inner moons receive a mass in rock comparable to their current total rock content, while Dione and Rhea receive an order-of-magnitude less rock than their current rock content. This suggests that external contamination may have been the primary source of rock in the inner moons, and that Dione and Rhea formed from much more rock-rich source material. Reproducing the distribution of rock among the current inner moons is challenging, and appears to require large impactors stochasticity and/or the presence of some rock in the initial ring.

  2. Comparative Evaluation of Three Automated Systems for DNA Extraction in Conjunction with Three Commercially Available Real-Time PCR Assays for Quantitation of Plasma Cytomegalovirus DNAemia in Allogeneic Stem Cell Transplant Recipients▿

    PubMed Central

    Bravo, Dayana; Clari, María Ángeles; Costa, Elisa; Muñoz-Cobo, Beatriz; Solano, Carlos; José Remigia, María; Navarro, David

    2011-01-01

    Limited data are available on the performance of different automated extraction platforms and commercially available quantitative real-time PCR (QRT-PCR) methods for the quantitation of cytomegalovirus (CMV) DNA in plasma. We compared the performance characteristics of the Abbott mSample preparation system DNA kit on the m24 SP instrument (Abbott), the High Pure viral nucleic acid kit on the COBAS AmpliPrep system (Roche), and the EZ1 Virus 2.0 kit on the BioRobot EZ1 extraction platform (Qiagen) coupled with the Abbott CMV PCR kit, the LightCycler CMV Quant kit (Roche), and the Q-CMV complete kit (Nanogen), for both plasma specimens from allogeneic stem cell transplant (Allo-SCT) recipients (n = 42) and the OptiQuant CMV DNA panel (AcroMetrix). The EZ1 system displayed the highest extraction efficiency over a wide range of CMV plasma DNA loads, followed by the m24 and the AmpliPrep methods. The Nanogen PCR assay yielded higher mean CMV plasma DNA values than the Abbott and the Roche PCR assays, regardless of the platform used for DNA extraction. Overall, the effects of the extraction method and the QRT-PCR used on CMV plasma DNA load measurements were less pronounced for specimens with high CMV DNA content (>10,000 copies/ml). The performance characteristics of the extraction methods and QRT-PCR assays evaluated herein for clinical samples were extensible at cell-based standards from AcroMetrix. In conclusion, different automated systems are not equally efficient for CMV DNA extraction from plasma specimens, and the plasma CMV DNA loads measured by commercially available QRT-PCRs can differ significantly. The above findings should be taken into consideration for the establishment of cutoff values for the initiation or cessation of preemptive antiviral therapies and for the interpretation of data from clinical studies in the Allo-SCT setting. PMID:21697323

  3. On the Evolution of Low-Mass X-Ray Binaries under the Influence of a Donor Stellar Wind Induced by X-Rays from the Accretor

    NASA Astrophysics Data System (ADS)

    Iben, Icko, Jr.; Tutukov, Alexander V.; Fedorova, Alexandra V.

    1997-09-01

    In a low-mass X-ray binary (LMXB), an intense stellar wind from the mass donor may be a consequence of the absorption of X-rays from the mass-accreting neutron star or black hole, and such a wind could change the evolution of these binaries dramatically compared with the evolution of cataclysmic variables (CVs), which are close binaries in which the accretor is a white dwarf. An analytical study and numerical models show that, in the closest and brightest LMXBs, a relativistic companion can capture up to ~10% of the mass lost in the induced stellar wind (ISW) from the main-sequence or subgiant donor, and this is enough to keep the X-ray luminosity of a typical LMXB on the level of LX ~ 5000 L⊙ and to accelerate the rotation of an old neutron star with a low magnetic field into the millisecond-period range. A self-sustained ISW may exist even if the donor does not fill its Roche lobe, but the system can be bright (LX > 100 L⊙) only if the radius of the donor is a substantial fraction (>~0.8) of the Roche lobe radius. A lower limit on the Roche lobe filling factor follows from the circumstance that both the rate Ėwind at which work must be done to lift wind matter off the donor and the rate Ėabs at which the donor absorbs X-ray energy are proportional to ṀISW (the ISW mass-loss rate) and from the requirement that Ėwind<Ėabs in order for energy to be conserved. The observed number (~100) of bright LMXBs in our Galaxy can be understood as the product of a relatively short lifetime (a few × 107 yr) and a small theoretical birthrate (~2 × 10-6-8 × 10-6 yr-1), which is comparable to semiempirical estimates of the birthrate of LMXBs and millisecond pulsars (~2 × 10-6 yr-1). The theoretical lifetime is ~10-60 times shorter than when the ISW is not taken into account, and the theoretical birthrate is ~3-6 times smaller, because of the fact that the ISW acts to expand the orbit and reduce the number of systems that can evolve through an X-ray bright stage under

  4. Falsely Elevated Plasma Creatinine Due to an Immunoglobulin M Paraprotein.

    PubMed

    McGill, Mitchell R; Vijayan, Anitha; Trulock, Elbert P; Witt, Chad A; Kohler, Giselle D; Scott, Mitchell G

    2016-11-01

    The most common method for measuring plasma creatinine is based on its reaction with picric acid. However, enzymatic methods are becoming more popular due to improved specificity. We present a case of falsely elevated plasma creatinine values obtained by an enzymatic method that turned out to be due to a monoclonal immunoglobulin M (IgM) paraprotein. A 63-year-old woman evaluated for lung transplantation had falsely increased plasma creatinine levels (1.54-1.71mg/dL; corresponding to estimated glomerular filtration rates of 32-36 mL/min/1.73m(2)) as measured by the Roche Creatinine plus enzymatic assay when compared with the picric acid-based procedure and several other enzymatic methods, which gave plasma creatinine values of 0.7 to 0.8mg/dL. Serum protein electrophoresis revealed an IgM κ light chain paraprotein. Removal of high-molecular-weight (>30kDa) proteins by ultrafiltration reduced the patient's plasma creatinine level by the Roche enzymatic method to 0.7mg/dL. Addition of the patient's immunoglobulin fraction to plasma from other patients with normal plasma creatinine levels resulted in values that were increased by 0.58 to 0.62mg/dL. Furthermore, removal of non-IgM immunoglobulins with protein G-coupled beads did not eliminate the interference from the patient's plasma. Taken together, these studies demonstrate that falsely elevated plasma creatinine values by the Roche enzymatic method can be due to an IgM paraprotein. Copyright © 2016 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

  5. Formation of regular satellites from the spreading of massive rings : Why some planets have one moon and other have many ?

    NASA Astrophysics Data System (ADS)

    Charnoz, Sebastien; Crida, A.

    2013-10-01

    Around giant planets, the regular satellites pile-up at a distance of a few planetary radii, their masses increasing with the distance to the pile-up. In contrast, terrestrial bodies are dominated by one large satellite (the Moon for the Earth, Charon for Pluto). Here we show that both cases can be understood in the frame of a new paradigm for satellite formation : the spreading of a debris disk initialy confined inside the Roche radius of the planet (a « tidal disk »). By definition, beyond the Roche radius, solids aggregate and accrete, forming new moons. Those moons then migrate outward, repelled by the disk. We find that if the life-time of the disk is short (the spreading is fast), then accretion is faster than migration and all the material gathers into one large satellite. If the life-time of the disk is long, many satellites form and migrate away ; merging events take place during the migration, so that the mass should be proportional to the distance to the Roche radius to the power 9/5 . This is in good agreement with the distribution of the inner satellites of Saturn, Uranus, and Neptune. Relating the life-time of the disk to its mass ratio to the planet, we find that a debris disk around a giant planet should give birth to many satellites, while the Moon forming disk should give birth to one large satellite of about one lunar mass, possibly with a smaller companion as recently suggested to explain the lunar highlands5.

  6. FROM DUST TO PLANETESIMALS: CRITERIA FOR GRAVITATIONAL INSTABILITY OF SMALL PARTICLES IN GAS

    SciTech Connect

    Shi, Ji-Ming; Chiang, Eugene

    2013-02-10

    Dust particles sediment toward the midplanes of protoplanetary disks, forming dust-rich sublayers encased in gas. What densities must the particle sublayer attain before it can fragment by self-gravity? We describe various candidate threshold densities. One of these is the Roche density, which is that required for a strengthless satellite to resist tidal disruption by its primary. Another is the Toomre density, which is that required for de-stabilizing self-gravity to defeat the stabilizing influences of pressure and rotation. We show that for sublayers containing aerodynamically well-coupled dust, the Toomre density exceeds the Roche density by many (up to about four) orders of magnitude. We present three-dimensional shearing box simulations of self-gravitating, stratified, dust-gas mixtures to test which of the candidate thresholds is relevant for collapse. All of our simulations indicate that the larger Toomre density is required for collapse. This result is sensible because sublayers are readily stabilized by pressure. Sound-crossing times for thin layers are easily shorter than free-fall times, and the effective sound speed in dust-gas suspensions decreases only weakly with the dust-to-gas ratio (as the inverse square root). Our findings assume that particles are small enough that their stopping times in gas are shorter than all other timescales. Relaxing this assumption may lower the threshold for gravitational collapse back down to the Roche criterion. In particular, if the particle stopping time becomes longer than the sound-crossing time, then sublayers may lose pressure support and become gravitationally unstable.

  7. Next-Generation Sequencing of 5' Untranslated Region of Hepatitis C Virus in Search of Minor Viral Variant in a Patient Who Revealed New Genotype While on Antiviral Treatment.

    PubMed

    Caraballo Cortes, Kamila; Bukowska-Ośko, Iwona; Pawełczyk, Agnieszka; Perlejewski, Karol; Płoski, Rafał; Lechowicz, Urszula; Stawiński, Piotr; Demkow, Urszula; Laskus, Tomasz; Radkowski, Marek

    2016-01-01

    The role of mixed infections with different hepatitis C virus (HCV) genotypes in viral persistence, treatment effects, and tissue tropism is unclear. Next-generation sequencing (NGS), which is suitable for analysis of large, genetically diverse populations offers unparalleled advantages for the study of mixed infections. The aim of the study was to determine, using two different deep sequencing strategies (pyrosequencing - 454 Life Sciences/Roche and reversible terminator sequencing-by-synthesis by Illumina), the origin of a novel HCV genotype transiently detectable during antiviral therapy (pre-existing minor population vs. de novo superinfection). Secondly, we compared 5' untranslated region (5'-UTR) variants obtained by the two NGS approaches. 5' UTR amplification products from 9 samples collected from genotype 1b infected patient before, during, and after treatment (4 serum and 5 peripheral blood mononuclear cell - PBMC - samples) were subjected to the next-generation sequencing. The sequencing revealed the presence of two (454/Roche) and one (Illumina) genotype 4 variants in PBMC at Week 16. None of these variants were present either in the preceding or following samples as revealed by both platforms. 454/Roche sequencing detected 24 different 5'-UTR variants: 8 were present in serum and PBMC, 4 only in serum and 12 only in PBMC. Illumina sequencing detected 11 different 5'-UTR variants: 5 in serum and PBMC, 4 only in serum and 2 only in PBMC. Six variants were identical for both sequencing platforms. The difference in variants number was primarily due to variability in two 5'-UTR homopolymeric regions. In conclusion, longitudinal analysis of HCV variants, employing two independent deep sequencing methods, suggests that the transient presence of a different genotype strain in PBMC was a result of superinfection and not a selection of pre-existing minor variant.

  8. Recovery of spiked troponin I in four routine assays

    PubMed Central

    Loh, Tze Ping; Lim, Xiong Chang; Kieu, Karize; Sajiir, Haressh; Neo, Siew Fong; Cheng, Wan Ling; Sethi, Sunil Kumar

    2016-01-01

    Introduction This study aimed to examine the recovery of spiked human cardiac troponin I (cTnI) results measured by four routine assays, and investigate possible interference from microclots. Materials and methods 457 consecutive samples with cTnI concentration below limit of quantitation (12 ng/L), declared by the Vitros TnI ES assay (reference assay), were measured on Beckman Coulter Accu TnI+3, Siemens TnI-Ultra and Roche TnI STAT assays. These samples were enriched with native full-length cTnI to a concentration of 100 ng/L and retested. A post-spiking result that exceeded the critical difference at a predefined probability of 0.0005 of the target concentration (the median post-spiking result for each individual assay) was considered as outlier. To determine whether microclots were a significant cause of critically discrepant outlier results, a separate 50 samples were centrifuged twice between two post-spiking measurements using the Vitros TnI ES assay. Results The median recovery of the enriched cTnI was highest with the Roche assay (271 ng/L) and lowest with the Vitros assay (29 ng/L). The Vitros assay had the highest percentage of results that exceeded the critical difference (49%), followed by the Siemens (38%), Roche (18%) and Beckman Coulter (7%) assays. None of the 50 additional samples produced a critically lower cTnI result after re-centrifugation. Conclusions Our findings underscored the variability of cTnI assays in measuring native cTnI. The lack of cTnI results that became significantly lower after re-centrifugation suggested that microclots are unlikely to be a major cause of the outlier results. PMID:27346968

  9. Recovery of spiked troponin I in four routine assays.

    PubMed

    Loh, Tze Ping; Lim, Xiong Chang; Kieu, Karize; Sajiir, Haressh; Neo, Siew Fong; Cheng, Wan Ling; Sethi, Sunil Kumar

    2016-01-01

    This study aimed to examine the recovery of spiked human cardiac troponin I (cTnI) results measured by four routine assays, and investigate possible interference from microclots. 457 consecutive samples with cTnI concentration below limit of quantitation (12 ng/L), declared by the Vitros TnI ES assay (reference assay), were measured on Beckman Coulter Accu TnI+3, Siemens TnI-Ultra and Roche TnI STAT assays. These samples were enriched with native full-length cTnI to a concentration of 100 ng/L and retested. A post-spiking result that exceeded the critical difference at a predefined probability of 0.0005 of the target concentration (the median post-spiking result for each individual assay) was considered as outlier. To determine whether microclots were a significant cause of critically discrepant outlier results, a separate 50 samples were centrifuged twice between two post-spiking measurements using the Vitros TnI ES assay. The median recovery of the enriched cTnI was highest with the Roche assay (271 ng/L) and lowest with the Vitros assay (29 ng/L). The Vitros assay had the highest percentage of results that exceeded the critical difference (49%), followed by the Siemens (38%), Roche (18%) and Beckman Coulter (7%) assays. None of the 50 additional samples produced a critically lower cTnI result after re-centrifugation. Our findings underscored the variability of cTnI assays in measuring native cTnI. The lack of cTnI results that became significantly lower after re-centrifugation suggested that microclots are unlikely to be a major cause of the outlier results.

  10. BD-21 3873: another yellow-symbiotic barium star.

    NASA Astrophysics Data System (ADS)

    Smith, V. V.; Cunha, K.; Jorissen, A.; Boffin, H. M. J.

    1997-08-01

    An abundance analysis of the yellow symbiotic system BD-21 3873 reveals it to be a metal-poor K-giant ([Fe/H]=-1.3) which is enriched in the heavy s-process elements. In that respect, this star appears to be a twin of AG Dra, another yellow symbiotic system analyzed in a previous paper (Smith et al., 1996A&A...315..179S). The heavy-element abundance distributions of AG Dra and BD-21 3873 are almost identical, and are best reproduced by a s-process with a neutron exposure parameter of 1.2-1.3mb^-1^ and a neutron density logN_n_=8.3 (as derived from the Rb/Zr ratio). These two systems thus link the symbiotic stars to the binary barium and CH stars which are also s-process enriched. These binary systems, which exhibit overabundances of the heavy elements, owe their abundance peculiarities to mass transfer from thermally-pulsing asymptotic giant branch stars, which have since evolved to become white-dwarf companions of the cool stars we now view as the chemically-peculiar primaries. The spectroscopic orbits of BD-21 3873 (derived from CORAVEL measurements) and AG Dra are similar to those of barium and CH stars. With an orbital period of 281.6d, BD-21 3873 is one of the closest systems in these families, and its light curve indeed suggests that variations due to reflection and ellipticity effects are present. The amplitude of the ellipsoidal variations indicates that the giant must be close to filling its Roche lobe. However, no acceptable solution simultaneously satisfies the constraints from the light curve, the orbital elements and the evolutionary tracks in the framework of the standard Roche lobe geometry. We suggest that this discrepancy may be resolved by taking into account the deformation of the Roche lobe caused by the force driving the large mass loss of the giant.

  11. A spectroscopic study of anomalous stellar populations in M67

    NASA Astrophysics Data System (ADS)

    McGahee, Courtney Elizabeth

    A population of stars exists in the old, open cluster M67, whose photometry, color magnitude diagram locations and associated evolutionary states cannot be explained by current, standard single star evolution theory. These stars are often referred to as "yellow straggler" stars. Yellow stragglers have been identified in multiple star clusters suggesting that these stars constitute a real population. Additionally, according to independent studies, at least some of the yellow straggler stars in M67 are likely cluster members. Therefore, cluster non-membership is not a sufficient explanation for the observed anomalous photometry of these stars. It is possible that the yellow stragglers occupy their precarious color magnitude diagram positions as a result of the evolution of mass transfer blue straggler stars. These are stars which have been formed by Roche Lobe overflow mass transfer in close binary systems. If this the case for the yellow stragglers, it is hypothesized that they could potentially exhibit two spectroscopic characteristics that can be indicative of this type of mass transfer system. Specifically, variable radial velocities can be used to indicate that the yellow stragglers exist in binary systems and enhancements of s-process elements in yellow stragglers can indicate Roche Lobe overflow mass transfer from a once asymptotic giant branch star which has since evolved into a white dwarf. This dissertation details the radial velocity survey and the chemical abundance analysis that have been conducted to investigate the yellow stragglers with regard to this hypothesis. The radial velocity survey revealed that eight of the ten yellow stragglers studied exhibit variable radial velocities indicating that the yellow straggler population of M67 possess a high binary frequency. However, the chemical abundance analysis revealed that none of the yellow stragglers exhibited enhancements of the s-process elements Y and Ba. Therefore, a history which involves Roche

  12. Formation of Janus and Epimetheus from Saturn's rings as coorbitals, thanks to Mimas' 2:3 inner Mean Motion Resonances

    NASA Astrophysics Data System (ADS)

    Aurélien, Crida; El Moutamid, Maryame

    2017-06-01

    Janus and Epimetheus orbit Saturn at 151461 km on average, on mutual horseshoe orbits with orbital separation 50 km, exchanging position every 4 years. This configuration is unique and intriguing : Lissauer et al. (1985) have shown that their orbital separation should converge to zero in about 20 Myrs only, and no satisfactory model for the origin of this co-orbital resonance exists yet. Charnoz et al. (2010) have shown that Janus and Epimetheus probably formed from the spreading of the rings beyond the Roche radius. Here, we study this phenomenon in the frame of the elliptical restricted 3-body problem, where ring particles are perturbed by the 2:3 mean motion resonances with the outer satellite Mimas.Two types of resonances play different roles. The Lindblad resonance (LR) confines the rings radially, and prevents their spreading (like the B-ring into the Cassini division). The Corotation resonance (CR) confines the rings azimuthally in two capture sites (akin Neptune's arcs). Because of Saturn's J_2, the CR is 130 km closer to Saturn than the LR. A few hundred million years ago, the 2:3 mean motion resonances with Mimas were just inside the Roche radius ; hence the rings could not spread and the two capture sites were full of ring material. When Mimas migrated outwards so that its 2:3 mean motion resonances receded past the Roche radius, the captured material agglomerated into two bodies of ~10^{15} kg on the exact same orbit. These bodies then migrated outwards together due to their interaction with the rings, in mutual horseshoe orbits. The rings then spawn new small satellites, eventually accreted by the proto-Janus and the proto-Epimetheus following the pyramidal regime of the ring spreading model (Crida & Charnoz 2012). The two bodies then grow in mass following a Fibonacci sequence, and this excites their orbital separation, leading to a configuration close to the present one.

  13. Body Mass Index in Pregnancy Does Not Affect Peroxisome Proliferator-activated Receptor Gamma Promoter Region (−359 to −260) Methylation in the Neonate

    PubMed Central

    Casamadrid, VRE; Amaya, CA; Mendieta, ZH

    2016-01-01

    Background: Obesity in pregnancy can contribute to epigenetic changes. Aim: To assess whether body mass index (BMI) in pregnancy is associated with changes in the methylation of the peroxisome proliferator-activated receptor γ (PPAR) promoter region (-359 to - 260) in maternal and neonatal leukocytes. Subjects and Methods: In this matched, cohort study 41 pregnant women were allocated into two groups: (a) Normal weight (n = 21) and (b) overweight (n = 20). DNA was extracted from maternal and neonatal leukocytes (4000-10,000 cells) in MagNA Pure (Roche) using MagNA Pure LC DNA Isolation Kit 1 (Roche, Germany). Treatment of DNA (2 μg) was performed with sodium bisulfite (EZ DNA Methylation-Direct™ Kit; Zymo Research). Real-time quantitative polymerase chain reaction (qPCR) was performed in a LightCycler 2.0 (Roche) using the SYBR® Advantage® qPCR Premix Kit (Clontech). The primers used for PPARγ coactivator (PPARG) M3 were 5’- aagacggtttggtcgatc-3’ (forward), and5’- cgaaaaaaaatccgaaatttaa-3’ (reverse) and those for PPARG unmethylated were: 5’-gggaagatggtttggttgatt-3’ (forward) and 5’- ttccaaaaaaaaatccaaaatttaa-3’ (reverse). Intergroup differences were calculated using the Mann-Whitney U-test, and intragroup differences, with the Wilcoxon test (IBM SPSS Statistics for Windows, Version 19.0. Armonk, NY: IBM Corp.). Results: Significant differences were found in BMI, pregestational weight, and postdelivery weight between groups but not in the methylation status of the PPARγ promoter region (-359 to - 260). Conclusion: The PPARγ promoter region (-359 to - 260) in peripheral leukocytes is unlikely to get an obesity-induced methylation in pregnancy. PMID:27144075

  14. Formation of Black Hole Low-mass X-Ray Binaries in Hierarchical Triple Systems

    NASA Astrophysics Data System (ADS)

    Naoz, Smadar; Fragos, Tassos; Geller, Aaron; Stephan, Alexander P.; Rasio, Frederic A.

    2016-05-01

    The formation of black hole (BH) low-mass X-ray binaries (LMXB) poses a theoretical challenge, as low-mass companions are not expected to survive the common-envelope scenario with the BH progenitor. Here we propose a formation mechanism that skips the common-envelope scenario and relies on triple-body dynamics. We study the evolution of hierarchical triples following the secular dynamical evolution up to the octupole-level of approximation, including general relativity, tidal effects, and post-main-sequence evolution such as mass loss, changes to stellar radii, and supernovae. During the dynamical evolution of the triple system the “eccentric Kozai-Lidov” mechanism can cause large eccentricity excitations in the LMXB progenitor, resulting in three main BH-LMXB formation channels. Here we define BH-LMXB candidates as systems where the inner BH-companion star crosses its Roche limit. In the “eccentric” channel (˜81% of the LMXBs in our simulations) the donor star crosses its Roche limit during an extreme eccentricity excitation while still on a wide orbit. Second, we find a “giant” LMXB channel (˜11%), where a system undergoes only moderate eccentricity excitations but the donor star fills its Roche-lobe after evolving toward the giant branch. Third, we identify a “classical” channel (˜8%), where tidal forces and magnetic braking shrink and circularize the orbit to short periods, triggering mass-transfer. Finally, for the giant channel we predict an eccentric (˜0.3-0.6) preferably inclined (˜40°, ˜140°) tertiary, typically on a wide enough orbit (˜104 au) to potentially become unbound later in the triple evolution. While this initial study considers only one representative system and neglects BH natal kicks, we expect our scenario to apply across a broad region of parameter space for triple-star systems.

  15. Performance of an Early Infant Diagnostic Test, AmpliSens DNA-HIV-FRT, Using Dried Blood Spots Collected from Children Born to Human Immunodeficiency Virus-Infected Mothers in Ukraine

    PubMed Central

    Shanmugam, Vedapuri; Azarskova, Marianna; Nguyen, Shon; Hurlston, Mackenzie; Sabatier, Jennifer; Zhang, Guoqing; Osmanov, Saladin; Ellenberger, Dennis; Yang, Chunfu; Vitek, Charles; Liulchuk, Maria; Nizova, Natalya

    2015-01-01

    An accurate accessible test for early infant diagnosis (EID) is crucial for identifying HIV-infected infants and linking them to treatment. To improve EID services in Ukraine, dried blood spot (DBS) samples obtained from 237 HIV-exposed children (≤18 months of age) in six regions in Ukraine in 2012 to 2013 were tested with the AmpliSens DNA-HIV-FRT assay, the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 Qual test, and the Abbott RealTime HIV-1 Qualitative assay. In comparison with the paired whole-blood results generated from AmpliSens testing at the oblast HIV reference laboratories in Ukraine, the sensitivity was 0.99 (95% confidence interval [CI], 0.95 to 1.00) for the AmpliSens and Roche CAP/CTM Qual assays and 0.96 (95% CI, 0.90 to 0.98) for the Abbott Qualitative assay. The specificity was 1.00 (95% CI, 0.97 to 1.00) for the AmpliSens and Abbott Qualitative assays and 0.99 (95% CI, 0.96 to 1.00) for the Roche CAP/CTM Qual assay. McNemar analysis indicated that the proportions of positive results for the tests were not significantly different (P > 0.05). Cohen's kappa (0.97 to 0.99) indicated almost perfect agreement among the three tests. These results indicated that the AmpliSens DBS and whole-blood tests performed equally well and were comparable to the two commercially available EID tests. More importantly, the performance characteristics of the AmpliSens DBS test meets the World Health Organization EID test requirements; implementing AmpliSens DBS testing might improve EID services in resource-limited settings. PMID:26447114

  16. Military Interoperable Digital Hospital Testbed (MIDHT) Phase II

    DTIC Science & Technology

    2011-07-01

    0.00058 -0.00388 -0.01639 -0.01833 P o r t a g e N O R C A M -0.02550 -0.01126 -0.00370 -0.05563 -0.00681 -0.00417 -0.01754 9 Survey opportunities...satisfaction results are much lower than those reported by DesRoches et al2 regarding a 2008 national survey of physicians on EHR’s. Only 34% of CMMC...71020, 70450) by time period is presented below: P O S T P R E (baseline) Phase 1 Phase 2 2008 2009 2010 July through December January through

  17. The Role of BRCA1 Domains and Motifs in Tumor Suppression

    DTIC Science & Technology

    2009-08-01

    hypersensitive to ionizing radiation (IR) and develop *Correspondence to: Alvaro N.A. Monteiro; H. Lee Moffitt Cancer Center; 12902 Magnolia Drive...cells were maintained in DMEM media supplemented with 7.5% FBS, 100 units/mL penicillin /streptomycin and 1.25 μg/ mL amphotericin B (Sigma, St...mL penicillin /streptomycin and 1.25 μg/mL amphotericin B. Transient transfections using Fugene 6 (Roche) were performed according to manufacturer’s

  18. [Setting up of 15 POC blood gas analyzers at Montpellier Hosptital (France)].

    PubMed

    Marrocco, Alexandre; Cristol, Jean-Paul; Boularan, Anne-Marie

    2016-01-01

    The purpose of this article is to describe the setting up of 15 blood gas analyzers GEM(®) Premier™ 4000 (IL) at Montpellier hospital. This experience includes analytical characterization (within and between run coefficient of variation) using GSE and GHE IL controls, correlation of 35 samples with a routinely used laboratory blood gas analyzer (Cobas b221, Roche(®)). We shall also develop the training, the habilitation and its follow-up for the user staff (450 people) of the different hospital's units in the aim of the accreditation.

  19. Development and Evaluation of Up-Converting Phosphor Technology-Based Lateral Flow Assay for Quantitative Detection of NT-proBNP in Blood

    PubMed Central

    Hao, Qingfang; Zou, Deyong; Zhang, Xiaoli; Zhang, Liping; Li, Hongmei; Qiao, Yong; Zhao, Huansheng; Zhou, Lei

    2017-01-01

    A newly assay, up-converting phosphor technology-based lateral flow (UPT-LF) assay, was developed for rapid and quantitative detection of N-terminal fragment of B-type natriuretic peptide precursor (NT-proBNP), one of the most important serum molecular maker of heat failure, in plasma samples as a point of care testing (POCT) method for diagnosis of acute heart failure. Human plasma from 197 patients with acute heart failure and 200 healthy controls was assessed using the UPT-LF assay, in a comparison with a Roche Elecsys assay. The limit of detection of the UPT-LF assay, with a coefficient of variation (CV) of less than 15%, was 116 ng/L, which is lower than the clinical diagnosis cutoff (150 ng/mL). The linear range was 50–35,000 ng/L. The CVs were less than 10% for both UPT-LF and Roche Elecsys assays for plasma samples under different storages, demonstrating the good stability and reproducibility. There are certain linear correlations between the results of UPT-LF and Roche Elecsys assay for EDTA-K2 and heparin-anticoagulated plasma, as well as for serum samples. For UPT-LF assay, there is a significant correlation between the values derived from analysis of EDTA-K2 and heparin-anticoagulated plasma samples (R = 0.995). No statistically significant difference was found between serum and plasma samples for UPT-LF assay. Our results demonstrate that NT-proBNP levels in healthy adults are elevated with age and had a relationship with sex, and with the age increase the NT-proBNP levels of females are significantly higher than those of males (p<0.01). The UPT-LF assay has a high reproducibility, stability, sensitivity, specificity, and is consistent with Roche Elecsys assay, and therefore it could be used as a POCT method for the quantitative detection of NT-proBNP in blood for clinical diagnosis and research of acute heart failure. PMID:28151978

  20. Evidence for an Accretion Stream in the Low Accretion Rate Polar (LARP) J2048

    NASA Astrophysics Data System (ADS)

    Honeycutt, R. Kent; Kafka, S.; Tappert, C.

    2010-01-01

    We present new red/near-IR spectra of the LARP J204827.9+005008.9 obtained with the (UT2) telescope. All emission lines in our spectra have two components. The sinusoidal low amplitude component corresponds to irradiation at the inner hemisphere of the M3 star. Our Doppler maps indicate that the larger amplitude component may correspond to a ballistic stream from L1. J2048 is thought to be accreting via a wind, so the detection of velocity features consistent with the velocities of Roche lobe overflow is unexpected. We briefly discuss scenarios that might explain this situation, but none are fully satisfactory.