Science.gov

Sample records for 03-02-1999 amplicor roche

  1. Comparison of Roche Cobas Amplicor Mycobacterium tuberculosis Assay with In-House PCR and Culture for Detection of M. tuberculosis

    PubMed Central

    Eing, Bodo R.; Becker, Andrea; Sohns, Arthur; Ringelmann, Ronald

    1998-01-01

    The new Roche Cobas Amplicor Mycobacterium tuberculosis assay, which is a semiautomated version of the manually performed Roche Amplicor M. tuberculosis test, was compared to culture and an IS6110-based in-house PCR protocol. A total of 1,681 specimens from 833 patients, including specimen types other than sputum, were tested in parallel by both the in-house PCR and the Cobas Amplicor M. tuberculosis assay. After we resolved discrepant PCR results, the sensitivity, specificity, and positive and negative predictive values for the Cobas Amplicor M. tuberculosis assay were 66.33, 99.71, 94.36, and 97.66%, respectively. The corresponding values for the in-house PCR were 91.08, 99.85, 97.87, and 99.37%, respectively. For culture- and smear-positive specimens, the sensitivity of the Cobas Amplicor M. tuberculosis test was 96.42% (in-house PCR, 100%). If only smear-negative sputum specimens were considered, the Cobas Amplicor M. tuberculosis assay exhibited a sensitivity of 45.45% (in-house PCR, 63.63%) relative to that of culture. With a modified protocol for DNA extraction (washing of samples plus ultrasonication), both PCR methods performed better with gastric aspirates than with sputum samples (sensitivity of the Cobas Amplicor M. tuberculosis assay with smear-negative gastric aspirates, 70.00%; sensitivity of in-house PCR, 90.00%). With dithiothreitol being used for liquefaction of specimens in this study, the Cobas Amplicor M. tuberculosis assay exhibited an inhibition rate of 9.16%. In our view, the new Cobas Amplicor M. tuberculosis test (i) is well suited for typing of smear-positive specimens, (ii) may also be applied to gastric aspirates and other types of specimens if DNA extraction methods are modified appropriately, and (iii) exhibits a sensitivity with smear-negative sputum specimens which makes it recommendable that a minimum of three samples from the same patient be tested. PMID:9650955

  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. 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.

  4. 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

  5. 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.

  6. Clinical Evaluation of the Automated COBAS AMPLICOR MTB Assay for Testing Respiratory and Nonrespiratory Specimens

    PubMed Central

    Reischl, Udo; Lehn, Norbert; Wolf, Hans; Naumann, Ludmila

    1998-01-01

    We evaluated the COBAS AMPLICOR PCR system (Roche Diagnostics) for the routine detection of Mycobacterium tuberculosis complex (MTBC) in clinical specimens. Diagnostic culture, considered as the reference method, was performed with BACTEC, Löwenstein-Jensen, Stonebrink, and Kirchner media. Occasionally MB-Redox, ESP, or MGIT medium was also used. A total of 643 respiratory and 506 nonrespiratory specimens collected from 807 patients were investigated. Of the 95 culture-positive specimens, 80 were COBAS AMPLICOR MTB positive, and of the 1,054 culture-negative specimens, 1,044 were COBAS AMPLICOR MTB negative. After resolving discrepancies by review of the medical history, the overall sensitivity, specificity, and positive and negative predictive values for the COBAS AMPLICOR MTB assay, respectively, were 83.5, 98.8, 86.7, and 98.6% compared to those of diagnostic culture. In smear-positive specimens, the sensitivity of the COBAS AMPLICOR MTB assay was 96%, versus 48% for smear-negative specimens. No significant differences in the test performance between respiratory and nonrespiratory specimens were observed. The overall inhibition rate was less than 2%, excluding stool specimens. The clear advantages of the COBAS AMPLICOR PCR system are standardized procedures and reagents for specimen processing as well as an internal control for reliable monitoring of PCR inhibitors. By simplifying the work flow through a completely automated amplification and amplicon detection procedure, the COBAS AMPLICOR PCR system proved itself as a very useful component for routine diagnostic procedures. PMID:9738032

  7. Clinical evaluation of the automated COBAS AMPLICOR MTB assay for testing respiratory and nonrespiratory specimens.

    PubMed

    Reischl, U; Lehn, N; Wolf, H; Naumann, L

    1998-10-01

    We evaluated the COBAS AMPLICOR PCR system (Roche Diagnostics) for the routine detection of Mycobacterium tuberculosis complex (MTBC) in clinical specimens. Diagnostic culture, considered as the reference method, was performed with BACTEC, Löwenstein-Jensen, Stonebrink, and Kirchner media. Occasionally MB-Redox, ESP, or MGIT medium was also used. A total of 643 respiratory and 506 nonrespiratory specimens collected from 807 patients were investigated. Of the 95 culture-positive specimens, 80 were COBAS AMPLICOR MTB positive, and of the 1,054 culture-negative specimens, 1,044 were COBAS AMPLICOR MTB negative. After resolving discrepancies by review of the medical history, the overall sensitivity, specificity, and positive and negative predictive values for the COBAS AMPLICOR MTB assay, respectively, were 83.5, 98.8, 86.7, and 98.6% compared to those of diagnostic culture. In smear-positive specimens, the sensitivity of the COBAS AMPLICOR MTB assay was 96%, versus 48% for smear-negative specimens. No significant differences in the test performance between respiratory and nonrespiratory specimens were observed. The overall inhibition rate was less than 2%, excluding stool specimens. The clear advantages of the COBAS AMPLICOR PCR system are standardized procedures and reagents for specimen processing as well as an internal control for reliable monitoring of PCR inhibitors. By simplifying the work flow through a completely automated amplification and amplicon detection procedure, the COBAS AMPLICOR PCR system proved itself as a very useful component for routine diagnostic procedures.

  8. 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.

  9. Assessment of Use of the COBAS AMPLICOR System with BACTEC 12B Cultures for Rapid Detection of Frequently Identified Mycobacteria

    PubMed Central

    Ninet, B.; Rohner, P.; Metral, C.; Auckenthaler, R.

    1999-01-01

    The use of the COBAS AMPLICOR System (Roche Molecular Diagnostics, Basel, Switzerland), the only automated system for PCR testing, was evaluated for a rapid identification of mycobacteria with positive BACTEC 12B cultures. Two hundred ninety-six specimens with a growth index of ≥30 were analyzed for the presence of Mycobacterium tuberculosis complex, Mycobacterium avium, and Mycobacterium intracellulare. Compared to traditional methods and provided that samples with PCR inhibition are retested at a 1:10 dilution, the sensitivity and specificity of the COBAS AMPLICOR System with BACTEC 12B cultures were 100 and 98%, respectively. The COBAS AMPLICOR method is rapid and reliable for identifying the most common mycobacteria in cultures. PMID:9986853

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Misidentification of Mycobacterium leprae as Mycobacterium intracellulare by the COBAS AMPLICOR M. intracellulare Test

    PubMed Central

    Lefmann, M.; Moter, A.; Schweickert, B.; Göbel, U. B.

    2005-01-01

    Commercially available nucleic acid probe- and amplification-based systems for detection and differentiation of mycobacteria are widely used in clinical microbiology laboratories. Here we report two cases of human leprosy in which the COBAS AMPLICOR Mycobacterium intracellulare test led to false- positive results. Correct identification of Mycobacterium leprae was possible only by amplification and comparative sequence analysis of the 16S rRNA gene. PMID:15815021

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Roche Potential with Luminous Accretion Disks

    NASA Astrophysics Data System (ADS)

    Fukue, Jun; Hanamoto, Keishi

    2002-12-01

    The radiative environments of an interacting binary, which contains a luminous accretion disk, are investigated. The disk radiation field has no effect in the direction of the orbital plane, while it significantly affects in the polar direction. As the disk luminosity increases, the Roche potential around the compact star becomes hollow in the polar direction. It further crashes toward the pole, and a cone of avoidance appears at the normalized luminosity Γd ≡ Ld/LE = 0.5, where Ld is the disk luminosity and LE the Eddington luminosity of the compact star. The disk corona, the wind-fed accretion flow, and the common envelope suffer a remarkable influence by the luminous disk in active binaries. Of these, the wind-fed accretion is briefly discussed.

  9. 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

  10. 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).

  11. ["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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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}.

  19. 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

  20. Performance of an IS6110-Based PCR Assay and the COBAS AMPLICOR MTB PCR System for Detection of Mycobacterium tuberculosis Complex DNA in Human Lymph Node Samples

    PubMed Central

    Rimek, Dagmar; Tyagi, Sachin; Kappe, Reinhard

    2002-01-01

    We compared the performance of two PCR assays, an IS6110-based in-house protocol and the COBAS AMPLICOR MTB PCR (COBAS MTB) system, for the detection of Mycobacterium tuberculosis complex in 43 human lymph node samples from 40 patients. For the in-house PCR and the COBAS MTB assays, respectively, sensitivities were 87.5% versus 45.5% (P < 0.05), specificities were 100.0% versus 91.3% (P > 0.05), and inhibition rates were 4.8% versus 19.5% (P < 0.05). For the COBAS MTB system, additional N-acetyl-l-cysteine-NaOH pretreatment of the samples changed neither the inhibition rate nor the sensitivity significantly. PMID:12149389

  1. 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...

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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).

  13. 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…

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  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. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. [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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  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. 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.

  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. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. [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.

  12. 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.

  13. 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

  14. 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.

  15. 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…

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. "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.

  14. 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.

  15. 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.

  16. 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…

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  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. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. [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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Accuracy of roche accu-chek inform whole blood capillary, arterial, and venous glucose values in patients receiving intensive intravenous insulin therapy after cardiac surgery.

    PubMed

    Karon, Brad S; Gandhi, Gunjan Y; Nuttall, Gregory A; Bryant, Sandra C; Schaff, Hartzell V; McMahon, M Molly; Santrach, Paula J

    2007-06-01

    Intravenous insulin protocols are increasingly common in the intensive care unit to maintain normoglycemia. Little is known about the accuracy of point-of-care glucometers for measuring glucose in this patient population or the impact of sample source (capillary, arterial, or venous whole blood) on the accuracy of glucometer results. We compared capillary, arterial, and venous whole blood glucose values with laboratory plasma glucose values in 20 patients after cardiac surgery. All 4 samples (capillary, arterial, and venous whole blood and laboratory plasma glucose) were analyzed hourly for the first 5 hours during intravenous insulin therapy in the intensive care unit. There were no significant differences between median capillary whole blood (149 mg/dL [8.3 mmol/L]) and laboratory plasma (151 mg/dL [8.4 mmol/L]) glucose levels. The median arterial (161 mg/dL [8.9 mmol/L]) and venous (162 mg/dL [9.0 mmol/L]) whole blood glucose levels were significantly higher than the median laboratory plasma glucose level. Capillary whole blood glucose levels correlate most closely with laboratory plasma glucose levels in patients receiving intensive intravenous insulin therapy after cardiac surgery.

  4. 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

  5. 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.

  6. 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.

  7. [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

  8. 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.

  9. 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.

  10. 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

    2007-11-02

    megaterium Bacillus polymyxa Bacillus sphaericus Bacillus stearothermophilus Bacillus subtilis subsp. niger Bacillus thuringiensis Bacillus popilliae...xylosoxydans Bacillus anthracis BA0068 Ames Sterne SPS 97.13.213 Bacillus cereus Bacillus coagulans Bacillus licheniformis Bacillus macerans Bacillus ...varicella- zoster virus, and Bacillus anthracis DNA by LightCycler polymerase chain reaction after

  11. 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…

  12. 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.

  13. 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.

  14. [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

  15. Center for the Advancement of Sustainability Innovations (CASI): A Summary of the Center’s First Year’s Activities

    DTIC Science & Technology

    2008-05-01

    www.sandia.gov/mission/energy/index.html ERDC POC: Tarek Abdullah, Tarek.Abdullah@usace.army.mil, 217-373-4432 Roch Ducey , Roch.Ducey...controls/storage. ERDC POCs: Thomas Hartranft and Roch Ducey , Roch.A.Ducey@usace.army.mil, 217-373-6760 SERDP POC: John Hall. Website...www.serdp.org Publication: Roch Ducey and William Goran drafted an article entitled “Potential Military Applications of Energy Micro-Grids” for October 2007

  16. 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

  17. 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.

  18. 78 FR 44577 - Senior Executive Service Performance Review Board

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-24

    ... Grade, Deborah C. Gramlick, Carl Graves, Margaret Greene, Jonathan Griffin, Robert Grimm, Michael Gross..., David M. Robinson, George A. Roche, William W. Rodriguez, Waldemar Rogers, Debra Rudolph, Alan...

  19. 77 FR 2071 - Medical Devices; Availability of Safety and Effectiveness Summaries for Premarket Approval...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-13

    ... date P100031, FDA-2011-M-0502...... Roche Diagnostics ELECSYS ANTI-HBC IMMUNOASSAY & June 22, 2011. Corp.. ELECSYS PRECICONTROL ANTI-HBC. P100032, FDA-2011-M-0503...... Roche Diagnostics ELECSYS ANTI-HBC... ANALYZER. P100001, FDA-2011-M-0563...... Ortho-Clinical VITROS IMMUNODIAGNOSTICS July 20, 2011....

  20. Insulin and Breast Cancer Risk

    DTIC Science & Technology

    2002-06-01

    of three standard samples. Serum glucose was determined on a Cobas Mira automated chemistry analyzer (Roche Diagnostic Systems, Indianapolis, IL). The...was determined on a Cobas Mira automated chemistry analyzer (Roche Diagnostic Systems, Indianapolis, IL). The intrabatch coefficient of variation

  1. 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

  2. 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…

  3. 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...

  4. 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

  5. 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...

  6. 76 FR 17776 - Animal Drugs, Feeds, and Related Products; Withdrawal of Approval of New Animal Drug Applications...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-31

    ... CFR section affected (sponsor's Sponsor (established name of drug) drug labeler code) Roche Vitamins...., Roche Vitamins, Inc., Waterloo Mills Co., and Wendt Laboratories, Inc., are no longer the sponsors of an... Vitamins, Inc.'', ``Waterloo Mills Co.'', and ``Wendt Laboratories, Inc.''; and in the table in...

  7. 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.

  8. 76 FR 59416 - Senior Executive Service Performance Review Board

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-26

    .... Gramlick, Carl Graves, Margaret Griffin, Robert P., Ph.D Grimm, Michael Gross-Davis, Leslie Grossman, Seth..., William Ratliff, Gerri L. Rhew, Perry J. Robles, Alfonso Roche, William Rogers, Debra Rossides, Gale...

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. Waste-to-Energy ECIP (Energy Conservation Investment Program) Project. Volume 1: An Analysis of Hydrogen Infrastructure Fuel Cell Technology

    DTIC Science & Technology

    2006-04-01

    Infrastructure Fuel Cell Technology Gonzalo Perez, Robert Neathammer, Franklin H. Holcomb, Roch A. Ducey , Byung J. Kim, and Fred Louis April 2006 C on...Analysis of Hydrogen Infrastructure Fuel Cell Technology Franklin H. Holcomb, Roch A. Ducey , and Byung J. Kim Construction Engineering Research...assistance in this project. Dr. Tho- mas Hartranft is Chief, CEERD-CF-E, and L. Michael Golish is Chief, CEERD-CF. The associated Technical Director was

  14. Energy Supply Options for Modernizing Army Heating Systems

    DTIC Science & Technology

    1999-01-01

    Modernizing Army Heating Systems Michael K. Brewer, Thomas E. Durbin, Chris Dilks, Roch A. Ducey , Vicki L. Van Blaricum, William T. Brown, William...NUMBERS 4A162784 AT45 UL-XC7 6. AUTHOR(S) Michael K. Brewer, Thomas E. Durbin, Chris Dilks, Roch A. Ducey , Vicki L. VanBlaricum, William T. Brown...Laboratories (USACERL). The USACERL principal investigator was Michael K. Brewer. Martin J. Savoie is Acting Chief, CECER-UL-U; Dr. John T. Bandy is

  15. Dietary Intake and Stress Fractures Among Elite Male Combat Recruits

    DTIC Science & Technology

    2012-03-13

    orthopedic surgeons in order to detect the presence of stress fracture and other overuse injuries. Anthropometric measurements Anthropometric measurements... immunoassay (Roche Elecsys®, Roche Diagnostics GmbH, Mannheim, Germany, reference: of 16–293 ng/ml). Serum iron was measured with a commercial kit on...measure 25(OH)D levels (DiaSorin, Stillwater, MN, reference range 30.0– 74.0 ng/ml). Parathyroid hormone (PTH) was measured by immunoassay with

  16. 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

  17. 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

  18. 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.

  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. 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.

  1. 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

  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. 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.

  4. 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.

  5. 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.

  6. 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

  7. Molecular Mechanisms and Treatment Strategies for Obesity-Associated Coronary Artery Disease, an Imminent Military Epidemic

    DTIC Science & Technology

    2008-12-01

    lesions that lacked nuclei and cytoplasm. In Situ TdT-Mediated dUTP Nick -End Labeling Assays Apoptotic cells in the intima of atherosclerotic lesions...were detected by the TdT-mediated dUTP nick -end labeling (TUNEL) technique using the TMR red in situ cell death detection kit (Roche Diagnos- tics...data were verified by TUNEL (Tdt-mediated dUTP nick end labeling) analysis, using the in-situ cell death detection kit, TMR red, from Roche (see

  8. 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.

  9. Inhibition of Estrogen-Induced Growth of Breast Cancer by Targeting Mitochondria Oxidants

    DTIC Science & Technology

    2010-04-01

    mM NaCl, 0.5% deoxycholate, 0.1% Nonidet P - 40 , 0.1% SDS, 50 mM Tris) containing protease and phosphatase inhibitors (Roche, CA). Equal amounts of...19 deoxycholate, 0.1% Nonidet P - 40 , 0.1% SDS, 50 mM Tris) containing protease and phosphatase inhibitors (Roche, CA). Whole cell lysates (WCL...modulators (MnSOD and catalase), were pre-treated with 40 μM ebselen or 1.0 mM NAC and then challenged with 100 pg/ml estrogensMCF-7 cells containing null

  10. 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.

  11. Trackline and Point Detection Probabilities for Acoustic Surveys of Cuvier’s and Blainville’s Beaked Whales

    DTIC Science & Technology

    2013-09-01

    La Jolla, California 92037 Peter L. Tyack and Mark P. Johnson Scottish Oceans Institute, East Sands, St. Andrews, Fife, Scotland KY15 5NT, United...survey,” Marine Mammal Sci. 21, 429–445. Baumann-Pickering, S., Wiggins, S. M., Roth , E. H., Roch, M. A., Schnitzler, H.-U., and Hildebrand, J. A

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. Effect of T-2 Toxin, Fasting, and 2-Methyl-thiazolidine-4-carboxylate, a Glutathione Prodrug, on Hepatic Glutathione Levels1,2

    DTIC Science & Technology

    1986-11-14

    method of Tietz (1969). This method3 was specifically modified for automated analysis on a Cobas-Bio Automated Chemistry Analyzer (Roche Analytical...automated analysis on a Cobas-Bio Automated Chemistry Analyzer . Enzymatic activity was determined in the linear range for both time and protein. Protein was

  19. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. Improving the Cybersecurity of U.S. Air Force Military Systems Throughout Their Life Cycles

    DTIC Science & Technology

    2015-01-01

    James D. Powers, Elizabeth Bodine-Baron, Bernard Fox, Lauren Kendrick, Michael H. Powell Report Documentation Page Form ApprovedOMB No. 0704...rather than by an inherently secure design. 7 See also Baldwin , Dahmann, and Goodnight, 2011. 7...of more proximate objectives. A common pitfall of analysis is to adopt as goals the most clearly defined and easily measured phenomena. James Roche

  1. 76 FR 14691 - Notice of Determinations Regarding Eligibility To Apply for Worker Adjustment Assistance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-17

    .... Florence, SC February 7, 2010. Hoffman-LA Roche, Pharmaceutical, Pharma Technical, Olsten Staffing, etc. 75... International, Roth Staffing. 75,277 Steelcase, Inc., Wood Plant. Caledonia, MI June 14, 2011. 75,277A Manpower, Working On-Site at Caledonia, MI February 1, 2010. Steelcase, Inc.; Wood Plant. The...

  2. 40 CFR Table 2 to Subpart Jj of... - List of Volatile Hazardous Air Pollutants

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (Aroclors) 1336363 Polycyclic Organic Matter b 1,3-Propane sultone 1120714 beta-Propiolactone 57578... glycol ethers with the structure: R-(OCH2CH2)n—OH. Polymers are excluded from the glycol category. b Includes organic compounds with more than one benzene ring, and which have a boiling point greater than...

  3. 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…

  4. 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.

  5. 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.…

  6. 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

  7. 76 FR 47210 - Medical Devices; Availability of Safety and Effectiveness Summaries for Premarket Approval...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-04

    .......... Roche Molecular cobas HPV test April 19, 2011. Systems, Inc. P100029 FDA-2011-M-0296....... St. Jude...). P930014 (S45) FDA-2011-M-0338. Alcon Research, Ltd... AcrySof toric IOL and AcrySof IQ May 3, 2011....

  8. The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  9. Comparison of the Media Coverage of the Vietnam War to the Media Coverage of the Invasions of Grenada and Panama: A Question of Legacies

    DTIC Science & Technology

    1991-01-01

    Advisory committee: Di.•t , .i ,’ u Professor Kathy McAda.ms, Advisor I Professor Steve Barkin Professor James Roche --- 4- ABSTRACT Title...administration. Commentators such as Walter Cronkite, David Brinkley, Frank McGee and Howard K. Smith became less objective and much more personal in

  10. 454-pyrosequencing: A tool for discovery and biomarker development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. 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.

  12. 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…

  13. Identification and initial characterization of a novel turkey-origin picobirnavirus using a metagenomic approach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  14. Genome Wide Characterization of Simple Sequence Repeats in Cucumber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  15. 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

  16. 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,…

  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. 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…

  19. 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…

  20. Swedish Defence Research Abstracts 82/83-2 (Froe Foersvars Forsknings Referat 82/83-2).

    DTIC Science & Technology

    1983-08-01

    alarm (78) Carbon dioxide retention inside motorcycle helmets (79) Vibration and decompression gas bubbles (80) No effects of nootropic drugs on memory... nootropic drugs on memory and psychomotor performance during reduced air pressure (in English) S. Levander and others Report I from the Roche Clinical Unit

  1. 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

  2. Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. VizieR Online Data Catalog: LMC X-3 formation history (Sorensen+, 2017)

    NASA Astrophysics Data System (ADS)

    Sorensen, M.; Fragos, T.; Steiner, J. F.; Antoniou, V.; Meynet, G.; Dosopoulou, F.

    2016-10-01

    Selected parameters of mass transfer sequence models computed with MESA that matches observational inferred data on the BH X-ray binary LMC X-3. Each record describes the initial configuration of the LMC X-3 binary the moment Roche lobe overflow begins. (1 data file).

  4. 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…

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. 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)

  14. 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.

  15. 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....

  16. 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}.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. [Sensitivity of the COBAS AmpliScreen™ HIV-1 test v1.5 for HIV-1 detection].

    PubMed

    Gomez, Lucía P; Balangero, Marcos C; Castro, Gonzalo; Kademian, Silvia; Mangeaud, Arnaldo; Barbas, María G; Cudolá, Analía; de León, Juan F; Carrizo, Horacio; Gallego, Sandra V

    2014-01-01

    The introduction of nucleic acid amplification techniques (NAT) in blood banks was intended to reduce the residual risk of transfusion-transmitted infections. Co-circulation of a great diversity of HIV-1 variants in Argentina portrays the need to assess the sensitivity of serological and molecular assays available for their detection. In this study, we evaluated the sensitivity of the COBAS AmpliScreen™ HIV-1 Test, version 1.5 (Roche) for the detection of HIV-1 RNA in plasma samples of infected individuals from Argentina. The results of this study reveal that this technique has high sensitivity for the detection of HIV-1 RNA under assay conditions: using mini-pool testing, pools ≥ 50 RNA copies per ml achieved ≥ 92 % sensitivity, whereas in the standard procedure, samples ≥ 207 RNA copies/ml achieved 100 % sensitivity. Moreover, the COBAS AmpliScreen™ HIV-1 Test, version 1.5 (Roche) is suitable for detecting prevailing HIV-1 variants.

  10. 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

  11. JPRS Report, Africa, (Sub-Sahara).

    DTIC Science & Technology

    2007-11-02

    by the sugar industry each year. The lime kilns are located at Ville Noire, Beau Champ, Riviere du Rempart, Baie du Tombeau, Roche Bois and Grande...proach to urbanisation (as set out in the relative White Paper) allows for greater inward indus- trialisation — that is, a process of economic...velopment. The latter does not clash with a simultaneous urbanisation programme or the consequential pro- cess of inward indus- trialisation. More than

  12. 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.

  13. Optical Observations With Milliarcsecond Resolution Of Stars, Their Environments And Companions

    DTIC Science & Technology

    2012-01-01

    eclipsing binary system con- sisting of a ~3 solar mass B6-8II star which has filled its Roche lobe and a ~13 solar mass early B star, which is completely...mass binaries, eclipsing binaries, and radio stars. These observations also reveal the previously unseen companions in single-lined spectroscopic...a number of stellar systems which include high-mass binaries, eclipsing binaries, and radio stars. These observations also reveal the previously

  14. 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

  15. Evolution of Very Close Binaries of Low Mass

    SciTech Connect

    Eggleton, P

    2009-07-17

    Binaries of low total mass (say 1-3 M{sub {circle_dot}}) and very short period (say {approx}< 4 d) are subject to a number of evolutionary processes, such as nuclear evolution, Roche-Lobe overflow, mass loss by stellar wind enhanced by rapid rotation, angular momentum loss by stellar wind with magnetic braking and tidal friction, mass transfer in contact (potentially in either direction), and heat transport from one component to the other during contact. Unfortunately all of these phenomena can be expected to occur on something like the same timescale. This makes it especially difficult to tie a particular system to a particular set of evolutionary processes. Theory suggests that very close binaries should appear in four morphological forms: detached binaries, semidetached binaries in which the more massive component is the one that fills its Roche lobe (reverse Algols), semidetached binaries in which the less massive component is the one that fills its Roche lobe (normal Algols), and contact, or, as some would say, overcontact binaries, where both components overfill their Roche lobes up to the same equipotential surface. This is not to say that perhaps some other configuration may be important, but I am not sure that any has yet been put forward that is incontrovertible. I have developed an evolutionary code in which the two components are solved simultaneously, and subject in principle to all six of the processes in the first paragraph. All four morphological forms are achievable by the code, as the physics demands. The code is still preliminary, partly at least because of the difficulty of quantifying all six processes. I will illustrate some possibly peculiar evolutionary scenarios that can emerge; but I will mainly argue, on the basis of observed data from a variety of systems, that it is indeed necessary to include all these processes, and not, for example, to ignore mass loss by stellar wind by claiming that it cannot be strong enough to be significant.

  16. 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.

  17. 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.

  18. 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

  19. Promotion of Tumor-Initiating Cells in Primary and Recurrent Breast Tumors

    DTIC Science & Technology

    2013-07-01

    Geneticin, Sigma - Aldrich, St Louis, MO, USA). The Her2 wild-type and mutant (V654E) plasmids were constructed previously (Li et al., 2004) (Addgene...instructions supplemented with protease inhibitor mix (Roche) and phosphatase inhibitor mix ( Sigma ). Nuclear and cytoplasmic extracts were prepared as...inhibitor cocktail ( Sigma -Aldrich). IKK complexes were immunoprecipitated from 500mg total protein extract using IKKg antibody (Santa Cruz Biotechnology). An

  20. Marine Mammal Demographics of the Outer Washington Coast During 2008-2009

    DTIC Science & Technology

    2011-08-01

    Širović, Erin M. Oleson, John Calambokidis, Simone Baumann-Pickering, Amanda Cummins, Sara Kerosky, Lauren Roche, Anne Simonis, Sean M. Wiggins, and...Science Center Simone Baumann-Pickering Amanda Cummins Sara Kerosky Scripps Institute of Scripps Institute of Scripps Institute of...AUTHOR(S) 5d. PROJECT NUMBER Ana Širović, Erin M. Oleson, John Calambokidis, Simone Baumann- Pickering, Amanda Cummins, Sara Kerosky, Lauren

  1. 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.

  2. Molecular Modeling in Drug Design for the Development of Organophosphorous Antidotes/Prophylactics

    DTIC Science & Technology

    1986-05-01

    5012 61102A 1102BS11 EB 025 11. TITLE (Include Security Classification) Molecular Modeling in Drug Design for the Development of Organophosphorous...t ....................................., ’ i.° AD MOLECULAR MODELING IN DRUG DESIGN FOR THE DEVELOPMENT OF ORGANOPHOSPHOROUS ANTIDOTES...Reed, W.J. Murray, E.B. Roche and L.N. Donelsmith, Gen. Pharmac., 12, 177-185 (1981). 5. L.B.Kier, "Molecular Orbital Theory in Drug Design ", Academic

  3. Autonomic Dysreflexia-Like Syndrome in a T12 Paraplegic During Thoracic Spine Surgery

    DTIC Science & Technology

    2010-11-01

    or lumbar spinal cord lesions and paraplegia have been reported to exhibit catecholamine-induced hypertension and autonomic dys- function of central...cord origin. Roche et al.17 reported a series of 5 African American male patients with low thoracic or lumbar traumatic paraplegia exhibiting severe...Am Paraplegia Soc 1992;15:171–86 4. Amzallag M. Autonomic hyperreflexia. Int Anesthesiol Clin 1993;31:87–102 5. Karlsson AK. Autonomic dysreflexia

  4. Bibliography of Technical Publications and Papers, October 1978 - September 1979

    DTIC Science & Technology

    1979-11-01

    C. ROCHE, D. RYU, and M. MANDELS. Cellulase production by a new mutant strain of Trichoderma reesei MCC 77. Biotech. Bioeng. Symp., 8: 89-101 (1978...Physiol. Psychol., 93(3): 538-547 (1979). 180. HANDELS, M., S. DORVAL, and J. MEDE1WS. Saccarification of cellulose with Trichoderma cellulase . Proc...pouches. J. Food Quality, 2(2): 75-103 (1978). 190. SPANO, L., A. ALLEN, T. TASSINARI, M. MANDELS, and D. RYU. Reassessment of economics of cellulase

  5. Bibliography of Technical Publications and Papers July 1976 - September 1977

    DTIC Science & Technology

    1977-10-01

    1976). 207. , and J. M. NYSTROM. Pilot scale production of cellulase and enzymatic hydrolysis of waste cellulose. Amer. Inst. Chem. Eng. Symp. Series...Org. Chem., 41(13): 2320-2326 (1976). 233. ,L.NDELS, M., R. ANDREOTTI, and C. ROCHE. Measurement of saccarifying cellulase . Biorechnol. & Bioeng...J. N1., and A. L. ALLEN. Pilot scale investigations and economics of cellulase production. Biotechnol. 6 Bioeng. Symp. No. 6, 55-74 (1976). 38 FOOD

  6. Acoustic Metadata Management and Transparent Access to Networked Oceanographic Data Sets

    DTIC Science & Technology

    2015-09-30

    Transparent Access to Networked Oceanographic Data Sets Marie A. Roch Dept. of Computer Science San Diego State University 5500 Campanile Drive San...derived from these recordings (metadata of the recordings) becomes crucial in order to combine data across disparate studies to provide information...The period over which effort was invested may not be the same as that of the acoustic data itself. Examples of this include gaps due to

  7. 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.

  8. Aerospace Materials Process Modelling

    DTIC Science & Technology

    1988-08-01

    des phdnombnes physico - chimiques , slors sal connus, notamment des rdactions do phase as produisant dana l intorvalle do solidification, par des...connaissance do donndos theraiques, sinai qua du comportement e~canique, physico - chimique at mdtaliurgique des pibees & order maim aussi des moules. des...W.T.Sbs 16 A NUMERICAL MODEL OF DIRECTIONAL SOLIDIFICATION OF CAST TURBINE BLADES by G,.Lammndu and L -Veruiot des Roches 17 Paper IS withdrawn Pape 19

  9. 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.

  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. The Report of the Working Group Concerning the Deterrence of and Response to Incidents of Sexual Assault at the U.S. Air Force Academy

    DTIC Science & Technology

    2003-06-01

    restricted and have the fewest privileges.730 Of all the year groups , the most pressure is placed on Fourth-Class cadets. Interviews with faculty...working group to review cadet complaints, and the policies, programs and practices of the Academy to deter and respond to incidents of sexual assault...with a view toward making recommendations as appropriate. Secretary Roche also tasked the Working Group to review cases of sexual assault that had

  13. The Impact of Electronic Knowledge-Based Nursing Content and Decision-Support on Nursing-Sensitive Patient Outcomes

    DTIC Science & Technology

    2015-02-01

    community health centers on patient activation. Patient Educ Couns, 84(2), 257-260. DesRoches, C., Donelan, K., Buerhaus, P., & Zhonghe, L. (2008...decision support (CDS) tools in electronic health records (EHR) hold great promise, but are relatively untested for nurses . Researchers have suggested that...Dissemination, Information.  Evidence-Based Nursing  Health Services Research  Nursing Evaluation Research  Nursing Informatics  Nursing Process Patient

  14. 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.

  15. 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

  16. Reducing DoD Fossil-Fuel Dependence

    DTIC Science & Technology

    2006-09-01

    Wheels Analysis of Vehicle/Fuel Systems 20Jul06: (VTC) Robert Roche and Peter Melik [Army, AMSAA]: Fuel Consumption Modeling and Support Insights In...grains DDGS Distiller’s dried grains with solubles 91 DICI Direct Injection Compression Ignition (engine) DME Dimethyl ether. Surrogate for diesel...and do not own the transmission lines. Joule The ( kinetic ) energy acquired by a mass of one kilogram moving at a speed of one meter per second kJ

  17. Reducing DoD Fossil-Fuel Dependence

    DTIC Science & Technology

    2006-09-01

    Analysis of Vehicle/Fuel Systems 20Ju106: (VTC) Robert Roche and Peter Melik [Army, AMSAA]: Fuel Consumption Modeling and Support Insights In addition...with solubles 90 DICI Direct Injection Compression Ignition (engine) DME Dimethyl ether. Surrogate for diesel. DOE Department of Energy. The federal...wholesale to the power market. IPPs own and operate their stations as non-utilities and do not own the transmission lines. Joule The ( kinetic ) energy acquired

  18. 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

  19. Airmen First: Shaping the Expeditionary Air Force for Counterinsurgency

    DTIC Science & Technology

    2006-09-01

    American Power (New York: Basic Books, 2002), 336-352. 3 Airpower has played a role in fighting insurgents since Brigadier General John J. Pershing led the...operational effects on specific targets. See Honorable James G. Roche, Secretary of the Air Force, and General John P. Jumper, Chief of Staff, U.S. Air Force...operations characterized by irregular warfare—operations in which 20 John A. Nagl, Learning to Eat Soup with

  20. 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

  1. 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

  2. Functional Analysis of the Beclin-1 Tumor Suppressor Interaction With hVps34 (Type-III P13-Kinase) in Breast Cancer Cells

    DTIC Science & Technology

    2006-06-01

    1% Nonidet P40 , 0.5% sodium deoxycholate, 0.1% SDS, 5 mM EDTA. Insoluble material was removed by centrifugation at 100,000 g for 45 minutes at 4°C...7.4, 2 mM EDTA, 0.5% Nonidet P-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with complete mini protease inhibitors (Roche). Insoluble material

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  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. 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⊕.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. [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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. AFRRI (Armed Forces Radiobiology Research Institute) Reports, October-December 1989

    DTIC Science & Technology

    1989-02-01

    PBS) just before intra - L:fects o/ allogeneic BHA transplantation. Since allo- peritoneal injection in a volume of 0.5 ml. The ttoffmann-L.aRoche c...was given im until the appetite returned, and was then given orally. Dexamethasone was administered once daily as an im injection at a rate of 2.2 mg... arterial blood pressure: Ah,,ence of hypertension alter excision of the area postrema in rats. Pfhuc,’erv Arch 1977:372:169- 173. 6. Rahin BN1, Hunt WA

  13. Molecular Medicine - CHI's 17th International Tri-Conference: Mastering Medicinal Chemistry - CHI's Seventh Annual Conference.

    PubMed

    Terrett, Nick

    2010-04-01

    CHI's 17th International Tri-Conference on Molecular Medicine, held in San Francisco, included topics covering new developments in the field of medicinal chemistry. This conference report highlights selected presentations on fragment-based drug discovery, quantum mechanical energy decomposition for the analysis of SARs, medicinal chemistry strategies and the role of imaging in drug discovery. Investigational drugs discussed include MLN-4924 (Millennium Pharmaceuticals Inc), GDC-0449 (Chugai Pharmaceutical Co Ltd/Curis Inc/F Hoffmann-La Roche Ltd/Genentech Inc/NCI), RDEA-119 (Ardea Biosciences Inc/Bayer HealthCare AG) and tafamidis (Fx-1006A; FoldRx Pharmaceuticals Inc).

  14. Transition Metal Doped ZnO for Spintronics

    DTIC Science & Technology

    2007-07-01

    34 Heo, Y. W.; Ip, K.; Pearton, S. J.; Norton, D. P.; Budai, J. D., Applied Surface Science (2006), 252(20), 7442-7448. 14. "ZnO spintronics and nanowire ...Ren, F., Applied Physics Letters, Volume 87, Issue 21,, 2005, Pages 212106-212101-3. 28. "Cubic (MgZn)O nanowire growth using catalyst-driven...Ren, S. Shojah-Ardalan, and R. Wilkins, J.Electron. Mater. 34 395 (2005). 40. "Fabrication Approaches to ZnO Nanowire Devices," J.R. LaRoche, Y.W. Heo

  15. Characterization of the Discoidin Domain Receptor 2 Kinase as a Novel Therapeutic Target for Squamous Cell Lung Cancer

    DTIC Science & Technology

    2012-09-01

    Immunoblots were performed using the Nupage System (Invitrogen) per the manufacturer’s protocol. Cells were lysed in 1% Nonidet P - 40 with protease (Roche...based on genetic lesions. J Clin Invest 2009;119:1727– 40 . 33. Du J, Bernasconi P , Clauser KR, Mani DR, Finn SP, Beroukhim R, et al. Bead-based...DDR2 mutations. DDR2 knockdown was associated with a decrease in both cell proliferation and in markers of DDR2 signaling including p -Src and p -STAT3

  16. Targeting Transforming Growth Factor Beta to Enhance the Fracture Resistance of Bone

    DTIC Science & Technology

    2013-01-01

    Nonidet P - 40 , and protease inhibitors (Complete ULTRA Protease InhibitorMix- ture Tablets, Roche Applied Science). Nuclear extracts were isolated using...25 30 35 40 45 mg/kg P ea k fo rc e (N ) 6 months 22 months * **(A) 13 C4 @ 5 1D 11 @ 1 1D 11 @ 5 13 C4 @ 5 1D 11 @ 1 1D 11 @ 5 0.0...0.075 0.368 13C4 1D11 0 20 40 60 80 P ea k fo rc e (N ) p =0.0035 0 0.15 0.20

  17. Minimizing the risk of chemically reactive metabolite formation of new drug candidates: implications for preclinical drug design.

    PubMed

    Brink, Andreas; Pähler, Axel; Funk, Christoph; Schuler, Franz; Schadt, Simone

    2016-11-27

    Many pharmaceutical companies aim to reduce reactive metabolite formation by chemical modification at early stages of drug discovery. A practice often applied is the detection of stable trapping products of electrophilic intermediates with nucleophilic trapping reagents to guide rational structure-based drug design. This contribution delineates this strategy to minimize the potential for reactive metabolite formation of clinical candidates during preclinical drug optimization, exemplified by the experience at Roche over the past decade. For the majority of research programs it was possible to proceed with compounds optimized for reduced covalent binding potential. Such optimized candidates are expected to have a higher likelihood of succeeding throughout the development processes, resulting in safer drugs.

  18. Evolutionary Processes in Multiple Systems

    SciTech Connect

    Eggleton, P P; Kisseleva-Eggleton, L

    2006-02-14

    There are several ways in which triple stars can evolve in somewhat unusual ways. They discuss two situations where Case A Roche-lobe overflow, followed by a merger, can produce anomalous wide binaries such as {gamma} Per; and Kozai cycles in triples with non-parallel orbits, which can produce merged rapidly-rotating stars like AB Dor, and which can also lead to the delayed ejection of one component of a multiple, as may have been observed in T Tau in 1998.

  19. New Developments in Eclipsing Binary Light Curve Modeling

    NASA Astrophysics Data System (ADS)

    Milone, E. F.; Stagg, C. R.

    1994-03-01

    The light curve modeling of binary stars has continued to evolve since its founding by Henry Norris Russell (see Russell and Merrill 1952 and citations therein) nearly a century ago, accelerated in the 1950s by Kopal's introduction of Roche geometry into models and by the development of synthetic light curve computer code in the 1970's. Improved physics and the use of more kinds of observational input are providing another round of important advances that promise to enlarge our knowledge of both binary stars and ensembles containing them. Here we discuss the newer horizons of light curve modeling and the steps being taken toward them.

  20. Identification of Biomarkers Associated with the Healing of Chronic Wounds. Addendum

    DTIC Science & Technology

    2012-09-01

    from Poly (L- lactic acid ) and Pluronic 104," Appl. Spectrosc. 2010, 64, 359-364. • P.J.R. Roche, M.C-K Cheung, K.Y. Yung, A.G. Kirk, V.P. Chodavarpu...hypertrophic scarring is the result of a protein imbalance at the injury site, the biochemical characterization of the burn wound from the time of...Characterize the protein biochemistry of burn wounds. a. Analyze wound fluid samples to determine proteins present a. Identify trends present in

  1. Numerical calculations of mass transfer flow in semi-detached binary systems. [of stars

    NASA Technical Reports Server (NTRS)

    Edwards, D. A.; Pringle, J. E.

    1987-01-01

    The details of the mass transfer flow near the inner Lagrangian point in a semidetached binary system are numerically calculated. A polytropic equation of state with n = 3/2 is used. The dependence of the mass transfer rate on the degree to which the star overfills its Roche lobe is calculated, and good agreement with previous analytic estimates is found. The variation of mass transfer rate which occurs if the binary system has a small eccentricity is calculated and is used to cast doubt on the model for superhumps in dwarf novae proposed by Papaloizou and Pringle (1979).

  2. Scientific Respiratory Symposium, Paris June 2010

    PubMed Central

    Dalglish, Gavin; Priestley, Graham

    2011-01-01

    At a 2010 Respiratory Symposium in Paris, chaired by Professors Bousquet and Roche of the University of Paris, recent trends in research, therapy and treatment guidelines for asthma and chronic obstructive pulmonary disease (COPD) were reviewed and discussed by a faculty of expert European and US respiratory physicians. This article reviews five key clinical presentations with particular emphasis given to the importance of small airways in the pathology and treatment of asthma and COPD. Further analysis of the economics of treatment in Europe and the US shows a wide variance in direct and indirect costs. PMID:21792320

  3. Doublet craters and the tidal disruption of binary asteroids

    NASA Technical Reports Server (NTRS)

    Melosh, H. J.; Stansberry, J. A.

    1991-01-01

    An evaluation is conducted of the possibility that the tidal disruption of a population of contact binary asteroids can account for terrestrial-impact 'doublet' craters. Detailed orbital integrations indicate that while such asteroids are often disrupted by tidal forces outside the Roche limit, the magnitude of the resulting separations is too small to account for the observed doublet craters. It is hypothesized that an initial population of km-scale earth-crossing objects encompassing 10-20 percent binaries must be responsible for doublet impacts, as may be verified by future observations of earth-approaching asteroids.

  4. Workshop Introduction - Building Energy Performance Improvement Through Advanced Technologies, Smart Organization, and Financing

    DTIC Science & Technology

    2004-09-01

    A&M University, ESL Continuous Commissioning—An Effective Method for Energy Reductions Ch 5 14:00-14:15 Mr. Michael Chimack, University of Illinois...PNNL Energy assessment and analysis using FEDS Ch 7 8:45-9:00 Dr. Michael Witte, GardAnalytics Whole building energy analysis using EnergyPlus 9:00-9...Assessment of HVAC systems reliability 14:30-15:00 Coffee break Ch 8 15:00-15:15 Mr. Roch Ducey , ERDC-CERL Energy Security 15:15-15:30 Mr

  5. The contribution of air-fluidization to the mobility of rapid flowslides involving fine particles

    NASA Astrophysics Data System (ADS)

    Stilmant, Frédéric; Dewals, Benjamin; Archambeau, Pierre; Erpicum, Sébastien; Pirotton, Michel

    2016-04-01

    Air-fluidization can be the origin of the long runout of gravitational flows involving fine particles such as ash. An excessive air pore pressure dramatically reduces the friction angle of the material as long as this pressure has not been dissipated, which occurs during the flow. This phenomenon can be modelled thanks to the 2D depth-averaged equations of mass and momentum conservation and an additional transport equation for basal pore pressure evolution (Iverson and Denlinger, 2001). In this contribution, we discuss the application of this model in relation to recent experimental results on air-fluidized flows by Roche et al. (2008) and Roche (2012). The experimental results were used to set a priori the value of the diffusion coefficient in the model, taking into account the difference of scale between the experiments and real-world applications. We also compare the model predictions against detailed observations of a well-documented historical event, the collapse of a fly-ash heap in Belgium (Stilmant et al., 2015). In particular, we analyse the influence of the different components of the model on the results (pore pressure dissipation vs. pore pressure generation). The diffusion coefficient which characterizes the dissipation of air pore pressure is found sufficiently low for maintaining a fluidized flow over hundreds of meters. The study concludes that an air-fluidization theory is consistent with the field observations. These findings are particularly interesting as they seem not in line with the mainstream acceptation in landslide modelling that air generally plays a secondary role (e.g., Legros, 2002). References Iverson, R.M., Denlinger, R.P., 2001. Flow of variably fluidized granular masses across three-dimensional terrain - 1. Coulomb mixture theory. J. Geophys. Res. 106, 537 552. Legros, F., 2002. The mobility of long-runout landslides. Eng. Geol. 63, 301-331. Roche, O., 2012. Depositional processes and gas pore pressure in pyroclastic flows: an

  6. Comparison of the Reference Intervals Used for the Evaluation of Maternal Thyroid Function During Pregnancy Using Sequential and Nonsequential Methods

    PubMed Central

    Fan, Jian-Xia; Yang, Shuai; Qian, Wei; Shi, Feng-Tao; Huang, He-Feng

    2016-01-01

    Background: Maternal thyroid dysfunction is common during pregnancy, and physiological changes during pregnancy can lead to the overdiagnosis of hyperthyroidism and misdiagnosis of hypothyroidism with nongestation-specific reference intervals. Our aim was to compare sequential with nonsequential methods for the evaluation of thyroid function in pregnant women. Methods: We tested pregnant women who underwent their trimester prenatal screening at our hospital from February 2011 to September 2012 for serum thyroid stimulating hormone (TSH) and free thyroxine (FT4) using the Abbott and Roche kits. There were 447 and 200 patients enrolled in the nonsequential and sequential groups, respectively. The central 95% range between the 2.5th and the 97.5th percentiles was used as the reference interval for the thyroid function parameter. Results: The nonsequential group exhibited a significantly larger degree of dispersion in the TSH reference interval during the 2nd and 3rd trimesters as measured using both the Abbott and Roche kits (all P < 0.05). The TSH reference intervals were significantly larger in the nonsequential group than in the sequential group during the 3rd trimester as measured with both the Abbott (4.95 vs. 3.77 mU/L, P < 0.001) and Roche kits (6.62 vs. 5.01 mU/L, P = 0.004). The nonsequential group had a significantly larger FT4 reference interval as measured with the Abbott kit during all trimesters (12.64 vs. 5.82 pmol/L; 7.96 vs. 4.77 pmol/L; 8.10 vs. 4.77 pmol/L, respectively, all P < 0.05), whereas a significantly larger FT4 reference interval was only observed during the 2nd trimester with the Roche kit (7.76 vs. 5.52 pmol/L, P = 0.002). Conclusions: It was more reasonable to establish reference intervals for the evaluation of maternal thyroid function using the sequential method during each trimester of pregnancy. Moreover, the exclusion of pregnancy-related complications should be considered in the inclusion criteria for thyroid function tests. PMID

  7. Active and realistic passive marijuana exposure tested by three immunoassays and GC/MS in urine

    SciTech Connect

    Mule, S.J.; Lomax, P.; Gross, S.J.

    1988-05-01

    Human urine samples obtained before and after active and passive exposure to marijuana were analyzed by immune kits (Roche, Amersham, and Syva) and gas chromatography/mass spectrometry (GC/MS). Seven of eight subjects were positive for the entire five-day test period with one immune kit. The latter correlated with GC/MS in 98% of the samples. Passive inhalation experiments under conditions likely to reflect realistic exposure resulted consistently in less than 10 ng/mL of cannabinoids. The 10-100-ng/mL cannabinoid concentration range essential for detection of occasional and moderate marijuana users is thus unaffected by realistic passive inhalation.

  8. 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

  9. Searches for Optical Counterparts to Fermi Unassociated Sources with the Intermediate Palomar Transient Factory

    NASA Astrophysics Data System (ADS)

    Bellm, Eric Christopher; Prince, Thomas A.; Kaplan, David L. A.; Kupfer, Thomas; DeCesar, Megan E.; Laher, Russ; Masci, Frank J.; Shupe, David L.; Intermediate Palomar Transient Factory Collaboration

    2017-01-01

    The Intermediate Palomar Transient Factory (iPTF) has accumulated an extensive optical variability dataset across the Northern Sky, including at low Galactic latitudes (|b| < 20 degrees). We are using this dataset to search for optical counterparts to unassociated Fermi gamma-ray sources, particular the companions of eclipsing binary millisecond pulsars. So-called redback binary millisecond pulsars are a key evolutionary stage in the recycling process that spins up millisecond pulsars. The Roche-distorted and irradiated pulsar companion produces a periodic signature at the orbital period that may be readily identified with iPTF. We report on the progress of this search and present interesting candidates found.

  10. The mass of the black hole in the X-ray binary LMC X-1

    NASA Astrophysics Data System (ADS)

    Abubekerov, M. K.; Antokhina, E. A.; Gostev, N. Yu.; Cherepashchuk, A. M.; Shimansky, V. V.

    2016-12-01

    A dynamical estimate of the mass of the black hole in the LMC X-1 binary system is obtained in the framework of a Roche model for the optical star, based on fitting of the He I 4471 Å and He II 4200 Å absorption lines assuming LTE. The mass of the black hole derived from the radial-velocity curve for the He II 4200 Å line is m x = 10.55 M ⊙, close to the value found earlier based on a model with two point bodies [1].

  11. Mass flow in the O7f binary UW Canis Majoris. II

    NASA Technical Reports Server (NTRS)

    Mccluskey, G. E., Jr.; Kondo, Y.

    1976-01-01

    The far-ultraviolet spectrum of UW CMa was obtained from the telescope spectrometer on the Copernicus satellite at about phase 0.25 in order to supplement earlier observations of the same kind made near phase 0.75. Analysis of the data shows that the high-temperature gas giving rise to the P Cygni features in the far-ultraviolet spectrum is located primarily around the entire binary system and does not share in the motion of either component. The effects of radiation pressure on the Roche (Jacobian) equipotential surfaces and in generating a stellar wind are discussed.

  12. Monte Carlo Simulations of the Post-Common-Envelope White-Dwarf Main-Sequence Binary Population

    SciTech Connect

    Camacho, Judit; Torres, Santiago; Garcia-Berro, Enrique; Schreiber, Matthias R.

    2010-12-22

    We present a detailed Monte Carlo simulator of the population of binary systems within the solar neighborhood. We have used the most up-to-date stellar evolutionary models, a complete treatment of the Roche lobe overflow episode, as well as a full implementation of the orbital evolution of the binary system. Preliminary results are presented for the population of white-dwarf main-sequence binaries, resulting from a common envelope episode. We also study the role played by the binding energy parameter, {lambda}, and by the common envelope efficiency, {alpha}{sub CE}. Finally, results are compared with the population of identified white-dwarf main-sequence binaries.

  13. New Spectroscopic Analysis and Light Curve Model of the Eclipsing Binary V356 Sgr

    NASA Astrophysics Data System (ADS)

    Cabezas, M.; Mennickent, R.; Djurasević, G.

    2017-02-01

    We present a new orbital solution for the V356 Sgr binary system based on new and accurate radial velocities. It consists of a B3 V star accreting matter from a Roche-Lobe filling A2 II star. The spectra were disentangled using KOREL. The UBV light curves by Popper (1957) and Wilson & Woodward (1995) as well as the ASAS V-band light curve were modeled with a multicomponent synthesis code including an accretion disk. The system parameters, such as the effective temperature and surface gravity for both stars as well as the disk temperature and radius, were determined.

  14. Photometric study of two neglected beta Lyr-type binaries: V342 Her & V387 Her

    NASA Astrophysics Data System (ADS)

    Aktoka, Ü.; Erdem, A.; Öztürk, O.; Sürgit, D.

    2017-02-01

    In this study, SuperWASP light curves of V342 Her and V387 Her were analyzed by means of the Wilson-Devinney (W-D) code with a Monte Carlo (MC) search method for the first time. The final photometric solutions of these two systems show that while V342 Her has an over contact configuration in which both components overflows their Roche limiting lobes, V387 Her has a detached configuration. Photometric mass ratios and approximate absolute parameters of the systems are obtained.

  15. Two-Color Multiplex Assay for the Identification of Orthopox Viruses with Real-Time LUX-PCR

    DTIC Science & Technology

    2005-07-14

    perfringens 13124 1000 0/2 0/2 Francisella tularensis NA 1000 0/2 0/2 Haemophlius influenzae 10211 1000 0/2 0/2 Listeia monocytogenes 15313 1000 0/2 0/2...Loveless BM, Norwood D, Zwiers SH, Mucker E, Hartmann C, et al. Smallpox and pan-orthopox virus detection by real-time 3 0-minor groove binder TaqMan ...Whitehouse CA, Hartmann C, Mucker E, et al. Monkeypox virus detection in rodents using real-time 3 0-minor groove binder TaqMan assays on the Roche

  16. F-22A Raptor

    DTIC Science & Technology

    2007-06-12

    Raptor’s attack capabilities raises two broad issues: are these capabilities needed? And are these capabilities worth the cost? CRS-10 26 GAO- 04 -39, pp. 7 -8...5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7 . PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES...Program,” Defense Daily, March 4, 2002. 6 Ron Laurenzo, “Roche Envisions Close Air Support F-22,” Defense Week. July 1, 2002. 7 Bill Sweetman. “Smarter

  17. F-22A Raptor

    DTIC Science & Technology

    2008-08-13

    GAO- 04 -39, pp. 7 -8 vendors. Therefore, keeping the F-22 line open will help protect the F-35s industrial base, supporters argue. F-35 proponents...5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7 . PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES...4, 2002. 7 Ron Laurenzo, “Roche Envisions Close Air Support F-22,” Defense Week. July 1, 2002. 8 Bill Sweetman. “Smarter Bomber,” Popular Science

  18. The Role of DN-GSK3beta in Mammary Tumorigenesis

    DTIC Science & Technology

    2006-07-01

    gene, in primary breast cancers. Cancer Sci 2003;94(6):515-8. 6. Lin SY, Xia W, Wang JC, et al. Beta-catenin, a novel prognostic marker for breast...regard, GSK3h has not been studied. In this article, we use a novel mouse model to explore the effect of Wnt pathway deregulation on the development of...anti–cyclin D1 (Calbiochem), anti-a- tubulin (Sigma), anti-HA.11 (Covance/Babco, Rich­ mond, CA), anti-c-myc (Roche, Indianapolis, IN), and anti-SP1

  19. Are we underdosing acne patients with generic isotretinoin?

    PubMed

    Mutizwa, Misha M; Sheinbein, David M

    2013-01-15

    With Roche's withdrawl of Accutane from the U.S. market in 2009, isotretinoin has only been available in its generic form. Many clinicians fail to realize that for approval by the U.S. Food and Drug Administration, a generic medication must have a bioequivalence between 80 percent and 125 percent of that of the innovator product. This potential variability in bioavailability between branded and generic medications is important to keep in mind with isotretinoin, given the implications for achieving a sustained remission in acne patients.

  20. Performance and Verification of a Real-Time PCR Assay Targeting the gyrA Gene for Prediction of Ciprofloxacin Resistance in Neisseria gonorrhoeae

    PubMed Central

    Hemarajata, P.; Yang, S.; Soge, O. O.; Klausner, J. D.

    2016-01-01

    In the United States, 19.2% of Neisseria gonorrhoeae isolates are resistant to ciprofloxacin. We evaluated a real-time PCR assay to predict ciprofloxacin susceptibility using residual DNA from the Roche Cobas 4800 CT/NG assay. The results of the assay were 100% concordant with agar dilution susceptibility test results for 100 clinical isolates. Among 76 clinical urine and swab specimens positive for N. gonorrhoeae by the Cobas assay, 71% could be genotyped. The test took 1.5 h to perform, allowing the physician to receive results in time to make informed clinical decisions. PMID:26739156

  1. [Cutaneous melanoma - "black death" of modern times? Traces in contemporary literature].

    PubMed

    Bahmer, F A; Bahmer, J A

    2013-11-01

    Cutaneous melanoma, sometimes labeled as "black skin cancer", is increasing in frequency and becoming a more common literary motive. In US literature, Sylvia Plath and Charles Bukowski depicted melanoma more than 50 years ago, later Stephen King and Thomas C. Boyle. In German literature, Charlotte Roche shortly mentioned this tumor. Jörg Pönnighaus, both poet and dermatologist, intensively deals in his poems with the effects melanoma has on patients and doctors alike. Melanoma definitely is not the "Black Death" of modern times. However, the perception of this tumor as extremely malignant and as life-threatening makes melanoma a metaphor of the deadly danger of cancer.

  2. The implications of a companion enhanced wind on millisecond pulsar production

    NASA Astrophysics Data System (ADS)

    Smedley, Sarah L.; Tout, Christopher A.; Ferrario, Lilia; Wickramasinghe, Dayal T.

    2017-01-01

    The most frequently seen binary companions to millisecond pulsars (MSPs) are helium white dwarfs. The standard rejuvenation mechanism, in which a low- to intermediate-mass companion to a neutron star fills its Roche lobe between central hydrogen exhaustion and core helium ignition, is the most plausible formation mechanism. We have investigated whether the observed population can realistically be formed via this mechanism. We used the Cambridge STARS code to make models of Case B Roche-lobe overflow with Reimers' mass-loss from the donor. We find that the range of initial orbital periods required to produce the currently observed range of orbital periods of MSPs is extremely narrow. To reduce this fine tuning, we introduce a companion enhanced wind (CEW) that strips the donor of its envelope more quickly so that systems can detach at shorter periods. Our models indicate that the fine tuning can be significantly reduced if a CEW is active. Because significant mass is lost owing to a CEW, we expect some binary pulsars to accrete less than the 0.1 M⊙ needed to spin them up to millisecond periods. This can account for mildly recycled pulsars present along the entire Mc-Porb relation. Systems with Pspin > 30 ms are consistent with this, but too few of these mildly recycled pulsars have yet been observed to make a significant comparison.

  3. A prescription and fast code for the long-term evolution of star clusters - III. Unequal masses and stellar evolution

    NASA Astrophysics Data System (ADS)

    Alexander, Poul E. R.; Gieles, Mark; Lamers, Henny J. G. L. M.; Baumgardt, Holger

    2014-08-01

    We present a new version of the fast star cluster evolution code EVOLVE ME A CLUSTER OF STARS (EMACSS). While previous versions of EMACSS reproduced clusters of single-mass stars, this version models clusters with an evolving stellar content. Stellar evolution dominates early evolution, and leads to: (1) reduction of the mean mass of stars due to the mass loss of high-mass stars; (2) expansion of the half-mass radius; (3) for (nearly) Roche Volume filling clusters, the induced escape of stars. Once sufficient relaxation has occurred (≃10 relaxation times-scales), clusters reach a second, `balanced' state whereby the core releases energy as required by the cluster as a whole. In this state: (1) stars escape due to tidal effects faster than before balanced evolution; (2) the half-mass radius expands or contracts depending on the Roche volume filling factor; and (3) the mean mass of stars increases due to the preferential ejection of low-mass stars. We compare the EMACSS results of several cluster properties against N-body simulations of clusters spanning a range of initial number of stars, mass, half-mass radius, and tidal environments, and show that our prescription accurately predicts cluster evolution for this data base. Finally, we consider applications for EMACSS, such as studies of galactic globular cluster populations in cosmological simulations.

  4. Antimetastatic effect of fluvastatin on breast and hepatocellular carcinoma cells in relation to SGK1 and NDRG1 genes.

    PubMed

    Salis, Osman; Okuyucu, Ali; Bedir, Abdulkerim; Gör, Ufuk; Kulcu, Canan; Yenen, Eser; Kılıç, Nermin

    2016-03-01

    Metastasis occurs due to migration of the cells from primary tumor toward other tissues by gaining invasive properties. Since metastatic invasion shows a strong resistance against conventional cancer treatments, the studies on this issue have been focused. Within this context, inhibition of migration and determination of the relationships at the gene level will contribute to treatment of metastatic cancer cases. We have aimed to demonstrate the impact of TGF-β1 and fluvastatin on human breast cancer (MCF-7) and human hepatocellular carcinoma (Hep3B) cell cultures via Real-Time Cell Analyzer (RTCA) and to test the expression levels of some genes (NDRG1, SGK1, TWIST1, AMPKA2) and to compare their gene expression levels according to RTCA results. Both of cell series were applied TGF-β1 and combinations of TGF-β1/fluvastatin. Primer and probes were synthesized using Universal Probe Library (UPL, Roche) software, and expression levels of genes were tested via qPCR using the device LightCycler 480 II (Roche). Consequently, fluvastatin dose-dependently inhibited migration induced by TGF-β1 in both groups. This inhibition was accompanied by low level of SGK1 messenger RNA (mRNA) and high levels of NDRG1 and AMPKA2 mRNA. Thus, we conclude that fluvastatin plays an important role in reducing resistance to chemotherapeutics and preventing metastasis.

  5. Small Satellites Embedded In The Rings : Accretion And Motion Of Material At The Surface Of Pan And Atlas

    NASA Astrophysics Data System (ADS)

    Brahic, André; Charnoz, S.; Déau, E.; Thomas, P.; Porco, C.

    2006-09-01

    Recent Cassini images have revealed the strange shapes of Pan and Atlas, with surprising bulges near the equator. We try here to understand the origin of the moons' equatorial bulges by examination of the detailed motion of material falling from the ring to the surface and then rolling on the surface. Two questions are treated: (1) where does the material fall on the surface? (2) where does the material roll once it is on the surface? Using numerical simulations, we show that the equatorial bulge maybe material accreted from the surrounding rings. But the resulting shape depends critically on both the orbital parameters of the satellites, and on the shape of the Roche Lobe compared to the 3D body surface which are similar (indeed Porco et al. -- LPSC 2006-- has shown that the overall shape and size of these bodies are close to that of the body's Roche lobe). We show that the complex interplay between the Saturn tidal forces, the shape and the body's gravity creates, on the surface, valleys of stability where the material is expected to migrate in a short time. All these elements may put some new constrains on the origin of Pan and Atlas, as well as on their dynamical history. This work was supported by the French space agency (CNES), Université Paris 7 and CEA

  6. Radial Velocity Monitoring of Composite-Spectra Hot Subdwarf Stars with the HET

    NASA Astrophysics Data System (ADS)

    Barlow, Brad; Wade, R. A.; Liss, S.

    2014-01-01

    The enigmatic hot subdwarf B (sdB) stars represent one of the least-understood stages of stellar evolution. Theory shows that they likely formed from red giant branch stars that lost their outer envelopes due to Roche lobe overflow and common envelope interactions with a companion. Binary population synthesis models are generally successful at reproducing the observed orbital periods of sdB binaries with M dwarf and white dwarf companions; the story for sdB+F/G/K binaries, however, is still being written. Relatively few observational constraints have been published for these composite-spectra systems. We have been monitoring the radial velocities (RVs) of 15 sdB binaries with F-K dwarf companions since 2005 using the Medium and High Resolution Spectrographs on the Hobby-Eberly Telescope. Here we present RV measurements and orbital parameter estimates for selected systems in our sample. We also present an up-to-date orbital period histogram for all known sdB binaries, including both short- and long-period systems. Our results suggest that those with F-K main sequence companions have periods on the order of 1.5 to 3 years. Several of the long-period binaries show strong evidence for non-circular orbits, challenging the conventional Roche Lobe overflow formation channel for hot subdwarf stars. This material is based upon work supported by the National Science Foundation under Grant No. AST-0908642.

  7. Evaluation of new oxidation methods for the measurement of bilirubin on the aeroset clinical chemistry analyzer and comparison with methods on the Hitachi 717.

    PubMed

    Sturm, Ernhard; Albrecht-Groos, Ragnhild; Seyfarth, Michael

    2002-01-01

    We evaluated analytical and performance quality of the new oxidation methods for direct and total bilirubin on the Abbott Aeroset clinical chemistry analyzer. Within-day imprecisions for Abbott Aeroset assays ranged from 0.7 to 2.9% and between-day imprecisions from 2.1 to 7.3%. Inaccuracies as compared with the control "target values" for the Jendrassik-Gróf method showed deviations of -18.2 to +4.2%. Limits of detection were determined and showed very low values of < or = 0.25 micromol/l and dilution linearities were confirmed up to > 300 micromol/l. A method comparison for 100 patient samples with established Jendrassik-Gróf and DPD methods on the Roche Hitachi 717 showed good linearities between the investigated methods (r > or = 0.995). Due to slopes that ranged from 0.829 to 0.950, reference ranges for the oxidation methods differ slightly from those of established Roche Jendrassik-Gróf methods, but results can be adapted by the introduction of converting factors. In conclusion, the oxidation bilirubin assays revealed convincing analytical and performance qualities for medical needs that were similar or even better than for established methods. Application of the oxidation methods on the Aeroset clinical chemistry analyzer also improves laboratory efficiency by increasing throughput, speed of obtaining results and lowered sample and reagent volumes compared to established methods.

  8. The design and use of a computer-based digital image acquisition, management, and communications system for conferencing in pathology.

    PubMed

    Wray, B E; Lai-Goldman, M

    1995-01-01

    The Roche ImageManager is a PC computer-based system, running under Windows 3.1. This system allows the storage, viewing, printing, and transmission of, and conferencing on large sets of high resolution, color images from various sources. Images may be acquired at resolutions up to 3072 x 2320 pixels under software control, and transmitted for conferencing or stored in the database using JPEG compression. Each image is stored with associated information, text notes, annotations, and a "thumbnail" image. The stored information may be searched for matching images, for example representative images of a particular disease for training, or images to be reviewed for a particular patient. Images may be transmitted with all associated information between sites which have telephone service, worldwide. Support is being added for LAN use with a multi-user database, ISDN and Switch56 communications, and remote microscope control. Interactive conferencing allows rapid transmission of low resolution images for specimen scanning, viewing of multiple high resolution still images, and real-time interactive pointers for detailed discussions of image features. The ImageManager is being used and evaluated for conferencing and training purposes. A study was performed by Roche Biomedical Laboratories to compare the ability of pathologists to make a diagnosis on complex cases using transmitted images vs. routine microscopic examination. The effectiveness of the system in providing images of a sufficient quality to allow diagnosis in a private practice setting will be presented.

  9. The Cyclic Nature of Martian Satellites

    NASA Astrophysics Data System (ADS)

    Hesselbrock, Andrew; Minton, David A.

    2016-10-01

    The inward tidal decay of Phobos will cause the satellite to rapidly disrupt into a ring as it reaches the Rigid Roche Limit at ~ 1.6 Mars radii in less than 70 My. This ring will viscously spread to eventually form a new generation of satellites at the Fluid Roche Limit at ~ 3.2 Mars radii. We have constructed a ring-satellite model to show that this is only the latest in a series of satellite-ring cycles that have occurred repeatedly throughout Martian history, beginning with a ring created by a giant impact. During each cycle, ring material is deposited onto Mars, decreasing the mass of the ring-satellite system, such that each cycle produces progressively less massive satellites. We find that at least ~ 5 ring/satellite cycles are needed to produce a Phobos mass satellite in its current orbit. Furthermore, the decay of each ring system would have deposited a significant volume of ring material onto Mars throughout the early Noachian and into the late Amazonian. Some anomalous sedimentary deposits on Mars may be linked to these periodic episodes of ring deposition.

  10. Hot White Dwarf Donors in Ultracompact X-Ray Binaries

    NASA Astrophysics Data System (ADS)

    Bildsten, Lars

    2002-09-01

    The discovery of two accreting millisecond X-ray pulsars in binaries with ~43 minute orbital periods allows for a new probe of the donor's structure. For XTE J1751-305, only a hot white dwarf (WD) can fill the Roche lobe. A cold He WD is a possible solution for XTE J0929-314, although I will show that evolutionary arguments make a hot WD more likely. In addition to being larger than the T=0 models, these finite entropy, low-mass (Mc<0.03 Msolar) WDs have a minimum mass for a fixed core temperature. If they remain hot as they lose mass and expand, they can ``evaporate'' to leave an isolated millisecond radio pulsar. They also adiabatically expand upon mass loss at a rate faster than the growth of the Roche radius if the angular momentum deposited in the disk is not returned to the donor. If the timescale of the resulting runaway mass transfer is shorter than the viscous timescale in the outer disk, then the mass transfer instability of Ruderman & Shaham for He WDs would be realized. However, my estimates of these timescales still make the instability unlikely for adiabatic responses. I close by noting the possible impact of finite temperature WDs on our understanding of AM CVn binaries.

  11. Origin of the use of the word magma in Earth Sciences

    NASA Astrophysics Data System (ADS)

    Gohau, , G.

    1998-05-01

    The word magma was originally used in pharmacy (1694), and then in chemistry (1773).It took its modern geological significance only during the XIXth century.Although it is generally considered to have been first used in geology in 1879 (Roches eruptives, by Fouque and Michel-Levy), the word was already used by Fournet as early as 1838, and soon by Durocher (1845).Both supported an igneous origin of the granite, and were opposed to the metamorphic origin interpretation which, at that time, was dominant in France.Le mot magma, issu de la pharmacie (1694), et utilise par les chimistes des 1773, ne prend son sens moderne, en geologie, qu'au XIX^e siecle.Quoiqu'on retienne habituellement la date de 1879 (Roches eruptives, par Fouque et Michel-Levy), le terme apparait en fait des 1838, chez Fournet, puis chez Durocher a partir de 1845.Partisans de l'origine ignee du granite, ces deux auteurs s'opposent a la these dominante, en France, de l'origine metamorphique.

  12. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software.

    PubMed

    Poulet, Axel; Privat, Maud; Ponelle, Flora; Viala, Sandrine; Decousus, Stephanie; Perin, Axel; Lafarge, Laurence; Ollier, Marie; El Saghir, Nagi S; Uhrhammer, Nancy; Bignon, Yves-Jean; Bidet, Yannick

    Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.

  13. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software

    PubMed Central

    Poulet, Axel; Privat, Maud; Viala, Sandrine; Decousus, Stephanie; Perin, Axel; Lafarge, Laurence; Ollier, Marie; El Saghir, Nagi S.

    2016-01-01

    Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts. PMID:27656653

  14. ON THE ORBIT OF THE SHORT-PERIOD EXOPLANET WASP-19b

    SciTech Connect

    Hellier, Coel; Anderson, D. R.; Smalley, B.; Southworth, J.; Collier-Cameron, A.; Miller, G. R. M.; Queloz, D.; Triaud, A. H. M. J.

    2011-04-01

    WASP-19b has the shortest orbital period of any known exoplanet, orbiting at only 1.2 times the Roche tidal radius. By observing the Rossiter-McLaughlin effect we show that WASP-19b's orbit is aligned, with {lambda} = 4.{sup 0}6 {+-} 5.{sup 0}2. Using, in addition, a spectroscopic vsin I and the observed rotation period we conclude that the obliquity, {psi}, is less than 20{sup 0}. Further, the eccentricity of the orbit is less than 0.02. We argue that hot Jupiters with orbital periods as short as that of WASP-19b are two orders of magnitude less common than hot Jupiters at the 3-4 day 'pileup'. We discuss the evolution of WASP-19b's orbit and argue that most likely it was first moved to near twice the Roche limit by third-body interactions, and has since spiralled inward to its current location under tidal decay. This is compatible with a stellar tidal-dissipation quality factor, Q'{sub *}, of order 10{sup 7}.

  15. Period studies and photometric models for two EB-type binaries EU Hya and AW Vul

    NASA Astrophysics Data System (ADS)

    Yang, Yuan-Gui; Li, Qun; Li, Hua-Li; Dai, Hai-Feng

    2016-02-01

    New photometry for two Algol-type binaries, EU Hya (P = 0.7782 d) and AW Vul (P = 0.8065 d), was carried out using the 60-cm telescope at Xinglong station of National Astronomical Observatories, Chinese Academy of Sciences. With the updated Wilson-Devinney code, photometric elements were derived from the multi-color light curves. The modeled results indicate that the two systems are near-contact binaries, whose secondary components fill their Roche lobes. The fill-out factors of the primaries are fp = 81.2 (±0.2)% for EU Hya and fp = 82.4 (±0.3)% for AW Vul. Period analysis implies that there exists a downward parabola with a light-time orbit from the (O - C) curve. This kind of periodic oscillation may be attributed to the light-time orbit effect of a third companion. The long-term period decrease may be caused by mass and angular momentum loss. When the orbital period decreases, the fill-out factor of fp will increase. Our results indicate that the primaries will also eventually fill their Roche lobes. EU Hya and AW Vul may possibly evolve from semi-detached binaries into contact ones.

  16. Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

    PubMed Central

    Hirakawa, Hideki; Shirasawa, Kenta; Kosugi, Shunichi; Tashiro, Kosuke; Nakayama, Shinobu; Yamada, Manabu; Kohara, Mistuyo; Watanabe, Akiko; Kishida, Yoshie; Fujishiro, Tsunakazu; Tsuruoka, Hisano; Minami, Chiharu; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Komaki, Akiko; Yanagi, Tomohiro; Guoxin, Qin; Maeda, Fumi; Ishikawa, Masami; Kuhara, Satoru; Sato, Shusei; Tabata, Satoshi; Isobe, Sachiko N.

    2014-01-01

    Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species. PMID:24282021

  17. Coupled Evolutions of the Stellar Obliquity, Orbital Distance, and Planet's Radius due to the Ohmic Dissipation Induced in a Diamagnetic Hot Jupiter around a Magnetic T Tauri Star

    NASA Astrophysics Data System (ADS)

    Chang, Yu-Ling; Bodenheimer, Peter H.; Gu, Pin-Gao

    2012-10-01

    We revisit the calculation of the ohmic dissipation in a hot Jupiter presented by Laine et al. by considering more realistic interior structures, stellar obliquity, and the resulting orbital evolution. In this simplified approach, the young hot Jupiter of one Jupiter mass is modeled as a diamagnetic sphere with a finite resistivity, orbiting across tilted stellar magnetic dipole fields in vacuum. Since the induced ohmic dissipation occurs mostly near the planet's surface, we find that the dissipation is unable to significantly expand the young hot Jupiter. Nevertheless, the planet inside a small corotation orbital radius can undergo orbital decay by the dissipation torque and finally overfill its Roche lobe during the T Tauri star phase. The stellar obliquity can evolve significantly if the magnetic dipole is parallel/antiparallel to the stellar spin. Our results are validated by the general torque-dissipation relation in the presence of the stellar obliquity. We also run the fiducial model of Laine et al. and find that the planet's radius is sustained at a nearly constant value by the ohmic heating, rather than being thermally expanded to the Roche radius as suggested by the authors.

  18. WOBBLING AND PRECESSING JETS FROM WARPED DISKS IN BINARY SYSTEMS

    SciTech Connect

    Sheikhnezami, Somayeh; Fendt, Christian E-mail: fendt@mpia.de

    2015-12-01

    We present results of the first ever three-dimensional (3D) magnetohydrodynamic (MHD) simulations of the accretion–ejection structure. We investigate the 3D evolution of jets launched symmetrically from single stars but also jets from warped disks in binary systems. We have applied various model setups and tested them by simulating a stable and bipolar symmetric 3D structure from a single star–disk–jet system. Our reference simulation maintains a good axial symmetry and also a bipolar symmetry for more than 500 rotations of the inner disk, confirming the quality of our model setup. We have then implemented a 3D gravitational potential (Roche potential) due by a companion star and run a variety of simulations with different binary separations and mass ratios. These simulations show typical 3D deviations from axial symmetry, such as jet bending outside the Roche lobe or spiral arms forming in the accretion disk. In order to find indications of precession effects, we have also run an exemplary parameter setup, essentially governed by a small binary separation of only ≃200 inner disk radii. This simulation shows a strong indication that we observe the onset of a jet precession caused by the wobbling of the jet-launching disk. We estimate the opening angle of the precession cone defined by the lateral motion of the jet axis to be about 4° after about 5000 dynamical time steps.

  19. Use of the UriSwab collection device for testing of Chlamydia trachomatis and Neisseria gonorrhoeae: implications for a postal testing service.

    PubMed

    McNicol, J; Debattista, J

    2013-06-01

    In order to demonstrate the reliability of UriSwab, a trial was conducted using urine samples that had previously returned a detected result for Chlamydia trachomatis and/or Neisseria gonorrhoeae. Urine specimens (115 samples) were received from sexual health clinics and tested using the Roche Cobas 4800 CT/NG method. Concurrently, the urine samples were pipetted directly on to the sponge applicator of the UriSwab, simulating micturition, and the urine harvested from the UriSwab was tested using the Roche Cobas 4800 method. Of the 87 standard urine specimens that were C. trachomatis detected, 85 (98%) were also detected in the corresponding UriSwab specimen (sensitivity 97.7%, specificity 95.7%). Of the 34 standard specimens that were N. gonorrhoeae detected, 33 (97%) were also detected in the corresponding UriSwab specimen (sensitivity 97.1%, specificity 100%). The performance of the UriSwab in this trial was comparable with the testing of neat first-catch urine specimens for both C. trachomatis and N. gonorrhoeae.

  20. FDA approval summary: vemurafenib for treatment of unresectable or metastatic melanoma with the BRAFV600E mutation.

    PubMed

    Kim, Geoffrey; McKee, Amy E; Ning, Yang-Min; Hazarika, Maitreyee; Theoret, Marc; Johnson, John R; Xu, Qiang Casey; Tang, Shenghui; Sridhara, Rajeshwari; Jiang, Xiaoping; He, Kun; Roscoe, Donna; McGuinn, W David; Helms, Whitney S; Russell, Anne Marie; Miksinski, Sarah Pope; Zirkelbach, Jeanne Fourie; Earp, Justin; Liu, Qi; Ibrahim, Amna; Justice, Robert; Pazdur, Richard

    2014-10-01

    On August 17, 2011, the U.S. Food and Drug Administration (FDA) approved vemurafenib tablets (Zelboraf, Hoffmann-LaRoche Inc.) for the treatment of patients with unresectable or metastatic melanoma with the BRAF(V600E) mutation as detected by an FDA-approved test. The cobas 4800 BRAF V600 Mutation Test (Roche Molecular Systems, Inc.) was approved concurrently. An international, multicenter, randomized, open-label trial in 675 previously untreated patients with BRAF(V600E) mutation-positive unresectable or metastatic melanoma allocated 337 patients to receive vemurafenib, 960 mg orally twice daily, and 338 patients to receive dacarbazine, 1,000 mg/m(2) intravenously every 3 weeks. Overall survival was significantly improved in patients receiving vemurafenib [HR, 0.44; 95% confidence interval (CI), 0.33-0.59; P < 0.0001]. Progression-free survival was also significantly improved in patients receiving vemurafenib (HR, 0.26; 95% CI, 0.20-0.33; P < 0.0001). Overall response rates were 48.4% and 5.5% in the vemurafenib and dacarbazine arms, respectively. The most common adverse reactions (≥30%) in patients treated with vemurafenib were arthralgia, rash, alopecia, fatigue, photosensitivity reaction, and nausea. Cutaneous squamous cell carcinomas or keratoacanthomas were detected in approximately 24% of patients treated with vemurafenib. Other adverse reactions included hypersensitivity, Stevens-Johnson syndrome, toxic epidermal necrolysis, uveitis, QT prolongation, and liver enzyme laboratory abnormalities.

  1. The Complex Circumstellar and Circumbinary Environment of V356 Sgr

    NASA Astrophysics Data System (ADS)

    Fullard, Andrew; Lomax, Jamie R.; Malatesta, Michael A.; Babler, Brian L.; Bednarski, Daniel; Berdis, Jodi; Bjorkman, Karen S.; Bjorkman, Jon Eric; Carciofi, Alex C.; Davidson, James W.; Keil, Marcus; Meade, Marilyn; Nordsieck, Kenneth H.; Scheffler, Matt; Hoffman, Jennifer L.; Wisniewski, John P.

    2017-01-01

    The eclipsing, interacting binary star V356 Sgr is a particularly exciting object for analysis due to its probable nonconservative mass loss and the possible progenitor link between Roche-lobe overflow systems and core-collapse supernovae. We present the results of 45 spectropolarimetric observations of V356 Sgr taken over 21 years, which we used to characterize the geometry of the system's circumstellar material. We find that V356 Sgr exhibits a large intrinsic polarization signature arising from electron scattering. The lack of repeatable eclipses in the polarization phase curves indicates the presence of a substantial pool of scatterers not occulted by either star. We suggest that these scatterers form either a circumbinary disk coplanar with the gainer's accretion disk, or an elongated structure perpendicular to the orbital plane of V356 Sgr, possibly formed by bipolar outflows.We also observe small-scale, cycle-to-cycle variations in the magnitude of intrinsic polarization at individual phases. These may indicate a mass transfer or mass loss rate that varies on the time-scale of the system's orbital period. Finally, we present a comparison of V356 Sgr with the well studied beta Lyr system; the significant differences observed between the two systems suggests diversity in the basic circumstellar geometry of Roche-lobe overflow binaries.

  2. THE HABITABILITY AND DETECTION OF EARTH-LIKE PLANETS ORBITING COOL WHITE DWARFS

    SciTech Connect

    Fossati, L.; Haswell, C. A.; Patel, M. R.; Busuttil, R.; Bagnulo, S.; Kowalski, P. M.; Shulyak, D. V.; Sterzik, M. F. E-mail: C.A.Haswell@open.ac.uk E-mail: r.busuttil@open.ac.uk E-mail: kowalski@gfz-potsdam.de E-mail: msterzik@eso.org

    2012-09-20

    Since there are several ways planets can survive the giant phase of the host star, we examine the habitability and detection of planets orbiting white dwarfs. As a white dwarf cools from 6000 K to 4000 K, a planet orbiting at 0.01 AU would remain in the continuous habitable zone (CHZ) for {approx}8 Gyr. We show that photosynthetic processes can be sustained on such planets. The DNA-weighted UV radiation dose for an Earth-like planet in the CHZ is less than the maxima encountered on Earth, and hence non-magnetic white dwarfs are compatible with the persistence of complex life. Polarization due to a terrestrial planet in the CHZ of a cool white dwarf (CWD) is 10{sup 2} (10{sup 4}) times larger than it would be in the habitable zone of a typical M-dwarf (Sun-like star). Polarimetry is thus a viable way to detect close-in rocky planets around white dwarfs. Multi-band polarimetry would also allow us to reveal the presence of a planet atmosphere, providing a first characterization. Planets in the CHZ of a 0.6 M{sub Sun} white dwarf will be distorted by Roche geometry, and a Kepler-11d analog would overfill its Roche lobe. With current facilities a super-Earth-sized atmosphereless planet is detectable with polarimetry around the brightest known CWD. Planned future facilities render smaller planets detectable, in particular by increasing the instrumental sensitivity in the blue.

  3. A Binary Teetering on the Edge

    NASA Astrophysics Data System (ADS)

    Motl, P. M.; D'Souza, M. C. R.; Tohline, J. E.; Frank, J.

    2005-05-01

    We present a fully three-dimensional hydrodynamical simulation of Roche lobe overflow in a binary near the stability boundary. This boundary separates evolutionary branches that correspond to either an accelerating mass transfer rate leading eventually to merger through tidal instability or to a decaying mass transfer rate as the orbit expands. The binary begins with a mass ratio of 0.4 (ratio of donor to accretor mass) and is initially assumed to be rotating synchronously. We treat the stellar components as simple polytropic fluids characterized by a polytropic index, n = 3/2. As the donor overflows its Roche lobe, the mass transfer rate initially accelerates before stabilizing and eventually dropping over a timescale of tens of orbits. We also note that for this particular binary, the accretion stream impacts on the surface of the donor rather than forming an accretion disk. This simulation allows us to measure the efficiency with which the accretion stream spins up the accretor in this "direct impact" scenario and the degree to which angular momentum is transfered back to the binary orbit via the tidal field.

  4. VizieR Online Data Catalog: Cataclysmic Binaries, LMXBs, and related objects (Ritter+, 2005)

    NASA Astrophysics Data System (ADS)

    Ritter, H.; Kolb, U.

    2005-03-01

    Cataclysmic Binaries are semi-detached binaries consisting of a white dwarf or a white dwarf precursor primary and a low-mass secondary which is filling its critical Roche lobe. The secondary is not necessarily unevolved, it may even be a highly evolved star as for example in the case of the AM CVn-type stars. Low-Mass X-Ray Binaries are semi-detached binaries consisting of either a neutron star or a black hole primary, and a low-mass secondary which is filling its critical Roche lobe. Related Objects are detached binaries consisting of either a white dwarf or a white dwarf precursor primary and of a low-mass secondary. The secondary may also be a highly evolved star. The catalogue lists coordinates, apparent magnitudes, orbital parameters, stellar parameters of the components and other characteristic properties of 599 cataclysmic binaries, 81 low-mass X-ray binaries and 147 related objects with known or suspected orbital periods together with a comprehensive selection of the relevant recent literature. In addition the catalogue contains a list of references to published finding charts for 796 of the 827 objects, and a cross- reference list of alias object designations. Literature published before 30 June 2005 has, as far as possible, been taken into account. Updated information will be provided regularly, currently every six months. Old editions include catalogue (5th edition), (6th edition) and (7th edition). (10 data files).

  5. Inter-strand coupling and base pairing sequences in DNA charge transport.

    NASA Astrophysics Data System (ADS)

    Yudiarsah, Efta; Ulloa, Sergio

    2006-03-01

    The electronic transport properties of double-stranded DNA are studied using a tight-binding Hamiltonian. Transfer and scattering matrix methods for double strands are employed simultaneously in the calculation, guaranteeing numerical stability. Realistic on-site energies [1] and hopping constants are used in the model [2]. The role of inter-strand coupling is shown to be extremely important for random sequences typical of genetic DNA. In contrast, inter-strand coupling only changes slightly the charge transport properties for more periodic sequences. The effect of base-pairing across strands and details of the sequences were investigated. Our model shows that the resistance of DNA depends on the sequences and the ratio of the bases. This agrees with previous results by Roche [3]. The resistance is also shown to increase with the concentration of different bases in a homogenous strand, and we find that for certain sequences only short-range electronic transport is possible.[1] H. Sugiyama and I. Saito, J. Am. Chem. Soc. 118, 7063 (1996).[2] A. A. Voityuk, J. Jortner, M. Bixon, and N. Rosch, J. Chem. Phys. 114, 5614 (2001).[3] S. Roche, Phys. Rev. Lett. 91, 108101 (2003).

  6. Performance of the HSV OligoGen kit for the diagnosis of herpes simplex virus type 1 and 2.

    PubMed

    Parra-Sánchez, Manuel; Marcuello López, Ana; García-Rey, Silvia; Zakariya-Yousef Breval, Ismail; Bernal Martínez, Samuel; Pueyo Rodríguez, Isabel; Martín-Mazuelos, Estrella; Palomares Folía, José Carlos

    2016-07-01

    PCR methods are nowadays between the most rapid and sensitive methods for screening and diagnosing herpes simplex virus (HSV) type 1 and 2. The aim of this study was to analyze the reliability, accuracy, and usefulness of the new assay HSV OligoGen kit in comparison with the Roche LightCycler HSV ½ Qual Kit assay for the detection of HSV in clinical samples. For this analysis, a prospective study was designed for detection of HSV-1 and HSV-2 including 110 ulcer specimens, 48 urine, 48 endocervical, 43 cerebral spinal fluids, 4 urethral and 3 pharyngeal swabs that were sent from a regional STI clinic or an Intensive Clinical Unit, both in Seville, Spain. In comparison to the Roche LightCycler HSV ½ Qual Kit assay, sensitivity, specificity, positive and negative predicative values, and kappa value for HSV detection using the HSV OligoGen kit were 96.2%, 100%, 100%, 98.3%, and 0.97 for HSV-1, respectively. For HSV-2, the corresponding values were 98.3%, 100%, 100%, 99.5%, and 0.98, respectively. Statistical data obtained in this study confirms the usefulness and reliable results of this new assay.

  7. OSI-774 OSI Pharmaceuticals.

    PubMed

    Norman, P

    2001-02-01

    OSI-774 (formerly CP-358774), a quinazoline derivative, is an orally active epidermal growth factor receptor (EGFR) inhibitor which was originally under joint development by Pfizer and OSI Pharmaceuticals (formerly Oncogene Science) for the potential treatment of cancer (eg, ovarian, non-small cell lung cancer (NSCLC) and head and neck). It is being evaluated in phase II trials [304305], [372201]. On 8 January 2001, OSI announced that it had signed an agreement with Roche and Genentech for the global co-development and marketing of OSI-774. The agreement with Genentech covers the United States, that with Roche the rest of the world [395371], [395526]. In June 2000, OSI gained all development and marketing rights for OSI-774 following Pfizer's merger with Warner-Lambert [371439]. In September 2000, Pfizer transferred the IND dossierfor OSI-774 to OSI ahead of the timeline agreed in the June 2000 development and marketing rights agreement [383786]. The phase II trials will assess OSI-774 both as a single agent and in combination with existing chemotherapy regimens [347783]. Phase III trials are expected to be initiated in 2001 [347783]. In October 2000, Lehman Brothers predicted that OSI-774 would move into pivotal trials in thefirst half of 2001 and that the drug would be launched in 2003. The analysts also estimated worldwide sales of US $66 million, $285 million and $461 million in 2003, 2004 and 2005, respectively, and peak sales in excess of US $500 million [395189].

  8. ACTIVITY ON THE M STAR OF QS Vir

    SciTech Connect

    Ribeiro, T.; Baptista, R.; Kafka, S.; Tappert, C.

    2010-03-15

    We report analysis of VRIJH photometry and phase-resolved optical spectroscopy of the eclipsing DA white dwarf (WD) plus dMe dwarf binary QS Vir. Modeling of the photometric data yields an inclination of i = 74.9 {+-} 0.6 and a mass ratio of q = M {sub 2}/M {sub 1} = 0.50 {+-} 0.05. Our Doppler maps indicate the presence of material in the Roche lobe of the WD, at a location near the M star, likely due to accretion from the stellar wind of the M star (as opposed to Roche-lobe overflow accretion). We also constructed images of the brightness distribution of the M star at different epochs which reveal the location of two stable active regions. Doppler tomography shows that the majority of the hydrogen and Ca II H and K emission originates on the active M dwarf, likely distributed in two preferred activity longitudes, similar to active regions on BY Dra and FK Comae systems.

  9. Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species.

    PubMed

    Hirakawa, Hideki; Shirasawa, Kenta; Kosugi, Shunichi; Tashiro, Kosuke; Nakayama, Shinobu; Yamada, Manabu; Kohara, Mistuyo; Watanabe, Akiko; Kishida, Yoshie; Fujishiro, Tsunakazu; Tsuruoka, Hisano; Minami, Chiharu; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Komaki, Akiko; Yanagi, Tomohiro; Guoxin, Qin; Maeda, Fumi; Ishikawa, Masami; Kuhara, Satoru; Sato, Shusei; Tabata, Satoshi; Isobe, Sachiko N

    2014-01-01

    Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species.

  10. HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data

    PubMed Central

    Churbanov, Alexander; Ryan, Rachael; Hasan, Nabeeh; Bailey, Donovan; Chen, Haofeng; Milligan, Brook; Houde, Peter

    2012-01-01

    Motivation: Microsatellites are among the most useful genetic markers in population biology. High-throughput sequencing of microsatellite-enriched libraries dramatically expedites the traditional process of screening recombinant libraries for microsatellite markers. However, sorting through millions of reads to distill high-quality polymorphic markers requires special algorithms tailored to tolerate sequencing errors in locus reconstruction, distinguish paralogous loci, rarify raw reads originating from the same amplicon and sort out various artificial fragments resulting from recombination or concatenation of auxiliary adapters. Existing programs warrant improvement. Results: We describe a microsatellite prediction framework named HighSSR for microsatellite genotyping based on high-throughput sequencing. We demonstrate the utility of HighSSR in comparison to Roche gsAssembler on two Roche 454 GS FLX runs. The majority of the HighSSR-assembled loci were reliably mapped against model organism reference genomes. HighSSR demultiplexes pooled libraries, assesses locus polymorphism and implements Primer3 for the design of PCR primers flanking polymorphic microsatellite loci. As sequencing costs drop and permit the analysis of all project samples on next-generation platforms, this framework can also be used for direct simple sequence repeats genotyping. Availability: http://code.google.com/p/highssr/ Contact: alexander@big.ac.cn Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22954626

  11. Characteristics and biotypes of Pasteurella multocida isolated from humans.

    PubMed Central

    Oberhofer, T R

    1981-01-01

    Fifty-two isolates of Pasteurella (48 strains of Pasteurella multocida and 4 strains of atypical Pasteurella) were identified by conventional and commercial test systems. All strains fermented glucose, sucrose, and fructose in purple broth base (Difco Laboratories) with bromocresol purple as indicator, although the atypical Pasteurella produced fermentation reactions that were barely perceptible. Eleven different biotypes were identified by fermentation reactions in maltose, mannitol, xylose, sorbitol, and trehalose media. There was a correlation of biotypes to cat bites, with 61% of cat bite isolates falling into biotype A and B. A correlation of biotype and dog bite isolates was not seen. The choice of medium used for fermentation tests was critical as evidenced by the inability of the organisms to grow in a second commercially purchased preparation of purple broth base. The reliability of commercial test systems in identifying Pasteurella was 81% for Oxi/Ferm (Roche Diagnostics, Div. Hoffmann-La Roche, Inc., Nutley, N.J.), 68% for API (Analytab Products, Plainview, N.Y.), and 11% for Minitek (BBL Microbiology Systems, Cockeysville, MD.). PMID:7240390

  12. Explaining the variability of WD 1145+017 with simulations of asteroid tidal disruption

    NASA Astrophysics Data System (ADS)

    Veras, Dimitri; Carter, Philip J.; Leinhardt, Zoë M.; Gänsicke, Boris T.

    2017-02-01

    Post-main-sequence planetary science has been galvanized by the striking variability, depth and shape of the photometric transit curves due to objects orbiting white dwarf WD 1145+017, a star which also hosts a dusty debris disc and circumstellar gas, and displays strong metal atmospheric pollution. However, the physical properties of the likely asteroid which is discharging disintegrating fragments remain largely unconstrained from the observations. This process has not yet been modelled numerically. Here, we use the N-body code PKDGRAV to compute dissipation properties for asteroids of different spins, densities, masses and eccentricities. We simulate both homogeneous and differentiated asteroids, for up to 2 yr, and find that the disruption time-scale is strongly dependent on density and eccentricity, but weakly dependent on mass and spin. We find that primarily rocky differentiated bodies with moderate (˜3-4 g cm-3) bulk densities on near-circular (e ≲ 0.1) orbits can remain intact while occasionally shedding mass from their mantles. These results suggest that the asteroid orbiting WD 1145+017 is differentiated, resides just outside of the Roche radius for bulk density but just inside the Roche radius for mantle density, and is more akin physically to an asteroid like Vesta instead of one like Itokawa.

  13. STABILITY OF GAS CLOUDS IN GALACTIC NUCLEI: AN EXTENDED VIRIAL THEOREM

    SciTech Connect

    Chen, Xian; Cuadra, Jorge; Amaro-Seoane, Pau E-mail: jcuadra@astro.puc.cl

    2016-03-10

    Cold gas entering the central 1–10{sup 2} pc of a galaxy fragments and condenses into clouds. The stability of the clouds determines whether they will be turned into stars or can be delivered to the central supermassive black hole (SMBH) to turn on an active galactic nucleus (AGN). The conventional criteria to assess the stability of these clouds, such as the Jeans criterion and Roche (or tidal) limit, are insufficient here, because they assume the dominance of self-gravity in binding a cloud, and neglect external agents, such as pressure and tidal forces, which are common in galactic nuclei. We formulate a new scheme for judging this stability. We first revisit the conventional Virial theorem, taking into account an external pressure, to identify the correct range of masses that lead to stable clouds. We then extend the theorem to further include an external tidal field, which is equally crucial for the stability in the region of our interest—in dense star clusters, around SMBHs. We apply our extended Virial theorem to find new solutions to controversial problems, namely, the stability of the gas clumps in AGN tori, the circum-nuclear disk in the Galactic Center, and the central molecular zone of the Milky Way. The masses we derive for these structures are orders of magnitude smaller than the commonly used Virial masses (equivalent to the Jeans mass). Moreover, we prove that these clumps are stable, contrary to what one would naively deduce from the Roche (tidal) limit.

  14. AN X-RAY AND OPTICAL LIGHT CURVE MODEL OF THE ECLIPSING SYMBIOTIC BINARY SMC3

    SciTech Connect

    Kato, Mariko; Hachisu, Izumi; Mikolajewska, Joanna

    2013-01-20

    Some binary evolution scenarios for Type Ia supernovae (SNe Ia) include long-period binaries that evolve to symbiotic supersoft X-ray sources in their late stage of evolution. However, symbiotic stars with steady hydrogen burning on the white dwarf's (WD) surface are very rare, and the X-ray characteristics are not well known. SMC3 is one such rare example and a key object for understanding the evolution of symbiotic stars to SNe Ia. SMC3 is an eclipsing symbiotic binary, consisting of a massive WD and red giant (RG), with an orbital period of 4.5 years in the Small Magellanic Cloud. The long-term V light curve variations are reproduced as orbital variations in the irradiated RG, whose atmosphere fills its Roche lobe, thus supporting the idea that the RG supplies matter to the WD at rates high enough to maintain steady hydrogen burning on the WD. We also present an eclipse model in which an X-ray-emitting region around the WD is almost totally occulted by the RG swelling over the Roche lobe on the trailing side, although it is always partly obscured by a long spiral tail of neutral hydrogen surrounding the binary in the orbital plane.

  15. LONG-TERM EVOLUTION OF DOUBLE WHITE DWARF BINARIES ACCRETING THROUGH DIRECT IMPACT

    SciTech Connect

    Kremer, Kyle; Kalogera, Vassiliki; Sepinsky, Jeremy E-mail: vicky@northwestern.edu

    2015-06-10

    We calculate the long-term evolution of angular momentum in double white dwarf binaries undergoing direct impact accretion over a broad range of parameter space. We allow the rotation rate of both components to vary and account for the exchange of angular momentum between the spins of the white dwarfs and the orbit, while conserving the total angular momentum. We include gravitational, tidal, and mass transfer effects in the orbital evolution, and allow the Roche radius of the donor star to vary with both the stellar mass and the rotation rate. We examine the long-term stability of these systems, focusing in particular on those systems that may be progenitors of AM CVn or SNe Ia. We find that our analysis yields an increase in the predicted number of stable systems compared to that in previous studies. Additionally, we find that by properly accounting for the effects of asynchronism between the donor and the orbit on the Roche-lobe size, we eliminate oscillations in the orbital parameters, which were found in previous studies. Removing these oscillations can reduce the peak mass transfer rate in some systems, keeping them from entering an unstable mass transfer phase.

  16. Constraining Engine Paradigms of Pre-Planetary Nebulae Using Kinematic Properties of their Outflows

    NASA Astrophysics Data System (ADS)

    Blackman, E.

    2014-04-01

    Binary interactions and accretion plausibly conspire to produce the ubiquitous collimated outflows from planetary nebulae (PN) and their presumed pre-planetary nebulae (PPN) progenitors. But which accretion engines are viable? The difficulty in observationally resolving the engines warrants indirect constraints. I discuss how momentum outflow data for PPN can be used to determine the minimum required accretion rate for presumed main sequence (MS) or white dwarf (WD) accretors by comparing to several example accretion rates inferred from published models. While the main goal is to show the method in anticipation of more data and better theoretical constraints, taking the present results at face value already rule out modes of accretion: Bondi-Hoyle Lyttleton (BHL) wind accretion and wind Roche lobe overflow (M-WRLOF, based on Mira parameters) are too feeble for all 19/19 objects for a MS accretor. For a WD accretor, BHL is ruled out for 18/19 objects and M-WRLOF for 15/19 objects. Roche lobe overflow from the primary can accommodate 7/19 objects but only common envelope evolution accretion modes seem to be able to accommodate all 19 objects. Sub-Eddington rates for a MS accretor are acceptable but 8/19 would require super-Eddington rates for a WD. I also briefly discuss a possible anti-correlation between age and maximum observed outflow speed, and the role of magnetic fields.

  17. COUPLED EVOLUTIONS OF THE STELLAR OBLIQUITY, ORBITAL DISTANCE, AND PLANET'S RADIUS DUE TO THE OHMIC DISSIPATION INDUCED IN A DIAMAGNETIC HOT JUPITER AROUND A MAGNETIC T TAURI STAR

    SciTech Connect

    Chang, Yu-Ling; Gu, Pin-Gao; Bodenheimer, Peter H.

    2012-10-01

    We revisit the calculation of the ohmic dissipation in a hot Jupiter presented by Laine et al. by considering more realistic interior structures, stellar obliquity, and the resulting orbital evolution. In this simplified approach, the young hot Jupiter of one Jupiter mass is modeled as a diamagnetic sphere with a finite resistivity, orbiting across tilted stellar magnetic dipole fields in vacuum. Since the induced ohmic dissipation occurs mostly near the planet's surface, we find that the dissipation is unable to significantly expand the young hot Jupiter. Nevertheless, the planet inside a small corotation orbital radius can undergo orbital decay by the dissipation torque and finally overfill its Roche lobe during the T Tauri star phase. The stellar obliquity can evolve significantly if the magnetic dipole is parallel/antiparallel to the stellar spin. Our results are validated by the general torque-dissipation relation in the presence of the stellar obliquity. We also run the fiducial model of Laine et al. and find that the planet's radius is sustained at a nearly constant value by the ohmic heating, rather than being thermally expanded to the Roche radius as suggested by the authors.

  18. The Moon's orbit history and inferences on its origin

    NASA Technical Reports Server (NTRS)

    Conway, B. A.

    1984-01-01

    A frequency dependent model of tidal friction was used to determine the evolution of the Earth-Moon system. The analysis considers the lunar orbit eccentricity and inclination, the solar tide on the Earth, Earth oblateness, and higher order terms in the tidal potential. A solution of the equations governing the precession of the Earth's rotational angular momentum and the lunar ascending node is found. The history is consistent with a capture origin for the Moon. It rules out the origin of the Moon by fission. Results are shown for a range of assumed values for the lunar tidal dissipation. Tidal dissipation within the Moon, during what would be the immediate postcapture period, is shown to be capable of significantly heating the Moon. The immediate postcapture orbit has a periapsis within the Earth's Roche limit. Capture into resonance with the Earth's gravitational field as this orbit tidally evolves is suggested to be a mechanism to prevent so close, an approach. It is shown that the probability of such capture is negligibly small and alternative hypotheses for the survival of the Roche limit passage is offered.

  19. The Crowded Magnetosphere Of The Post-Common-Envelope Binary QS Virginis

    NASA Astrophysics Data System (ADS)

    Hill, Colin

    2016-06-01

    We present high-speed photometry and high-resolution spectroscopy of the short-period (Prot = 3.6 h) eclipsing post-common-envelope binary QS Virginis (QS Vir). Our UVES spectra span in excess of 6 orbits, over more than a year, and reveal the presence of several large prominences passing in front of both the M star and its white dwarf (WD) companion. Despite showing small variations on a time-scale of days, they persist for more than a year and may last decades. Roche tomography reveals a heavily spotted M star, with long-lived spots remaining in fixed locations, preferentially found on the hemisphere facing the WD. We find the 14,220 ± 350 K WD is relatively massive at 0.782 ± 0.013 M(_{odot}),with a radius of0.01068 ± 0.00007 R(_{odot}), consistent with evolutionary models. The tidally distorted M star has a mass of 0.382 ± 0.006 M(_{odot})and a radius of0.381 ± 0.003 R(_{odot}), also consistent with evolutionary models. Since the M star's radius is still within its Roche lobe and there is no evidence that it is overinflated, we conclude that QS Vir is most likely a pre-cataclysmic binary just about to become semidetached.

  20. NG6: Integrated next generation sequencing storage and processing environment

    PubMed Central

    2012-01-01

    Background Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increase the number of laboratories hosting a sequencer. In such a context, it is important to provide these teams with an easily manageable environment to store and process the produced reads. Results We describe a user-friendly information system able to manage large sets of sequencing data. It includes, on one hand, a workflow environment already containing pipelines adapted to different input formats (sff, fasta, fastq and qseq), different sequencers (Roche 454, Illumina HiSeq) and various analyses (quality control, assembly, alignment, diversity studies,…) and, on the other hand, a secured web site giving access to the results. The connected user will be able to download raw and processed data and browse through the analysis result statistics. The provided workflows can easily be modified or extended and new ones can be added. Ergatis is used as a workflow building, running and monitoring system. The analyses can be run locally or in a cluster environment using Sun Grid Engine. Conclusions NG6 is a complete information system designed to answer the needs of a sequencing platform. It provides a user-friendly interface to process, store and download high-throughput sequencing data. PMID:22958229

  1. Prevalence of use study for amphetamine (AMP), methamphetamine (MAMP), 3,4-methylenedioxy-amphetamine (MDA), 3,4-methylenedioxy-methamphetamine (MDMA), and 3,4-methylenedioxy-ethylamphetamine (MDEA) in military entrance processing stations (MEPS) specimens.

    PubMed

    Klette, Kevin L; Kettle, Aaron R; Jamerson, Matthew H

    2006-06-01

    The Roche Abuscreen Onlinetrade mark Amphetamine immunoassay (IA), modified to include sodium periodate, and the Microgenics DRI Ecstasy IA were used to determine the prevalence of amphetamine (AMP), methamphetamine (MAMP), 3,4-methylenedioxyamphetamine (MDA), 3,4-methylenedioxymethamphetamine (MDMA), and 3,4-methylenedioxyethylamphetamine (MDEA) in urine specimens from applicants seeking to join the United States Armed Forces. Over a 4-month period, a total of 85,658 specimens were IA screened using the Department of Defense 500 ng/mL administrative cutoff level for AMP and MDMA. All presumptively positive specimens were confirmed using a solid-phase extraction procedure coupled with simultaneous analysis of AMP, MAMP, MDA, MDMA, and MDEA by fast gas chromatography-mass spectrometry using the same cutoff levels as the IA. The Roche Online Amphetamine IA identified 216 specimens as presumptively positive; of these, 70 specimens confirmed positive for AMP and 87 specimens confirmed positive for AMP and/or MAMP, resulting in a confirmation rate of 73%. The Microgenics DRI Ecstasy IA identified eight specimens as presumptively positive; of these, five specimens confirmed positive for MDMA and/or MDA, resulting in a confirmation rate of 63%. The total use prevalence for AMP, MAMP, MDA, MDMA, and/or MDEA in military entrance processing stations specimens over the testing period was determined to be 0.19%.

  2. Evaluation of commercial kits for extraction of DNA and RNA from Clostridium difficile.

    PubMed

    Metcalf, Devon; Weese, J Scott

    2012-12-01

    Commercial nucleic acid extraction kits are a cost effective, efficient and convenient way to isolate DNA and RNA from bacteria. Despite the increasing importance of the gastrointestinal pathogen, Clostridium difficile, and the increased use of nucleic acids in its identification, characterization, and investigation of virulence factors, no standardized or recommended methods for nucleic acid isolation exist. Here, we sought to evaluate 4 commercial DNA extraction kits and 3 commercial RNA extraction kits assessing cost, labor intensity, purity, quantity and quality of nucleic acid preparations. The DNA extraction kits produced a range of concentrations (20.9-546 ng/ml) and A(260/280) ratios (1.92-2.11). All kits were suitable for DNA extraction with the exception of the Roche MagNA pure LC DNA isolation kit III which produced DNA of high yield but with substantial shearing, but that did not affect downstream PCR amplifications. For RNA extraction, the Qiagen RNeasy mini kit stood out producing preparations of consistently higher concentrations and higher RNA integrity numbers (RIN). The Roche MagNA pure LC RNA isolation kit produced preparations that could not be properly assigned RINs due to a failure to remove small RNAs which were interpreted as degradation. Good DNA and RNA yield are critical but methods are often overlooked. This study highlights the potential for critical variation between established commercial systems and the need for assessment of any extraction methods that are used.

  3. Simultaneous detection of human mitochondrial DNA and nuclear-inserted mitochondrial-origin sequences (NumtS) using forensic mtDNA amplification strategies and pyrosequencing technology.

    PubMed

    Bintz, Brittania J; Dixon, Groves B; Wilson, Mark R

    2014-07-01

    Next-generation sequencing technologies enable the identification of minor mitochondrial DNA variants with higher sensitivity than Sanger methods, allowing for enhanced identification of minor variants. In this study, mixtures of human mtDNA control region amplicons were subjected to pyrosequencing to determine the detection threshold of the Roche GS Junior(®) instrument (Roche Applied Science, Indianapolis, IN). In addition to expected variants, a set of reproducible variants was consistently found in reads from one particular amplicon. A BLASTn search of the variant sequence revealed identity to a segment of a 611-bp nuclear insertion of the mitochondrial control region (NumtS) spanning the primer-binding sites of this amplicon (Nature 1995;378:489). Primers (Hum Genet 2012;131:757; Hum Biol 1996;68:847) flanking the insertion were used to confirm the presence or absence of the NumtS in buccal DNA extracts from twenty donors. These results further our understanding of human mtDNA variation and are expected to have a positive impact on the interpretation of mtDNA profiles using deep-sequencing methods in casework.

  4. Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use

    PubMed Central

    Raymond, Stéphanie; Nicot, Florence; Jeanne, Nicolas; Delfour, Olivier; Carcenac, Romain; Lefebvre, Caroline; Cazabat, Michelle; Sauné, Karine; Delobel, Pierre; Izopet, Jacques

    2017-01-01

    The coreceptor used by HIV-1 must be determined before a CCR5 antagonist, part of the arsenal of antiretroviral drugs, is prescribed because viruses that enter cells using the CXCR4 coreceptor are responsible for treatment failure. HIV-1 tropism is also correlated with disease progression and so must be determined for virological studies. Tropism can be determined by next-generation sequencing (NGS), but not all of these new technologies have been fully validated for use in clinical practice. The Illumina NGS technology is used in many laboratories but its ability to predict HIV-1 tropism has not been evaluated while the 454 GS-Junior (Roche) is used for routine diagnosis. The genotypic prediction of HIV-1 tropism is based on sequencing the V3 region and interpreting the results with an appropriate algorithm. We compared the performances of the MiSeq (Illumina) and 454 GS-Junior (Roche) systems with a reference phenotypic assay. We used clinical samples for the NGS tropism predictions and assessed their ability to quantify CXCR4-using variants. The data show that the Illumina platform can be used to detect minor CXCR4-using variants in clinical practice but technical optimization are needed to improve quantification. PMID:28186189

  5. Microarray oligonucleotide probe designer (MOPeD): A web service.

    PubMed

    Patel, Viren C; Mondal, Kajari; Shetty, Amol Carl; Horner, Vanessa L; Bedoyan, Jirair K; Martin, Donna; Caspary, Tamara; Cutler, David J; Zwick, Michael E

    2010-11-01

    Methods of genomic selection that combine high-density oligonucleotide microarrays with next-generation DNA sequencing allow investigators to characterize genomic variation in selected portions of complex eukaryotic genomes. Yet choosing which specific oligonucleotides to be use can pose a major technical challenge. To address this issue, we have developed a software package called MOPeD (Microarray Oligonucleotide Probe Designer), which automates the process of designing genomic selection microarrays. This web-based software allows individual investigators to design custom genomic selection microarrays optimized for synthesis with Roche NimbleGen's maskless photolithography. Design parameters include uniqueness of the probe sequences, melting temperature, hairpin formation, and the presence of single nucleotide polymorphisms. We generated probe databases for the human, mouse, and rhesus macaque genomes and conducted experimental validation of MOPeD-designed microarrays in human samples by sequencing the human X chromosome exome, where relevant sequence metrics indicated superior performance relative to a microarray designed by the Roche NimbleGen proprietary algorithm. We also performed validation in the mouse to identify known mutations contained within a 487-kb region from mouse chromosome 16, the mouse chromosome 16 exome (1.7 Mb), and the mouse chromosome 12 exome (3.3 Mb). Our results suggest that the open source MOPeD software package and website (http://moped.genetics.emory.edu/) will make a valuable resource for investigators in their sequence-based studies of complex eukaryotic genomes.

  6. Obinutuzumab: first global approval.

    PubMed

    Cameron, Fiona; McCormack, Paul L

    2014-01-01

    Obinutuzumab (Gazyva™) is an intravenously administered, humanized and glycoengineered, type II anti-CD20 monoclonal antibody for the treatment of B-cell malignancies. It is approved in the US for use in combination with chlorambucil for the first-line treatment of chronic lymphocytic leukaemia (CLL), and has been filed for approval in the EU in this indication. The antibody is based on GlycArt Biotechnology's (later Roche Glycart AG) proprietary GlycoMAb® technology, which uses glycoengineered antibodies that specifically increase antibody-dependent cellular cytotoxicity and thereby increase immune-mediated target cell death. Obinutuzumab is a type II anti-CD20 antibody that induces enhanced direct cell death. The monoclonal antibody is in worldwide phase III development with Roche and its subsidiaries, Genentech and Chugai Pharmaceutical, as well as Biogen Idec, for diffuse large B-cell lymphoma and non-Hodgkin's lymphoma generally, and is also in phase III development in countries outside of the US and EU for CLL.

  7. Mind the Gap when Data Mining the Ritter-Kolb Cataclysmic Variable Catalogue

    NASA Astrophysics Data System (ADS)

    Sparks, Warren M.; Sion, Edward M.

    2017-01-01

    The cataclysmic variable (CV) binary consists of a white dwarf primary and a low-mass secondary which overflows its Roche lobe. The Ritter-Kolb catalogue (2003, A&A, 404, 301) is a collection (~1000) of CV binaries and related objects. We have mined this catalogue for CVs with unevolved secondaries whose mass ratio (secondary/primary) is known (~130). A plot of the secondary mass verses the log of the orbital period exhibits the well-known period gap at 2-3 hrs. In addition, this plot shows that the secondary masses just above the period gap are collectively much larger than those just below. The average of the first ten secondary masses above the period is 180% larger than the average below the gap.The disrupted magnetic braking hypothesis (Howell, Nelson, and Rappaport 2001, ApJ, 550, 897 [HNR]) predicts that when the secondary becomes fully convective, the magnetic braking, which has driven the secondary out of thermal equilibrium, stops. In adjusting to thermal equilibrium the secondary shrinks below its Roche lobe and no longer loses mass. The binary system ceases to appear as a CV until gravitational radiation loss brings the secondary back in contact with its Roche lobe. This scenario is at odds with the apparent secondary mass loss across the period gap. Either the secondary continues to lose mass while crossing the period gap or the secondary masses are miscalculated!Magnetic braking causes the secondary to expand or inflate larger than its single star counterpart. Any orbital parameter calculation which assumes a radius-mass relationship based on single main-sequence stars will overestimate the mass of the secondary. We can approximate this mass overestimation from calculations by HNR which take into account the thermal heating from magnetic braking. Using this approximation as a first-order correction to the secondary mass, we replot the deflated secondary mass versus the binary period. The deflated masses immediately above and below the period gap are

  8. Formation and early evolution of narrow planetary rings following the tidal disruption of satellites

    NASA Astrophysics Data System (ADS)

    Ogilvie, G. I.; Leinhardt, Z. M.; Latter, H. N.; Kokubo, E.

    2012-09-01

    Satellites that are formed inside the corotation radius of a planet migrate slowly inwards as a result of tidal dissipation in the central body. Eventually they are tidally disrupted and form planetary rings. We use N-body simulations of gravitational aggregates (rubble piles) to study the tidal disruption of both homogeneous satellites and differentiated bodies containing a denser core. These bodies are initially placed in synchronous rotation on circular orbits at different distances from the planet. In cases where tidal disruption occurs, we analyse the disruption process and the properties of the rings that are formed. We find that the Roche limit for a rubble pile is closer to the planet than for a fluid body of the same mean density, and this effect is enhanced if the satellite is differentiated. Significant zones exist around Uranus and Neptune in which inward migration and tidal disruption may occur; similar zones may have existed around the early Jupiter and Saturn. Within its Roche limit, a homogeneous satellite is totally disrupted and forms a narrow ring. The initial stages of the disruption are similar to the evolution of a viscous fluid ellipsoid, which can be computed semianalytically. Later, however, gravitational instability produces irregular structure and dynamics within the ring. On the other hand, a differentiated satellite tends to undergo a disruption of its mantle only. This process is similar to Roche-lobe overflow in interacting binary stars, although proceeding simultaneously through both Lagrange points L1 and L2, and produces streams of ejected particles whose trajectories are initially well described by solutions of the restricted three-body problem. Again, however, gravitational instability affects the streams near nodes where the particles comes almost to rest in the corotating frame and the density is enhanced. This type of disruption process produces two narrow rings on either side of a remnant satellite. If a differentiated

  9. Three decades of structure- and property-based molecular design.

    PubMed

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been involved in this transformation process, to have been able to collaborate with, direct, guide, or simply encourage outstanding experts in various disciplines to build and further develop what has become a major pillar of modern small-molecule drug discovery. This article is an account of major events that took place since the early decision of Roche to implement computer-assisted molecular modeling 32 years ago and is devoted to the key players involved. It highlights the internal build-up of structural biology, with protein X-ray structure determination at its core, and the early setup of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries. These developments were accompanied by the rise of miniaturized parallel compound property analytics which resulted in a major paradigm shift in medicinal chemistry from linear to multi-dimensional lead optimization. The rapid growth of huge collections of property data stimulated the development of various novel data mining concepts with 'matched molecular pair' analysis and novel variants thereof playing crucial roles. As compound properties got more prominent in molecular design, exploration of specific structural motifs for property modulation became a research activity complementary to target-oriented medicinal chemistry. The exploration of oxetane is given as an example. For the sake of brevity, this account cannot detail all further developments that have taken place in each individual area of

  10. Forming Inner Ice-Rich Moons at Saturn from a Massive Early Ring

    NASA Astrophysics Data System (ADS)

    Salmon, Julien; Canup, Robin M.

    2014-11-01

    Saturn’s rings are 90 to 95% water ice. As a group, Saturn’s moons interior to and including Tethys are also about 90% ice. The small inner moons (interior to and including Janus) are dynamically young with histories tied to that of the rings (e.g., Goldreich & Tremaine 1982; Esposito 1986). Charnoz et al. (2010) showed that ring material viscously spreading outward across the Roche limit can produce these small moons and their observed mass vs. distance relationship within the last 107 years. Canup (2010) proposed that at the end of Saturn’s formation, tidal stripping from a differentiated Titan-sized moon as it spiraled into Saturn could have produced a massive 1024 - 1025 g initial ice ring, and that Mimas, Enceladus and Tethys could have been similarly spawned from this primordial ring as it viscously evolved. Charnoz et al. (2011) considered a massive ice-rock ring and a tidal dissipation factor for Saturn of Q ˜ 103, and found that satellites out to Rhea could be spawned from such a ring. However the likelihood of such a small value for Q is debated. In addition, capture into mutual mean motion resonances and resulting eccentricity growth (not included in the Charnoz et al. model) could lead to orbital destabilization as the moons tidally expand over large distances (Peale & Canup 2014). Here we consider a dissipation factor for Saturn Q ˜ 104 - 105 and investigate whether Mimas, Enceladus and Tethys could have been spawned from a massive initial ice ring. In this scenario, the rock in these moons would be delivered by material from outside the rings, e.g. by heliocentric impactors during the LHB (Canup 2013). We have expanded a numerical model developed to study the accretion of Earth's Moon (Salmon and Canup 2012, 2014), which couples an analytic Roche-interior disk model to the N-body code SyMBA for material exterior to the Roche limit, so that we can directly track the accretion and mutual interactions of growing satellites (including mean

  11. Pharmaceutical quality of seven generic Levodopa/Benserazide products compared with original Madopar® / Prolopa®

    PubMed Central

    2013-01-01

    Background By definition, a generic product is considered interchangeable with the innovator brand product. Controversy exists about interchangeability, and attention is predominantly directed to contaminants. In particular for chronic, degenerative conditions such as in Parkinson’s disease (PD) generic substitution remains debated among physicians, patients and pharmacists. The objective of this study was to compare the pharmaceutical quality of seven generic levodopa/benserazide hydrochloride combination products marketed in Germany with the original product (Madopar® / Prolopa® 125, Roche, Switzerland) in order to evaluate the potential impact of Madopar® generics versus branded products for PD patients and clinicians. Methods Madopar® / Prolopa® 125 tablets and capsules were used as reference material. The generic products tested (all 100 mg/25 mg formulations) included four tablet and three capsule formulations. Colour, appearance of powder (capsules), disintegration and dissolution, mass of tablets and fill mass of capsules, content, identity and amounts of impurities were assessed along with standard physical and chemical laboratory tests developed and routinely practiced at Roche facilities. Results were compared to the original “shelf-life” specifications in use by Roche. Results Each of the seven generic products had one or two parameters outside the specifications. Deviations for the active ingredients ranged from +8.4% (benserazide) to −7.6% (levodopa) in two tablet formulations. Degradation products were measured in marked excess (+26.5%) in one capsule formulation. Disintegration time and dissolution for levodopa and benserazide hydrochloride at 30 min were within specifications for all seven generic samples analysed, however with some outliers. Conclusions Deviations for the active ingredients may go unnoticed by a new user of the generic product, but may entail clinical consequences when switching from original to generic during a

  12. Models for various aspects of dwarf novae and nova-like stars

    NASA Technical Reports Server (NTRS)

    Ladous, Constanze

    1993-01-01

    The first attempts to explain the nature of dwarf novae were based on the assumption of single-star phenomena, in which emission lines were assumed to be caused by circumstellar gas shells. The outburst behavior was tentatively ascribed to the kind of (also not understood) mechanism leading to nova outbursts. The realization that some, and possibly all, dwarf novae and nova-like stars (and novae) are binaries eventually led to models which bore more and more similarities to the modern interpretation on the basis of the Roche model. Not all cataclysmic variables are known binaries. In fact, with respect to the entire number of known objects, the proven binaries are still the minority, but all the brightest variables are in fact known to binaries. Not a single system is known which exhibits the usual characteristics of a cataclysmic variable and at the same time can be declared with certainty to be a single star. Two systems are known, the dwarf nova EY Cyg and the recurrent nova V1017 Sgr, in which, in spite of intensive search, no radial velocity variations have been found; but they still exhibit composite spectra consisting of a bright continuum, an emission spectrum, and a cool absorption spectrum. If the Roche model is correct, it is to be expected that a small percentage of objects is viewed pole-on, so orbital motions do not make themselves felt as Doppler shifts of spectral lines. So even these two systems support the hypothesis that all cataclysmic variables (with the possible exception of symbiotic stars) are binaries. In cataclysmic variables, it seems that the brightness changes observed in dwarf novae and nova-like stars in the optical and the UV are due directly to changes in the accretion disks. The study and understanding of accretion disks in these systems can bear potentially valuable consequences for many other fields in astronomy. The observed spectra of dwarf novae and nova-like stars comprise a fairly large range: pure emission spectra, pure

  13. CONSTRAINTS ON THE COMPACT OBJECT MASS IN THE ECLIPSING HIGH-MASS X-RAY BINARY XMMU J013236.7+303228 IN M 33

    SciTech Connect

    Bhalerao, Varun B.; Harrison, Fiona A.; Van Kerkwijk, Marten H.

    2012-09-20

    We present optical spectroscopic measurements of the eclipsing high-mass X-ray binary (HMXB) XMMU J013236.7+303228 in M 33. Based on spectra taken at multiple epochs of the 1.73 day binary orbital period we determine physical as well as orbital parameters for the donor star. We find the donor to be a B1.5IV subgiant with effective temperature T = 22, 000-23, 000 K. From the luminosity, temperature, and known distance to M 33 we derive a radius of R 8.9 {+-} 0.5 R{sub Sun }. From the radial-velocity measurements, we determine a velocity semi-amplitude of K{sub opt} = 63 {+-} 12 km s{sup -1}. Using the physical properties of the B star determined from the optical spectrum, we estimate the star's mass to be M{sub opt} = 11 {+-} 1 M{sub Sun }. Based on the X-ray spectrum, the compact companion is likely a neutron star, although no pulsations have yet been detected. Using the spectroscopically derived B star mass we find the neutron star companion mass to be M{sub X} = 2.0 {+-} 0.4 M{sub Sun }, consistent with the neutron star mass in the HMXB Vela X-1, but heavier than the canonical value of 1.4 M{sub Sun} found for many millisecond pulsars. We attempt to use as an additional constraint that the B star radius inferred from temperature, flux, and distance should equate to the Roche radius, since the system accretes by Roche lobe overflow. This leads to substantially larger masses, but by trying to apply the technique to known systems, we find that the masses are consistently overestimated. Attempting to account for that in our uncertainties, we derive M{sub X} = 2.2{sup +0.8}{sub -0.6} M{sub Sun} and M{sub opt} = 13 {+-} 4 M{sub Sun }. We conclude that precise constraints require detailed modeling of the shape of the Roche surface.

  14. Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

    PubMed Central

    2010-01-01

    Background Several recent studies have demonstrated the use of Roche 454 sequencing technology for de novo transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis. Further, estimating the effectiveness of transcript discovery using Roche 454 transcriptome data is still a difficult task. Results Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, Erynnis propertius (Lepidoptera: Hesperiidae) and the Anise swallowtail, Papilio zelicaon (Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments. Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6× on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (Bombyx mori) protein--this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. In the final assemblies, 1,413 E. propertius and 1,940 P. zelicaon unigenes had a ratio > 0.8; 2,866 E. propertius and 4,015 P. zelicaon unigenes had a ratio > 0.5. Conclusions Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining

  15. Probing the Masses and Radii of Donor Stars in Eclipsing X-Ray Binaries with the Swift Burst Alert Telescope

    NASA Astrophysics Data System (ADS)

    Coley, Joel B.; Corbet, Robin H. D.; Krimm, Hans A.

    2015-08-01

    Physical parameters of both the mass donor and compact object can be constrained in X-ray binaries with well-defined eclipses, as our survey of wind-fed supergiant X-ray binaries IGR J16393-4643, IGR J16418-4532, IGR J16479-4514, IGR J18027-2016, and XTE J1855-026 reveals. Using the orbital period and Kepler’s third law, we express the eclipse half-angle in terms of radius, inclination angle, and the sum of the masses. Pulse-timing and radial velocity curves can give masses of both the donor and compact object as in the case of the “double-lined” binaries IGR J18027-2016 and XTE J1855-026. The eclipse half angles are {15}-2+3, {31.7}-0.8+0.7, 32 ± 2,34 ± 2, and 33.6+/- 0.7 degrees for IGR J16393-4643, IGR J16418-4532, IGR J16479-4514, IGR J18027-2016, and XTE 1855-026, respectively. In wind-fed systems, the primary not exceeding the Roche-lobe size provides an upper limit on system parameters. In IGR J16393-4643, spectral types of B0 V or B0-5 III are found to be consistent with the eclipse duration and Roche-lobe, but the previously proposed donor stars in IGR J16418-4532 and IGR J16479-4514 were found to be inconsistent with the Roche-lobe size. Stars with spectral types O7.5 I and earlier are possible. For IGR J18027-2016, the mass and radius of the donor star lie between 18.6-19.4 {M}⊙ and 17.4-19.5 {R}⊙ . We constrain the neutron star mass between 1.37 and 1.43 {M}⊙ .We find the mass and radius of the donor star in XTE J1855-026 to lie between 19.6-20.2 {M}⊙ and 21.5-23.0 {R}⊙ . The neutron star mass was constrained to 1.77-1.82 {M}⊙ . Eclipse profiles are asymmetric in IGR J18027-2016 and XTE J1855-026, which we attribute to accretion wakes.

  16. CHARACTERIZING THE THERMOSPHERE OF HD209458b WITH UV TRANSIT OBSERVATIONS

    SciTech Connect

    Koskinen, T. T.; Yelle, R. V.; Lavvas, P.; Lewis, N. K.

    2010-11-01

    Transmission spectroscopy at UV wavelengths is a rich and largely unexplored source of information about the upper atmospheres of extrasolar planets. So far, UV transit observations have led to the detection of atomic hydrogen, oxygen, and ionized carbon in the upper atmosphere of HD209458b. The interpretation of these observations is controversial-it is not clear if the absorption arises from an escaping atmosphere interacting with the stellar radiation and stellar wind, or from the thermosphere inside the Roche lobe. In this paper, we introduce an empirical model that can be used to analyze UV transit depths of extrasolar planets. We use this model to interpret the transits of HD209458b in the H I 1216 and the O I 1304 triplet emission lines. The results indicate that the mean temperature of the thermosphere is T = 8000-11,000 K and that the H{sub 2}/H dissociation front is located at pressures between p = 0.1 and 1 {mu}bar, which correspond to a distance r{approx} 1.1 R{sub p} from the center of the planet. The upper boundary of the model thermosphere is located at r = 2.7-3 R{sub p} , above which the atmosphere is mostly ionized. We find that the H I transit depth in the wings of the H Ly{alpha} line reflects the optical depth of the thermosphere, but that the atmosphere also overflows the Roche lobe. By assuming a solar mixing ratio of oxygen, we obtain an O I transit depth that is statistically consistent with the observations. An O I transit depth comparable to the H I transit depth is possible if the atmosphere is undergoing fast hydrodynamic escape, the O/H ratio is supersolar, or if a significant quantity of neutral oxygen is found outside the Roche lobe. We find that the observations can be explained solely by absorption in the upper atmosphere and extended clouds of energetic neutral atoms or atoms strongly perturbed by radiation pressure are not required. Due to the large uncertainty in the data, repeated observations are necessary to better constrain

  17. Touchdown Enzyme Time Release-PCR for Detection and Identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci Using the 16S and 16S-23S Spacer rRNA Genes

    PubMed Central

    Madico, Guillermo; Quinn, Thomas C.; Boman, Jens; Gaydos, Charlotte A.

    2000-01-01

    Three touchdown enzyme time release (TETR)-PCR assays were used to amplify different DNA sequences in the variable regions of the 16S and 16S-23S spacer rRNA genes specific for Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci as improved tests for sensitive diagnosis and rapid species differentiation. The TETR-PCR protocol used 60 cycles of amplification, which provided improved analytical sensitivity (0.004 to 0.063 inclusion-forming unit of Chlamydia species per PCR). The sensitivity of TETR-PCR with primer set CTR 70-CTR 71 was 96.7%, and the specificity was 99.6%, compared to those of the AMPLICOR PCR for the detection of C. trachomatis in vaginal swab samples. TETR-PCR for C. pneumoniae with primer set CPN 90-CPN 91 was 90% sensitive and 93.3% specific compared with a nested PCR with primer set CP1/2-CPC/D for clinical respiratory samples. TETR-PCR for C. psittaci with primer set CPS 100-CPS 101 showed substantial agreement with cell culturing (κ, 0.78) for animal tissue samples. Primer sets were then combined into a single multiplex TETR-PCR test. The respective 315-, 195-, and 111-bp DNA target products were precisely amplified when DNA from each of the respective Chlamydia species or combinations of them was used. Multiplex chlamydia TETR-PCR correctly identified one strain of each of the 15 serovars of C. trachomatis, 22 isolates of C. pneumoniae, and 20 isolates of C. psittaci. The primer sets were specific for each species. No target products were amplified when DNA from C. pecorum or a variety of other microorganisms was tested for specificity. TETR-PCR with primers selected for specific sequences in the 16S and 16S-23S spacer rRNA genes is a valuable test that could be used either with individual primers or in a multiplex assay for the identification and differentiation of Chlamydia species from culture isolates or for the detection of chlamydiae in clinical samples. PMID:10699002

  18. Prevalence and risk factors of hepatitis B and C virus infections among the general population and blood donors in Morocco

    PubMed Central

    2013-01-01

    Background Viral hepatitis is a serious public health problem affecting billions of people globally. Limited information is available on this issue in Morocco. This cross-sectional study was undertaken with the aim of determining the seroprevalence and risk factors of hepatitis B virus (HBV) and hepatitis C virus (HCV) among the general population and among blood donors. Methods Blood samples from volunteers, have been screened with ELISA tests for detecting the hepatitis-B surface antigen (HBsAg) and anti-HCV. Within the seroreactive patients for HCV in the general population, RT-PCR was performed by the Cobas Ampliprep/Cobas Amplicor. Results HCV and HBV-seropositivity was documented in 1.58% and 1.81% out of 41269 and 23578 participants respectively from the general population. Two patients were found to be co-infected. HCV-RNA was detected by PCR in 70.9% of the 195 anti-HCV positive subjects. The anti-HCV prevalence was not different among males and females (P = 0.3). It increased with age; the highest prevalence was observed among subjects with >50 years old (3.12%). Various risk factors for acquiring HCV infection were identified; age, dental treatment, use of glass syringes and surgical history. In addition to these factors, gender and sexual risk behaviors were found to be associated with higher prevalence of hepatitis B. The HBV positivity was significantly higher among males than females participants in all age groups (P < 0.01). The peak was noticed among males aged 30–49 years (2.4%). None of the 152 persons younger than 20 years had HBsAg or anti-HCV. The prevalence of anti-HCV and HBsAg among 169605 blood donors was 0.62% and 0.96% respectively. Conclusions Our study provided much important information concerning hepatitis B and C prevalence and risk factors; it confirmed the intermediate endemicity for HCV infection and pointed to a decreasing trend of HBV incidence, which might reclassify Morocco in low HBV endemicity area. This could be

  19. Mortality during the first 24 months after delivery in relation to CD4 T-lymphocyte levels and viral load in a cohort of breast-feeding HIV-1-infected women in Dar es Salaam, Tanzania.

    PubMed

    Kilewo, Charles; Karlsson, Katarina; Swai, Andrew; Massawe, Augustine; Lyamuya, Eligius; Mhalu, Fred; Biberfeld, Gunnel

    2005-04-15

    The objective of this study was to analyze the mortality during the first 24 months after delivery in relation to CD4 T-lymphocyte levels and viral load at enrollment (36 weeks of gestation) in a cohort of HIV-1-seropositive breast-feeding women at the Dar es Salaam site of the multicenter Petra trial (a mother-to-child HIV-1 transmission intervention trial using antiretroviral therapy). Antiretroviral treatment was not available in this setting apart from the short treatment given within the trial around delivery to prevent mother-to-child transmission of HIV. T-lymphocyte subsets were determined by flow cytometry. Plasma HIV-1 RNA was quantified by the Amplicor HIV-1 RNA Monitor v 1.5 assay. Mortality after delivery was analyzed using the life-table technique and Cox regression. The analysis included 266 mothers. The CD4 cell counts at enrollment were <200 cells/mm in 14.5% of the mothers. The viral load at enrollment was >100,000 RNA copies/mL in 33.6% of the mothers. The mortality 24 months after delivery was 6.7% (95% CI = 3.1-10.1%). The mortality 24 months after delivery was 29.9% (95% CI = 13.1-46.9%) for mothers with <200 CD4 cells/mm at enrollment, 3.3% (95% CI = 0-6.6%) for mothers with 200-499 CD4 cells/mm, 2.9% (95% CI = 0-7.1%) for mothers with >500 CD4 cells/mm (P = 0.0000), 15.0% (95% CI = 6.6-23.4%) for mothers with viral load >100,000 copies/mL at enrollment, and 2.8% (95% CI = 0-5.6%) for mothers with viral load <100,000 copies/mL (P = 0.0000). In the multivariate analysis CD4 cell counts and viral load were both independent risk factors for mortality (P < 0.001 and P = 0.004, respectively). In conclusion, the mortality was high among women with severe immunosuppression or high viral load at enrollment, but not in the rest of the women. CD4 lymphocyte count in late pregnancy was a better predictor of death within 2 years than was viral load. The results support the World Health Organization recommendation to initiate antiretroviral treatment in

  20. Community Risk Factors for Ocular Chlamydia Infection in Niger: Pre-Treatment Results from a Cluster-Randomized Trachoma Trial

    PubMed Central

    Amza, Abdou; Kadri, Boubacar; Nassirou, Baido; Stoller, Nicole E.; Yu, Sun N.; Zhou, Zhaoxia; Chin, Stephanie; West, Sheila K.; Bailey, Robin L.; Mabey, David C. W.; Keenan, Jeremy D.; Porco, Travis C.; Lietman, Thomas M.; Gaynor, Bruce D.

    2012-01-01

    Background Trachoma control programs utilize mass azithromycin distributions to treat ocular Chlamydia trachomatis as part of an effort to eliminate this disease world-wide. But it remains unclear what the community-level risk factors are for infection. Methods This cluster-randomized, controlled trial entered 48 randomly selected communities in a 2×2 factorial design evaluating the effect of different treatment frequencies and treatment coverage levels. A pretreatment census and examination established the prevalence of risk factors for clinical trachoma and ocular chlamydia infection including years of education of household head, distance to primary water source, presence of household latrine, and facial cleanliness (ocular discharge, nasal discharge, and presence of facial flies). Univariate and multivariate associations were tested using linear regression and Bayes model averaging. Findings There were a total of 24,536 participants (4,484 children aged 0–5 years) in 6,235 households in the study. Before treatment in May to July 2010, the community-level prevalence of active trachoma (TF or TI utilizing the World Health Organization [WHO] grading system) was 26.0% (95% CI: 21.9% to 30.0%) and the mean community-level prevalence of chlamydia infection by Amplicor PCR was 20.7% (95% CI: 16.5% to 24.9%) in children aged 0–5 years. Univariate analysis showed that nasal discharge (0.29, 95% CI: 0.04 to 0.54; P = 0.03), presence of flies on the face (0.40, 95% CI: 0.17 to 0.64; P = 0.001), and years of formal education completed by the head of household (0.07, 95% CI: 0.07 to 0.13; P = 0.03) were independent risk factors for chlamydia infection. In multivariate analysis, facial flies (0.26, 95% CI: 0.02 to 0.49; P = 0.03) and years of formal education completed by the head of household (0.06, 95% CI: 0.008 to 0.11; P = 0.02) were associated risk factors for ocular chlamydial infection. Interpretation We have found that the presence of facial

  1. Residual Stress Analysis in Thick Uranium Films

    SciTech Connect

    Hodge, A M; Foreman, R J; Gallegos, G F

    2004-12-06

    Residual stress analysis was performed on thick, 1.0 to 25 {micro}m, depleted Uranium (DU) films deposited on an Al substrate by magnetron sputtering. Two distinct characterization techniques were used to measure substrate curvature before and after deposition. Stress evaluation was performed using the Benabdi/Roche equation, which is based on beam theory of a bi-layer material. The residual stress evolution was studied as a function of coating thickness and applied negative bias voltage (0-300V). The stresses developed were always compressive; however, increasing the coating thickness and applying a bias voltage presented a trend towards more tensile stresses and thus an overall reduction of residual stresses.

  2. Linearity analysis and comparison study on the epoc(®) point-of-care blood analysis system in cardiopulmonary bypass patients.

    PubMed

    Chen, Jianing; Gorman, Monique; O'Reilly, Bill; Chen, Yu

    2016-03-01

    The epoc(®) blood analysis system (Epocal Inc., Ottawa, Ontario, Canada) is a newly developed in vitro diagnostic hand-held analyzer for testing whole blood samples at point-of-care, which provides blood gas, electrolytes, ionized calcium, glucose, lactate, and hematocrit/calculated hemoglobin rapidly. The analytical performance of the epoc(®) system was evaluated in a tertiary hospital, see related research article "Analytical evaluation of the epoc(®) point-of-care blood analysis system in cardiopulmonary bypass patients" [1]. Data presented are the linearity analysis for 9 parameters and the comparison study in 40 cardiopulmonary bypass patients on 3 epoc(®) meters, Instrumentation Laboratory GEM4000, Abbott iSTAT, Nova CCX, and Roche Accu-Chek Inform II and Performa glucose meters.

  3. A Preparation of (−)-Nutlin-3 Using Enantioselective Organocatalysis at Decagram Scale

    PubMed Central

    Davis, Tyler A.; Vilgelm, Anna E.; Richmond, Ann; Johnston, Jeffrey N.

    2013-01-01

    Chiral nonracemic cis-4,5-bis(aryl) imidazolines have emerged as a powerful platform for the development of cancer chemotherapeutics, stimulated by the Hoffmann-La Roche discovery that Nutlin-3 can restore apoptosis in cells with wild-type p53. The lack of efficient methods for the enantioselective synthesis of cis-imidazolines, however, has limited their more general use. Our disclosure of the first enantioselective synthesis of (−)-Nutlin-3 provided a basis to prepare larger amounts of this tool used widely in cancer biology. Key to the decagram-scale synthesis described here was the discovery of a novel bis(amidine) organocatalyst that provides high enantioselectivity at warmer reaction temperature (−20 °C) and low catalyst loadings. Further refinements to the procedure led to the synthesis of (−)-Nutlin-3 in a 17 gram batch, and elimination of all but three chromatographic purifications. PMID:24127627

  4. A late Neandertal femur from Les Rochers-de-Villeneuve, France

    PubMed Central

    Beauval, Cédric; Maureille, Bruno; Lacrampe-Cuyaubère, François; Serre, David; Peressinotto, David; Bordes, Jean-Guillaume; Cochard, David; Couchoud, Isabelle; Dubrasquet, David; Laroulandie, Véronique; Lenoble, Arnaud; Mallye, Jean-Baptiste; Pasty, Sylvain; Primault, Jérôme; Rohland, Nadin; Pääbo, Svante; Trinkaus, Erik

    2005-01-01

    In 2002, a Neandertal partial femoral diaphysis was discovered at Les Rochers-de-Villeneuve (Vienne, France). Radiocarbon dated to ≈40,700 14C years before present, this specimen is one of the most recent Middle Paleolithic Neandertals. The diaphysis derives from an archeological level indicating alternating human and carnivore (mostly hyena) occupation of the cave, reinforcing the close proximity and probable competition of Middle Paleolithic humans with large carnivores for resources and space. Morphological aspects of the diaphysis and ancient DNA extracted from it indicate that it is aligned with the Neandertals and is distinct from early modern humans. However, its midshaft cortical bone distribution places it between other Middle Paleolithic Neandertals and the Châtelperronian Neandertal from La Roche-à-Pierrot, supporting a pattern of changing mobility patterns among late Middle Paleolithic Neandertals on the eve of modern human dispersals into Europe. PMID:15878988

  5. Patient Recruitment 2.0: Become a Partner in the Patient Journey Using Digital Media.

    PubMed

    Lindemann, Michael; Freeman, Tobe; Kilchenmann, Timothy; Harrison, Shuree; Chan, Margaret; Wygonik, Mark; Haines, Lea; Gossens, Christian

    2016-01-27

    We describe a digital platform, Pioneering Healthcare, designed to inform and empower people who are impacted by lung cancer. The platform enables Roche to support an online conversation with patients and caregivers about lung cancer, and about the role of lung cancer clinical studies in the development of future treatment options. This conversation is live and ongoing on the platform. It provides insights about the views and motivations of patients, and about how to better support patients pursuing treatment for life-threatening illness. We discuss the strategies used to deploy Pioneering Healthcare, and the advantages of using digital platforms for raising disease awareness, increasing patient engagement and, ultimately, for boosting patient enrollment into clinical trials.

  6. International society for antiviral research - 23rd international conference.

    PubMed

    Mason, Vicki L

    2010-06-01

    The 23rd International Conference on Antiviral Research (ICAR), organized by the International Society for Antiviral Research (ISAR) and held in San Francisco, included topics covering new therapeutic developments in the field of antivirals. This conference report highlights selected presentations on CD4-BFFI (Roche Holding AG), a CD4 mAb-based bifunctional HIV entry inhibitor; a CLDC-HBsAg vaccine (Juvaris BioTherapeutics Inc/China National Biotec Group) against HBV; ODE-(S)-MPMPA (University of California San Diego), a potent anti-HCV compound; the anti-human CMV activity exhibited by tricin; the protective activity of Ingavirin against influenza A; and Prosetta Bioconformatics's approach to identifying small-molecule antivirals.

  7. 1,3-Oxazines as BACE1 and/or BACE2 inhibitors: a patent evaluation (WO2012156284).

    PubMed

    Gilbert, Eric J

    2013-08-01

    This patent review covers the contents of Hoffman-La Roche and Siena Biotech's patent application WO2012156284 titled '1,3-Oxazines as BACE1 and/or BACE2 Inhibitors.' Beta-site amyloid precursor protein-converting enzyme (BACE1) and BACE2 activities are reported to support the claimed compounds' use as therapeutics for Alzheimer's disease and type II diabetes, respectively. A common core motif of the claimed compounds is the six-membered 1,3-oxazine system. To gain access to the S3 and S3 subpocket of the BACE1 active site, various linkers are described including nitrogen- and oxygen-based, aryl, and amide-based linkers. Of the 65 compounds claimed, 6 had IC50s less than 100 nM in the BACE1 cell assay. Cellular BACE2 inhibition data are reported for 20 compounds with 2 under 100 nM.

  8. GRAVITY DARKENING AND BRIGHTENING IN BINARIES

    SciTech Connect

    White, Helen E.; Baumgarte, Thomas W.; Shapiro, Stuart L.

    2012-06-20

    We apply a von Zeipel gravity darkening model to corotating binaries to obtain a simple, analytical expression for the emergent radiative flux from a tidally distorted primary orbiting a point-mass secondary. We adopt a simple Roche model to determine the envelope structure of the primary, assumed massive and centrally condensed, and use the results to calculate the flux. As for single rotating stars, gravity darkening reduces the flux along the stellar equator of the primary, but, unlike for rotating stars, we find that gravity brightening enhances the flux in a region around the stellar poles. We identify a critical limiting separation beyond which hydrostatic equilibrium no longer is possible, whereby the flux vanishes at the point on the stellar equator of the primary facing the companion. For equal-mass binaries, the total luminosity is reduced by about 13% when this limiting separation is reached.

  9. On the structure of contact binaries. I - The contact discontinuity

    NASA Technical Reports Server (NTRS)

    Shu, F. H.; Lubow, S. H.; Anderson, L.

    1976-01-01

    The problem of the interior structure of contact binaries is reviewed, and a simple resolution of the difficulties which plague the theory is suggested. It is proposed that contact binaries contain a contact discontinuity between the lower surface of the common envelope and the Roche lobe of the cooler star. This discontinuity is maintained against thermal diffusion by fluid flow, and the transition layer is thin to the extent that the dynamical time scale is short in comparison with the thermal time scale. The idealization that the transition layer has infinitesimal thickness allows a simple formulation of the structure equations which are closed by appropriate jump conditions across the discontinuity. The further imposition of the standard boundary conditions suffices to define a unique model for the system once the chemical composition, the masses of the two stars, and the orbital separation are specified.

  10. RNA-Seq Assembly – Are We There Yet?

    PubMed Central

    Schliesky, Simon; Gowik, Udo; Weber, Andreas P. M.; Bräutigam, Andrea

    2012-01-01

    Transcriptomic sequence resources represent invaluable assets for research, in particular for non-model species without a sequenced genome. To date, the Next Generation Sequencing technologies 454/Roche and Illumina have been used to generate transcriptome sequence databases by mRNA-Seq for more than fifty different plant species. While some of the databases were successfully used for downstream applications, such as proteomics, the assembly parameters indicate that the assemblies do not yet accurately reflect the actual plant transcriptomes. Two different assembly strategies have been used, overlap consensus based assemblers for long reads and Eulerian path/de Bruijn graph assembler for short reads. In this review, we discuss the challenges and solutions to the transcriptome assembly problem. A list of quality control parameters and the necessary scripts to produce them are provided. PMID:23056003

  11. Comparison of two dry chemistry analyzers and a wet chemistry analyzer using canine serum.

    PubMed

    Lanevschi, Anne; Kramer, John W.

    1996-01-01

    Canine serum was used to compare seven chemistry analytes on two tabletop clinical dry chemistry analyzers, Boehringer's Reflotron and Kodak's Ektachem. Results were compared to those obtained on a wet chemistry reference analyzer, Roche Diagnostic's Cobas Mira. Analytes measured were urea nitrogen (BUN), creatinine, glucose, aspartate aminotransferase (AST), alanine aminotransferase (ALT), cholesterol and bilirubin. Nine to 12 canine sera with values in the low, normal, and high range were evaluated. The correlations were acceptable for all comparisons with correlation coefficients greater than 0.98 for all analytes. Regression analysis resulted in significant differences for both tabletop analyzers when compared to the reference analyzer for cholesterol and bilirubin, and for glucose and AST on the Kodak Ektachem. Differences appeared to result from proportional systematic error occurring at high analyte concentrations.

  12. Discovering drug–drug interactions: a text-mining and reasoning approach based on properties of drug metabolism

    PubMed Central

    Tari, Luis; Anwar, Saadat; Liang, Shanshan; Cai, James; Baral, Chitta

    2010-01-01

    Motivation: Identifying drug–drug interactions (DDIs) is a critical process in drug administration and drug development. Clinical support tools often provide comprehensive lists of DDIs, but they usually lack the supporting scientific evidences and different tools can return inconsistent results. In this article, we propose a novel approach that integrates text mining and automated reasoning to derive DDIs. Through the extraction of various facts of drug metabolism, not only the DDIs that are explicitly mentioned in text can be extracted but also the potential interactions that can be inferred by reasoning. Results: Our approach was able to find several potential DDIs that are not present in DrugBank. We manually evaluated these interactions based on their supporting evidences, and our analysis revealed that 81.3% of these interactions are determined to be correct. This suggests that our approach can uncover potential DDIs with scientific evidences explaining the mechanism of the interactions. Contact: luis.tari@roche.com PMID:20823320

  13. A Spectroscopic Study of Anomalous Stellar Populations in M67

    NASA Astrophysics Data System (ADS)

    McGahee, Courtney; King, Jeremy R.; Deliyannis, Constantine P.

    2015-01-01

    A population of so-called "yellow straggler" stars occupy precarious color magnitude diagram positions in the old open cluster M67 that cannot be explained by standard single star evolution theory. These stars may have been formed by Roche lobe overflow mass transfer in close binary systems. We present new radial velocities and spectroscopic abundances of M67 yellow stragglers to test this hypothesis, and find that these objects possess a high binary frequency, but no enhancements of s-process elements that might be a smoking gun signature of mass transfer. Observations were conducted using the WIYN 3.5 m telescope in conjunction with the HYDRA spectrograph at Kitt Peak National Observatory. Support for this project was provided by NSF grants AST 09-08342, AST 0607567, and AST 1211699.

  14. Targeting PRMT5 as a Novel Radiosensitization Approach for Primary and Recurrent Prostate Cancer Treatment

    DTIC Science & Technology

    2013-08-01

    and anti-Flag M2 (F3165) antibodies were from sigma . Monoclonal Anti-Human PARP antibody (4C10-5) was purchased from BD Biosciences (San Diego, CA... sigma ). Plasmids encoding c-Jun63A/73A, c-JunDLZ (c-JunD280-317), c-Jun A?D265 In265 and TAM67 (c-JunD3-122) were generated by PCR or ligation PCR (Ali...cotransfected with 2 lg of pLVX-Tet-On, 1.5 lg of pHR0- CMV -DR8.20vpr, and 0.5 lg of pHR0- CMV -VSV-G using Fugene HD reagent (Roche Ap- plied Science

  15. Patient Recruitment 2.0: Become a Partner in the Patient Journey Using Digital Media

    PubMed Central

    Lindemann, Michael; Freeman, Tobe; Kilchenmann, Timothy; Harrison, Shuree; Chan, Margaret; Wygonik, Mark; Haines, Lea

    2016-01-01

    We describe a digital platform, Pioneering Healthcare, designed to inform and empower people who are impacted by lung cancer. The platform enables Roche to support an online conversation with patients and caregivers about lung cancer, and about the role of lung cancer clinical studies in the development of future treatment options. This conversation is live and ongoing on the platform. It provides insights about the views and motivations of patients, and about how to better support patients pursuing treatment for life-threatening illness. We discuss the strategies used to deploy Pioneering Healthcare, and the advantages of using digital platforms for raising disease awareness, increasing patient engagement and, ultimately, for boosting patient enrollment into clinical trials. PMID:26818938

  16. A Fortunate Story of an Unusual AK-47 Bullet Trajectory: Always Keep a Smartphone in Your Pocket.

    PubMed

    Thabouillot, Oscar; Perrier, Pierre; Roche, Nicolas-Charles; Agard, David; Barbier, Olivier; Martin, Guillaume; Viant, Eric; Leclere, Jean-Baptiste

    2016-06-01

    This is a report of a fortunate story of an unusual AK-47 bullet trajectory which took place during the Paris (France) attack of November 13th, 2015. A young man, trying to protect his girlfriend, interfered between her and a shooter. He had been wounded in the posterior compartment of the thigh. The bullet penetrated him and, instead of exiting, rebound against his Smartphone, which was in the front pocket of his pants. Thanks to that, the missile bullet did not injure his girlfriend but ended its trajectory in the fat tissue of his thigh. Thabouillot O , Perrier P , Roche NC , Agard D , Barbier O , Martin G , Viant E , Leclere JB . A fortunate story of an unusual AK-47 bullet trajectory: always keep a Smartphone in your pocket. Prehosp Disaster Med, 2016;31(3):343-345.

  17. Theoretical Studies of Accreting Neutron Stars

    NASA Technical Reports Server (NTRS)

    Taam, Ronald E.

    2003-01-01

    Among the newly discovered classes of X-ray sources which have attracted wide attention are close binary systems in which mass is transferred via Roche lobe overflow from a low mass donor star to its neutron star companion. Many of these sources exhibit intense bursts of X-ray radiation as well as periodic and quasi-periodic phenomena. Intensive analysis of these sources as a class has provided insight into the accretion process in binary star systems and into the magnetic field, rotational, and nuclear evolution of the underlying neutron star. In this proposal we have focused on theoretical studies of the hydrodynamical and nuclear processes that take place on the surface of accreting neutron stars in these systems. The investigation of these processes is critical for providing an understanding of a number of outstanding problems related to their transient behavior and evolution.

  18. Sesquinary catenae on the Martian satellite Phobos from reaccretion of escaping ejecta

    NASA Astrophysics Data System (ADS)

    Nayak, M.; Asphaug, E.

    2016-08-01

    The Martian satellite Phobos is criss-crossed by linear grooves and crater chains whose origin is unexplained. Anomalous grooves are relatively young, and crosscut tidally predicted stress fields as Phobos spirals towards Mars. Here we report strong correspondence between these anomalous features and reaccretion patterns of sesquinary ejecta from impacts on Phobos. Escaping ejecta persistently imprint Phobos with linear, low-velocity crater chains (catenae) that match the geometry and morphology of prominent features that do not fit the tidal model. We prove that these cannot be older than Phobos' current orbit inside Mars' Roche limit. Distinctive reimpact patterns allow sesquinary craters to be traced back to their source, for the first time across any planetary body, creating a novel way to probe planetary surface characteristics. For example, we show that catena-producing craters likely formed in the gravity regime, providing constraints on the ejecta velocity field and knowledge of source crater material properties.

  19. Sesquinary catenae on the Martian satellite Phobos from reaccretion of escaping ejecta.

    PubMed

    Nayak, M; Asphaug, E

    2016-08-30

    The Martian satellite Phobos is criss-crossed by linear grooves and crater chains whose origin is unexplained. Anomalous grooves are relatively young, and crosscut tidally predicted stress fields as Phobos spirals towards Mars. Here we report strong correspondence between these anomalous features and reaccretion patterns of sesquinary ejecta from impacts on Phobos. Escaping ejecta persistently imprint Phobos with linear, low-velocity crater chains (catenae) that match the geometry and morphology of prominent features that do not fit the tidal model. We prove that these cannot be older than Phobos' current orbit inside Mars' Roche limit. Distinctive reimpact patterns allow sesquinary craters to be traced back to their source, for the first time across any planetary body, creating a novel way to probe planetary surface characteristics. For example, we show that catena-producing craters likely formed in the gravity regime, providing constraints on the ejecta velocity field and knowledge of source crater material properties.

  20. TT Aurigae - A B-type semi-detached eclipsing binary

    NASA Astrophysics Data System (ADS)

    Wachmann, A. A.; Popper, D. M.; Clausen, J. V.

    1986-07-01

    The Hamburg B, V photometry and Lick spectroscopic material on TT Aur are analyzed. In conjunction with the Wilson-Devinney program of light curve analysis, an iterative scheme is employed for matching the model to the photometric observations and the observed color index of the system in order to obtain temperatures and luminosities. The system is semidetached. The less massive, cooler component fills its Roche lobe. This component is the larger one, so that mass exchange has occurred, whereas Bell and Hilditch (1984) conclude it is the smaller. The color indices derived for the components correspond to spectral types B1 and B2.5. The mass of the hotter star, evaluated from the measured radial velocities, is significantly lower than for stars of similar temperatures with known masses. This apparent discrepancy can be reduced by estimated correction of the velocities for blending of the lines of the components.

  1. Linearity analysis and comparison study on the epoc® point-of-care blood analysis system in cardiopulmonary bypass patients

    PubMed Central

    Chen, Jianing; Gorman, Monique; O’Reilly, Bill; Chen, Yu

    2016-01-01

    The epoc® blood analysis system (Epocal Inc., Ottawa, Ontario, Canada) is a newly developed in vitro diagnostic hand-held analyzer for testing whole blood samples at point-of-care, which provides blood gas, electrolytes, ionized calcium, glucose, lactate, and hematocrit/calculated hemoglobin rapidly. The analytical performance of the epoc® system was evaluated in a tertiary hospital, see related research article “Analytical evaluation of the epoc® point-of-care blood analysis system in cardiopulmonary bypass patients” [1]. Data presented are the linearity analysis for 9 parameters and the comparison study in 40 cardiopulmonary bypass patients on 3 epoc® meters, Instrumentation Laboratory GEM4000, Abbott iSTAT, Nova CCX, and Roche Accu-Chek Inform II and Performa glucose meters. PMID:26937460

  2. Catalogue and properties of δ Scuti stars in binaries

    NASA Astrophysics Data System (ADS)

    Liakos, Alexios; Niarchos, Panagiotis

    2017-02-01

    The catalogue contains 199 confirmed cases of binary systems containing at least one pulsating component of δ Sct type. The sample is divided into subgroups in order to describe the properties and characteristics of the δ Sct-type stars in binaries according to their Roche geometry. Demographics describing quantitatively our knowledge for these systems as well as the distributions of their pulsating components in the mass-radius, colour-magnitude, and evolutionary status-temperature diagrams are presented and discussed. It is shown that a threshold of ∼13 d of the orbital period regarding the influence of binarity on the pulsations is established. Finally, the correlations between the pulsation periods and the orbital periods, evolutionary status, and companion's gravity influence are updated based on the largest sample to date.

  3. ORBITAL SOLUTIONS AND ABSOLUTE ELEMENTS OF THE ECLIPSING BINARY EE AQUARII

    SciTech Connect

    Wronka, Marissa Diehl; Gold, Caitlin; Sowell, James R.; Williamon, Richard M. E-mail: rwilliamon@physics.emory.edu

    2010-04-15

    EE Aqr is a 7.9 mag Algol variable with a 12 hr orbital period. The Wilson-Devinney program is used to simultaneously solve 11 previously published light curves together with two existing radial velocity curves. The resulting masses are M {sub 1} = 2.24 {+-} 0.13 M {sub sun} and M {sub 2} = 0.72 {+-} 0.04 M {sub sun}, and the radii are R {sub 1} = 1.76 {+-} 0.03 R {sub sun} and R {sub 2} = 1.10 {+-} 0.02 R {sub sun}. The system has the lower-mass component completely filling its Roche lobe. Its distance from Hipparcos observations is 112 {+-} 10 pc. An improved ephemeris is derived, and no deviations in the period over time were seen. Light and velocity curve parameters, orbital elements, and absolute dimensions are presented, plus a comparison is made with previous solutions.

  4. PHOTOMETRIC STUDY OF THE NEAR CRITICAL CONTACT SYSTEM, GSC 3355 0394

    SciTech Connect

    Samec, R. G.; Melton, R. A.; Figg, E. R.; Labadorf, C. M.; Martin, K. P.; Chamberlain, H. A.; Faulkner, D. R.; Van Hamme, W.

    2010-11-15

    GSC 3355 0394 has an EB-type light curve, which is dominated by hot and cool spot activities. It displays night-to-night variations in light-curve shapes. The period study yields six new times of minimum light and the first precision ephemeris, HJD T{sub min}I = 2, 454, 408.9547 {+-} 0.0017 + 0.4621603 {+-} 0.0000008d*E. VR{sub c}I{sub c} standard magnitudes are presented. BVRI Wilson synthetic light-curve solutions are calculated for both a Mode 4 (V1010 Oph-type, semidetached, more massive component filling its Roche lobe) configuration and a Mode 3, contact configuration (fill-out 100% or critical contact). The critical contact is the lowest residual solution. Four major spot regions are needed to model this binary, at least one is evidently a stream spot.

  5. AY Vulpeculae, observations and analysis of a binary with an undermassive secondary

    SciTech Connect

    Walker, R.L.; Chambliss, C.R. Kutztown Univ., PA )

    1991-02-01

    AY Vulpeculae is an Algol-type eclipsig binary with P = 2.4124 days, and V = 11.70 at maximum light. The primary eclipse is very deep (2.2 mag), which makes the system of special interest. Complete light curves in UBV were obtained in 1986 using the 1.0 m reflector at the USNO Flagstaff Station. A revised ephemeris is presented which shows that the period has increased slightly over the past few decades. The light curves were analyzed using both the WINK method and the SIMPLEX algorithm. AY Vulpeculae is a semidetached system with the secondary filling its Roche lobe. The values derived for r1, r2, and the mass ratio (q) are 0.24, 0.26, and 0.24, respectively. The primary component has the characteristics of a subgiant of spectral class F0, while the secondary is a K-type subgiant and is decidedly undermassive. 24 refs.

  6. Comparison of the MagNA pure LC automated system and the RiboPure-Blood RNA manual method for RNA extraction from multiple myeloma bone marrow samples conserved in an RNA stabilizer.

    PubMed

    Garcia-Effron, G; Gamarra, S; Crooke, A; Martínez-Sánchez, P; Lahuerta, J; Martínez-López, J

    2007-04-01

    A total of 62 frozen bone marrow specimens conserved in RNA later (Ambion) were processed using two different extraction methods, the MagNA Pure LC system (MAG; Roche) and the manual RiboPure-Blood RNA method (RIBO; Ambion); Beta glucoronidase RNA (GUS) was amplified by LightCycler PCR to evaluate the quality of both extraction procedures. Less than 1000 GUS copies/ml was detected in 26 of 62 specimens (41.94%) processed by MAG and in five of 62 specimens (8.06%) processed by RIBO. Moreover, RNA recovery from the 62 specimens by MAG is, on average, 2.91 cycle threshold-fold higher than RIBO (P = 0.0008). Furthermore, we compared the extraction times and reagent costs of both methods. In conclusion, RNA extraction using MAG is faster to process 32 samples and less expensive than RIBO but it is not sensitive enough to be employed for research purpose in our laboratory.

  7. Pharmacogenetic testing in psychiatry: a review of features and clinical realities.

    PubMed

    de Leon, José; Arranz, Maria J; Ruaño, Gualberto

    2008-12-01

    This article focuses on the first generation of pharmacogenetic tests that are potentially useful in psychiatry. All pharmacogenetic tests currently on the market, or soon to be marketed in psychiatry, for which some information has been published in peer-reviewed journal articles (or abstracts), were selected. Five pharmacogenetic tests are reviewed in detail: the Roche AmpliChip CYP450 Test, the Luminex Tag-It Mutation Detection Kit, the LGC clozapine response test, the PGxPredict: Clozapine test, and the Genomas PhyzioType system. After reviewing these tests, three practical aspects of implementing pharmacogenetic testing in psychiatric clinical practice are briefly reviewed: (1) the evaluation of these tests in clinical practice, (2) cost-effectiveness, and (3) regulatory oversight. Finally, the future of these and other pharmacogenetic tests in psychiatry is discussed.

  8. The socioeconomic burden of cancer in member countries of the Association of Southeast Asian Nations (ASEAN)--stakeholder meeting report.

    PubMed

    Jan, Stephen; Kimman, Merel; Kingston, David; Woodward, Mark

    2012-01-01

    The ACTION (Asean CosTs In ONcology) Study will be one of the largest observational studies of the burden of cancer ever conducted in Asia. The study will involve 10,000 newly diagnosed patients with cancer and will be carried out across eight low- and middle income countries within the ASEAN region (Indonesia, Thailand, Malaysia, Cambodia, Myanmar, Viet Nam, Laos and the Philippines). Patients will be interviewed three times over 12 months to assess their health, use of health care services, out of pocket costs related to their illness, social and quality of life issues. The project is a collaboration between the George Institute for Global Health, the ASEAN Foundation and Roche. The aim of the study is to assess the health and socioeconomic impact of cancer on patients in ASEAN communities, and the factors that may impact on these outcomes.

  9. Photometric Analysis and Period Investigation of the EW Type Eclipsing Binary V441 Lac

    NASA Astrophysics Data System (ADS)

    Li, K.; Hu, S.-M.; Guo, D.-F.; Jiang, Y.-G.; Gao, D.-Y.; Chen, X.

    2016-09-01

    Four color light curves of the EW type eclipsing binary V441 Lac were presented and analyzed by the W-D code. It is found that V441 Lac is an extremely low mass ratio ( q = 0.093±0.001) semi-detached binary with the less massive secondary component filling the inner Roche lobe. Two dark spots on the primary component were introduced to explain the asymmetric light curves. By analyzing all times of light minimum, we determined that the orbital period of V441 Lac is continuously increasing at a rate of d P/d t = 5.874(±0.007) × 10-7 d yr-1. The semi-detached Algol type configuration of V441 Lac is possibly formed by a contact configuration destroyed shallow contact binary due to mass transfer from the less massive component to the more massive one predicted by the thermal relaxation oscillation theory.

  10. A synthetic light curve solution of the OAO-2 ultraviolet light curves of u Herculis

    NASA Technical Reports Server (NTRS)

    Eaton, J. A.

    1978-01-01

    OAO 2 ultraviolet photometry of the eclipsing binary u Her is reported and interpreted. The light curve of u Her is found to be intrinsically variable, the variable light curve is rectified, and the adjusted light and color curves are plotted. A simultaneous solution to three adjusted OAO 2 light curves (at respective wavelengths of 3320, 1910, and 1550 A) is obtained by using the Roche model. The results indicate that the system is semidetached if the gravity darkening of the secondary is not significantly larger than expected. It is suggested that the primary is responsible for the variable light curve, that the monochromatic albedo of the secondary is very low at short wavelengths, and that the depth of primary eclipse is strongly dependent on the primary's limb darkening.

  11. EK TrA, a close relative of VW HYI

    NASA Astrophysics Data System (ADS)

    Gänsicke, B. T.; Beuermann, K.; Thomas, H.-C.

    1997-08-01

    The southern dwarf nova EK TrA has been suggested to show the spectrum of its white dwarf primary in the single available International Ultraviolet Explorer (IUE) post-outburst spectrum. We demonstrate that this spectrum is still disc-dominated. However, a careful analysis reveals a white dwarf contribution of ~25 per cent of the SWP flux and a white dwarf temperature of T_wd~18000K. Our optical spectroscopy of the system deep in quiescence confirms the flux level of the white dwarf derived from the IUE data. Additional optical emission arises from a cool (T~6500K) accretion disc, possibly extending over the whole Roche lobe radius of the primary. Both optical and UV data yield a distance of d~180pc.

  12. Identification of a novel human rhinovirus C type by antibody capture VIDISCA-454.

    PubMed

    Jazaeri Farsani, Seyed Mohammad; Oude Munnink, Bas B; Canuti, Marta; Deijs, Martin; Cotten, Matthew; Jebbink, Maarten F; Verhoeven, Joost; Kellam, Paul; Loens, Katherine; Goossens, Herman; Ieven, Margareta; van der Hoek, Lia

    2015-01-19

    Causative agents for more than 30 percent of respiratory infections remain unidentified, suggesting that unknown respiratory pathogens might be involved. In this study, antibody capture VIDISCA-454 (virus discovery cDNA-AFLP combined with Roche 454 high-throughput sequencing) resulted in the discovery of a novel type of rhinovirus C (RV-C). The virus has an RNA genome of at least 7054 nt and carries the characteristics of rhinovirus C species. The gene encoding viral protein 1, which is used for typing, has only 81% nucleotide sequence identity with the closest known RV-C type, and, therefore, the virus represents the first member of a novel type, named RV-C54.

  13. Quantum dots: a new tool for studying quantum phase transitions (QPT)

    NASA Astrophysics Data System (ADS)

    Roch, N.; Florens, S.; Bouchiat, V.; Wernsdorfer, W.; Balestro, F.

    2009-03-01

    QPT were studied in many different systems: spin chains, strongly correlated materials, high Tc superconductors, etc. but all the properties (magnetism, superconductivity ...) of these materials can be difficult to control. On the other hand, thanks to microelectronic technologies, it is now possible to obtain taylor-made quantum dots in which all the interactions can be tuned finely. It was then proposed by several theoretic papers [1] to use them as model systems for probing QPT. In this experimental work, we observed a screening/non screening QPT transition in a single-molecule transistor. We will present a full study as a function of magnetic field, bias voltage and temperature [2].[3pt] [1] M.Vojta, Philosophical Magazine,86:13,1807 - 1846 (2006)[0pt] [2] N.Roch et al. , Nature 453, 633-637 (2008)

  14. Comparison of Next-Generation Sequencing Systems

    PubMed Central

    Liu, Lin; Li, Yinhu; Li, Siliang; Hu, Ni; He, Yimin; Pong, Ray; Lin, Danni; Lu, Lihua; Law, Maggie

    2012-01-01

    With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized. PMID:22829749

  15. Development of real-time PCR assays for the detection of Moraxella macacae associated with bloody nose syndrome in rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques

    PubMed Central

    Whitehouse, Chris A.; Chase, Kitty; Embers, Monica E.; Kulesh, David A.; Ladner, Jason T.; Palacios, Gustavo F.; Minogue, Timothy D.

    2016-01-01

    Background Moraxella macacae is a recently described bacterial pathogen that causes epistaxis or so-called bloody nose syndrome in captive macaques. The aim of this study was to develop specific molecular diagnostic assays for M. macacae and to determine their performance characteristics. Methods We developed six real-time PCR assays on the Roche LightCycler. The accuracy, precision, selectivity, and limit of detection (LOD) were determined for each assay, in addition to further validation by testing nasal swabs from macaques presenting with epistaxis at the Tulane National Primate Research Center. Results All assays exhibited 100% specificity and were highly sensitive with an LOD of 10 fg for chromosomal assays and 1 fg for the plasmid assay. Testing of nasal swabs from 10 symptomatic macaques confirmed the presence of M. macacae in these animals. Conclusions We developed several accurate, sensitive, and species-specific real-time PCR assays for the detection of M. macacae in captive macaques. PMID:26365904

  16. Dispersing agents for an aqueous slurry of coal powder

    SciTech Connect

    Moriyama, N.; Watanabe, S.; Yamamura, M.

    1981-11-24

    Aqueous dispersions of coal powder having good flowability properties are provided by employing, as the dispersing agent, an anionic surface active agent. The formula of the additives: (R-O-CH2CH2O-MSO3)nm wherein R is an alkyl or alkenyl group having 6 to 22 carbon atoms or an alkyl- or alkenyl-substituted aryl group having 4 to 22 carbon atoms in the substituent thereof, M is an integer from 2 to 50, N is a number of from 1 to 3 and is the same as the valence of the counter ion m, and M is a cation having a valence of from 1 to 3.

  17. A circumbinary debris disk in a polluted white dwarf system

    NASA Astrophysics Data System (ADS)

    Farihi, J.; Parsons, S. G.; Gänsicke, B. T.

    2017-03-01

    Planetary systems commonly survive the evolution of single stars, as evidenced by terrestrial-like planetesimal debris observed orbiting and polluting the surfaces of white dwarfs 1,2 . Here, we report the identification of a circumbinary dust disk surrounding a white dwarf with a substellar companion in a 2.27 h orbit. The system bears the dual hallmarks of atmospheric metal pollution and infrared excess 3,4 ; however, the standard (flat and opaque) disk configuration is dynamically precluded by the binary. Instead, the detected reservoir of debris must lie well beyond the Roche limit in an optically thin configuration, where erosion by stellar irradiation is relatively rapid. This finding shows that rocky planetesimal formation is robust around close binaries, even those with low mass ratios.

  18. A Knock-in Reporter for a Novel AR-Targeted Therapy

    DTIC Science & Technology

    2016-05-01

    In brief, cells were lysed in RIPA buffer containing 50mM Tris-HCl, pH 7.4, 1% Nonidet P-40, 0.25% sodium deoxycholate, 150 mM NaCl, 1 mM EDTA, 1 mM...PMSF, and 1mM NaF, 1 mM Na3VO4 and protease inhibitor cocktail (Roche, Indianapolis, IN, USA), and then resolved in sodium dodecyl sulfate...cells irradiated with UV were lysed in modified RIPA buffer containing 50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium

  19. Studies of Transient X-Ray Sources with the Ariel 5 All-Sky Monitor. Ph.D. Thesis - Maryland Univ.

    NASA Technical Reports Server (NTRS)

    Kaluzienski, L. J.

    1977-01-01

    The All-Sky Monitor, an imaging X-ray detector launched aboard the Ariel 5 satellite, was used to obtain detailed light curves of three new sources. Additional data essential to the determination of the characteristic luminosities, rates of occurrence (and possible recurrence), and spatial distribution of these objects was also obtained. The observations are consistent with a roughly uniform galactic disk population consisting of at least two source sub-classes, with the second group (Type 2) at least an order of magnitude less luminous and correspondingly more frequent than the first (Type 1). While both subtypes are probably unrelated to the classical optical novae (or supernovae), they are most readily interpreted within the standard mass exchange X-ray binary model, with outbursts triggered by Roche-lobe overflow (Type 1) or enhancements in the stellar wind density of the companion (Type 2), respectively.

  20. Ordinary tales from endoscopic odysseys: fiction, ethics, and the gastroenterological journey.

    PubMed

    Meulenberg, Frans; de Beaufort, Inez D

    2014-04-01

    Fiction (i.e. novels, short stories, and movies) provides an opportunity for imaginative moral reflection and can serve as a basis for moral argument. Narratives play a role in moral reasoning because they are exemplars as well as tests. Those who care for sick people, should be interested in patient's and literary stories. Exploring the representation of gastroenterological ailments in fiction gives insight in the experience of undergoing colonoscopy, farting, pain, the borders of intimacy, hygiene and the lack of it, taboos and the doctor-patient-relationship. Included authors are, among others: Michel Faber, Alan Bennett, Charles Bukowski, Charlotte Roche and James Joyce. Several movies are discussed as well. Though in general gastroenterological problems don't seem often at foreground in fiction, in some cases they are represented in a more symbolic way, and touch upon some fundamental aspects of the human condition.

  1. Disk Accretion of Tidally Disrupted Rocky Bodies onto White Dwarfs

    NASA Astrophysics Data System (ADS)

    Feng, W.; Desch, S.

    2017-03-01

    The prevailing model for the pollution of white dwarf photospheres invokes accretion from a disk of gas and solid particles, fed by tidal disruption of rocky bodies inside the Roche radius. Current models can successfully explain the accretion rates of metals onto white dwarfs, provided the gaseous disks viscously spread at rates consistent with a partially suppressed magnetorotational instability (Metzger et al. 2012); however, these models do not explore the extent of the magnetorotational instability in disks by calculating the degree of ionization. We present ionization fractions for thermal and non-thermal processes to assess the extent of the magnetorotational instability in white dwarf disks. We determine that the disk viscosity parameter α can be as high as 0.1 in white disks, implying that the magnetorotational instability must be carefully modeled.

  2. Eccentricity Pumping Through Circumbinary Disks in Hot Subdwarf Binaries

    NASA Astrophysics Data System (ADS)

    Vos, J.

    2015-12-01

    Hot subdwarf-B stars in long-period binaries are found to be on eccentric orbits, even though current binary-evolution theory predicts these objects to be circularized before the onset of Roche-lobe overflow (RLOF). We have tested three different eccentricity pumping processes on their viability to reproduce the observed wide sdB population; tidally-enhanced wind mass-loss, phase-dependent RLOF on eccentric orbits and the interaction between a circumbinary (CB) disk and the binary. The binary module of the stellar-evolution code Modules for Experiments in Stellar Astrophysics (MESA) is extended to include the eccentricity-pumping processes, and a parameter study is carried out. We find that models including phase-dependent RLOF or a CB disk can reach the observed periods and eccentricities. However, the models cannot explain the observed correlation between period and eccentricity. Nor can circular short period systems be formed when eccentricity pumping mechanisms are active.

  3. Evidence of Accretion in Saturn's F Ring (Invited)

    NASA Astrophysics Data System (ADS)

    Agnor, C. B.; Buerle, K.; Murray, C. D.; Evans, M. W.; Cooper, N. J.; Williams, G. W.

    2010-12-01

    Lying slightly outside the classical Roche radius and being strongly perturbed by the adjacent moons Prometheus and Pandora, Saturn's F ring represents a unique astrophysical laboratory for examining the processes of mass accretion and moonlet formation. Recent images from the Cassini spacecraft reveal optically thick clumps, capable of casting shadows, and associated structures in regions of the F ring following close passage by Prometheus. Here we examine the accretion environment of the F ring and Prometheus' role in moonlet formation and evolution. Using the observed structures adjacent to these clumps and dynamical arguments we estimate the masses of these clumps and find them comparable to that of ~10-20-km contiguous moonlets. Further, we show that Prometheus' perturbations on the F ring create regions of enhanced density and low relative velocity that may accelerate the accretion of clumps and moonlets.

  4. [Identification of yeast-like fungi: evaluation of 4 commercial systems].

    PubMed

    Russolo, S; Sala, A; Crotti, D

    1984-12-01

    Four different commercial systems were compared to identify 110 medically important yeast-like fungi found out in as many pathologic materials in three Medical Centers. The systems were: a) API 20C Aux (Ayerst), which represented the reference method in conjunction with the germ-tube test, aggregates 19 carbohydrate substrates for assimilation reactions; b) Uni-Yeast Tek (Flow) and Mycotube (Roche) were used to indicate assimilation and fermentation of 7 carbohydrate substrates and to determine other biochemical tests; c) Candida-Check (Poli) was based on agglutination reaction by specific antisera. Comparative testing of the methods provided correct identifications for 99.1% by API 20C Aux, 95.4% by Candida-Check, 89.1% by Mycotube, 88.2% by Uni-Yeast Tek. The good concordance of the methods and their optimal manuality, rapidity, and economy suggest a wider diffusion in microbiological laboratories.

  5. Simultaneous X-ray and optical observations of the flaring X-ray source, Aquila A-1

    NASA Technical Reports Server (NTRS)

    Bowyer, C. S.; Charles, P. A.

    1979-01-01

    During the summer of 1978 the recurrent transient X-ray source, Aquila X-1, underwent its first major outburst in two years. The results of extensive observations at X-ray and optical wavelengths throughout this event, which lasted for approximately two months are presented. The peak X-ray luminosity was approximately 1.3 times that of the Crab and exhibited spectral dependent flickering on timescales approximately 5 minutes. The observations are interpreted in terms of a standard accretion disk model withparticular emphasis on the similarities to Sco X-1 and other dward X-ray systems, although the transient nature of the system remains unexplained. It was found that Aquila X-1 can be described adequately by the semi-detached Roche lobe model and yields a mass ratio of less than or approximate to 3.5.

  6. Automated Triplex (HBV, HCV and HIV) NAT Assay Systems for Blood Screening in India

    PubMed Central

    2016-01-01

    This review is confined to triplex nucleic acid testing (NAT) assays to be used on fully automated platform. Around the world, these assays are being used at various transfusion medicine centres or blood banks to screen blood units for HBV, HCV and HIV. These assay systems can screen up to 1000 blood units for HBV, HCV and HIV simultaneously in a day. This area has been dominated by mainly two manufacturers: M/s Gen-Probe-Novartis and M/s Roche Molecular Systems. The triplex NAT assay systems of both manufacturers are licensed by United States Food and Drug Administration. There is not much awareness about the technology and procedures used in these assays. The main objective of this review is to create awareness about the technology and procedure of these assays. PMID:27042485

  7. Chromospherically active stars. I - HD 136905

    NASA Technical Reports Server (NTRS)

    Fekel, F. C.; Hall, D. S.; Africano, J. L.; Gillies, K.; Quigley, R.

    1985-01-01

    The variable star HD 136905, recently designated GX Librae, is a chromospherically active K1 III single-lined spectroscopic binary with a period of 11.1345 days. It has moderate strength Ca II H and K and ultraviolet emission features, while H-alpha is strongly in absorption. The inclination of the system is 58 + or - 17 deg and the unseen secondary is most likely a G or K dwarf. The v sin i of the primary, 32 + or - 2 km/s, results in a minimum radius of 7.0 + or - 0.4 solar radii. Since the star fills a substantial fracture of its Roche lab, the double-peaked limit curve seen by photometric observers is predominantly ellipsoidal in nature. Both the photometry and the spectroscopy yield values for the period and the time of conjunction that are identical within their uncertainties.

  8. Testing Common Envelopes on Double White Dwarf Binaries

    NASA Astrophysics Data System (ADS)

    Nandez, Jose L. A.; Ivanova, Natalia; Lombardi, James C., Jr.

    2015-06-01

    The formation of a double white dwarf binary likely involves a common envelope (CE) event between a red giant and a white dwarf (WD) during the most recent episode of Roche lobe overflow mass transfer. We study the role of recombination energy with hydrodynamic simulations of such stellar interactions. We find that the recombination energy helps to expel the common envelope entirely, while if recombination energy is not taken into account, a significant fraction of the common envelope remains bound. We apply our numerical methods to constrain the progenitor system for WD 1101+364 - a double WD binary that has well-measured mass ratio of q=0.87±0.03 and an orbital period of 0.145 days. Our best-fit progenitor for the pre-common envelope donor is a 1.5 ⊙ red giant.

  9. A search for planetary eclipses of white dwarfs in the Pan-STARRS1 medium-deep fields

    SciTech Connect

    Fulton, B. J.; Tonry, J. L.; Flewelling, H.; Burgett, W. S.; Chambers, K. C.; Hodapp, K. W.; Huber, M. E.; Kaiser, N.; Wainscoat, R. J.; Waters, C.

    2014-12-01

    We present a search for eclipses of ∼1700 white dwarfs (WDs) in the Pan-STARRS1 medium-deep fields. Candidate eclipse events are selected by identifying low outliers in over 4.3 million light curve measurements. We find no short-duration eclipses consistent with being caused by a planetary size companion. This large data set enables us to place strong constraints on the close-in planet occurrence rates around WDs for planets as small as 2 R {sub ⊕}. Our results indicate that gas giant planets orbiting just outside the Roche limit are rare, occurring around less than 0.5% of WDs. Habitable-zone super-Earths and hot super-Earths are less abundant than similar classes of planets around main-sequence stars. These constraints provide important insight into the ultimate fate of the large population of exoplanets orbiting main-sequence stars.

  10. Sesquinary catenae on the Martian satellite Phobos from reaccretion of escaping ejecta

    PubMed Central

    Nayak, M.; Asphaug, E.

    2016-01-01

    The Martian satellite Phobos is criss-crossed by linear grooves and crater chains whose origin is unexplained. Anomalous grooves are relatively young, and crosscut tidally predicted stress fields as Phobos spirals towards Mars. Here we report strong correspondence between these anomalous features and reaccretion patterns of sesquinary ejecta from impacts on Phobos. Escaping ejecta persistently imprint Phobos with linear, low-velocity crater chains (catenae) that match the geometry and morphology of prominent features that do not fit the tidal model. We prove that these cannot be older than Phobos' current orbit inside Mars' Roche limit. Distinctive reimpact patterns allow sesquinary craters to be traced back to their source, for the first time across any planetary body, creating a novel way to probe planetary surface characteristics. For example, we show that catena-producing craters likely formed in the gravity regime, providing constraints on the ejecta velocity field and knowledge of source crater material properties. PMID:27575002

  11. Premature ventricular contractions associated with isotretinoin use*

    PubMed Central

    Alan, Sevil; Ünal, Betül; Yildirim, Aytül

    2016-01-01

    Isotretinoin has been considered a unique drug for acne treatment. However, it is associated with numerous adverse effects. Isotretinoin can trigger premature ventricular contractions. This report describes a 33-year-old-woman who presented with palpitations for 1 week while undergoing 1-month isotretinoin treatment for mild-moderate facial acne. An electrocardiogram and Holter monitoring showed premature ventricular contractions during isotretinoin (Roaccutane, Roche) treatment. Isotretinoin-related premature ventricular contractions were strongly suggested in this case due to the existence of documented premature ventricular contractions on electrocardiograms and the disappearance of these premature ventricular contractions two weeks after termination of the treatment To the authors' knowledge, there has been 1 reported case of premature ventricular contractions linked to isotretinoin use; this report describes a second such case. PMID:28099609

  12. Photometric study of the pulsating, eclipsing binary OO DRA

    SciTech Connect

    Zhang, X. B.; Deng, L. C.; Tian, J. F.; Wang, K.; Yan, Z. Z.; Luo, C. Q.; Sun, J. J.; Liu, Q. L.; Xin, H. Q.; Zhou, Q.; Luo, Z. Q.

    2014-12-01

    We present a comprehensive photometric study of the pulsating, eclipsing binary OO Dra. Simultaneous B- and V-band photometry of the star was carried out on 14 nights. A revised orbital period and a new ephemeris were derived from the data. The first photometric solution of the binary system and the physical parameters of the component stars are determined. They reveal that OO Dra could be a detached system with a less-massive secondary component nearly filling its Roche lobe. By subtracting the eclipsing light changes from the data, we obtained the intrinsic pulsating light curves of the hotter, massive primary component. A frequency analysis of the residual light yields two confident pulsation modes in both B- and V-band data with the dominant frequency detected at 41.865 c/d. A brief discussion concerning the evolutionary status and the pulsation nature of the binary system is finally given.

  13. The Genome of Yoka Poxvirus ▿

    PubMed Central

    Zhao, Guoyan; Droit, Lindsay; Tesh, Robert B.; Popov, Vsevolod L.; Little, Nicole S.; Upton, Chris; Virgin, Herbert W.; Wang, David

    2011-01-01

    Yoka poxvirus was isolated almost four decades ago from a mosquito pool in the Central African Republic. Its classification as a poxvirus is based solely upon the morphology of virions visualized by electron microscopy. Here we describe sequencing of the Yoka poxvirus genome using a combination of Roche/454 and Illumina next-generation sequencing technologies. A single consensus contig of ∼175 kb in length that encodes 186 predicted genes was generated. Multiple methods were used to show that Yoka poxvirus is most closely related to viruses in the Orthopoxvirus genus, but it is clearly distinct from previously described poxviruses. Collectively, the phylogenetic and genomic sequence analyses suggest that Yoka poxvirus is the prototype member of a new genus in the family Poxviridae. PMID:21813608

  14. THE DISCOVERY OF ELLIPSOIDAL VARIATIONS IN THE KEPLER LIGHT CURVE OF HAT-P-7

    SciTech Connect

    Welsh, William F.; Orosz, Jerome A.; Seager, Sara; Fortney, Jonathan J.; Jenkins, Jon; Rowe, Jason F.; Koch, David; Borucki, William J.

    2010-04-20

    We present an analysis of the early Kepler observations of the previously discovered transiting planet HAT-P-7b. The light curve shows the transit of the star, the occultation of the planet, and the orbit phase-dependent light from the planet. In addition, phase-dependent light from the star is present, known as 'ellipsoidal variations'. The very nearby planet (only four stellar radii away) gravitationally distorts the star and results in a flux modulation twice per orbit. The ellipsoidal variations can confuse interpretation of the planetary phase curve if not self-consistently included in the modeling. We fit the light curve using the Roche potential approximation and derive improved planet and orbit parameters.

  15. LED illumination effects on proliferation and survival of meningioma cellular cultures

    NASA Astrophysics Data System (ADS)

    Solarte, Efrain; Urrea, Hernan; Criollo, William; Gutierrez, Oscar

    2010-02-01

    Meningioma cell cultures were prepared from frozen cell samples in 96 wells culture plates. Semiconductor light sources (LED) in seven different wavelength ranges were used to illuminate the wells, three different irradiation doses were selected per LED. Control cultures using three different concentrations of FBS were processed for comparison. Cell proliferation, viability, and cytotoxicity were measured every 24 hours for 6 days, using the XTT colorimetric assay (RocheR). None of the irradiated cultures exhibit cytotoxicity; but some of them exhibit proliferation inhibition. The larger proliferation was detected at a 0.05J/cm2 dose, for all LEDs; but for the orange and violet LEDs generated the bigger proliferation rate was measured. Results show the improvement of meningioma cell proliferation using illumination in some given wavelength ranges.

  16. Low power laser and LED irradiation effect on proliferation and differentiation of Wistar rats mesenchymal stem cells

    NASA Astrophysics Data System (ADS)

    Mancera, Diana; Solarte, Efrain; Fierro, Leonardo; Criollo, William

    2013-11-01

    It has been demonstrated that appropriately cultured and stimulated mesenchymal cells, can give rise to cells of all tissues of the body. We evaluate the cell proliferation and differentiation induced by low power light irradiation in cell cultures of mesenchymal cells, isolated and previously characterized, from Wistar rats. Roche® XTT and LDH tests were used to assess proliferation and cytotoxicity. Cellular differentiation was determined by optical microscopy and using specific fluorescent markers. We report laser cellular proliferation enhancement by 532 and 473 nm, and the best cell culture response by a dose of 2 Jcm-2. Although a three day irradiation protocol the cultures grown and no cytotoxicity was detected. Cellular differentiation occurred, and the production of cardiomyocytes was promoted by the cell proliferation stimulated by low power laser irradiation.

  17. Detecting Two-Spirit erotics: The fiction of Carole laFavor.

    PubMed

    Tatonetti, Lisa

    2016-01-01

    This article examines the life and novels of Carole laFavor, arguing for her importance to and influence in Two-Spirit studies. Along with being a writer, laFavor was a powerful voice for social justice and Indigenous health sovereignty in Minnesota and the nation. Her two novels, Along the Journey River and Evil Dead Center, which both focus on Anishinaabe lesbian detective protagonist Renee LaRoche, are the first lesbian detective fiction published by a Native author. Renee's embrace of a specifically Two-Spirit erotics anchors her to family and brings her tribal community a powerful healing when she employs her skills to protect her people from instances of racism, abuse, and injustice. This article, then, reads these novels as the first of an emerging genre of texts that claim an overtly Two-Spirit erotic as well as vital precursors to the present embrace of sovereign erotics in Indigenous studies.

  18. Combining next-generation sequencing and online databases for microsatellite development in non-model organisms

    PubMed Central

    Rico, Ciro; Normandeau, Eric; Dion-Côté, Anne-Marie; Rico, María Inés; Côté, Guillaume; Bernatchez, Louis

    2013-01-01

    Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes. PMID:24296905

  19. The Flow Structure in the Vicinity of the Inner Lagrangian Point in Magnetic Cataclysmic Variables

    NASA Astrophysics Data System (ADS)

    Isakova, P. B.; Zhilkin, A. G.; Bisikalo, D. V.

    2017-03-01

    The mass transfer between the components of the magnetic cataclysmic variables occurs through the inner Lagrangian point. The results of 3D numerical simulations of the flow structure in magnetic cataclysmic variables show that the magnetic field of the accretor essentially influences the flow structure. In polars (with magnetic fields of 10–100 MG at the surface of the white dwarf) the material streaming from the donor splits into the several flows as soon as it leaves the inner Lagrangian point. These flows move along the magnetic field lines and reach the magnetic poles of the accretor. This picture does not correspond to the classical situation of the flow formation when material flows from the donor into the Roche lobe of the accretor along the ballistic trajectory. The aim of our study is to investigate in detail the features of the flow splitting in the vicinity of the inner Lagrangian point in classic polars.

  20. The genome of Yoka poxvirus.

    PubMed

    Zhao, Guoyan; Droit, Lindsay; Tesh, Robert B; Popov, Vsevolod L; Little, Nicole S; Upton, Chris; Virgin, Herbert W; Wang, David

    2011-10-01

    Yoka poxvirus was isolated almost four decades ago from a mosquito pool in the Central African Republic. Its classification as a poxvirus is based solely upon the morphology of virions visualized by electron microscopy. Here we describe sequencing of the Yoka poxvirus genome using a combination of Roche/454 and Illumina next-generation sequencing technologies. A single consensus contig of ∼175 kb in length that encodes 186 predicted genes was generated. Multiple methods were used to show that Yoka poxvirus is most closely related to viruses in the Orthopoxvirus genus, but it is clearly distinct from previously described poxviruses. Collectively, the phylogenetic and genomic sequence analyses suggest that Yoka poxvirus is the prototype member of a new genus in the family Poxviridae.

  1. LongISLND: in silico sequencing of lengthy and noisy datatypes

    PubMed Central

    Lau, Bayo; Mohiyuddin, Marghoob; Mu, John C.; Fang, Li Tai; Bani Asadi, Narges; Dallett, Carolina; Lam, Hugo Y. K.

    2016-01-01

    Summary: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling. Availability and Implementation: LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd Contact: hugo.lam@roche.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27667791

  2. Evaluation of enzyme-linked immunosorbent and alternative assays for detection of HIV antibodies using panels of Brazilian sera.

    PubMed

    Ivo-Dos-Santos, J; Mello, D L; Couto-Fernandez, J C; Passos, R M; Dias-Carneiro, L A; Castilho, E A; Galvão-Castro, B

    1990-01-01

    Sera from 472 Brazilian subjects, confirmed to be either positive or negative for HIV antibodies and comprising the total clinical spectrum of HIV infection, were utilized in the evaluation of six commercially available enzyme-linked immunosorbent assays (ELISA), as well as of four alternative assays, namely indirect immunofluorescence (IIF), passive hemagglutination (PHA), dot blot and Karpas AIDS cell test. The sensitivities ranged from 100% (Abbott and Roche ELISA) to 84.2% (PHA) and the specificities ranged from 99.3% (IIF) to 80.2% (PHA). The sensitivity and specificity of the PHA and the sensitivity of the Karpas cell test were significantly lower than those of the other tests. Although the IFF and dot blot had good sensitivities and specificities, the six ELISA were more attractive than those tests when other parameters such as ease of reading and duration of assay were considered.

  3. EDTA interference in electrochemiluminescence ACTH assay.

    PubMed

    Toprak, Burak; Yalcin, Hulya; Arı, Elif; Colak, Ayfer

    2016-11-01

    Background As plasma is the recommended sample type for Roche adrenocorticotropic hormone (ACTH) assay, we evaluated the effect of EDTA concentration on Cobas ACTH assay. Methods Samples containing twofold and fourfold higher concentrations of EDTA were prepared by adding plasma to empty K2EDTA tubes and by making under-filled EDTA tubes. All measurements were performed with four replicates. Results Increased EDTA concentration resulted in a significant decrease in ACTH concentration. Fifty-per cent-filled EDTA tube showed 19% decrease in ACTH concentration and 25% filled EDTA tube showed 50% decrease in ACTH concentration. Conclusion We recommend that inadequately filled EDTA specimens should be rejected when using Cobas ACTH assay.

  4. A real-time PCR diagnostic method for detection of Naegleria fowleri.

    PubMed

    Madarová, Lucia; Trnková, Katarína; Feiková, Sona; Klement, Cyril; Obernauerová, Margita

    2010-09-01

    Naegleria fowleri is a free-living amoeba that can cause primary amoebic meningoencephalitis (PAM). While, traditional methods for diagnosing PAM still rely on culture, more current laboratory diagnoses exist based on conventional PCR methods; however, only a few real-time PCR processes have been described as yet. Here, we describe a real-time PCR-based diagnostic method using hybridization fluorescent labelled probes, with a LightCycler instrument and accompanying software (Roche), targeting the Naegleria fowleriMp2Cl5 gene sequence. Using this method, no cross reactivity with other tested epidemiologically relevant prokaryotic and eukaryotic organisms was found. The reaction detection limit was 1 copy of the Mp2Cl5 DNA sequence. This assay could become useful in the rapid laboratory diagnostic assessment of the presence or absence of Naegleria fowleri.

  5. Assembly Algorithms for Next-Generation Sequencing Data

    PubMed Central

    Miller, Jason R.; Koren, Sergey; Sutton, Granger

    2010-01-01

    The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly. PMID:20211242

  6. Mass flow in close binary systems

    NASA Technical Reports Server (NTRS)

    Kondo, Y.; Mccluskey, G. E.

    1976-01-01

    The manner of mass flow in close binary systems is examined with a special view to the role of the so-called critical Roche (or Jacobian) lobe, taking into consideration relevant physical conditions such as radiation pressure that may affect the restricted three-body problem treatment. The mass does not necessarily flow from component one to component two through the L1 point to form a gaseous ring surrounding the latter. These considerations are applied to X-ray binaries with early-type optical components, such as Cyg X-1 (HDE 226868) and 3U 1700 - 37 (HD 153919). In the two bright close binary systems Beta Lyr and UW CMa, which are believed to be undergoing dynamic mass transfer, recent Copernicus observations show that the gas giving rise to the prominent ultraviolet emission lines surrounds the entire binary system rather than merely component two. Implications of these observations are also discussed.

  7. Recent advances in nanopore sequencing

    PubMed Central

    Maitra, Raj D.; Kim, Jungsuk; Dunbar, William B.

    2013-01-01

    The prospect of nanopores as a next-generation sequencing (NGS) platform has been a topic of growing interest and considerable government-sponsored research for more than a decade. Oxford Nanopore Technologies recently announced the first commercial nanopore sequencing devices, to be made available by the end of 2012, while other companies (Life, Roche, IBM) are also pursuing nanopore sequencing approaches. In this paper, the state of the art in nanopore sequencing is reviewed, focusing on the most recent contributions that have or promise to have NGS commercial potential. We consider also the scalability of the circuitry to support multichannel arrays of nanopores in future sequencing devices, which is critical to commercial viability. PMID:23138639

  8. Assembly algorithms for next-generation sequencing data.

    PubMed

    Miller, Jason R; Koren, Sergey; Sutton, Granger

    2010-06-01

    The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly.

  9. METER-SIZED MOONLET POPULATION IN SATURN'S C RING AND CASSINI DIVISION

    SciTech Connect

    Baillie, Kevin; Colwell, Joshua E.; Esposito, Larry W.; Lewis, Mark C.

    2013-06-01

    Stellar occultations observed by the Cassini Ultraviolet Imaging Spectrograph reveal the presence of transparent holes a few meters to a few tens of meters in radial extent in otherwise optically thick regions of the C ring and the Cassini Division. We attribute the holes to gravitational disturbances generated by a population of {approx}10 m boulders in the rings that is intermediate in size between the background ring particle size distribution and the previously observed {approx}100 m propeller moonlets in the A ring. The size distribution of these boulders is described by a shallower power-law than the one that describes the ring particle size distribution. The number and size distribution of these boulders could be explained by limited accretion processes deep within Saturn's Roche zone.

  10. Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions

    PubMed Central

    2014-01-01

    Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review applications of deep sequencing to pathogen evolution. Pioneering deep sequencing studies from the virology literature are discussed, such as whole genome Roche-454 sequencing analyses of the dynamics of the rapidly mutating pathogens hepatitis C virus and HIV. Extension of the deep sequencing approach to bacterial populations is then discussed, including the impacts of emerging sequencing technologies. While it is clear that deep sequencing has unprecedented potential for assessing the genetic structure and evolutionary history of pathogen populations, bioinformatic challenges remain. We summarise current approaches to overcoming these challenges, in particular methods for detecting low frequency variants in the context of sequencing error and reconstructing individual haplotypes from short reads. PMID:24428920

  11. Evidence for CNO processed material in the accretion disk of GP Comae

    NASA Technical Reports Server (NTRS)

    Marsh, T. R.; Horne, Keith; Rosen, Simon

    1991-01-01

    NIR spectroscopic observations of GP Com are reported. Data obtained using the 2.5-m Isaac Newton Telescope and the 4.2-m William Herschel Telescope at La Palma during April and June 1988 and with the 5-m Hale reflector at Palomar Observatory during January 1983 are presented in tables and sample spectra and discussed in detail. Number ratios H/He less than 0.00001, N/O = about 50, and N/C greater than 100 are calculated under the assumption of a uniform optically thin slab of gas in LTE. From the N overabundance it is inferred that the material observed is being extracted by Roche-lobe overflow from the secondary's H-exhausted core, at a time after most C and O have been converted to N in the CNO cycle.

  12. Evidence for CNO processed material in the accretion disk of GP Comae

    SciTech Connect

    Marsh, T.R.; Horne, K.; Rosen, S. London Univ. College, Dorking )

    1991-01-01

    NIR spectroscopic observations of GP Com are reported. Data obtained using the 2.5-m Isaac Newton Telescope and the 4.2-m William Herschel Telescope at La Palma during April and June 1988 and with the 5-m Hale reflector at Palomar Observatory during January 1983 are presented in tables and sample spectra and discussed in detail. Number ratios H/He less than 0.00001, N/O = about 50, and N/C greater than 100 are calculated under the assumption of a uniform optically thin slab of gas in LTE. From the N overabundance it is inferred that the material observed is being extracted by Roche-lobe overflow from the secondary's H-exhausted core, at a time after most C and O have been converted to N in the CNO cycle. 33 refs.

  13. Radial velocity measurements of the chromospherically-active stars (2): HD 28591 = V492 Per

    NASA Technical Reports Server (NTRS)

    Dadonas, V.; Sperauskas, J.; Fekel, F. C.; Morton, M. D.

    1994-01-01

    From two sets of the spectroscopic observations covering a ten year period we have obtained 59 radial velocities of the chromospherically-active star HD 28591 = V492 Per. It is a G9III single-lined spectroscopic binary with a period of 21.2910 days and a circular orbit. The upsilon sin i of 24.6 km/sec, results in a minimum radius 10.3 solar radii. We estimate a distance of 165 +/- 40 pc and an orbital inclination of 65 +/- 25 degrees. The secondary is probably a mid to late-type K dwarf. The star is brighter than the limiting magnitude of the Bright Star Catalogue. The mean photometric and the orbital periods are identical within their uncertainties. Since the star fills a significant fraction of its Roche lobe, about 62%, the photometric light curve may be the result of starspots and a modest ellipticity effect.

  14. Agitating mass transfer with a warped disc's shadow

    NASA Astrophysics Data System (ADS)

    Cambier, H.

    2015-10-01

    For compact objects fed by Roche lobe overflow, accretion-generated X-rays irradiating the donor star can alter gas flow towards the Lagrange point thus varying mass transfer. The latest work specific to this topic consists of simple yet insightful two-dimensional hydrodynamics simulations stressing the role of global flow. To explore how a time-varying disc shadow affects mass transfer, I generalize the geometry, employ a robust hydrodynamics solver, and use phase space analysis near the nozzle to include coriolis lift there. Without even exposing the nozzle, a warped disc's shadow can drive mass transfer cycles by shifting the equatorial edges of the irradiation patches in turns: drawing in denser ambient gas before sweeping it into the nozzle. Other important effects remain missing in two-dimensional models, which I discuss along with prospects for more detailed yet efficient models.

  15. CNO abundances and hydrodynamic models of the Nova outbursts. 4: Comparison with observations

    NASA Technical Reports Server (NTRS)

    Sparks, W. M.; Starrfield, S.; Truran, J. W.

    1975-01-01

    A variety of observations of novae are discussed in light of theoretical models. It is proposed that the nearly constant bolometric luminosity of FH Ser originates in the non-degenerate hydrogen-burning region at the bottom of the hydrogen-rich envelope which remains after the primary ejection. The shift of the wavelength of peak emission from the visual to shortward of the ultraviolet is caused by the decrease of the photospheric radius of the remnant envelope as the bolometric luminosity stays nearly constant. The oscillations in the light curve of GK Per during the transition stage can be explained by a pulsation of the remnant envelope when it is the size of the Roche lobe. The CNO over-abundances in novae reported by various observers are strongly suggestive of this nova mechanism. Finally, the implications of the upper limits of C-13 and N-15 in DQ Her are discussed.

  16. Development of twelve microsatellite loci in the red tree corals Primnoa resedaeformis and Primnoa pacifica

    USGS Publications Warehouse

    Morrison, Cheryl; Springmann, Marcus J.; Shroades, Kelsey; Stone, Robert P.

    2015-01-01

    A suite of tetra-, penta-, and hexa-nucleotide microsatellite loci were developed from Roche 454 pyrosequencing data for the cold-water octocorals Primnoa resedaeformis and P. pacifica. Twelve of 98 primer sets tested consistently amplified in 30 P. resedaeformis samples from Baltimore Canyon (western North Atlantic Ocean) and in 24 P. pacifica samples (Shutter Ridge, eastern Gulf of Alaska). The loci displayed moderate levels of allelic diversity (average 7.5 alleles/locus) and heterozygosity (average 47 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and to distinguish species. These common species are long-lived (hundreds of years) and provide essential fish habitat (P. pacifica), yet populations are provided little protection from human activities. These loci will be used to determine regional patterns of population connectivity to inform effective marine spatial planning and ecosystem-based fisheries management.

  17. A comparison between observed Algol-type double stars in the solar neighborhood and evolutionary computations of galactic case A binaries with a B-type primary at birth

    NASA Astrophysics Data System (ADS)

    Mennekens, N.; Vanbeveren, D.

    2017-03-01

    We first discuss a large set of evolutionary calculations of close binaries with a B-type primary at birth and with a period such that the Roche lobe overflow starts during the core hydrogen burning phase of the primary (intermediate mass and massive case A binaries). The evolution of both components is followed simultaneously allowing us to check for the occurrence of contact binaries. We consider various models to treat a contact system and the influence of these models on the predicted Algol-type system population is investigated. We critically discuss the available observations of Algol-type binaries with a B-type primary at birth. Comparing these observations with the predictions allows us to put constraints on the contact star physics. We find that mass transfer in Algols is most probably not conservative, that contact during this phase does not necessarily lead to a merger, and that angular momentum loss must be moderate.

  18. SV Cam spot activity in February 2001 - March 2002

    NASA Astrophysics Data System (ADS)

    Zboril, M.; Djurašević, G.

    2003-07-01

    We present the analysis of new BVR light curves for the active star SV Cam. The Roche model with spotted areas on the hotter primary component fits satisfactorily all filter observations yielding two spots in intermediate latitudes and covering about 1.5% each of the stellar surface. Both are ~ 1000 K cooler than surrounding photosphere. The comparison with an earlier season (January/February 2000) suggests that the spots probably evolved in area longitude and latitude but basic and preferred orientation from previous season is confirmed. Data are available only in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/406/193

  19. Lead optimization of the VU0486321 series of mGlu1 PAMs. Part 1: SAR of modifications to the central aryl core.

    PubMed

    Garcia-Barrantes, Pedro M; Cho, Hyekyung P; Blobaum, Anna L; Niswender, Colleen M; Conn, P Jeffrey; Lindsley, Craig W

    2015-11-15

    This Letter describes the lead optimization of the VU0486321 series of mGlu1 positive allosteric modulators (PAMs). While first generation PAMs from Roche were reported in the late 1990s, little effort has focused on the development of mGlu1 PAMs since. New genetic data linking loss-of-function mutant mGlu1 receptors to schizophrenia, bipolar disorder and other neuropsychiatric disorders has rekindled interest in the target, but the ideal in vivo probe, for example, with good PK, brain penetration and low plasma protein binding, for robust target validation has been lacking. Here we describe the first modifications to the central aryl core of the VU0486321 series, where robust SAR was noted. Moreover, structural variants were identified that imparted selectivity (up to >793-fold) versus mGlu4.

  20. Isolation and characterization of microsatellite markers for an endemic tree in East Asia, Quercus variabilis (Fagaceae)1

    PubMed Central

    Wang, Xian; Li, Jing; Li, Yong

    2015-01-01

    Premise of the study: Microsatellite markers of Quercus variabilis (Fagaceae) were isolated for population genetic and landscape genetic studies. Methods and Results: Roche 454 pyrosequencing combined with the magnetic bead enrichment protocol were used to isolate microsatellite markers for Q. variabilis. A total of 2121 microsatellites were identified from 63,851 individual sequence reads. One hundred microsatellite loci were selected to test primer amplification efficiency among 24 individuals from two wild populations. Among the 100 tested markers, 34 primer pairs were successfully amplified. Of these, 14 yielded polymorphic amplification products, whereas the remaining 20 loci were monomorphic. The number of alleles for polymorphic loci ranged from two to six, and the observed heterozygosity ranged from 0.042 to 0.750. Conclusions: These microsatellite loci will provide useful tools for further population genetic and landscape genetic studies on Q. variabilis. PMID:26082882

  1. Detection of Staphylococcus aureus enterotoxin production genes from patient samples using an automated extraction platform and multiplex real-time PCR.

    PubMed

    Chiefari, Amy K; Perry, Michael J; Kelly-Cirino, Cassandra; Egan, Christina T

    2015-12-01

    To minimize specimen volume, handling and testing time, we have developed two TaqMan(®) multiplex real-time PCR (rtPCR) assays to detect staphylococcal enterotoxins A-E and Toxic Shock Syndrome Toxin production genes directly from clinical patient stool specimens utilizing a novel lysis extraction process in parallel with the Roche MagNA Pure Compact. These assays are specific, sensitive and reliable for the detection of the staphylococcal enterotoxin encoding genes and the tst1 gene from known toxin producing strains of Staphylococcus aureus. Specificity was determined by testing a total of 47 microorganism strains, including 8 previously characterized staphylococcal enterotoxin producing strains against each rtPCR target. Sensitivity for these assays range from 1 to 25 cfu per rtPCR reaction for cultured isolates and 8-20 cfu per rtPCR for the clinical stool matrix.

  2. Tidal interaction in compact binaries: A post-Newtonian affine framework

    NASA Astrophysics Data System (ADS)

    Ferrari, V.; Gualtieri, L.; Maselli, A.

    2012-02-01

    We develop a semianalytical approach, based on the post-Newtonian expansion and on the affine approximation, to model the tidal deformation of neutron stars in the coalescence of black hole-neutron star or neutron star-neutron star binaries. Our equations describe, in a unified framework, both the system orbital evolution, and the neutron star deformations. These are driven by the tidal tensor, which we expand at 1/c3 post-Newtonian order, including spin terms. We test the theoretical framework by simulating black hole-neutron star coalescence up to the onset of mass shedding, which we determine by comparing the shape of the star with the Roche lobe. We validate our approach by comparing our results with those of fully relativistic, numerical simulations.

  3. Spin-down of radio millisecond pulsars at genesis.

    PubMed

    Tauris, Thomas M

    2012-02-03

    Millisecond pulsars are old neutron stars that have been spun up to high rotational frequencies via accretion of mass from a binary companion star. An important issue for understanding the physics of the early spin evolution of millisecond pulsars is the impact of the expanding magnetosphere during the terminal stages of the mass-transfer process. Here, I report binary stellar evolution calculations that show that the braking torque acting on a neutron star, when the companion star decouples from its Roche lobe, is able to dissipate >50% of the rotational energy of the pulsar. This effect may explain the apparent difference in observed spin distributions between x-ray and radio millisecond pulsars and help account for the noticeable age discrepancy with their young white dwarf companions.

  4. SW Sextantis in an excited, low state

    NASA Astrophysics Data System (ADS)

    Groot, P. J.; Rutten, R. G. M.; van Paradijs, J.

    2001-03-01

    We present low-resolution spectrophotometric optical observations of the eclipsing nova-like cataclysmic variable SW Sex, the prototype of the SW Sex stars. We observed the system when it was in an unusual low state. The spectrum is characterized by the presence of strong Heii and Civ emission lines as well as the normal single peaked Balmer emission lines. The radial temperature profile of the disk follows the expected T~ R-3/4 only in the outer parts and flattens off inside 0.5 times the white dwarf Roche lobe radius. The single peaked emission lines originate in a region above the plane of the disk, at the position of the hot spot.

  5. Vismodegib in the treatment of advanced BCC.

    PubMed

    O'Kane, G M; Lyons, T; McDonald, I; Mulligan, N; Moloney, F J; Murray, D; Kelly, C M

    2014-01-01

    Basal-cell carcinoma (BCC) is the most commonly diagnosed malignancy, comprising over 80 per thousand of non-melanoma skin cancers. Surgical excision is adequate treatment for most BCC's. Options are however limited for the minority of patients presenting with locally advanced inoperable or metastatic BCC. The Hedgehog signalling pathway is a critical driver in the pathogenesis of both sporadic and hereditary BCC. On 31st January 2012, based on a phase II clinical trial the US Food and Drug Administration approved Vismodegib (Erivedge, Roche) a first-in-class, small-molecule oral Hedgehog-inhibitor for the treatment of locally advanced inoperable and metastatic BCC. We present our experience treating the first Irish patient with this agent.

  6. American Chemical Society-239th national meeting--Investigating new therapeutic candidates: part 2. 21-25 March 2010, San Francisco, CA, USA.

    PubMed

    Kirkham, Konrad

    2010-05-01

    The American Chemical Society 239th National Meeting, held in San Francisco, included topics covering developments related to the chemical optimization of therapeutics. This conference report highlights selected presentations on second-generation cholesterol absorption inhibitors (CAIs), CCK2 receptor antagonists to prevent acid rebound, HIF-PH inhibitors for anemia, the neonatal Fc receptor (FcRn) as a target for autoimmune disease, and GPR119 agonists and GLP-1 receptor agonists for the treatment of diabetes. Investigational drugs discussed include LPD-608 (Lipideon Biotechnology AG), a second-generation CAI series from Merck & Co Inc, JNJ-26070109 and JNJ-42041935 (both Johnson & Johnson), SYN-1436 (Syntonix Pharmaceuticals Inc), a series of GPR119 agonists from Roche Holding AG and Schering-Plough Research Institute, and a series of GLP-1 receptor agonists from Bristol-Myers Squibb Co.

  7. The Tamiflu saga continues: will our conduct change after the publication of the latest systematic review on benefits and harms of oseltamivir?

    PubMed

    Bachelet, Vivienne C

    2014-05-20

    In 2013, we wrote about the harm, waste and deception stemming from conducts adopted by the pharmaceutical industry, by concealing raw data and Clinical Study Reports (CSRs) from the regulator’s view when requesting the marketing patent. We described the case of Tamiflu (Roche), a drug that has been widely used in our population and profusely prescribed by physicians. Health authorities, entailing a great cost for the countries in the region, have also purchased it. In this editorial, we will show how the idea of using antivirals for prophylaxis and treatment of influenza took hold, starting from the first enthusiastic recommendations up to the systematic review published last month in the BMJ.

  8. The Effects of Common Envelope and Tidal Evolution On the Properties of X-ray Binaries, CVs and SN Ia

    NASA Astrophysics Data System (ADS)

    Moe, Maxwell C.; Di Stefano, R.

    2011-09-01

    Population synthesis studies provide an excellent testbed for determining the consequences and significance of certain binary processes that lead to accretion onto a compact object. We investigated the recent observational constraints of the common envelope (CE) efficiency parameter with particular regard to the dependence on the mass ratio of the binary. In our population synthesis calculations, we also implemented binary tidal interactions prior to Roche lobe overflow, such as tidal capture of and spin up by the companion, synchronization, and enhanced equatorial mass loss of the giant that can significantly alter the evolution of the system. Finally, we analyzed these binary interactions in the context of nuclear burning on white dwarfs, accreting X-ray binaries, cataclysmic variables, progenitors of Type Ia supernovae, and other high energy binary phenomena.

  9. Metagenomic characterization of biodiversity in the extremely arid desert soils of Kazakhstan

    NASA Astrophysics Data System (ADS)

    Kutovaya, O. V.; Lebedeva, M. P.; Tkhakakhova, A. K.; Ivanova, E. A.; Andronov, E. E.

    2015-05-01

    For the first time, the composition of microbiomes in the biological crust (AKL) horizons of extremely arid desert soils (Aridic Calcisols) developed from saline and nonsaline alluvial deposits in the Ili Depression (eastern Kazakhstan) was analyzed. To describe the diversity of microorganisms in the soil samples, a novel method of pyrosequencing (Roche/454 Life Sciences) was applied. It was shown that bacteria from the Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, Acidobacteria, and Bacteroidetes phyla predominate in all the samples; these are typical representatives of the microbiome of soil crusts. A distinctive feature of the extremely arid soils is the high contribution of cyanobacteria (25-30%) to the total DNA. In the soils developed from saline sediments, representatives from the Rubrobacteraceae, Streptococcaceae, and Caulobacteraceae families and from the Firmicutes phylum predominated. In the soils developed from nonsaline gypsiferous deposits, bacteria from the class of Acidobacteria, subgroup Gp3, of the Methylobacteriaceae family and the class of Subdivision 3 from the Verrucomicrobia phylum predominated.

  10. Evolutionary history of four binary blue stragglers from the globular clusters ω Cen, M 55, 47 Tuc, and NGC 6752

    NASA Astrophysics Data System (ADS)

    Stȩpień, K.; Pamyatnykh, A. A.; Rozyczka, M.

    2017-01-01

    Context. Origin and evolution of blue stragglers in globular clusters is still a matter of debate. Aims: The aim of the present investigation is to reproduce the evolutionary history of four binary blue stragglers in four different clusters, for which precise values of global parameters are known. Methods: Using the model for cool close binary evolution that we developed, progenitors of all investigated binaries were found and their parameters evolved into the presently observed values. Results: The results show that the progenitors of the binary blue stragglers are cool close binaries with period of a few days, which transform into stragglers by rejuvenation of the initially less massive component as a result of mass transfer from its more massive companion overflowing the inner critical Roche surface. The parameters of V209 from ω Cen indicate that the binary is substantially enriched in helium. This is an independent and strong evidence of the existence of the helium rich subpopulation in this cluster.

  11. Quiescent accretion disks in black hole X-ray novae

    NASA Technical Reports Server (NTRS)

    Orosz, Jerome A.; Bailyn, Charles D.; Remillard, Ronald A.; Mcclintock, Jeffrey E.; Foltz, Craig B.

    1994-01-01

    We present detailed time-resolved spectroscopy of the Balmer emission lines from two black hole binary systems in quiescence, A0620-00 and Nova Muscae 1991. We find extraordinary similarities between the two systems. There are 30-40 km/s velocity variations of the emission lines over the orbital period, the phases of which are not aligned with the expected phase of the motion of the compact primary. Detailed modeling of both systems is complicated by variable hot spot components, regions of optical thickness, and intermittent excess emission in the blue line wings of the H-alpha lines. Both sources also display low velocities at the outer edge of the accretion disk, implying a large primary Roche lobe and extreme mass ratios. These complications suggest that although simple optically thin, Keplerian alpha-disk models provide a useful parameterization of emission lines from these systems, the straightforward physical models they imply should be treated with great caution.

  12. 2-Year follow-up to STeP trial shows sustainability of structured self-monitoring of blood glucose utilization: results from the STeP practice logistics and usability survey (STeP PLUS).

    PubMed

    Friedman, Kevin; Noyes, Jeannette; Parkin, Christopher G

    2013-04-01

    We report findings from a follow-up survey of clinicians from the STeP study that assessed their attitudes toward and current use of the Accu-Chek(®) 360° View tool (Roche Diagnostics, Indianapolis, IN) approximately 2 years after the study was completed. The Accu-Chek 360° View tool enables patients to record/plot a seven-point self-monitoring of blood glucose (SMBG) profile (fasting, preprandial/2-h postprandial at each of the three meals, and bedtime) on 3 consecutive days, document meal sizes and energy levels, and comment on their SMBG experiences. Our findings showed that the majority of these physicians continue to use the tool with their patients, citing enhanced patient understanding and engagement, better discussions with patients regarding the impact of lifestyle behaviors, improved clinical outcomes, and better practice efficiencies as significant benefits of the tool.

  13. Spin-Down of Radio Millisecond Pulsars at Genesis

    NASA Astrophysics Data System (ADS)

    Tauris, Thomas M.

    2012-02-01

    Millisecond pulsars are old neutron stars that have been spun up to high rotational frequencies via accretion of mass from a binary companion star. An important issue for understanding the physics of the early spin evolution of millisecond pulsars is the impact of the expanding magnetosphere during the terminal stages of the mass-transfer process. Here, I report binary stellar evolution calculations that show that the braking torque acting on a neutron star, when the companion star decouples from its Roche lobe, is able to dissipate >50% of the rotational energy of the pulsar. This effect may explain the apparent difference in observed spin distributions between x-ray and radio millisecond pulsars and help account for the noticeable age discrepancy with their young white dwarf companions.

  14. [Profile of Shohei Ninomiya (pharmacist), the first Japanese medical representative to practice modern European-style propaganda in the late Meiji era].

    PubMed

    Nishikawa, Takashi

    2007-01-01

    A Swiss pharmaceutical company (F-Hoffmann-La Roche Ltd.), first introduced the profession of "propagandist" in Japan in 1912. At the time, Shohei Ninomiya was a chief hospital pharmacist, but he changed his vocation to become the first "propah" (Japanese abbreviation for propagandist). The German physician Dr. Rudolf Ebering initiated Dr. Ninomiya in the methods and principles of "propah," and he faithfully practiced them. The defining principle of a modern European propagandist is one who is far from sales-centered. From the late 1970s through 1980s, however, Japanese pharmaceutical companies indulged in pursuing sales and neglected this principle, resulting in numerous abuses and adverse effects. Today, use of the description "medical representative" (MR) is more common than "propah." Even with this different description, pharmaceutical companies and MRs should never neglect the founding principle to avoid repeating such abuses.

  15. An extended upper atmosphere around the extrasolar planet HD209458b.

    PubMed

    Vidal-Madjar, A; Des Etangs, A Lecavelier; Désert, J-M; Ballester, G E; Ferlet, R; Hébrard, G; Mayor, M

    2003-03-13

    The planet in the system HD209458 is the first one for which repeated transits across the stellar disk have been observed. Together with radial velocity measurements, this has led to a determination of the planet's radius and mass, confirming it to be a gas giant. But despite numerous searches for an atmospheric signature, only the dense lower atmosphere of HD209458b has been observed, through the detection of neutral sodium absorption. Here we report the detection of atomic hydrogen absorption in the stellar Lyman alpha line during three transits of HD209458b. An absorption of 15 +/- 4% (1sigma) is observed. Comparison with models shows that this absorption should take place beyond the Roche limit and therefore can be understood in terms of escaping hydrogen atoms.

  16. Drugs from marine organisms

    NASA Astrophysics Data System (ADS)

    von Berlepsch, Klaus

    1980-07-01

    A modern approach to the search for biologically active substances of potential therapeutic use isolated from marine organisms is illustrated by a presentation of the multidisciplinary project pursued by the Roche Research Institute of Marine Pharmacology near Sydney, Australia. This specialized insitute is part of the world-wide research endeavour of our company and has now been in operation for five years. Following a brief outline of the technical functions the main scientific achievements published by the scientists of the institute are reviewed. This institute is, to our knowledge, the only one of its kind in private industry and we have attempted to demonstrate how its activities should be viewed in the overall context of today's drug or product development.

  17. A multi-frequency study of symbiotic stars. I - Near-simultaneous optical and radio observations

    NASA Astrophysics Data System (ADS)

    Ivison, R. J.; Bode, M. F.; Roberts, J. A.; Meaburn, J.; Davis, R. J.; Nelson, R. F.; Spencer, R. E.

    1991-03-01

    The relationship between optical line flux and 5 GHz radio flux is investigated for a sample of 17 northern sky symbiotic stars. Data were obtained near-simultaneously with the Manchester Echelle Spectrograph mounted on the Issac Newton Telescope, La Palma and the Broad Band Interferometer at Jodrell Bank. Color excesses, calculated from Balmer hydrogen line fluxes assuming Case B recombination ratios, are compared with other reddening estimates and also combined with extinction maps to provide improved distance estimates. Optical line fluxes are used in combination with radio fluxes to estimate physical parameters of these objects, including mass-loss rates. The suggestion that the ionized regions of D-type symbiotics are much more extensive than those in S-type is confirmed. This in turn strengthens the hypothesis that S-type symbiotics are more likely to be undergoing Roche-lobe overflow than their D-type counterparts.

  18. Accretion disks in Algols: Progenitors and evolution

    NASA Astrophysics Data System (ADS)

    Van Rensbergen, W.; De Greve, J. P.

    2016-08-01

    Context. There are only a few Algols with measured accretion disk parameters. These measurements provide additional constraints for tracing the origin of individual systems, narrowing down the initial parameter space. Aims: We investigate the origin and evolution of six Algol systems with accretion disks to find the initial parameters and evolutionary constraints for them. Methods: With a modified binary evolution code, series of close binary evolution are calculated to obtain the best match for observed individual systems. Results: Initial parameters for six Algol systems with accretion disks were determined matching both the present system parameters and the observed disk characteristics. Conclusions: When Roche lobe overflow (RLOF) starts during core hydrogen burning of the donor, the disk lifetime was found to be short. The disk luminosity is comparable to the luminosity of the gainer during a large fraction of the disk lifetime.

  19. Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.)

    PubMed Central

    2011-01-01

    The microbes in the gastrointestinal (GI) tract are of high importance for the health of the host. In this study, Roche 454 pyrosequencing was applied to a pooled set of different 16S rRNA gene amplicons obtained from GI content of common carp (Cyprinus carpio) to make an inventory of the diversity of the microbiota in the GI tract. Compared to other studies, our culture-independent investigation reveals an impressive diversity of the microbial flora of the carp GI tract. The major group of obtained sequences belonged to the phylum Fusobacteria. Bacteroidetes, Planctomycetes and Gammaproteobacteria were other well represented groups of micro-organisms. Verrucomicrobiae, Clostridia and Bacilli (the latter two belonging to the phylum Firmicutes) had fewer representatives among the analyzed sequences. Many of these bacteria might be of high physiological relevance for carp as these groups have been implicated in vitamin production, nitrogen cycling and (cellulose) fermentation. PMID:22093413

  20. Toxic Profile of Benznidazole in Patients with Chronic Chagas Disease: Risk Factors and Comparison of the Product from Two Different Manufacturers

    PubMed Central

    Salvador, F.; Sánchez-Montalvá, A.; Treviño, B.; Serre, N.; Sao Avilés, A.; Almirante, B.

    2015-01-01

    Benznidazole is considered the first-line treatment option against Chagas disease. The major drawback of benznidazole is its toxicity profile. The main objectives of this study were to describe the adverse events (AEs) in patients with chronic Chagas disease treated with benznidazole, determine the risk factors involved and compare the toxic profiles of two different preparations of the drug from ELEA and Roche. A total of 746 patients were diagnosed with Chagas disease in a 5-year period, and of these 472 were treated with benznidazole. A high proportion of patients (n = 360 [76%]) suffered AEs, the most frequent being those related to hypersensitivity (52.9% of patients), headache (12.5%), and epigastric pain (10.4%). In 72 (12.7%) cases, treatment was discontinued. Overall, women had a higher incidence of AEs compared to men (81.3% versus 66%, P = 0.001) and were subject to higher levels of hypersensitivity-related events. Dermatological events, digestive tract manifestations, and general symptoms had a greater likelihood to appear around day 10 and neurological AEs around day 40 after starting treatment. With respect to liver function and hematological tests, the majority of patients did not suffer significant perturbation of liver enzymes or altered blood cell counts. However, 14 patients suffered from neutropenia, and 14 patients had aminotransferase levels that were more than four times the upper limit of the normal range. Patients treated with the ELEA benznidazole product experienced more arthromyalgia, neutropenia, and neurological disorders (mainly paresthesias) than those treated with the Roche product. Both drug products resulted in approximately the same percentage of permanent withdrawals. PMID:26195525