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Sample records for 03-02-1999 amplicor roche

  1. Use of Roche AMPLICOR Mycobacterium tuberculosis PCR in Early Diagnosis of Tuberculous Meningitis

    PubMed Central

    Bonington, Alec; Strang, J. I. George; Klapper, Paul E.; Hood, Steven V.; Rubombora, William; Penny, Miranda; Willers, Rose; Wilkins, Edmund G. L.

    1998-01-01

    Several nucleic acid-based amplification tests are available for the detection of Mycobacterium tuberculosis, but few data are available on their use in the diagnosis of tuberculous meningitis (TBM). We performed a prospective study to assess the Roche AMPLICOR Mycobacterium tuberculosis PCR test (TB AMPLICOR) for use in the diagnosis of TBM and compared it with direct Ziehl-Neelsen staining of smears, radiometric culture for M. tuberculosis, and clinical and cerebrospinal fluid (CSF) findings. Eighty-three CSF specimens collected from 69 patients with suspected meningitis in South Africa were tested by TB AMPLICOR. On the basis of clinical and laboratory findings, 40 of these patients were treated for TBM and 29 patients were not treated for TBM. Ten CSF samples from 10 patients were positive by TB AMPLICOR. Seven of these 10 patients were classified as having definite TBM, 2 were classified as having probable TBM, and 1 was classified as having possible TBM. The sensitivity of TB AMPLICOR for detecting cases of definite and probable TBM in patients from whom CSF specimens had been collected less than 10 days into antituberculosis treatment was 60.0%. Specimens from all 29 patients not treated for TBM were negative by the TB AMPLICOR, giving a 100% specificity. TB AMPLICOR is therefore more sensitive than the combination of Ziehl-Neelsen staining of smears and radiometric culture for M. tuberculosis and is a rapid and highly specific diagnostic test for TBM. PMID:9574686

  2. Cytomegalovirus quantification in plasma with Abbott RealTime CMV and Roche Cobas Amplicor CMV assays.

    PubMed

    Tremblay, Maxime-Antoine; Rodrigue, Marc-André; Deschênes, Louise; Boivin, Guy; Longtin, Jean

    2015-12-01

    We assessed the performance of Abbott RealTime CMV assay (ARC) compared to Roche Cobas Amplicor CMV Monitor Test (RCM) for quantification of CMV in plasma of transplant patients. Commercial panels were used to test linearity, precision and interference and 83 clinical samples were used for the accuracy and precision analyses. All 43 RCM-positive clinical samples tested positive by ARC. The overall concordance between the two tests was good (98%). Based on 17 samples, the inter-assay median coefficient of variation was 13%. A linearity panel ranging from approximately 1 to 7log10copies/mL was used to confirm linearity (R(2)=0.99). CMV viral load measurement was not affected by different concentrations of HSV-1 or EBV DNA. We conclude that The Abbott RealTime CMV assay offers good sensitivity, precision and linearity and is suitable for monitoring CMV viral loads in transplant recipients. Standardization with the WHO CMV standard allows for comparison with other assays. PMID:26341060

  3. 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

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

    PubMed

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

    2009-07-01

    To improve the control of Chlamydia trachomatis infection in India, a rapid, specific and cost-effective method is much needed. We developed an in-house PCR assay by targeting a unique genomic sequence encoding a protein from the C. trachomatis phospholipase D endonuclease superfamily that produces an amplified fragment of 368 bp. The specificity of the primers was confirmed using genomic DNA from other sexually transmitted disease-causing and related micro-organisms and from humans. The assay was highly sensitive and could detect as low as 10 fg C. trachomatis DNA. Clinical evaluation of the in-house-developed PCR was carried out using 450 endocervical specimens that were divided in two groups. In group I (n=274), in-house PCR was evaluated against the direct fluorescence assay. The resolved sensitivity of the in-house PCR method was 97.22 % compared with 88 % for the direct fluorescent antibody assay. In group II (n=176), the in-house PCR was compared with the commercial Roche AMPLICOR MWP CT detection kit. The resolved sensitivity of the in-house PCR assay reported here was 93.1 % and the specificity was 97.46 %, making it a cost-effective alternative for routine diagnosis of genital infection by C. trachomatis. The method should facilitate early detection leading to better prevention and treatment of genital infection in India. PMID:19502371

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

    PubMed Central

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

    2014-01-01

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

  6. Comparison of the Digene Hybrid Capture 2 Assay and Roche AMPLICOR and LINEAR ARRAY Human Papillomavirus (HPV) Tests in Detecting High-Risk HPV Genotypes in Specimens from Women with Previous Abnormal Pap Smear Results▿

    PubMed Central

    Stevens, Matthew P.; Garland, Suzanne M.; Rudland, Elice; Tan, Jeffrey; Quinn, Michael A.; Tabrizi, Sepehr N.

    2007-01-01

    The development of cervical cancer is strongly associated with the presence of persistent high-risk (HR) human papillomavirus (HPV) infection. Recently, the commercially manufactured PCR-based Roche AMPLICOR (AMP) and LINEAR ARRAY (LA) HPV tests have become available for HPV detection. However, knowledge of their clinical performance compared to the U.S. Food and Drug Administration-approved Hybrid Capture 2 (HC2) assay is limited. This study evaluated the concordance between the HC2, AMP, and LA tests in detecting HR-HPV among a cohort of 1,679 women with previous abnormal Pap smear results. Overall, 1,393 specimens (81.3%) generated concordant results for HR-HPV presence or absence by the three assays. The concordance levels were substantial between the HC2 and AMP tests (84.4%, κ = 0.6419) and between the HC2 and LA tests (84.0%, κ = 0.6341) and nearly perfect between the AMP and LA tests (97.8%, κ = 0.9441). HR-HPV prevalence, as detected by the AMP or LA tests, was significantly higher among women with cytological or histological high-grade disease (CIN2 or greater) than that detected by HC2 (P < 0.0001). The AMP and LA tests exhibited greater sensitivity, but lower specificity, than HC2 for detecting HR-HPV among this cohort of women with underlying cervical abnormalities, particularly among subjects with histologically proven high-grade disease. Both PCR-based HPV tests may be valuable in the management of care for women with underlying cervical abnormalities, in predicting treatment success, and in studying the clearance or acquisition of new infections. PMID:17494721

  7. Comparison of Amplicor and GeneXpert MTB/RIF Tests for Diagnosis of Tuberculous Meningitis

    PubMed Central

    Patel, Vinod B.; Connolly, Cathy; Singh, Ravesh; Lenders, Laura; Matinyenya, Brian; Theron, Grant; Ndung'u, Thumbi

    2014-01-01

    There are no data about the comparative accuracy of commercially available nucleic acid amplification tests (GeneXpert MTB/RIF and Roche Amplicor) for the diagnosis of tuberculous meningitis (TBM). A total of 148 patients with suspected TBM were evaluated, and cultures served as the reference standard. The sensitivities and specificities (95% confidence interval [CI]) for the Amplicor and Xpert MTB/RIF tests were similar: 46 (31–60) versus 50 (33–67) and 99 (93–100) and 94 (84–99), respectively. PMID:25056328

  8. Performance of the Amplicor human immunodeficiency virus type 1 PCR and analysis of specimens with false-negative results.

    PubMed Central

    Barlow, K L; Tosswill, J H; Parry, J V; Clewley, J P

    1997-01-01

    Over a 4-year period, the Roche Amplicor kit was used in a United Kingdom reference laboratory for the detection or confirmation of human immunodeficiency virus (HIV) type 1 infection, particularly in infants born to HIV-infected mothers. Of 408 specimens from adults and older children tested, the 122 seronegative specimens were all Amplicor negative. Of the 286 seropositive specimens, 268 were Amplicor positive. On the basis of these results, the Amplicor assay has a specificity of 100% and a sensitivity of 93.7%. In addition, for 247 specimens from infants and young children, serological results may not have been diagnostic because of placental transfer of maternal antibodies. Forty-eight were Amplicor positive, and of the 199 Amplicor-negative specimens, 19 were assumed to be false negative on the basis of clinical data, serological markers (including p24 antigen), and/or results for previous or follow-up specimens. This represents a sensitivity of 75% for the Amplicor test for specimens from patients under 2 years of age. Of these 37 false-negative specimens plus 2 specimens from other laboratories, 31 could be characterized by amplifying extracted material from them by an in-house nested gag PCR spanning the Amplicor target region. The amplicons were sequenced and found to represent subtypes A (35.5%), B (22.6%), C (22.6%), D (16.1%), and G (3.2%). False-negative results by the Amplicor assay may be ascribed to low-target copy number, the physical behavior of one primer (SK462), and sequence variation in the target region of the other primer (SK431). PMID:9350745

  9. Reproducibility problems with the AMPLICOR PCR Chlamydia trachomatis test.

    PubMed Central

    Peterson, E M; Darrow, V; Blanding, J; Aarnaes, S; de la Maza, L M

    1997-01-01

    In an attempt to use an expanded "gold standard" in an evaluation of an antigen detection test for Chlamydia trachomatis, the AMPLICOR (Roche Diagnostics Systems, Inc., Branchburg, N.J.) PCR Chlamydia trachomatis test and culture were used with 591 sets of cervical specimens. Of the 591 specimens assayed, 35 were retested due to either an equivocal result by the PCR (19 samples) or a discrepancy between the results of culture, PCR, and the antigen detection method. During the repeat testing of the samples with equivocal and discrepant results, all but one interpretation change was due to the PCR result. In addition, upon repeat testing the PCR assay value measured in optical density units varied widely for 13 of these specimens. These 13 specimens were then tested in triplicate by the manufacturer with primers to the chlamydia plasmid and in duplicate with primers to the major outer membrane protein. Only 3 of the 13 specimens gave the same interpretation with these five replicates. In summary, reproducibility problems with the AMPLICOR test should be considered before it is incorporated as part of routine testing or used as an expanded gold standard for chlamydia testing. PMID:9157161

  10. Comparison of AMPLICOR and Hybrid Capture II assays for high risk HPV detection in normal and abnormal liquid-based cytology: use of INNO-LiPA Genotyping assay to screen the discordant results.

    PubMed

    Mo, L Z; Monnier-Benoit, S; Kantelip, B; Petitjean, A; Riethmuller, D; Prétet, J L; Mougin, C

    2008-02-01

    The study was aimed to evaluate the feasibility of detecting human papillomavirus (HPV) in women with normal or abnormal cervical smears using the Roche Amplicor MWP HPV Test. We compared by AMPLICOR Test and Hybrid Capture II (HCII) Test, the prevalence of HR-HPV in 470 cervical samples including 55 samples with WNL cytology, 208 ASC-US, 193 LGSIL and 14 HGSIL. Samples with discordant results were retested with INNO-LiPA Genotyping HPV Test v2. The HR-HPV positivity in WNL cytology samples was similar (21.8%) by AMPLICOR and HCII. In ASC-US, the HPV positivity was 42.3% by both tests. In LGSIL, HPV positivity was 66.3% and 66.8% by AMPLICOR and HCII, respectively. In HGSIL, 92.8% of samples were positive by AMPLICOR and 85.7% by HCII. The agreement of both tests was 96.2% with a Kappa value of 0.92. Eighteen cases were discordant: 9 HCII positive/AMPLICOR negative and 9 HCII negative/AMPLICOR positive. The INNO-LiPA test revealed HPV positivity in every case. Interestingly, all HCII+/AMPLICOR- samples were found to harbour HPV53. As for the HCII-/AMPLICOR+ samples, 8 demonstrated a multiple infection with HR 16- and/or 18- and/or 56-phylogenetically related HPV types. Moreover, two of these samples were co-infected with HPV6 and two other with HPV54. By using consensus HR-HPV as our reference HPV positivity, the sensitivity (96.6%) and specificity (100%) of AMPLICOR was similar to that of HCII Test. The AMPLICOR HPV Test is sensitive, specific, feasible and appropriate for routine HPV detection. PMID:18036888

  11. A Java Interface for Roche Lobe Calculations

    NASA Astrophysics Data System (ADS)

    Leahy, D. A.; Leahy, J. C.

    2015-09-01

    A JAVA interface for calculating various properties of the Roche lobe has been created. The geometry of the Roche lobe is important for studying interacting binary stars, particularly those with compact objects which have a companion which fills the Roche lobe. There is no known analytic solution to the Roche lobe problem. Here the geometry of the Roche lobe is calculated numerically to high accuracy and made available to the user for arbitrary input mass ratio, q.

  12. 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. PMID:26706730

  13. 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.

  14. Assessment of agreement between the AMPLICOR HIV-1 MONITOR test versions 1.0 and 1.5.

    PubMed

    Hill, Charles E; Green, Alicia M; Ingersoll, Jessica; Easley, Kirk A; Nolte, Frederick S; Caliendo, Angela M

    2004-01-01

    The agreement of the microwell plate AMPLICOR HIV-1 MONITOR version 1.0 (MWP 1.0), the microwell plate AMPLICOR HIV-1 MONITOR version 1.5 (MWP 1.5), and the COBAS AMPLICOR HIV-1 MONITOR version 1.5 (COBAS 1.5) tests was evaluated using clinical specimens and well-characterized control material. Two hundred patient plasma specimens and a panel of known human immunodeficiency virus type 1 (HIV-1) subtypes were tested. All data were log(10) transformed prior to analysis. The 95% limits of agreement for the three tests at the average of 3.66 log(10) copies/ml were +/- 0.28 log(10), +/- 0.34 log(10), and +/- 0.34 log(10) copies/ml for MWP 1.0-MWP 1.5, MWP 1.0-COBAS 1.5, and MWP 1.5-COBAS 1.5, respectively. Ten specimens (6.1%) had differences exceeding the limits of agreement for the MWP 1.0 and MWP 1.5 tests. Correlation coefficients among the three tests were high (r >or=0.96). The viral-load values obtained with the MWP 1.0 test were only 2.1% higher on average than those measured with the MWP 1.5 test and 1.6% higher than those seen with the COBAS 1.5 test. The MWP 1.5 test values were 0.8% higher than the COBAS 1.5 test values. Overall, there was less agreement among the different tests for viral-load values near the lower limit of quantification. The MWP 1.0 test underquantified subtypes A, E, F, G, and H by 1.0 to 2.0 log(10) copies/ml; this problem was not observed with the MWP 1.5 test. The close agreement among the results obtained with the different test versions and formats suggests that it is not necessary to reestablish a baseline viral load when changing AMPLICOR HIV-1 MONITOR tests, unless the patient is known to be infected with a non-B subtype. PMID:14715766

  15. Roche limit of a solid body

    NASA Technical Reports Server (NTRS)

    Aggarwal, H. R.; Oberbeck, V. R.

    1974-01-01

    Tidal fission of both impacting and orbiting linear elastic solid bodies based on Kelvin's theory of earth tides is considered. It is shown that there can be more than one mutually exclusive modes of fracture - the particular mode in which a body fractures depending on its size and strength. The analysis gives a vivid picture of the propagation of the fracture with a decreasing distance from the planet. Expressions for the initiation and completion of fracture are obtained which are displayed graphically for a rigid body. The effect of elasticity on the breakup altitude is discussed. For orbiting solid bodies, the study gives the upper limit of the breakup altitude as 0.38R (where R is the radius of planet), which is much less than the value 1.44R used for such bodies in the past. The results presented include a previously given theory by Sekiguchi as a part. For the special case of a liquid body, comparison is made with Roche's calculation and the difference explained.

  16. Impact of Human Immunodeficiency Virus Type 1 (HIV-1) Genetic Diversity on Performance of Four Commercial Viral Load Assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT

    PubMed Central

    Swanson, Priscilla; de Mendoza, Carmen; Joshi, Yagnya; Golden, Alan; Hodinka, Richard L.; Soriano, Vincent; Devare, Sushil G.; Hackett, John

    2005-01-01

    Human immunodeficiency virus type 1 (HIV-1) evolution and changing strain distribution present a challenge to nucleic acid-based assays. Reliable patient monitoring of viral loads requires the detection and accurate quantification of genetically diverse HIV-1. A panel of 97 HIV-1-seropositive plasma samples collected from Cameroon, Brazil, and South Africa was used to compare the performance of four commercially available HIV RNA quantitative tests: Abbott LCx HIV RNA Quantitative assay (LCx), Bayer Versant HIV-1 RNA 3.0 (bDNA), Roche AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5), and bioMérieux NucliSens HIV-1 QT (NucliSens). The panel included group M, group O, and recombinant viruses based on sequence analysis of gag p24, pol integrase, and env gp41. The LCx HIV assay quantified viral RNA in 97 (100%) of the samples. In comparison, bDNA, Monitor v1.5, and NucliSens quantified viral RNA in 96.9%, 94.8%, and 88.6% of the samples, respectively. The two group O specimens were quantified only by the LCx HIV assay. Analysis of nucleotide mismatches at the primer/probe binding sites for Monitor v1.5, NucliSens, and LCx assays revealed that performance characteristics reflected differences in the level of genetic conservation within the target regions. PMID:16081923

  17. 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).

  18. The flat Grothendieck-Riemann-Roch theorem without adiabatic techniques

    NASA Astrophysics Data System (ADS)

    Ho, Man-Ho

    2016-09-01

    In this paper we give a simplified proof of the flat Grothendieck-Riemann-Roch theorem. The proof makes use of the local family index theorem and basic computations of the Chern-Simons form. In particular, it does not involve any adiabatic limit computation of the reduced eta-invariant.

  19. ["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. PMID:20617296

  20. Biotech Meets Chemistry: Roche Invests in Customized Training.

    PubMed

    Heinzelmann, Elsbeth

    2015-01-01

    In response to current needs, Roche is offering its employees an intensive course in biotechnology under the auspices of biotechnet Switzerland. Lecturers from ZHAW Wädenswil [university of applied science] give participants the benefit of their expertise in theory and laboratory practice. One valuable spin-off from this is that this extra-mural course will allow participants to create a permanent network. PMID:26507351

  1. 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.

  2. Plasmonic Roche lobe in metal-dielectric-metal structure

    SciTech Connect

    Shiu, Ruei-Cheng; Lan, Yung-Chiang

    2013-07-15

    This study investigates a plasmonic Roche lobe that is based on a metal-dielectric-metal (MDM) structure using finite-difference time-domain simulations and theoretical analyses. The effective refractive index of the MDM structure has two centers and is inversely proportional to the distance from the position of interest to the centers, in a manner that is analogous to the gravitational potential in a two-star system. The motion of surface plasmons (SPs) strongly depends on the ratio of permittivities at the two centers. The Lagrange point is an unstable equilibrium point for SPs that propagate in the system. After the SPs have passed through the Lagrange point, their spread drastically increases.

  3. 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}.

  4. Analysis of cytomegalovirus (CMV) viremia using the pp65 antigenemia assay, the amplicor CMV test, and a semi-quantitative polymerase chain reaction test after allogeneic marrow transplantation.

    PubMed

    Ksouri, H; Eljed, H; Greco, A; Lakhal, A; Torjman, L; Abdelkefi, A; Ben Othmen, T; Ladeb, S; Slim, A; Zouari, B; Abdeladhim, A; Ben Hassen, A

    2007-03-01

    A pp65 antigenemia assay for polymorphonuclear leukocytes (PMNLs) (CINAkit Rapid Antigenemia), and a qualitative polymerase chain reaction (PCR) test for plasma 'PCR-P qual' (Amplicor cytomegalovirus [CMV] test) were performed for 126 samples (blood and plasma) obtained from 18 bone marrow transplant patients, over a 9-month surveillance period. Among those samples, 92 were assayed with a semi-quantitative PCR test for PMNLs 'PCR-L quant.' The number of samples with a positive CMV test for antigenemia and PCR-P qual assays was 20.63% and 12.7%, respectively, whereas the PCR-L quant assay was positive in 48 of the 92 samples assayed (52.17%). The rates of concordance of the results of PCR-P qual and antigenemia, PCR-P qual and PCR-L quant, antigenemia and PCR-L quant were 92%, 65.2% and 66.8%, respectively. The analysis of the results for the 92 specimens tested by all 3 methods showed a rate of concordance of 63% among all methods. Good agreement (kappa=0.72) was found only between pp65 Ag and PCR-P qual assays. Clinical disease correlates with an antigenemia high viral load. Three patients had CMV disease despite preemptive therapy, and all of them had graft-versus-host-disease (GVHD). PMNLs-based assays are more efficient in monitoring CMV reactivation, but for high-risk patients with GVHD, more sensitive assays (real-time PCR) must be done. PMID:17313466

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

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

    SciTech Connect

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

    2014-09-20

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

  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. 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.

  9. 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

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

    PubMed

    Bencivenga, Alessandro; Di Luigi, Gianluca

    2015-01-01

    Ex voto are devotional objects, widely used in Italy as a form of prayer or wish, or as thanksgiving for a grace received. In a broader historical perspective, votive offerings are hung in Greek, Etruscan, Roman shrines and later in churches or to show gratitude for miracles obtained, healing from illness or infirmity, or as a simple supplication and prayer. The ex voto here presented seem to be unique in the world: made of majolica, they come from the church of St. Roch in Castelli (Abruzzo). They depict breast benign and malignant lesions (mastitis, abscess, fat necrosis, inflammatory cancer, infiltrating carcinoma) in three dimensions, performing an accurate and personalized portrait of breast diseases (in some cases with the depicted name of the sick woman), showing fine details of each disease, and demonstrating accurate knowledge of the female anatomy and pathology. PMID:26946819

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  12. 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…

  13. 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

  14. Roche lobe underfilling of the secondary star in PSR J102347.6+003841?

    NASA Astrophysics Data System (ADS)

    McConnell, O.; Callanan, P. J.; Kennedy, M.; Hurley, D.; Garnavich, P.; Menzies, J.

    2015-08-01

    PSR J102347.6+003841 is a radio pulsar system with a spin period of 1.69 ms and an orbital period of 4.75 h. Uniquely, it undergoes periods of transient accretion from its companion star: it occupies an important position in the evolutionary track from X-ray binary to isolated millisecond radio pulsar. Here, we present a spectroscopic study of this system showing late-type absorption features which match those of a G2V star. We find a semi-amplitude of 286 ± 3 kms-1 and a best-fitting orbital period of 0.198 0966(1) d. We combine these measurements with optical photometry which suggests the secondary star may be underfilling its Roche lobe by between 15 and 20 per cent. We weakly constrain the mass of the neutron star to be ≤2.2 M⊙ at the 2σ level. We also discuss the possible origins of the Hα emission line in our template subtracted, averaged spectrum. Finally, we present and discuss new optical photometry of J1023 taken during the recent outburst of the system.

  15. 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.

  16. 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.

  17. Somersaulting techniques used in high-scoring and low-scoring Roche vaults performed by male Olympic gymnasts.

    PubMed

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

    2007-04-01

    The aim of this study was to compare the somersaulting techniques used in the 16 highest-scoring and 16 lowest-scoring Roche vaults. Our hypothesis was that the gymnasts performing the highest-scoring Roche vaults would demonstrate a better technique than those performing the lowest-scoring Roche vaults while on the horse (pushing off the horse more effectively), somersaulting (executing most of the required somersaults higher in flight), and landing (showing a greater control). A 16-mm motion picture camera, operating at 100 Hz, recorded the vaults during the official competition. The two-dimensional direct linear transformation was used for spatial reconstruction. The results of t-tests (P < 0.05) indicated that, compared with the low-scoring gymnasts, the high-scoring gymnasts had: (1) greater height of body centre of mass and a more fully extended body position at the horse take-off; (2) greater height of body centre of mass at the peak of post-flight, knee release, and touchdown on the mat; (3) greater horizontal and vertical displacements of body centre of mass, greater somersaulting rotation, and longer time from the knee release to mat touchdown; and (d) markedly smaller landing point deductions. In conclusion, a successful Roche vault is likely when the focus is on: (a) leaving the horse with a large vertical velocity in an extended body position to achieve a high trajectory of centre of mass by first extending the legs, then immediately pushing off the horse vigorously, using the muscles of the upper extremity; (b) grasping the knees immediately after the take-off from the horse, achieving the tightly tucked body position early during the ascent to the peak, and completing two-thirds of the required somersaults at a great height; (c) releasing the knees and extending the body above the top level of the horse; and (d) contacting the mat with a high body centre of mass position. PMID:17454535

  18. 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

    2016-06-01

    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.

  19. An evaluation of the New Roche Diagnostics Kit for the rapid identification of clinically important non-dextrose, non-fastidious gram-negative rods.

    PubMed

    Elegbe, I A

    1980-01-01

    The evaluation of the new Roche Diagnostics Commercial kit (Roche Diagnostics, 1975) for the identification of non-dextrose fermenting, non-fastidious gram-negative rods has been compared with conventional methods in the recognition and identification of these non-dextrose, non-fastidious gram-negative bacteria. This new kit has definite advantages over and above the conventional methods in a number of ways. It is cheaper to run, and above all it is less cumbersome, less time consuming and it is accurate. Apart from all these, the new method makes use of the odour test (Roche Diagnostics, 1975) and other additional conventional tests recommended by the Oxi/ferm manufacturer. PMID:6283862

  20. The Quasi-Roche Lobe Overflow State in the Evolution of Close Binary Systems Containing a Radio Pulsar

    NASA Astrophysics Data System (ADS)

    Benvenuto, O. G.; De Vito, M. A.; Horvath, J. E.

    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.

  1. 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.

  2. 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. PMID:25502520

  3. Comparison of Hybribio GenoArray and Roche Human Papillomavirus (HPV) Linear Array for HPV Genotyping in Anal Swab Samples

    PubMed Central

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

    2014-01-01

    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 χ2 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. PMID:25502520

  4. Performance Evaluation of Siemens ADVIA Centaur and Roche MODULAR Analytics E170 Total 25-OH Vitamin D Assays

    PubMed Central

    Chen, Yu; Kinney, Lois; Božović, Andrea; Smith, Hilary; Tarr, Heather; Diamandis, Eleftherios P.; LeBlanc, Adrien

    2014-01-01

    Objectives To evaluate the newly developed Roche MODULAR Analytics E170 Total Vitamin D and the Siemens ADVIA Centaur® Vitamin D Total assays. Materials and Methods Assays were evaluated using the Clinical and Laboratory Standards Institute protocols. Split patient samples were compared with LC-MS/MS and DiaSorin LIAISON assays (n=79 including 15 specimens with detectable endogenous 25-OH vitamin D2). Assay accuracy was also evaluated using the Vitamin D External Quality Assessment Scheme samples. Results The ADVIA Centaur and E170 assays demonstrated maximum total CVs of 14.1% and 5.9%, respectively. Both showed excellent linearity (R2 >0.99). The ADVIA Centaur assay demonstrated interference with bilirubin at 800 μmol/L, hemolysis at 1.25 g/L, and triglycerides at 2.8 mmol/L. Compared to LC-MS/MS, the ADVIA Centaur assay demonstrated a R2 value of 0.893, average bias of −8.8%; the E170 assay an R2 value of 0.872, average bias of 14.3% with underestimation of 25-OH vitamin D2. Compared to the LIAISON assay, the ADVIA Centaur assay demonstrated an R2 value of 0.781, average bias of −17.3%; the E170 assay an R2 value of 0.823, average bias of 11.4%. The ADVIA Centaur and E170 assays demonstrated a biases of <20% in 10/10 and 8/10 samples, respectively. Conclusions The ADVIA Centaur and E170 vitamin D assays demonstrated acceptable linearity, imprecision, and accuracy. The E170 assay demonstrated consistent underestimation of 25-OH vitamin D2 levels. Compared with LC-MS/MS, the ADVIA Centaur assay demonstrated a higher R2 value and a smaller average bias than the E170 assay. PMID:22705028

  5. 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.

  6. Robe's restricted problem of 2+2 bodies when the bigger primary is a Roche ellipsoid and the smaller primary is an oblate body

    NASA Astrophysics Data System (ADS)

    Kaur, Bhavneet; Aggarwal, Rajiv

    2014-01-01

    In this problem, one of the primaries of mass m 1 is a Roche ellipsoid filled with a homogeneous incompressible fluid of density ρ 1. The smaller primary of mass m 2 is an oblate body outside the Ellipsoid. The third and the fourth bodies (of mass m 3 and m 4 respectively) are small solid spheres of density ρ 3 and ρ 4 respectively inside the Ellipsoid, with the assumption that the mass and the radius of the third and the fourth body are infinitesimal. We assume that m 2 is describing a circle around m 1. The masses m 3 and m 4 mutually attract each other, do not influence the motions of m 1 and m 2 but are influenced by them. We have extended the Robe's restricted three-body problem to 2+2 body problem under the assumption that the fluid body assumes the shape of the Roche ellipsoid (Chandrashekhar in Ellipsoidal figures of equilibrium, Chap. 8, Dover, New York, 1987). We have taken into consideration all the three components of the pressure field in deriving the expression for the buoyancy force viz (i) due to the own gravitational field of the fluid (ii) that originating in the attraction of m 2 (iii) that arising from the centrifugal force. In this paper, equilibrium solutions of m 3 and m 4 and their linear stability are analyzed. We have proved that there exist only six equilibrium solutions of the system, provided they lie within the Roche ellipsoid. In a system where the primaries are considered as Earth-Moon and m 3, m 4 as submarines, the equilibrium solutions of m 3 and m 4 respectively when the displacement is given in the direction of x 1-axis or x 2-axis are unstable.

  7. Comparison of the Roche Septi-Chek blood culture bottle with a brain heart infusion biphasic medium bottle and with a tryptic soy broth bottle.

    PubMed Central

    Henry, N K; Grewell, C M; McLimans, C A; Washington, J A

    1984-01-01

    In a comparison of 1,368 positive blood cultures, a vented Roche Septi-Chek (V-RSC) blood culture bottle was superior to an unvented tryptic soy broth-containing bottle (Difco) for the recovery of all aerobic and facultatively anaerobic microorganisms. Anaerobic bacteria were recovered more frequently and earlier in the unvented tryptic soy broth-containing bottle. A separate comparison of 529 positive blood cultures was conducted to examine the performance of the V-RSC bottle with that of a vented brain heart infusion biphasic medium. The V-RSC bottle recovered significantly more isolates of Enterobacteriaceae and of anaerobic bacteria than did the vented brain heart infusion biphasic medium. The V-RSC bottle is a reliable blood culture system for all aerobic and facultatively anaerobic microorganisms. Because of its suboptimal recovery of anaerobic bacteria, it is recommended that the V-RSC bottle be used in combination with an unvented vacuum blood culture bottle. PMID:6371039

  8. Quantitative DNA analysis of fresh solid tumors by flow and image cytometric methods: a comparison using the Roche Pathology Workstation Image Analyzer.

    PubMed

    Ellison, D A; Maygarden, S J; Novotny, D B

    1995-04-01

    The clinical utility of DNA ploidy and cell cycle parameters as prognostic indicators has been demonstrated for selected malignant tumors. Previous quantitative DNA analysis studies have used various tumor sample preparation methods and analyzers. We undertook a pilot study to compare the results of DNA analysis of fresh solid tumors by flow cytometry with the new Roche Pathology Workstation Image Analyzer. Flow cytometric DNA analysis was done on cell suspensions of fine needle aspirates from fresh tumor specimens and analyzed for ploidy and cell cycle statistics with a Becton-Dickinson FACScan Analyzer, using a rectangular model. Small aliquots from these same aspirates were prepared as direct cytologic smears and Feulgen stained for DNA analysis with the Roche Image Analyzer. Additional smears were stained with Diff-Quik for morphologic correlation with DNA histograms. The study group consisted of 40 malignant neoplasms. There was a high correlation between the flow and image DNA indices (R = 0.93, slope = 1.0036, P < 0.001) but a weaker relationship between the flow and image estimated S-phase fractions (R = 0.57, slope = 0.5401, P < 0.01). DNA ploidy categorization for the two methods was concordant in 30 (75%) cases, discordant in seven (17.5%) cases, and equivocal in three (7.5%) cases. In our experience, quantitative DNA analysis of fresh tumor aspirates by flow and image cytometric methods yielded comparable and/or complementary results, with each method having certain advantages and disadvantages. Proposed reasons for false and true discordances and an approach for evaluation are discussed. PMID:7617654

  9. Vitamin B(12) Immunoassay on Roche Elecsys 2010: Effects of High Excess Concentration of Serum Vitamin B(12) in CKD Patients on Parenteral Administration.

    PubMed

    Basu, Surupa; Chaudhuri, Subimal

    2011-10-01

    Vitamin B(12) being water soluble is excreted in the urine when administered in excess. The probability of finding an abnormally excess serum concentration would be almost surreal. We report a peculiar clinical situation that may impact the vitamin B(12) immunoassay on the Roche Elecsys 2010 due to excess analyte concentration. In separate episodes (Feb and June 2010), the Biochemistry laboratory of a tertiary-care hospital, Kolkata, India, encountered two critically ill patients with background chronic kidney disease (CKD), low urine output, and on cyanocoabalamin supplementation, who had serum vitamin B(12) concentrations far exceeding expected values; even post dialysis. The B(12) assays (pmol/l) were performed using electrochemiluminiscence immunoassay on Roche Elecsys 2010, the assay validity confirmed by concomitant quality control runs. The immunoassays failed to deliver results, flagged with "signal level below limit". Biotin therapy was ruled out as a possible interferent. In the first episode, re-assay of a repeat draw yielded same outcome; outsourcing on Immulite provided concentration of >738 pmol/l. Serial dilution gave result of >29520 pmol/l on Elecsys 2010. In the second, we gained from past experience. Vitamin B(12) concentration >59040 pmol/l was conveyed to the treating nephrologist the very day. The B(12) immunoassay on the Elecsys 2010 employs sequential incubation steps for competitive binding that is compromised in the event of abnormally excess B(12) concentration in patient sera akin to the prozone effect. This knowledge may be beneficial while assaying sera of CKD patients to avoid financial loss due unnecessary repeats and delay in turnaround time. PMID:23024480

  10. 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)

  11. 10Be dating of the Main Terrace level in the Amblève valley (Ardennes, Belgium): new age constraint on the archaeological and palaeontological filling of the Belle-Roche palaeokarst

    NASA Astrophysics Data System (ADS)

    Rixhon, Gilles; Bourlès, Didier L.; Braucher, Régis; Siame, Lionel; Cordy, Jean-Marie; Demoulin, Alain

    2014-05-01

    It is still disputed whether very old archaeological and palaeontological remains found in the Belle-Roche palaeocave (eastern Belgium) pertain to the Early (˜1 Ma) or Middle (˜0.5 Ma) Pleistocene. Here, in situ-produced cosmogenic 10Be concentrations from a depth profile in nearby sediments of the Belle-Roche terrace (Amblève Main Terrace level) are used as an indirect solution of this chronological issue. The distribution of 10Be concentrations in the upper 3 m of this profile displays the theoretically expected exponential decrease with depth. Assuming a single exposure episode, we obtain a best fit age of 222.5±31 ka for the time of terrace abandonment. However, below 3 m, the 10Be concentrations show a marked progressive increase with depth. This distinctive cosmogenic signal is interpreted as the result of slow aggradation of the fluvial deposits over a lengthy interval. Modelling of the whole profile thus suggests that the onset of the terrace formation occurred at around 550 ka, with a sediment accumulation rate of ˜20 mm/ka. Based on two slightly different reconstructions of the geomorphic evolution of the area and a discussion of the temporal link between the cave and Main Terrace levels, we conclude that the fossil-bearing layers in the palaeokarst pertain most probably to MIS 14-13 (or possibly MIS 12-11) and the artifact-bearing layer to MIS 13 (or possibly MIS 11). This age estimate for the large mammal association identified in the Belle-Roche palaeokarst and the attribution to MIS 14-13 of a similar fauna found in the lowermost fossiliferous layers of the Caune de l'Arago (Tautavel) are in mutual support. Our results therefore confirm the status of the Belle-Roche site as a reference site for the Cromerian mammal association and the Early Palaeolithic industry in NW Europe.

  12. Characterization of a Novel Melt Curve by Use of the Roche LightCycler HSV 1/2 Analyte-Specific Reagent Real-Time PCR Assay: Frequencies of This Novel (Low) Melt Curve and Commonly Encountered (Intermediate) Melt Curves

    PubMed Central

    Almradi, Amro; Espy, Mark J.; Prada, Anne E.; Gibson, John P.; Pritt, Bobbi S.

    2014-01-01

    We characterize a novel probe binding-site polymorphism detectable solely by melt curve analysis using the Roche LightCycler HSV 1/2 analyte-specific reagent real-time PCR assay. The frequencies of this novel (47°C) and previously described intermediate (60 to 62°C) melt curves were 0.016% and 4.9%, respectively. PMID:24352998

  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. Analytical evaluation of the Dade Behring Dimension RxL automated N-Terminal proBNP (NT-proBNP) method and comparison with the Roche Elecsys 2010.

    PubMed

    Di Serio, Francesca; Ruggieri, Vincenzo; Varraso, Lucia; De Sario, Rosalisa; Mastrorilli, Angela; Pansini, Nicola

    2005-01-01

    Methods to quantify B-type natriuretic peptide (BNP) and N-terminal-propeptide (NT-proBNP) in plasma or serum samples are well established. We assessed the analytical performance of the Dimension RxL NT-proBNP method (Dade-Behring). Evaluation of different sample types was carried out. Controls and heparin plasma pools were used to determine the detection limit, precision, and linearity. Sample stability and the effect of interfering substances on the NT-proBNP concentrations were evaluated. Agreement between Dimension RxL and Elecsys 2010 (Roche Diagnostics) NT-proBNP methods was assessed. The influence of age and sex on NT-proBNP concentrations was evaluated in healthy subjects. Heparin plasma should be the matrix of choice. The detection limit was 2.0 ng/L. The total imprecision was 2.6-3.6% for concentrations from 231 to 9471 ng/L; mean NT-proBNP concentrations of 21 and 15 ng/L were associated with coefficients of variation of 9.9% and 14.7%, respectively. The method was linear up to 32,650 ng/L. There was no effect of temperature, freeze-thaw cycles and interfering substances. A bias was detected when Dimension RxL and Elecsys 2010 NT-proBNP methods were compared. Age and sex were significantly and independently related to NT-proBNP concentrations. The Dimension RxL NT-proBNP method, like the Elecsys 2010, is suitable for routine use in the diagnosis of heart failure. PMID:16232094

  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. EUROarray human papillomavirus (HPV) assay is highly concordant with other commercial assays for detection of high-risk HPV genotypes in women with high grade cervical abnormalities.

    PubMed

    Cornall, A M; Poljak, M; Garland, S M; Phillips, S; Machalek, D A; Tan, J H; Quinn, M A; Tabrizi, S N

    2016-06-01

    The purpose of this study was to evaluate the performance of the EUROIMMUN EUROArray HPV genotyping assay against the Roche Cobas 4800, Roche HPV Amplicor, Roche Linear Array and Qiagen Hybrid Capture 2 assays in the detection of high-risk HPV (HR-HPV) from liquid based cervical cytology samples collected from women undergoing follow-up for abnormal cervical cytology results. Cervical specimens from 404 women undergoing management of high-grade cytological abnormality were evaluated by EUROarray HPV for detection of HR-HPV genotypes and prediction of histologically-confirmed cervical intraepithelial neoplasia grade 2 or higher (≥CIN2). The results were compared to Hybrid Capture 2, Cobas 4800 HPV, Amplicor and Linear Array HPV. Positivity for 14 HR-HPV types was 80.0 % for EUROarray (95 % CI; 75.7-83.8 %). Agreement (κ, 95 % CI) between the EUROarray and other HPV tests for detection of HR-HPV was good to very good [Hybrid Capture κ = 0.62 (0.54-0.71); Cobas κ = 0.81 (0.74-0.88); Amplicor κ = 0.68 (0.60-0.77); Linear Array κ = 0.77 (0.70-0.85)]. For detection of HR-HPV, agreement with EUROarray was 87.90 % (Hybrid Capture), 93.58 % (Cobas), 92.84 % (Amplicor) and 92.59 % (Linear Array). Detection of HR-HPV was not significantly different between EUROarray and any other test (p < 0.001). EUROarray was concordant with other assays evaluated for detection of high-risk HPV and showed sensitivity and specificity for detection of ≥ CIN2 of 86 % and 71 %, respectively. PMID:27048314

  17. Ability of Two Commercially Available Assays (Abbott RealTime HIV-1 and Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Version 2.0) To Quantify Low HIV-1 RNA Levels (<1,000 Copies/Milliliter): Comparison with Clinical Samples and NIBSC Working Reagent for Nucleic Acid Testing Assays

    PubMed Central

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

    2014-01-01

    Concordance between molecular assays may be suboptimal at low HIV-1 viremia levels (<1,000 copies/ml); therefore, it may be difficult to define and compare virologic endpoints for successful and failed therapy. We compared two commercial assays (the Abbott RealTime HIV-1 and the Roche Cobas AmpliPrep/TaqMan HIV-1 version 2.0) for their ability to detect and quantify low viral loads. A comparison was performed using 167 residual clinical samples (with values ranging from “not detected” to 1,000 copies/ml, as measured by the Abbott assay) and the National Institute and Biological Standards and Control (NIBSC) HIV-1 RNA working reagent 1 for nucleic acid amplification techniques (NAT) assays (serially diluted to a range from 1 to 1,000 copies/ml). Quantitative results were compared using Lin's concordance correlation coefficient and a Bland-Altman plot. Concordance with the qualitative results was measured by Cohen's kappa statistic. With clinical samples, the degree of interassay concordance of the qualitative results at a 40-copies/ml HIV-1 RNA threshold was substantial (κ = 0.762); the correlation among the quantified samples was suboptimal (concordance correlation coefficient, 0.728; P < 0.0001); the mean difference of the values between the Roche and Abbott assays was 0.193 log10 copies/ml. Using the HIV-1 RNA working reagent 1 for NAT assays, the results provided by the Roche assay were, on average, 3 times higher than expected, while the Abbott assay showed high accuracy. The Roche assay was highly sensitive, being able to detect a level as low as 3.5 copies/ml HIV-1 RNA with 95% probability. The performance characteristics of each molecular assay should be taken into account when HIV-1 RNA threshold values for “virologic suppression,” “virologic failure,” “persistent low viral loads,” etc., are defined and indicated in the support of clinical decisions. PMID:24671791

  18. Development and Evaluation of a Next-Generation Digital PCR Diagnostic Assay for Ocular Chlamydia trachomatis Infections

    PubMed Central

    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.

    2013-01-01

    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 (r2 = 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. PMID:23637300

  19. Development and verification of an automated sample processing protocol for quantitation of human immunodeficiency virus type 1 RNA in plasma.

    PubMed

    Lee, Brenda G; Fiebelkorn, Kristin R; Caliendo, Angela M; Nolte, Frederick S

    2003-05-01

    We developed and verified an automated sample processing protocol for use with the AMPLICOR HIV-1 MONITOR test, version 1.5 (Roche Diagnostics, Indianapolis, Ind.). The automated method uses the MagNA Pure LC instrument and total nucleic acid reagents (Roche Applied Science, Indianapolis, Ind.) to extract human immunodeficiency virus type 1 (HIV-1) RNA from plasma specimens. We compared the HIV-1 load results for a dilution series (1 to 5 nominal log(10) copies/ml) and 175 clinical specimens processed by the automated method to those for the same samples processed by the manual methods specified by the manufacturer. The sensitivity, dynamic range, and precision of the viral load assay obtained by automated processing of specimens were similar to those obtained by an ultrasensitive manual processing method. The results were highly correlated (R(2), 0.95), and were in close agreement, with a mean difference of 0.09 log(10) (standard deviation, 0.292). The limits of agreement were +/-0.58 log(10) for results for samples processed by both the manual and the automated methods. These performance characteristics were achieved with a smaller sample volume (200 versus 500 microl) and without a high-speed centrifugation step and required only 15 min of labor for a batch of 32 samples. In conclusion, the automated sample preparation protocol can replace both the standard and the ultrasensitive manual methods used with the AMPLICOR HIV-1 MONITOR test and can substantially reduce the labor associated with this test. PMID:12734249

  20. 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.

  1. 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…

  2. "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. PMID:22375299

  3. Utility of PCR in diagnosing pulmonary tuberculosis.

    PubMed Central

    Bennedsen, J; Thomsen, V O; Pfyffer, G E; Funke, G; Feldmann, K; Beneke, A; Jenkins, P A; Hegginbothom, M; Fahr, A; Hengstler, M; Cleator, G; Klapper, P; Wilkins, E G

    1996-01-01

    At present, the rapid diagnosis of pulmonary tuberculosis rests with microscopy. However, this technique is insensitive and many cases of pulmonary tuberculosis cannot be initially confirmed. Nucleic acid amplification techniques are extremely sensitive, but when they are applied to tuberculosis diagnosis, they have given variable results. Investigators at six centers in Europe compared a standardized PCR system (Amplicor; Roche) against conventional culture methods. Defined clinical information was collected. Discrepant samples were retested, and inhibition assays and backup amplification with a separate primer pair were performed. Mycobacterium tuberculosis complex organisms were recovered from 654 (9.1%) of 7,194 samples and 293 (7.8%) of 3,738 patients. Four hundred fifty-two of the M. tuberculosis isolates from 204 patients were smear positive and culture positive. Among the culture-positive specimens, PCR had a sensitivity of 91.4% for smear-positive specimens and 60.9% for smear-negative specimens, with a specificity of 96.1%. Analysis of 254 PCR-positive, culture-negative specimens with discrepant results revealed that 130 were from patients with recently diagnosed tuberculosis and 94 represented a presumed laboratory error. Similar analysis of 118 PCR-negative, culture-positive specimens demonstrated that 27 discrepancies were due to presumed uneven aliquot distribution and 11 were due to presumed laboratory error; PCR inhibitors were detected in 8 specimens. Amplicor enables laboratories with little previous experience with nucleic acid amplification to perform PCR. Disease in more than 60% of the patients with tuberculosis with smear-negative, culture-positive specimens can be diagnosed at the time of admission, and potentially all patients with smear-positive specimens can immediately be confirmed as being infected with M. tuberculosis, leading to improved clinical management. PMID:8735089

  4. 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

  5. Urogenital Mycoplasmas and Human Papilloma Virus in Hemodialysed Women

    PubMed Central

    Ekiel, Alicja; Pietrzak, Bronisława; Aptekorz, Małgorzata; Mazanowska, Natalia; Kamiński, Paweł; Martirosian, Gayane

    2013-01-01

    Bacterial infections, especially endogenous, are the frequent complications among hemodialyzed and renal transplant patients. In this study we assumed the prevalence of urogenital mycoplasmas and HPV among hemodialysed women. We examined 32 hemodialysed women aged 20–48 (mean 35.6 ± 8.23) and 100 healthy controls of the same ages. Two swabs were collected for detection of mycoplasmas and HPV. Culture of Ureaplasma spp. and M. hominis was performed using Mycoplasma IST2 (bioMérieux, France), Identificaton of U. parvum and U. urealyticum was performed by Kong. Primers described by Jensen were used for M. genitalium. For detection of high-risk HPV types Amplicor HPV (Roche Molecular System, CA) was used. Prevalence of urogenital mycoplasmas in the hemodialysed women (53.1%) was significantly higher (P = 0.0059), compared with controls (25%). In both groups, U. parvum was the most frequently isolated. Cooccurrence of urogenital mycoplasmas was shown in 75% of the HPV-positive hemodialysed women and in 30.4% of HPV-positive controls (P = 0.0461). Cooccurrence of urogenital mycoplasmas with HPV was significantly higher in hemodialysed women. The need to take into account these microorganisms in routine diagnostic, especially for hemodialysed patients, was demonstrated. Further studies to demonstrate the role of this cooccurrence in etiopathogenesis of infection in hemodialysed patients are required. PMID:24363622

  6. Diagnosis of Neisseria gonorrhoeae Using Molecular Beacon

    PubMed Central

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

    2015-01-01

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

  7. 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. PMID:24088864

  8. Urogenital mycoplasmas and human papilloma virus in hemodialysed women.

    PubMed

    Ekiel, Alicja; Pietrzak, Bronisława; Wiechuła, Barbara; Aptekorz, Małgorzata; Mazanowska, Natalia; Rady, Dominika; Kamiński, Paweł; Martirosian, Gayane

    2013-01-01

    Bacterial infections, especially endogenous, are the frequent complications among hemodialyzed and renal transplant patients. In this study we assumed the prevalence of urogenital mycoplasmas and HPV among hemodialysed women. We examined 32 hemodialysed women aged 20-48 (mean 35.6 ± 8.23) and 100 healthy controls of the same ages. Two swabs were collected for detection of mycoplasmas and HPV. Culture of Ureaplasma spp. and M. hominis was performed using Mycoplasma IST2 (bioMérieux, France), Identificaton of U. parvum and U. urealyticum was performed by Kong. Primers described by Jensen were used for M. genitalium. For detection of high-risk HPV types Amplicor HPV (Roche Molecular System, CA) was used. Prevalence of urogenital mycoplasmas in the hemodialysed women (53.1%) was significantly higher (P = 0.0059), compared with controls (25%). In both groups, U. parvum was the most frequently isolated. Cooccurrence of urogenital mycoplasmas was shown in 75% of the HPV-positive hemodialysed women and in 30.4% of HPV-positive controls (P = 0.0461). Cooccurrence of urogenital mycoplasmas with HPV was significantly higher in hemodialysed women. The need to take into account these microorganisms in routine diagnostic, especially for hemodialysed patients, was demonstrated. Further studies to demonstrate the role of this cooccurrence in etiopathogenesis of infection in hemodialysed patients are required. PMID:24363622

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

    PubMed Central

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

    2014-01-01

    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. PMID:24667303

  10. A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms.

    PubMed

    Indugu, Nagaraju; Bittinger, Kyle; Kumar, Sanjay; Vecchiarelli, Bonnie; Pitta, Dipti

    2016-01-01

    Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M (2) = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed. PMID:26870608

  11. A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms

    PubMed Central

    Indugu, Nagaraju; Bittinger, Kyle; Kumar, Sanjay; Vecchiarelli, Bonnie

    2016-01-01

    Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M2 = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed. PMID:26870608

  12. Elevated Cytokine and Chemokine Levels in the Placenta Are Associated With in utero HIV-1 Mother-To-Child Transmission

    PubMed Central

    Kumar, Surender B.; Rice, Cara E.; Milner, Danny A.; Ramirez, Nilsa C.; Ackerman, William E.; Mwapasa, Victor; Turner, Abigail Norris; Kwiek, Jesse J.

    2012-01-01

    Objective To determine if there is an association between cytokine and chemokine levels in plasma isolated from the placenta and HIV-1 mother-to-child transmission (MTCT). Design We designed a case-control study of HIV-infected, pregnant women enrolled in the Malaria and HIV in Pregnancy cohort. Participants were recruited in Blantyre, Malawi from 2000-04. Cases were women whose children were HIV-1 DNA-positive at birth (in utero MTCT) or HIV-1 DNA-negative at birth and HIV-1 DNA-positive at 6-weeks post-partum (intrapartum MTCT); controls were women whose children were HIV-1 DNA-negative both at birth and 6-weeks post-partum. Methods After delivery, blood was isolated from an incision on the basal plate of the placenta. We used a Luminex assay to simultaneously quantify 27 cytokines, chemokines, and growth factors in placental plasma. HIV-1 RNA copies were quantified with the Roche Amplicor kit. Results Levels of IL-4, IL-5, IL-6, IL-7, IL-9, eotaxin, IL1Ra and IP-10 were significantly elevated in placental plasma isolated from cases of in utero HIV-1 MTCT. In contrast, only GCSF was elevated in placental plasma isolated from cases of intrapartum MTCT. After adjusting for maternal age, gestational age, and peripheral CD4+ T cell count, every log10 increase in placental IP-10 was associated with a three-fold increase in the prevalence of in utero HIV-1 MTCT. Conclusions Elevated cytokine and chemokine levels in placental plasma were associated with in utero and not intrapartum MTCT. IP-10, which is both a T-cell chemokine and potentiator of HIV-replication, was robustly and independently associated with prevalent, in utero MTCT. PMID:22301415

  13. Detection of endocervical anti-Chlamydia trachomatis immunoglobulin A in pregnant women by a rapid, 6-minute enzyme-linked immunosorbent assay: comparison with PCR and chlamydial antigen detection methods.

    PubMed Central

    Witkin, S S; Bongiovanni, A M; Inglis, S R

    1997-01-01

    There is a need for a rapid, uncomplicated, and inexpensive test for Chlamydia trachomatis infection in women. We evaluated the ability of a 6-min enzyme-linked immunosorbent assay (ELISA) that requires no laboratory equipment (IgA Rapid SeroTest; Savyon Diagnostics) to detect C. trachomatis immunoglobulin A (IgA) in the endocervices of 167 inner-city pregnant women and compared the results with DNA amplification (Amplicor PCR; Roche Diagnostics) and antigen detection (Chlamydiazyme; Abbott Laboratories) performed on the same women. Anti-C. trachomatis IgA was detected in the cervices of 32 women (19.2%). Samples from 23 women (13.8%) were PCR positive, while chlamydial antigen was present in 20 women (12.0%). There was only 1 sample (4.3%) that was positive by PCR but negative by ELISA; 10 samples were ELISA positive and PCR negative. In contrast, seven samples (30.4%) were PCR positive but Chlamydiazyme negative and four were Chlamydiazyme positive and PCR negative. Compared to PCR, the IgA ELISA had a sensitivity of 95.7%, a specificity of 93.1%, a positive predictive value of 68.8%, and a negative predictive value of 99.3%. The antigen assay had a sensitivity of only 69.6%, a specificity of 97.2%, a positive predictive value of 80.0%, and a negative predictive value of 95.2%. In high-risk groups where laboratory testing is not available, or where the patient might not return to obtain her testing result and be treated, the Rapid IgA SeroTest is a viable alternative for detection of cervical C. trachomatis in pregnant women. PMID:9196193

  14. Abbott RealTime PCR assay is useful for evaluating virological response to antiviral treatment for chronic hepatitis C.

    PubMed

    Ikezaki, Hiroaki; Furusyo, Norihiro; Ihara, Takeshi; Hayashi, Takeo; Ogawa, Eiichi; Toyoda, Kazuhiro; Taniai, Hiroaki; Kainuma, Mosaburo; Murata, Masayuki; Hayashi, Jun

    2011-12-01

    This study was done to evaluate the utility of the Abbott RealTime PCR assay (ART) for the monitoring of chronic hepatitis C patients. The serum samples of 183 patients infected with hepatitis C virus (HCV) genotype 1b who had completed a 48-week period of pegylated interferon (PEG-IFN) alpha-2b plus ribavirin treatment were prospectively analyzed. Serum HCV RNA levels were measured both by ART and by the Roche COBAS Amplicor Monitor test, version2.0 (CAM) at baseline and at weeks 4, 12, 24, 36, and 48 of treatment, and at 24 weeks after the end of treatment (EOT). A significant positive correlation of pretreatment HCV RNA levels was found between ART and CAM (r = 0.595, P < 0.0001). Of the 183 patients, 66 (36.0%) achieved a sustained virological response (SVR). The logarithmic decline of the HCV RNA level from the pretreatment level determined by ART in SVR patients was significantly higher than that in non-SVR patients at all time points tested. The logarithmic decline determined by CAM in SVR patients was significantly higher than that in non-SVR patients only at week 4, but there was no significant difference at other weeks. Of 124 patients who were HCV RNA-negative at EOT by ART, 58 (46.8%) had a relapse of viremia at 24 weeks after EOT, whereas 77 of 143 patients (53.8%) who were HCV RNA-negative at EOT by CAM had a relapse. The relapse rate was lower when determined by ART than by CAM, but not significantly so. ART is more useful than CAM for evaluating the virological response to antiviral treatment for chronic hepatitis C. PMID:21528383

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-08-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2005-01-01

    The follow up of patients with chronic liver diseases and the data from multicentric clinical studies are affected by the variability of assay results for the same parameter between the different laboratories. Today, the main objective in clinical chemistry throughout the world is to harmonise the assay results between the laboratories after the confirmation of their traceability, in relation to defined reference systems. In this context, the purpose of our study was to verify the homogeneity of haptoglobin, apolipoprotein A1, total bilirubin, GGT activity, ALAT activity results, which are combined in Fibrotest and Actitest, between Dimension Analysers RXL, ARX and X-PAND (Dade Behring Society). Moreover, we verified the transferability of Fibrotest and Actitest results between the RXL, and either the BN2 (haptoglobin and apolipoprotein A1) or the Modular DP (total bilirubin, GGT and ALAT activity concentrations). The serum samples from 150 hospitalised patients were analysed on the different analysers. Specific protein assays were calibrated using solutions standardised against reference material on Dimension and BN2 analysers. Total bilirubin assays were performed by a diazoreaction on Dimension and Modular DP analysers. The GGT and ALAT activity measurements on the Dimension analysers were performed in accordance with the reference methods defined by the International Federation of Clinical Chemisty and Laboratory Medicine (IFCC). On the Modular, enzyme activity measurements were performed according to the Szasz method (L-gamma- glutamyl-4-nitroanilide as substrate) modified by Persijn and van der Slik (L-gamma- glutamyl-3-carboxy- 4-nitroanilide as substrat) for GGT and according to the IFCC specifications for ALAT. The methods of enzymatic activity measurement were calibrated on the Modular only. Liver fibrosis and necroinflammatory activity indices were determined using calculation algorithms, after having adjusted each component's result of Fibrotest and Actitest for gender and age. Our study has shown, for each parameter, harmonious results between the Dimension analysers and between RXL and BN2- Modular DP. Disregarding alpha-2 macroglobulin which cannot be assayed on RXL, the results of Fibrotest and Actitest were similar as performed on BN2- Modular DP and RXL. PMID:15951262

  19. 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. PMID:22154424

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

    PubMed

    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. PMID:25381805

  1. 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. PMID:17600936

  2. The Diaphragm and Lubricant Gel for Prevention of Cervical Sexually Transmitted Infections: Results of a Randomized Controlled Trial

    PubMed Central

    Ramjee, Gita; van der Straten, Ariane; Chipato, Tsungai; de Bruyn, Guy; Blanchard, Kelly; Shiboski, Stephen; Cheng, Helen; Montgomery, Elizabeth; Padian, Nancy

    2008-01-01

    Background We evaluated the effectiveness of the Ortho All-Flex Diaphragm, lubricant gel (Replens®) and condoms compared to condoms alone on the incidence of chlamydial and gonococcal infections in an open-label randomized controlled trial among women at risk of HIV/STI infections. Methods We randomized 5045 sexually-active women at three sites in Southern Africa. Participants who tested positive for curable STIs were treated prior to enrollment as per local guidelines. Women were followed quarterly and tested for Chlamydia trachomatis (CT) or Neisseria gonorrhoeae (GC) infection by nucleic-acid amplification testing (Roche Amplicor®) using first-catch urine specimens. STIs detected at follow-up visits were treated. We compared the incidence of first infection after randomization between study arms in both intent-to-treat (ITT) and per-protocol populations. Findings Baseline demographic, behavioral and clinical characteristics were balanced across study arms. Nearly 80% of participants were under 35 years of age. Median follow-up time was 21 months and the retention rate was over 93%. There were 471 first chlamydia infections, 247 in the intervention arm and 224 in the control arm with an overall incidence of 6.2/100 woman-years (wy) (relative hazard (RH) 1.11, 95% Confidence Interval (CI): 0.93–1.33; p = 0.25) and 192 first gonococcal infections, 95 in the intervention arm and 97 in the control arm with an overall incidence of 2.4/100wy (RH 0.98, 95%CI: 0.74–1.30; p = 0.90). Per protocol results indicated that when diaphragm adherence was defined as “always use” since the last visit, there was a significant reduction in the incidence of GC infection among women randomized to the intervention arm (RH 0.61, 95%CI: 0.41–0.91, P = 0.02). Interpretation There was no difference by study arm in the rate of acquisition of CT or GC. However, our per-protocol results suggest that consistent use of the diaphragm may reduce acquisition of GC. Trial

  3. 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.

  4. Comparing Abbott m2000 RealTime HIV test and Roche COBAS Ampliprep/COBAS Taqman HIV test, v2.0 in treated HIV-1 B and non-B subjects with low viraemia.

    PubMed

    Margariti, Apostolia; Chatzidimitriou, Dimitrios; Metallidis, Simeon; Pilalas, Dimitrios; Kourelis, Andreas; Papadimitriou, Evangelia; Haidich, Anna-Bettina; Malisiovas, Nicolaos; Skoura, Lemonia

    2016-04-01

    Viral load testing is a valuable tool in HIV clinical care and research. Discrepancies among diverse viral load assays, especially with regard to non-B HIV-1 subtypes have been reported. Our study aimed to explore the impact of HIV subtype (B versus non-B) on the agreement between CAP/CTM, v2.0 and m2000 RealTime in treated HIV patients, focusing on low viral loads (<200 copies/ml). Our findings indicate that there is a significant difference in the performance of the compared assays in the low-viremic range and non-B subtypes, suggesting that a single assay should be used for follow-up. PMID:26331699

  5. Les amas sulfurés du massif miocène d'El Aouana (Algérie)— I. Dynamisme de mise en place des roches volcaniques et implications métallogéniques

    NASA Astrophysics Data System (ADS)

    Villemaire, Cl.

    Two main units have been distinguished in the Miocene El Aouana area. A tectonic event occurs between their respective deposits inducing faulting, tilting of the lower volcanic unit and caldeira structure. The lower unit comprises first continental air fall pyroclastic rocks and dacitic flows, then marine flow pyroclastic rocks, dacitic flows and epiclastic rocks. The upper volcanic unit, announced by extensive andesitic flows, is characterized by pyroclastic flow sheets. The two units are intruded by dacitic domes. These volcanic rocks belong to the calco-alcaline succession, with well-expressed acidic terms. The ore deposits are formed by lenses, stockworks and lodes. They are massive sulphides ore type. Mineralizations are strictly localized at the contact boundary between dacitic intrusive rocks and marine pyroclastic flows and epiclastic rocks. We suggest that the systematic research of dacitic domes would be successful to increase the mining reserves of this area.

  6. Présence de sills de roches ignées acides dans la mine Sb-Au de Ribeiro da Serra, district Dúrico-Beirão, Nord Portugal. Implications métallogéniques

    NASA Astrophysics Data System (ADS)

    Couto, Helena; Roger, Guy; Fonteilles, Michel

    1999-11-01

    In the Ribeiro da Serra mine, subconcordant and locally discordant veins composed mainly of quartz and albite, hosted by the bedded sequence of the schist-greywacke complex, are interpreted as sills of albitized felsic igneous rocks. They were emplaced after major Hercynian folding, in the same faulted structure as a mineralized quartz vein, and probably only a short time before the latter. The existence of this magmatic activity supports the hypothesis of an indirect relationship between the Sb-Au veins and a hidden granitic intrusion in the Dúrico-Beirão district.

  7. 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

    2016-09-01

    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. PMID:27602422

  8. Benefit of hepatitis C virus core antigen assay in prediction of therapeutic response to interferon and ribavirin combination therapy.

    PubMed

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

    2005-01-01

    A highly sensitive second-generation hepatitis C virus (HCV) core antigen assay has recently been developed. We compared viral disappearance and first-phase kinetics between commercially available core antigen (Ag) assays, Lumipulse Ortho HCV Ag (Lumipulse-Ag), and a quantitative HCV RNA PCR assay, Cobas Amplicor HCV Monitor test, version 2 (Amplicor M), to estimate the predictive benefit of a sustained viral response (SVR) and non-SVR in 44 genotype 1b patients treated with interferon (IFN) and ribavirin. HCV core Ag negativity could predict SVR on day 1 (sensitivity = 100%, specificity = 85.0%, accuracy = 86.4%), whereas RNA negativity could predict SVR on day 7 (sensitivity = 100%, specificity = 87.2%, accuracy = 88.6%). None of the patients who had detectable serum core Ag or RNA on day 14 achieved SVR (specificity = 100%). The predictive accuracy on day 14 was higher by RNA negativity (93.2%) than that by core Ag negativity (75.0%). The combined predictive criterion of both viral load decline during the first 24 h and basal viral load was also predictive for SVR; the sensitivities of Lumipulse-Ag and Amplicor-M were 45.5 and 47.6%, respectively, and the specificity was 100%. Amplicor-M had better predictive accuracy than Lumipulse-Ag in 2-week disappearance tests because it had better sensitivity. On the other hand, estimates of kinetic parameters were similar regardless of the detection method. Although the correlations between Lumipulse-Ag and Amplicor-M were good both before and 24 h after IFN administration, HCV core Ag seemed to be relatively lower 24 h after IFN administration than before administration. Lumipulse-Ag seems to be useful for detecting the HCV concentration during IFN therapy; however, we still need to understand the characteristics of the assay. PMID:15634970

  9. The phosphatic crusts from basalts of the Abrolhos Archipelago (Bahia, Brazil): rocks formed from guanos during the Late QuaternaryLes croûtes phosphatées des basaltes de l'archipel d'Abrolhos (Bahia, Brésil) : des roches formées au Quaternaire récent à partir de guanos

    NASA Astrophysics Data System (ADS)

    Flicoteaux, René; Melfi, Adolpho

    2000-02-01

    Basalts from the Abrolhos Archipelago are capped (1) by argilloferruginous saprolite formed under intense weathering conditions at the expense of the basalts and (2) by phosphatic leucophosphite and variscite-rich crusts developed at the expense of both saprolite and basalts. Phosphorus, as indicated by the associated organic compounds, is provided by the leaching of nitrogenous guanos. In the Siriba Island, the crusts affecting the basalts are overlain by a conglomerate related to the Quaternary transgressive-regressive phase at 5 100 years BP. Therefore, the leaching of the guanos certainly began before the transgression.

  10. Nouvelles données pétrographiques, géochimiques et géochronologiques du massif 'granitique' de Bondoukou (Côte d'Ivoire) mise en évidence d'un âge Burkinien, par isochrone Rb/Sr sur roches totales

    NASA Astrophysics Data System (ADS)

    Toure, S.; Caen-Vachette, M.; Tempier, P.

    The locality of Bondoukou, NE of Ivory Coast, gave its name to a granite type, opposite to the Baoulé-type granite in Bodin's classification (1951, Bull. Dir. Mines AOF, Dakar, N° 12). This classification has been progressively enlarged to the whole of West Africa. The Bondoukou granite is subcircular in form, intrusive and discordant in the tufaceous schists and had not been dated previously. Recent age determinations on 15 samples from this massif have been done with the Rb/Sr isochron method on whole rocks. The age obtained is approx. 2170 Ma. Consequently, these new data yield a Burkinian age (ex early Eburnean) which was not expected since a lot of works on Birrimian granites of West Africa assigned a post tectonic character and consequently a later age to the Bondoukou granite, related to the Baoulé-type granites. Other age determinations with the same Rb/Sr method were done on granitic massifs which were assigned to the Bondoukou type; they yielded ages slightly younger than 2000 Ma in Senegal and Burkina Faso respectively (Bassot, J. P. and Caen-Vachette, M. 1984. In: 12th coll. Inter. Géol. africaine, Bruxelles, et géol. africaine (Edited by Klerkx, J. et Michot, J.),pp. 191-209. Tervuren, Belgique; and Gamsonre, P. E. and Rossy, M. 1974. Esquisse géologique de la région de Ouahi Gouya (N. W. de la Hte Volta). Chronologie des divers types de granitoîdes, p. 181. 2ème Rast, Nancy). So, these few results point out the complex position of the Bondoukou type granites. Their meaning in the main Eburnean orogeny must be considered.

  11. The Cobas® EGFR Mutation Test v2 assay.

    PubMed

    Brown, Paul

    2016-02-01

    Paul Brown speaks to Gemma Westcott, Commissioning Editor: Paul Brown has served as the Head of Roche Molecular Diagnostics at Roche Diagnostics Corporation since February 2010 having previously held a variety of positions within Roche Pharma. After completing his doctorate in organic chemistry he was awarded a post-doctoral fellowship at the California Institute of Technology in Pasadena, CA, USA, but soon returned to his native UK to join Roche Pharma Research. Paul's first post within Roche was as group leader, doing drug discovery and making new small molecule drugs, but later moved into the business part of the company. Since then, he has enjoyed roles such as lifecycle leader for brands such as Tamiflu(®) and Xenical, vice president of sales and marketing of the pharmaceutical division and most recently general manager of Roche Pharma, Sweden. PMID:26838018

  12. Choosing, Creating and Using Story Problems: Some Helpful Hints

    ERIC Educational Resources Information Center

    Roche, Anne

    2013-01-01

    In this article Anne Roche describes some of the different types of story problems defined in the Cognitively Guided Instruction professional development program. Teachers will find the table reproduced on page 32 to be very helpful in designing word problems. Roche then gives some suggestions for improving the way division stories are used in the…

  13. 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…

  14. 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...

  15. Chemiluminescence enzyme immunoassay for monitoring hepatitis C virus core protein during interferon-alpha2b and ribavirin therapy in patients with genotype 1 and high viral loads.

    PubMed

    Enomoto, Masaru; Nishiguchi, Shuhei; Tamori, Akihiro; Kohmoto, Modoka; Habu, Daiki; Sakaguchi, Hiroki; Takeda, Tadashi; Kawada, Norifumi; Seki, Shuichi; Shiomi, Susumu

    2005-09-01

    This study evaluated an updated chemiluminescence enzyme immunoassay (CLEIA) for hepatitis C virus (HCV) core protein for monitoring viral kinetics during treatment with interferon (IFN)-alpha and ribavirin. Using the CLEIA, serum levels of HCV core protein were measured in 17 patients with genotype 1 and high baseline viral loads during the first 4 weeks of combination therapy. HCV RNA was measured by the Amplicor Monitor test for comparison. At the start of therapy, the median HCV level (interquartile range) was 700 (540-940) kIU/ml of viral RNA and 11,310 (5,528-14,238) fmol/L of core protein. HCV RNA was above the upper limit of the linear range of the Amplicor Monitor test in 13 of the 17 patients, while the core protein level was within the linear range of the CLEIA in all patients. During therapy, the proportion of patients with HCV levels below the cutoff values at each time point was less with the Amplicor Monitor test than with CLEIA. Serum HCV core protein level decreased rapidly during the first 24 hr of therapy and more slowly thereafter, with median exponential decays of 1.08 and 0.046 log10/day, respectively. In the second phase, between day 1 and 28, the median decrease in HCV core protein level was higher in four patients with sustained virologic response (0.13 log10/day) than in 13 patients with no response (0.028 log10/day, P = 0.042). The wide linear range of the HCV core protein assay is appropriate for measuring viral loads during therapy with IFN-alpha and ribavirin. PMID:16032731

  16. 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

  17. 75 FR 52932 - Notice of Intent To Grant an Exclusive License; Doar, Pekuin, Sall Limited Liability Company

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-30

    ... Technology Transfer Program, 9800 Savage Road, Suite 6541, Fort George G. Meade, MD 20755-6541. FOR FURTHER INFORMATION CONTACT: Marian T. Roche, Director, Technology Transfer Program, 9800 Savage Road, Suite...

  18. 1st HPV Test for Use with Preservative Fluid

    MedlinePlus

    ... https://medlineplus.gov/news/fullstory_159789.html 1st HPV Test for Use With Preservative Fluid Human papillomavirus ... Food and Drug Administration has approved Roche's cobas HPV Test -- the first diagnostic to be used with ...

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

    ERIC Educational Resources Information Center

    Roche, Anne; Clarke, Doug

    2014-01-01

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

  20. On the origin of X-ray variability of SS 433

    NASA Technical Reports Server (NTRS)

    Band, D. L.; Grindlay, J. E.

    1984-01-01

    The X-ray flares observed from the central source in SS 433 by the Einstein telescope are attributed to surges in the mass transfer rate due to changes in the critical Roche volume of the companion. Analysis of the Roche potential for a primary with spin misaligned with the orbital axis, as required by the slaved disk model, predicts that the critical Roche volume will contract twice per orbit if the orbit is circular. A critical Roche volume fractional change of 1-2 percent is found by applying this potential to SS 433. The nutation of the companion should not affect the steady precession of its spin. Aspects of this work strengthen the evidence that the compact object might be a black hole.

  1. 75 FR 36694 - Importer of Controlled Substances; Notice of Registration

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-28

    ..., 2010, and published in the Federal Register on March 24, 2010 (75 FR 14186), Roche Diagnostics... (7315) I Tetrahydrocannabinols (7370) I Alphamethadol (9605) I Cocaine (9041) II Ecgonine (9180)...

  2. 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.

  3. 78 FR 61358 - Mylan, Inc., Agila Specialties Global Pte. Limited, Agila Specialties Private Limited and Strides...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-03

    ... the growth of cytomegalovirus, a form of herpes virus that can lead to blindness. Currently, Roche... resort to treat serious bacterial infections in an intensive care setting. There are currently...

  4. Hepatitis C virus RNA assays: a comparison of SuperQuant and Monitor.

    PubMed

    Hadziyannis, E; Hadziyannis, A; Yen-Lieberman, B; Kiwi, M L; Hodnick, S; Spanou, F; Starkey, C; Younossi, Z M

    2001-07-01

    Hepatitis C RNA testing has been used extensively to assess the efficacy of antiviral therapy and has increasingly become an integral part of clinical management of patients with chronic hepatitis C. A variety of commercially available hepatitis C virus (HCV) RNA tests are used to detect HCV RNA qualitatively or quantitatively. These commercial tests have fundamental differences that are reflected on the values they generate. We compared two widely used assays, HCV SuperQuant (SQ) and Amplicor HCV Monitor (M1 and M2), in sera of patients with chronic hepatitis C. A total of 506 sera from 79 patients were tested with both assays. The data were logarithmically transformed and analyzed by linear regression and measurement of agreement. Two hundred thirty-eight sera had HCV RNA values within the dynamic range of both assays. The correlation between the assays was fair, with a correlation coefficient (r) of 0.699. Overall, SQ generated higher values than M1 with a mean difference of 0.558 log (SD = 0.624). One hundred ninety-four (38%) and 121 (24%) of the sera were below the dynamic range of M1 and SQ, respectively. Seventy-three sera, undetectable by M1, were positive by SQ. The Amplicor HCV Monitor 2.0 (M2) was performed in 66 sera. All were positive by SQ and M2, but only 38 were within the dynamic range of M1. The correlations between these tests were good (r = 0.68-0.78), but the agreement was rather poor. In conclusion, this study confirms that both SQ and M2 are more sensitive than M1. Additionally, our results show rather poor agreements between these assays. The recent attempts in standardizing the reporting of these assays should make their results more easily interchangeable. PMID:11418790

  5. 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

  6. 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. PMID:26851121

  7. A comparison between two different automated total 25-hydroxyvitamin D immunoassay methods using liquid chromatography-tandem mass spectrometry

    PubMed Central

    Kocak, Fatma Emel; Ozturk, Bahadir; Isiklar, Ozben Ozden; Genc, Ozlem; Unlu, Ali; Altuntas, Irfan

    2015-01-01

    Introduction Total 25-hydroxyvitamin D [25(OH)D] is the most reliable indicator of vitamin D status. In this study, we compared two automated immunoassay methods, the Abbott Architect 25-OH Vitamin D assay and the Roche Cobas Vitamin D total assay, with the liquid chromatography-tandem mass spectrometry (LC-MS/MS). Materials and methods One hundred venous blood samples were randomly selected from routine vitamin D tests. Two of the serum aliquots were analyzed at the Abbott Architect i2000 and the Roche Cobas 6000’s module e601 in our laboratory within the same day. The other serum aliquots were analyzed at the LC-MS/MS in different laboratory. Passing-Bablok regression analysis and Bland-Altman plot were used to compare methods. Inter-rater agreement was analyzed using kappa (κ) analysis. Results The Roche assay showed acceptable agreement with the LC-MS/MS based on Passing-Bablok analysis (intercept: -5.23 nmol/L, 95% CI: -8.73 to 0.19; slope: 0.97, 95% CI: 0.77 to 1.15). The Abbott assay showed proportional (slope: 0.77, 95% CI: 0.67 to 0.85) and constant differences (intercept: 17.08 nmol/L; 95% CI: 12.98 to 21.39). A mean bias of 15.1% was observed for the Abbott and a mean bias of -14.1% was observed for the Roche based on the Bland-Altman plots. We found strong to nearly perfect agreement in vitamin D status between the immunoassays and LC-MS/MS. (κ: 0.83 for Abbott, κ: 0.93 for Roche) using kappa analysis. Conclusion Both immunoassays demonstrated acceptable performance, but the Roche Cobas assay demonstrated better performance than the Abbott Architect in the studied samples. PMID:26526462

  8. Listening Walks and Singing Maps

    ERIC Educational Resources Information Center

    Cardany, Audrey Berger

    2011-01-01

    The Listening Walk by Paul Showers and illustrated by Aliki, and "It's My City: A Singing Map" by April Pulley Sayre with pictures by Denis Roche, provide two examples of texts that aid in building children's phonological awareness for reading and music. The author describes each narrative and discusses its function as a springboard to composition…

  9. 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)

  10. 78 FR 64232 - Notice of Adjustment of Disaster Grant Amounts

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-28

    ... SECURITY Federal Emergency Management Agency Notice of Adjustment of Disaster Grant Amounts AGENCY: Federal Emergency Management Agency, DHS. ACTION: Notice. SUMMARY: FEMA gives notice of an increase of the maximum... Roche, Recovery Directorate, Federal Emergency Management Agency, 500 C Street SW., Washington, DC...

  11. 78 FR 25259 - Notice of Intent To Grant an Exclusive License; Integrata Security, LLC

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-30

    ... filed with the National Security Agency Technology Transfer Program, 9800 Savage Road, Suite 6848, Fort George G. Meade, MD 20755-6848. FOR FURTHER INFORMATION CONTACT: Marian T. Roche, Director, Technology Transfer Program, 9800 Savage Road, Suite 6848, Fort George G. Meade, MD 20755-6848, telephone (443)...

  12. 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...

  13. 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...

  14. Comparison of Two Commercial Automated Nucleic Acid Extraction and Integrated Quantitation Real-Time PCR Platforms for the Detection of Cytomegalovirus in Plasma

    PubMed Central

    Tsai, Huey-Pin; Tsai, You-Yuan; Lin, I-Ting; Kuo, Pin-Hwa; Chen, Tsai-Yun; Chang, Kung-Chao; Wang, Jen-Ren

    2016-01-01

    Quantitation of cytomegalovirus (CMV) viral load in the transplant patients has become a standard practice for monitoring the response to antiviral therapy. The cut-off values of CMV viral load assays for preemptive therapy are different due to the various assay designs employed. To establish a sensitive and reliable diagnostic assay for preemptive therapy of CMV infection, two commercial automated platforms including m2000sp extraction system integrated the Abbott RealTime (m2000rt) and the Roche COBAS AmpliPrep for extraction integrated COBAS Taqman (CAP/CTM) were evaluated using WHO international CMV standards and 110 plasma specimens from transplant patients. The performance characteristics, correlation, and workflow of the two platforms were investigated. The Abbott RealTime assay correlated well with the Roche CAP/CTM assay (R2 = 0.9379, P<0.01). The Abbott RealTime assay exhibited higher sensitivity for the detection of CMV viral load, and viral load values measured with Abbott RealTime assay were on average 0.76 log10 IU/mL higher than those measured with the Roche CAP/CTM assay (P<0.0001). Workflow analysis on a small batch size at one time, using the Roche CAP/CTM platform had a shorter hands-on time than the Abbott RealTime platform. In conclusion, these two assays can provide reliable data for different purpose in a clinical virology laboratory setting. PMID:27494707

  15. 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…

  16. Last Rites for Cataclysmic Variables: Death by Fire, or Ice? (Abstract)

    NASA Astrophysics Data System (ADS)

    Patterson, J.

    2016-06-01

    (Abstract only) Cataclysmic binaries lose angular momentum as they age, and thus the component stars in the binary spiral ever closer together. As the spiraling-in proceeds, the shrinking Roche lobe "strangles" the donor star, forcing it to transfer mass. Since we can measure the rate of mass transfer pretty well, we know the rate of angular momentum loss pretty well.

  17. Analysis of genetic diversity using SNP markers in oat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A large-scale single nucleotide polymorphism (SNP) discovery was carried out in cultivated oat using Roche 454 sequencing methods. DNA sequences were generated from cDNAs originating from a panel of 20 diverse oat cultivars, and from Diversity Array Technology (DArT) genomic complexity reductions fr...

  18. 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...

  19. 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 ...

  20. Catholic Schools as Schools of Academic Excellence: A Summary of the Third Catholic Higher Education Collaborative Conference Proceedings

    ERIC Educational Resources Information Center

    Weitzel-O'Neill, Patricia; Torres, Aubrey Scheopner

    2011-01-01

    This article summarizes the content and outcomes of the third Catholic Higher Education Collaborative Conference (CHEC), cosponsored by the Roche Center for Catholic Education at Boston College and the Center for Catholic School Leadership at Fordham University. The conference focused on how Catholic higher education can assist in developing and…

  1. 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…

  2. Next generation sequencing of crown and rhizome transcriptome from an upland, tetraploid switchgrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The crown and rhizome transcriptome of a winter-adapted, upland tetraploid switchgrass cultivar Summer, was investigated using the Roche 454-FLX pyrosequencing platform. In all approximately 1 million reads consisting of 216 million bases were assembled into 27,687 contigs and 43,094 singletons. A...

  3. EFFECT OF ZINC EXPOSURE ON SUBSEQUENT ACUTE TOLERANCE TO HEAVY METALS IN RAINBOW TROUT

    EPA Science Inventory

    Fish usually show increased tolerance to metals in solution if proviously given an opportunity to acclimate to near lethal concentrations of the metal (Dixon and Sprngue 1981a; McCarter and Roch 1983; Bradley et al. 1985; Chapman 1985), and tolerence has been correlated with an i...

  4. 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.…

  5. 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...

  6. Do Items that Measure Self-Perceived Physical Appearance Function Differentially across Gender Groups? An Application of the MACS Model

    ERIC Educational Resources Information Center

    Gonzalez-Roma, Vicente; Tomas, Ines; Ferreres, Doris; Hernandez, Ana

    2005-01-01

    The aims of this study were to investigate whether the 6 items of the Physical Appearance Scale (Marsh, Richards, Johnson, Roche, & Tremayne, 1994) show differential item functioning (DIF) across gender groups of adolescents, and to show how this can be done using the multigroup mean and covariance structure (MG-MACS) analysis model. Two samples…

  7. 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

  8. 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.

  9. 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...

  10. Ultra high-throughput nucleic acid sequencing as a tool for virus discovery in the turkey gut.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recently, the use of the next generation of nucleic acid sequencing technology (i.e., 454 pyrosequencing, as developed by Roche/454 Life Sciences) has allowed an in-depth look at the uncultivated microorganisms present in complex environmental samples, including samples with agricultural importance....

  11. Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content and rearrangements revealed by next generation sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete plastid genome sequence of the American cranberry was reconstructed using next-generation sequencing data by in silico procedures. We used Roche 454 shotgun sequence data to isolate cranberry plastid-specific sequences of the cultivar ‘HyRed’ via homology comparisons with complete seque...

  12. 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…

  13. Spiral concentrators recover fine coal

    SciTech Connect

    Fiscor, S.

    2005-12-15

    Compound spirals offer better performance in a more efficient configuration. Prep plant operators in the US are increasingly opting to use spiral concentrators. They are easy to install, operate and maintain but their downfall is low capacity. The article describes spirals available from PrepTech/Multotec, Krebs Engineers and Roche MT. It reports on research on spiral concentrator technology. 1 ref., 4 figs.

  14. 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,…

  15. 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...

  16. The gene space in wheat: the complete y-gliadin gene family from the wheat cultivar Chinese Spring

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete set of unique y-gliadin genes is described for the wheat cultivar Chinese Spring using a combination of EST and Roche 454 DNA sequences. Assemblies of Chinese Spring ESTs yielded eleven different gamma-gliadin gene sequences. Two of the sequences encode identical polypeptides and are ...

  17. Reach for the stars: education & public outreach special

    NASA Astrophysics Data System (ADS)

    2007-08-01

    Over the next 15 pages we present a snapshot of current astronomy outreach programmes, targeting schools, children and adults, by means of observatories, robotic telescopes, podcasts and more. Much of this activity was presented and discussed at the National Astronomy Meeting this year in Preston, in a well-attended session organized by Paul Roche and Carolina Ödman.

  18. Nonlinear Time Series Analysis via Neural Networks

    NASA Astrophysics Data System (ADS)

    Volná, Eva; Janošek, Michal; Kocian, Václav; Kotyrba, Martin

    This article deals with a time series analysis based on neural networks in order to make an effective forex market [Moore and Roche, J. Int. Econ. 58, 387-411 (2002)] pattern recognition. Our goal is to find and recognize important patterns which repeatedly appear in the market history to adapt our trading system behaviour based on them.

  19. Transcriptome sequencing to produce a SNP-based genetic map of onion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sequencing the onion genome is challenging because of its enormous size (16 giga base pairs DNA per haploid genome). Pilot sequencing of onion transcripts showed sufficient numbers of single nucleotide polymorphisms (SNPs) to develop a detailed genetic map. We sequenced 2.5 Roche-454 plates of norma...

  20. Evaluation of New Quantitative Assays for Diagnosis and Monitoring of Cytomegalovirus Disease in Human Immunodeficiency Virus-Positive Patients

    PubMed Central

    Pellegrin, Isabelle; Garrigue, Isabelle; Binquet, Christine; Chene, Genevieve; Neau, Didier; Bonot, Pascal; Bonnet, Fabrice; Fleury, Herve; Pellegrin, Jean-Luc

    1999-01-01

    Cobas Amplicor CMV Monitor (CMM) and Quantiplex CMV bDNA 2.0 (CMV bDNA 2.0), two new standardized and quantitative assays for the detection of cytomegalovirus (CMV) DNA in plasma and peripheral blood leukocytes (PBLs), respectively, were compared to the CMV viremia assay, pp65 antigenemia assay, and the Amplicor CMV test (P-AMP). The CMV loads were measured in 384 samples from 58 human immunodeficiency virus (HIV) type 1-infected, CMV-seropositive subjects, including 13 with symptomatic CMV disease. The assays were highly concordant (agreement, 0.88 to 0.97) except when the CMV load was low. Quantitative results for plasma and PBLs were significantly correlated (Spearman ρ = 0.92). For PBLs, positive results were obtained 125 days before symptomatic CMV disease by CMV bDNA 2.0 and 124 days by pp65 antigenemia assay, whereas they were obtained 46 days before symptomatic CMV disease by CMM and P-AMP. At the time of CMV disease diagnosis, the sensitivity, specificity, and positive and negative predictive values of CMV bDNA 2.0 were 92.3, 97.8, 92.3, and 97.8%, respectively, whereas they were 92.3, 93.3, 80, and 97.8%, respectively, for the pp65 antigenemia assay; 84.6, 100, 100, and 95.7%, respectively, for CMM; and 76.9, 100, 100, and 93.8%, respectively, for P-AMP. Considering the entire follow-up, the sensitivity, specificity, and positive and negative predictive values of CMV bDNA 2.0 were 92.3, 73.3, 52.1, and 97.1%, respectively, whereas they were 100, 55.5, 39.4, and 100%, respectively, for the pp65 antigenemia assay; 92.3, 86.7, 66.7, and 97.5%, respectively, for CMM; and 84.6, 91.1, 73.3, and 95.3%, respectively, for P-AMP. Detection of CMV in plasma is technically easy and, despite its later positivity (i.e., later than in PBLs), can provide enough information sufficiently early so that HIV-infected patients can be effectively treated. In addition, these standardized quantitative assays accurately monitor the efficacy of anti-CMV treatment. PMID:10488165

  1. 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}.

  2. Evaluation of in-house polymerase chain reaction assay sensitivity, can it be utilized in limited-resources settings?

    PubMed Central

    Dorudinia, Atosa; Shamaei, Masoud; Karimi, Shirin; Javadi, Alireza; Mohammadi Ziazi, Leila; Pourabdollah, Mihan

    2014-01-01

    Background: Polymerase chain reaction (PCR) assay has widely used for the detection of tuberculosis (TB). This study tried to compare in-house PCR with some well-known commercial PCR kits for detection of TB agent. Methods: Clinical samples obtained from 620 TB suspected patients were analyzed for the diagnosis of Mycobacterium tuberculosis complex (MTC) by in-house PCR. All samples were obtained through pulmonary specimens consisted of 384 sputum, 148 bronchial aspirates and 88 pleural effusions. Results: Considering culture as a golden criterion, in which its diagnostic sensitivity and specificity of PCR assay were 87.7% and 85.6%, respectively. The findings of this study also indicate 22.1% (137/620) of the specimens were detected as MTC by PCR. Both PCR and culture confirmed presence of MTC in 57 of the samples. In comparison to culture, the diagnostic sensitivity of PCR for sputum was 87.5% (42/48), bronchial aspirates 100% (12/12), and 60% (3/5) for pleural effusions. The sensitivity of in-house PCR method is comparable with the sensitivity of Amplicor and Cobas TaqMan for MTC. Conclusion: The study illustrates the in-house PCR assay for detection of MTC has high sensitivity and specificity versus approved commercial kits. This could be reliable test in the diagnosis of MTC in resource-limited countries. PMID:25679005

  3. Responding to pandemic (H1N1) 2009 influenza: the role of oseltamivir

    PubMed Central

    Reddy, David

    2010-01-01

    Pandemic (H1N1) 2009 influenza is affecting countries in all five continents, with most cases so far having been reported in North and South America and Europe, and children and young adults being the most susceptible age groups. To date, the clinical course of disease is typically mild, with low hospitalization and mortality rates. Pandemic (H1N1) 2009 is susceptible to oseltamivir and, although few clinical data are yet available, current information suggests that treatment with oseltamivir appears to be beneficial. Only isolated cases of resistance to the drug have been reported to date, in keeping with the low frequency observed in clinical studies involving patients infected with seasonal influenza viruses. Current health authority guidelines recommend the use of oseltamivir in infected adults and children who have or are at elevated risk for severe disease, including pregnant women; use during the pandemic in infants <1 year has also been authorized in Europe and a number of other countries, including the USA and Canada. Before the onset of the current pandemic, F. Hoffmann-La Roche Ltd expanded annual production capacity for oseltamivir to 400 million treatment courses per year to meet anticipated demand. However, during an influenza pandemic, and despite increased production capabilities, resources are nonetheless likely to be initially in short supply. For this reason, Roche, in line with WHO recommendations, has advocated advance stockpiling of antivirals by governments as a pandemic preparedness measure. Between 2004 and December 2009, 350 million treatment courses were supplied to governments worldwide. Support for developing countries has been a priority. Roche has established a cluster of initiatives aimed at increasing access to Tamiflu for the world's developing economies, including, making donations to the WHO, establishing the Tamiflu Reserves Program (TRP) and sub-licensing and manufacturing contracts with local companies in Asia and Africa

  4. Small-scale lunar farside volcanism

    NASA Astrophysics Data System (ADS)

    Pasckert, Jan Hendrik; Hiesinger, Harald; van der Bogert, Carolyn H.

    2015-09-01

    We identified and mapped 28 mare basalt occurrences, between the Australe and South Pole-Aitken basins on the southern lunar farside, and determined their absolute model ages (AMAs) by performing crater size-frequency distribution (CSFD) measurements. Our study area can be subdivided into seven major mare basalt occurrences in and around Bolyai, Roche V, Rosseland, Pauli, and Roche craters, south of both Rosseland and Coblentz craters, as well as mare patches between Eötvös and Roche craters. The AMAs of the mare basalts in and around Bolyai crater range from 2.1 Ga to 3.5 Ga (two units), varying drastically within short distances. The mare patches south of Coblentz crater contain nine units that have AMAs ranging from 2.1 Ga to 3.8 Ga. The mare basalts in Roche V crater show an AMA of 2.2 Ga. We mapped seven volcanic units in Rosseland crater and derived AMAs for five of these units. The mare basalts in Rosseland crater show the youngest AMAs found in our study area, ranging from 1.5 Ga to 2.9 Ga. The mare basalt occurrence south of Rosseland crater shows significantly older ages with an AMA of 3.3 Ga. The mare basalts in Pauli and Roche craters show AMAs from 1.7 Ga to 3.1 Ga. The mare patches between Eötvös and Roche craters show a similar range of AMAs from 1.9 Ga to 3.1 Ga. The AMAs of the mare basalts in our study show that the lunar farside was volcanically active for nearly as long as the lunar nearside (1.2 Ga ago), or at least longer than previously thought (2.5 Ga ago) and predicted by models of the ascent and eruption of lunar basalts. In addition, we calculated thicknesses and volumes of the investigated mare basalts. With thicknesses between ∼21 m and ∼172 m and volumes from ∼0.1 km3 to ∼379 km3, the mare basalts in our study area show a wide range of dimensions, similar to other mare basalts of the lunar near- and farsides.

  5. VizieR Online Data Catalog: Simulations of hot gas planets atmospheres (Salz+, 2016)

    NASA Astrophysics Data System (ADS)

    Salz, M.; Czesla, S.; Schneider, P. C.; Schmitt, J. H. M. M.

    2015-11-01

    The following tables contain the simulation results from the publication. Each table contains a 1D spherically symmetric, hydrodynamically escaping thermosphere of a hot gas planet. The atmospheres contain hydrogen and helium, and no molecules. The simulations were performed with the PLUTO-CLOUDY interface (Salz et al., Cat. J/A+A/576/A21). Each table contains a header, which specifies the system parameters, that where used for the simulations. The simulation region extends to 12/15 planetary radii, but the atmospheres are only approximately valid up to the Roche-lobe height, above which the spherical approximation is invalid. The Roche-lobe height is also given in the header. In the cases of WASP-10 b and WASP-8 b the atmospheres are hydrodynamically stable and the atmospheres extend only up to the exobase defined for proton-proton scattering as given in the publication. (17 data files).

  6. Formation of Regular Satellites from Ancient Massive Rings in the Solar System

    NASA Astrophysics Data System (ADS)

    Crida, A.; Charnoz, S.

    2012-11-01

    When a planetary tidal disk—like Saturn’s rings—spreads beyond the Roche radius (inside which planetary tides prevent aggregation), satellites form and migrate away. Here, we show that most regular satellites in the solar system probably formed in this way. According to our analytical model, when the spreading is slow, a retinue of satellites appear with masses increasing with distance to the Roche radius, in excellent agreement with Saturn’s, Uranus’, and Neptune’s satellite systems. This suggests that Uranus and Neptune used to have massive rings that disappeared to give birth to most of their regular satellites. When the spreading is fast, only one large satellite forms, as was the case for Pluto and Earth. This conceptually bridges the gap between terrestrial and giant planet systems.

  7. SATELLITE FORMATION from ancient massive rings

    NASA Astrophysics Data System (ADS)

    Crida, Aurélien; Charnoz, Sébastien

    2013-07-01

    When a planetary tidal disk - like Saturn's rings - spreads beyond the Roche radius (inside which planetary tides prevent aggregation), satellites form and migrate away. Here, we show that most regular satellites in the solar system probably formed in this way. According to our analytical model, when the spreading is slow, a retinue of satellites appear with masses increasing with distance to the Roche radius, in excellent agreement with Saturn's, Uranus', and Neptune's satellite systems. This suggests that Uranus and Neptune used to have massive rings that disappeared to give birth to most of their regular satellites. In contrast, when the spreading is fast, only one large satellite forms, as was the case for Pluto and Earth. This conceptually bridges the gap between terrestrial and giant planet systems. (Ref: Crida & Charnoz 2012, Science, 338, 1196-1199)

  8. Tidal evolution in the Neptune-Triton system

    NASA Technical Reports Server (NTRS)

    Chyba, C. F.; Jankowski, D. G.; Nicholson, P. D.

    1989-01-01

    Triton, which is currently spiralling toward Neptune due to tides raised on both bodies, possesses an obliquity which may lie close to either a zero-deg 'state 1' or a 100-deg 'state 2' which correspond to the two stable Cassini extrema of its rotational Hamiltonian. The Kaula (1966) tidal formalism is presently used to model the past and future evolution of the system in both states. For nominal parameters in state 1, Triton will reach Neptune's Roche limit in about 3.6 Gyr with a decrease in orbital inclination to 145 deg from the current 159 deg; in the case of state 2, Triton's inclination will increase to 180 deg in 10-100 million years and then transition to state 1, subsequently reaching the Neptune Roche limit in about 1.4 Gyr.

  9. 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.

  10. On the shape of rapidly rotating stars

    NASA Astrophysics Data System (ADS)

    Zahn, J.-P.; Ranc, C.; Morel, P.

    2010-07-01

    Aims: The critical surface of a rapidly rotating star is determined, assuming that the rotation is either uniform or shellular (angular velocity constant on level surfaces, but increasing with depth). Methods: A step beyond the classical Roche model, where the entire mass is assumed to be gathered at the center of the star, here the quadrupolar moment of the mass distribution is taken into account through a linear perturbation method. Results: The flattening (defined here as the ratio between the equatorial and the polar radius) can somewhat exceed the 3/2 value of the Roche model, depending on the strength of the interior rotation. The result is applied to a star of 7 solar masses, which is the mass of Achernar, the star with the largest flattening detected so far through optical interferometry.

  11. 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. PMID:23197530

  12. Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline

    PubMed Central

    Zhao, Guoyan; Krishnamurthy, Siddharth; Cai, Zhengqiu; Popov, Vsevolod L.; Travassos da Rosa, Amelia P.; Guzman, Hilda; Cao, Song; Virgin, Herbert W.; Tesh, Robert B.; Wang, David

    2013-01-01

    Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens. PMID:24167629

  13. 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.

  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. On the Birational Invariance of the BCOV Torsion of Calabi-Yau Threefolds

    NASA Astrophysics Data System (ADS)

    Maillot, V.; Rössler, D.

    2012-04-01

    Fang et al. (J. Diff. Geom. 80(2):175-259, 2008, Sect. 4, Conj. 4.17) conjecture that a certain spectral string-theoretic invariant of Calabi-Yau threefolds (the BCOV torsion) is a birational invariant. We prove a weak form of this conjecture. The proof combines the arithmetic Riemann-Roch theorem in Arakelov geometry with some inputs from motivic integration theory.

  16. Hydrodynamical evolution of coalescing binary neutron stars

    NASA Technical Reports Server (NTRS)

    Rasio, Frederic A.; Shapiro, Stuart L.

    1992-01-01

    The hydrodynamics of the final merging of two neutron stars and the corresponding gravitational wave emission is studied in detail. Various test calculations are presented, including the compressible Roche and Darwin problems and the head-on collision of two polytropes. A complete coalescence calculation is presented for the simplest case of two identical neutron stars, represented by Gamma = 2 polytropes, in a circular orbit, with their spins aligned and synchronized with the orbital rotation.

  17. 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.

  18. Effet Hall quantique, liquides de Luttinger et charges fractionnaires

    NASA Astrophysics Data System (ADS)

    Roche, Patrice; Rodriguez, V.; Glattli, D. Christian

    We review some basic properties of the Fractional Quantum Hall Effect and particularly address the physics of the edge states. The chiral Luttinger liquid properties of the edges are discussed and probed experimentally using transport measurements. Shot noise measurements, which allow determination of the quasiparticle charge are also discussed. To cite this article: P. Roche et al., C. R. Physique 3 (2002) 717-732.

  19. 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. PMID:25151890

  20. Aspects of computer vision in surgical endoscopy

    NASA Astrophysics Data System (ADS)

    Rodin, Vincent; Ayache, Alain; Berreni, N.

    1993-09-01

    This work is related to a project of medical robotics applied to surgical endoscopy, led in collaboration with Doctor Berreni from the Saint Roch nursing-home in Perpignan, France). After taking what Doctor Berreni advises, two aspects of endoscopic color image processing have been brought out: (1) The help to the diagnosis by the automatic detection of the sick areas after a learning phase. (2) The 3D reconstruction of the analyzed cavity by using a zoom.

  1. The very short-period extreme mass ratio binary 75 Pegasi - Photometry and model

    SciTech Connect

    Martin, B.E.; Hube, D.P.; Brown, C. Alberta, University, Edmonton Glenlea Astronomical Observatory Manitoba, University, Winnipeg )

    1991-05-01

    The bright star 75 Peg is a close binary ellipsoidal variable with a short period (0.5021035-day) and an extreme mass ratio of 0.104 B, V, and R photometric data, along with previously published radial-velocity data, are analyzed; they suggest that the primary of the 75 Peg system may be, or is very close to, filling its critical Roche lobe. 11 refs.

  2. Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples.

    PubMed

    Mosher, Jennifer J; Bernberg, Erin L; Shevchenko, Olga; Kan, Jinjun; Kaplan, Louis A

    2013-11-01

    Longer sequences of the bacterial 16S rRNA gene could provide greater phylogenetic and taxonomic resolutions and advance knowledge of population dynamics within complex natural communities. We assessed the accuracy of a Pacific Biosciences (PacBio) single molecule, real time (SMRT) sequencing based on DNA polymerization, a promising 3rd generation high-throughput technique, and compared this to the 2nd generation Roche 454 pyrosequencing platform. Amplicons of the 16S rRNA gene from a known isolate, Shewanella oneidensis MR1, and environmental samples from two streambed habitats, rocks and sediments, and a riparian zone soil, were analyzed. On the PacBio we analyzed ~500 bp amplicons that covered the V1-V3 regions and the full 1500 bp amplicons of the V1-V9 regions. On the Roche 454 we analyzed the ~500 bp amplicons. Error rates associated with the isolate were lowest with the Roche 454 method (2%), increased by more than 2-fold for the 500 bp amplicons with the PacBio SMRT chip (4-5%), and by more than 8-fold for the full gene with the PacBio SMRT chip (17-18%). Higher error rates with the PacBio SMRT chip artificially inflated estimates of richness and lowered estimates of coverage for environmental samples. The 3rd generation sequencing technology we evaluated does not provide greater phylogenetic and taxonomic resolutions for studies of microbial ecology. PMID:23999276

  3. 4th European Antibody Congress 2008

    PubMed Central

    2009-01-01

    The Fourth European Antibody meeting, organized by Terrapin Ltd., was held in Geneva, a center of the European biopharmaceutical industry. Merck-Serono, NovImmune, Pierre Fabre and Therapeomic are located nearby, as are R&D centers of Boehringer-Ingelheim, Novartis, Roche and Sanofi-Aventis. Over 40 speakers and more than 200 delegates attended the event. Companies represented included Abbott, Ablynx, Adnexus/ BMS, Astra-Zeneca/ CAT/ Medimmune, BiogenIdec, BioRad, Centocor (Johnson & Johnson), Crucell/DSM, Domantis, Dyax, Genmab, Genzyme, Glycart/ Roche, Haptogen, Immunogen, Kyowa-Kirin, LFB, Medarex, Merck-Serono, Micromet, Novartis, Pierre Fabre Laboratories, Roche, Sanofi-Aventis, Seattle-Genetics, Transgene, UCB Celltech and Wyeth. Other attendees included those based in academe or government (University of Amsterdam, University of Zurich, Univeristy Hospital-Lyon, Ecole Polytechnique Federale de Lausanne, INSERM, Tufts University, US National Institutes of Health), consultants, and patent attorneys (Edwards, Angell, Palmer & Dodge). The meeting was very interactive and included exchanges during the many scheduled networking times (exhibitions, speed-networking, lunches and evening receptions). The first day of the three day conference was dedicated to advances in understanding antibody structure-function relationships. Challenges and opportunities in antibody development were the focus of the second day and the third day featured discussion of innovative antibodies and antibody alternatives. PMID:20061813

  4. Formation of Centaurs’ Rings through Their Partial Tidal Disruption during Planetary Encounters

    NASA Astrophysics Data System (ADS)

    Hyodo, Ryuki; Charnoz, Sébastien; Genda, Hidenori; Ohtsuki, Keiji

    2016-09-01

    Centaurs are minor planets orbiting between Jupiter and Neptune that have or had crossing orbits with one or more giant planets. Recent observations and reinterpretation of previous observations have revealed the existence of ring systems around 10199 Chariklo and 2060 Chiron. However, the origin of the ring systems around such a minor planet is still an open question. Here, we propose that the tidal disruption of a differentiated object that experiences a close encounter with a giant planet could naturally form diverse ring–satellite systems around the Centaurs. During the close encounter, the icy mantle of the passing object is preferentially ripped off by the planet's tidal force and the debris is distributed mostly within the Roche limit of the largest remnant body. Assuming the existence of a 20‑50 wt% silicate core below the icy mantle, a disk of particles is formed when the objects pass within 0.4–0.8 of the planet's Roche limit with the relative velocity at infinity 3‑6 km s‑1 and 8 hr initial spin period of the body. The resultant ring mass is 0.1%–10% of the central object's mass. Such particle disks are expected to spread radially, and materials spreading beyond the Roche limit would accrete into satellites. Our numerical results suggest that ring formation would be a natural outcome of such extreme close encounters, and Centaurs can naturally have such ring systems because they cross the orbits of the giant planets.

  5. 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.

  6. A Quantitative Study of S Cancri: An Algol Binary at the Terminal State of Mass Transfer

    NASA Astrophysics Data System (ADS)

    Polidan, Ronald S.

    The Algol binary S Cnc is a 9.5 day totally eclipsing system with a very low mass (0.23M(sun)) K0III-IV secondary star. The system has an extensive archive of optical data, the analysis of which argues that this system has ceased mass transfer and that the secondary is now detached from its critical Roche lobe and has an "extended atmosphere" between its photosphere and Roche lobe. Existing low S/N IUE eclipse spectra show strong emission in C IV, Si IV, Mg II and other lines. The derived luminosities in these UV lines are an order of magnitude greater than the luminosities for the most chromospherically active single or binary stars. We propose to use low and high resolution IUE spectra to investigate S Cnc in order to derive a better understanding of the origins of the UV emission lines seen during eclipse and to define the geometrical properties and physical conditions in the gas giving rise to the extended atmosphere detected near eclipse in optical spectra. These new data will advance our understanding of the mass-transfer process in the late stages of close binary-star evolution and provide the first measures of the level of chromospheric activity in the low mass, Roche-lobe-filling secondary in this system.

  7. SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching.

    PubMed

    Zhbannikov, Ilya Y; Hunter, Samuel S; Settles, Matthew L; Foster, James A

    2013-08-01

    With the advent of Next-Generation (NG) sequencing, it has become possible to sequence a entire genomes quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or characterizing exomes. With the raw DNA-library of a complete genome it would appear to be a trivial problem to identify reads of interest. But it is not always easy to incorporate well-known tools such as BLAST, BLAT, Bowtie, and SOAP directly into a bioinformatics pipelines before the assembly stage, either due to incompatibility with the assembler's file inputs, or because it is desirable to incorporate information that must be extracted separately. For example, in order to incorporate flowgrams from a Roche 454 sequencer into the Newbler assembler it is necessary to first extract them from the original SFF files. We present SlopMap, a bioinformatics software utility that allows quickly identification similar to the provided reference reads from either Roche 454 or Illumnia DNA library. With simple and intuitive command-line interface along with file output formats compatible to assembly programs, SlopMap can be directly embedded to biological data processing pipeline without any additional programming work. In addition, SlopMap preserves flowgram information needed for Roche 454 assembler. PMID:24404406

  8. SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching

    PubMed Central

    Zhbannikov, Ilya Y.; Hunter, Samuel S.; Settles, Matthew L.; Foster, James A.

    2013-01-01

    With the advent of Next-Generation (NG) sequencing, it has become possible to sequence a entire genomes quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or characterizing exomes. With the raw DNA-library of a complete genome it would appear to be a trivial problem to identify reads of interest. But it is not always easy to incorporate well-known tools such as BLAST, BLAT, Bowtie, and SOAP directly into a bioinformatics pipelines before the assembly stage, either due to incompatibility with the assembler’s file inputs, or because it is desirable to incorporate information that must be extracted separately. For example, in order to incorporate flowgrams from a Roche 454 sequencer into the Newbler assembler it is necessary to first extract them from the original SFF files. We present SlopMap, a bioinformatics software utility that allows quickly identification similar to the provided reference reads from either Roche 454 or Illumnia DNA library. With simple and intuitive command-line interface along with file output formats compatible to assembly programs, SlopMap can be directly embedded to biological data processing pipeline without any additional programming work. In addition, SlopMap preserves flowgram information needed for Roche 454 assembler. PMID:24404406

  9. 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.

  10. Mass-loss evolution of close-in exoplanets: Evaporation of hot Jupiters and the effect on population

    SciTech Connect

    Kurokawa, H.; Nakamoto, T.

    2014-03-01

    During their evolution, short-period exoplanets may lose envelope mass through atmospheric escape owing to intense X-ray and extreme ultraviolet (XUV) radiation from their host stars. Roche-lobe overflow induced by orbital evolution or intense atmospheric escape can also contribute to mass loss. To study the effects of mass loss on inner planet populations, we calculate the evolution of hot Jupiters considering mass loss of their envelopes and thermal contraction. Mass loss is assumed to occur through XUV-driven atmospheric escape and the following Roche-lobe overflow. The runaway effect of mass loss results in a dichotomy of populations: hot Jupiters that retain their envelopes and super Earths whose envelopes are completely lost. Evolution primarily depends on the core masses of planets and only slightly on migration history. In hot Jupiters with small cores (≅ 10 Earth masses), runaway atmospheric escape followed by Roche-lobe overflow may create sub-Jupiter deserts, as observed in both mass and radius distributions of planetary populations. Comparing our results with formation scenarios and observed exoplanets populations, we propose that populations of closely orbiting exoplanets are formed by capturing planets at/inside the inner edges of protoplanetary disks and subsequent evaporation of sub-Jupiters.

  11. The narrow rings of Jupiter, Saturn and Uranus

    NASA Technical Reports Server (NTRS)

    Dermott, S. F.; Murray, C. D.; Sinclair, A. T.

    1980-01-01

    The origin of the newly discovered narrow ring systems around Jupiter, Saturn and Uranus is considered. It is pointed out that both the Uranian and Jovian ring systems have mean orbital radii of 1.8 planetary radii and lie within the Roche zones of their respective planets, and it is suggested that the Jovian ring is the product of the disintegration of a satellite that entered the Roche zone, and that large numbers of small particles are now in horseshoe orbits about the Lagrangian equilibrium points of the remnant chunks. Analysis of the path of a ring particle in a horseshoe orbit is shown to result in ring structures in agreement with those observed for the circular rings of Jupiter and the highly eccentric ring of Uranus. The stability of these ring systems is then considered, and it is suggested that the F ring of Saturn, which lies outside the Roche zone, represents primordial matter not yet accreted by small satellites just inside the Mimas first-order resonances.

  12. Formation and Evolution of Binary Planetary Nebula Nuclei and Related Objects

    NASA Astrophysics Data System (ADS)

    Iben, Icko, Jr.; Tutukov, Alexander V.

    1993-11-01

    A study is made of the evolution of close binaries in which the primary first fills its Roche lobe after the exhaustion of helium at its center and before the onset of thermal pulses. Initial masses are in the range 3-6 M0. Also examined is the evolution of a 1 Msun model which fills its Roche lobe on the first giant branch when the mass of its helium degenerate core reaches 0.4 M0. In all cases, a common envelope scenario is assumed, and mass is removed from the model primary on a timescale shorter than the initial thermal timescale of the envelope of the primary until the model contracts within a final Roche lobe of predetermined size. After the removal of the common envelope, systems are very close binaries in which the evolved remnant has either a carbon-oxygen (CO) core and a helium-burning shell (progenitor of mass 2.3-8 Msun) or a helium core and a hydrogen-burning shell (progenitor of mass 1-2.3 Msun). The more massive remnants fill their Roche lobes for an extended period, transferring first hydrogen-rich material at a rate ˜10-8±1 Msun yr-1 for up to 106 yr, and then helium at a rate ˜10-6±1 Msun yr-1 for (1-4) × 105 yr. As much as ˜0.4 Msun of nearly pure helium can be transferred to an accretor. A possible real analog of the hydrogen-transferring models is U Sco, although, in many instances, a hydrogen-transferring episode may be bypassed or considerably shortened if the hot remnant blows a strong enough wind. Possible observational analogs of helium transferring models are bright ultrasoft X-ray sources like CAL 83 and CAL 87 in the Large Magellanic Cloud and some classes of supernova precursors. Our models help to explain the number and properties of hot helium OB subdwarfs. A method for estimating initial orbital periods of binary planetary nebula nuclei is introduced and used to infer the initial characteristics of binary systems which have produced close binary central stars, precataclysmic variables, and related systems. Using existing

  13. The Effect of Multiple Rounds of Mass Drug Administration on the Association between Ocular Chlamydia trachomatis Infection and Follicular Trachoma in Preschool-Aged Children

    PubMed Central

    Lee, Jennifer S.; Muñoz, Beatriz E.; Mkocha, Harran; Gaydos, Charlotte A.; Quinn, Thomas C.; West, Sheila K.

    2014-01-01

    Purpose To examine the relationship between ocular Chlamydia trachomatis infection and follicular trachoma (TF) in children prior to and following multiple rounds of annual mass drug administration (MDA) with azithromycin. Methodology/principal findings Thirty-two communities with endemic trachoma in Kongwa District, Tanzania, were offered annual MDA as part of a district-wide trachoma control program. Presence of ocular C. trachomatis infection and TF were assessed in 3,200 randomly sampled children aged five years and younger, who were examined prior to each MDA. Infection was detected using the Amplicor CT/NG assay and TF was identified by clinical examination using the World Health Organization (WHO) simplified grading system. The association between chlamydial infection and TF in children was evaluated at baseline prior to any treatment, and 12 months after each of three annual rounds of mass treatment. Factors associated with infection were examined using generalized estimating equation models. At baseline, the overall prevalence of chlamydial infection and TF was 22% and 31%, respectively. Among children with clinical signs of TF, the proportion of those with infection was 49% prior to treatment and declined to 30% after three MDAs. The odds of infection positivity among children with clinical signs of TF decreased by 26% (OR 0.74, 95% CI 0.65 to 0.84, p = <0.01) with each MDA, after adjusting for age. For children aged under one year, who did not receive treatment, the relationship was unchanged. Conclusions/significance The association between ocular C. trachomatis infection and TF weakened in children with each MDA, as both infection and clinical disease prevalence declined. However, there was still a significant proportion of TF cases with infection after three rounds of MDA. New strategies are needed to assess this residual infection for optimal treatment distribution. PMID:24722392

  14. Ag(I)-coordinated hairpin DNA for homogenous electronic monitoring of hepatitis C virus accompanying isothermal cycling signal amplification strategy.

    PubMed

    Lu, Minghua; Xu, Linfang; Zhang, Xiaona; Xiao, Rui; Wang, Youmei

    2015-11-15

    This work designs a new homogenous electronic monitoring platform for sensitive detection of hepatitis C virus (HCV) on an immobilization-free Ag(I)-assisted hairpin DNA through the cytosine-Ag(+)-cytosine coordination chemistry. The assay consists of target-induced Ag(+) dissociation from hairpin DNA and an isothermal circular strand-displacement polymerization (ICSDP) reaction. Upon target analyte introduction, HCV DNA initially hybridizes with hairpin DNA to disrupt the Ag(I)-coordinated hairpin probe and releases the coordinated Ag(+) ion, then the newly formed DNA duplex induces the ICSDP reaction with the aid of primer and polymerase, and then the displaced target DNA retriggers Ag(I)-coordinated hairpin DNA with target recycling, thereby resulting in formation of numerous free Ag(+) ions in the detection cell. The released Ag(+) ions can be readily captured by the negatively charged screen-printed carbon electrode, and subsequent anodic-stripping voltammetric detection of the captured Ag(+) ions are conducted to form the anodic current for the production of the electrochemical signal within the applied potential. Under optimal conditions, the ICSDP-based homogenous sensing system can be utilized for the detection of HCV DNA at a concentration as low as 2.3 pM. Intra- and inter-assay coefficients of variation with identical batches are below 9.5% and 10.5%, respectively. The analysis in 5 clinical serum specimens shows good accordance between results obtained by the developed method and commercial Cobas® Amplicor HCV Test Analyzer. PMID:26071691

  15. Rapid Quantification of Hepatitis B Virus DNA by Automated Sample Preparation and Real-Time PCR

    PubMed Central

    Stelzl, Evelyn; Muller, Zsofia; Marth, Egon; Kessler, Harald H.

    2004-01-01

    Monitoring of hepatitis B virus (HBV) DNA in serum by molecular methods has become the standard for assessment of the replicative activity of HBV. Several molecular assays for the detection and quantification of HBV DNA have been described. However, they usually lack automated sample preparation. Moreover, those assays, which are based on PCR, are limited by a short dynamic range (2 to 3 log units). In the present study, the use of RealArt HBV LC PCR Reagents in conjunction with automated extraction on the COBAS AMPLIPREP analyzer was evaluated. Members of an HBV proficiency program panel were tested; linearity, interassay, and intra-assay variations were determined. The performance of the assay in a routine clinical laboratory was evaluated with a total of 117 clinical specimens. When members of the HBV proficiency program panel were tested by the new molecular assay, the results were found to be within ±0.5 log unit of the results obtained by reference laboratories. Determination of linearity resulted in a quasilinear curve over more than 6 log units. The interassay variation of the RealArt HBV LC PCR Reagents by use of the automated sample preparation protocol ranged from 16 to 73%, and the intra-assay variation ranged from 9 to 40%. When clinical samples were tested by the new assay with the automated sample preparation protocol and the results were compared with those obtained by the COBAS AMPLICOR HBV MONITOR Test with manual sample preparation, the results for 76% of all samples with positive results by both tests were found to be within ±0.5 log unit and the results for another 18% were found to be within between 0.5 and 1.0 log unit. In conclusion, the real-time PCR assay with automated sample preparation proved to be suitable for the routine molecular laboratory and required less hands-on time. PMID:15184417

  16. Geospatial Distribution and Clustering of Chlamydia trachomatis in Communities Undergoing Mass Azithromycin Treatment

    PubMed Central

    Yohannan, Jithin; He, Bing; Wang, Jiangxia; Greene, Gregory; Schein, Yvette; Mkocha, Harran; Munoz, Beatriz; Quinn, Thomas C.; Gaydos, Charlotte; West, Sheila K.

    2014-01-01

    Purpose. We detected spatial clustering of households with Chlamydia trachomatis infection (CI) and active trachoma (AT) in villages undergoing mass treatment with azithromycin (MDA) over time. Methods. We obtained global positioning system (GPS) coordinates for all households in four villages in Kongwa District, Tanzania. Every 6 months for a period of 42 months, our team examined all children under 10 for AT, and tested for CI with ocular swabbing and Amplicor. Villages underwent four rounds of annual MDA. We classified households as having ≥1 child with CI (or AT) or having 0 children with CI (or AT). We calculated the difference in the K function between households with and without CI or AT to detect clustering at each time point. Results. Between 918 and 991 households were included over the 42 months of this analysis. At baseline, 306 households (32.59%) had ≥1 child with CI, which declined to 73 households (7.50%) at 42 months. We observed borderline clustering of households with CI at 12 months after one round of MDA and statistically significant clustering with growing cluster sizes between 18 and 24 months after two rounds of MDA. Clusters diminished in size at 30 months after 3 rounds of MDA. Active trachoma did not cluster at any time point. Conclusions. This study demonstrates that CI clusters after multiple rounds of MDA. Clusters of infection may increase in size if the annual antibiotic pressure is removed. The absence of growth after the three rounds suggests the start of control of transmission. PMID:24906862

  17. Dried-Plasma Transport Using a Novel Matrix and Collection System for Human Immunodeficiency Virus and Hepatitis C Virus Virologic Testing▿

    PubMed Central

    Lloyd, R. M.; Burns, D. A.; Huong, J. T.; Mathis, R. L.; Winters, M. A.; Tanner, M.; De La Rosa, A.; Yen-Lieberman, B.; Armstrong, W.; Taege, A.; McClernon, D. R.; Wetshtein, J. L.; Friedrich, Brian M.; Ferguson, Monique R.; O'Brien, William; Feorino, P. M.; Holodniy, M.

    2009-01-01

    A novel method for the collection and transportation of dried-blood-plasma samples, SampleTanker (ST), was developed and compared to standard shipping protocols for frozen-plasma specimens containing human immunodeficiency virus type 1 (HIV-1) and/or hepatitis C virus (HCV). Matched frozen and dried 1-ml EDTA-containing plasma samples were collected and analyzed by several molecular-based virologic assays. After addition of 1.175 ml of reconstitution buffer, 1.035 ml of dried plasma was recovered. Mean intra-assay variances were 0.05, 0.05, and 0.06 log10 copies/ml for the Versant, Amplicor, and NucliSens QT HIV-1 load assays, respectively (P, not significant). However, mean HIV-1 viral load was consistently reduced in dried samples by 0.32 to 0.51 log10 copies/ml, depending on assay type (P < 0.05). Infectious HIV-1 was not recovered from dried ST plasma. There was no significant difference in HIV-1 viral load results obtained using ST after 8 weeks of storage at ambient temperature. Compared to frozen plasma, HIV-1 genotypic results were >99% concordant at the nucleotide and amino acid levels, as well as for resistance-associated mutations. We further demonstrated successful detection of multiple analytes, including HIV-1 viral load, HIV-1 antiretroviral resistance genotype, and HCV genotype, from a single ST unit. Dried plasma collected with ST yielded comparable results to frozen samples for multiple-analyte clinical testing. As such, ST could be a useful alternative for virologic tests and clinical trials worldwide by significantly diminishing transportation cost and the sample volume restrictions associated with dried-blood-spot technology. PMID:19321732

  18. Magnitude of Virologic Blips Is Associated With a Higher Risk for Virologic Rebound in HIV-Infected Individuals: A Recurrent Events Analysis

    PubMed Central

    Grennan, J. Troy; Loutfy, Mona R.; Su, DeSheng; Harrigan, P. Richard; Cooper, Curtis; Klein, Marina; Machouf, Nima; Montaner, Julio S. G.; Rourke, Sean; Tsoukas, Christos; Hogg, Bob

    2012-01-01

    (See the editorial commentary by Taiwo and Bosch, on pages 1189–91.) Background. The importance of human immunodeficiency virus (HIV) blip magnitude on virologic rebound has been raised in clinical guidelines relating to viral load assays. Methods. Antiretroviral-naive individuals initiating combination antiretroviral therapy (cART) after 1 January 2000 and achieving virologic suppression were studied. Negative binomial models were used to identify blip correlates. Recurrent event models were used to determine the association between blips and rebound by incorporating multiple periods of virologic suppression per individual. Results. 3550 participants (82% male; median age, 40 years) were included. In a multivariable negative binomial regression model, the Amplicor assay was associated with a lower blip rate than branched DNA (rate ratio, 0.69; P < .01), controlling for age, sex, region, baseline HIV-1 RNA and CD4 count, AIDS-defining illnesses, year of cART initiation, cART type, and HIV-1 RNA testing frequency. In a multivariable recurrent event model controlling for age, sex, intravenous drug use, cART start year, cART type, assay type, and HIV-1 RNA testing frequency, blips of 500–999 copies/mL were associated with virologic rebound (hazard ratio, 2.70; P = .002), whereas blips of 50–499 were not. Conclusions. HIV-1 RNA assay was an important determinant of blip rates and should be considered in clinical guidelines. Blips ≥500 copies/mL were associated with increased rebound risk. PMID:22438396

  19. Mass-loss rates of "hot-Jupiter" exoplanets with various types of gaseous envelopes

    NASA Astrophysics Data System (ADS)

    Cherenkov, A. A.; Bisikalo, D. V.; Kaigorodov, P. V.

    2014-10-01

    According to the compuations results obtained by Bisikalo et al. (2013) for the gas-dynamical effect of stellar winds on exoplanet atmospheres, three types of gaseous envelopes can form around hot Jupiters: closed, quasi-closed, and open. The type of envelope that forms depends on the position of the frontal collision point (where the dynamical pressure of the wind is equal to the pressure of the surrounding atmosphere) relative to the Roche-lobe boundaries. Closed envelopes are formed around planets whose atmospheres lie completely within their Roche lobes. If the frontal collision point is located outside the Roche lobe, the atmospheric material begins to flow out through the Lagrangian points L1 and L2, which can result in the formation of quasi-closed (if the dynamical pressure of the stellar wind stops the outflow through L1) or open gaseous envelopes. The example of the typical hot Jupiter HD 209458b is considered for four sets of atmospheric parameters, to determine the mass-loss rates for the different types of envelopes arising with these parameters. The mass-loss rates based on the modeling results were estimated to be Ṁ ≤ 109 g/s for a closed atmosphere, Ṁ ≃ 3 × 109 g/s for a quasi-closed atmosphere, and Ṁ ≃ 3 × 1010 g/s for an open atmosphere. The matter in the closed and quasi-closed atmospheres flows out mainly through L2, and the matter in open envelopes primarily through L1.

  20. 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

  1. Formation of regular satellites from the spreading of massive rings : Why some planets have one moon and other have many ?

    NASA Astrophysics Data System (ADS)

    Charnoz, Sebastien; Crida, A.

    2013-10-01

    Around giant planets, the regular satellites pile-up at a distance of a few planetary radii, their masses increasing with the distance to the pile-up. In contrast, terrestrial bodies are dominated by one large satellite (the Moon for the Earth, Charon for Pluto). Here we show that both cases can be understood in the frame of a new paradigm for satellite formation : the spreading of a debris disk initialy confined inside the Roche radius of the planet (a « tidal disk »). By definition, beyond the Roche radius, solids aggregate and accrete, forming new moons. Those moons then migrate outward, repelled by the disk. We find that if the life-time of the disk is short (the spreading is fast), then accretion is faster than migration and all the material gathers into one large satellite. If the life-time of the disk is long, many satellites form and migrate away ; merging events take place during the migration, so that the mass should be proportional to the distance to the Roche radius to the power 9/5 . This is in good agreement with the distribution of the inner satellites of Saturn, Uranus, and Neptune. Relating the life-time of the disk to its mass ratio to the planet, we find that a debris disk around a giant planet should give birth to many satellites, while the Moon forming disk should give birth to one large satellite of about one lunar mass, possibly with a smaller companion as recently suggested to explain the lunar highlands5.

  2. 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

    Chang, Joy; Tarasova, Tetyana; Shanmugam, Vedapuri; Azarskova, Marianna; Nguyen, Shon; Hurlston, Mackenzie; Sabatier, Jennifer; Zhang, Guoqing; Osmanov, Saladin; Ellenberger, Dennis; Yang, Chunfu; Vitek, Charles; Liulchuk, Maria; Nizova, Natalya

    2015-12-01

    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

  3. 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.

  4. 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

  5. Crystallization-induced dynamic resolution R-epimer from 25-OCH3-PPD epimeric mixture.

    PubMed

    Zhang, Sainan; Tang, Yun; Cao, Jiaqing; Zhao, Chen; Zhao, Yuqing

    2015-11-15

    25-OCH3-PPD is a promising antitumor dammarane sapogenin isolated from the total saponin-hydrolyzed extract of Panax ginseng berry and Panax notoginseng leaves. 20(R)-25-OCH3-PPD was more potent as an anti-cancer agent than 20(S)-25-OCH3-PPD and epimeric mixture of 25-OCH3-PPD. This paper describes the rapid separation process of the R-epimer of 25-OCH3-PPD from its epimeric mixture by crystallization-induced dynamic resolution (CIDR). The optimized CIDR process was based on single factor analysis and nine well-planned orthogonal design experiments (OA9 matrix). A rapid and sensitive reverse phase high-performance liquid chromatographic (HPLC) method with evaporative light-scattering detector (ELSD) was developed and validated for the quantitation of 25-OCH3-PPD epimeric mixture and crystalline product. Separation and quantitation were achieved with a silica column using a mobile phase consisting of methanol and water (87:13, v/v) at a flow rate of 1.0mL/min. The ELSD detection was performed at 50°C and 3L/min. Under conditions involving 3mL of 95% ethanol, 8% HCl, and a hermetically sealed environment for 72h, the maximum production of 25(R)-OCH3-PPD was achieved with a chemical purity of 97% and a total yield of 87% through the CIDR process. The 25(R)-OCH3-PPD was nearly completely separated from the 220mg 25-OCH3-PPD epimeric mixture. Overall, a simple and steady small-batch purification process for the large-scale production of 25(R)-OCH3-PPD from 25-OCH3-PPD epimeric mixture was developed. PMID:26491820

  6. 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. PMID:24007886

  7. Laboratory Evaluation of the Liat HIV Quant (IQuum) Whole-Blood and Plasma HIV-1 Viral Load Assays for Point-of-Care Testing in South Africa

    PubMed Central

    Gous, Natasha; Carmona, Sergio; Stevens, Wendy

    2015-01-01

    Point-of-care (POC) HIV viral load (VL) testing offers the potential to reduce turnaround times for antiretroviral therapy monitoring, offer near-patient acute HIV diagnosis in adults, extend existing centralized VL services, screen women in labor, and prompt pediatrics to early treatment. The Liat HIV Quant plasma and whole-blood assays, prerelease version, were evaluated in South Africa. The precision, accuracy, linearity, and agreement of the Liat HIV Quant whole-blood and plasma assays were compared to those of reference technologies (Roche CAP CTMv2.0 and Abbott RealTime HIV-1) on an HIV verification plasma panel (n = 42) and HIV clinical specimens (n = 163). HIV Quant plasma assay showed good performance, with a 2.7% similarity coefficient of variation (CV) compared to the Abbott assay and a 1.8% similarity CV compared to the Roche test on the verification panel, and 100% specificity. HIV Quant plasma had substantial agreement (pc [concordance correlation] = 0.96) with Roche on clinical specimens and increased variability (pc = 0.73) in the range of <3.0 log copies/ml range with the HIV Quant whole-blood assay. HIV Quant plasma assay had good linearity (2.0 to 5.0 log copies/ml; R2 = 0.99). Clinical sensitivity at a viral load of 1,000 copies/ml of the HIV Quant plasma and whole-blood assays compared to that of the Roche assay (n = 94) was 100% (confidence interval [CI], 95.3% to 100%). The specificity of HIV Quant plasma was 88.2% (CI, 63.6% to 98.5%), and that for whole blood was 41.2% (CI, 18.4% to 67.1%). No virological failure (downward misclassification) was missed. Liat HIV Quant plasma assay can be interchanged with existing VL technology in South Africa. Liat HIV Quant whole-blood assay would be advantageous for POC early infant diagnosis at birth and adult adherence monitoring and needs to be evaluated further in this clinical context. LIAT cartridges currently require cold storage, but the technology is user-friendly and robust. Clinical cost and

  8. The development and use of a general route to brassinolide, its biosynthetic precursors, metabolites and analogues.

    PubMed

    Hurski, A L; Ermolovich, Yu V; Zhabinskii, V N; Khripach, V A

    2015-02-01

    A new method for the construction of steroid side chains through the addition of lithium salts of dithianes to a C-22 aldehyde was developed. An efficient one-pot procedure for the preparation of a suitable C-22 aldehyde from commercial epibrassinolide in three steps in 86% isolated yield was described. Enantioselective hydroxymethylation of isovaleraldehyde and Kulinkovich cyclopropanation of silylated Roche esters were used as key steps for the dithiane syntheses. The method was applied for the preparation of brassinolide, its biosynthetic precursors and metabolites. In addition, a number of brassinosteroids with a double bond in the side chain were prepared as precursors for tritiated derivatives for biosynthetic studies. PMID:25473936

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

    PubMed

    Hemarajata, P; Yang, S; Soge, O O; Humphries, R M; Klausner, J D

    2016-03-01

    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

  10. How Zantac became the best-selling drug in history.

    PubMed

    Wright, R

    1996-01-01

    Glaxo's Zantac began its dominance of the acid/peptic marketplace with a launch strategy, taking advantage of the established Roche sales force to rapidly promote the product. Educational symposia for physicians were instrumental in disseminating both disease and product information to primary care physicians and specialists. This technique not only pleased physicians (more referrals), but also increased public awareness of gastrointestinal disease, further expanding the patient market. Several novel marketing strategies contributed to Zantac's success, including the public-service announcements, celebrity media tours, and consumer-awareness bulletins, which brought the drug to the lay public and encouraged individuals to seek advice from their physicians. PMID:10169076

  11. Parameters of the Centaurus X-3 binary system

    SciTech Connect

    Khruzina, T.S.; Cherepashchuk, A.M.

    1986-06-01

    The paper provides an interpretation of the average (composite) V779 Cen light curve and of the two phase intervals of the 26-day cycle. Consideration is given to eclipses of the optical star by an accretion disk confined to the orbit plane of the binary stem and to eclipses of the disk by the star. It is shown that changes in the apparent radius and luminosity of the accretion disk around the compact member of the system could produce the long-period variability in the optical light curve if the optical star nearly fills its Roche lobe (filling factor 0.995 + or - 0.005). 36 references.

  12. The black hole binary A0620-00

    NASA Technical Reports Server (NTRS)

    Mcclintock, J. E.; Remillard, R. A.

    1986-01-01

    CCD photometry obtained with the 1.3-m McGraw-Hill telescope during 1981-1985 and 490-560-nm spectra obtained at KPNO on Jan. 17, 1985, are reported for A0620-00. The mass of the compact X-ray source is found to have lower limit 3.20 solar mass, strongly implying that it is a black hole; its mass is shown to exceed 7.3 solar mass if the K dwarf fills its Roche lobe during quiescence.

  13. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing.

    PubMed

    Mosher, Jennifer J; Bowman, Brett; Bernberg, Erin L; Shevchenko, Olga; Kan, Jinjun; Korlach, Jonas; Kaplan, Louis A

    2014-09-01

    Improved sequencing accuracy was obtained with 16S amplicons from environmental samples and a known pure culture when upgraded Pacific Biosciences (PacBio) hardware and enzymes were used for the single molecule, real-time (SMRT) sequencing platform. The new PacBio RS II system with P4/C2 chemistry, when used with previously constructed libraries (Mosher et al., 2013) surpassed the accuracy of Roche/454 pyrosequencing platform. With accurate read lengths of >1400 base pairs, the PacBio system opens up the possibility of identifying microorganisms to the species level in environmental samples. PMID:24978594

  14. Effects of radiation pressure on the equipotential surfaces in X-ray binaries

    NASA Technical Reports Server (NTRS)

    Kondo, Y.; Mccluskey, G. E., Jr.; Gulden, S. L.

    1976-01-01

    Equipotential surfaces incorporating the effect of radiation pressure were computed for the X-ray binaries Cen X-3, Cyg X-1 = HDE 226868, Vela XR-1 = 3U 0900-40 = HD 77581, and 3U 1700-37 = HD 153919. The topology of the equipotential surfaces is significantly affected by radiation pressure. In particular, the so-called critical Roche (Jacobian) lobes, the traditional figure 8's, do not exist. The effects of these results on modeling X-ray binaries are discussed.

  15. MASS TRANSFER VARIATIONS IN UX MONOCEROTIS: EIGHT YEARS OF AUTOMATED PHOTOMETRIC MONITORING

    SciTech Connect

    Olson, Edward C.; Henry, Gregory W.; ETZEL, PAUL B. E-mail: henry@schwab.tsuniv.edu

    2009-11-15

    We analyze eight years (1999-2007) of automated photometric observations of the active Algol binary UX Monocerotis to search for mass transfer bursts similar to those seen in U Cephei. The largest photometric anomaly is the mean gainer luminosity difference between the stream-impact hemisphere and the opposite hemisphere. We find an updated Wilson-Devinney solution for earlier six-color observations. The UX Mon donor star fills its Roche lobe and the gainer nearly fills its rotational lobe. Instead of isolated bursts of the U Cep type, we found nearly continuous brightness fluctuations likely produced by variable mass transfer. We discuss implications for mass transfer.

  16. 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.

  17. Search for contact systems among EB-type binaries. II - ES Lib and AR Boo

    NASA Astrophysics Data System (ADS)

    Milano, L.; Barone, F.; Mancuso, S.; Russo, G.

    1989-03-01

    In a search of contact systems among EB-type binaries, the existing photometric observations of ES Lib and AR Boo have been analyzed. It is found that ES Lib is a semi-detached system, with the primary filling the Roche lobe. AR Boo is instead found to be a contact system, with no lobe overfilling, and with a large temperature difference between the components, but this solution has to be considered as temptative, because of the poor quality of the data and the lack of any spectroscopic information.

  18. The Journal Microarrays

    PubMed Central

    Lin, Shu-Kun

    2011-01-01

    Our publishing company MDPI AG has its headquarters in Basel, Switzerland where there are thousands of scientists working in the laboratories of pharmaceutical companies and institutes including Novartis [1], F. Hoffmann-La Roche [2] and institutes affiliated with University of Basel [3]. In 1996, the first annual microplate conference MipTec was held in Basel, and the MipTec 2011 was held a few days ago in Basel [4]. I published a paper on microplate standardization presented at MipTec 1996 in MDPI’s longest-running journal Molecules [5-7]. [....

  19. 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

  20. SNP discovery in non-model organisms using 454 next generation sequencing.

    PubMed

    Wheat, Christopher W

    2012-01-01

    Roche 454 sequencing of the transcriptome has become a standard approach for efficiently obtaining single nucleotide polymorphisms (SNPs) in non-model species. In this chapter, the primary issues facing the development of SNPs from the transcriptome in non-model species are presented: tissue and sampling choices, mRNA preparation, considerations of normalization, pooling and barcoding, how much to sequence, how to assemble the data and assess the assembly, calling transcriptome SNPs, developing these into genomic SNPs, and publishing the work. Discussion also covers the comparison of this approach to RAD-tag sequencing and the potential of using other sequencing platforms for SNP development. PMID:22665274

  1. 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.

  2. 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.

  3. Celestial: Common astronomical conversion routines and functions

    NASA Astrophysics Data System (ADS)

    Robotham, Aaron S. G.

    2016-02-01

    The R package Celestial contains common astronomy conversion routines, particularly the HMS and degrees schemes, and a large range of functions for calculating properties of different cosmologies (as used by the cosmocalc website). This includes distances, ages, growth rate/factor and densities (e.g., Omega evolution and critical energy density). It also includes functions for calculating thermal properties of the CMB and Planck's equations and virial properties of halos in different cosmologies, and standard NFW and weak-lensing formulas and low level orbital routines for calculating Roche properties, Vis-Viva and free-fall times.

  4. YAG laser therapy in opthalmology

    NASA Astrophysics Data System (ADS)

    Vorosmarthy, Daniel

    1994-02-01

    The author gives first a short report about the history of light application as a therapeutic method in medicine and about the xenon- and sunlight-photocoagulators first used. He commemorates Prof. Gerd Meyer-Schwickerath, who was not only the inventor of this new method, but also a leading person in ophthalmology in the post-war years. The first YAG- LASER instrument for ophthalmology in Hungary was set up in 1986 in the Saint Roch Hospital. Up to the end laser year 2762 YAG-LASEr treatments have been performed. The form and the effectiveness of the YAG-LASER treatment will be discussed and evaluated.

  5. 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.

  6. 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.

  7. [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. PMID:24135905

  8. 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

  9. [The study and evaluation of a method for identifying Escherichia coli by using fluorescent disks].

    PubMed

    Niebla Pérez, A; Pascual Marqui, C

    1992-01-01

    A study was carried out with 101 strains, 79 of Escherichia coli and 22 of other genera isolated from clinical samples at several hospitals in Havana form October 1989 to January 1990. In all the strains, beta-glycuronidase enzyme was detected in conditions established by our laboratory and was compared with the results reached by the ROCHE enterotube method. Of the 79 Escherichia coli strains, 74 were positive to the beta-glycuronidase detection test. Sensitivity was 94% and specificity, was 100%. PMID:1344689

  10. Ultraviolet spectra of planetary nebulae. VII - The abundance of carbon in the very low excitation nebula He 2-131

    NASA Astrophysics Data System (ADS)

    Adams, S.; Seaton, M. J.

    1982-07-01

    Features observed in infrared spectra suggest that certain very low excitation (VLE) nebulae have low C/O abundance ratios (Cohen & Barlow 1980; Aitken & Roche 1982). Fluxes in the multiplets [O II] sun2470 and [O II] λ2326 have been measured for the VLE nebula He 2-131 = HD 138403 using lUE high-dispersion spectra. An analysis similar to that of Harrington et al. (1980) for IC 418 gives C/O = 0.3 for He 2-131, compared with C/O = 1.3 for IC 418 and 0.6 for the Sun.

  11. X-ray burst sources

    NASA Technical Reports Server (NTRS)

    Lewin, W. H. G.

    1986-01-01

    There are about 100 bright X-ray sources in the Galaxy that are accretion-driven systems composed of a neutron star and a low mass companion that fills its critical Roche lobe. Many of these systems generate recurring X-ray bursts that are the result of thermonuclear flashes in the neutron star's surface layers, and are accompanied by a somewhat delayed optical burst due to X-ray heating of accretion disk. The Rapid Burster discovered in 1976 exhibits an interval between bursts that is strongly correlated with the energy in the preceding burst. There is no optical identification for this object.

  12. Diagnosis and management of Paget-Schroetter's syndrome.

    PubMed

    Hart, Sarah Dean

    2010-10-01

    Paget-Schroetter's syndrome (PSS) is an effort-related syndrome involving upper extremity deep vein thromboses (UEDVTs) that usually occur in the subclavian or axillary veins. The aetiology is distinct from that of lower extremity DVTs (LEDVTs). Although rare, the syndrome can occur in young, otherwise healthy people who participate in upper extremity activity (Roche-Nagle et al 2007) such as footballer Gary Cahill, a defender at Bolton Wanderers, whose hopes of playing football at international level this season have diminished as a result of developing a UEDVT (BBC Sport 2010). This article discusses the incidence and aetiology, and provides a case study, of the syndrome. PMID:21066922

  13. Equilibrium Structure of Rotationally and Tidally Distorted Prasad Model Including the Effect of Mass Variation Inside the Star

    NASA Astrophysics Data System (ADS)

    Saini, Seema; Lal, A. K.; Kumar, Sunil

    2014-03-01

    In this paper we propose suitable modifications in the concept of Roche equipotentials to account for the effect of mass distribution inside the star on its equipotential surfaces and use this in conjunction with the approach of Kippenhahn and Thomas, in a manner earlier used by Prasad and Mohan, to incorporate the effects of rotational and tidal forces in the equations of stellar structure parameters. The proposed method has been used to compute the structure parameters of the rotationally and tidally distorted Prasad model of the star.

  14. Effects of rotation and tidal distortions on the periods of adiabatic oscillations of composite models of stars

    NASA Astrophysics Data System (ADS)

    Mohan, C.; Agarwal, S. R.

    1987-01-01

    Mohan and Saxena's approach of using the averaging technique of Kippenhahn and Thomas in conjunction with Kopal's method of evaluating various parameters on the Roche equipotentials has been used to compute the effects of rotation and tidal distortions on the periods of small adiabatic radial and nonradial modes of oscillations of a series of composite models of stars. In these stars the density decreases slowly in the core from the centre to the interface and then falls of rapidly in the envelope from the interface to the outer surface.

  15. 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

  16. Metal Impurities Cause False Positives in High-Throughput Screening Campaigns

    PubMed Central

    2012-01-01

    Organic impurities in compound libraries are known to often cause false-positive signals in screening campaigns for new leads, but organic impurities do not fully account for all false-positive results. We discovered inorganic impurities in our screening library that can also cause positive signals for a variety of targets and/or readout systems, including biochemical and biosensor assays. We investigated in depth the example of zinc for a specific project and in retrospect in various HTS screens at Roche and propose a straightforward counter screen using the chelator TPEN to rule out inhibition caused by zinc. PMID:24900642

  17. Continuum viscoplastic simulation of a granular column collapse on large slopes : μ(I) rheology and lateral wall effects

    NASA Astrophysics Data System (ADS)

    Martin, Nathan; Mangeney, Anne; Ionescu, Ioan; Bouchut, Francois

    2016-04-01

    The description of the mechanical behaviour of granular flows and in particular of the static/flowing transition is still an open and challenging issue with strong implication for hazard assessment [{Delannay et al.}, 2016]. In particular, {detailed quantitative} comparison between numerical models and observations is necessary to go further in this direction. We simulate here dry granular flows resulting from the collapse of granular columns on an inclined channel (from horizontal to 22^o) and compare precisely the results with laboratory experiments performed by {Mangeney et al.} [2010] and {Farin et al.} [2014]. Incompressibility is assumed despite the dilatancy observed in the experiments (up to 10%). The 2-D model is based on the so-called μ(I) rheology that induces a Drucker-Prager yield stress and a variable viscosity. A nonlinear Coulomb friction term, representing the friction on the lateral walls of the channel is added to the model. We demonstrate that this term is crucial to accurately reproduce granular collapses on slopes higher than 10o whereas it remains of little effect on horizontal slope [{Martin et al.}, 2016]. We show that the use of a variable or a constant viscosity does not change significantly the results provided that these viscosities are of the same order [{Ionescu et al.}, 2015]. However, only a fine tuning of the constant viscosity (η = 1 Pa.s) makes it possible to predict the slow propagation phase observed experimentally on large slopes. This was not possible when using, without tuning, the variable viscosity calculated from the μ(I) rheology with the parameters estimated from experiments. Finally, we discuss the well-posedness of the model with variable and constant viscosity based in particular on the development of shear bands observed in the numerical simulations. References Delannay, R., Valance, A., Mangeney, A., Roche, O., and Richard, P., 2016. Granular and particle-laden flows: from laboratory experiments to field

  18. The complete mitochondrial genome of Crassostrea gasar (Bivalvia: Ostreidae).

    PubMed

    Cavaleiro, Nathalia P; Solé-Cava, Antonio M; Melo, Cláudio M R; de Almeida, Luiz G; Lazoski, Cristiano; Vasconcelos, Ana Tereza R

    2016-07-01

    The complete mitochondrial genome of Crassostrea gasar was sequenced using the Ion Proton technology in combination with 454 Roche GS-FLX plataform data. We assembled a 17,686 bp complete circular mitochondrial genome, containing 13 protein-coding genes, a major non-coding region (MNR), two ribosomal RNA genes and 24 transfer RNA genes. Phylogenetic analysis of concatenated amino acid sequences from mitochondria showed monophyletic clades formed with high bootstrap values. This is the first complete mitochondrial sequence of an oyster from South America. Mitogenome sequence was deposited in GenBank under the accession number KR856227. PMID:27158791

  19. 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

  20. Performance of a commercial assay for the diagnosis of influenza A (H1N1) infection in comparison to the Centers for Disease Control and Prevention protocol of real time RT-PCR.

    PubMed

    Barbás, María G; Gallego, Sandra V; Castro, Gonzalo M; Baumeister, Elsa; Kademian, Silvia; De Leon, Juan; Cudolá, Analía

    2012-01-01

    At the time of influenza A (H1N1) emergency, the WHO responded with remarkable speed by releasing guidelines and a protocol for a real-time RT-PCR assay (rRT-PCR). The aim of the present study was to evalúate the performance of the "Real Time Ready Influenza A/H1N1 Detection Set" (June 2009)-Roche kit in comparison to the CDC reference rRT-PCR protocol. The overall sensitivity of the Roche assay for detection of the Inf A gene in the presence or absence of the H1 gene was 74.5 %. The sensitivity for detecting samples that were only positive for the Inf A gene (absence of the H1 gene) was 53.3 % whereas the sensitivity for H1N1-positive samples (presence of the Inf A gene and any other swine gene) was 76.4 %. The specificity of the assay was 97.1 %. A new version of the kit (November 2009) is now available, and a recent evaluation of its performance showed good sensitivity to detect pandemic H1N1 compared to other molecular assays. PMID:22610294

  1. Detection of surreptitious administration of analog insulin to an 8-week-old infant.

    PubMed

    Green, Rebecca P; Hollander, Abby S; Thevis, Mario; Thomas, Andreas; Dietzen, Dennis J

    2010-05-01

    An 8-week-old infant presented to the emergency department with lethargy, tachycardia, and a blood glucose concentration of 1.8 mmol/L. After admission, hypoglycemia recurred on 3 additional occasions. Initial urinalysis results were negative for ketones, and the results of additional laboratory tests did not support the diagnosis of cortisol or growth hormone deficiency, oral hypoglycemic ingestion, or an inborn error of metabolism. Difficulty restoring and maintaining glucose concentrations along with a transient response to glucagon during 1 hypoglycemic episode suggested hyperinsulinism. In 1 hypoglycemic episode, elevated insulin and low C-peptide concentrations suggested exogenous insulin administration, but 2 subsequent blood samples obtained during hypoglycemia contained appropriately decreased concentrations of insulin. The insulin immunoassay initially used in this case (Roche ElecSys/cobas [Roche Diagnostics, Indianapolis, IN]) was insensitive to insulin analogs. Two additional immunoassays, 1 with intermediate (Immulite [Siemens, Deerfield, IL]) and 1 with broad (radioimmunoassay [Millipore, Inc, Billerica, MA]) reactivity to insulin analogs were used to characterize insulin in each of the critical blood samples. Samples obtained during hypoglycemia displayed a graded reactivity similar to that observed in type 1 diabetic patients prescribed insulin analogs, whereas a sample obtained from the patient and a control subject during euglycemia showed equal reactivity among the 3 assays. These data suggested administration of insulin analog to the child, and further characterization of insulin by using tandem mass spectrometry confirmed the presence of Humalog. The child was subsequently placed in foster care with no further recurrence of hypoglycemia. PMID:20385635

  2. 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. PMID:26419593

  3. [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. PMID:25444127

  4. 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.

  5. Genome sequencing and analysis of a granulovirus isolated from the Asiatic rice leafroller, Cnaphalocrocis medinalis.

    PubMed

    Zhang, Shan; Zhu, Zheng; Sun, Shifeng; Chen, Qijin; Deng, Fei; Yang, Kai

    2015-12-01

    The complete genome of Cnaphalocrocis medinalis granulovirus (CnmeGV) from a serious migratory rice pest, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), was sequenced using the Roche 454 Genome Sequencer FLX system (GS FLX) with shotgun strategy and assembled by Roche GS De Novo assembler software. Its circular double-stranded genome is 111,246 bp in size with a high A+T content of 64.8% and codes for 118 putative open reading frames (ORFs). It contains 37 conserved baculovirus core ORFs, 13 unique ORFs, 26 ORFs that were found in all Lepidoptera baculoviruses and 42 common ORFs. The analysis of nucleotide sequence repeats revealed that the CnmeGV genome differs from the rest of sequenced GVs by a 23 kb and a 17kb gene block inversions, and does not contain any typical homologous region (hr) except for a region of non-hr-like sequence. Chitinase and cathepsin genes, which are reported to have major roles in the liquefaction of the hosts, were not found in the CnmeGV genome, which explains why CnmeGV infected insects do not show the phenotype of typical liquefaction. Phylogenetic analysis, based on the 37 core baculovirus genes, indicates that CnmeGV is closely related to Adoxophyes orana granulovirus. The genome analysis would contribute to the functional research of CnmeGV, and would benefit to the utilization of CnmeGV as pest control reagent for rice production. PMID:26712716

  6. 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.

  7. Changes in potassium and sodium concentrations in stored blood.

    PubMed

    Opoku-Okrah, Clement; Acquah, Benjamin Kojo Safo; Dogbe, Elliot Eli

    2015-01-01

    Potassium is the principal intracellular cation with sodium being the principal extracellular cation. Maintenance of the distribution of potassium and sodium between the intracellular and the extracellular compartments relies on several homeostatic mechanisms. This study analysed the effect of blood storage on the concentrations of potassium and sodium in stored blood and also determine any variations that may exist in their concentrations. 50 mls of blood was sampled each from 28 units of evenly mixed donated blood in citrate phosphate dextrose adenine (CPDA-1) bags immediately after donation into satellite bag and stored at 4oC. Potassium and sodium concentration determinations were done on each of the 28 samples on day 0 (before blood was initially stored in the fridge), day 5, day 10, day 15 and day 20 of storage using the Roche 9180 ISE Electrolyte Analyser (Hoffmann-La Roche Ltd, Switzerland). data analysis showed significant changes in the potassium and sodium concentrations with a continuous rise in potassium and a continuous fall in sodium. A daily change of 0.59 mmol/l and 0.50 mmol/l was observed in the potassium and sodium concentrations respectively. We showed steady but increased daily concentrations of potassium and decrease concentrations of sodium in blood stored over time at 4oC. PMID:27386032

  8. The ROSAT bright source 1RXS J201607.0 + 251645: an active Algol-type binary

    NASA Astrophysics Data System (ADS)

    Li, Hua-Li; Yang, Yuan-Gui; Su, Wei; Wang, Hui-Juan; Wei, Jian-Yan

    2009-09-01

    1RXS J201607.0+251645 is identified as an eclipsing binary. We present preliminary observations in the V band with the 0.6-m telescope for three years and extensive observations in the V and R bands with the 0.8-m telescope for six nights, respectively. The light curve of the system is EB type. Five light minimum times were obtained and the orbital period of 0.388058d(±0.00044d) is determined. The photometric solution given by the 2003-version of the Wilson-Devinney program suggests that the binary is a semidetached system with photometric mass ratio 0.895(±0.006), which is probably comprised of a G5 primary and an oversized K5 secondary. The less massive component has completely filled its Roche lobe, while the other one almost fills its Roche lobe with a filling factor of 93.4%. The system shows a varying O'Connell effect in its phase folded diagrams from 2005 to 2007, and is X-ray luminous with log LX/Lbol ~ -3.27. Possible mechanisms to account for these two phenomena are discussed. Finally, we infer that the binary may be in thermal oscillation or may evolve into a contact binary.

  9. Formation of the Double Neutron Star System PSR J1930-1852

    NASA Astrophysics Data System (ADS)

    Shao, Yong; Li, Xiang-Dong

    2016-01-01

    The spin period (185 ms) and period derivative (1.8× {10}-17 {{s}} {{{s}}}-1) of the recently discovered double neutron star (DNS) system PSR J1930-1852 indicate that the pulsar was mildly recycled through the process of Roche-lobe overflow. This system has the longest orbital period (45 days) of the known DNS systems, and can be formed from a helium star-NS binary if the initial mass of the helium star was ≲ 4.0{M}⊙ ; otherwise, the helium star would never fill its Roche-lobe. At the moment of the supernova explosion, the mass of the helium star was ≲ 3.0{M}⊙ . We find that the probability distribution of the velocity kick imparted to the new-born neutron star has a maximum at about 30 {km} {{{s}}}-1 (and a tail up to 260 {km} {{{s}}}-1), indicating that this NS probably received a low kick velocity at birth.

  10. Orbital period changes in massive X-ray binaries

    NASA Technical Reports Server (NTRS)

    Kelley, Richard L.

    1986-01-01

    Data from long-term pulse-timing observations of Cen X-3 are compiled and analyzed to determine the evolution of the orbital period, and the implications of the results for other massive X-ray binaries are discussed. Third-body effects, tidal effects, and mass-loss/transfer effects are considered as possible causes for the orbital-period decay observed in Cen X-3, and it is concluded that strong tidal coupling between the companion star and the orbital causes the period decay via orbital instability and/or mass loss. Applying these results to the Roche-lobe-overflow models of Savonije (1983), the evolutionary expansion rate of the Cen X-3 companion and the Roche-lobe shrinking rate are estimated as about 2 x 10 to the -7th/yr and about 1 x 10 to the -6th/yr, respectively, implying an X-ray lifetime of about 5000 yr. Estimates of the companion mass-change rate and period decay for Cen X-3 and four other objects are presented in a table.

  11. Trends, prospects and challenges in quantifying flow and transport through fractured rocks

    NASA Astrophysics Data System (ADS)

    Neuman, Shlomo P.

    2005-03-01

    of these trends in light of recent experimental and theoretical findings, ending with a short list of prospects and challenges for the future. Parmis les problèmes aucquels font face les hydrogéologues, il y a celui de la caractérisation des roches fracturées (Faybishenko and Benson, 2000). Cet article discute des solutions associées aux quantifications des écoulements et des transports à travers les roches fracturées à l'échelles des essais de puits et des essais de traçage. Une part importante de la litérature traite des roches cristallines, des roches sédimentaires consolidées telles les grés, les calcaires (exeptés les karsts) et la craie. De fait, cet article traitera la même panoplie de roches. La quantification directe des écoulements et du transport dans de tels milieux est généralement abordée via la géométrie des fractures, les données de pression et de traçage, qui déslors sont les objets principaux de notre étude. La géologie, la géophysique et la géochimie (incluant la géochimie isotopique) sont criticables car elles donnent des informations qualitatives sur l'écoulement et le transport des aquifères fracturés, et son intégrées graduellement dans des modèles qualitatifs. La manière d'intégrer ces données dépasse malheureusement cet article. L'hydrogéologie des aquifères de fractures et les autres sciences de la terre s'intéressant aux roches fracturées méritent des traîtements différents. En toute évidence il est suggéré que rarement un modèle d'écoulement et de transport dans une roche fracturée puisse être traité comme un milieu isotropique continu, uniforme ou moyennement non-uniforme. Par ailleurs, il est admis la dépendance entre la forte hétérogénéité erratique et la variété de natures et de comportements des roches fracturées. Une manière de régler le problème est de considérer le milieu comme un réseau de fractures discrètes (avec une perméabilité de matrice ou de bloc). Une

  12. 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.

  13. Facts and fictions about polymorphism.

    PubMed

    Cruz-Cabeza, Aurora J; Reutzel-Edens, Susan M; Bernstein, Joel

    2015-12-01

    We present new facts about polymorphism based on (i) crystallographic data from the Cambridge Structural Database (CSD, a database built over 50 years of community effort), (ii) 229 solid form screens conducted at Hoffmann-La Roche and Eli Lilly and Company over the course of 8+ and 15+ years respectively and (iii) a dataset of 446 polymorphic crystals with energies and properties computed with modern DFT-d methods. We found that molecular flexibility or size has no correlation with the ability of a compound to be polymorphic. Chiral molecules, however, were found to be less prone to polymorphism than their achiral counterparts and compounds able to hydrogen bond exhibit only a slightly higher propensity to polymorphism than those which do not. Whilst the energy difference between polymorphs is usually less than 1 kcal mol(-1), conformational polymorphs are capable of differing by larger values (up to 2.5 kcal mol(-1) in our dataset). As overall statistics, we found that one in three compounds in the CSD are polymorphic whilst at least one in two compounds from the Roche and Lilly set display polymorphism with a higher estimate of up to three in four when compounds are screened intensively. Whilst the statistics provide some guidance of expectations, each compound constitutes a new challenge and prediction and realization of targeted polymorphism still remains a holy grail of materials sciences. PMID:26400501

  14. Plume shot noise in convection: evidence of a boundary layer instability consistent with the triggering of the Ultimate regime of convection

    NASA Astrophysics Data System (ADS)

    Salort, Julien

    2008-11-01

    A sudden enhancement of the heat transfer for Rayleigh numbers Ra>1e12 was reported in a Rayleigh Bénard cell in 1997 (Chavanne et al. PRL).This observation was interpreted as the occurrence of Kraichnan's ``Ultimate'' regime of convection, which is characterized by turbulent boundary layers. This interpretation has been indirectly supported by the outcome a test experiment, using a cell with corrugated surfaces. A more direct test would consist in probing fluctuations within the boundary layer, but its thinness (order 100 microns) causes instrumentation challenges. To overcome this difficulty, we recorded the shot noise induced by the thermal plumes leaving the bottom plate. We find that the heat transfer enhancement at Ra˜1e12, is accompanied by a significant increase of shot noise. This observation is interpreted as the signature of a boundary layer instability, in agreement with the Ultime regime scenario. [ Gauthier F. and Roche P.-E et al., EPL 83:24005 (2008) ] [3pt] In collaboration with Frédéric Gauthier and Philippe-E. Roche, Institut NEEL, CNRS.

  15. A Neutron Star–White Dwarf Binary Model for Repeating Fast Radio Burst 121102

    NASA Astrophysics Data System (ADS)

    Gu, Wei-Min; Dong, Yi-Ze; Liu, Tong; Ma, Renyi; Wang, Junfeng

    2016-06-01

    We propose a compact binary model for the fast radio burst (FRB) repeaters, where the system consists of a magnetic white dwarf (WD) and a neutron star (NS) with strong bipolar magnetic fields. When the WD fills its Roche lobe, mass transfer will occur from the WD to the NS through the inner Lagrange point. The accreted magnetized materials may trigger magnetic reconnection when they approach the NS surface, and therefore the electrons can be accelerated to an ultra-relativistic speed. In this scenario, the curvature radiation of the electrons moving along the NS magnetic field lines can account for the characteristic frequency and the timescale of an FRB. Owing to the conservation of angular momentum, the WD may be kicked away after a burst, and the next burst may appear when the system becomes semi-detached again through the gravitational radiation. By comparing our analyses with the observations, we show that such an intermittent Roche-lobe overflow mechanism can be responsible for the observed repeating behavior of FRB 121102.

  16. Atlantic salmon skin and fillet color changes effected by perimortem handling stress, rigor mortis, and ice storage.

    PubMed

    Erikson, U; Misimi, E

    2008-03-01

    The changes in skin and fillet color of anesthetized and exhausted Atlantic salmon were determined immediately after killing, during rigor mortis, and after ice storage for 7 d. Skin color (CIE L*, a*, b*, and related values) was determined by a Minolta Chroma Meter. Roche SalmoFan Lineal and Roche Color Card values were determined by a computer vision method and a sensory panel. Before color assessment, the stress levels of the 2 fish groups were characterized in terms of white muscle parameters (pH, rigor mortis, and core temperature). The results showed that perimortem handling stress initially significantly affected several color parameters of skin and fillets. Significant transient fillet color changes also occurred in the prerigor phase and during the development of rigor mortis. Our results suggested that fillet color was affected by postmortem glycolysis (pH drop, particularly in anesthetized fillets), then by onset and development of rigor mortis. The color change patterns during storage were different for the 2 groups of fish. The computer vision method was considered suitable for automated (online) quality control and grading of salmonid fillets according to color. PMID:18298716

  17. Risk factors for acquisition and clearance of oral human papillomavirus infection among HIV-infected and HIV-uninfected adults.

    PubMed

    Beachler, Daniel C; Sugar, Elizabeth A; Margolick, Joseph B; Weber, Kathleen M; Strickler, Howard D; Wiley, Dorothy J; Cranston, Ross D; Burk, Robert D; Minkoff, Howard; Reddy, Susheel; Xiao, Weihong; Guo, Yingshi; Gillison, Maura L; D'Souza, Gypsyamber

    2015-01-01

    Human papillomavirus (HPV) causes the majority of oropharyngeal cancers in the United States, yet the risk factors for and natural history of oral HPV infection are largely unknown. In 2010-2011, a US-based longitudinal cohort study of 761 human immunodeficiency virus (HIV)-infected and 469 at-risk HIV-uninfected participants from the Multicenter AIDS Cohort Study and the Women's Interagency HIV Study was initiated. Semiannually collected oral rinses were evaluated for 37 HPV genotypes using the Roche LINEAR ARRAY HPV Genotyping Test (Roche Molecular Systems, Pleasanton, California), and factors associated with oral HPV incidence and clearance were explored using adjusted Wei-Lin-Weissfeld modeling. Through 2013, the 2-year cumulative incidence of any type of oral HPV infection was 34% in HIV-infected persons and 19% in HIV-uninfected persons. However, many of these infections cleared. Seven percent of incident infections and 35% of prevalent infections persisted for at least 2 years. After adjustment for other risk factors, HIV infection (adjusted hazard ratio = 2.3, 95% confidence interval: 1.7, 3.2), reduced current CD4 cell count, and increased numbers of oral sex and "rimming" partners increased the risk of incident oral HPV infection, whereas male sex, older age, and current smoking increased the risk of oral HPV persistence (each P < 0.05). This helps explain the consistent associations observed between these factors and prevalent oral HPV infection in previous cross-sectional studies. PMID:25480823

  18. Constraints on common envelope magnetic fields from observations of jets in planetary nebulae

    NASA Astrophysics Data System (ADS)

    Tocknell, James; De Marco, Orsola; Wardle, Mark

    2014-04-01

    The common envelope (CE) interaction describes the swallowing of a nearby companion by a growing, evolving star. CEs that take place during the asymptotic giant branch phase of the primary may lead to the formation of a planetary nebula (PN) with a post-CE close binary in the middle. We have used published observations of masses and kinematics of jets in four post-CE PN to infer physical characteristics of the CE interaction. In three of the four systems studied, Abell 63, ETHOS 1 and the Necklace PN, the kinematics indicate that the jets were launched a few thousand years before the CE and we favour a scenario where this happened before Roche lobe overflow, although better models of wind accretion and wind Roche lobe overflow are needed. The magnetic fields inferred to launch pre-CE jets are of the order of a few gauss. In the fourth case, NGC 6778, the kinematics indicate that the jets were launched about 3000 yr after the CE interaction. Magnetic fields of the order of a few hundreds to a few thousands gauss are inferred in this case, approximately in line with predictions of post-CE magnetic fields. However, we remark that in the case of this system, we have not been able to find a reasonable scenario for the formation of the two jet pairs observed: the small orbital separation may preclude the formation of even one accretion disc able to supply the necessary accretion rate to cause the observed jets.

  19. A photometric study of the W UMa-type system U Pegasi

    NASA Astrophysics Data System (ADS)

    Djurašević, G.; Rovithis-Livaniou, H.; Rovithis, P.; Erkapić, S.; Milovanović, N.

    2001-03-01

    In the present study, the activity of the eclipsing binary of the W UMa-type system U Peg is examined by analysing the photoelectric observations covering the period from 1950 to 1989. During this period, the light curves show significant differences and asymmetries. The analysis of the corresponding light curves is made using Djurašević's inverse problem method. To explain the light-curve asymmetries and variations, we used a Roche model that involved regions containing spots on the components. The analysis shows that the system U Peg is in an overcontact configuration (fover ~ 14.9%). The Roche model with spotted areas on the cooler component yields a good fit of the observations for the whole set of the analysed light curves without any changes of the basic system parameters. This indicates that the complex nature of the light-curve variations during the examined period can be explained by the evolution and motion of spotted areas on the cooler component. According to the obtained results, the spotted areas cover a significant part of the stellar surface; the changes in their location and size with time are examined.

  20. Hematological and Biochemical Markers of Iron Status in a Male, Young, Physically Active Population

    PubMed Central

    Nunes, Lázaro Alessandro Soares; Grotto, Helena Zerlotti W.; Brenzikofer, René; Macedo, Denise Vaz

    2014-01-01

    The aim of this study was to establish reference intervals (RIs) for the hemogram and iron status biomarkers in a physically active population. The study population included male volunteers (n = 150) with an average age of 19 ± 1 years who had participated in a regular and controlled exercise program for four months. Blood samples were collected to determine hematological parameters using a Sysmex XE-5000 analyzer (Sysmex, Kobe, Japan). Iron, total iron-binding capacity (TIBC), transferrin saturation and ferritin, and high-sensitivity C-reactive protein (CRP) concentrations in serum samples were measured using commercial kits (Roche Diagnostics, GmbH, Mannheim, Germany) and a Roche/Hitachi 902 analyzer. The RIs were established using the RefVal program 4.1b. The leucocyte count, TIBC, and CRP and ferritin concentrations exhibited higher RIs compared with those in a nonphysically active population. Thirty volunteers (outliers) were removed from the reference population due to blood abnormalities. Among the outliers, 46% exhibited higher CRP concentrations and lower concentrations of iron and reticulocyte hemoglobin compared with the nonphysically active population (P < 0.001). Our results showed that it is important to establish RIs for certain laboratory parameters in a physically active population, especially for tests related to the inflammatory response and iron metabolism. PMID:25045665

  1. LUT Reveals a New Mass-transferring Semi-detached Binary

    NASA Astrophysics Data System (ADS)

    Qian, S.-B.; Zhou, X.; Zhu, L.-Y.; Zejda, M.; Soonthornthum, B.; Zhao, E.-G.; Zhang, J.; Zhang, B.; Liao, W.-P.

    2015-12-01

    GQ Dra is a short-period eclipsing binary in a double stellar system that was discovered by Hipparcos. Complete light curves in the UV band were obtained with the Lunar-based Ultraviolet Telescope in 2014 November and December. Photometric solutions are determined using the W-D (Wilson and Devinney) method. It is discovered that GQ Dra is a classical Algol-type semi-detached binary where the secondary component is filling the critical Roche lobe. An analysis of all available times of minimum light suggests that the orbital period is increasing continuously at a rate of \\dot{P}=+3.48(+/- 0.23)× {10}-7 days yr-1. This could be explained by mass transfer from the secondary to the primary, which is in agreement with the semi-detached configuration with a lobe-filling secondary. By assuming a conservation of mass and angular momentum, the mass transfer rate is estimated as \\dot{m}=9.57(+/- 0.63)× {10}-8 {M}⊙ {{yr}}-1. All of these results reveal that GQ Dra is a mass-transferring semi-detached binary in a double system that was formed from an initially detached binary star. After the massive primary evolves to fill the critical Roche lobe, the mass transfer will be reversed and the binary will evolve into a contact configuration with two sub-giant or giant component stars.

  2. Controlled evaluation of the agar-slide and radiometric blood culture systems for the detection of bacteremia and fungemia.

    PubMed Central

    Weinstein, M P; Reller, L B; Mirrett, S; Stratton, C W; Reimer, L G; Wang, W L

    1986-01-01

    A commercially available agar-slide blood culture bottle (Septi-Chek; Roche Diagnostics, Div. Hoffman-La Roche, Inc., Nutley, N.J.) was compared with the radiometric blood culture system (BACTEC; Johnston Laboratories, Inc., Towson, Md.) in 8,544 paired blood cultures from adult patients. The systems were inoculated with equal volumes (10 ml) of blood. Overall, there was no statistically significant difference between the two systems in the recovery of clinically important microorganisms, but significantly more members of the family Enterobacteriaceae other than Escherichia coli were detected by the agar-slide system (P less than 0.005). The agar-slide system detected more fungi, and the BACTEC detected more anaerobic bacteria; however, small numbers of recovered organisms precluded statistical significance. When microorganisms grew in both systems, their presence was detected one or more days earlier in the BACTEC (P less than 0.001). More contaminants grew in the agar-slide system (P less than 0.001). Both systems performed well, and either system should provide high yield and prompt detection of positive blood cultures in patients with bacteremia and fungemia if used in an optimal way as recommended by the respective manufacturers. PMID:3517047

  3. Risk Factors for Acquisition and Clearance of Oral Human Papillomavirus Infection Among HIV-Infected and HIV-Uninfected Adults

    PubMed Central

    Beachler, Daniel C.; Sugar, Elizabeth A.; Margolick, Joseph B.; Weber, Kathleen M.; Strickler, Howard D.; Wiley, Dorothy J.; Cranston, Ross D.; Burk, Robert D.; Minkoff, Howard; Reddy, Susheel; Xiao, Weihong; Guo, Yingshi; Gillison, Maura L.; D'Souza, Gypsyamber

    2015-01-01

    Human papillomavirus (HPV) causes the majority of oropharyngeal cancers in the United States, yet the risk factors for and natural history of oral HPV infection are largely unknown. In 2010–2011, a US-based longitudinal cohort study of 761 human immunodeficiency virus (HIV)-infected and 469 at-risk HIV-uninfected participants from the Multicenter AIDS Cohort Study and the Women's Interagency HIV Study was initiated. Semiannually collected oral rinses were evaluated for 37 HPV genotypes using the Roche LINEAR ARRAY HPV Genotyping Test (Roche Molecular Systems, Pleasanton, California), and factors associated with oral HPV incidence and clearance were explored using adjusted Wei-Lin-Weissfeld modeling. Through 2013, the 2-year cumulative incidence of any type of oral HPV infection was 34% in HIV-infected persons and 19% in HIV-uninfected persons. However, many of these infections cleared. Seven percent of incident infections and 35% of prevalent infections persisted for at least 2 years. After adjustment for other risk factors, HIV infection (adjusted hazard ratio = 2.3, 95% confidence interval: 1.7, 3.2), reduced current CD4 cell count, and increased numbers of oral sex and “rimming” partners increased the risk of incident oral HPV infection, whereas male sex, older age, and current smoking increased the risk of oral HPV persistence (each P < 0.05). This helps explain the consistent associations observed between these factors and prevalent oral HPV infection in previous cross-sectional studies. PMID:25480823

  4. 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.

  5. RY Aquarius a Binary System with Pulsating delta-scuti Primary Component

    NASA Astrophysics Data System (ADS)

    Manzoori, Davood; Salar, Abbasvand

    2016-07-01

    We present simultaneous new BVI light curves along with radial velocity curve analysis of the RY Aqr system, using the PHysics Of Eclipsing BinariEs code. The analysis indicates that while the primary is completely inside its Roche critical surface, the secondary has filled out its Roche surface. In addition, the positions of the system components on M–R, H–R diagrams are specified, which show that the primary is a main-sequence or nearly main-sequence star while the secondary is an evolved subgiant. In addition, analysis of the period and luminosity variations of the system were carried out. Fourier frequency analysis of light variation indicates that the primary is a pulsating, δ-scuti variable star. Moreover, O–C curve analysis shows that the period of the system is secularly decreasing with a rate of dp/dt = 0.074 s yr‑1. This decrease in the orbital period variations was attributed to a mass and angular momentum loss from the system with a rate of 2.57× {10}-10{M}ȯ {{yr}}-1. Apart from the secular period decreases, the orbital period of the system is modulated by a cyclic period of 72.69 year, which was attributed to a third body orbiting around the barycenter of the system.

  6. Oseltamivir: a first line defense against swine flu.

    PubMed

    Agrawal, Ritesh; Rewatkar, Prarthana V; Kokil, Ganesh R; Verma, Arunima; Kalra, Atin

    2010-07-01

    Oseltamivir (has known by its brand name 'Tamiflu') is a prodrug, requiring ester hydrolysis for conversion to the active form, Oseltamivir carboxylate. Oseltamivir was the first orally active neuraminidase inhibitor commercially developed by US based Gilead Sciences and is currently marketed by F. Hoffmann-La Roche (Roche). Oseltamivir is an antiviral drug which works by blocking the function of the viral neuraminidase protein. US FDA approved Oseltamivir for prophylaxis of uncomplicated influenza A and B. Currently, Oseltamivir is the only first line defense drug available for the treatment of Swine Flu. Orally Oseltamivir is well tolerated and effective in treatment of influenza in adolescents and adults, including the elderly and patients with chronic cardiac and/or respiratory disease. Many of the pharmaceutical companies targeted Oseltamivir as a block buster molecule. In present review, we have tried to cover chemistry, mode of binding, total synthesis, current patent status, adverse effect and clinical status of Oseltamivir giving emphasis on medicinal chemistry aspect. PMID:20843284

  7. In Vitro Metabolism of 20(R)-25-Methoxyl-Dammarane-3, 12, 20-Triol from Panax notoginseng in Human, Monkey, Dog, Rat, and Mouse Liver Microsomes

    PubMed Central

    Li, Wei; Liu, Li; Sun, Baoshan; Guo, Zhenghong; Shi, Caihong; Zhao, Yuqing

    2014-01-01

    The present study characterized in vitro metabolites of 20(R)-25-methoxyl-dammarane-3β, 12β, 20-triol (20(R)-25-OCH3-PPD) in mouse, rat, dog, monkey and human liver microsomes. 20(R)-25-OCH3-PPD was incubated with liver microsomes in the presence of NADPH. The reaction mixtures and the metabolites were identified on the basis of their mass profiles using LC-Q/TOF and were quantified using triple quadrupole instrument by multiple reaction monitoring. A total of 7 metabolites (M1–M7) of the phase I metabolites were detected in all species. 25(R)-OCH3-PPD was metabolized by hydroxylation, dehydrogenation, and O-demethylation. Enzyme kinetic of 20(R)-25-OCH3-PPD metabolism was evaluated in rat and human hepatic microsomes. Incubations studies with selective chemical inhibitors demonstrated that the metabolism of 20(R)-25-OCH3-PPD was primarily mediated by CYP3A4. We conclude that 20(R)-25-OCH3-PPD was metabolized extensively in mammalian species of mouse, rat, dog, monkey, and human. CYP3A4-catalyzed oxygenation metabolism played an important role in the disposition of 25(R)-OCH3-PPD, especially at the C-20 hydroxyl group. PMID:24736630

  8. Short clones or long clones? A simulation study on the use of paired reads in metagenomics

    PubMed Central

    2010-01-01

    Background Metagenomics is the study of environmental samples using sequencing. Rapid advances in sequencing technology are fueling a vast increase in the number and scope of metagenomics projects. Most metagenome sequencing projects so far have been based on Sanger or Roche-454 sequencing, as only these technologies provide long enough reads, while Illumina sequencing has not been considered suitable for metagenomic studies due to a short read length of only 35 bp. However, now that reads of length 75 bp can be sequenced in pairs, Illumina sequencing has become a viable option for metagenome studies. Results This paper addresses the problem of taxonomical analysis of paired reads. We describe a new feature of our metagenome analysis software MEGAN that allows one to process sequencing reads in pairs and makes assignments of such reads based on the combined bit scores of their matches to reference sequences. Using this new software in a simulation study, we investigate the use of Illumina paired-sequencing in taxonomical analysis and compare the performance of single reads, short clones and long clones. In addition, we also compare against simulated Roche-454 sequencing runs. Conclusion This work shows that paired reads perform better than single reads, as expected, but also, perhaps slightly less obviously, that long clones allow more specific assignments than short ones. A new version of the program MEGAN that explicitly takes paired reads into account is available from our website. PMID:20122183

  9. 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.

  10. Wobbling and Precessing Jets from Warped Disks in Binary Systems

    NASA Astrophysics Data System (ADS)

    Sheikhnezami, Somayeh; Fendt, Christian

    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.