Science.gov

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 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.

  15. 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.

  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

    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.

  1. 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.

  2. 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

  3. 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

  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. 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

  14. 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

  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. "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

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

    ERIC Educational Resources Information Center

    American Association of University Professors, 2014

    2014-01-01

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

  3. 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. 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

  7. 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

  8. 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

  9. 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

  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. 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

  14. 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

  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. [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

  18. 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

  19. 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...

  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. 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.

  18. 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.

  19. 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)...

  20. 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.

  1. 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...

  2. 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 ...

  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. 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

  5. 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

  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. 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…

  9. 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…

  10. 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...

  11. 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...

  12. 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.…

  13. 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...

  14. 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…

  15. 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

  16. 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.

  17. 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...

  18. 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…

  19. 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)

  20. 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...

  1. 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)...

  2. 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...

  3. 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...

  4. 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

  5. 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…

  6. 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.

  7. 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...

  8. 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…

  9. 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 ...

  10. 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.

  11. 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,…

  12. 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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using the Genome Sequencer FLX Titanium technology (Roche, 454 Life Sciences), a ribonucleic acid (RNA) virus-specific metagenome was prepared using the pooled intestinal contents collected from North Carolina turkey flocks experiencing enteric disease signs. This analysis produced 6526 contigs rang...

  14. Genome Wide Characterization of Simple Sequence Repeats in Cucumber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The whole genome sequence of the cucumber cultivar Gy14 was recently sequenced at 15× coverage with the Roche 454 Titanium technology. The microsatellite DNA sequences (simple sequence repeats, SSRs) in the assembled scaffolds were computationally explored and characterized. A total of 112,073 SSRs ...

  15. 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. 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....

  17. 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...

  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. 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.

  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. 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.

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Crida, A.; Charnoz, S.

    2012-11-01

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

  6. 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)

  7. 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.

  8. 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.

  9. 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).

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  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. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

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

    SciTech Connect

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

    1988-05-01

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. [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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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]. [....

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. [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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. [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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline

    PubMed Central

    2010-01-01

    Background Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions. Results We developed an integrated database oriented software pipeline for analysis of 454/Roche GS-FLX amplicon resequencing experiments using Perl and a relational database. The pipeline enables variation detection, variation detection validation, and advanced data analysis, which provides information that can be used to optimize PCR efficiency using traditional means. The modular approach enables customization of the pipeline where needed and allows researchers to adopt their analysis pipeline to their experiments. Clear documentation and training data is available to test and validate the pipeline prior to using it on real sequencing data. Conclusions We designed an open-source database oriented pipeline that enables advanced analysis of 454/Roche GS-FLX amplicon resequencing experiments using SQL-statements. This modular database approach allows easy coupling with other pipeline modules such as variant interpretation or a LIMS system. There is also a set of standard reporting scripts available. PMID:20487544

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  2. ACTIVITY ON THE M STAR OF QS Vir

    SciTech Connect

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

    2010-03-15

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

  3. Unexpectedly dangerous escargot stew: oleandrin poisoning through the alimentary chain.

    PubMed

    Gechtman, Cecilia; Guidugli, Federico; Marocchi, Alessandro; Masarin, Adriano; Zoppi, Francesco

    2006-01-01

    A female, aged 43 and a male, aged 66, experienced gastrointestinal and cardiovascular symptoms after a meal including snail stew. Twelve hours after the ingestion, they presented with nausea, vomiting, diarrhea, and cardiovascular symptoms typical of acute toxic digoxin ingestion and were hospitalized. The man's electrocardiogram was altered, and the woman's was normal. Serum digoxin levels, measured on a Roche COBAS Integra 800 with the Roche On-Line Digoxin reagent, were 1.14 and 1.00 nmol/L, respectively. Potassium levels were normal in both patients. The serum digoxin concentration decreased on the second day, and symptoms resolved on the third day with patients fully recovered (i.e., reversion to a normal sinus rhythm). Cardiac-glycoside-like intoxication symptoms follow the ingestion of leaves or flowers of Nerium oleander. The consumed snails were suspected to be responsible for the intoxication. In the homogenized snail tissue, the concentration expressed in digoxin equivalents was 0.282 nmol/g. The presence of oleandrin and oleandrigenin in the snails was confirmed by liquid chromatography-tandem mass spectrometry analysis, which was performed on a ionic-trap Finnigan LXQ instrument using an electrospray ionization interface. High-pressure liquid chromatographic separation was performed on a C18 column with a gradient of methanol/water. An extract of oleander leaves was used as reference. PMID:17137529

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

    SciTech Connect

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

    2012-10-01

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

  5. A Variant of the Mukai Pairing via Deformation Quantization

    NASA Astrophysics Data System (ADS)

    Ramadoss, Ajay C.

    2012-06-01

    Let X be a smooth projective complex variety. The Hochschild homology HH•( X) of X is an important invariant of X, which is isomorphic to the Hodge cohomology of X via the Hochschild-Kostant-Rosenberg isomorphism. On HH•( X), one has the Mukai pairing constructed by Caldararu. An explicit formula for the Mukai pairing at the level of Hodge cohomology was proven by the author in an earlier work (following ideas of Markarian). This formula implies a similar explicit formula for a closely related variant of the Mukai pairing on HH•( X). The latter pairing on HH•( X) is intimately linked to the study of Fourier-Mukai transforms of complex projective varieties. We give a new method to prove a formula computing the aforementioned variant of Caldararu's Mukai pairing. Our method is based on some important results in the area of deformation quantization. In particular, we use part of the work of Kashiwara and Schapira on Deformation Quantization modules together with an algebraic index theorem of Bressler, Nest and Tsygan. Our new method explicitly shows that the "Noncommutative Riemann-Roch" implies the classical Riemann-Roch. Further, it is hoped that our method would be useful for generalization to settings involving certain singular varieties.

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

    PubMed

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

    2014-07-01

    Next-generation sequencing technologies enable the identification of minor mitochondrial DNA variants with higher sensitivity than Sanger methods, allowing for enhanced identification of minor variants. In this study, mixtures of human mtDNA control region amplicons were subjected to pyrosequencing to determine the detection threshold of the Roche GS Junior(®) instrument (Roche Applied Science, Indianapolis, IN). In addition to expected variants, a set of reproducible variants was consistently found in reads from one particular amplicon. A BLASTn search of the variant sequence revealed identity to a segment of a 611-bp nuclear insertion of the mitochondrial control region (NumtS) spanning the primer-binding sites of this amplicon (Nature 1995;378:489). Primers (Hum Genet 2012;131:757; Hum Biol 1996;68:847) flanking the insertion were used to confirm the presence or absence of the NumtS in buccal DNA extracts from twenty donors. These results further our understanding of human mtDNA variation and are expected to have a positive impact on the interpretation of mtDNA profiles using deep-sequencing methods in casework. PMID:24738853

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

    PubMed

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

    2016-07-01

    PCR methods are nowadays between the most rapid and sensitive methods for screening and diagnosing herpes simplex virus (HSV) type 1 and 2. The aim of this study was to analyze the reliability, accuracy, and usefulness of the new assay HSV OligoGen kit in comparison with the Roche LightCycler HSV ½ Qual Kit assay for the detection of HSV in clinical samples. For this analysis, a prospective study was designed for detection of HSV-1 and HSV-2 including 110 ulcer specimens, 48 urine, 48 endocervical, 43 cerebral spinal fluids, 4 urethral and 3 pharyngeal swabs that were sent from a regional STI clinic or an Intensive Clinical Unit, both in Seville, Spain. In comparison to the Roche LightCycler HSV ½ Qual Kit assay, sensitivity, specificity, positive and negative predicative values, and kappa value for HSV detection using the HSV OligoGen kit were 96.2%, 100%, 100%, 98.3%, and 0.97 for HSV-1, respectively. For HSV-2, the corresponding values were 98.3%, 100%, 100%, 99.5%, and 0.98, respectively. Statistical data obtained in this study confirms the usefulness and reliable results of this new assay. PMID:27185644

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

    NASA Astrophysics Data System (ADS)

    Blackman, E.

    2014-04-01

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

  9. Simultaneous CCD Photometry of Two Eclipsing Binary Stars in Pegasus - Part2: BX Peg

    NASA Astrophysics Data System (ADS)

    Alton, K. B.

    2013-05-01

    BX Peg is an overcontact W UMa binary system (P = 0.280416 d) which has been rather well studied, but not fully understood due to complex changes in eclipse timings and light curve variations attributed to star spots. Photometric data collected in three bandpasses (B, V, and Ic) produced nineteen new times of minimum for BX Peg. These were used to update the linear ephemeris and further analyze potential changes in orbital periodicity by examining long-term changes in eclipse timings. In addition, synthetic fitting of light curves by Roche modeling was accomplished with the assistance of three different programs, two of which employ the Wilson-Devinney code. Different spotted solutions were necessary to achieve the best Roche model fits for BX Peg light curves collected in 2008 and 2011. Overall, the long-;term decrease (9.66 × 10-3 sec y-1) in orbital period defined by the parabolic fit of eclipse timing data could arise from mass transfer or angular momentum loss. The remaining residuals from observed minus predicted eclipse timings for BX Peg exhibit complex but non-random behavior. These may be related to magnetic activity cycles and/or the presence of an unseen mass influencing the times of minimum, however, additional minima need to be collected over a much longer timescale to resolve the nature of these complex changes.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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

  19. Changes in potassium and sodium concentrations in stored blood

    PubMed Central

    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. 50mls 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 0.59mmol/l and 0.50mmol/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.

  20. Stability of Gas Clouds in Galactic Nuclei: An Extended Virial Theorem

    NASA Astrophysics Data System (ADS)

    Chen, Xian; Amaro-Seoane, Pau; Cuadra, Jorge

    2016-03-01

    Cold gas entering the central 1-102 pc of a galaxy fragments and condenses into clouds. The stability of the clouds determines whether they will be turned into stars or can be delivered to the central supermassive black hole (SMBH) to turn on an active galactic nucleus (AGN). The conventional criteria to assess the stability of these clouds, such as the Jeans criterion and Roche (or tidal) limit, are insufficient here, because they assume the dominance of self-gravity in binding a cloud, and neglect external agents, such as pressure and tidal forces, which are common in galactic nuclei. We formulate a new scheme for judging this stability. We first revisit the conventional Virial theorem, taking into account an external pressure, to identify the correct range of masses that lead to stable clouds. We then extend the theorem to further include an external tidal field, which is equally crucial for the stability in the region of our interest—in dense star clusters, around SMBHs. We apply our extended Virial theorem to find new solutions to controversial problems, namely, the stability of the gas clumps in AGN tori, the circum-nuclear disk in the Galactic Center, and the central molecular zone of the Milky Way. The masses we derive for these structures are orders of magnitude smaller than the commonly used Virial masses (equivalent to the Jeans mass). Moreover, we prove that these clumps are stable, contrary to what one would naively deduce from the Roche (tidal) limit.

  1. 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

  2. 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

  3. Erlotinib: CP 358774, NSC 718781, OSI 774, R 1415.

    PubMed

    2003-01-01

    Erlotinib [Tarceva, R 1415, CP 358774, OSI 774, NSC 718781] is a small molecular, once-a-day, orally active inhibitor of the epidermal growth factor receptor tyrosine kinase. This profile has been selected from R&D Insight, a pharmaceutical intelligence database produced by Adis International Ltd. It is one of a class of anticancer drugs that target the underlying molecular mechanism involving oncogenes and tumour suppressor genes, which play critical roles in the conversion of normal cells into a cancerous state. Erlotinib is undergoing clinical development as an oral tablet by an alliance between OSI Pharmaceuticals, Genentech and Roche. OSI Pharmaceuticals, Genentech and Roche have entered an agreement for the global development and commercialisation of erlotinib. Under the terms of the agreement, Genentech and OSI will share costs and profit-taking for commercialising the product in the US. The overall costs of the development programme will be shared equally between the three companies. OSI will keep certain co-promotion rights in the US and Genentech will be responsible for commercialising the drug in the US should the FDA approve it. Roche will take the responsibility for obtaining regulatory approval and commercialisation in territories outside the US and pay royalties to OSI on net sales of the product in these markets. Initially, the alliance partners intend to pursue development of erlotinib in all the major tumour markets, particularly for non-small cell lung cancer (NSCLC) in which the group will focus on front-line combination approaches. Pfizer and OSI Pharmaceuticals in the US were developing erlotinib as a treatment for solid tumours. However, in June 2000, Pfizer merged with Warner-Lambert. The resulting company retained the Pfizer name, but in order to meet Federal Trade Commission requirements for the merger Pfizer granted all developmental and marketing rights for erlotinib to OSI Pharmaceuticals. This divestiture of the erlotinib portfolio, in

  4. ISA 247: trans-ISA 247, trans-R 1524, ISA(TX)247, ISAtx 247, ISATx247, LX 211, LX211, R 1524, R-1524.

    PubMed

    2007-01-01

    Isotechnika is developing the immunosuppressive drug ISA 247, a calcineurin inhibitor that is undergoing clinical development for the treatment of psoriasis (phase III) and prevention of organ rejection after transplantation (phase II). Preclinical development for uveitis is also underway. Other autoimmune disease indications that could be explored include arthritis, type I diabetes and Crohn's disease. ISA 247 was being co-developed as R 1524 by Isotechnika and Roche. However, Roche is no longer involved in the development of this compound. Based on analysis of previously collected data, the trans-ISA 247 isomer was found to be more bioavailable and it is expected that this isomer can be administered at a lower dose compared with the previous formulation that consisted of an equivalent mixture of the two geometric isomers (cis and trans). Preclinical observations indicate that ISA 247 has the potential to be more potent and less toxic than other marketed immunosuppressants in its class used for the prevention of transplant rejection. Experiments to date suggest that ISA 247 is about three times as potent as ciclosporin, while genotoxicity studies in animals have shown that the compound has a significantly reduced tendency to cause renal toxicity. The combination of reduced toxicity and improved potency would give ISA 247 a therapeutic benefit over existing calcineurin-based treatments. Isotechnika and Roche entered into a co-development and commercialisation agreement in April 2002, with Roche gaining the exclusive worldwide marketing rights for ISA 247; Isotechnika received milestone payments of $US4 million and $CAN21.9 million in September 2002 and May 2003, respectively. The agreement was restructured in April 2004, under which Isotechnika will now solely manage and fund the clinical development of trans-ISA 247. Upon successful completion of these trials, Isotechnika will conduct at its own expense a phase IIb study in renal transplantation and phase III

  5. Control of Trachoma from Achham District, Nepal: A Cross-Sectional Study from the Nepal National Trachoma Program

    PubMed Central

    Pant, Bidya Prasad; Bhatta, Ramesh C.; Chaudhary, J. S. P.; Awasthi, Suresh; Mishra, Sailesh; Sharma, Shekhar; Cuddapah, Puja A.; Gwyn, Sarah E.; Stoller, Nicole E.; Martin, Diana L.; Keenan, Jeremy D.; Lietman, Thomas M.; Gaynor, Bruce D.

    2016-01-01

    Background The WHO seeks to control trachoma as a public health problem in endemic areas. Achham District in western Nepal was found to have TF (trachoma follicular) above 20% in a 2006 government survey, triggering 3 annual mass drug administrations finishing in 2010. Here we assess the level of control that has been achieved using surveillance for clinical disease, ocular chlamydia trachomatis infection, and serology for antibodies against chlamydia trachomatis protein antigens. Methods We conducted a cross-sectional survey of children aged 1–9 years in communities in Achham District in early 2014 including clinical examination validated with photographs, conjunctival samples for Chlamydia trachomatis (Amplicor PCR), and serological testing for antibodies against chlamydia trachomatis protein antigens pgp3 and CT694 using the Luminex platform. Findings In 24 randomly selected communities, the prevalence of trachoma (TF and/or TI) in 1–9 year olds was 3/1124 (0.3%, 95% CI 0.1 to 0.8%), and the prevalence of ocular chlamydia trachomatis infection was 0/1124 (0%, 95% CI 0 to 0.3%). In 18 communities selected because they had the highest prevalence of trachoma in a previous survey, the prevalence of TF and/or TI was 7/716 (1.0%, 95% CI 0.4 to 2.0%) and the prevalence of ocular chlamydia trachomatis infection was 0/716 (0%, 95% CI 0 to 0.5%). In 3 communities selected for serological testing, the prevalence of trachoma was 0/68 (0%, 95% CI 0 to 5.3%), the prevalence of ocular chlamydia trachomatis infection was 0/68 (0%, 95% CI 0 to 0.5%), the prevalence of antibodies against chlamydia trachomatis protein antigen pgp3 was 1/68 (1.5%, 95% CI 0.04% to 7.9%), and the prevalence of antibodies against chlamydia trachomatis protein antigen CT694 was 0/68 (0%, 95% CI 0 to 5.3%). Conclusion/Significance This previously highly endemic district in Nepal has little evidence of recent clinical disease, chlamydia trachomatis infection, or serological evidence of trachoma

  6. Diagnostic Accuracy of a Prototype Point-of-Care Test for Ocular Chlamydia trachomatis under Field Conditions in The Gambia and Senegal

    PubMed Central

    Harding-Esch, Emma M.; Holland, Martin J.; Schémann, Jean-François; Molina, Sandra; Sarr, Isatou; Andreasen, Aura A.; Roberts, Chrissy h.; Sillah, Ansumana; Sarr, Boubacar; Harding, Edward F.; Edwards, Tansy; Bailey, Robin L.; Mabey, David C. W.

    2011-01-01

    Background The clinical signs of active trachoma are often present in the absence of ocular Chlamydia trachomatis infection in low prevalence and mass treated settings. Treatment decisions are currently based on the prevalence of clinical signs, and this may result in the unnecessary distribution of mass antibiotic treatment. We aimed to evaluate the diagnostic accuracy of a prototype point-of-care (POC) test, developed for field diagnosis of ocular C. trachomatis, in low prevalence settings of The Gambia and Senegal. Methodology/Principal Findings Three studies were conducted, two in The Gambia and one in Senegal. Children under the age of 10 years were screened for the clinical signs of trachoma. Two ocular swabs were taken from the right eye. The first swab was tested by the POC test in the field and the result independently graded by two readers. The second swab was tested for the presence of C. trachomatis by Amplicor Polymerase Chain Reaction. In Senegal, measurements of humidity and temperature in the field were taken. A total of 3734 children were screened, 950 in the first and 1171 in the second Gambian study, and 1613 in Senegal. The sensitivity of the prototype POC test ranged between 33.3–67.9%, the specificity between 92.4–99.0%, the positive predictive value between 4.3–21.0%, and the negative predictive value between 98.0–99.8%. The rate of false-positives increased markedly at temperatures above 31.4°C and relative humidities below 11.4%. Conclusions/Significance In its present format, this prototype POC test is not suitable for field diagnosis of ocular C. trachomatis as its specificity decreases in hot and dry conditions: the environment in which trachoma is predominantly found. In the absence of a suitable test for infection, trachoma diagnosis remains dependent on clinical signs. Under current WHO recommendations, this is likely resulting in the continued mass treatment of non-infected communities. PMID:21829735

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

    NASA Astrophysics Data System (ADS)

    Salmon, Julien; Canup, Robin M.

    2014-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    NASA Technical Reports Server (NTRS)

    Ladous, Constanze

    1993-01-01

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

  10. 25-hydroxy-Vitamin D status: limitations in comparison and clinical interpretation of serum-levels across different assay methods.

    PubMed

    Enko, Dietmar; Fridrich, Leo; Rezanka, Erwin; Stolba, Robert; Ernst, Juliane; Wendler, Iris; Fabian, Daniel; Hauptlorenz, Susanne; Halwachs-Baumann, Gabriele

    2014-01-01

    Background: Over the last decade, clinical interest to evaluate human 25-hydroxy-vitamin D (25[OH]D) serum levels has increased exponentially. In the present study, four chemiluminescence immunoassays (CLIA), one radioimmunoassy (RIA), and one high performance liquid chromatography (HPLC) method were compared and also with the liquid chromatography-tandem mass spectrometry (LC-MS/MS) method in view of 25(OH)D serum level determination. Methods: For the method comparison, blood samples from 133 consecutive patients were prospectively collected. All participants gave written informed consent for their blood samples to be used in this study. They came to the Department of Nuclear Medicine of the Central Hospital Steyr (Austria) for osteodensidometric measurement as part of their preventive medical check-up. Pearson's correlation coefficients, Bland-Altman plots, and paired t-tests were calculated. Assay-specific reference ranges were considered using blood samples from persons with normal parathormone, calcium, and total-protein values (n = 97). Results: The highest correlation was between the HPLC and the LC-MS/MS method (r = 0.96). The lowest correlation was between the cobas Vitamin D3 assay (Roche) and any of the evaluated assays (r = 0.46 - 0.63). Bland-Altman plots revealed a big negative mean bias in three assays (cobas Vitamin D3 assay [Roche]: -22.8; DiaSorin LIAISON [25[OH]D total CLIA [Diasorin]: -18.4; Diasorin 25[OH]D125 I RIA [Diasorin]: -23.8 [nmol/L]) and a much smaller positive mean bias in the other assays (ClinRep complete 25[OH]D2/D3 HPLC kit [Recipe]: 2.7; ADVIA Centaur Vitamin D total assay [Siemens]: 8.2; IDS total vitamin D assay [Immunodiagnostic Systems]: 12.1 [nmol/L]) compared to the LC-MS/MS method. Meanwhile, the manufacturer has withdrawn the cobas Vitamin D3 assay from the market. Conclusions: Poor antibody specificity with cross-reactivity to other vitamin D metabolites, incomplete extraction of the 25(OH)D analyte from the vitamin D

  11. Performance of an Optimized Paper-Based Test for Rapid Visual Measurement of Alanine Aminotransferase (ALT) in Fingerstick and Venipuncture Samples

    PubMed Central

    Noubary, Farzad; Coonahan, Erin; Schoeplein, Ryan; Baden, Rachel; Curry, Michael; Afdhal, Nezam; Kumar, Shailendra; Pollock, Nira R.

    2015-01-01

    Background A paper-based, multiplexed, microfluidic assay has been developed to visually measure alanine aminotransferase (ALT) in a fingerstick sample, generating rapid, semi-quantitative results. Prior studies indicated a need for improved accuracy; the device was subsequently optimized using an FDA-approved automated platform (Abaxis Piccolo Xpress) as a comparator. Here, we evaluated the performance of the optimized paper test for measurement of ALT in fingerstick blood and serum, as compared to Abaxis and Roche/Hitachi platforms. To evaluate feasibility of remote results interpretation, we also compared reading cell phone camera images of completed tests to reading the device in real time. Methods 96 ambulatory patients with varied baseline ALT concentration underwent fingerstick testing using the paper device; cell phone images of completed devices were taken and texted to a blinded off-site reader. Venipuncture serum was obtained from 93/96 participants for routine clinical testing (Roche/Hitachi); subsequently, 88/93 serum samples were captured and applied to paper and Abaxis platforms. Paper test and reference standard results were compared by Bland-Altman analysis. Findings For serum, there was excellent agreement between paper test and Abaxis results, with negligible bias (+4.5 U/L). Abaxis results were systematically 8.6% lower than Roche/Hitachi results. ALT values in fingerstick samples tested on paper were systematically lower than values in paired serum tested on paper (bias -23.6 U/L) or Abaxis (bias -18.4 U/L); a correction factor was developed for the paper device to match fingerstick blood to serum. Visual reads of cell phone images closely matched reads made in real time (bias +5.5 U/L). Conclusions The paper ALT test is highly accurate for serum testing, matching the reference method against which it was optimized better than the reference methods matched each other. A systematic difference exists between ALT values in fingerstick and paired

  12. EMS in Viracept--the course of events in 2007 and 2008 from the non-clinical safety point of view.

    PubMed

    Müller, Lutz; Singer, Thomas

    2009-11-12

    Viracept (nelfinavir) is an HIV protease inhibitor supplied by Roche outside the US, Canada and Japan. Viracept was first introduced by Roche in 1998. Although newer protease inhibitors have become available for the treatment of HIV, it is viewed as a useful medicine for patients who are intolerant to ritonavir (since it does not require ritonavir boosting), pregnant women, and patients in resource-limited settings, since the formulation is heat-stable and does not require refrigeration. The relatively high prevalence of HIV in some of the third world countries means that it was also a product of choice for young women of childbearing age, pregnant and nursing women and young children. On 18 May 2007 F. Hoffmann-La Roche received first reports of a "bad smell" of blisterpacked Viracept tablets and one adverse drug report of nausea and vomiting from patients in Spain. Subsequently, ethyl methanesulfonate (EMS), an established mutagen, carcinogen and teratogen was identified as the potential source of the bad smell. On 6 June 2007, Viracept was globally recalled as the extent of the contamination exceeded the guidances for permissible levels set by regulatory authorities by more than 1000-fold and hence human risk was not readily assessable. In the following, a compilation of the course of events from a non-clinical point of view is presented. This compilation only partially reflects the complexity of the case and the interactions between all parties between May/June 2007 and September 2008 and hence necessarily remains partly a subjective compilation of the authors of this article. This compilation serves also as an introduction into this Special Issue of Toxicology Letters. The data on the cause and levels of contamination, likely duration of intake and affected patient population can be found in the subsequent contributions. Most importantly, we share in other parts of this Special Issue with the scientific community the data and risk assessment arguments that

  13. Photometric evolution, orbital modulation and progenitor of Nova Mon 2012

    NASA Astrophysics Data System (ADS)

    Munari, U.; Dallaporta, S.; Castellani, F.; Valisa, P.; Frigo, A.; Chomiuk, L.; Ribeiro, V. A. R. M.

    2013-10-01

    We present and discuss accurate and densely mapped BVRCIC light curves of the neon Nova Mon 2012, supplemented by the evolution in Stromgren b and y bands and in the integrated flux of relevant emission lines. Our monitoring started with the optical discovery of the nova (50 days past the first detection in gamma-rays by Fermi-LAT) and extend to day +270, well past the end of the super-soft phase in X-rays. The nova was discovered during the nebular decline, well past t3 and the transition to optically thin ejecta. It displayed very smoothly evolving light curves. A bifurcation between y and V light curves took place at the start of the super-soft X-ray source (SSS) phase, and a knee developed towards the end of the SSS phase. The apparent magnitude of the nova at the unobserved optical maximum is constrained to +3 ≤ V ≤ 4.5. The appearance, grow in amplitude and then demise of a 0.29585 (±0.00002) days orbital modulation of the optical brightness was followed along the nova evolution. The observed modulation, identical in phase and period with the analogue seen in the X-ray and satellite ultraviolet, has a near-sinusoidal shape and a weak secondary minimum at phase 0.5. We favour an interpretation in terms of super-imposed ellipsoidal distortion of the Roche lobe filling companion and irradiation of its side facing the WD. Similar light curves are typical of symbiotic stars where a Roche lobe filling giant is irradiated by a very hot WD. Given the high orbital inclination, mutual occultation between the donor star and the accretion disc could contribute to the observed modulation. The optical+infrared spectral energy distribution of Nova Mon 2012 during the quiescence preceding outburst is nicely fitted by an early K-type main-sequence star (˜K3V) at 1.5 kpc distance, reddened by E(B - V) = 0.38, with a WD companion and an accretion disc contributing to the observed blue excess and moderate Hα emission. A typical early K-type main-sequence star with a mass

  14. CHARACTERIZING THE THERMOSPHERE OF HD209458b WITH UV TRANSIT OBSERVATIONS

    SciTech Connect

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

    2010-11-01

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

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

    SciTech Connect

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

    2012-09-20

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

  16. Screening Brucella spp. in bovine raw milk by real-time quantitative PCR and conventional methods in a pilot region of vaccination, Edirne, Turkey.

    PubMed

    Kaynak-Onurdag, F; Okten, S; Sen, B

    2016-05-01

    Brucellosis is a worldwide zoonotic disease transmitted to humans by consumption of contaminated milk and milk products. Brucellosis is endemic in Turkey, and Edirne has a high Brucella prevalence. Brucellosis is prevented by live-attenuated vaccines for animals and the vaccination program has been in place since 1984 in Turkey. Thrace is the pilot region for this vaccination program. The gold standard diagnostic technique for brucellosis is still the isolation of suspicious bacterial colonies followed by bacteriological identification, but it is very time consuming and laborious. In many studies, Brucella has been investigated by PCR techniques. However, PCR-based methods cannot differentiate between the vaccine strain and the virulent strain; thus, the vaccine strain may interfere with the virulent strain and causes false-positive reactions. To monitor brucellosis control programs effectively, it is important to distinguish vaccine and field strains of Brucella spp. In this study, raw milk samples were collected from 99 cows at 12 different barns in 5 villages of Edirne (Turkey). Bacteriological analyses and real-time quantitative (q)PCR experiments were applied to all samples. The DNA was isolated using Biospeedy DNA-Tricky Purification Kit (Bioeksen, Istanbul, Turkey). For all reactions, Roche Light Cycler Nano (Roche Diagnostics, Mannheim, Germany) instrument and Biospeedy EvaGreen qPCR Pre-Mix (Bioeksen) were used. The data were analyzed using Roche LightCycler NanoSoftware 1.0. For samples that were negative by bacteriological analyses and positive by qPCR, we developed a novel qPCR-based method to differentiate the virulent B. abortus strains and B. abortus S19 vaccine strain. We designed qPCR primers targeting the outer membrane protein of B. abortus. The qPCR products were sequenced using the ABI Prism Big Dye Terminator Cycle Sequencing Ready Reaction Kit on an ABI Prism 377 DNA sequencer (Applied Biosystems, Foster City, CA). In total, 2.02% of the

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

    SciTech Connect

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

    2010-04-20

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

  18. The Effect of Tidal Inflation Instability on the Mass and Dynamical Evolution of Extrasolar Planets with Ultrashort Periods

    NASA Astrophysics Data System (ADS)

    Gu, Pin-Gao; Lin, Douglas N. C.; Bodenheimer, Peter H.

    2003-05-01

    We investigate the possibility of substantial inflation of short-period Jupiter-mass planets, as a result of their internal tidal dissipation associated with the synchronization and circularization of their orbits. We employ the simplest prescription based on an equilibrium model with a constant lag angle for all components of the tide. We show the following: (1) In the low-eccentricity limit, the synchronization of the planets' spin with their mean motion is established before tidal dissipation can significantly modify their internal structure. (2) However, above a critical eccentricity, which is a function of the planets' semimajor axis, tidal dissipation of energy during the circularization process can induce planets to inflate in size before their eccentricity is damped. (3) For moderate eccentricities, the planets adjust to stable thermal equilibria in which the rate of their internal tidal dissipation is balanced by the enhanced radiative flux associated with their enlarged radii. (4) For sufficiently large eccentricities, the planets swell beyond two Jupiter radii and their internal degeneracy is partially lifted. Thereafter, their thermal equilibria become unstable and they undergo runaway inflation until their radii exceed the Roche radius. (5) We determine the necessary and sufficient condition for this tidal inflation instability. (6) These results are applied to study short-period planets. We show that for young Jupiter-mass planets, with a period of less than 3 days, an initial radius of about 2RJ, and an orbital eccentricity greater than 0.2, the energy dissipated during the circularization of their orbits is sufficiently intense and protracted to inflate their sizes up to their Roche radii. (7) We estimate the mass-loss rate, the asymptotic planetary masses, and the semimajor axes for various planetary initial orbital parameters. The possibility of gas overflow through both inner (L1) and outer (L2) Lagrangian points for the planets with short

  19. IUE observations of V Sagittae

    NASA Technical Reports Server (NTRS)

    Koch, R. H.; Corcoran, M. F.; Holenstein, B. D.; Mccluskey, G. E., Jr.

    1986-01-01

    Observations of the nova-like variable V Sge are discussed, and the ground-based light curve is analyzed, compensating for the component interaction effect. Low-dispersion IUE spectra indicate that interstellar reddening is smaller than suggested from visible-band observations. The UV and visible continuum are modeled by a He-rich model and by a simple accretion disk, and the UV spectrum emission lines are used to determine ionization temperatures and a lower N(e) limit. The present data are consistent with the picture of the companion to the He star being embedded in an accretion disk, with the disk being large (of dimension comparable to that of the embedding Roche lobe as a result of vigorous mass transfer) at the time of the ground-based data, and with the disk having been diminished to a radius of the order of 200 times of the neutron star, at the time of the IUE spectra.

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

    NASA Technical Reports Server (NTRS)

    Kaluzienski, L. J.

    1977-01-01

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

  1. Theoretical Studies of Accreting Neutron Stars

    NASA Technical Reports Server (NTRS)

    Taam, Ronald E.

    2003-01-01

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

  2. Strange star equation of state fits the refined mass measurement of 12 pulsars and predicts their radii

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, Taparati; Ray, Subharthi; Li, Xiang-Dong; Dey, Jishnu; Dey, Mira

    2013-06-01

    There are three categories of stars whose masses have been found accurately in recent times: (1) two for which Shapiro delay is used, which is possible due to GR light bending as the partner is heavy - PSR J1614-2230 and PSR J1903+0327, (2) six eclipsing stars for which numerical Roche lobe geometry is used and (3) three stars for which spectroscopic methods are used and in fact for these three the mass and radii both are estimated. Motivated by large colour (Nc) expansion using a modified Richardson potential, along with density-dependent quark masses thereby allowing chiral symmetry restoration, we get compact strange stars fitting all the observed masses.

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

    PubMed

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

    2016-01-01

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

  4. Canadian seismic agreement. Annual report, 1 July 1981 to 30 June 1982

    SciTech Connect

    Lyons, J.A.; Wetmiller, R.J.; Andersen, F.; Drysdale, J.A.; Shannon, W.E.; Hayman, R.B.; Basham, P.W.

    1982-11-01

    Activities undertaken by the Earth Physics Branch (EPB) during the past year are described. Data concentrators were established at Hauterive and Riviere-du-Loup in Quebec and St. John in New Brunswick to handle new stations in eastern Quebec and the Maritimes. Six new stations have been installed at Hauterive and Grosses-Roches, Quebec and Edmunston, Caledonia Mountain, St. George and Mount McKendrick, New Brunswick. Network developments are outlined. A more sophisticated version of the multiplexing outstation software developed under contract and currently being tested is outlined. Version 1 of the Seismic Analysis Monitor (SAM) software package (formerly DISDAP) has just gone into production. A summary of the performance of ECTN over the past year is given. A summary of eastern Canadian seismicity during the reporting period is included.

  5. Resolution of Persistent Cystoid Macular Edema due to Central Retinal Vein Occlusion in a Vitrectomized Eye following Intravitreal Implant of Dexamethasone 0.7 mg

    PubMed Central

    Reibaldi, Michele; Russo, Andrea; Zagari, Marco; Toro, Mario; Grande De, Vittorio; Cifalinò, Valentina; Rametta, Stefania; Faro, Salvatore; Longo, Antonio

    2012-01-01

    We report the case of a 62-year-old woman with a history of vitreoretinal surgery for vitreous hemorrhage secondary to central retinal vein occlusion (CRVO). Because of the persistence of macular edema (ME), she received 2 intravitreal injections of bevacizumab 0.5 mg (Avastin®, Genentech/Roche) three months after vitrectomy, without functional or anatomical improvement. Six months after vitrectomy, she therefore received an intravitreal implant of dexamethasone 0.7 mg (Ozurdex®). An improvement in her best-corrected visual acuity and central macular thickness, as measured by optical coherence tomography, was detected 7 days after the injection, and complete resolution of the ME and retinal hemorrhages was observed 6 months after the injection. Dexamethasone intravitreal implant might be an effective treatment option in ME secondary to CRVO, also in vitrectomized eyes. PMID:22615698

  6. Prevention, diagnosis, and treatment of influenza: current and future options.

    PubMed

    Poehling, K A; Edwards, K M

    2001-02-01

    Because influenza significantly affects the health of children, this review describes the current and future options for preventing, diagnosing, and treating influenza infections. Currently, the inactivated influenza vaccine is recommended for prevention of influenza; however, the live, attenuated, intranasal influenza vaccine is a potential future option. For diagnosis, viral culture is the gold standard, although four rapid diagnostic tests are available for more immediate results. The impetus for rapid results is the availability of effective antiviral agents indicated for early influenza infection. The four currently approved antiviral agents are amantadine, rimantadine, zanamivir [Relenza, Glaxo Wellcome, Inc., Research Triangle Park, NC] and oseltamivir [Tamiflu, Roche Pharmaceuticals, Nutley, NJ]. The indications, benefits, side effects and ages for which each drug is approved are reviewed. PMID:11176246

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

    SciTech Connect

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

    2013-06-01

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

  8. Saturn ring particles as dynamic ephemeral bodies.

    PubMed

    Davis, D R; Weidenschilling, S J; Chapman, C R; Greenberg, R

    1984-05-18

    Although Saturn's rings are within the Roche zone, the accretion of centimeter-sized particles into large aggregates many meters in diameter occurs readily, on a time scale of weeks. These aggregates are disrupted when tidal stresses exceed their very low strengths; thus most of the mass of the ring system is continually processed through a population of large "dynamic ephemeral bodies," which are continually forming and disintegrating. These large aggregates are not at all like the idealized ice spheres often used in modeling Saturn's ring dynamics. Their coefficient of restitution is low, hence they form a monolayer in the ring plane. The optically observable characteristics of the rings are dominated by the swarm of centimeter-sized particles. PMID:17780622

  9. [FT4 immunoassay interference : A case report].

    PubMed

    Chaabouni, Khansa; Hargafi, Khaoula; Elleuch, Aida; Messedi, Mariem; Turki, Mouna; Lahyani, Amina; Ayedi, Fatma

    2015-04-01

    Measurement of thyrotropin and free thyroxin made using immunoassays are usually needed in clinical endocrinology. Here, we report a case of a patient with type 2 diabetes who presented a weight loss. To eliminate hyperthyroidism, thyroid function tests were performed. Free thyroxin (FT4) was decreased using two automated immunoassays TOSOH AIA 1800 and Roche ELECSYS 2010, with a normal thyrotropin value. Thyroid function tests repeated a month later were normal. The patient's history revealed contact with sheep, which may partly explain the interference. Investigations into the patient's serum were carried out using both the PEG test and dilution test. Interference factors were probably antibodies. Despite progress in immunoassays, we should be aware of interference occurrence since it can lead to false results, unnecessary investigations and incorrect treatment. Thus, simple tests must be carried out as if interference in immunoassays were suspected. Dilutions and PEG tests are generally performed as first line investigations. PMID:26375746

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

    PubMed Central

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

    2013-01-01

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

  11. Origin and Evolution of the Uranian and Neptunian Satellites: Some Dynamical Considerations

    NASA Technical Reports Server (NTRS)

    Dermott, S. F.

    1984-01-01

    The satellite system of Neptune is so irregular that some formation mechanism or subsequent dynamical evolution that sets it apart from the other, more regular, satellite systems is obviously indicated. McKinnon argued that satellite capture is the most likely possibility and has shown that tidal circularization of Triton's presumably highly eccentric initial orbit probably resulted in melting of the satellite's interior. The satellite system of Uranus, although somewhat bland, also has a number of special features that indicate an interesting dynamical history. These include the anomalously high orbital inclination of Miranda and the probable coexistence of small satellites and narrow rings inside the plant's Roche limit. The possibility that orbital evolution due to tidal dissipation is involved in both of these phenomena is discussed. Other topics discussed are: the origin of rings; the formation of coorbital satellites; the lack of stable orbit-orbit resonances in the Uranian satellite system; and chaos, tidal heating and the shapes of Miranda and Ariel.

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

    SciTech Connect

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

    2010-04-15

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

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

    SciTech Connect

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

    1991-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

  15. Abuse of flunitrazepam (Rohypnol) and other benzodiazepines in Austin and south Texas.

    PubMed

    Calhoun, S R; Wesson, D R; Galloway, G P; Smith, D E

    1996-01-01

    Flunitrazepam (Rohypnol) is a benzodiazepine sedative-hypnotic that has generated significant media attention in the United States because of its abuse and its association with "date rape." A field investigation was conducted in south Texas to ascertain the nature and consequences of the abuse of flunitrazepam. In semistructured interviews, 66 subjects identified as flunitrazepam users were asked about their use of alcohol and other drugs and their sexual behaviors. Many subjects identified the drugs they had used as "roches" and gave descriptions of tablets of other benzodiazepines that were not consistent with flunitrazepam. Almost all subjects used other drugs, primarily alcohol and marijuana. Adverse consequences included amnesia, discoordination, automobile accidents, sexual assault, and respiratory depression or arrest. A significant proportion of the subjects reported that continued use was unappealing to them. The abuse of sedative-hypnotics in southeast Texas involves several benzodiazepines and is not limited to flunitrazepam. PMID:8811586

  16. Simple sequence repeat markers for the endangered species Clianthus puniceus and C. maximus (Fabaceae)1

    PubMed Central

    Houliston, Gary J.; Ramón-Laca, Ana; Jain, Reema; Mitchell, Caroline M.; Goeke, Dagmar F.

    2015-01-01

    • Premise of the study: Microsatellite markers were developed for Clianthus puniceus using a shotgun sequencing library and tested for cross amplification in the closely related C. maximus to inform population management of these two endangered species. • Methods and Results: We constructed a shotgun sequencing library using a Roche 454 sequencer and searched the resulting data set for putative microsatellite regions. We optimized 12 of these regions to produce polymorphic markers for Clianthus. We tested these markers on four populations of C. maximus and on four C. puniceus individuals of known provenance. Alleles per locus ranged from two to nine, while observed and expected heterozygosities per locus ranged from 0.000 to 1.000 and 0.178 to 0.600, respectively. • Conclusions: These markers will be valuable for ongoing monitoring of the genetic variation in naturally occurring populations of Clianthus and for the selection of individuals for revegetation projects in the species’ former range. PMID:25606358

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

    PubMed

    Nayak, M; Asphaug, E

    2016-01-01

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

  18. Residual Stress Analysis in Thick Uranium Films

    SciTech Connect

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

    2004-12-06

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

  19. Ultraviolet photometry from the Orbiting Astronomical Observatory. XXXIII - The symbiotic star AG Pegasi

    NASA Technical Reports Server (NTRS)

    Gallagher, J. S.; Webbink, R. F.; Holm, A. V.; Anderson, C. M.

    1979-01-01

    Ultraviolet broadband photometry obtained with the Wisconsin Experiment Package on OAO 2 is presented for the symbiotic binary star AG Peg. The hot component of the binary is found to be a luminous ultraviolet source, with an energy distribution consistent with its WN6 optical spectral type. Total luminosities of 1000 and 17,000 suns are found for the hot star by assuming, respectively, that the giant primary of AG Peg is a normal M3 III star and that it fills its Roche lobe. The eruptive behavior of AG Peg is shown to require the higher luminosity, and the activity in AG Peg is discussed in terms of a very slow novalike nuclear-powered event.

  20. Chromospherically active stars. I - HD 136905

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  1. [History of the discovery of the Lasègue phenomenon and its variants].

    PubMed

    Karbowski, K

    1984-07-10

    Ernest Charles Lasègue (1816-1883) discovered, but did not describe himself, the straight-leg-raising sign. This sign was described by one of this disciples, J.-J. Forst, in a doctoral thesis in Paris in 1881. Almost at the same time, L.K. Lazarević in Belgrade dealt with the same subject. The crossed-sciatic phenomenon was described for the first time by a Polish neurologist, J. Fajersztajn. In the same publication he mentioned the possibility of the activation of sciatica as a result of dorsiflexion of the foot. Independently of Fajersztajn, the Genevan specialist for internal medicine, Maurice Roch, observed the same phenomenon and called it "Lasègue du pied". The eponym "Bragard sign" for this manoeuvre is not correct. PMID:6382594

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

    PubMed

    Meulenberg, Frans; de Beaufort, Inez D

    2014-04-01

    Fiction (i.e. novels, short stories, and movies) provides an opportunity for imaginative moral reflection and can serve as a basis for moral argument. Narratives play a role in moral reasoning because they are exemplars as well as tests. Those who care for sick people, should be interested in patient's and literary stories. Exploring the representation of gastroenterological ailments in fiction gives insight in the experience of undergoing colonoscopy, farting, pain, the borders of intimacy, hygiene and the lack of it, taboos and the doctor-patient-relationship. Included authors are, among others: Michel Faber, Alan Bennett, Charles Bukowski, Charlotte Roche and James Joyce. Several movies are discussed as well. Though in general gastroenterological problems don't seem often at foreground in fiction, in some cases they are represented in a more symbolic way, and touch upon some fundamental aspects of the human condition. PMID:24810195

  3. [Metagenomic Analysis of Microbial Communities of the Sediments of the Kara Sea Shelf and the Yenisei Bay].

    PubMed

    Mamaeva, E V; Galach'yants, Yu P; Khabudaev, K V; Petrova, D P; Pogodaeva, T V; Khodzher, T B; Zemskaya, T I

    2016-01-01

    Microbial diversity in the sediments of the Kara Sea shelf and the southern Yenisei Bay, differing in pore water mineralization, was studied using massive parallel pyrosequencing according to the 454 (Roche) technology. Members of the same phyla (Cyanobacteria, Verrucomicrobia, Actinobacteria, Proteobacteria, and Bacteroidetes) predominated in bacterial communities of the sediments, while their ratio and taxonomic composition varied within the phyla and depended on pore water mineralization. Increasing salinity gradient was found to coincide with increased share of the γ-Proteobacteria and decreased abundance of α- and β-Proteo- bacteria, as well as of the phyla Verrucomicrobia, Chloroflexi, Chlorobi, and Acidobacteria. Archaeal diversity was lower, with Thaumarchaeota predominant in the sediments with high and low mineralization, while Crenarchaeota predominated in moderately mineralized sediments. Microbial communities of the Kara Sea shelf and Yenisei Gulf sediments were found to contain the organisms capable of utilization of a broad spectrum of carbon sources, including gaseous and petroleum hydrocarbons. PMID:27476207

  4. Institutional review board (IRB) and ethical issues in clinical research

    PubMed Central

    2012-01-01

    Clinical research has expanded tremendously in the past few decades and consequently there has been growing interest in the ethical guidelines that are being followed for the protection of human subjects. This review summarizes historical scandals and social responses chronologically from World War II to the Death of Ellen Roche (2001) to emphasize the lessons we must learn from history. International ethical guidelines for studies with human subjects are also briefly described in order to understand the circumstances of clinical research. The tasks and responsibilities of the institutions and investigators in human subject research to preserve the safety and welfare of research subjects are summarized. Next, several debated ethical issues and insights are arranged as controversial topics. This brief review and summary seeks to highlight important arguments and make suggestions to institutional review boards (IRBs) to contribute to the future evolution of ethics in clinical research as we advance forward. PMID:22323947

  5. Dynamic assessment of cell viability, proliferation and migration using real time cell analyzer system (RTCA).

    PubMed

    Roshan Moniri, Mani; Young, Ada; Reinheimer, Kelsey; Rayat, Jarrett; Dai, Long-Jun; Warnock, Garth L

    2015-03-01

    Cell viability and cell migration capacities are critical parameters for cell culture-related studies. It is essential to monitor the dynamic changes of cell properties under various co-culture conditions to our better understanding of their behaviours and characteristics. The real time cell analyzer (RTCA, xCELLigence, Roche) is an impedance-based technology that can be used for label-free and real-time monitoring of cell properties, such as cell adherence, proliferation, migration and cytotoxicity. The practicality of this system has been proven in our recent cancer studies. In the present method, we intend to use co-cultures of pancreatic cancer cells (HP62) and mesenchymal stem cells to describe in detail, the procedures and benefits of RTCA. PMID:24443077

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

    PubMed Central

    2014-01-01

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

  7. HST images of the eclipsing pulsar B1957+20

    NASA Technical Reports Server (NTRS)

    Fruchter, Andrew S.; Bookbinder, Jay; Bailyn, Charles D.

    1995-01-01

    We have obtained images of the eclipsing pulsar binary PSR B1957+20 using the Planetary Camera of the Hubble Space Telescope (HST). The high spatial resolution of this instrument has allowed us to separate the pulsar system from a nearby background star which has confounded ground-based observations of this system near optical minimum. Our images limit the temperature of the backside of the companion to T less than or approximately = 2800 K, about a factor of 2 less than the average temperature of the side of the companion facing the pulsar, and provide a marginal detection of the companion at optical minimum. The magnitude of this detection is consistent with previous work which suggests that the companion nearly fills its Roche lobe and is supported through tidal dissipation.

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

    PubMed Central

    2016-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

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

    2016-01-01

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

  11. Adiabatic Mass Loss Model in Binary Stars

    NASA Astrophysics Data System (ADS)

    Ge, H. W.

    2012-07-01

    Rapid mass transfer process in the interacting binary systems is very complicated. It relates to two basic problems in the binary star evolution, i.e., the dynamically unstable Roche-lobe overflow and the common envelope evolution. Both of the problems are very important and difficult to be modeled. In this PhD thesis, we focus on the rapid mass loss process of the donor in interacting binary systems. The application to the criterion of dynamically unstable mass transfer and the common envelope evolution are also included. Our results based on the adiabatic mass loss model could be used to improve the binary evolution theory, the binary population synthetic method, and other related aspects. We build up the adiabatic mass loss model. In this model, two approximations are included. The first one is that the energy generation and heat flow through the stellar interior can be neglected, hence the restructuring is adiabatic. The second one is that he stellar interior remains in hydrostatic equilibrium. We model this response by constructing model sequences, beginning with a donor star filling its Roche lobe at an arbitrary point in its evolution, holding its specific entropy and composition profiles fixed. These approximations are validated by the comparison with the time-dependent binary mass transfer calculations and the polytropic model for low mass zero-age main-sequence stars. In the dynamical time scale mass transfer, the adiabatic response of the donor star drives it to expand beyond its Roche lobe, leading to runaway mass transfer and the formation of a common envelope with its companion star. For donor stars with surface convection zones of any significant depth, this runaway condition is encountered early in mass transfer, if at all; but for main sequence stars with radiative envelopes, it may be encountered after a prolonged phase of thermal time scale mass transfer, so-called delayed dynamical instability. We identify the critical binary mass ratio for the

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

    PubMed Central

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

    2016-01-01

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

  13. Cobimetinib: First Global Approval.

    PubMed

    Garnock-Jones, Karly P

    2015-10-01

    Genentech (a subsidiary of Roche) and Exelixis are developing cobimetinib, an orally available small molecule, for the treatment of various cancers, including malignant melanoma and breast cancer. Cobimetinib inhibits the MEK (mitogen-activated protein kinase) component of the MAPK/ERK signalling pathway, which is frequently over-activated in human tumours. The product has been approved in Switzerland in combination with vemurafenib for the treatment of patients with unresectable or metastatic BRAF V600 mutation-positive melanoma, and is under regulatory review for the same indication in several countries, including the USA and the EU. This article summarizes the milestones in the development of cobimetinib leading to this first approval for unresectable or metastatic BRAF V600 mutation-positive melanoma melanoma. PMID:26452567

  14. [Anti-angiogenic therapies: from theory to practice].

    PubMed

    Bidart, Marie; Berger, François; Pelletier, Laurent

    2013-01-01

    During recent years clear progress has been made in support of tumor pathology. However, the treatment of metastatic disease is now a real therapeutic challenge. Among the new therapeutic strategies, blocking angiogenesis has been the subject of numerous clinical trials. However, if this approach was validated in 2004 by the approval of the first humanized anti-VEGF antibody (bevacizumab or Avastin(®), Roche, 2004), the pre-clinical and clinical studies conducted in the last 5 years have moderated the enthusiasm that these therapies had led in the early 2000s. In November 2011, the US Food and drug administration (FDA) revoke the agency's approval of the breast cancer indication for Avastin(®) because of benefit-risk balance appears negative. This review describes successively the mechanisms of action of antiangiogenic agents, the main anti-angiogenic drugs and the theoretical advantages and practical limitations of these therapies. PMID:24113438

  15. Spectroscopic observations of the optical counterpart of Centaurus X-4

    NASA Technical Reports Server (NTRS)

    Van Paradijs, J.; Verbunt, F.; Van Der Linden, T.; Pedersen, H.; Wamsteker, W.

    1980-01-01

    The optical spectrum of the transient X-ray burst source Centaurus X-4 was observed about 5 weeks after the source reached its maximum. The brightness of the optical counterpart had decreased to V = 18.2, and the star had become appreciably redder (B - V = 0.7) compared to its color at maximum. The spectrum of Centaurus X-4 is similar to that of cataclysmic variables showing strong emission lines of H-1 and weaker lines of He-1 and He-2. The N03 lambda 4640 line is not visible. The continuum energy distribution of Centaurus X-4 shows the presence of a main-sequence star in the system, with spectral type between K3 and K7. This is consistent with the orbital period of 8.2 hr proposed by Kaluzienski et al (1980), if the main-sequence star is close to filling its Roche lobe.

  16. Monocyte chemotactic protein-1 secretion and expression after Toxoplasma gondii infection in vitro depend on the stage of the parasite.

    PubMed

    Brenier-Pinchart, Marie-Pierre; Vigan, Inés; Jouvin-Marche, Evelyne; Marche, Patrice Noél; Pelet, Elisabeth; Gross, Uwe; Ambroise-Thomas, Pierre; Pelloux, Hervé

    2002-08-27

    Infection of human fibroblasts with tachyzoites of RH and Prugniaud strains, two different strains of Toxoplasma gondii, significantly increased monocyte chemotactic protein (MCP)-1 secretion contrary to what happened with bradyzoites of the cystogenetic strain. Quantification of MCP-1 mRNA by RT-PCR showed that this phenomenon is regulated at the transcriptional level. Thus, the stage of parasite can be deciding in MCP-1 induction since only tachyzoites induced MCP-1 expression and secretion. MCP-1 induced by tachyzoites could be involved in cell recruitment, as shown by the quantification of MCP1 ARNm by real-time PCR (LightCycler, Roche Diagnostics), in the pathogenesis of T. gondii infection. PMID:12204371

  17. Massive Binaries: Dynamical and Evolutionary Transformations

    NASA Astrophysics Data System (ADS)

    Gies, D. R.

    2012-12-01

    Observations of massive binaries offer us key insight about the formation, evolution, and destinies of massive stars. Here I review some advances in observational and theoretical studies of massive binaries. Surveys for binaries using radial velocity, photometric, and high angular resolution methods show that the binary frequency is high for O stars in clusters. Evolutionary models for interacting binaries demonstrate the importance of angular momentum transfer during Roche lobe overflow. The mass gainer may reach critical rotation and stem further accretion, and there are many observed cases that show the consequences of such mass loss and transfer. New hydrodynamical models describe colliding wind physics in eccentric binaries such as η Carinae and WR 140. All these research topics are championed by Tony Moffat, and the current richness of this field is due in large measure to his energetic pursuits.

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

    SciTech Connect

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

    2014-12-01

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

  19. A Real-World Perspective on Molecular Design.

    PubMed

    Kuhn, Bernd; Guba, Wolfgang; Hert, Jérôme; Banner, David; Bissantz, Caterina; Ceccarelli, Simona; Haap, Wolfgang; Körner, Matthias; Kuglstatter, Andreas; Lerner, Christian; Mattei, Patrizio; Neidhart, Werner; Pinard, Emmanuel; Rudolph, Markus G; Schulz-Gasch, Tanja; Woltering, Thomas; Stahl, Martin

    2016-05-12

    We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction. PMID:26878596

  20. ADIABATIC MASS LOSS IN BINARY STARS. I. COMPUTATIONAL METHOD

    SciTech Connect

    Ge Hongwei; Chen Xuefei; Han Zhanwen; Webbink, Ronald F. E-mail: mshjell@gmail.co

    2010-07-10

    The asymptotic response of donor stars in interacting binary systems to very rapid mass loss is characterized by adiabatic expansion throughout their interiors. In this limit, energy generation and heat flow through the stellar interior can be neglected. We model this response by constructing model sequences, beginning with a donor star filling its Roche lobe at an arbitrary point in its evolution, holding its specific entropy and composition profiles fixed as mass is removed from the surface. The stellar interior remains in hydrostatic equilibrium. Luminosity profiles in these adiabatic models of mass-losing stars can be reconstructed from the specific entropy profiles and their gradients. These approximations are validated by comparison with time-dependent binary mass transfer calculations. We describe how adiabatic mass-loss sequences can be used to quantify threshold conditions for dynamical timescale mass transfer, and to establish the range of post-common envelope binaries that are allowed energetically. In dynamical timescale mass transfer, the adiabatic response of the donor star drives it to expand beyond its Roche lobe, leading to runaway mass transfer and the formation of a common envelope with its companion star. For donor stars with surface convection zones of any significant depth, this runaway condition is encountered early in mass transfer, if at all; but for main-sequence stars with radiative envelopes, it may be encountered after a prolonged phase of thermal timescale mass transfer, a so-called delayed dynamical instability. We identify the critical binary mass ratio for the onset of dynamical timescale mass transfer as that ratio for which the adiabatic response of the donor star radius to mass loss matches that of its Roche lobe at some point during mass transfer; if the ratio of donor to accretor masses exceeds this critical value, dynamical timescale mass transfer ensues. In common envelope evolution, the dissipation of orbital energy of the

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

    PubMed

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

    2013-01-01

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

  2. Black widow pulsars: the price of promiscuity

    NASA Astrophysics Data System (ADS)

    King, A. R.; Davies, M. B.; Beer, M. E.

    2003-10-01

    The incidence of evaporating `black widow' pulsars (BWPs) among all millisecond pulsars is far higher in globular clusters than in the field. This implies a special formation mechanism for them in clusters. Cluster millisecond pulsars in wide binaries with white dwarf companions exchange them for turnoff-mass stars. These new companions eventually overflow their Roche lobes because of encounters and tides. The millisecond pulsars eject the overflowing gas from the binary, giving mass loss on the binary evolution time-scale. The systems are only observable as BWPs at epochs where this evolution is slow, making the mass loss transparent and the lifetime long. This explains why observed BWPs have low-mass companions. We suggest that at least some field BWPs were ejected from globular clusters or entered the field population when the cluster itself was disrupted.

  3. Testing Common Envelopes on Double White Dwarf Binaries

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  4. A search and modeling of peculiar narrow transient line components in novae spectra

    NASA Astrophysics Data System (ADS)

    Takeda, Larissa; Diaz, Marcos

    2015-08-01

    The formation of peculiar transient narrow emission line components observed in the spectra of a few novae is discussed. We aim to constrain the possible physical sources responsible for those unexpected components that present orbital radial velocity modulations, which were first observed in the post-outburst recombination lines of Nova U Sco 2010. A search for candidates showing similar narrow components is presented. Exploratory photoionization simulations indicate that the forming region cannot be restricted to the Roche Lobe of the primary, but could be located around the outer Lagrangian point L3 . Further analysis disfavors an origin at the companion star. In addition, we analyze possible correlations between the presence of the narrow components, the basic nova parameters and the spectral classification in the initial permitted line phase.

  5. Revised Photometric Elements of the Eclipsing Binary Di-Pegasi

    NASA Astrophysics Data System (ADS)

    Mardirossian, F.; Predolin, F.; Giuricin, G.

    1980-11-01

    Using Wood's (1972) model we have analyzed Binnendijk's (1973) two-colour photoelectric observations - as yet unsolved - of the eclipsing binary DI Peg and the photoelectric lightcurves published by Rucin'ski (1967). Our photoelectric elements, though still in favour of a semidetached configuration considerably differ from Ruciński's previous solution. The F4 primary is accompanied by a fainter and smaller (probably late G) cooler star, which fills its Roche lobe for our photometric mass ratio q = 0.3. The absolute elements of DI Peg, tentatively estimated by assuming for the primary a mass of 1.4 Msun, reveal that the secondary appears to be clearly undermassive for its temperature, size and luminosity, like common mass-exchange cooler remnants of Algol-type binaries.

  6. The shape of stretched Spandex

    NASA Astrophysics Data System (ADS)

    White, Gary

    2002-10-01

    What is the shape that results when a flat rubber sheet is warped by placing a heavy ball upon it? We show that, at distance R far from the center of a ball of mass M, the height h of the surface above the ball's center is given by h(R) = A*M^1/3*R^2/3, where A is a constant determined by the stretchiness of the rubber and the earth's gravitational constant. This happy result allows one to analyze the orbits of marbles and coins as they roll across the surface in some detail, providing very nice analogues for a wealth of topics in celestial mechanics, from Kepler's Laws to tides and the Roche limit.

  7. The shape of ``the Spandex'' and orbits upon its surface

    NASA Astrophysics Data System (ADS)

    White, Gary D.; Walker, Michael

    2002-01-01

    What is the shape that results when a flat rubber sheet is warped by placing a heavy ball upon it? We show that, at distance R far from the center of a ball of mass M, the height h of the surface above the ball's center is given by h(R)=AM1/3R2/3, where A is a constant determined by the stretchiness of the rubber and the earth's gravitational constant. This happy result allows one to analyze the orbits of marbles and coins as they roll across the surface in some detail, providing very nice analogues for a wealth of topics in celestial mechanics, from Kepler's laws to tides and the Roche limit.

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

    PubMed

    Bachelet, Vivienne C

    2014-01-01

    In 2013, we wrote about the harm, waste and deception stemming from conducts adopted by the pharmaceutical industry, by concealing raw data and Clinical Study Reports (CSRs) from the regulator’s view when requesting the marketing patent. We described the case of Tamiflu (Roche), a drug that has been widely used in our population and profusely prescribed by physicians. Health authorities, entailing a great cost for the countries in the region, have also purchased it. In this editorial, we will show how the idea of using antivirals for prophylaxis and treatment of influenza took hold, starting from the first enthusiastic recommendations up to the systematic review published last month in the BMJ. PMID:25383799

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

    PubMed Central

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

    2012-01-01

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

  10. High-throughput microsatellite marker development for the distylous herb Primula mistassinica (Primulaceae)1

    PubMed Central

    Matheny, Hannah; Edwards, Joan; Maroja, Luana S.

    2013-01-01

    • Premise of the study: Twelve microsatellite markers were developed for Primula mistassinica, a distylous, diploid arctic-alpine plant. The markers will be used to investigate the landscape genetics of a disjunct population on Isle Royale, Michigan, and the phylogeographic patterns of the species. • Methods and Results: We used Roche/454 high-throughput technology to sequence microsatellite-enriched regions in the P. mistassinica genome. We developed 12 polymorphic microsatellite primer sets. These loci contained di-, tri-, and tetranucleotide repeats with two to nine alleles per locus when assessed in 23 individuals. • Conclusions: Understanding the historical movements of P. mistassinica will provide insight to the survival prospects of current Arctic plant populations, which face the pressures of global, anthropogenic climate change. PMID:25202573

  11. Novel genomic microsatellite markers for genetic population and diversity studies of tropical scalloped spiny lobster (Panulirus homarus) and their potential application in related Panulirus species.

    PubMed

    Delghandi, M; Goddard, S; Jerry, D R; Dao, H T; Al Hinai, M S N; Al-Amry, W; Al-Marzouqi, A

    2016-01-01

    Fourteen polymorphic microsatellites with perfect di-, tri-, and tetra-nucleotide repeats were identified for Panulirus homarus using Roche 454 whole-genome sequencing method. Microsatellites were efficiently co-amplified in four multiplexes and a singleplex, providing consistent and easily interpretable genotypes. The number of alleles per locus ranged from 2 to 11 with the observed and expected heterozygosity ranging between 0.000-0.532 and 0.031-0.836, respectively. A significant deviation from Hardy-Weinberg equilibrium was observed for majority of the loci, probably due to homozygote excess. Genetic linkage disequilibrium analysis between all the possible pairs of the loci showed significant departure from the null hypothesis in the loci pairs Pho-G11-Pho-G33 and Pho-G33-Pho-G57. High success in primer cross-species amplification of these microsatellite markers indicates their utility for genetic studies of different Panulirus species. PMID:27173289

  12. Doppler tomography in cataclysmic variables: an historical perspective

    NASA Astrophysics Data System (ADS)

    Echevarría, J.

    To mark the half-century anniversary of this newly-born field of Cataclysmic Variables, a special emphasis is made in this review, on the Doppler Effect as a tool in astrophysics. The Doppler Effect was in fact, discovered almost 170 years ago, and has been since, one of the most important tools which helped to develop modern astrophysics. We describe and discuss here, its use in Cataclysmic Variables which, combined with another important tool, the tomography, first devised for medical purposes 70 years ago, helped to devise the astronomical Doppler Tomography, developed only two decades ago. A discussion is made since the first trailed spectra provided a one dimensional analysis of these binaries; on the establishment of a 2D velocity profiling of the accretion discs; and unto modern techniques, which include Roche Tomography, time modulation and 3D imaging.

  13. The interpretation of optical light variations of Centaurus X-3

    NASA Technical Reports Server (NTRS)

    Mauder, H.

    1976-01-01

    The interpretation of optical light variations of X-ray binaries is discussed for the case of negligible reflection effect. The limiting cases of synchronous rotation of the visible star (Roche configuration) and of no rotation (pure tidal deformation) are considered. The theoretical results are compared with the available light curves of Cen X-3. X-ray data of the Copernicus satellite are used to get an impression of the atmospheric structure of the outer layers of the visible component. It is shown, that the X-ray eclipse duration is in good agreement with the mass ration derived from the optical variations. The X-ray eclipse duration is discussed with respect to the extended low states, and a possible correlation of the extended lows with the appearance of the optical light curves is considered.

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

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

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

    SciTech Connect

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

    1991-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  17. Identification of genome-specific transcripts in wheat–rye translocation lines

    PubMed Central

    Lee, Tong Geon; Seo, Yong Weon

    2015-01-01

    Studying gene expression in wheat–rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [1]; Devos et al., 1995 [2]; Lee et al., 2010 [3]; Lee et al., 2013 [4]). To overcome limitations of current gene expression studies on wheat–rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat–rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis. PMID:26484243

  18. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

    PubMed Central

    Holt, Kathryn E; Parkhill, Julian; Mazzoni, Camila J; Roumagnac, Philippe; Weill, François-Xavier; Goodhead, Ian; Rance, Richard; Baker, Stephen; Maskell, Duncan J; Wain, John; Dolecek, Christiane; Achtman, Mark; Dougan, Gordon

    2009-01-01

    Isolates of Salmonella enterica serovar Typhi (Typhi), a human-restricted bacterial pathogen that causes typhoid, show limited genetic variation. We generated whole-genome sequences for 19 Typhi isolates using 454 (Roche) and Solexa (Illumina) technologies. Isolates, including the previously sequenced CT18 and Ty2 isolates, were selected to represent major nodes in the phylogenetic tree. Comparative analysis showed little evidence of purifying selection, antigenic variation or recombination between isolates. Rather, evolution in the Typhi population seems to be characterized by ongoing loss of gene function, consistent with a small effective population size. The lack of evidence for antigenic variation driven by immune selection is in contrast to strong adaptive selection for mutations conferring antibiotic resistance in Typhi. The observed patterns of genetic isolation and drift are consistent with the proposed key role of asymptomatic carriers of Typhi as the main reservoir of this pathogen, highlighting the need for identification and treatment of carriers. PMID:18660809

  19. Photometric Study of Near Contact Binaries

    NASA Astrophysics Data System (ADS)

    Zhu, L.; Qian, S.

    2009-08-01

    Near Contact Binary (NCB) is a kind of close binary in which both components fill or nearly fill their critical Roche Lobes. They are not in contact like W UMa systems, and show EB-type light variations. These characters make the NCB an interesting object. They are important observational targets which may be lying in key evolutionary states. According to the geometric definition of this subclass, NCBs actually comprise semi-detached with primary filling (SD1) or secondary filling (SD2), marginal-contact (C), and marginal-detached (D) systems. We have observed a group of NCBs (e.g. BL and, GW Tau, AS Ser, UU Lyn, RU UMi, GSC3658-0076 etc. ) and constructed an evolutionary sequence of case A mass transfer in observation. Finally, the available orbital period variations and absolute parameters of NCBs are collected and the preliminary statistical results are presented.

  20. Polarization in massive X-ray binaries. I - A low-inclination model for Cygnus X-1

    NASA Technical Reports Server (NTRS)

    Friend, D. B.; Cassinelli, J. P.

    1986-01-01

    The possibility that variable linear polarization in massive X-ray binaries is produced by electron scattering in an asymmetric stellar wind is investigated. The stellar wind is asymmetric because of the gravitational field of the secondary (X-ray source). The degree of asymmetry and the magnitude of the linear polarization are controlled by the degree to which the primary star fills its Roche lobe. For the well-observed X-ray binary Cyg X-1, the present model can produce the correct magnitude for the polarization. Provided that the inclination of the system is less than about 20 deg, the present model should also predict the correct phase dependence of the polarization. Modifications to the model are described which would enable it to apply to systems with higher inclination.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  2. How to get the reduced B fields of millisecond pulsars: Flux expulsion by spindown before the LMXB phase

    NASA Astrophysics Data System (ADS)

    Alpar, Mehmet Ali; Gügercinoǧlu, Erbil

    2016-07-01

    The physical interaction between quantized flux lines of the Type II proton superconductor and the quantized vortex lines of the neutron superfluid is re-visited. Srinivasan et al. (1990) had proposed that this interaction led to reduction of the magnetic field to the B ˜10^9 G range as the flux lines were expelled together with vortex lines during the spindown of the neutron star in an early epoch of binary evolution. The model is discussed with reference to spindown by the wind from the companion prior to the Roche lobe filling LMXB phase. An evolutionary model for the magnetic field and the rotation rate is presented, with application to the 11 Hz accreting pulsar in the LMXB IGR J17480-2446 in Terzan 5 (Patruno et al 2012) as well as 'standard' accreting and radio millisecond pulsar evolution.

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

    SciTech Connect

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

    2010-11-15

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

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

    PubMed

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

    1990-01-01

    Sera from 472 Brazilian subjects, confirmed to be either positive or negative for HIV antibodies and comprising the total clinical spectrum of HIV infection, were utilized in the evaluation of six commercially available enzyme-linked immunosorbent assays (ELISA), as well as of four alternative assays, namely indirect immunofluorescence (IIF), passive hemagglutination (PHA), dot blot and Karpas AIDS cell test. The sensitivities ranged from 100% (Abbott and Roche ELISA) to 84.2% (PHA) and the specificities ranged from 99.3% (IIF) to 80.2% (PHA). The sensitivity and specificity of the PHA and the sensitivity of the Karpas cell test were significantly lower than those of the other tests. Although the IFF and dot blot had good sensitivities and specificities, the six ELISA were more attractive than those tests when other parameters such as ease of reading and duration of assay were considered. PMID:2095632

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

    PubMed

    Rajput, Manoj Kumar

    2016-02-01

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

  6. Comparison of Next-Generation Sequencing Systems

    PubMed Central

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

    2012-01-01

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

  7. Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii

    PubMed Central

    2013-01-01

    Background The yeast Saccharomyces boulardii is used worldwide as a probiotic to alleviate the effects of several gastrointestinal diseases and control antibiotics-associated diarrhea. While many studies report the probiotic effects of S. boulardii, no genome information for this yeast is currently available in the public domain. Results We report the 11.4 Mbp draft genome of this probiotic yeast. The draft genome was obtained by assembling Roche 454 FLX + shotgun data into 194 contigs with an N50 of 251 Kbp. We compare our draft genome with all other Saccharomyces cerevisiae genomes. Conclusions Our analysis confirms the close similarity of S. boulardii to S. cerevisiae strains and provides a framework to understand the probiotic effects of this yeast, which exhibits unique physiological and metabolic properties. PMID:24148866

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

    PubMed Central

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

    2013-01-01

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

  9. Orbital angular momentum loss in PSR 1957 + 20

    NASA Technical Reports Server (NTRS)

    Banit, Menashe; Shaham, Jacob

    1992-01-01

    It is suggested that the companion winds, excited by the radiation from the neutron star in PSR 1957 + 20 form only through the combined action of the radiation heat on the companion's atmosphere and the radiation force on the slowly lifting wind. Ballistic simulations suggest that these winds leave only from selected areas of the illuminated surface of the companion; surface currents channel into these regions relatively hot (but altogether cooler than the companion escape velocity) 'coronal' matter from the whole illuminated area. Under suitable conditions, wind particles spend some time trailing the companion at close distances before taking off to escape from the system. This can torque the binary into angular momentum loss that will be as efficient as the one recently observed in PSR 1957 + 20 if the companion is bloated to dimensions close to that of the Roche lobe.

  10. The Algol-like binary TT Hydrae - The stars, circumstellar matter, and superionized plasma

    NASA Technical Reports Server (NTRS)

    Plavec, Mirek J.

    1988-01-01

    This paper reports on superionized UV emission lines discovered in TT Hydrae (HD 97528), a semidetached eclipsing binary system in the Southern-Hemisphere sky. The list of emission lines observed is typical for interacting nondegenerate binaries of the Algol type, but with system-specific relative-intensity characteristics. The primary component of the system is a B9.5 V main-sequence star with effective temperature of 9800 K. Its mass equals 2.25 solar masses; the radius is 1.9 solar radii; and surface gravity log g equals 4.23. The secondary star has a mass of 0.41 solar mass and fills its critical Roche lobe. Evidence obtained on mass interaction supports the conclusion that HD 97528 is a normal semidetached system.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    PubMed Central

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

    2005-01-01

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

  13. Urinary microalbumin measurement using a homogeneous liposomal immunoassay.

    PubMed

    Frost, S J; Chakraborty, J; Firth, G B

    1996-08-14

    A homogeneous colorimetric immunoassay which has been developed for urinary microalbumin utilizes complement-mediated immunolysis of liposomes containing the dye, sulphorhodamine B. Unlike a previously described model complement-mediated liposomal assay for serum albumin (Frost et al., 1994) which was competitive, this assay uses a sandwich-type format and Fab' (antialbumin)-coated liposomes to increase the assay sensitivity. The liposomal assay, performed using a Cobas Bio analyser (Roche, Welwyn Garden City, UK), gave an acceptable correlation with a radioimmunoassay (NETRIA, London, UK): r = 0.94; y (liposomal assay) = 1.09 x (radioimmunoassay) - 1.54 mg/1. The imprecisions of the assays were similar and matrix effects due to the use of urine samples were determined to be acceptably small. The assay demonstrates the advantage of using Fab'-coated liposomes in sandwich-type liposomal immunoassays over liposomes coated with intact antibody, which failed to elicit complement-mediated immunolysis. PMID:8765163

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

    NASA Technical Reports Server (NTRS)

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

    1979-01-01

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

  15. Short communication: Single molecule, real-time sequencing technology revealed species- and strain-specific methylation patterns of 2 Lactobacillus strains.

    PubMed

    Zhang, Wenyi; Sun, Zhihong; Menghe, Bilige; Zhang, Heping

    2015-05-01

    Pacific Biosciences' (Menlo Park, CA) single molecule, real-time sequencing technology was reported to have some advantages in generating finished genomes and characterizing the epigenome of bacteria. In the present study, this technology was used to sequence 2 Lactobacillus strains, Lactobacillus casei Zhang and Lactobacillus plantarum P-8. Previously, the former bacterium was sequenced by an Applied Biosystems 3730 DNA analyzer (Grand Island, NY), whereas the latter one was analyzed with Roche 454 (Indianapolis, IN) and Illumina sequencing technologies (San Diego, CA). The results showed that single molecule, real-time sequencing resulted in high-quality, finished genomes for both strains. Interestingly, epigenome analysis indicates the presence of 1 active N(6)-methyladenine methyltransferase in L. casei Zhang, but none in L. plantarum P-8. Our study revealed for the first time a completely different methylation pattern in 2 Lactobacillus strains. PMID:25747834

  16. Drug companies, UNAIDS make drugs available.

    PubMed

    1998-01-01

    The United Nations AIDS (UNAIDS) initiative is working with several drug companies and four countries on a pilot program to build a health infrastructure that provides affordable drugs to insure that combination therapies are used appropriately. The countries involved in the program are Uganda, Chile, Vietnam and Cote d'Ivoire, and the drug companies are Glaxo Wellcome, Hoffmann-La Roche, and Virco NV. Each country agreed to form national HIV/AIDS drug advisory boards, and non-profit companies will act as clearinghouses. Financing will come from the pharmaceutical companies, local health ministries, and a $1 million grant from UNAIDS. The program will be evaluated in terms of improvements to overall health care delivery, number of people treated, the impact on emergency care, and the rate of illness and death. PMID:11364863

  17. Ultraviolet, optical, infrared, and microwave observations of HR 5110

    NASA Technical Reports Server (NTRS)

    Little-Marenin, I. R.; Simon, T.; Ayres, T. R.; Cohen, N. L.; Feldman, P. A.

    1986-01-01

    Near-IR JHKLM photometric data and VLBI and IUE radio burst data collected on the short-period spectroscopic binary HR 5110 are analyzed to classify the object. The observed broadband colors were indicative of an F2 IV primary and a spotted K0 IV secondary. The system is being viewed pole-on, so is observable in the UV since the K companion has filled its Roche lobe. In comparisons of such features of Algol and RS VCn stars as the mass ratio, orbital inclination, presence or absence of evidence for mass streams, accretion disks, and active regions, spectral signatures, etc., sufficient similarities are found to classify HR 5110 as an Algol system.

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

    PubMed

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

    2016-06-01

    This is a report of a fortunate story of an unusual AK-47 bullet trajectory which took place during the Paris (France) attack of November 13th, 2015. A young man, trying to protect his girlfriend, interfered between her and a shooter. He had been wounded in the posterior compartment of the thigh. The bullet penetrated him and, instead of exiting, rebound against his Smartphone, which was in the front pocket of his pants. Thanks to that, the missile bullet did not injure his girlfriend but ended its trajectory in the fat tissue of his thigh. Thabouillot O , Perrier P , Roche NC , Agard D , Barbier O , Martin G , Viant E , Leclere JB . A fortunate story of an unusual AK-47 bullet trajectory: always keep a Smartphone in your pocket. Prehosp Disaster Med, 2016;31(3):343-345. PMID:27086713

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Tauris, Thomas M

    2012-02-01

    Millisecond pulsars are old neutron stars that have been spun up to high rotational frequencies via accretion of mass from a binary companion star. An important issue for understanding the physics of the early spin evolution of millisecond pulsars is the impact of the expanding magnetosphere during the terminal stages of the mass-transfer process. Here, I report binary stellar evolution calculations that show that the braking torque acting on a neutron star, when the companion star decouples from its Roche lobe, is able to dissipate >50% of the rotational energy of the pulsar. This effect may explain the apparent difference in observed spin distributions between x-ray and radio millisecond pulsars and help account for the noticeable age discrepancy with their young white dwarf companions. PMID:22301314

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

    PubMed

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

    2003-03-13

    The planet in the system HD209458 is the first one for which repeated transits across the stellar disk have been observed. Together with radial velocity measurements, this has led to a determination of the planet's radius and mass, confirming it to be a gas giant. But despite numerous searches for an atmospheric signature, only the dense lower atmosphere of HD209458b has been observed, through the detection of neutral sodium absorption. Here we report the detection of atomic hydrogen absorption in the stellar Lyman alpha line during three transits of HD209458b. An absorption of 15 +/- 4% (1sigma) is observed. Comparison with models shows that this absorption should take place beyond the Roche limit and therefore can be understood in terms of escaping hydrogen atoms. PMID:12634780

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

    NASA Astrophysics Data System (ADS)

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

    1991-03-01

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

  3. H-beta photometry of V1010 Ophiuchi

    NASA Technical Reports Server (NTRS)

    Corcoran, M. F.; Siah, M. J.; Guinan, E. F.

    1991-01-01

    An analysis is presented of previously unpublished intermediate and narrow band H-beta light curves of the short period eclipsing binary V1010 Oph. The temperature of the primary is determined directly by comparing the UV continuum with Kurucz model atmospheres and solve the broadband lightcurve using the Wilson-Devinney program. The present solution has the primary filling its Roche lobe while the secondary is detached from its lobe. An asymmetry in the light curve in which first quadrature (0.25 P) is brighter than the second quadrature (0.75 P) may be the result of local heating of the inner surface of the secondary by mass transfer from the primary. The present semidetached solution indicates that the system is probably evolved.

  4. Identification of a Novel Human Rhinovirus C Type by Antibody Capture VIDISCA-454

    PubMed Central

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

    2015-01-01

    Causative agents for more than 30 percent of respiratory infections remain unidentified, suggesting that unknown respiratory pathogens might be involved. In this study, antibody capture VIDISCA-454 (virus discovery cDNA-AFLP combined with Roche 454 high-throughput sequencing) resulted in the discovery of a novel type of rhinovirus C (RV-C). The virus has an RNA genome of at least 7054 nt and carries the characteristics of rhinovirus C species. The gene encoding viral protein 1, which is used for typing, has only 81% nucleotide sequence identity with the closest known RV-C type, and, therefore, the virus represents the first member of a novel type, named RV-C54. PMID:25606972

  5. Evolution of planetesimals. I - Dynamics: Relaxation in a thin disk. II - Numerical simulations

    NASA Astrophysics Data System (ADS)

    Palmer, P. L.; Lin, D. N. C.; Aarseth, S. J.

    1993-01-01

    The study examines the effects of density inhomogeneity and differential rotation as well as inelastic collisions on the dynamical evolution of planetesimals. Consideration is given to a three-step analysis: the dynamical evolution of the planetesimals, collisions and mass accumulation, and interaction with gas. It is shown that the velocity dispersion of a cold system of planetesimals increases rapidly due to elastic gravitational scattering. When the dispersion in the epicycle amplitude becomes comparable to the planetesimals' Roche radius, energy is transferred from the systematic Keplerian shear to the dispersive motion. With a numerical N-body scheme, gravitational scattering and physical collisions among a system of planetesimals is simulated. It is shown that dynamical equilibrium is attained with a velocity dispersion comparable to the surface escape velocity of those planetesimals which contribute most of the system mass.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  7. XMM-Newton Proposal 02022304

    NASA Astrophysics Data System (ADS)

    Barnard, Robin

    2003-03-01

    A Z-source candidate has been identified in the core of M31 using data from existing XMM-Newton observations. Z-sources are perhaps the most extreme form of neutron star binary; powered by Roche lobe overflow from a low mass secondary via disc accretion, their X-ray luminosities can reach 10^39 erg/s,and exhibit complex correlations between luminosity and X-ray spectra so thatthey trace out Z-shapes in colour-colour diagrams over a few days. We propose a programme of four 20 ks observations over 4 days to trace the Z-track, which will conclusively prove whether or not the candidate is a Z-source. Also, the programme would access for the first time variability over time-scales of a few days in the 120 sources in the field of view.

  8. Mode of action and application of Scorpion primers to mutation detection

    PubMed Central

    Thelwell, Nicola; Millington, Stephen; Solinas, Antonio; Booth, James; Brown, Tom

    2000-01-01

    Scorpion primers can be used to detect PCR products in homogeneous solution. Their structure promotes a unimolecular probing mechanism. We compare their performance with that of the same probe sequence forced to act in a bimolecular manner. The data suggest that Scorpions indeed probe by a unimolecular mechanism which is faster and more efficient than the bimolecular mechanism. This mechanism is not dependent on enzymatic cleavage of the probe. A direct comparison between Scorpions, TaqMan and Molecular Beacons on a Roche LightCycler indicates that Scorpions perform better, particularly under fast cycling conditions. Development of a cystic fibrosis mutation detection assay shows that Scorpion primers are selective enough to detect single base mutations and give good sensitivity in all cases. Simultaneous detection of both normal and mutant alleles in a single reaction is possible by combining two Scorpions in a multiplex reaction. Such favourable properties of Scorpion primers should make the technology ideal in numerous applications. PMID:11000267

  9. On the Definition of Mass in Mechanics: Why Is It So Difficult?

    NASA Astrophysics Data System (ADS)

    Coelho, Ricardo Lopes

    2012-05-01

    In spite of the concerted efforts of physicists, philosophers, mathematicians, and logicians, no final clarification of the concept of mass has been reached. So concludes Jammer in his book on the history of the concept. The Nobel laureate Wilczek called our attention to the problem in his papers on the concepts of the fundamental equation of dynamics.2 In 2005, Roche wrote a paper whose title asks the question "What is mass?"3 Hecht sums up the situation in textbooks in the title of his article "There Is No Really Good Definition of Mass."4 Where the difficulty in defining mass in classical mechanics lies is the question addressed in the present paper. Before dealing with this topic, it is important to make explicit what the problem consists of, since sometimes people think that there is no problem with mass at all.

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

  11. A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing1

    PubMed Central

    Garaycochea, Silvia; Speranza, Pablo; Alvarez-Valin, Fernando

    2015-01-01

    Premise of the study: We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. Methods: A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. Results: From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs. This weedy rice was classified based on 23 polymorphic regions identified by comparison with reference chloroplast genomes. We detected recent and past events of genetic material transfer between the chloroplast and nuclear genomes and estimated their occurrence frequency. Discussion: We obtained a high-quality complete chloroplast genome sequence from low-coverage sequencing data. Intergenome DNA transfer appears to be more frequent than previously thought. PMID:26504677

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

    PubMed

    Tatonetti, Lisa

    2016-01-01

    This article examines the life and novels of Carole laFavor, arguing for her importance to and influence in Two-Spirit studies. Along with being a writer, laFavor was a powerful voice for social justice and Indigenous health sovereignty in Minnesota and the nation. Her two novels, Along the Journey River and Evil Dead Center, which both focus on Anishinaabe lesbian detective protagonist Renee LaRoche, are the first lesbian detective fiction published by a Native author. Renee's embrace of a specifically Two-Spirit erotics anchors her to family and brings her tribal community a powerful healing when she employs her skills to protect her people from instances of racism, abuse, and injustice. This article, then, reads these novels as the first of an emerging genre of texts that claim an overtly Two-Spirit erotic as well as vital precursors to the present embrace of sovereign erotics in Indigenous studies. PMID:27254762

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  14. Period change investigation of the low mass ratio contact binary BO Ari

    NASA Astrophysics Data System (ADS)

    Kriwattanawong, W.; Tasuya, O.; Poojon, P.

    2016-04-01

    A photometric study and period change analysis for the A-type low mass ratio contact binary BO Ari is presented. The BVR light curves were fitted by using the Wilson-Devinney method. The photometric solution yields a low mass ratio of q = 0.1754(±0.0016) with a contact degree of f = 27.72%(±2.37%). We found a long-term orbital period decrease at a rate of dPdt = - 3.49 ×10-7 d yr-1. This result indicates that the system is undergoing mass transfer from the primary component to the secondary with a mass transfer rate of m˙1m1 = - 7.77 ×10-8 yr-1. With the period decrease, the inner and outer critical Roche surfaces will tighten and cause the degree of contact to increase. Therefore, BO Ari may evolve into a deeper contact system.

  15. Lax operator algebras and integrable systems

    NASA Astrophysics Data System (ADS)

    Sheinman, O. K.

    2016-02-01

    A new class of infinite-dimensional Lie algebras, called Lax operator algebras, is presented, along with a related unifying approach to finite-dimensional integrable systems with a spectral parameter on a Riemann surface such as the Calogero-Moser and Hitchin systems. In particular, the approach includes (non-twisted) Kac-Moody algebras and integrable systems with a rational spectral parameter. The presentation is based on quite simple ideas about the use of gradings of semisimple Lie algebras and their interaction with the Riemann-Roch theorem. The basic properties of Lax operator algebras and the basic facts about the theory of the integrable systems in question are treated (and proved) from this general point of view. In particular, the existence of commutative hierarchies and their Hamiltonian properties are considered. The paper concludes with an application of Lax operator algebras to prequantization of finite-dimensional integrable systems. Bibliography: 51 titles.

  16. GRAVITY DARKENING AND BRIGHTENING IN BINARIES

    SciTech Connect

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

    2012-06-20

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

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

    SciTech Connect

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

    2014-12-01

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

  18. Accretion disks in Algols: Progenitors and evolution

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  19. A new Vitreoscilla filiformis extract grown on spa water-enriched medium activates endogenous cutaneous antioxidant and antimicrobial defenses through a potential Toll-like receptor 2/protein kinase C, zeta transduction pathway.

    PubMed

    Mahe, Yann F; Perez, Marie-Jesus; Tacheau, Charlotte; Fanchon, Chantal; Martin, Richard; Rousset, Françoise; Seite, Sophie

    2013-01-01

    Vitreoscilla filiformis (VF) biomass (VFB) has been widely used in cosmetic preparations and shown to modulate the major inducible free-radical scavenger mitochondrial superoxide dismutase in skin cells. By adding La Roche-Posay (LRP) thermal spring water to the VF culture medium, we obtained a biomass (LRP-VFB) with a similar mitochondrial superoxide dismutase activation capacity to VF. Also, the new biomass more powerfully stimulated mRNA expression and antimicrobial peptides in reconstructed epidermis. Interestingly, a predictive computer model that analyzed transducing events within skin epidermal cells suggested that this protective activity may involve the Toll-like receptor 2/protein kinase C, zeta transduction pathway. Protein kinase C, zeta inhibition was effectively shown to abolish VFB-induced gene stimulation and confirmed this hypothesis. This thus opens new avenues for investigation into the improvement of skin homeostatic defense in relation to the control of its physiological microbiota and innate immunity. PMID:24039440

  20. 1,3-Oxazines as BACE1 and/or BACE2 inhibitors: a patent evaluation (WO2012156284).

    PubMed

    Gilbert, Eric J

    2013-08-01

    This patent review covers the contents of Hoffman-La Roche and Siena Biotech's patent application WO2012156284 titled '1,3-Oxazines as BACE1 and/or BACE2 Inhibitors.' Beta-site amyloid precursor protein-converting enzyme (BACE1) and BACE2 activities are reported to support the claimed compounds' use as therapeutics for Alzheimer's disease and type II diabetes, respectively. A common core motif of the claimed compounds is the six-membered 1,3-oxazine system. To gain access to the S3 and S3 subpocket of the BACE1 active site, various linkers are described including nitrogen- and oxygen-based, aryl, and amide-based linkers. Of the 65 compounds claimed, 6 had IC50s less than 100 nM in the BACE1 cell assay. Cellular BACE2 inhibition data are reported for 20 compounds with 2 under 100 nM. PMID:23837729

  1. Institutional review board (IRB) and ethical issues in clinical research.

    PubMed

    Kim, Won Oak

    2012-01-01

    Clinical research has expanded tremendously in the past few decades and consequently there has been growing interest in the ethical guidelines that are being followed for the protection of human subjects. This review summarizes historical scandals and social responses chronologically from World War II to the Death of Ellen Roche (2001) to emphasize the lessons we must learn from history. International ethical guidelines for studies with human subjects are also briefly described in order to understand the circumstances of clinical research. The tasks and responsibilities of the institutions and investigators in human subject research to preserve the safety and welfare of research subjects are summarized. Next, several debated ethical issues and insights are arranged as controversial topics. This brief review and summary seeks to highlight important arguments and make suggestions to institutional review boards (IRBs) to contribute to the future evolution of ethics in clinical research as we advance forward. PMID:22323947

  2. VizieR Online Data Catalog: HL Aur light curves and minima (Zhang+ 1997)

    NASA Astrophysics Data System (ADS)

    Zhang, R. X.; Fang, M. J.; Zhai, D. S.

    1996-11-01

    Photoelectric observations of HL Aur were carried out with the 60cm reflector of Beijing Astronomical Observatory in 1990 and 1994, and the first photoelectric BV light curves were obtained along with a newly derived ephemeris. The period of the system appears to be constant over the past 65-years. Using the Wilson-Devinney program a photometric analysis of the B and V light curves is performed. It is evident that HL Aur is a near-contact binary with a mass ratio of q=m2/m1=0.722+/-0.011. The primary component of the system is essentially in contact with its Roche lobe, while the secondary is detached but nearly in contact with its lobe. It is found that the components of the system are slightly evolved and located near the terminal-age main sequence. The binary is consistent with the general evolutionary picture for near-contact systems. (3 data files).

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

    PubMed Central

    2011-01-01

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

  4. The complete mitochondrial genome of the sandbar shark Carcharhinus plumbeus.

    PubMed

    Blower, Dean C; Ovenden, Jennifer R

    2016-01-01

    The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one individual were assembled into a 16,706 bp mitogenome with 33× average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA's, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure. PMID:24938089

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

    NASA Astrophysics Data System (ADS)

    Cambier, H.

    2015-10-01

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

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

    PubMed

    Nishikawa, Takashi

    2007-01-01

    A Swiss pharmaceutical company (F-Hoffmann-La Roche Ltd.), first introduced the profession of "propagandist" in Japan in 1912. At the time, Shohei Ninomiya was a chief hospital pharmacist, but he changed his vocation to become the first "propah" (Japanese abbreviation for propagandist). The German physician Dr. Rudolf Ebering initiated Dr. Ninomiya in the methods and principles of "propah," and he faithfully practiced them. The defining principle of a modern European propagandist is one who is far from sales-centered. From the late 1970s through 1980s, however, Japanese pharmaceutical companies indulged in pursuing sales and neglected this principle, resulting in numerous abuses and adverse effects. Today, use of the description "medical representative" (MR) is more common than "propah." Even with this different description, pharmaceutical companies and MRs should never neglect the founding principle to avoid repeating such abuses. PMID:18548887

  7. Accretion mode of the Ultra-Luminous X-ray source M82 X-2

    NASA Astrophysics Data System (ADS)

    Karino, S.; Miller, J. C.

    2016-05-01

    Periodic pulsations have been found in emission from the ultra-luminous X-ray source (ULX) M82 X-2, strongly suggesting that the emitter is a rotating neutron star rather than a black hole. However, the radiation mechanisms and accretion mode involved have not yet been clearly established. In this paper, we examine the applicability to this object of standard accretion modes for high mass X-ray binaries (HMXBs). We find that spherical wind accretion, which drives OB-type HMXBs, cannot apply here but that there is a natural explanation in terms of an extension of the picture for standard Be-type HMXBs. We show that a neutron star with a moderately strong magnetic field, accreting from a disc-shaped wind emitted by a Be-companion, could be compatible with the observed relation between spin and orbital period. A Roche lobe overflow picture is also possible under certain conditions.

  8. The rings of Uranus - Nature and origin

    NASA Technical Reports Server (NTRS)

    Dermott, S. F.; Gold, T.; Sinclair, A. T.

    1979-01-01

    Effects of a resonance between a set of ring particles and individual satellites are considered. It is suggested that the resonances are 1:1 for the rings of Uranus and that each ring must contain an as-yet unseen satellite. A model is proposed in which the rings of Uranus were caused by small satellites that entered the Roche zone due to tidal drag. According to this model, the satellites gradually lost material from their surfaces in this zone, the particles left a satellite with relatively low speeds and must have entered orbits similar to that of the satellite, and the gravitational force of the satellite compelled these particles to remain in a narrow sharply defined ring.

  9. Study on the decomposition mechanism of alkyl carbonate on lithium metal by pyrolysis-gas chromatography-mass spectroscopy

    NASA Astrophysics Data System (ADS)

    Mogi, Ryo; Inaba, Minoru; Iriyama, Yasutoshi; Abe, Takeshi; Ogumi, Zempachi

    The surface films formed on deposited lithium in electrolyte solutions based on ethylene carbonate (EC), diethyl carbonate (DEC), and dimethyl carbonate (DMC) were analyzed by pyrolysis-gas chromatography-mass spectroscopy (Py-GC-MS). In 1 M LiClO 4/EC, the main component of the surface film was easily hydrolyzed to give ethylene glycol after exposure to air, and hence was considered to have a chemical structure of ROCH 2CH 2OR', of which OR and OR' are OLi or OCO 2Li. Ethylene oxide, acetaldehyde, and 1,4-dioxane were detected in decomposition products, and they were considered to have been formed by pyrolysis of ROCH 2CH 2OR' in the pyrolyzer. The presence of ethanol in decomposition products confirmed that ring cleavage at the CH 2O bonds of EC occurs by one electron reduction. In addition, the presence of methanol implied the cleavage of the CC bond of EC upon reduction. From the surface films formed in 1 M LiClO 4/DEC and /DMC, ethanol and methanol, respectively, were detected, which suggested that corresponding lithium alkoxides and/or lithium alkyl carbonates were the main components. In 1 M LiClO 4/EC+DEC (1:1), EC dominantly decomposed to form the surface film. The surface film formed in 1 M LiPF 6/EC+DEC (1:1) contained a much smaller amount of organic compounds.

  10. Design and optimization of lipid-modified poly(amidoamine) dendrimer coated iron oxide nanoparticles as probes for biomedical applications

    NASA Astrophysics Data System (ADS)

    Boni, A.; Bardi, G.; Bertero, A.; Cappello, V.; Emdin, M.; Flori, A.; Gemmi, M.; Innocenti, C.; Menichetti, L.; Sangregorio, C.; Villa, S.; Piazza, V.

    2015-04-01

    Superparamagnetic iron oxide nanoparticles with a wide size range (2.6-14.1 nm) were synthesized and coated with the amphiphilic poly(amidoamine) PAMAM-C12 dendrimer. The resulting well dispersed and stable water suspensions were fully characterized in order to explore their possible use in biomedical applications. The structural and magnetic properties of the nanoparticles were preserved during the coating and were related to their relaxometric behaviour. The Nuclear Magnetic Resonance Dispersion (NMRD) profiles were found to be in accordance with the Roch model. The biocompatibility was assessed by means of cell viability tests and Transmission Electron Microscopy (TEM) analysis. The nanoparticles' capability of being detected via Magnetic Resonance Imaging (MRI) was investigated by means of clinical MRI scanners both in water and agar gel phantoms, and in a mouse model.Superparamagnetic iron oxide nanoparticles with a wide size range (2.6-14.1 nm) were synthesized and coated with the amphiphilic poly(amidoamine) PAMAM-C12 dendrimer. The resulting well dispersed and stable water suspensions were fully characterized in order to explore their possible use in biomedical applications. The structural and magnetic properties of the nanoparticles were preserved during the coating and were related to their relaxometric behaviour. The Nuclear Magnetic Resonance Dispersion (NMRD) profiles were found to be in accordance with the Roch model. The biocompatibility was assessed by means of cell viability tests and Transmission Electron Microscopy (TEM) analysis. The nanoparticles' capability of being detected via Magnetic Resonance Imaging (MRI) was investigated by means of clinical MRI scanners both in water and agar gel phantoms, and in a mouse model. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01148e

  11. The Starspots Activity of SV Cam

    NASA Astrophysics Data System (ADS)

    Djuravsevic, G.

    The paper is devoted to the problem of the orbital and physical parameters estimation of the active eclipsing binary SV Cam based on the interpretation of photometric observations made by {pa} during the period 1973-1981. The problem is solved in two stages: by obtaining a synthetic light curve in the case when the parameters of the corresponding Roche model {dja} are given a priori (direct problem), and by determining the parameters of the model for which the best fit between the synthetic light curve and the observations is achieved (inverse problem) {djb}. A total of 18 light curves are analysed in the framework of the Roche model, involving one and two spotted regions on the primary component of the system (Sp G3 V), for the temperature contrast between the spotted area and the surrounding photosphere A_s = T_s / T_1 = 0.65. The basic parameters of the system and of the spotted areas are estimated. According to the obtained results the spotted areas are formed at high latitudes and cover a significant part of the stellar surface. No clear cyclicity of the system's activity is noted from the analysed observations. There are some indications that spotted area at high latitudes (above 70circ) correspond to an enhanced activity. Since the system's period is short (P = 0^d.59), the presence of spotted regions at high latitudes can be explained by the dynamo mechanism for rapid rotators {sch}. During the analysed period the spotted areas tend to fall into a specially active longitude sectors, on high latitude, near stellar polar regions. Due to a selection effect it is possible that a more extensive observational material would correct this result to some extent. The light curve analysis allowed an estimation of the system parameters and of the active spotted regions.

  12. NMR relaxation induced by iron oxide particles: testing theoretical models.

    PubMed

    Gossuin, Y; Orlando, T; Basini, M; Henrard, D; Lascialfari, A; Mattea, C; Stapf, S; Vuong, Q L

    2016-04-15

    Superparamagnetic iron oxide particles find their main application as contrast agents for cellular and molecular magnetic resonance imaging. The contrast they bring is due to the shortening of the transverse relaxation time T 2 of water protons. In order to understand their influence on proton relaxation, different theoretical relaxation models have been developed, each of them presenting a certain validity domain, which depends on the particle characteristics and proton dynamics. The validation of these models is crucial since they allow for predicting the ideal particle characteristics for obtaining the best contrast but also because the fitting of T 1 experimental data by the theory constitutes an interesting tool for the characterization of the nanoparticles. In this work, T 2 of suspensions of iron oxide particles in different solvents and at different temperatures, corresponding to different proton diffusion properties, were measured and were compared to the three main theoretical models (the motional averaging regime, the static dephasing regime, and the partial refocusing model) with good qualitative agreement. However, a real quantitative agreement was not observed, probably because of the complexity of these nanoparticulate systems. The Roch theory, developed in the motional averaging regime (MAR), was also successfully used to fit T 1 nuclear magnetic relaxation dispersion (NMRD) profiles, even outside the MAR validity range, and provided a good estimate of the particle size. On the other hand, the simultaneous fitting of T 1 and T 2 NMRD profiles by the theory was impossible, and this occurrence constitutes a clear limitation of the Roch model. Finally, the theory was shown to satisfactorily fit the deuterium T 1 NMRD profile of superparamagnetic particle suspensions in heavy water. PMID:26933908

  13. Virtual microscopy in the undergraduate teaching of pathology

    PubMed Central

    Ordi, Oriol; Bombí, Josep Antoni; Martínez, Antonio; Ramírez, Josep; Alòs, Llúcia; Saco, Adela; Ribalta, Teresa; Fernández, Pedro L.; Campo, Elias; Ordi, Jaume

    2015-01-01

    Background: Little evidence is available concerning the impact of virtual microscopy (VM) in the undergraduate teaching of pathology. We aimed: (1) to determine the impact in student scores when moving from conventional microscopy (CM) to VM; (2) to assess the students’ impressions and changes in study habits regarding the impact of this tool. Methods: We evaluated two groups taking the discipline of pathology in the same course, one using CM and the other VM. The same set of slides used in the CM classes was digitized in a VENTANA iScan HT (Roche Diagnostics, Sant Cugat, Spain) at ×20 and observed by the students using the Virtuoso viewer (Roche Diagnostics). We evaluated the skill level reached by the students with an online test. A voluntary survey was undertaken by the VM group to assess the students’ impressions regarding the resource. The day and time of any accession to the viewer were registered. Results: There were no differences between the two groups in their marks in the online test (mean marks for the CM and the VM groups: 9.87 ± 0.34 and 9.86 ± 0.53, respectively; P = 0.880). 86.6% of the students found the software friendly, easy-to-use and effective. 71.6% of the students considered navigation easier with VM than with CM. The most appreciated feature of VM was the possibility to access the images anywhere and at any time (93.3%). 57.5% of the accesses were made on holidays and 41.9% later than 6:00 pm. Conclusions: Virtual microscopy can effectively replace the traditional methods of learning pathology, providing mobility and convenience to medical students. PMID:25722941

  14. Constraints on Common Envelope Magnetic Fields from Observations of Jets in Planetary Nebulae

    NASA Astrophysics Data System (ADS)

    De Marco, Orsola; Tocknell, J.; Wardle, M.

    2014-01-01

    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 and 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 years 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 cannot find a reasonable scenario for the formation of the two jet pairs observed: the small orbital separation would preclude the formation of even one accretion disk able to supply the necessary accretion rate to cause the observed jets. Additional and improved observations of post-CE PN will provide a powerful tool to constrain the CE interaction.

  15. Validation of an automated method for compounding monoclonal antibody patient doses

    PubMed Central

    Peters, Bas J.M.; Capelle, Martinus A.H.; Arvinte, Tudor; van de Garde, Ewoudt M.W.

    2013-01-01

    Automation robots have recently come to the market as an alternative for manual compounding of drugs for intravenous administration. Our aim was to assess whether robotic compounding can be performed with monoclonal antibodies (mAbs) without influencing the aggregation state of the proteins. Three frequently used mAbs were studied: infliximab (Remicade®, Janssen Biotech) and trastuzumab (Herceptin®, Roche) in lyophilised form, and bevacizumab (Avastin®, Roche) as a liquid formulation stored at 2°C to 8°C. The effects of different procedures to prepare the patient doses on antibody aggregation were evaluated. Remicade® and Herceptin® were reconstituted both manually and by a robotic arm (i.v.STATION®, Health Robotics). Additionally, the influence of vigorous shaking during reconstitution was investigated. The effects of rapid aspiration and dispensing on antibody aggregation were investigated for all three mAbs. Aggregation state was assessed by UV-Vis absorbance, 90° light scatter, fluorescence spectroscopy, Nile red fluorescence microscopy, and field flow fractionation without cross and focus flow. Robotic reconstituted samples showed similar findings compared with manual reconstitution if performed exactly according to the summary of product characteristics (SPC). Vials that were vigorously shaken showed a significant increase in aggregates. Similarly, rapid aspiration/dispense cycles resulted in a strong increase in the number and sizes of aggregates for all three mAbs; this result was observed after just one rapid aspiration/dispense cycle. Our study showed that robotic compounding of mAbs is feasible if the robot is exactly programmed according to the SPC, indicating that robotic compounding can be used to achieve reproducible high-quality compounding for delicate formulations. PMID:23255057

  16. NMR relaxation induced by iron oxide particles: testing theoretical models

    NASA Astrophysics Data System (ADS)

    Gossuin, Y.; Orlando, T.; Basini, M.; Henrard, D.; Lascialfari, A.; Mattea, C.; Stapf, S.; Vuong, Q. L.

    2016-04-01

    Superparamagnetic iron oxide particles find their main application as contrast agents for cellular and molecular magnetic resonance imaging. The contrast they bring is due to the shortening of the transverse relaxation time T 2 of water protons. In order to understand their influence on proton relaxation, different theoretical relaxation models have been developed, each of them presenting a certain validity domain, which depends on the particle characteristics and proton dynamics. The validation of these models is crucial since they allow for predicting the ideal particle characteristics for obtaining the best contrast but also because the fitting of T 1 experimental data by the theory constitutes an interesting tool for the characterization of the nanoparticles. In this work, T 2 of suspensions of iron oxide particles in different solvents and at different temperatures, corresponding to different proton diffusion properties, were measured and were compared to the three main theoretical models (the motional averaging regime, the static dephasing regime, and the partial refocusing model) with good qualitative agreement. However, a real quantitative agreement was not observed, probably because of the complexity of these nanoparticulate systems. The Roch theory, developed in the motional averaging regime (MAR), was also successfully used to fit T 1 nuclear magnetic relaxation dispersion (NMRD) profiles, even outside the MAR validity range, and provided a good estimate of the particle size. On the other hand, the simultaneous fitting of T 1 and T 2 NMRD profiles by the theory was impossible, and this occurrence constitutes a clear limitation of the Roch model. Finally, the theory was shown to satisfactorily fit the deuterium T 1 NMRD profile of superparamagnetic particle suspensions in heavy water.

  17. A Comparison of Stellar Mass-Transfer & Merger Simulations

    NASA Astrophysics Data System (ADS)

    Tohline, Joel E.; Motl, P.; Diehl, S.; Even, W.; Clayton, G.; Fryer, C.

    2011-01-01

    We present detailed comparisons of 3D stellar mass-transfer and merger simulations that have been carried out using two very different numerical hydrodynamic algorithms -- a finite-volume "grid" code (typically using 4M cylindrical grid cells) and a smoothed-particle hydrodynamics (SPH) code (typically using 1M particles). In all cases the initial binary models contain synchronously rotating, n = 3/2 polytropic stars of a specified mass ratio (q = Mdonor/Maccretor) that are in circular orbit with one star (the donor) marginally filling its Roche lobe. In our "base" set of 8 comparison simulations, we have followed the evolution of binaries having four different initial mass ratios (q0 = 1.3, 0.7, 0.5, 0.4) and each is evolved using two different equations of state: polytropic (P) and ideal-gas (I). In addition, some evolutions are repeated using a different numerical resolution and/or a different initial episode of "driving" to initiate mass-transfer. In the case of the binary systems with q0 = 1.3 and q0 = 0.7, the codes show a remarkable level of quantitative agreement; in the former case, the two stars merge and, in the latter case, the donor gets tidally disrupted. Binary systems with q0 = 0.5 or 0.4 enter a long phase (> 10-20 orbits) of stable mass-transfer during which the binary separation steadily increases; tidal disruption of the donor may ultimately occur if sufficiently deep contact is made between the Roche lobe and the donor during an initial episode of "driving." This work has been supported by grants AST-0708551 and DGE-0504507 from the U.S. National Science Foundation; by grants NNX07AG84G and NNX10AC72G from NASA's ATP program; and by grants of high-performance computing time on the TeraGrid, at LSU and across LONI (Louisiana Optical Network Initiative).

  18. Tidal Decay and Disruption of Gaseous Exoplanets

    NASA Astrophysics Data System (ADS)

    Jackson, Brian K.; Arras, Phil; Jensen, Emily; Peacock, Sarah; Marchant, Pablo; Penev, Kaloyan

    2015-11-01

    Many gaseous exoplanets in short-period orbits are on the verge of Roche-lobe overflow, and observations, along with orbital stability analysis, show tides probably drive significant orbital decay. Thus, the coupled processes of orbital evolution and tidal disruption likely shape the observed distribution of close-in exoplanets and may even be responsible for producing the shortest-period solid planets. However, the exact outcome for an overflowing planet depends on its internal response to mass loss and variable stellar insolation, and the accompanying orbital evolution can act to enhance or inhibit the disruption process. The final orbits of the denuded remnants of gas giants may be predictable from their mass-radius relationship, and so a distinctive mass-period relationship for some short-period solid planets may provide evidence for their origins as gaseous planets. In this presentation, we will discuss our work on tidal decay and disruption of close-in gaseous planets using a new model that accounts for the fact that short-period planets have hot, distended atmospheres, which can result in overflow even for planets that are not officially in Roche lobe contact. We will also point out that the orbital expansion that can accompany mass transfer may be less effective than previously realized because the resulting accretion disk may not return all of its angular momentum to the donor, as is usually assumed. Both of these effects have bee incorporated into the fully-featured and robust Modules for Experiments in Stellar Astrophysics (MESA) suite.

  19. Understanding the Evolution of Close Binary Systems with Radio Pulsars

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    We calculate the evolution of close binary systems (CBSs) formed by a neutron star (behaving as a radio pulsar) and a normal donor star, which evolve either to a helium white dwarf (HeWD) or to ultra-short orbital period systems. We consider X-ray irradiation feedback and evaporation due to radio pulsar irradiation. We show that irradiation feedback leads to cyclic mass transfer episodes, allowing CBSs to be observed in between episodes as binary radio pulsars under conditions in which standard, non-irradiated models predict the occurrence of a low-mass X-ray binary. This behavior accounts for the existence of a family of eclipsing binary systems known as redbacks. We predict that redback companions should almost fill their Roche lobe, as observed in PSR J1723-2837. This state is also possible for systems evolving with larger orbital periods. Therefore, binary radio pulsars with companion star masses usually interpreted as larger than expected to produce HeWDs may also result in such quasi-Roche lobe overflow states, rather than hosting a carbon-oxygen WD. We found that CBSs with initial orbital periods of Pi < 1 day evolve into redbacks. Some of them produce low-mass HeWDs, and a subgroup with shorter Pi becomes black widows (BWs). Thus, BWs descend from redbacks, although not all redbacks evolve into BWs. There is mounting observational evidence favoring BW pulsars to be very massive (gsim 2 M ⊙). As they should be redback descendants, redback pulsars should also be very massive, since most of the mass is transferred before this stage.

  20. A near-contact binary: CN Andromedae

    NASA Astrophysics Data System (ADS)

    Çiçek, C.; Erdem, A.; Soydugan, F.

    2005-02-01

    New BVR light curves and photometric analysis of the eclipsing binary star CN And are presented. The shape of the light curves are typical of β Lyr type, and there are large asymmetries between maxima. The BVR light curves and the radial velocity curves (from Rucinski et al. 2000) were solved with the Wilson-Devinney method, simultaneously. The results suggest that CN And is a almost contact binary system, in which the component stars are filling ˜99% of their Roche lobes. We discuss the model with a large dark starspot on the more massive star and a bright substellar spot on the companion to account for the light curve asymmetries. The absolute parameters of the system were also derived. The system resembles the near contact binary V1010 Oph according to its Roche configuration and light curve asymmetries. We, also, discuss the evolution of the system: it seems to be in a transition phase to the contact era. All previous times of minimum light were collected and combined with the new ones presented in this work. The variation of the orbital period of the system was then analyzed. The results reveal that the orbital period has a secular decrease of about 1.98±0.04 sec per century, which corresponds to a conservative mass transfer from the more to the less massive component at a rate of (1.52±0.09)×10-7m_⊙/yr or a mass loss from the primary component due to magnetic stellar winds at a rate of (7.83±0.09)×10-8m_⊙/yr.

  1. The Effect of Tides on the Population of PN from Interacting Binaries

    NASA Astrophysics Data System (ADS)

    Madappatt, Niyas; De Marco, Orsola; Villaver, Eva

    2016-08-01

    We have used the tidal equations of Zahn to determine the maximum orbital distance at which companions are brought into Roche lobe contact with their giant primary, when the primary expands during the giant phases. This is a key step when determining the rates of interaction between giants and their companions. Our stellar structure calculations are presented as maximum radii reached during the red and asymptotic giant branch (RGB and AGB, respectively) stages of evolution for masses between 0.8 and 4.0 M⊙ (Z=0.001 - 0.04) and compared with other models to gauge the uncertainty on radii deriving from details of these calculations. We find overall tidal capture distances that are typically 1-4 times the maximum radial extent of the giant star, where companions are in the mass range from 1 MJ to a mass slightly smaller than the mass of the primary. We find that only companions at initial orbital separations between ˜320 and ˜630 R⊙ will be typically captured into a Roche lobe-filling interaction or a common envelope on the AGB. Comparing these limits with the period distribution for binaries that will make PN, we deduce that in the standard scenario where all ˜1-8 M⊙ stars make a PN, at most 2.5 per cent of all PN should have a post-common envelope central star binary, at odds with the observational lower limit of 15-20 per cent. The observed over-abundance of post-interaction central stars of PN cannot be easily explained considering the uncertainties. We examine a range of explanations for this discrepancy.

  2. Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

    PubMed Central

    Hale, Matthew C; McCormick, Cory R; Jackson, James R; DeWoody, J Andrew

    2009-01-01

    Background Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads. Results Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 bp). These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences). Over 4,000 sequencing reads (~19%) were assigned gene ontologies, mostly to protein, RNA, and ion binding. A total of 877 candidate SNPs were identified from > 50 different genes. We employed an analytical approach from theoretical ecology (rarefaction) to evaluate depth of sequencing coverage relative to gene discovery. We also considered the relative merits of normalized versus native cDNA libraries when using next-generation sequencing platforms. Not surprisingly, fewer genes from the normalized libraries were rRNA subunits. Rarefaction suggests that normalization has little influence on the efficiency of gene discovery, at least when working with thousands of reads from a single tissue type. Conclusion Our data indicate that titration runs on 454 sequencers can characterize thousands of expressed sequence tags which can be used to identify SNPs, gene ontologies, and levels of gene expression in species of conservation concern. We anticipate that rarefaction will be useful in evaluations of gene discovery and that next-generation sequencing technologies hold great potential for the study of other non-model organisms. PMID:19402907

  3. Multiple Human Papilloma Virus 16 Infection Presenting as Various Skin Lesions.

    PubMed

    Choi, Hwan Jun; Lee, Jun Ho

    2016-06-01

    The 53-year-old woman admitted with multiple persistent, progressive, slightly raised, red, and crusted plague form masses that suddenly occurred on left thumb, both upper and lower extremity about 10 years ago. There was no induration in the lesion or in its surrounding skin. There was no unusual opinion on a radiologic test and family history. And she had no history of working in the business related to any chemical product such as arsenic or tar which was carcinogen. The patient has had total hysterectomy to treat uterine myoma 10 years ago. The wide excision and split thickness skin graft of 2 × 1.5 cm was performed around mass in the size of 1.5 × 1.2 cm on the left thumb and wide excision and local advancement flap was done on the other sites. As a result of biopsy, masses were diagnosed as Bowen disease, actinic keratosis, and Seborrheic keratosis. These specimens were obtained during surgery: broom-type cell sampling devices were used to collect samples from the specimens, and they were placed into PreservCyt solution (Cytyc Corp, Boxborough, MA). Then, the collected samples underwent the Roche Linear Array HPV Genotyping Test (Roche Diagnostics, Branchburg, NJ) that allows for the simultaneous identification of human papilloma virus (HPV) types from liquid-based cell preparations. On histopathological examination of the surgical specimen, atypical squamous cells proliferate through the whole thickness of the epidermis. The entire tumor was confined to the epidermis and did not invade into the dermis. The cells were often highly atypical. That were the irregular shape which the resection margin of masses had a negative tumor component. And HPV 16 genotyping test was positive although vaginal examination of HPV 16 genotyping was negative. PMID:27192658

  4. FORMATION OF MULTIPLE-SATELLITE SYSTEMS FROM LOW-MASS CIRCUMPLANETARY PARTICLE DISKS

    SciTech Connect

    Hyodo, Ryuki; Ohtsuki, Keiji; Takeda, Takaaki E-mail: ohtsuki@tiger.kobe-u.ac.jp

    2015-01-20

    Circumplanetary particle disks would be created in the late stage of planetary formation either by impacts of planetary bodies or disruption of satellites or passing bodies, and satellites can be formed by accretion of disk particles spreading across the Roche limit. Previous N-body simulation of lunar accretion focused on the formation of single-satellite systems from disks with large disk-to-planet mass ratios, while recent models of the formation of multiple-satellite systems from disks with smaller mass ratios do not take account of gravitational interaction between formed satellites. In the present work, we investigate satellite accretion from particle disks with various masses, using N-body simulation. In the case of accretion from somewhat less massive disks than the case of lunar accretion, formed satellites are not massive enough to clear out the disk, but can become massive enough to gravitationally shepherd the disk outer edge and start outward migration due to gravitational interaction with the disk. When the radial location of the 2:1 mean motion resonance of the satellite reaches outside the Roche limit, the second satellite can be formed near the disk outer edge, and then the two satellites continue outward migration while being locked in the resonance. Co-orbital satellites are found to be occasionally formed on the orbit of the first satellite. Our simulations also show that stochastic nature involved in gravitational interaction and collision between aggregates in the tidal environment can lead to diversity in the final mass and orbital architecture, which would be expected in satellite systems of exoplanets.

  5. Figure of the double Asteroid 90 Antiope from adaptive optics and lightcurve observations

    NASA Astrophysics Data System (ADS)

    Descamps, P.; Marchis, F.; Michalowski, T.; Vachier, F.; Colas, F.; Berthier, J.; Assafin, M.; Dunckel, P. B.; Polinska, M.; Pych, W.; Hestroffer, D.; Miller, K. P. M.; Vieira-Martins, R.; Birlan, M.; Teng-Chuen-Yu, J.-P.; Peyrot, A.; Payet, B.; Dorseuil, J.; Léonie, Y.; Dijoux, T.

    2007-04-01

    A long-term adaptive optics (AO) campaign of observing the double Asteroid (90) Antiope has been carried out in 2003-2005 using 8-10-m class telescopes, allowing prediction of the circumstances of mutual events occurring during the July 2005 opposition [Marchis, F., Descamps, P., Hestroffer, D., Berthier, J., de Pater, I., 2004. Bull. Am. Astron. Soc. 36, 1180]. This is the first opportunity to use complementary lightcurve and AO observations to extensively study the (90) Antiope system, an interesting visualized binary doublet system located in the main belt. The orbital parameters derived from the AO observations have served as input quantities for the derivation of a whole set of other physical parameters (namely shapes, surface scattering, bulk density, and internal properties) from analysis of collected lightcurves. To completely model the observed lightcurves, we employed Roche figures to construct an overall shape solution. The combination of these complementary observations has enabled us to derive a reliable physical and orbital solution for the system. Our model is consistent with a system of slightly non-spherical components, having a size ratio of 0.95 (with R=42.9±0.5 km, separation =171±1 km), and exhibiting equilibrium figures for homogeneous rotating bodies. A comparison with grazing occultation event lightcurves suggests that the real shapes of the components do not depart from Roche equilibrium figures by more than 10%. The J2000 ecliptic coordinates of the pole of the system are λ=200°±2° and α=38°±2°. The orbital period was refined to P=16.5051±0.0001 h, and the density is found to be slightly lower than previous determinations, with a value of 1.25±0.05 g/cm, leading to a significant macro-porosity of 30%. Possible scenarios for the origin of the system are also discussed.

  6. New Low Accretion Rate Magnetic Binary Systems and their Significance for the Evolution of Cataclysmic Variables

    NASA Astrophysics Data System (ADS)

    Schmidt, Gary D.; Szkody, Paula; Vanlandingham, Karen M.; Anderson, Scott F.; Barentine, J. C.; Brewington, Howard J.; Hall, Patrick B.; Harvanek, Michael; Kleinman, S. J.; Krzesinski, Jurek; Long, Dan; Margon, Bruce; Neilsen, Eric H., Jr.; Newman, Peter R.; Nitta, Atsuko; Schneider, Donald P.; Snedden, Stephanie A.

    2005-09-01

    Discoveries of two new white dwarf plus M star binaries with striking optical cyclotron emission features from the Sloan Digital Sky Survey (SDSS) brings to six the total number of X-ray-faint, magnetic accretion binaries that accrete at rates M˙<~10-13 Msolar yr-1, or <1% of the values normally encountered in cataclysmic variables. This fact, coupled with donor stars that underfill their Roche lobes and very cool white dwarfs, brand the binaries as post-common-envelope systems whose orbits have not yet decayed to the point of Roche lobe contact. They are premagnetic cataclysmic variables, or pre-Polars. The systems exhibit spin-orbit synchronism and apparently accrete by efficient capture of the stellar wind from the secondary star, a process that has been dubbed a ``magnetic siphon.'' Because of this, period evolution of the binaries will occur solely by gravitational radiation, which is very slow for periods >3 hr. Optical surveys for the cyclotron harmonics appear to be the only means of discovery, so the space density of pre-Polars could rival that of Polars, and the binaries provide an important channel of progenitors (in addition to the asynchronous intermediate Polars). Both physical and SDSS observational selection effects are identified that may help to explain the clumping of all six systems in a narrow range of magnetic field strength around 60 MG. A portion of the results presented here was obtained with the MMT Observatory, a facility operated jointly by the University of Arizona and the Smithsonian Institution. Based in part on observations with the Apache Point Observatory 3.5 m telescope and the Sloan Digital Sky Survey, which are owned and operated by the Astrophysical Research Consortium (ARC).

  7. [The biolaw and bioethics encyclopedia].

    PubMed

    del Barrio Seoane, Jaime

    2011-01-01

    On 4 April 2011, as part of the XVIII Conference in Law and the Human Genome, the official presentation took place of the first Spanish language Encyclopedia of Biolaw and Bioethics, in an event organised by the Inter-University Chair in Law and the Human Genome held, on this occasion, in the new Auditorium of the University of the Basque Country. The Encyclopedia of Biolaw and Bioethics is a project which was conceived and driven forward by the Inter-University Chair in Law and the Human Genome. It was an ambitious project which was supported by the Roche Institute Foundation. It was therefore a magnum opus which began more than three years ago and which has required the work of more than 200 professionals from various disciplines in Spain, Latin America and Portugal. The encyclopaedia tries to make up for the lack of a suitable publication in the Spanish language that could be used as a reference and be consulted by different experts who have to tackle controversies and doubts posed in the field of biolaw and bioethics as part of their everyday work. The work makes it possible to ascertain the situation in this field regarding the most controversial issues and emerging conflicts, find out which values, assets or rights are involved or confronted, what solutions have been proposed by bioethics and the social positions that have been established through legal regulations. All in all, the encyclopaedia was the culmination of an ambitious undertaking, a pioneering work in the Spanish speaking countries due to its characteristics and scope. It is essential to have such a resource in today's cultural environment. The presentation of the Encyclopedia of Biolaw and Bioethics given by Mr. Del Barrio Seoane as Director General of the Roche Institute Foundation during the Conference deservers a special mention. The project has been consolidated through the support of this institution. PMID:22977954

  8. Rms-flux relation and fast optical variability simulations of the nova-like system MV Lyr

    NASA Astrophysics Data System (ADS)

    Dobrotka, A.; Mineshige, S.; Ness, J.-U.

    2015-03-01

    The stochastic variability (flickering) of the nova-like system (subclass of cataclysmic variable) MV Lyr yields a complicated power density spectrum with four break frequencies. Scaringi et al. analysed high-cadence Kepler data of MV Lyr, taken almost continuously over 600 d, giving the unique opportunity to study multicomponent Power Density Spectra (PDS) over a wide frequency range. We modelled this variability with our statistical model based on disc angular momentum transport via discrete turbulent bodies with an exponential distribution of the dimension scale. Two different models were used, a full disc (developed from the white dwarf to the outer radius of ˜1010 cm) and a radially thin disc (a ring at a distance of ˜1010 cm from the white dwarf) that imitates an outer disc rim. We succeed in explaining the two lowest observed break frequencies assuming typical values for a disc radius of 0.5 and 0.9 times the primary Roche lobe and an α parameter of 0.1-0.4. The highest observed break frequency was also modelled, but with a rather small accretion disc with a radius of 0.3 times the primary Roche lobe and a high α value of 0.9 consistent with previous findings by Scaringi. Furthermore, the simulated light curves exhibit the typical linear rms-flux proportionality linear relation and the typical log-normal flux distribution. As the turbulent process is generating fluctuations in mass accretion that propagate through the disc, this confirms the general knowledge that the typical rms-flux relation is mainly generated by these fluctuations. In general, a higher rms is generated by a larger amount of superposed flares which is compatible with a higher mass accretion rate expressed by a larger flux.

  9. The crowded magnetosphere of the post-common-envelope binary QS Virginis

    NASA Astrophysics Data System (ADS)

    Parsons, S. G.; Hill, C. A.; Marsh, T. R.; Gänsicke, B. T.; Watson, C. A.; Steeghs, D.; Dhillon, V. S.; Littlefair, S. P.; Copperwheat, C. M.; Schreiber, M. R.; Zorotovic, M.

    2016-05-01

    We present high-speed photometry and high-resolution spectroscopy of the eclipsing post-common-envelope binary QS Virginis (QS Vir). Our Ultraviolet and Visual Echelle Spectrograph (UVES) spectra span multiple orbits over more than a year and reveal the presence of several large prominences passing in front of both the M star and its white dwarf companion, allowing us to triangulate their positions. Despite showing small variations on a time-scale of days, they persist for more than a year and may last decades. One large prominence extends almost three stellar radii from the M star. Roche tomography reveals that the M star is heavily spotted and that these spots are long-lived and in relatively fixed locations, preferentially found on the hemisphere facing the white dwarf. We also determine precise binary and physical parameters for the system. We find that the 14 220 ± 350 K white dwarf is relatively massive, 0.782 ± 0.013 M⊙, and has a radius of 0.010 68 ± 0.000 07 R⊙, consistent with evolutionary models. The tidally distorted M star has a mass of 0.382 ± 0.006 M⊙ and a radius of 0.381 ± 0.003 R⊙, also consistent with evolutionary models. We find that the magnesium absorption line from the white dwarf is broader than expected. This could be due to rotation (implying a spin period of only ˜700 s), or due to a weak (˜100 kG) magnetic field, we favour the latter interpretation. Since the M star's radius is still within its Roche lobe and there is no evidence that it is overinflated, we conclude that QS Vir is most likely a pre-cataclysmic binary just about to become semidetached.

  10. Empirical Constraints on Common Envelope Evolution in Wide Binaries

    NASA Astrophysics Data System (ADS)

    Geller, Aaron M.; Hurley, J. R.; Mathieu, R. D.

    2012-01-01

    If a giant star in a binary overfills its Roche lobe, the giant's convective envelope may respond by expanding faster than its Roche lobe, transferring mass on a dynamical time scale, and creating a common envelope (CE) that engulfs both stars. Orbital energy may then be transferred from the binary to the envelope, which can shrink the orbit and drive away the material, leaving behind a detached system containing the white dwarf core of the giant. Such a CE event is thought to be critical for explaining certain populations of exotic stars (e.g., cataclysmic variables). Yet the application of CE evolution to binary population synthesis and N-body or Monte Carlo star cluster models requires many poorly constrained assumptions, which may lead to unphysical evolutionary paths. In fact, we find that such fictitious systems are created regularly within our N-body models of the old (7 Gyr) open cluster NGC 188. Most notably, the model predicts a population of post-CE long-period ( 1000 days) circular solar-type main sequence - white dwarf binaries, that are not present in our observations of the true binaries in NGC 188, or any other solar-type binary population in the literature (in star clusters or in the field). The absence of such post-CE systems in real binary populations places important limits on parameters used in most models of CE evolution, and may suggest that more binaries undergo stable mass transfer than has previously been assumed. We discuss how various solutions to this problem would impact other observable stellar populations, including cataclysmic variables, symbiotic stars and blue stragglers.

  11. Synthetic Spectra and Light Curves of Interacting Binaries and Exoplanets with Circumstellar Material: SHELLSPEC

    NASA Astrophysics Data System (ADS)

    Budaj, Ján

    2012-04-01

    Program SHELLSPEC is designed to calculate light-curves, spectra and images of interacting binaries and extrasolar planets immersed in a moving circumstellar environment which is optically thin. It solves simple radiative transfer along the line of sight in moving media. The assumptions include LTE and optional known state quantities and velocity fields in 3D. Optional (non)transparent objects such as a spot, disc, stream, jet, shell or stars may be defined (embedded) in 3D and their composite synthetic spectrum calculated. The Roche model can be used as a boundary condition for the radiative transfer. Recently, a new model of the reflection effect, dust and Mie scattering were incorporated into the code. ɛ Aurigae is one of the most mysterious objects on the sky. Prior modeling of its light-curve assumed a dark, inclined, disk of dust with a central hole to explain the light-curve with a sharp mid-eclipse brightening. Our model consists of two geometrically thick flared disks: an internal optically thick disk and an external optically thin disk which absorbs and scatters radiation. Shallow mid-eclipse brightening may result from eclipses by nearly edge-on flared (dusty or gaseous) disks. Mid-eclipse brightening may also be due to strong forward scattering and optical properties of the dust which can have an important effect on the light-curves. There are many similarities between interacting binary stars and transiting extrasolar planets. The reflection effect which is briefly reviewed is one of them. The exact Roche shape and temperature distributions over the surface of all currently known transiting extrasolar planets have been determined. In some cases (HAT-P-32b, WASP-12b, WASP-19b), departures from the spherical shape can reach 7-15%.

  12. TIDAL AND MAGNETIC INTERACTIONS BETWEEN A HOT JUPITER AND ITS HOST STAR IN THE MAGNETOSPHERIC CAVITY OF A PROTOPLANETARY DISK

    SciTech Connect

    Chang, S.-H.; Gu, P.-G.; Bodenheimer, P. H.

    2010-01-10

    We present a simplified model to study the orbital evolution of a young hot Jupiter inside the magnetospheric cavity of a proto-planetary disk. The model takes into account the disk locking of stellar spin as well as the tidal and magnetic interactions between the star and the planet. We focus on the orbital evolution starting from the orbit in 2:1 resonance with the inner edge of the disk, followed by the inward and then outward orbital migration driven by the tidal and magnetic torques as well as the Roche-lobe overflow of the tidally inflated planet. The goal in this paper is to study how the orbital evolution inside the magnetospheric cavity depends on the cavity size, planet mass, and orbital eccentricity. In the present work, we only target the mass range from 0.7 to 2 Jupiter masses. In the case of the large cavity corresponding to the rotational period approx7 days, the planet of mass >1 Jupiter mass with moderate initial eccentricities (approx>0.3) can move to the region <0.03 AU from its central star in 10{sup 7} yr, while the planet of mass <1 Jupiter mass cannot. We estimate the critical eccentricity beyond which the planet of a given mass will overflow its Roche radius and finally lose all of its gas onto the star due to runaway mass loss. In the case of the small cavity corresponding to the rotational period approx3 days, all of the simulated planets lose all of their gas even in circular orbits. Our results for the orbital evolution of young hot Jupiters may have the potential to explain the absence of low-mass giant planets inside approx0.03 AU from their dwarf stars revealed by transit surveys.

  13. INTERACTING BINARIES WITH ECCENTRIC ORBITS. III. ORBITAL EVOLUTION DUE TO DIRECT IMPACT AND SELF-ACCRETION

    SciTech Connect

    Sepinsky, J. F.; Willems, B.; Kalogera, V.; Rasio, F. A. E-mail: b-willems@northwestern.ed E-mail: rasio@northwestern.ed

    2010-11-20

    The rapid circularization and synchronization of the stellar components in an eccentric binary system at the onset of Roche lobe overflow is a fundamental assumption common to all binary stellar evolution and population synthesis codes, even though the validity of this assumption is questionable both theoretically and observationally. Here we calculate the evolution of the orbital elements of an eccentric binary through the direct three-body integration of a massive particle ejected through the inner Lagrangian point of the donor star at periastron. The trajectory of this particle leads to three possible outcomes: direct accretion onto the companion star within a single orbit, self-accretion back onto the donor star within a single orbit, or a quasi-periodic orbit around the companion star, possibly leading to the formation of a disk. We calculate the secular evolution of the binary orbit in the first two cases and conclude that direct impact accretion can increase as well as decrease the orbital semimajor axis and eccentricity, while self-accretion always decreases the orbital semimajor axis and eccentricity. In cases where mass overflow contributes to circularizing the orbit, circularization can set in on timescales as short as a few percent of the mass-transfer timescale. In cases where mass overflow increases the eccentricity, the orbital evolution is governed by competition between mass overflow and tidal torques. In the absence of tidal torques, mass overflow results in direct impact can lead to substantially subsynchronously rotating donor stars. Contrary to assumptions common in the literature, direct impact accretion furthermore does not always provide a strong sink of orbital angular momentum in close mass-transferring binaries; in fact, we instead find that a significant part can be returned to the orbit during the particle orbit. The formulation presented in this paper together with our previous work can be combined with stellar and binary evolution

  14. Orbital evolution of eccentric interacting binary star systems

    NASA Astrophysics Data System (ADS)

    Sepinsky, Jeremy Francis

    2009-06-01

    We provide a comprehensive description of the long-term (secular) orbital evolution of eccentric interacting binary systems. The evolution of circular interacting binary systems is a well studied phenomenon, but observations have shown the existence of a small but significant number of eccentric interacting binary systems. We begin by extending the commonly accepted Roche formalism for binary interacting to include eccentric orbits and asynchronously rotating stars. Using this, we calculate orbital trajectories for particles ejected from a Roche lobe-filling donor star at the periastron of the eccentric orbit. These particles admit of three possible trajectories: direct impact onto the secondary star, self accretion back onto the donor star, and the formation of a disk about the accretor. We provide a proscription for determining a priorithe trajectory of the particle given the initial system parameters, as well as describe the secular evolution of the system for each of the three cases described above. We find that these orbital evolution timescales are comparable to the mass transfer timescale which can be significantly longer than expected from the literature. Furthermore, while it is commonly assumed that any mass transfer interactions will act to circularize the orbit, we find that there are regimes of parameter space where mass transfer can cause an increase in eccentricity, and can do so at a timescale comparable to the circularization timescale created by tidal interactions. The formalism presented here can be incorporated into binary evolution and population synthesis models to create a self-consistent treatment of mass transfer in eccentric binaries.

  15. Stellar Archeology in the Galactic Halo with Ultra-faint Dwarfs. VII. Hercules

    NASA Astrophysics Data System (ADS)

    Musella, Ilaria; Ripepi, Vincenzo; Marconi, Marcella; Clementini, Gisella; Dall'Ora, Massimo; Scowcroft, Victoria; Moretti, Maria Ida; Di Fabrizio, Luca; Greco, Claudia; Coppola, Giuseppina; Bersier, David; Catelan, Márcio; Grado, Aniello; Limatola, Luca; Smith, Horace A.; Kinemuchi, Karen

    2012-09-01

    We present the first time-series study of the ultra-faint dwarf galaxy Hercules. Using a variety of telescope/instrument facilities we secured about 50 V and 80 B epochs. These data allowed us to detect and characterize 10 pulsating variable stars in Hercules. Our final sample includes six fundamental-mode (ab-type) and three first-overtone (c-type) RR Lyrae stars, and one Anomalous Cepheid. The average period of the ab-type RR Lyrae stars, langP abrang = 0.68 days (σ = 0.03 days), places Hercules in the Oosterhoff II group, as found for almost the totality of the ultra-faint dwarf galaxies investigated so far for variability. The RR Lyrae stars were used to obtain independent estimates of the metallicity, reddening, and distance to Hercules, for which we find [Fe/H] = -2.30 ± 0.15 dex, E(B - V) = 0.09 ± 0.02 mag, and (m - M)0 = 20.6 ± 0.1 mag, in good agreement with the literature values. We have obtained a V, B - V color-magnitude diagram (CMD) of Hercules that reaches V ~ 25 mag and extends beyond the galaxy's half-light radius over a total area of 40' × 36'. The CMD and the RR Lyrae stars indicate the presence of a population as old and metal-poor as (at least) the Galactic globular cluster M68. Based on data collected at the 2.5 m Isaac Newton Telescope, La Palma, Canary Islands, Spain, at the 4.2 m William Herschel Telescope, Roche de los Muchachos, Canary Islands, Spain, at the 2.2 m ESO/MPI telescope, La Silla, Chile, Proposal 079.D-0587, at the 2 m Liverpool Telescope, Roche de los Muchachos, Canary Islands, Spain, and at the 2 m Faulkes Telescope North, Haleakala Observatory, Hawaii, USA.

  16. UNDERSTANDING THE EVOLUTION OF CLOSE BINARY SYSTEMS WITH RADIO PULSARS

    SciTech Connect

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

    2014-05-01

    We calculate the evolution of close binary systems (CBSs) formed by a neutron star (behaving as a radio pulsar) and a normal donor star, which evolve either to a helium white dwarf (HeWD) or to ultra-short orbital period systems. We consider X-ray irradiation feedback and evaporation due to radio pulsar irradiation. We show that irradiation feedback leads to cyclic mass transfer episodes, allowing CBSs to be observed in between episodes as binary radio pulsars under conditions in which standard, non-irradiated models predict the occurrence of a low-mass X-ray binary. This behavior accounts for the existence of a family of eclipsing binary systems known as redbacks. We predict that redback companions should almost fill their Roche lobe, as observed in PSR J1723-2837. This state is also possible for systems evolving with larger orbital periods. Therefore, binary radio pulsars with companion star masses usually interpreted as larger than expected to produce HeWDs may also result in such quasi-Roche lobe overflow states, rather than hosting a carbon-oxygen WD. We found that CBSs with initial orbital periods of P{sub i} < 1 day evolve into redbacks. Some of them produce low-mass HeWDs, and a subgroup with shorter P{sub i} becomes black widows (BWs). Thus, BWs descend from redbacks, although not all redbacks evolve into BWs. There is mounting observational evidence favoring BW pulsars to be very massive (≳ 2 M {sub ☉}). As they should be redback descendants, redback pulsars should also be very massive, since most of the mass is transferred before this stage.

  17. High-sensitive Troponin T measurements early after heart transplantation predict short- and long-term survival.

    PubMed

    Erbel, Christian; Taskin, Rukiye; Doesch, Andreas; Dengler, Thomas J; Wangler, Susanne; Akhavanpoor, Mohammadreza; Ruhparwar, Arjang; Giannitsis, Evangelos; Katus, Hugo A; Gleissner, Christian A

    2013-03-01

    Following heart transplantation, cardiac biomarkers remain elevated for several weeks eventually as a result of membrane leakage of the donor organ. We now test the predictive power of blood levels of troponin T (TNT) measured by the new hsTNT assay (Roche Diagnostics, Roche Diagnostics, Mannheim, Germany) early after heart transplantation. TNT was determined in 141 cardiac allograft recipients and 40 controls. Our findings demonstrate that patients who died within the first year after transplantation had significantly higher median hsTNT serum levels 6 weeks after transplantation (156 ng/l ± 203 vs. 29 ng/l ± 21, P = 0.0002). Using ROC analysis, a serum hsTNT concentration of 33.55 ng/l 6 weeks after transplantation was found to be the best cutoff to predict death at 1 year (HR 0.16, 95%CI:0.05-0.46, P = 0.001) with a sensitivity of 90.91% and a specificity of 70.97%. In addition, survival at 5 years (HR 0.15, 95% CI 0.06-0.35, P < 0.0001) was significantly better among patients below that cutoff value. In multivariate analysis, hsTNT serum level 6 weeks after transplantation emerged as an independent predictor for first-year mortality (hsTNT-HR 0.90, 95% CI: 0.81-1.00, P = 0.03). Cardiac troponin T concentrations early after transplantation as measured with a highly sensitive assay represent a strong and independent risk predictor of death after heart transplantation. PMID:23252662

  18. PSR J1723–2837: AN ECLIPSING BINARY RADIO MILLISECOND PULSAR

    SciTech Connect

    Crawford, Fronefield; Lyne, Andrew G.; Stairs, Ingrid H.; Kaplan, David L.; McLaughlin, Maura A.; Lorimer, Duncan R.; Freire, Paulo C. C.; Kramer, Michael; Burgay, Marta; D'Amico, Nichi; Possenti, Andrea; Camilo, Fernando; Faulkner, Andrew; Manchester, Richard N.; Steeghs, Danny

    2013-10-10

    We present a study of PSR J1723–2837, an eclipsing, 1.86 ms millisecond binary radio pulsar discovered in the Parkes Multibeam survey. Radio timing indicates that the pulsar has a circular orbit with a 15 hr orbital period, a low-mass companion, and a measurable orbital period derivative. The eclipse fraction of ∼15% during the pulsar's orbit is twice the Roche lobe size inferred for the companion. The timing behavior is significantly affected by unmodeled systematics of astrophysical origin, and higher-order orbital period derivatives are needed in the timing solution to account for these variations. We have identified the pulsar's (non-degenerate) companion using archival ultraviolet, optical, and infrared survey data and new optical photometry. Doppler shifts from optical spectroscopy confirm the star's association with the pulsar and indicate a pulsar-to-companion mass ratio of 3.3 ± 0.5, corresponding to a companion mass range of 0.4 to 0.7 M{sub ☉} and an orbital inclination angle range of between 30° and 41°, assuming a pulsar mass range of 1.4-2.0 M{sub ☉}. Spectroscopy indicates a spectral type of G for the companion and an inferred Roche-lobe-filling distance that is consistent with the distance estimated from radio dispersion. The features of PSR J1723–2837 indicate that it is likely a 'redback' system. Unlike the five other Galactic redbacks discovered to date, PSR J1723–2837 has not been detected as a γ-ray source with Fermi. This may be due to an intrinsic spin-down luminosity that is much smaller than the measured value if the unmeasured contribution from proper motion is large.

  19. A wind accretion model for HLX-1

    SciTech Connect

    Miller, M. Coleman; Farrell, Sean A.; Maccarone, Thomas J.

    2014-06-20

    The brightest ultraluminous X-ray source currently known, HLX-1, has been observed to undergo five outburst cycles. The periodicity of these outbursts, and their high inferred maximum accretion rates of ∼few × 10{sup –4} M {sub ☉} yr{sup –1}, naturally suggest Roche lobe overflow at the pericenter of an eccentric orbit. It is, however, difficult for the Roche lobe overflow model to explain the apparent trend of decreasing decay times over the different outbursts while the integrated luminosity also drops. Thus, if the trend is real rather than simply being a reflection of the complex physics of accretion disks, a different scenario may be necessary. We present a speculative model in which, within the last decade, a high-mass giant star had most of its envelope tidally stripped by the ∼10{sup 4–5} M {sub ☉} black hole in HLX-1, and the remaining core plus low-mass hydrogen envelope now feeds the hole with a strong wind. This model can explain the short decay time of the disk, and could explain the fast decrease in decay time if the wind speed changes with time. A key prediction of this model is that there will be excess line absorption due to the wind; our analysis does in fact find a flux deficit in the ∼0.9-1.1 keV range that is consistent with predictions, albeit at low significance. If this idea is correct, we also expect that within years to dacades the bound material from the original disruption will return and will make HLX-1 a persistently bright source.

  20. High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species

    PubMed Central

    Razgour, Orly; Clare, Elizabeth L; Zeale, Matt R K; Hanmer, Julia; Schnell, Ida Bærholm; Rasmussen, Morten; Gilbert, Thomas P; Jones, Gareth

    2011-01-01

    Sympatric cryptic species, characterized by low morphological differentiation, pose a challenge to understanding the role of interspecific competition in structuring ecological communities. We used traditional (morphological) and novel molecular methods of diet analysis to study the diet of two cryptic bat species that are sympatric in southern England (Plecotus austriacus and P. auritus) (Fig. 1). Using Roche FLX 454 (Roche, Basel, CH) high-throughput sequencing (HTS) and uniquely tagged generic arthropod primers, we identified 142 prey Molecular Operational Taxonomic Units (MOTUs) in the diet of the cryptic bats, 60% of which were assigned to a likely species or genus. The findings from the molecular study supported the results of microscopic analyses in showing that the diets of both species were dominated by lepidopterans. However, HTS provided a sufficiently high resolution of prey identification to determine fine-scale differences in resource use. Although both bat species appeared to have a generalist diet, eared-moths from the family Noctuidae were the main prey consumed. Interspecific niche overlap was greater than expected by chance (Ojk = 0.72, P < 0.001) due to overlap in the consumption of the more common prey species. Yet, habitat associations of nongeneralist prey species found in the diets corresponded to those of their respective bat predator (grasslands for P. austriacus, and woodland for P. auritus). Overlap in common dietary resource use combined with differential specialist prey habitat associations suggests that habitat partitioning is the primary mechanism of coexistence. The performance of HTS is discussed in relation to previous methods of molecular and morphological diet analysis. By enabling species-level identification of dietary components, the application of DNA sequencing to diet analysis allows a more comprehensive comparison of the diet of sympatric cryptic species, and therefore can be an important tool for determining fine

  1. Gravity darkening in binary stars

    NASA Astrophysics Data System (ADS)

    Espinosa Lara, F.; Rieutord, M.

    2012-11-01

    Context. Interpretation of light curves of many types of binary stars requires the inclusion of the (cor)relation between surface brightness and local effective gravity. Until recently, this correlation has always been modeled by a power law relating the flux or the effective temperature and the effective gravity, namely Teff ∝ geffβ . Aims: We look for a simple model that can describe the variations of the flux at the surface of stars belonging to a binary system. Methods: This model assumes that the energy flux is a divergence-free vector anti-parallel to the effective gravity. The effective gravity is computed from the Roche model. Results: After explaining in a simple manner the old result of Lucy (1967, Z. Astrophys., 65, 89), which says that β ~ 0.08 for solar type stars, we first argue that one-dimensional models should no longer be used to evaluate gravity darkening laws. We compute the correlation between log Teff and log geff using a new approach that is valid for synchronous, weakly magnetized, weakly irradiated binaries. We show that this correlation is approximately linear, validating the use of a power law relation between effective temperature and effective gravity as a first approximation. We further show that the exponent β of this power law is a slowly varying function, which we tabulate, of the mass ratio of the binary star and the Roche lobe filling factor of the stars of the system. The exponent β remains mostly in the interval [0.20,0.25] if extreme mass ratios are eliminated. Conclusions: For binary stars that are synchronous, weakly magnetized and weakly irradiated, the gravity darkening exponent is well constrained and may be removed from the free parameters of the models.

  2. [Multicenter evaluation of the reliability of five blood glucose monitoring systems].

    PubMed

    Jday-Daly, Ismahen; Augereau-Vacher, Christine; De Curraize, Claire; Fonfrède, Michèle; Lefevre, Guillaume; Lacour, Bernard; Hennequin-Le Meur, Carole

    2011-01-01

    As part of a tender AP-HP Paris Hospitals, an assessment of the reliability record of five blood glucose monitoring systems (BGMSs) (Optium Xceed (Abbott), Contour TS (Bayer), One Touch Ultra (Lifescan), Stat Strip Xpress (Nova) and Accu Check (Roche) and an evaluation of their sensitivity to changes in hematocrit were conducted in 4 hospitals of Paris. In terms of inaccuracy, all BGMSs have submitted CV repetability under the limits of acceptability. One BGMS (Lifescan) presented a CV of reproducibility outside limit of acceptability (13.1%). The inaccuracy was measured by a comparison method on multiparameter analyser relative to the hexokinase method for two sites, the glucose oxidase for the two others. The coefficients of correlation varied from 0.8405 to 0.9303. However, according to both defined acceptability criteria (absolute value difference between the result acquired on analyzer and those determined with the BGMS), the percentage of results outside acceptability was above 20% for two BGMSs (Abbott and Lifescan). Similarly, a net effect of changes in hematocrit was observed on the results of those two BGMSs. BGMS Nova was the most reliable, because of the correction device for hematocrit and blank substractions owed to interferences. In terms of expertise, BGMSs Nova and Roche have been selected with the best analytical performance and practicability satisfactory. In the future, accreditation with standard NF/EN 22870 requested for point of care testing, will require a close collaboration between biologists and clinicians to establish a system of strict quality control to detect deviations of these BGMSs. PMID:21463996

  3. Performance Characteristics of the QUANTIPLEX HIV-1 RNA 3.0 Assay for Detection and Quantitation of Human Immunodeficiency Virus Type 1 RNA in Plasma

    PubMed Central

    Erice, Alejo; Brambilla, Donald; Bremer, James; Jackson, J. Brooks; Kokka, Robert; Yen-Lieberman, Belinda; Coombs, Robert W.

    2000-01-01

    The QUANTIPLEX HIV-1 RNA assay, version 3.0 (a branched DNA, version 3.0, assay [bDNA 3.0 assay]), was evaluated by analyzing spiked and clinical plasma samples and was compared with the AMPLICOR HIV-1 MONITOR Ultrasensitive (ultrasensitive reverse transcription-PCR [US-RT-PCR]) method. A panel of spiked plasma samples that contained 0 to 750,000 copies of human immunodeficiency virus type 1 (HIV-1) RNA per ml was tested four times in each of four laboratories (1,344 assays). Negative results (<50 copies/ml) were obtained in 30 of 32 (94%) assays with seronegative samples, 66 of 128 (52%) assays with HIV-1 RNA at 50 copies/ml, and 5 of 128 (4%) assays with HIV-1 RNA at 100 copies/ml. The assay was linear from 100 to 500,000 copies/ml. The within-run standard deviation (SD) of the log10 estimated HIV-1 RNA concentration was 0.08 at 1,000 to 500,000 copies/ml, increased below 1,000 copies/ml, and was 0.17 at 100 copies/ml. Between-run reproducibility at 100 to 500 copies/ml was <0.10 log10 in most comparisons. Interlaboratory differences across runs were ≤0.10 log10 at all concentrations examined. A subset of the panel (25 to 500 copies/ml) was also analyzed by the US-RT-PCR assay. The within-run SD varied inversely with the log10 HIV-1 RNA concentration but was higher than the SD for the bDNA 3.0 assay at all concentrations. Log-log regression analysis indicated that the two methods produced very similar estimates at 100 to 500 copies/ml. In parallel testing of clinical specimens with low HIV-1 RNA levels, 80 plasma samples with <50 copies/ml by the US-RT-PCR assay had <50 copies/ml when they were retested by the bDNA 3.0 assay. In contrast, 11 of 78 (14%) plasma samples with <50 copies/ml by the bDNA 3.0 assay had ≥50 copies/ml when they were retested by the US-RT-PCR assay (median, 86 copies/ml; range, 50 to 217 copies/ml). Estimation of bDNA 3.0 values of <50 copies/ml by extending the standard curve of the assay showed that these samples with discrepant

  4. Efectos difusivos en la formación de enanas blancas de Helio de baja masa en sistemas binarios cerrados

    NASA Astrophysics Data System (ADS)

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

    ., & Benvenuto, O. G. (2001, MNRAS, 323, 471) but in that paper the mass transfer was mimicked by subtracting mass to a progenitor of 1 M⊙ to obtain the mass for the desired object. Actually, our binary code has a full nuclear reactions network for hydrogen and helium burning that allowed us to follow the abundances of fifteen isotopes throughout the entire evolution of the star. We have also included a detailed equation of state. The mass loss treatment is non conservative. We have modified the conditions for the beginning and end of mass transfer episodes. In our previous version, we assumed it to occur when the stellar radius was greater or smaller, respectively, that the Roche Lobe radius for the star. This introduced numerical problems, especially at the end of mass transfer phases. We adopted H. Ritter (1988, A&A, 202, 93) formulation that considers a finite scale height in the stellar atmosphere. The numerical behaviour in much more satisfactory, besides that it constitutes a more appropriate description for the physical problem. We perform the calculations for the evolution of the primary star in a close binary system of initial mass 2 M⊙, initial period of 1 day, initial mass ratio of 1.4142 and solar metallicity. We have done the calculations in four cases: A) with diffusion and all Roche Lobe overflows, B) with diffusion and only the first Roche Lobe overflow, C) without diffusion and all Roche Lobe overflows, D) without diffusion and only the first Roche Lobe overflow. Cases B) and D) where performed to compare with results obtained for Althaus et al. (2001). The main conclusion of this work is that the age of these objects is mainly determined by diffusive effects, and the late stages of mass transfer, not considered in Althaus et al. (2001), constituted a minor effect on the scales of cooling times.

  5. [Development of a real-time polymerase chain reaction method for the identification of Candida species].

    PubMed

    Ağca, Harun; Dalyan Cilo, Burcu; Özmerdiven, Gülşah Ece; Sağlam, Sezcan; Ener, Beyza

    2015-01-01

    Candida species are one of the major causes of nosocomial infections and are the fourth most common agent involved in bloodstream infections. The impact of non-albicans Candida species is increasing, however C.albicans is still the most common species. Since the antifungal susceptibility pattern among Candida spp. may be different, rapid diagnosis and identification of non-albicans Candida spp. are important for the determination of antifungal agents that will be used for treatment. The aim of the study was to describe a real-time polymerase chain reaction (Rt-PCR) assay that rapidly detects, identifies and quantitates Candida species from blood culture samples. A total of 50 consecutive positive blood culture bottles (BACTEC, Beckton Dickinson, USA) identified at our laboratory between June-November 2013, were included in the study. Reference strains of Candida spp. (C.albicans ATCC 10231, C.glabrata ATCC 90030, C.tropicalis ATCC 1021, C.krusei ATCC 6258, C.parapsilosis ATCC 22019 and C. dubliniensis CD36) grown on Sabouraud dextrose agar were used for quality control. BACTEC bottles that were positive for Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus were also studied to search the cross-reactivity. A commercial kit (Zymo Research, USA) was used for DNA extraction. Real-time PCR was performed on LightCycler 480 (Roche, Germany) with primers and probes specific for 18S rRNA of Candida species. Twenty microlitres of the reaction mix contained 2 μl of extracted DNA, 2 μl of LightCycler Fast Start DNA Master Probe (Roche Diagnostics, Germany), 2 μl of MgCl(2) (5 mmol), 2 μl of 10x PCR buffer (Roche Diagnostics, Germany), 0.5 μl of each primer (0.01 nmol/μl) and 1 μl of each probe (0.1 μmol/μl) (TibMolBiol, Germany). Amplification was performed using the following conditions; 95°C for 10 mins and 50 cycles of denaturation at 95°C for 10 secs, annealing at 62°C for 10 secs and polymerisation at 72°C for 20 secs. A melting curve was

  6. Representing Icebergs In A Fully Coupled Climate Model

    NASA Astrophysics Data System (ADS)

    Bügelmayer, Marianne; Roche, Didier; Renssen, Hans

    2014-05-01

    Changes in the global climate during past and current times strongly impact the Polar Regions, which in turn affect the global climate due to several mechanisms, such as albedo, topography, ablation and ice discharge. Icebergs are an important part of the climate system as they interact with the ocean, atmosphere and cryosphere. Several approaches have been taken to incorporate iceberg calving into numerical models under different climate forcings. The studies done so far have in common that the icebergs were moved by reconstructed or modelled forcing fields and that the initial size distribution of the icebergs was prescribed according to present day observations. Hence, uncertainties in the forcing fields and in the parameterization of the iceberg size may alter the results. To investigate the impact of the background forcing (atmosphere, ocean) and the pre-defined size distribution on the icebergs and consequently on the Northern hemisphere climate and the Greenland ice sheet, we have coupled an earth system model of intermediate complexity (iLOVECLIM, Roche et al., 2013) to an ice sheet/ice shelf model (GRISLI, Ritz et al., 2001) and an iceberg module (Jongma et al., 2009; Bügelmayer et al., 2014). Using this set-up, we performed 15 sensitivity experiments that differ in the applied forcing (atmosphere, ocean), the applied boundary conditions (pre-industrial, 4xCO2, 1/4 x CO2) and the initial size distribution of the icebergs. In the presented study only the Greenland ice sheet is considered. We find that, under pre-industrial conditions, the atmospheric forcing pushes the icebergs further away from their calving sites and further into the North Atlantic, whereas the ocean currents transport the bergs along the Greenland coast and southward along the Canadian coast. Although the purely atmospheric-forced bergs cause warmer oceanic conditions than the oceanic-driven bergs, the overall effect on climate and the resulting ice sheet due to variations in the

  7. The Effect of Solar Forcing on the Greenland Ice Sheet during the Holocene - A Model Study

    NASA Astrophysics Data System (ADS)

    Bügelmayer, Marianne; Roche, Didier; Renssen, Hans

    2014-05-01

    Abrupt climate changes did not only happen during glacials but also during interglacials such as the Holocene. Marine sediments provide evidence for the periodic occurrence of centennial-scale events with enhanced iceberg discharge during the past 11.000 years (Bond et al., 2001). These events were chronologically linked to reduced solar activity as reconstructed using cosmogenic isotopes (Bond et al., 2001), indicating that even an external forcing that is considered to be small, has a potential impact on climate due to several feedback mechanisms (Renssen et al., 2006). The interactions between climate and solar irradiance have been investigated using numerical models (e.g. Haigh, 1996; Renssen et al, 2006), but so far without dynamically computing the Greenland ice sheet and iceberg calving. Thus, the impact of solar variations on iceberg discharge and the underlying mechanisms have not been analysed so far. To analyse the effect of variations in solar activity on the Greenland ice sheet (GIS) and the iceberg calving, as well as possible feedback mechanisms that enhance the impact of the total solar irradiance, we use the earth system model of intermediate complexity (iLOVECLIM, Roche et al., 2013), coupled to the ice sheet/ice shelf model GRISLI (Ritz et al., 2001) and to a dynamic-thermodynamic iceberg module (Jongma et al., 2009, Bügelmayer et al., 2014) to perform transient experiments of the last 6000 years. The experiments are conducted applying reconstructed atmospheric greenhouse gas concentrations, volcanic aerosol loads, orbital parameters and variations in the total solar irradiance. We present the response of the coupled model to different solar irradiance scenarios to evaluate modeled GIS sensitivity to relatively modest variations in radiative forcing. Moreover, we investigate the dependence of the model results on the chosen model sensitivity. References: Bond, G., Kromer, B., Beer, J., Muscheler, R., Evans, M. N., Showers, W., … Bonani, G

  8. CCD Photometric Observations and Light Curve Synthesis of the Near-Contact Binary XZ Canis Minoris

    NASA Astrophysics Data System (ADS)

    Kim, Chun-Hwey; Park, Jang-Ho; Lee, Jae Woo; Jeong, Jang-Hae

    2009-06-01

    Through the photometric observations of the near-contact binary, XZ CMi, new BV light curves were secured and seven times of minimum light were determined. An intensive period study with all published timings, including ours, confirms that the period of XZ CMi has varied in a cyclic period variation superposed on a secular period decrease over last 70 years. Assuming the cyclic change of period to occur by a light-time effect due to a third-body, the light-time orbit with a semi-amplitude of 0.0056d, a period of 29y and an eccentricity of 0.71 was calculated. The observed secular period decrease of -5.26× 10^{-11} d/P was interpreted as a result of simultaneous occurrence of both a period decrease of -8.20 × 10^{-11} d/P by angular momentum loss (AML) due to a magnetic braking stellar wind and a period increase of 2.94 × 10^{-11} d/P by a mass transfer from the less massive secondary to the primary components in the system. In this line the decreasi! ng rate of period due to AML is about 3 times larger than the increasing one by a mass transfer in their absolute values. The latter implies a mass transfer of dot M_{s}= 3.21 × 10^{-8} M_⊙ y^{-1} from the less massive secondary to the primary. The BV light curves with the latest Wilson-Devinney binary code were analyzed for two separate models of 8200K and 7000K as the photospheric temperature of the primary component. Both models confirm that XZ CMi is truly a near-contact binary with a less massive secondary completely filling Roche lobe and a primary inside the inner Roche lobe and there is a third-light corresponding to about 15-17% of the total system light. However, the third-light source can not be the same as the third-body suggested from the period study. At the present, however, we can not determine which one between two models is better fitted to the observations because of a negligible difference of sum (O-C)^2 between them. The diversity of mass ratios, with which previous investigators were in

  9. Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles

    PubMed Central

    2011-01-01

    Background Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes in its size, color, sweetness, texture and aroma. In order to better understand the genetic and molecular basis of these changes and significantly expand the watermelon transcript catalog, we have selected four critical stages of watermelon fruit development and used Roche/454 next-generation sequencing technology to generate a large expressed sequence tag (EST) dataset and a comprehensive transcriptome profile for watermelon fruit flesh tissues. Results We performed half Roche/454 GS-FLX run for each of the four watermelon fruit developmental stages (immature white, white-pink flesh, red flesh and over-ripe) and obtained 577,023 high quality ESTs with an average length of 302.8 bp. De novo assembly of these ESTs together with 11,786 watermelon ESTs collected from GenBank produced 75,068 unigenes with a total length of approximately 31.8 Mb. Overall 54.9% of the unigenes showed significant similarities to known sequences in GenBank non-redundant (nr) protein database and around two-thirds of them matched proteins of cucumber, the most closely-related species with a sequenced genome. The unigenes were further assigned with gene ontology (GO) terms and mapped to biochemical pathways. More than 5,000 SSRs were identified from the EST collection. Furthermore we carried out digital gene expression analysis of these ESTs and identified 3,023 genes that were differentially expressed during watermelon fruit development and ripening, which provided novel insights into watermelon fruit biology and a comprehensive resource of candidate genes for future functional analysis. We then generated profiles of several interesting metabolites that are important to fruit quality including pigmentation and sweetness. Integrative analysis of metabolite and digital gene

  10. The origin of extended interstellar shells around Wolf-Rayet stars having bright optical ring nebulae

    NASA Technical Reports Server (NTRS)

    Nichols, J. S.; Fesen, R. A.

    1994-01-01

    during a Roche Lobe overflow stage of the binary after the supernova explosion. In either of these cases the bright optical ring nebulae associated with these three WR stars may signify recent Roche Lobe overflows consistent with spectroscopic abundance analysis.

  11. THE REFLECTION EFFECT IN INTERACTING BINARIES OR IN PLANET-STAR SYSTEMS

    SciTech Connect

    Budaj, J.

    2011-02-15

    There are many similarities between interacting binary stars and stars with a close-in giant extrasolar planet. The reflection effect is a well-known example. Although the generally accepted treatment of this effect in interacting binaries is successful in fitting light curves of eclipsing binaries, it is not very suitable for studying cold objects irradiated by hot objects or extrasolar planets. The aim of this paper is to develop a model of the reflection effect which could be easily incorporated into the present codes for modeling of interacting binaries so that these can be used to study the aforementioned objects. Our model of the reflection effect takes into account the reflection (scattering), heating, and heat redistribution over the surface of the irradiated object. The shape of the object is described by the non-spherical Roche potential expected for close objects. Limb and gravity darkening are included in the calculations of the light output from the system. The model also accounts for the orbital revolution and rotation of the exoplanet with appropriate Doppler shifts for the scattered and thermal radiation. Subsequently, light curves and/or spectra of several exoplanets have been modeled and the effects of the heat redistribution, limb darkening/brightening, (non-)gray albedo, and non-spherical shape have been studied. Recent observations of planet-to-star flux ratio of HD189733b, WASP12b, and WASP-19b at various phases were reproduced with very good accuracy. It was found that HD189733b has a low Bond albedo and intense heat redistribution, while WASP-19b has a low Bond albedo and low heat redistribution. The exact Roche geometries and temperature distributions over the surface of all 78 transiting extrasolar planets have been determined. Departures from the spherical shape may vary considerably but departures of about 1% in the radius are common within the sample. In some cases, these departures can reach 8%, 12%, or 14%, for WASP-33b, WASP-19b, and

  12. SAMBA HIV semiquantitative test, a new point-of-care viral-load-monitoring assay for resource-limited settings.

    PubMed

    Ritchie, Allyson V; Ushiro-Lumb, Ines; Edemaga, Daniel; Joshi, Hrishikesh A; De Ruiter, Annemiek; Szumilin, Elisabeth; Jendrulek, Isabelle; McGuire, Megan; Goel, Neha; Sharma, Pia I; Allain, Jean-Pierre; Lee, Helen H

    2014-09-01

    Routine viral-load (VL) testing of HIV-infected individuals on antiretroviral therapy (ART) is used to monitor treatment efficacy. However, due to logistical challenges, implementation of VL has been difficult in resource-limited settings. The aim of this study was to evaluate the performance of the SAMBA semi-Q (simple amplification-based assay semiquantitative test for HIV-1) in London, Malawi, and Uganda. The SAMBA semi-Q can distinguish between patients with VLs above and below 1,000 copies/ml. The SAMBA semi-Q was validated with diluted clinical samples and blinded plasma samples collected from HIV-1-positive individuals. SAMBA semi-Q results were compared with results from the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 test, v2.0. Testing of 96 2- to 10-fold dilutions of four samples containing HIV-1 subtype C as well as 488 samples from patients in the United Kingdom, Malawi, and Uganda yielded an overall accuracy for the SAMBA semi-Q of 99% (95% confidence interval [CI], 93.8 to 99.9%) and 96.9% (95% CI 94.9 to 98.3%), respectively, compared to to the Roche test. Analysis of VL data from patients in Malawi and Uganda showed that the SAMBA cutoff of 1,000 copies/ml appropriately distinguished treated from untreated individuals. Furthermore, analysis of the viral loads of 232 patients on ART in Malawi and Uganda revealed similar patterns for virological control, defined as either <1,000 copies/ml (SAMBA cutoff) or <5,000 copies/ml (WHO 2010 criterion; WHO, Antiretroviral Therapy for HIV Infection in Adults and Adolescents: Recommendations for a Public Health Approach, 2010). This study suggests that the SAMBA semi-Q has adequate concurrency with the gold standard measurements for viral load. This test can allow VL monitoring of patients on ART at the point of care in resource-limited settings. PMID:25031444

  13. Strong orbital expansion of Saturn’s inner ice-rich moons through ring torques and mutual resonances during their accretion from a massive ring

    NASA Astrophysics Data System (ADS)

    Salmon, Julien; Canup, Robin M.

    2015-11-01

    Saturn has a diversity of moons with possibly diverse origins. Titan likely formed in Saturn’s sub-nebula (e.g., Canup & Ward 2006). The small moons interior to Mimas are likely recent aggregates of ring’s material spreading through the Roche limit (Charnoz et al. 2010). The origin of the mid-size moons, Mimas through Rhea, is debated. Charnoz et al. (2011) considered a massive ice-rock ring and strong tidal dissipation in Saturn (Q ~ 103), and found that moons out to Rhea could be spawned from such a ring. However such a small value for Q for Saturn is debated. In addition, capture into mutual Mean Motion Resonances (MMR) and resulting eccentricity growth (not included in the Charnoz et al. (2011) model) could lead to orbital destabilization as the moons tidally expand over such large distances (Peale & Canup 2015).Here we consider weak planetary tides (Q ≥ 104) and investigate whether Mimas, Enceladus and Tethys could have been spawned from a massive ice ring (Canup 2010). In this scenario, the rock in these moons would be delivered by material from outside the rings, e.g. by heliocentric impactors during the LHB (Canup 2013). We have expanded a numerical model developed to study the Moon’s accretion (Salmon and Canup 2012, 2014), which couples an analytic Roche-interior disk model to the N-body code SyMBA (Duncan et al. 1998) for satellites, so that we can directly track their accretion and mutual interactions (including MMRs), as well as their tidal interaction with the planet. We consider an initially large Saturn (Fortney et al. 2007) and its progressive contraction, which impacts the strength of tides and the location of the corotation resonance. We perform simulations with and without Dione and Rhea, and study the influence of tidal dissipation into the moons.We find that recoil of the moons due to ring torques, together with capture of moons into MMRs, can produce a distribution similar to that observed. If tidal dissipation in the moons was weak

  14. Rotation and evolution of A and F stars

    NASA Astrophysics Data System (ADS)

    Yoon, Jinmi

    Rapid rotation can significantly affect stellar evolution. Perhaps more importantly, rapid rotation obscures the interpretation of the measurements of the intrinsic properties of the star. Thus, it is important to determine the actual rotational velocity of a star, whereas generally only the line of sight projection is known. Reported here are three investigations of the effects of rotation using high resolution spectroscopy and high angular resolution interferometry. First, a list of potential targets and a series of catalogs of potential calibrators for existing ground-based interferometry were produced. A and F stars are subject to distortion if rotating rapidly, which can add significant uncertainty in interferometric measurements if used as calibrators. The catalogs characterize these uncertainties. Next, the discovery that Vega is a rapidly rotating pole-on star creates uncertainties over its assumed age and composition. A full spectral synthesis with the Roche model derived from NPOI interferometry demonstrates that the temperature gradient over the surface produces a variety of peculiar line shapes in addition to the flat-bottomed line profiles previously recognized. ELODIE spectra show excellent agreement with the calculations if an additional 10 km s-1 of macroturbulence is added to the predicted spectra. The suggestion that Vega has the peculiar composition of a lambda Boo star is also confirmed. Rapid rotation argues strongly that the star is well mixed. Hence the deduced composition is a bulk property, not limited to its surface, leading to a significant revision of Vega's mass and age as estimated from evolutionary calculations. Lastly, simultaneously fitting the interferometric and spectroscopic observations with a Roche model providing the maximum possible number of constraints on the model gives a more direct determination of Vega's physical characteristics, particularly its mass. These calculations confirm independently that Vega has a much lower

  15. A simplified methodology to approach the complexity of foraminiferal calcite oxygen-isotope data - model comparison

    NASA Astrophysics Data System (ADS)

    Roche, Didier; Waelbroeck, Claire

    2016-04-01

    Since the pioneering work of Epstein (Epstein et al., 1953), numerous calcite isotopic records from the ocean have been used to attempt reconstructing paleoclimatic information. Additional to the well known complexity brought by the fact that foraminiferal calcite records both temperature and isotopic composition of the surrounding oceanic waters, an additional effect for surface - dwelling foraminifers is the fact that two different species do not have the same habitat and may thus record different signals. This is obvious when comparing paleoclimatic records where different species have been measured for the isotopic composition of the calcite. The difference in habitat produces a three dimensional spatial complexity (a foraminifera living in preferred climatic conditions at a specific location, but also at a specific depth, sometimes far from the surface) but also a temporal uncertainty (foraminifers generally live for only a few weeks and their growth season may be evolving through time with climate change). While the different species habitats potentially contain a wealth of information that could be used to better understand the sequences of climate change, this has seldom been used in modeling studies, most models deriving calcite isotopic signal from surface and annual mean conditions (e.g. Roche et al., 2014). In the present work, we propose a reduced complexity approach to compute the calcite for several planktonic foraminifers from climate model simulations under pre-industrial conditions. We base our approach on simple functions describing the temperature dependence of the different species growth rates (Lombard et al., 2009) and on probability of presence based on the physical variables computed in the climate model. We present a comparison to available sediment traps and core tops data as a validation of the methodology, focusing on the possibility for future applicability towards inversion of the signal measured in oceanic sediment cores. References

  16. Thyroglobulin (Tg) Testing Revisited: Tg Assays, TgAb Assays, and Correlation of Results With Clinical Outcomes

    PubMed Central

    Netzel, Brian C.; Grebe, Stefan K. G.; Carranza Leon, B. Gisella; Castro, M. Regina; Clark, Penelope M.; Hoofnagle, Andrew N.; Spencer, Carole A.; Turcu, Adina F.

    2015-01-01

    Context: Measurement of thyroglobulin (Tg) by mass spectrometry (Tg-MS) is emerging as a tool for accurate Tg quantification in patients with anti-Tg autoantibodies (TgAbs). Objective: The objective of the study was to perform analytical and clinical evaluations of two Tg-MS assays in comparison with immunometric Tg assays (Tg-IAs) and Tg RIAs (Tg-RIAs) in a cohort of thyroid cancer patients. Methods: A total of 589 samples from 495 patients, 243 TgAb−/252 TgAb+, were tested by Beckman, Roche, Siemens-Immulite, and Thermo-Brahms Tg and TgAb assays, two Tg-RIAs, and two Tg-MS assays. Results: The frequency of TgAb+ was 58%, 41%, 27%, and 39% for Roche, Beckman, Siemens-Immulite, and Thermo-Brahms, respectively. In TgAb− samples, clinical sensitivities and specificities of 100% and 74%–100%, respectively, were observed across all assays. In TgAb+ samples, all Tg-IAs demonstrated assay-dependent Tg underestimation, ranging from 41% to 86%. In TgAb+ samples, the use of a common cutoff (0.5 ng/mL) for the Tg-MS, three Tg-IAs, and the USC-RIA improved the sensitivity for the Tg-MSs and Tg-RIAs when compared with the Tg-IAs. In up to 20% of TgAb+ cases, Tg-IAs failed to detect Tg that was detectable by Tg-MS. In Tg-RIAs false-high biases were observed in TgAb+ samples containing low Tg concentrations. Conclusions: Tg-IAs remain the method of choice for Tg quantitation in TgAb− patients. In TgAb+ patients with undetectable Tg by immunometric assay, the Tg-MS will detect Tg in up to 20% additional cases. The Tg-RIA will detect Tg in approximately 35% cases, but a significant proportion of these will be clinical false-positive results. The undetectable Tg-MS seen in approximately 40% of TgAb+ cases in patients with disease need further evaluation. PMID:26079778

  17. Characterization of the heart transcriptome of the white shark (Carcharodon carcharias)

    PubMed Central

    2013-01-01

    Background The white shark (Carcharodon carcharias) is a globally distributed, apex predator possessing physical, physiological, and behavioral traits that have garnered it significant public attention. In addition to interest in the genetic basis of its form and function, as a representative of the oldest extant jawed vertebrate lineage, white sharks are also of conservation concern due to their small population size and threat from overfishing. Despite this, surprisingly little is known about the biology of white sharks, and genomic resources are unavailable. To address this deficit, we combined Roche-454 and Illumina sequencing technologies to characterize the first transciptome of any tissue for this species. Results From white shark heart cDNA we generated 665,399 Roche 454 reads (median length 387-bp) that were assembled into 141,626 contigs (mean length 503-bp). We also generated 78,566,588 Illumina reads, which we aligned to the 454 contigs producing 105,014 454/Illumina consensus sequences. To these, we added 3,432 non-singleton 454 contigs. By comparing these sequences to the UniProtKB/Swiss-Prot database we were able to annotate 21,019 translated open reading frames (ORFs) of ≥ 20 amino acids. Of these, 19,277 were additionally assigned Gene Ontology (GO) functional annotations. While acknowledging the limitations of our single tissue transcriptome, Fisher tests showed the white shark transcriptome to be significantly enriched for numerous metabolic GO terms compared to the zebra fish and human transcriptomes, with white shark showing more similarity to human than to zebra fish (i.e. fewer terms were significantly different). We also compared the transcriptome to other available elasmobranch sequences, for signatures of positive selection and identified several genes of putative adaptive significance on the white shark lineage. The white shark transcriptome also contained 8,404 microsatellites (dinucleotide, trinucleotide, or tetranucleotide motifs

  18. Pursuing the link between Scientific Research and Communication: the experience of the OAVdA and the Planetarium in the Aosta Valley

    NASA Astrophysics Data System (ADS)

    Ettore Bernagozzi, Andrea; Bertolini, Enzo; Calcidese, Paolo; Carbognani, Albino; Carlo Cenadelli, Davide; Christille, Jean Marc; Pellissier, Paolo; Recaldini, Paolo; Soldi, Matteo

    2015-08-01

    The Astronomical Observatory of the Autonomous Region of the Aosta Valley (OAVdA) and the Planetarium of Lignan are located in the Saint-Barthélemy Valley, in the Italian Alps at the border with France and Switzerland. They are managed by the non-profit organisation Fondazione Clément Fillietroz-ONLUS. The OAVdA opened in 2003, then the Planetarium followed in 2009.Scientific Research has been the main activity at the OAVdA since 2006, when an official agreement of cooperation was set up with the Italian National Institute for Astrophysics (INAF). Scientific Research made at the OAVdA contributes greatly to the development of high quality Public Outreach and Education programs. We adopt the principle that knowledge teachers and students meet in school is the result of scientific researches made by scientists in the past; then, knowledge they will meet in life tomorrow is the result of scientific researches that scientists are making today. To put this in practice, researchers are effectively involved, for at least 30% of their working time, in a vast spectrum of Public Outreach and Education initiatives where they illustrate several aspects of their work.In the presentation we explain why the theoretical framework informing our Public Outreach and Education programs was identified and how it has caused, after almost 10 years, a major change in the perception of the OAVdA and the Planetarium by all the stakeholders: institutional funding sources, other funding sources, participants to the initiatives (both schools and public at large), media, the researchers themselves. Among the activities, we report about three experiences strongly based on the establishment of a 'virtuous link' between Research and Communication: the Summer School in Astronomy in Saint-Barthélemy (targeted to public at large); "Saint-Roch Etoiles", a 5-year project with the Saint-Roch School in Aosta (students aged 5-12); the ESO Astronomy Camp co-organised in Lignan with the European Southern

  19. Código para imageamento indireto de estrelas em sistemas binarios: simulação de variações elipsoidais e do perfil das linhas

    NASA Astrophysics Data System (ADS)

    Souza, T. R.; Baptista, R.

    2003-08-01

    As estrelas secundárias em variáveis cataclí smicas (VCs) e binárias-x de baixa massa (BXBMs) são cruciais para o entendimento da origem, evolução e comportamento destas binárias interagentes. Elas são estrelas magneticamente ativas submetidas a condições ambientais extremas [e.g., estão muito próximas de uma fonte quente e irradiante; têm rotação extremamente rápida e forma distorcida; estão perdendo massa a taxas de 10-8-10-10 M¤/ano] que contribuem para que suas propriedades sejam distintas das de estrelas de mesma massa na seqüência principal. Por outro lado, o padrão de irradiação na face da secundária fornece informação sobre a geometria das estruturas de acréscimo em torno da estrela primária. Assim, a obtenção de imagens da superfície destas estrelas é de grande interesse astrofísico. A Tomografia Roche usa as variações no perfil das linhas de emissão/absorção da estrela secundária em função da fase orbital para mapear a distribuição de brilho em sua superfície. Neste trabalho apresentamos os resultados iniciais do desenvolvimento de um programa para o mapeamento da distribuição de brilho na superfí cie das estrelas secundárias em VCs e BXBMs com técnicas de astro-tomografia. Presentemente temos em operação um código que simula as variações no perfil das linhas em conseqüência de efeito Doppler resultante da combinação de rotação e translação de uma estrela em forma de lobo de Roche em torno do centro de massa da binária, em função da distribuição de brilho na superfície desta estrela. O código igualmente produz a curva de luz resultante das variações de aspecto da estrela em função da fase orbital (variações elipsoidais).

  20. The Near-Earth Flyby of Asteroid 2012 DA14 (Invited)

    NASA Astrophysics Data System (ADS)

    Moskovitz, N. A.; Endicott, T.; Lister, T.; Ryan, B.; Ryan, E. V.; Willman, M.; Hergenrother, C.; Binzel, R. P.; Polishook, D.; DeMeo, F.; Bennechi, S.; Sheppard, S.; Marchis, F.; Angusteijn, T.; Birthwhistle, P.; Verveer, A.; Gulbis, A.; Nagayama, T.; Gilmore, A.; Kilmartin, P.

    2013-12-01

    On UT 2013 February 15, the elongated 20x40 meter near-Earth asteroid 2012 DA14 made a close flyby of the Earth at a distance of approximately 27,000 km or 4 Earth-radii. This passage was inside the orbital distance of geosynchronous satellites and close to the Earth's Roche limit. This close encounter was unprecedented in our advance knowledge of the incoming trajectory, thereby allowing us to forge a detailed coordinated plan for observation and testing of physical models predicting tidal effects near our planet's Roche limit. Predicted outcomes of such close encounters include tidal disruption, changes in rotation state, and mass loss or mass redistribution due to seismic shaking. Each of these effects sensitively depend on how tidal energy is dissipated in the interior of the asteroid: a rubble pile will dissipate tidal energy differently than a solid or partially fractured monolith. The internal properties of asteroids in general and particularly those in the size range of 2012 DA14 are largely unknown. This encounter represents one of the first ever opportunities to observationally test models of the interior structure of small planetary bodies. We will present the results of a large multi-observatory campaign focused on 2012 DA14. This campaign includes data from shortly after discovery in 2012 and surrounding the close approach of the asteroid in February of 2013. These data were collected with over a dozen telescopes worldwide, ranging in aperture from 1m to 8m and include major facilities in Chile, Australia, New Zealand, South Africa, Israel, Hawaii, Arizona, New Mexico, and the Canary Islands. We will highlight the outcome of pre- and post-flyby visible-wavelength photometric and spectroscopic observations. This will include clear evidence that 2012 DA14 is now in a non-principal axis rotation state, requiring a multi-periodic tumbling model to fit its post-flyby rotational light curve. Such a complex rotation state is consistent with models for the

  1. Formation of Large Regular Satellites of Giant Planets in an Extended Gaseous Nebula: Subnebula Model and Accretion of Satellites

    NASA Technical Reports Server (NTRS)

    Mosqueira, I.; Estrada, P. R.

    2000-01-01

    We model the subnebulae of Jupiter and Saturn wherein satellite accretion took place. We expect a giant planet subnebula to be composed of an optically thick (given gaseous opacity) inner region inside of the planet's centrifugal radius (located at r(sub c, sup J) = l5R(sub J) for Jupiter and r(sub c, sup S) = 22R(sub S) for Saturn), and an optically thin, extended outer disk out to a fraction of the planet's Roche lobe, which we choose to be R(sub roche)/5 (located at approximately 150R(sub J) near the inner irregular satellites for Jupiter, and approximately 200R(sub S) near Phoebe for Saturn). This places Titan and Ganymede in the inner disk, Callisto and Iapetus in the outer disk, and Hyperion in the transition region. The inner disk is the leftover of the gas accreted by the protoplanet. The outer disk results from the solar torque on nebula gas flowing into the protoplanet during the time of giant planet gap opening. For the sake of specificity, we use a cosmic mixture 'minimum mass' model to constrain the gas densities of the inner disks of Jupiter and Saturn (and also Uranus). For the total mass of the outer disk we use the simple scaling M(sub disk) = M(sub P)tau(sub gap)/tau(sub acc), where M(sub P) is the mass of the giant planet, tau(sub gap) is the gap opening timescale, and tau(sub acc) is the giant planet accretion time. This gives a total outer disk mass of approximately 100M(sub Callisto) for Jupiter and possibly approximately 200M(sub Iapetus) for Saturn (which contain enough condensables to form Callisto and Iapetus respectively). Our model has Ganymede at a subnebula temperature of approximately 250 K and Titan at approximately 100 K. The outer disks of Jupiter and Saturn have constant temperatures of 130 K and 90 K respectively.

  2. Non-convex model of the binary asteroid (809) Lundia and its density estimation

    NASA Astrophysics Data System (ADS)

    Kryszczynska, A.; Bartczak, P.; Polinska, M.; Colas, F.

    2014-07-01

    Introduction: (809) Lundia was classified as a V-type asteroid in the Flora family (Florczak et.al. 2002). The binary nature of (809) Lundia was discovered in September 2005 based on photometric observations. The first modeling of the Lundia synchronous binary system was based on 22 lightcurves obtained at Borowiec and Pic du Midi Observatories during two oppositions in 2005/2006 and 2006/2007. Two methods of modeling --- modified Roche ellipsoids and kinematic --- gave similar parameters for the system (Kryszczynska et al. 2009). The poles of the orbit in ecliptic coordinates were: longitude 118° and latitude 28° in the modified Roche model and 120°, 18°, respectively, in the kinematic model. The orbital period obtained from the lightcurve analysis as well as from modeling was 15.418 h. The obtained bulk density of both components was 1.64 or 1.71 g/ccm. Observations: We observed (809) Lundia in the 2008, 2009/2010, 2011, and 2012 oppositions at the Borowiec, Pic du Midi, Prompt, and Rozhen Observatories. As predicted, the visible eclipses/occultation events were observed only in 2011. Currently, our dataset consists of 45 individual lightcurves and they were all used in the new modeling. Method: We used new method of modeling based on a genetic algorithm that is able to create a non-convex asteroid shape model, rotational period, and spin-axis orientation of a single or binary asteroid, using only photometric observations. The details of the method are presented in the poster by Bartczak et al., at this conference. Results: The new non-convex model of (809) Lundia is presented in the figure. The parameters of the system in the ecliptic coordinates are: longitude 122°, latitude 22°, and sidereal period 15.41574 h. They are very similar to the values obtained before. However, assuming an equivalent diameter of a single body of 9.1 km from the Spitzer observations (Marchis et al. 2012) and the volume of the two modeled bodies, the separation of the components

  3. 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

  4. Hepatitis B and D viruses replication interference: Influence of hepatitis B genotype

    PubMed Central

    Madejón, Antonio; Romero, Míriam; Hernández, Ángela; García-Sánchez, Araceli; Sánchez-Carrillo, Marta; Olveira, Antonio; García-Samaniego, Javier

    2016-01-01

    AIM: To study the hepatitis B virus (HBV) and hepatitis D virus (HDV) replication interferences in patients with chronic hepatitis delta infected with different HBV genotypes. METHODS: We conducted a transversal study including 68 chronic hepatitis delta (CHD) (37 HIV-positive) patients and a control group of 49 chronic hepatitis B (CHB) (22 HIV-positive) patients. In addition, a dynamic follow-up was performed in 16 CHD patients. In all the samples, the surface antigen of hepatitis B (HBsAg) serum titers were analyzed with the Monolisa HBsAg Ultra system (Bio-Rad), using as quantification standard a serial dilution curve of an international HBsAg standard. Serum HBV-DNA titers were analyzed using the Roche Cobas TaqMan (Roche, Barcelona, Spain), and the serum HDV-RNA using an in-house real-time qRT-PCR method, with TaqMan probes. HBV genotype was determined with the line immunoassay LiPA HBV genotyping system (Innogenetics, Ghent, Belgium). In those patients negative for LiPA assay, a nested PCR method of complete HBsAg coding region, followed by sequence analysis was applied. RESULTS: No differences in the HBV-DNA levels were found in CHB patients infected with different HBV genotypes. However, in CHD patients the HBV-DNA levels were lower in those infected with HBV-A than in those with HBV-D, both in HIV negative [median (IQR): 1.25 (1.00-1.35) vs 2.95 (2.07-3.93) log10 (copies/mL), P = 0.013] and HIV positive patients [2.63 (1.24-2.69) vs 7.25 (4.61-7.55) log10 (copies/mL), P < 0.001]. This was confirmed in the dynamic study of the HBV/HDV patients. These differences induce an under-estimation of HBV-A incidence in patients with CHD analyzed with LiPA assay. Finally, the HBsAg titers reflected no significant differences in CHD patients infected with HBV-A or D. CONCLUSION: Viral replication interference between HBV and HDV is HBV-genotype dependent, and more evident in patients infected with HBV-genotype A, than with HBV-D or E. PMID:27003993

  5. Internal quality control system for non-stationary, non-ergodic analytical processes based upon exponentially weighted estimation of process means and process standard deviation.

    PubMed

    Jansen, Rob T P; Laeven, Mark; Kardol, Wim

    2002-06-01

    The analytical processes in clinical laboratories should be considered to be non-stationary, non-ergodic and probably non-stochastic processes. Both the process mean and the process standard deviation vary. The variation can be different at different levels of concentration. This behavior is shown in five examples of different analytical systems: alkaline phosphatase on the Hitachi 911 analyzer (Roche), vitamin B12 on the Access analyzer (Beckman), prothrombin time and activated partial thromboplastin time on the STA Compact analyzer (Roche) and PO2 on the ABL 520 analyzer (Radiometer). A model is proposed to assess the status of a process. An exponentially weighted moving average and standard deviation was used to estimate process mean and standard deviation. Process means were estimated overall and for each control level. The process standard deviation was estimated in terms of within-run standard deviation. Limits were defined in accordance with state of the art- or biological variance-derived cut-offs. The examples given are real, not simulated, data. Individual control sample results were normalized to a target value and target standard deviation. The normalized values were used in the exponentially weighted algorithm. The weighting factor was based on a process time constant, which was estimated from the period between two calibration or maintenance procedures. The proposed system was compared with Westgard rules. The Westgard rules perform well, despite the underlying presumption of ergodicity. This is mainly caused by the introduction of the starting rule of 12s, which proves essential to prevent a large number of rule violations. The probability of reporting a test result with an analytical error that exceeds the total allowable error was calculated for the proposed system as well as for the Westgard rules. The proposed method performed better. The proposed algorithm was implemented in a computer program running on computers to which the analyzers were

  6. Morphine and codeine concentrations in human urine following controlled poppy seeds administration of known opiate content.

    PubMed

    Smith, Michael L; Nichols, Daniel C; Underwood, Paula; Fuller, Zachary; Moser, Matthew A; LoDico, Charles; Gorelick, David A; Newmeyer, Matthew N; Concheiro, Marta; Huestis, Marilyn A

    2014-08-01

    Opiates are an important component for drug testing due to their high abuse potential. Proper urine opiate interpretation includes ruling out poppy seed ingestion; however, detailed elimination studies after controlled poppy seed administration with known morphine and codeine doses are not available. Therefore, we investigated urine opiate pharmacokinetics after controlled oral administration of uncooked poppy seeds with known morphine and codeine content. Participants were administered two 45 g oral poppy seed doses 8 h apart, each containing 15.7 mg morphine and 3mg codeine. Urine was collected ad libitum up to 32 h after the first dose. Specimens were analyzed with the Roche Opiates II immunoassay at 2000 and 300 μg/L cutoffs, and the ThermoFisher CEDIA(®) heroin metabolite (6-acetylmorphine, 6-AM) and Lin-Zhi 6-AM immunoassays with 10 μg/L cutoffs to determine if poppy seed ingestion could produce positive results in these heroin marker assays. In addition, all specimens were quantified for morphine and codeine by GC/MS. Participants (N=22) provided 391 urine specimens over 32 h following dosing; 26.6% and 83.4% were positive for morphine at 2000 and 300 μg/L GC/MS cutoffs, respectively. For the 19 subjects who completed the study, morphine concentrations ranged from <300 to 7522 μg/L with a median peak concentration of 5239 μg/L. The median first morphine-positive urine sample at 2000 μg/L cutoff concentration occurred at 6.6 h (1.2-12.1), with the last positive from 2.6 to 18 h after the second dose. No specimens were positive for codeine at a cutoff concentration of 2000 μg/L, but 20.2% exceeded 300 μg/L, with peak concentrations of 658 μg/L (284-1540). The Roche Opiates II immunoassay had efficiencies greater than 96% for the 2000 and 300 μg/L cutoffs. The CEDIA 6-AM immunoassay had a specificity of 91%, while the Lin-Zhi assay had no false positive results. These data provide valuable information for interpreting urine opiate results. PMID

  7. Genome wide expression profiling of two accession of G. herbaceum L. in response to drought

    PubMed Central

    2012-01-01

    Background Genome-wide gene expression profiling and detailed physiological investigation were used for understanding the molecular mechanism and physiological response of Gossypium herbaceum, which governs the adaptability of plants in drought conditions. Recently, microarray-based gene expression analysis is commonly used to decipher genes and genetic networks controlling the traits of interest. However, the results of such an analysis are often plagued due to a limited number of genes (probe sets) on microarrays. On the other hand, pyrosequencing of a transcriptome has the potential to detect rare as well as a large number of transcripts in the samples quantitatively. We used Affymetrix microarray as well as Roche's GS-FLX transcriptome sequencing for a comparative analysis of cotton transcriptome in leaf tissues under drought conditions. Results Fourteen accessions of Gossypium herbaceum were subjected to mannitol stress for preliminary screening; two accessions, namely Vagad and RAHS-14, were selected as being the most tolerant and most sensitive to osmotic stress, respectively. Affymetrix cotton arrays containing 24,045 probe sets and Roche's GS-FLX transcriptome sequencing of leaf tissue were used to analyze the gene expression profiling of Vagad and RAHS-14 under drought conditions. The analysis of physiological measurements and gene expression profiling showed that Vagad has the inherent ability to sense drought at a much earlier stage and to respond to it in a much more efficient manner than does RAHS-14. Gene Ontology (GO) studies showed that the phenyl propanoid pathway, pigment biosynthesis, polyketide biosynthesis, and other secondary metabolite pathways were enriched in Vagad under control and drought conditions as compared with RAHS-14. Similarly, GO analysis of transcriptome sequencing showed that the GO terms responses to various abiotic stresses were significantly higher in Vagad. Among the classes of transcription factors (TFs) uniquely

  8. Retrograde binaries of massive black holes in circumbinary accretion discs

    NASA Astrophysics Data System (ADS)

    Amaro-Seoane, Pau; Maureira-Fredes, Cristián; Dotti, Massimo; Colpi, Monica

    2016-06-01

    Context. We explore the hardening of a massive black hole binary embedded in a circumbinary gas disc under a specific circumstance: when the binary and the gas are coplanar and the gas is counter-rotating. The binary has unequal mass and the interaction of the gas with the lighter secondary black hole is the main cause of the braking torque on the binary that shrinks with time. The secondary black hole, revolving in the direction opposite to the gas, experiences a drag from gas-dynamical friction and from direct accretion of part of it. Aims: In this paper, using two-dimensional (2D) hydrodynamical grid simulations we investigate the effect of changing the accretion prescriptions on the dynamics of the secondary black hole, which in turn affect the binary hardening and eccentricity evolution. Methods: We find that realistic accretion prescriptions lead to results that differ from those inferred assuming accretion of all the gas within the Roche Lobe of the secondary black hole. Results: When considering gas accretion within the gravitational influence radius of the secondary black hole (which is smaller than the Roche Lobe radius) to better describe gas inflows, the shrinking of the binary is slower. In addition, in this case, a smaller amount of accreted mass is required to reduce the binary separation by the same amount. Different accretion prescriptions result in different discs' surface densities, which alter the black hole's dynamics back. Full 3D Smoothed-particle hydrodynamics realizations of a number of representative cases, run over a shorter interval of time, validate the general trends observed in the less computationally demanding 2D simulations. Conclusions: Initially circular black hole binaries increase their eccentricity only slightly, which then oscillates around small values (<0.1) while they harden. By contrast, initially eccentric binaries become more and more eccentric. A semi-analytical model describing the black hole's dynamics under

  9. The Rings Around the Egg Nebula

    NASA Technical Reports Server (NTRS)

    Harpaz, Amos; Rappaport, Saul; Soker, Noam

    1997-01-01

    We present an eccentric binary model for the formation of the proto-planetary nebula CRL 2688 (the Egg Nebula) that exhibits multiple concentric shells. Given the apparent regularity of the structure in the Egg Nebula, we postulate that the shells are caused by the periodic passages of a companion star. Such an orbital period would have to lie in the range of 100-500 yr, the apparent time that corresponds to the spacing between the rings. We assume, in this model, that an asymptotic giant branch (AGB) star, which is the origin of the matter within the planetary nebula, loses mass in a spherically symmetric wind. We further suppose that the AGB star has an extended atmosphere (out to approximately 10 stellar radii) in which the outflow speed is less than the escape speed; still farther out, grains form and radiation pressure accelerates the grains along with the trapped gas to the escape speed. Once escape speed has been attained, the presence of a companion star will not significantly affect the trajectories of the matter leaving in the wind and the mass loss will be approximately spherically symmetric. On the other hand, if the companion star is sufficiently close that the Roche lobe of the AGB star moves inside the extended atmosphere, then the slowly moving material will be forced to flow approximately along the critical potential surface (i.e., the Roche lobe) until it flows into the potential lobe of the companion star. Therefore, in our model, the shells are caused by periodic cessations of the isotropic wind rather than by any periodic enhancement in the mass-loss process. We carry out detailed binary evolution calculations within the context of this scenario, taking into account the nuclear evolution and stellar wind losses of the giant as well as the effects of mass loss and mass transfer on the evolution of the eccentric binary orbit. From the initial binary parameters that we find are required to produce a multiple concentric shell nebula and the known

  10. The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing

    PubMed Central

    2012-01-01

    Background This study describes how the complete mitogenome of a terrestrial snail, Cylindrus obtusus (Draparnaud, 1805) was sequenced without PCRs from a collection specimen that had been in 70% ethanol for 8 years. The mitogenome was obtained with Illumina GAIIx shot gun sequencing. Although the used specimen was collected relatively recently and kept in a DNA-friendly preservative (not formalin as frequently used with old museum specimens), we believe that the exclusion of PCRs as facilitated by NGS (Next Generation Sequencing) removes a great obstacle in DNA sequencing of collection specimens. A brief comparison is made between our Illumina GAIIx approach and a similar study that made use of the Roche 454-FLX platform. Results The mtDNA sequence of C. obtusus is 14,610 bases in length (about 0.5 kb larger than other stylommatophoran mitogenomes reported hitherto) and contains the 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs) typical for metazoans. Except for a swap between the position of tRNA-Pro and tRNA-Ala, the gene arrangement of C. obtusus is identical to that reported for Cepaea nemoralis. The 'aberrant' rearrangement of tRNA-Thr and COIII compared to that of other Sigmurethra (and the majority of gastropods), is not unique for C. nemoralis (subfamily Helicinae), but is also shown to occur in C. obtusus (subfamily Ariantinae) and might be a synapomorphy for the family Helicidae. Conclusions Natural history collections potentially harbor a wealth of information for the field of evolutionary genetics, but it can be difficult to amplify DNA from such specimens (due to DNA degradation for instance). Because NGS techniques do not rely on primer-directed amplification (PCR) and allow DNA to be fragmented (DNA gets sheared during library preparation), NGS could be a valuable tool for retrieving DNA sequence data from such specimens. A comparison between Illumina GAIIx and the Roche 454 platform suggests that the former might be more suited for de

  11. Cross-reactivity of steroid hormone immunoassays: clinical significance and two-dimensional molecular similarity prediction

    PubMed Central

    2014-01-01

    Background Immunoassays are widely used in clinical laboratories for measurement of plasma/serum concentrations of steroid hormones such as cortisol and testosterone. Immunoassays can be performed on a variety of standard clinical chemistry analyzers, thus allowing even small clinical laboratories to do analysis on-site. One limitation of steroid hormone immunoassays is interference caused by compounds with structural similarity to the target steroid of the assay. Interfering molecules include structurally related endogenous compounds and their metabolites as well as drugs such as anabolic steroids and synthetic glucocorticoids. Methods Cross-reactivity of a structurally diverse set of compounds were determined for the Roche Diagnostics Elecsys assays for cortisol, dehydroepiandrosterone (DHEA) sulfate, estradiol, progesterone, and testosterone. These data were compared and contrasted to package insert data and published cross-reactivity studies for other marketed steroid hormone immunoassays. Cross-reactivity was computationally predicted using the technique of two-dimensional molecular similarity. Results The Roche Elecsys Cortisol and Testosterone II assays showed a wider range of cross-reactivity than the DHEA sulfate, Estradiol II, and Progesterone II assays. 6-Methylprednisolone and prednisolone showed high cross-reactivity for the cortisol assay, with high likelihood of clinically significant effect for patients administered these drugs. In addition, 21-deoxycortisol likely produces clinically relevant cross-reactivity for cortisol in patients with 21-hydroxylase deficiency, while 11-deoxycortisol may produce clinically relevant cross-reactivity in 11β-hydroxylase deficiency or following metyrapone challenge. Several anabolic steroids may produce clinically significant false positives on the testosterone assay, although interpretation is limited by sparse pharmacokinetic data for some of these drugs. Norethindrone therapy may impact immunoassay measurement

  12. Analysis of the Skin Transcriptome in Two Oujiang Color Varieties of Common Carp

    PubMed Central

    Wang, Chenghui; Wachholtz, Michael; Wang, Jun; Liao, Xiaolin; Lu, Guoqing

    2014-01-01

    Background Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding. Methodology/Principal Findings In this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW. Conclusions The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism

  13. Parturition in dairy cows temporarily alters the expression of genes in circulating neutrophils.

    PubMed

    Crookenden, M A; Heiser, A; Murray, A; Dukkipati, V S R; Kay, J K; Loor, J J; Meier, S; Mitchell, M D; Moyes, K M; Walker, C G; Roche, J R

    2016-08-01

    Extensive metabolic and physiologic changes occur during the peripartum, concurrent with a high incidence of infectious disease. Immune dysfunction is a likely contributor to the increased risk of disease at this time. Studies using high-yielding, total mixed ration-fed cows have indicated that neutrophil function is perturbed over the transition period; however, this reported dysfunction has yet to be investigated in moderate-yielding, grazing dairy cows. Therefore, we investigated changes in the expression of genes involved in neutrophil function. Blood was collected from cows at 5 time points over the transition period: precalving (-1wk; n=46), day of calving (d 0; n=46), and postcalving at wk 1 (n=46), wk 2 (n=45), and wk 4 (n=43). Neutrophils were isolated by differential centrifugation and gene expression was investigated. Quantitative reverse transcriptase PCR with custom-designed primer pairs and Roche Universal Probe Library (Roche, Basel, Switzerland) chemistry, combined with microfluidics integrated fluidic circuit chips (96.96 Dynamic Array, San Francisco, CA) were used to investigate the expression of 78 genes involved in neutrophil function and 18 endogenous control genes. Statistical significance between time points was determined using a repeated measures ANOVA. Genes that were differentially expressed over the transition period included those involved in neutrophil adhesion (SELL, ITGB2, and ITGBX), mediation of the immune response (TLR4, HLA-DRA, and CXCR2), maturation, cell cycle progression, apoptosis (MCL1, BCL2, FASLG, and RIPK1), and control of gene expression (PPARG, PPARD, and STAT3). We noted reduced gene expression of proinflammatory cytokines (IFNG, TNF, IL12, and CCL2) on the day of calving, whereas anti-inflammatory cytokine gene expression (IL10) was upregulated. Increased gene expression of antimicrobial peptides (BNBD4, DEFB10, and DEFB1) occurred on the day of calving. Collectively, transcription profiles are indicative of

  14. Orbital Evolution and Migration of Extrasolar Planets

    NASA Astrophysics Data System (ADS)

    Trilling, D. E.; Benz, W.; Guillot, T.; Lunine, J. I.; Hubbard, W. B.; Burrows, A.

    1997-07-01

    Giant planets in circumstellar disks can migrate inward from their initial (formation) positions. Migration is caused by inward torques between the planet and the disk; by outward torques between the planet and the spinning star; and by outward torques due to Roche lobe overflow and mass loss from the planet. Summing torques on planets in disks with various physical parameters, we find that Jupiter-mass planets can stably arrive and survive at small heliocentric distances. Inward migration timescales can be approximately equal to or less than disk lifetimes and star spindown timescales. Therefore, the range of fates of Jupiter-mass planets is broad, and generally comprises three classes: (I) planets which migrate inward too rapidly and lose all their mass due to Roche lobe overflow; (II) planets which migrate inward and survive in very small orbits; and (III) planets which do not migrate very far. Some, but not all, of the planets in Class II lose mass during their evolution and migration times, resulting in planets with final masses smaller than their initial masses. For example, in our model, we produce planets similar to 51 Peg b which have lost ~ 75% of their initial mass. The observed extrasolar planets, both those with extremely small semi-major axes (51 Peg b at 0.05 AU, tau Boo b (0.046 AU), upsilon And b (0.057 AU), and 55 Cnc b (0.11 AU)) and those with more moderate semi-major axes (rho Cor Bor b (0.23 AU), 47 UMa b (2.1 AU)) form a subset of the potential outcomes of the system, in that Jupiter-mass objects can stably survive in orbits with a wide range of semi-major axes. Our numerical model produces planets which have similar characteristics to the observed planets, as well as planets similar to Jupiter, and many intermediate cases. Since Jupiters can stably migrate to various orbital separations, we predict that, as planetary detection techniques improve, Jupiter-mass planets will be found in a wide range of orbits, from much less than 1 AU to

  15. Nanoemulsified orlistat-embedded multi-unit pellet system (MUPS) with improved dissolution and pancreatic lipase inhibition.

    PubMed

    Sangwai, Mayur; Sardar, Surendra; Vavia, Pradeep

    2014-02-01

    The present research work explores an innovative technological solution to constraints in efficient oral delivery of poorly water-soluble anti-obesity drug orlistat. Nanoemulsion of orlistat and its subsequent transformation into multi-unit pellet system (MUPS) for improved oral delivery was developed. Orlistat nanoemulsion was developed with capryol PGMC as an oil phase and cremophor RH40 as an emulsifier using high-pressure homogenization. Influence of critical processing parameters on globule size distribution, polydispersity index and physical stability of nanoemulsion was evaluated. The optimized nanoemulsion was transformed into MUPS using an extrusion spheronization technique. Optimized formulation was characterized at nanoemulsion as well as MUPS stage. DLS and nanoparticle tracking analysis studies of orlistat nanoemulsion exhibited unimodal size distribution with polydispersity value <0.1. Confocal laser scanning microscopy (CLSM) studies confirmed the presence of uniform spherical nanosized oil droplets of nanoemulsified orlistat. DSC and PXRD studies of MUPS confirmed amorphization of embedded nanoemulsified orlistat. In-vitro dissolution studies in surfactant-reduced media demonstrated remarkable improvement in dissolution compared to pure orlistat and marketed formulation (Xenical Capsules 120 mg, Hoffman-La Roche, Basle, Switzerland). Comparative in-vitro bovine porcine pancreatic lipase inhibition studies of pure orlistat, marketed product and developed MUPS showed 13.57- and 2.41-fold higher lipase inhibition with developed MUPS compared to pure orlistat and marketed products, respectively. PMID:23259606

  16. [Interest in periodic health examinations for young people in the judicial system].

    PubMed

    North, S

    2003-12-01

    The Centre for Health Examinations (CES) in Roche sur Yon has experience with the Periodic Health Examinations (EPS) on population groups in fragile or disadvantaged situations and young people in the process of integration. Minors followed by the Judicial Protection of the Youth (PJJ) are in a preoccupying state of health. Professionals led a working group for reflection from two institutions working in health management. This study aims to explore the representations of young people's health under the care of the judicial system in order to evaluate the pertinence of EPS in the health course of youth in the judicial correctional system. 23 semi-directed interviews allowed the team to show that if the youth have a somatic definition of health, they are nevertheless open to a comprehensive approach to health. Their parents are unavoidable reference points. The readability of the speakers in terms of mental health remains average. The resources in health documentation are under-utilised. The treating doctor remains a special partner for health. The knowledge of social rights is insufficient. The notion of risk and the need for more information concerns the areas of drunk driving, sexuality and road rage. The EPS very logically places itself in the health course of the youth. The partnership between the health and the justice systems should be constructed in the framework of a convention between the two institutions. PMID:14964014

  17. Transcriptomic Analysis of Cadmium Stress Response in the Heavy Metal Hyperaccumulator Sedum alfredii Hance

    PubMed Central

    Yang, Xiaoe; Liu, Jian-Xiang

    2013-01-01

    The Sedum alfredii Hance hyperaccumulating ecotype (HE) has the ability to hyperaccumulate cadmium (Cd), as well as zinc (Zn) and lead (Pb) in above-ground tissues. Although many physiological studies have been conducted with these plants, the molecular mechanisms underlying their hyper-tolerance to heavy metals are largely unknown. Here we report on the generation of 9.4 gigabases of adaptor-trimmed raw sequences and the assembly of 57,162 transcript contigs in S. alfredii Hance (HE) shoots by the combination of Roche 454 and Illumina/Solexa deep sequencing technologies. We also have functionally annotated the transcriptome and analyzed the transcriptome changes upon Cd hyperaccumulation in S. alfredii Hance (HE) shoots. There are 110 contigs and 123 contigs that were up-regulated (Fold Change ≧2.0) and down-regulated (Fold Change ≦0.5) by chronic Cd treatment in S. alfredii Hance (HE) at q-value cutoff of 0.005, respectively. Quantitative RT-PCR was employed to compare gene expression patterns between S. alfredii Hance (HE) and non-hyperaccumulating ecotype (NHE). Our results demonstrated that several genes involved in cell wall modification, metal translocation and remobilization were more induced or constitutively expressed at higher levels in HE shoots than that in NHE shoots in response to Cd exposure. Together, our study provides large-scale expressed sequence information and genome-wide transcriptome profiling of Cd responses in S. alfredii Hance (HE) shoots. PMID:23755133

  18. Transcriptomic analysis of cadmium stress response in the heavy metal hyperaccumulator Sedum alfredii Hance.

    PubMed

    Gao, Jun; Sun, Ling; Yang, Xiaoe; Liu, Jian-Xiang

    2014-01-01

    The Sedum alfredii Hance hyperaccumulating ecotype (HE) has the ability to hyperaccumulate cadmium (Cd), as well as zinc (Zn) and lead (Pb) in above-ground tissues. Although many physiological studies have been conducted with these plants, the molecular mechanisms underlying their hyper-tolerance to heavy metals are largely unknown. Here we report on the generation of 9.4 gigabases of adaptor-trimmed raw sequences and the assembly of 57,162 transcript contigs in S. alfredii Hance (HE) shoots by the combination of Roche 454 and Illumina/Solexa deep sequencing technologies. We also have functionally annotated the transcriptome and analyzed the transcriptome changes upon Cd hyperaccumulation in S. alfredii Hance (HE) shoots. There are 110 contigs and 123 contigs that were up-regulated (Fold Change ≥ 2.0) and down-regulated (Fold Change

  19. CONSTRAINTS ON TYPE Ia SUPERNOVA PROGENITOR COMPANIONS FROM EARLY ULTRAVIOLET OBSERVATIONS WITH SWIFT

    SciTech Connect

    Brown, Peter J.; Dawson, Kyle S.; Harris, David W.; Olmstead, Matthew; Milne, Peter; Roming, Peter W. A.

    2012-04-10

    We compare early ultraviolet (UV) observations of Type Ia supernovae (SNe Ia) with theoretical predictions for the brightness of the shock associated with the collision between SN ejecta and a companion star. Our simple method is independent of the intrinsic flux from the SN and treats the flux observed with the Swift/Ultra-Violet Optical Telescope as conservative upper limits on the shock brightness. Comparing this limit with the predicted flux for various shock models, we constrain the geometry of the SN progenitor-companion system. We find the model of a 1 M{sub Sun} red supergiant companion in Roche-lobe overflow to be excluded at a 95% confidence level for most individual SNe for all but the most unfavorable viewing angles. For the sample of 12 SNe taken together, the upper limits on the viewing angle are inconsistent with the expected distribution of viewing angles for red gaint stars as the majority of companions with high confidence. The separation distance constraints do allow main-sequence companions. A better understanding of the UV flux arising from the SN itself as well as continued UV observations of young SNe Ia will further constrain the possible progenitors of SNe Ia.

  20. The genome sequence of ectromelia virus Naval and Cornell isolates from outbreaks in North America.

    PubMed

    Mavian, Carla; López-Bueno, Alberto; Bryant, Neil A; Seeger, Kathy; Quail, Michael A; Harris, David; Barrell, Bart; Alcami, Antonio

    2014-08-01

    Ectromelia virus (ECTV) is the causative agent of mousepox, a disease of laboratory mouse colonies and an excellent model for human smallpox. We report the genome sequence of two isolates from outbreaks in laboratory mouse colonies in the USA in 1995 and 1999: ECTV-Naval and ECTV-Cornell, respectively. The genome of ECTV-Naval and ECTV-Cornell was sequenced by the 454-Roche technology. The ECTV-Naval genome was also sequenced by the Sanger and Illumina technologies in order to evaluate these technologies for poxvirus genome sequencing. Genomic comparisons revealed that ECTV-Naval and ECTV-Cornell correspond to the same virus isolated from independent outbreaks. Both ECTV-Naval and ECTV-Cornell are extremely virulent in susceptible BALB/c mice, similar to ECTV-Moscow. This is consistent with the ECTV-Naval genome sharing 98.2% DNA sequence identity with that of ECTV-Moscow, and indicates that the genetic differences with ECTV-Moscow do not affect the virulence of ECTV-Naval in the mousepox model of footpad infection. PMID:24999046

  1. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

    PubMed Central

    Haas, Brian J.; Gevers, Dirk; Earl, Ashlee M.; Feldgarden, Mike; Ward, Doyle V.; Giannoukos, Georgia; Ciulla, Dawn; Tabbaa, Diana; Highlander, Sarah K.; Sodergren, Erica; Methé, Barbara; DeSantis, Todd Z.; Petrosino, Joseph F.; Knight, Rob; Birren, Bruce W.

    2011-01-01

    Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys. PMID:21212162

  2. PROTOTYPING NON-EQUILIBRIUM VISCOUS-TIMESCALE ACCRETION THEORY USING LMC X-3

    SciTech Connect

    Cambier, Hal J.; Smith, David M.

    2013-04-10

    Explaining variability observed in the accretion flows of black hole X-ray binary systems remains challenging, especially concerning timescales less than, or comparable to, the viscous timescale but much larger than the inner orbital period despite decades of research identifying numerous relevant physical mechanisms. We take a simplified but broad approach to study several mechanisms likely relevant to patterns of variability observed in the persistently high-soft Roche-lobe overflow system LMC X-3. Based on simple estimates and upper bounds, we find that physics beyond varying disk/corona bifurcation at the disk edge, Compton-heated winds, modulation of total supply rate via irradiation of the companion, and the likely extent of the partial hydrogen ionization instability is needed to explain the degree, and especially the pattern, of variability in LMC X-3 largely due to viscous dampening. We then show how evaporation-condensation may resolve or compound the problem given the uncertainties associated with this complex mechanism and our current implementation. We briefly mention our plans to resolve the question, refine and extend our model, and alternatives we have not yet explored.

  3. How Can Viral Dynamics Models Inform Endpoint Measures in Clinical Trials of Therapies for Acute Viral Infections?

    PubMed Central

    Cori, Anne; de Wolf, Frank; Anderson, Roy M.

    2016-01-01

    Acute viral infections pose many practical challenges for the accurate assessment of the impact of novel therapies on viral growth and decay. Using the example of influenza A, we illustrate how the measurement of infection-related quantities that determine the dynamics of viral load within the human host, can inform investigators on the course and severity of infection and the efficacy of a novel treatment. We estimated the values of key infection-related quantities that determine the course of natural infection from viral load data, using Markov Chain Monte Carlo methods. The data were placebo group viral load measurements collected during volunteer challenge studies, conducted by Roche, as part of the oseltamivir trials. We calculated the values of the quantities for each patient and the correlations between the quantities, symptom severity and body temperature. The greatest variation among individuals occurred in the viral load peak and area under the viral load curve. Total symptom severity correlated positively with the basic reproductive number. The most sensitive endpoint for therapeutic trials with the goal to cure patients is the duration of infection. We suggest laboratory experiments to obtain more precise estimates of virological quantities that can supplement clinical endpoint measurements. PMID:27367230

  4. The new photometric solution and light curve study of the semi-detached binary system ASAS ID 211049-3657.9

    NASA Astrophysics Data System (ADS)

    Tanrıver, Mehmet

    2014-08-01

    This work is targeted on the photometric (light curve) analysis of the stars with G2 spectral type. The sun like star (ASAS ID 211049-3657.9) located in the ASAS catalogue was subjected to its photometric solutions and the light curve analysis in V band. The light curve of ASAS ID 211049-3657.9 binary system which belongs to the Southern Hemisphere shows the variation of β Lyr type. The solution of light curve was carried out using the PHOBE code. The photometric solution reveals a semi-detached configuration with a less-massive component filling its own Roche lobe. The absolute parameters, very close to the astrophysical fundamental values of the sun, are obtained as a result of the solution. A spotted solution for ASAS ID 211049-3657.9 binary system with the Sun-like selected from the solar analogue star list of Tanrıver (2012, 2013) is conducted. The masses of the primary and secondary components for ASAS ID 211049-3657.9 are M1 = 1.00741 M⊙ and M2 = 0.37535 M⊙, respectively. While the radius for the primary was R1 = 1.00097 R⊙, and for the secondary R2 = 1.19107 R⊙ and the temperature of the primary and secondary are T1 = 5850 K and T2 = 5150 K, respectively. The positions in the HR diagram of the components are also discussed.

  5. A field guide to the binary stars

    NASA Astrophysics Data System (ADS)

    Trimble, V.

    1983-05-01

    Details and examples of the six phases of existence for a binary star system are described. The birth and pre-main-sequence contraction is generally obscured from observation by the presence of gas and dust clouds; it comprises 1/1000th of a system's lifetime. The main sequence, i.e., hydrogen burning, takes up to 90 pct of a star's lifetime, and has been detected in stars with masses ranging from 0.07-32 solar masses. In binary systems, the main sequence stars may or may not interact, or one companion may burn out before the other leaves the main sequence. The primary in a binary system expands to fill its Roche lobe before mass transfer begins, then continues on a Kelvin-Helmholtz time scale until the primary is smaller than the secondary, when transfer proceeds on a nuclear time scale. The depletion of hydrogen fuel or He ignition stops the mass transfer, leading to formation of a white dwarf, neutron star, or supernova that sends both the neutron star and the OB secondary off at high speeds. Back transfer can be initiated in a fifth phase and can produce black holes or dwarf novae, or supernovae. Finally, the system terminates when both stars are extinguished and fall into one another, which can also yield supernovae or black holes.

  6. Effects of Stealth adulterant on immunoassay testing for drugs of abuse.

    PubMed

    Cody, J T; Valtier, S

    2001-09-01

    Stealth is an adulterant advertised as being undetectable by adulteration tests. It has been described as peroxidase and peroxide, which, when added to urine samples, are intended to prevent a positive drug test. Characterization of the effect of Stealth on urine samples and immunoassay results was undertaken to assist in detection of this adulterant. Stealth was added to a number of urine matrices, and various parameters were evaluated including pH, specific gravity, color, creatinine, chloride, urea, blood, glucose, and nitrite. Samples were spiked with THC acid metabolite, benzoylecgonine, morphine, secobarbital, PCP, amphetamine, and lysergic acid diethylamide (LSD) then tested by Roche OnLine and Microgenics CEDIA immunoassay reagents. Results of these analyses showed Stealth did not cause the urine sample to exceed any of the monitored parameters including those routinely used in drug-testing laboratories that would indicate adulteration of a sample. It did, however, cause samples positive for the marijuana metabolite (11-nor-delta9-tetrahydrocannibinol-9-carboxylic acid), LSD, and opiate (morphine) at 125-150% of cutoff to screen negative by immunoassay. Adulterating an authentic positive sample provided by a marijuana user caused that sample to screen negative using these immunoassay reagents as well. PMID:11550822

  7. XZ And a semidetached asynchronous binary system

    NASA Astrophysics Data System (ADS)

    Manzoori, Davood

    2016-05-01

    In this work the light curves (LCs) solutions along with the radial velocity curve of the semidetached binary systemXZ And are presented using the PHOEBE program(ver 0.31a). Absolute parameters of the stellar components were then determined, enabling us to discuss structure and evolutionary status of the system. The analysis indicates that the primary is a non-synchronous (i.e., F1 = 3.50 ± 0.01) Main Sequence (MS) star and the secondary is a bit more evolved, and fills its Roche critical surface. In addition, times of minima data (" O - C curve") were analyzed. Apart from an almost parabolic variation in the general trend of O - C data, which was attributed to a mass transfer from the secondary with the rate ˙2 = (9.52 ± 0.41) × 10-10 M ⊙ yr-1; two cyclic variations with mean periods of 34.8 ± 2.4 and 23.3 ± 3.0 yr, modulating the orbital period, were found, which were attributed to a third body orbiting around the system, and magnetic activity cycle effect, respectively.

  8. Can Long-Range PCR Be Used to Amplify Genetically Divergent Mitochondrial Genomes for Comparative Phylogenetics? A Case Study within Spiders (Arthropoda: Araneae)

    PubMed Central

    Briscoe, Andrew G.; Goodacre, Sara; Masta, Susan E.; Taylor, Martin I.; Arnedo, Miquel A.; Penney, David; Kenny, John; Creer, Simon

    2013-01-01

    The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput sequencing. Here we assess the effectiveness of a wide range of targeted long-range PCR strategies, encapsulating single and dual fragment primer design approaches to provide full mitogenomic coverage within the Araneae (Spiders). Despite extensive rounds of optimisation, full mitochondrial genome PCR amplifications were stochastic in most taxa, although 454 Roche sequencing confirmed the successful amplification of 10 mitochondrial genomes out of the 33 trialled species. The low success rates of amplification using long-Range PCR highlights the difficulties in consistently obtaining genomic amplifications using currently available DNA polymerases optimised for large genomic amplifications and suggests that there may be opportunities for the use of alternative amplification methods. PMID:23667474

  9. A comparison of different pre-lysis methods and extraction kits for recovery of Streptococcus agalacticae (Lancefield group B Streptococcus) DNA from whole blood.

    PubMed

    Burke, Rachael M; McKenna, James P; Cox, Ciara; Coyle, Peter V; Shields, Michael D; Fairley, Derek J

    2016-10-01

    Sub-optimal recovery of bacterial DNA from whole blood samples can limit the sensitivity of molecular assays to detect pathogenic bacteria. We compared 3 different pre-lysis protocols (none, mechanical pre-lysis and achromopeptidase pre-lysis) and 5 commercially available DNA extraction platforms for direct detection of Group B Streptococcus (GBS) in spiked whole blood samples, without enrichment culture. DNA was extracted using the QIAamp Blood Mini kit (Qiagen), UCP Pathogen Mini kit (Qiagen), QuickGene DNA Whole Blood kit S (Fuji), Speed Xtract Nucleic Acid Kit 200 (Qiagen) and MagNA Pure Compact Nucleic Acid Isolation Kit I (Roche Diagnostics Corp). Mechanical pre-lysis increased yields of bacterial genomic DNA by 51.3 fold (95% confidence interval; 31.6-85.1, p<0.001) and pre-lysis with achromopeptidase by 6.1 fold (95% CI; 4.2-8.9, p<0.001), compared with no pre-lysis. Differences in yield due to pre-lysis were 2-3 fold larger than differences in yield between extraction methods. Including a pre-lysis step can improve the limits of detection of GBS using PCR or other molecular methods without need for culture. PMID:27546716

  10. SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

    USGS Publications Warehouse

    Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

  11. Expression and purification of a functional recombinant aspartate aminotransferase (AST) from Escherichia coli.

    PubMed

    Zou, Lihui; Zhao, Haijian; Wang, Daguang; Wang, Meng; Zhang, Chuanbao; Xiao, Fei

    2014-07-01

    Aspartate aminotransferase (AST; E.C. 2.6.1.1), a vitamin B6-dependent enzyme, preferentially promotes the mutual transformation of aspartate and α-ketoglutarate to oxaloacetate and glutamate. It plays a key role in amino acid metabolism and has been widely recommended as a biomarker of liver and heart damage. Our study aimed to evaluate the extensive preparation of AST and its application in quality control in clinical laboratories. We describe a scheme to express and purify the 6His-AST fusion protein. An optimized sequence coding AST was synthesized and transformed into Escherichia coli BL21 (DE3) strain for protein expression. Ideally, the fusion protein has a volumetric productivity achieving 900 mg/l cultures. After affinity chromatography, the enzyme activity of purified AST reached 150,000 U/L. Commutability assessment between the engineered AST and standard AST from Roche suggested that the engineered AST was the better candidate for the reference material. Moreover, the AST showed high stability during long-term storage at -20ºC. In conclusion, the highly soluble 6His-tagged AST can become a convenient tool for supplying a much better and cheaper standard or reference material for the clinical laboratory. PMID:24722375

  12. Characterization of mineral phosphate solubilization traits from a barley rhizosphere soil functional metagenome.

    PubMed

    Chhabra, Sagar; Brazil, Dina; Morrissey, John; Burke, James I; O'Gara, Fergal; N Dowling, David

    2013-10-01

    Mineral phosphate solubilization (MPS) microorganisms are important for their provision of orthophosphate anions for plant growth promotion activity in soil. In this study, we applied a functional metagenomic approach to identify this trait directly from the microbiome in barley rhizosphere soil that had not received P fertilizer over a 15-year period. A fosmid system was used to clone the metagenome of which 18,000 clones (~666 Mb of DNA) was screened for MPS. Functional assays and High Performance Liquid Chromatography analysis recognized gluconic acid production and MPS activity in the range 24.8-77.1 mmol/L and 27.6-38.16 μg/mL, respectively, when screened in an Escherichia coli host (at frequency of one MPS-positive clone hit per 114 Mb DNA tested). The MPS clones (with average insert size of ~37 kb) were analysed by 454 Roche sequencing and annotated. A number of genes/operons with homology to Phosphorous (P) uptake, regulatory and solubilization mechanisms were identified, linking the MPS function to the uncultivated microbiome present in barley rhizosphere soil. PMID:23894099

  13. In Search of Pathogens: Transcriptome-Based Identification of Viral Sequences from the Pine Processionary Moth (Thaumetopoea pityocampa)

    PubMed Central

    Jakubowska, Agata K.; Nalcacioglu, Remziye; Millán-Leiva, Anabel; Sanz-Carbonell, Alejandro; Muratoglu, Hacer; Herrero, Salvador; Demirbag, Zihni

    2015-01-01

    Thaumetopoea pityocampa (pine processionary moth) is one of the most important pine pests in the forests of Mediterranean countries, Central Europe, the Middle East and North Africa. Apart from causing significant damage to pinewoods, T. pityocampa occurrence is also an issue for public and animal health, as it is responsible for dermatological reactions in humans and animals by contact with its irritating hairs. High throughput sequencing technologies have allowed the fast and cost-effective generation of genetic information of interest to understand different biological aspects of non-model organisms as well as the identification of potential pathogens. Using these technologies, we have obtained and characterized the transcriptome of T. pityocampa larvae collected in 12 different geographical locations in Turkey. cDNA libraries for Illumina sequencing were prepared from four larval tissues, head, gut, fat body and integument. By pooling the sequences from Illumina platform with those previously published using the Roche 454-FLX and Sanger methods we generated the largest reference transcriptome of T. pityocampa. In addition, this study has also allowed identification of possible viral pathogens with potential application in future biocontrol strategies. PMID:25626148

  14. Illumina Production Sequencing at the DOE Joint Genome Institute - Workflow and Optimizations

    SciTech Connect

    Tarver, Angela; Fern, Alison; Diego, Matthew San; Kennedy, Megan; Zane, Matthew; Daum, Christopher; Hack, Christopher; Tang, Eric; Deshpande, Shweta; Cheng, Jan-Fang; Roberts, Simon; Alexandre, Melanie; Harmon-Smith, Miranda; Lucas, Susan

    2010-06-18

    The U.S. Department of Energy (DOE) Joint Genome Institute?s (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the DOE mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI?s Production Sequencing group, the Illumina Genome Analyzer pipeline has been established as one of three sequencing platforms, along with Roche/454 and ABI/Sanger. Optimization of the Illumina pipeline has been ongoing with the aim of continual process improvement of the laboratory workflow. These process improvement projects are being led by the JGI?s Process Optimization, Sequencing Technologies, Instrumentation& Engineering, and the New Technology Production groups. Primary focus has been on improving the procedural ergonomics and the technicians? operating environment, reducing manually intensive technician operations with different tools, reducing associated production costs, and improving the overall process and generated sequence quality. The U.S. DOE JGI was established in 1997 in Walnut Creek, CA, to unite the expertise and resources of five national laboratories? Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest ? along with HudsonAlpha Institute for Biotechnology. JGI is operated by the University of California for the U.S. DOE.

  15. The Tamiflu fiasco and lessons learnt.

    PubMed

    Gupta, Yogendra Kumar; Meenu, Meenakshi; Mohan, Prafull

    2015-01-01

    Oseltamivir (Tamiflu), a neuraminidase inhibitor, was approved for seasonal flu by US Food and Drug Administration in 1999. A number of randomized controlled trials, systematic reviews, and meta-analysis emphasized a favorable efficacy and safety profile. Majority of them were funded by Roche, which also first marketed and promoted this drug. In 2005 and 2009, the looming fear of pandemic flu led to recommendation by prominent regulatory bodies such as World Health Organization (WHO), Centers for Disease Control and Prevention, European Medicines Agency and others for its use in treatment and prophylaxis of influenza, and it's stockpiling as a measure to tide over the crisis. Serious Adverse Events, especially neuropsychiatric events associated with Tamiflu started getting reported leading to a cascade of questions on clinical utility of this drug. A recent Cochrane review and related articles have questioned the risk-benefit ratio of the drug, besides raising doubts about the regulatory decision of approving it. The recommendations for stockpiling the said drug as given by various international organizations viz WHO have also been put to scrutiny. Although many reviewers have labeled the Tamiflu saga as a "costly mistake," the episode leaves us with some important lessons. This article takes a comprehensive relook on the subject, and we proceed to suggest some ways and means to avoid a similar situation in the future. PMID:25821304

  16. Formation Channels for Blue Straggler Stars

    NASA Astrophysics Data System (ADS)

    Davies, Melvyn B.

    In this chapter we consider two formation channels for blue straggler stars: (1) the merger of two single stars via a collision, and (2) those produced via mass transfer within a binary. We review how computer simulations show that stellar collisions are likely to lead to relatively little mass loss and are thus effective in producing a young population of more-massive stars. The number of blue straggler stars produced by collisions will tend to increase with cluster mass. We review how the current population of blue straggler stars produced from primordial binaries decreases with increasing cluster mass. This is because exchange encounters with third, single stars in the most massive clusters tend to reduce the fraction of binaries containing a primary close to the current turn-off mass. Rather, their primaries tend to be somewhat more massive and have evolved off the main sequence, filling their Roche lobes in the past, often converting their secondaries into blue straggler stars (but more than 1 Gyr or so ago and thus they are no longer visible today as blue straggler stars).

  17. Bio-transformation of agri-food wastes by newly isolated Neurospora crassa and Lactobacillus plantarum for egg production.

    PubMed

    Liu, P; Li, J; Deng, Z

    2016-03-01

    Using bio-transferred feedstuff was a cost-effective approach to improve egg quality and production; particularly, the nutritive diet came from agri-food wastes. In this study, optimization of fermentation conditions and co-cultivation of Neurospora crassa with Lactobacillus plantarum was performed in a simple bioreactor. The optimized fermentation of beer lees substrates through N. crassa led to the hydrolysis rates of crude fiber increasing to 43.27%. Compared to that of using N. crassa alone, the combination of N. crassa and L. plantarum enhanced the content of amino acids (13,120 to 18,032 mg/100 g) on oil-tea seed cake substrates particularly. When hens were fed 10% fermented oil-tea seedcake substrate, the ratio of feed to egg decreased from 3.1 to 2.6, egg production ratio increased from 65.71 to 80.10%, and color of vitelline (Roche) increased from 8.20 to 10.20. Fifteen kinds of carotenoids were identified by HPLC in fermented oil-tea seed cake substrates. The results of this study highlighted that the mixed-fermentation by N. crassa and L. plantarum may be an effective way to convert agri-food wastes into high-valued biomass products, which could have a positive effect on hens and their eggs. PMID:26740129

  18. FullSSR: Microsatellite Finder and Primer Designer

    PubMed Central

    Metz, Sebastián; Cabrera, Juan Manuel; Rueda, Eva; Giri, Federico; Amavet, Patricia

    2016-01-01

    Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user. PMID:27366148

  19. Optical Observations of the Binary Pulsar System PSR B1718-19: Implications for Tidal Circularization

    NASA Astrophysics Data System (ADS)

    van Kerkwijk, M. H.; Kaspi, V. M.; Klemola, A. R.; Kulkarni, S. R.; Lyne, A. G.; Van Buren, D.

    2000-01-01

    We report on Keck and Hubble Space Telescope optical observations of the eclipsing binary pulsar system PSR B1718-19, in the direction of the globular cluster NGC 6342. These reveal a faint star (mF702W=25.21+/-0.07 Vega system) within the pulsar's 0.5" radius positional error circle. This may be the companion. If it is a main-sequence star in the cluster, it has radius RC~=0.3 Rsolar, temperature Teff~=3600 K, and mass MC~=0.3 Msolar. In many formation models, however, the pulsar (spun-up by accretion or newly formed) and its companion are initially in an eccentric orbit. If so, for tidal circularization to have produced the present-day highly circular orbit, a large stellar radius is required, i.e., the star must be bloated. Using constraints on the radius and temperature from the Roche and Hayashi limits, we infer from our observations that RC<~0.44 Rsolar and Teff>~3300 K. Even for the largest radii, the required efficiency of tidal dissipation is larger than expected for some prescriptions.

  20. Development of an electrostatic dust detector for tungsten dust

    NASA Astrophysics Data System (ADS)

    Starkey, D.; Hammond, K.; Roquemore, L.; Skinner, C. H.

    2012-10-01

    Next-step fusion reactors, such as ITER, are expected to have large quantities of dust that will present hazards that have yet to be encountered in current fusion devices. To manage the amount of dust within the reactors a real-time dust detector must be implemented to ensure that dust does not reach hazardous levels. An electrostatic device that accomplishes this has already been tested on NSTX and Tore Supra [1,2]. We will present modifications of this device to improve its ruggedness to withstand the conditions that will be present in ITER. The detector consists of two tungsten wires wrapped around a macor cylinder that are biased at 100-300 V. Incident dust causes a measurable transient short circuit. Initial results have demonstrated the detection of tungsten particles. We will also present a potential method of electrostatic cleaning of residual dust from the detector.[4pt] [1] C. H. Skinner et al., Rev. Sci. Instrum., 81, 10E102 (2010)[0pt] [2] H. Roche et al., Phys. Scr., T145, (2011).

  1. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

    PubMed Central

    Penton, C. Ryan; Gupta, Vadakattu V. S. R.; Yu, Julian; Tiedje, James M.

    2016-01-01

    We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation. PMID:27313569

  2. Total synthesis of tetraacylated phosphatidylinositol hexamannoside and evaluation of its immunomodulatory activity

    PubMed Central

    Patil, Pratap S.; Cheng, Ting-Jen Rachel; Zulueta, Medel Manuel L.; Yang, Shih-Ting; Lico, Larry S.; Hung, Shang-Cheng

    2015-01-01

    Tuberculosis, aggravated by drug-resistant strains and HIV co-infection of the causative agent Mycobacterium tuberculosis, is a global problem that affects millions of people. With essential immunoregulatory roles, phosphatidylinositol mannosides are among the cell-envelope components critical to the pathogenesis and survival of M. tuberculosis inside its host. Here we report the first synthesis of the highly complex tetraacylated phosphatidylinositol hexamannoside (Ac2PIM6), having stearic and tuberculostearic acids as lipid components. Our effort makes use of stereoelectronic and steric effects to control the regioselective and stereoselective outcomes and minimize the synthetic steps, particularly in the key desymmetrization and functionalization of myo-inositol. A short synthesis of tuberculostearic acid in six steps from the Roche ester is also described. Mice exposed to the synthesized Ac2PIM6 exhibit increased production of interleukin-4 and interferon-γ, and the corresponding adjuvant effect is shown by the induction of ovalbumin- and tetanus toxoid-specific antibodies. PMID:26037164

  3. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).

    PubMed

    Bonatelli, Isabel A S; Carstens, Bryan C; Moraes, Evandro M

    2015-01-01

    Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms. PMID:26561396

  4. Characterization of 12 Novel Microsatellite Markers of Sogatella furcifera (Hemiptera: Delphacidae) Identified From Next-Generation Sequence Data

    PubMed Central

    Nam, Hwa Yeun; Coates, Brad; Kim, Kyung Seok; Park, Marana; Lee, Joon-Ho

    2015-01-01

    The white-backed planthopper, Sogatella furcifera (Horváth) (Hemiptera: Delphacidae), is a major pest of rice and has long-range migratory behavior in Asia. Microsatellite markers (simple sequence repeats) have been widely used to determine the origins and genetic diversity of insect pests. We identified novel microsatellite loci for S. furcifera samples collected from Laos, Vietnam, and three localities in Bangladesh from next-generation Roche 454 pyrosequencing data. Size polymorphism at 12 microsatellite loci was verified for 40 adult individuals collected from Shinan, South Korea. The average number of alleles per locus was 7.92. The mean values of observed (Ho) and expected heterozygosities (HE) were 0.615 and 0.757, respectively. These new microsatellite markers will be a resource for future ecological genetic studies of S. furcifera samples across more broad geographic regions in Asia and may assist in estimations of genetic differentiation and gene flow among populations for implementation of more effective management strategies to control this serious rice pest. PMID:26163593

  5. Comprehensive transcriptome profiling of squamous cell carcinoma of horn in Bos indicus.

    PubMed

    Koringa, P G; Jakhesara, S J; Bhatt, V D; Meshram, C P; Patel, A K; Fefar, D T; Joshi, C G

    2016-06-01

    Squamous cell carcinoma (SCC) of horn is frequently observed in Bos indicus affecting 1% of cattle population and accounting 83.34% of total tumours found. The transcriptome profile of horn cancer (HC) tissue and the matched normal (HN) tissue were analysed by RNA-seq using Roche 454 sequencing. A total of 1 504 900 reads comprising of 612 MB data were used to identify differentially expressed genes using CLC Genomic Workbench. These include up-regulation of KRT6A, KRT6B, KRT6C, KRT14, SFN, KRT84, PI3, COL17A1, ANLN, SERPINB5 and down-regulation of BOLA, SCGB1A1, CXCL17, KRT19, BPIFB1, NR4A1 and TFF3 in HC, which are involved in regulation of gene transcription, cell proliferation, apoptosis, cell survival and metabolic pathways. The qPCR analysis of several targets suggested concordance of gene expression profile with RNA-seq analysis. The present findings would provide basis for further screening of genes and identification of markers for early diagnosis and therapeutic intervention of HC. PMID:24314272

  6. Characterisation of the hydrogeology of the Augustus River catchment, Western Australia

    NASA Astrophysics Data System (ADS)

    Wilkes, Shane M.; Clement, T. Prabhakar; Otto, Claus J.

    Understanding the hydrogeology of weathered rock catchments is integral for the management of various problems related to increased salinity within the many towns of Western Australia. This paper presents the results of site characterisation investigations aimed at improving the overall understanding of the hydrogeology of the southern portion of the Augustus River catchment, an example of a weathered rock catchment. Site data have highlighted the presence of both porous media aquifers within the weathered profile and fractured rock aquifers within the basement rocks. Geophysical airborne surveys and other drilling data have identified a large number of dolerite dykes which crosscut the site. Fractured quartz veins have been found along the margins of these dolerite dykes. Detailed groundwater-level measurements and barometric efficiency estimates indicate that these dolerite dykes and fractured quartz veins are affecting groundwater flow directions, promoting a strong hydraulic connection between all aquifers, and also influencing recharge mechanisms. The hydrogeological significance of the dolerite dykes and fractured quartz veins has been assessed using a combination of high-frequency groundwater-level measurements (30-min sampling interval), rainfall measurements (5-min sampling interval) and barometric pressure fluctuations (30-min sampling interval). A conceptual model was developed for describing various hydrogeological features of the study area. The model indicates that fractured quartz veins along the margins of dolerite dykes are an important component of the hydrogeology of the weathered rock catchments. Comprendre l'hydrogéologie des bassins en roches altérées est essentiel pour la gestion de différents problèmes liés à l'augmentation de la salinité dans de nombreuses villes d'Australie occidentale. Cet article présente les résultats d'études de caractérisation de sites conduites pour améliorer la compréhension de l'hydrogéologie de la

  7. A massive neutron star in the millisecond pulsar PSR J2215+5135

    NASA Astrophysics Data System (ADS)

    Shahbaz, Tariq

    2016-07-01

    Binary evolution may increase neutron masses via accretion. Hence the most massive neutron stars (NSs) are expected to be located amongst the binary millisecond pulsars (MSPs) spun-up within X-ray binaries. Most MSPs are found with brown dwarf lookalikes or ˜0.2 M stars in systems called "black widows" and "redbacks", respectively, because these companions are ablated by the pulsar wind. These systems offer some advantages over white dwarf-pulsar binaries: they are typically brighter, they present strongly irradiated hemispheres, and they fill significant fractions of their Roche lobes. As a result, their optical light curves exhibit variability due to a combination of their ellipsoidal shape and irradiation, which can be modelled in order to determine orbital parameters such as the mass ratio and inclination. Combining these with optical spectroscopy and/or pulsar timing enables one to determine a reliable NS masses. Here we present the results of our detailed modelling of the optical lightcurves and radial velocity curves of J2215+5135, which allows us to determine various ystem parameters, including the NS mass.

  8. Encounters between binaries and neutron stars

    NASA Technical Reports Server (NTRS)

    Davies, M. B.; Benz, W.; Hills, J. G.

    1993-01-01

    We simulated encounters between a neutron star and primordial and tidal-capture binaries. In the case of encounters involving a tidal-capture binary, comprising a white dwarf and a main-sequence star, we find that most exchange encounters will produce a single merged object with the white dwarf and neutron star engulfed in a common envelope of gas donated by the main-sequence primary of the original binary. A small fraction of exchanges induce a merger of the white dwarf and main-sequence star, with this object being unbound to the neutron star, and the two objects having a large relative speed at infinity. For encounters involving a primordial binary, fewer encounters require the inclusion of hydrodynamical effects. Those involving collisions or close encounters tend to produce a binary comprised of the two merged stars (now forming one star) and the third star. The binaries produced typically have large enough separations to prevent the formation of a single merged object until subsequent stellar evolution of one of the components causes it to fill its Roche lobe. Clean exchanges produce binaries with large eccentricities; they are typically sufficiently wide to avoid circularization.

  9. Formation of millisecond pulsars with low-mass helium white dwarf companions in very compact binaries

    SciTech Connect

    Jia, Kun; Li, X.-D.

    2014-08-20

    Binary millisecond pulsars (BMSPs) are thought to have evolved from low-mass X-ray binaries (LMXBs). If the mass transfer in LMXBs is driven by nuclear evolution of the donor star, the final orbital period is predicted to be well correlated with the mass of the white dwarf (WD), which is the degenerate He core of the donor. Here we show that this relation can be extended to very small WD mass (∼0.14-0.17 M {sub ☉}) and narrow orbital period (about a few hours), depending mainly on the metallicities of the donor stars. There is also discontinuity in the relation, which is due to the temporary contraction of the donor when the H-burning shell crosses the hydrogen discontinuity. BMSPs with low-mass He WD companions in very compact binaries can be accounted for if the progenitor binary experienced very late Case A mass transfer. The WD companion of PSR J1738+0333 is likely to evolve from a Pop II star. For PSR J0348+0432, to explain its extreme compact orbit in the Roche-lobe-decoupling phase, even lower metallicity (Z = 0.0001) is required.

  10. The signature of single-degenerate accretion-induced collapse

    SciTech Connect

    Piro, Anthony L.

    2014-10-10

    The accretion-induced collapse (AIC) of a white dwarf to a neutron star has long been suggested as a natural theoretical outcome in stellar evolution, but there has never been a direct detection of such an event. This is not surprising since the small amount of radioactive nickel synthesized (∼10{sup –3} M {sub ☉}) implies a relatively dim optical transient. Here we argue that a particularly strong signature of an AIC would occur for an oxygen-neon-magnesium (ONeMg) white dwarf accreting from a star that is experiencing Roche-lobe overflow as it becomes a red giant. In such cases, the ∼10{sup 50} erg explosion from the AIC collides with and shock-heats the surface of the extended companion, creating an X-ray flash lasting ∼1 hr followed by an optical signature that peaks at an absolute magnitude of ∼ – 16 to –18 and lasts for a few days to a week. These events would be especially striking in old stellar environments where hydrogen-rich supernova-like transients would not normally be expected. Although the rate of such events is not currently known, we describe observing strategies that could be utilized with high cadence surveys that should either detect these events or place strong constraints on their rates.

  11. Formation of Short-Period Binary Pulsars in Globular Clusters.

    PubMed

    Rasio; Pfahl; Rappaport

    2000-03-20

    We present a new dynamical scenario for the formation of short-period binary millisecond pulsars in globular clusters. Our work is motivated by the recent observations of 20 radio pulsars in 47 Tuc. In a dense cluster such as 47 Tuc, most neutron stars acquire binary companions through exchange interactions with primordial binaries. The resulting systems have semimajor axes in the range approximately 0.1-1 AU and neutron star companion masses approximately 1-3 M middle dot in circle. For many of these systems, we find that when the companion evolves off the main sequence and fills its Roche lobe, the subsequent mass transfer is dynamically unstable. This leads to a common envelope phase and the formation of short-period neutron star-white dwarf binaries. For a significant fraction of these binaries, the decay of the orbit due to gravitational radiation will be followed by a period of stable mass transfer driven by a combination of gravitational radiation and tidal heating of the companion. The properties of the resulting short-period binaries match well those of observed binary pulsars in 47 Tuc. PMID:10702129

  12. Disuse bone loss in hindquarter suspended rats: partial weightbearing, exercise and ibandronate treatment as countermeasures

    NASA Technical Reports Server (NTRS)

    Schultheis, L.; Ruff, C. B.; Rastogi, S.; Bloomfield, S.; Hogan, H. A.; Fedarko, N.; Thierry-Palmer, M.; Ruiz, J.; Bauss, F.; Shapiro, J. R.

    2000-01-01

    The purpose of this study was to evaluate potential countermeasures for bone loss during long-term space missions in the hindquarter suspended rat, including partial weight bearing (surrogate for artificial gravity) episodic full weight bearing (2 hour/day full weight bearing) and treatment with the third generation bisphosphonate ibandronate (Roche). Graded mechanical loading was studied by housing the animals on a novel servo controlled force plate system which permitted the titration of mechanical force at varying frequency and amplitude and different levels of weight bearing. The force plate, which forms the cage floor, is a glass platform supported by an 18" diameter speaker cone filled with expanding polyurethane foam. An infrared optical sensor attached to the speaker cone yields a voltage linearly related to vertical displacement of the glass platform. The dynamic force on the paw was computed as a product of the apparent mass of the animal on the platform at rest and the acceleration of the platform determined from the second derivative of the optical sensor output. The mass of the animal on the platform was varied by adjusting tension on the tether suspending the animal. Mechanical impact loading was titrated with the force plate resonating at different frequencies, including 3 Hz and 16 Hz.

  13. Development of an RNA Interference Tool, Characterization of Its Target, and an Ecological Test of Caste Differentiation in the Eusocial Wasp Polistes

    PubMed Central

    Havukainen, Heli; Henshaw, Michael T.; Amdam, Gro V.

    2011-01-01

    Recent advancements in genomics provide new tools for evolutionary ecological research. The paper wasp genus Polistes is a model for social insect evolution and behavioral ecology. We developed RNA interference (RNAi)-mediated gene silencing to explore proposed connections between expression of hexameric storage proteins and worker vs. gyne (potential future foundress) castes in naturally-founded colonies of P. metricus. We extended four fragments of putative hexamerin-encoding P. metricus transcripts acquired from a previous study and fully sequenced a gene that encodes Hexamerin 2, one of two proposed hexameric storage proteins of P. metricus. MALDI-TOF/TOF, LC-MSMS, deglycosylation, and detection of phosphorylation assays showed that the two putative hexamerins diverge in peptide sequence and biochemistry. We targeted the hexamerin 2 gene in 5th (last)-instar larvae by feeding RNAi-inducing double-stranded hexamerin 2 RNA directly to larvae in naturally-founded colonies in the field. Larval development and adult traits were not significantly altered in hexamerin 2 knockdowns, but there were suggestive trends toward increased developmental time and less developed ovaries, which are gyne characteristics. By demonstrating how data acquisition from 454/Roche pyrosequencing can be combined with biochemical and proteomics assays and how RNAi can be deployed successfully in field experiments on Polistes, our results pave the way for functional genomic research that can contribute significantly to learning the interactions of environment, development, and the roles they play in paper wasp evolution and behavioral ecology. PMID:22069460

  14. An upper limit on the sizes of shepherding satellites at Saturn's ring G

    NASA Technical Reports Server (NTRS)

    Van Allen, James A.

    1987-01-01

    An accurate analytical theory of the absorption of energetic magnetospheric particles by an inert satellite is developed for the case in which the radius b of the satellite is much less than the equatorial gyroradius r(g) of the particles and in which r(g) is in turn much less than the radius r of the satellite's orbit. In previous interpretations of Pioneer 11 observations, an estimate of the lifetime against absorption of energetic protons at Saturn's ring G has been made. This lifetime is used in the framework of the absorption theory to establish an upper limit on the sizes of shepherding satellites associated with the ring. The resulting upper limit, ignoring the absorption of the optically observed particulate matter, is given for an assemblage of N satellites of various radii. It is noted that ring G lies outside the Roche limit. No shepherding satellites at ring G were detected optically by Voyagers 1 and 2, and the searches were not comprehensive in longitudinal coverage.

  15. Head-to-head comparison of B-type natriuretic peptide (BNP) and NT-proBNP in daily clinical practice.

    PubMed

    Mair, Johannes; Gerda, Falkensammer; Renate, Hiemetzberger; Ulmer, Hanno; Andrea, Griesmacher; Pachinger, Otmar

    2008-02-29

    B-type natriuretic peptide (BNP; Abbott Diagnostics) and N-terminal proBNP (NT-proBNP, Roche Diagnostics) were compared in consecutive samples of 458 patients (mean age 60 years+/-16 years; 159 female, 299 male) sent for NT-proBNP measurement to investigate influences on both markers. BNP and NT-proBNP showed a close correlation with each other (r=0.89, p<0.0001). Using age- and gender-adjusted upper reference values the inter-rater agreement of both parameters was satisfactory (83%, Cohen's kappa coefficient=0.7). The combination of normal BNP and elevated NT-proBNP was significantly more frequent than vice versa (61 vs. 16 patients), and a calculated glomerular filtration rate<60 ml/min/1.73 m(2) was found in 39% of these patients. Multiple linear regression analysis revealed a significant influence of a reduced ejection fraction (<50%), renal dysfunction (calculated glomerular filtration rate<60 ml/min/1.73 m(2)), anemia, hypertension, age, and gender on both BNP and NT-proBNP. In conclusion, despite a close correlation and a satisfactory agreement between both markers in classification, frequent discrepancies in individual patients demonstrate that both markers are clinically not completely equivalent. PMID:17360054

  16. Comparative study of a portable prothrombin time monitor employing three different systems in oral anticoagulant units.

    PubMed

    Vacas, M; Fernández, M A; Martínez-Brotons, F; Lafuente, P J; Ripoll, F; Alvarez, C; Iriarte, J A

    2001-01-01

    The aim of this study was to evaluate the accuracy of the portable coagulometer CoaguChek (Roche Diagnostics) as a prothrombin time (PT) monitor, and to correlate capillary blood results with those of three different routine methods used for monitoring oral anticoagulant therapy (OAT): capillary, plasma and whole blood samples. Three hospitals participated in the study with a total of 235 patients on OAT. The international normalized ratio (INR) results obtained with CoaguChek were compared with those obtained using each of the routine methods. The study presents a good correlation between the PT monitor and the three methods studied: r = 0.9745 (hospital A), r = 0.9283 (hospital B), r = 0.9136 (hospital C). A simplified concordance test of the methods results in a nine-field comparison table showing concordances of 87.2, 85.7 and 68.4%, respectively. The absolute difference (mean +/- SD) between laboratory A and CoaguChek INRs was 0.0571 +/- 0.2042, with values of 0.04286 +/- 0.3906 for laboratory B and 0.6986 +/- 0.6170 for laboratory C. These results confirm that CoaguChek could be used as a new method for oral anticoagulant monitoring, and is in best agreement with the capillary blood PT system. PMID:11408745

  17. Kyste hydatique de la surrénale: à propos d'un cas

    PubMed Central

    Mahmoudi, Ammar; Maâtouk, Mezri; Noomen, Faouzi; Nasr, Mohamed; Zouari, Khadija; Hamdi, Abdelaziz

    2015-01-01

    Le kyste hydatique de la surrénale reste une affection exceptionnelle et une localisation inhabituelle du kyste hydatique, même dans les pays où l'hydatidose sévit à l’état endémique. Nous rapportons un cas de kyste hydatique surrénalien révélé par des douleurs de l'hypochondre droit. Le diagnostic a été évoqué en préopératoire sur les données de la tomodensitométrie abdominale qui avait objectivé une masse kystique surrénalienne droite. La sérologie hydatique était positive. Le traitement chirurgical avait consisté en une résection du dôme saillant et avait permis de conserver la glande. Le kyste était univésiculaire contenant un liquide eau de roche avec une membrane proligère. Les suites opératoires étaient simples. La surveillance à distance, échographique et immunologique, n'avait pas décelé de récidive avec un recul de deux ans PMID:26587122

  18. Performance evaluation of a new fourth-generation HIV Ag/Ab combination electrochemiluminescence immunoassay - evaluation of a new HIV assay.

    PubMed

    Wang, Tingting; Li, Dongdong; Yan, Kening; Yuan, Yu; Yang, Tingfu; Du, Xiaoqing; Yan, Xuedan; Tao, Chuanmin; Wang, Lanlan

    2014-03-01

    A new fourth-generation HIV Ag/Ab electrochemiluminescence immunoassay for screening of HIV infection, the Elecsys HIV Combi PT (Roche Diagnostics, Penzberg, Germany) assay, is going to be commercially available in clinical laboratories in China. This assay was evaluated and compared with two commonly used assays: Elecsys HIV Combi assay and the Livzon anti-HIV-1/2 ELISA. Commercially available panels and 30 established HIV infection samples were tested to evaluate the sensitivity. In addition, a total of 675 routine clinical samples were collected and tested in West China Hospital to compare the specificity. Any reactive result from a screening test was retested and all reactive retested samples were confirmed with Western blot assay, Elecsys HIV Ag test, Elecsys HIV Ag confirmatory test or HIV-1 RNA NAT testing. According to the results of the HIV seroconversion panels, the Elecsys HIV Combi PT could detect seroconversion at the same bleed or at least one bleed earlier compared to the other two assays. Among the 675 clinical samples, most results were consistent except for one specimen with a false-negative result using Elecsys HIV Combi assay. In conclusion, the Elecsys HIV Combi PT has shown satisfactory sensitivity and specificity to be a screening test for HIV infection. PMID:23970655

  19. On the Origin of the Sub-Jovian Desert in the Orbital-period-Planetary-mass Plane

    NASA Astrophysics Data System (ADS)

    Matsakos, Titos; Königl, Arieh

    2016-03-01

    Transit and radial velocity observations indicate a dearth of sub-Jupiter-mass planets on short-period orbits, outlined roughly by two oppositely sloped lines in the period-mass plane. We interpret this feature in terms of high-eccentricity migration of planets that arrive in the vicinity of the Roche limit, where their orbits are tidally circularized, long after the dispersal of their natal disk. We demonstrate that the two distinct segments of the boundary are a direct consequence of the different slopes of the empirical mass-radius relation for small and large planets, and show that this relation also fixes the mass coordinate of the intersection point. The period coordinate of this point, as well as the detailed shape of the lower boundary, can be reproduced with a plausible choice of a key parameter in the underlying migration model. The detailed shape of the upper boundary, on the other hand, is determined by the post-circularization tidal exchange of angular momentum with the star and can be reproduced with a stellar tidal quality factor {Q}*\\prime ˜ {10}6.

  20. WW Geminorum: An early B-type eclipsing binary evolving into the contact phase

    SciTech Connect

    Yang, Y.-G.; Dai, H.-F.; Yin, X.-G.; Yang, Y. E-mail: yangyg@chnu.edu.cn

    2014-11-01

    WW Gem is a B-type eclipsing binary with a period of 1.2378 days. The CCD photometry of this binary was performed in 2013 December using the 85 cm telescope at the Xinglong Stations of the National Astronomical Observatories of China. Using the updated W-D program, the photometric model was deduced from the VRI light curves. The results imply that WW Gem is a near-contact eclipsing binary whose primary component almost fills its Roche lobe. The photometric mass ratio is q {sub ph} = 0.48(± 0.05). All collected times of minimum light, including two new ones, were used for the period studies. The orbital period changes of WW Gem could be described by an upward parabola, possibly overlaid by a light-time orbit with a period of P {sub mod} = 7.41(± 0.04) yr and a semi-amplitude of A = 0.0079 days(± 0.0005 days), respectively. This kind of cyclic oscillation may be attributed to the light-travel time effect via the third body. The long-term period increases at a rate of dP/dt = +3.47(±0.04) × 10{sup –8} day yr{sup –1}, which may be explained by the conserved mass transfer from the less massive component to the more massive one. With mass transfer, the massive binary WW Gem may be evolving into a contact binary.