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Sample records for 03-02-1999 amplicor roche

  1. Evaluation of Roche Amplicor PCR assay for Mycobacterium tuberculosis.

    PubMed Central

    Wobeser, W L; Krajden, M; Conly, J; Simpson, H; Yim, B; D'costa, M; Fuksa, M; Hian-Cheong, C; Patterson, M; Phillips, A; Bannatyne, R; Haddad, A; Brunton, J L; Krajden, S

    1996-01-01

    The Roche Amplicor Mycobacterium tuberculosis PCR test (RMtb-PCR) was compared with mycobacterial culture, with the BACTEC 460 system and inoculation on Lowenstein-Jensen media. Results were interpreted with an adjusted "gold standard" incorporating clinical diagnosis. A total of 1,480 clinical specimens from 1,155 patients, including tissues and fluids, as well as 141 specimens which demonstrated a positive growth index on the BACTEC 460 system were assessed. The sensitivity, specificity, and positive and negative predictive values of RMtb-PCR compared with the adjusted gold standard for clinical specimens were 79, 99, 93, and 98%, respectively. In smear-positive specimens, the sensitivity of RMtb-PCR was 98% versus 53% for smear-negative specimens. When RMtb-PCR was performed two times per week, PCR results were available an average of 21 days before the culture results. For specimens demonstrating a positive growth index on the BACTEC 460 system, RMtb-PCR had a sensitivity and specificity of 98 and 100%, respectively. This study demonstrates the value of a commercial nucleic acid amplification kit for rapid diagnosis of M. tuberculosis, particularly in smear-positive specimens or BACTEC culture-positive specimens. PMID:8748289

  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. Assessment of MagNA Pure LC Extraction System for Detection of Human Papillomavirus (HPV) DNA in PreservCyt Samples by the Roche AMPLICOR and LINEAR ARRAY HPV Tests

    PubMed Central

    Stevens, Matthew P.; Rudland, Elice; Garland, Suzanne M.; Tabrizi, Sepehr N.

    2006-01-01

    Roche Molecular Systems recently released two PCR-based assays, AMPLICOR and LINEAR ARRAY (LA), for the detection and genotyping, respectively, of human papillomaviruses (HPVs). The manual specimen processing method recommended for use with both assays, AmpliLute, can be time-consuming and labor-intensive and is open to potential specimen cross-contamination. We evaluated the Roche MagNA Pure LC (MP) as an alternative for specimen processing prior to use with either assay. DNA was extracted from cervical brushings, collected in PreservCyt media, by AmpliLute and MP using DNA-I and Total Nucleic Acid (TNA) kits, from 150 patients with histologically confirmed cervical abnormalities. DNA was amplified and detected by AMPLICOR and the LA HPV test. Concordances of 96.5% (139 of 144) (κ = 0.93) and 95.1% (135 of 142) (κ = 0.90) were generated by AMPLICOR when we compared DNA extracts from AmpliLute to MP DNA-I and TNA, respectively. The HPV genotype profiles were identical in 78.7 and 74.7% of samples between AmpliLute and DNA-I or TNA, respectively. To improve LA concordance, all 150 specimens were extracted by MP DNA-I protocol after the centrifugation of 1-ml PreservCyt samples. This modified approach improved HPV genotype concordance levels between AmpliLute and MP DNA-I to 88.0% (P = 0.043) without affecting AMPLICOR sensitivity. Laboratories that have an automated MP extraction system would find this procedure more feasible and easier to handle than the recommended manual extraction method and could substitute such extractions for AMPLICOR and LA HPV tests once internally validated. PMID:16825360

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

    PubMed

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

    2000-11-01

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

  5. Comparison of PapType to Digene Hybrid Capture 2, Roche linear array, and Amplicor for detection of high-risk human papillomavirus genotypes in women with previous abnormal pap smears.

    PubMed

    Tabrizi, Sepehr N; Stevens, Matthew P; Khan, Zaheer A; Chow, Conan; Devitt, Martin A; Garland, Suzanne M

    2012-08-01

    PapType human papillomavirus (HPV) assay was compared to Hybrid Capture 2 (HC2), Amplicor (Amp), and Linear Array (LA) HPV tests in 894 women undergoing management for a high-grade Pap smear abnormality. The sensitivity in detection of underlying high-grade histological diagnosis by PapType was 90.3% and by HC2 was 79.8%, while by Amp and LA it was 92.4% and 91.6%, respectively. The specificities were 52.5%, 55.3%, 49.4%, and 51.7% for PapType, HC2, Amp, and LA, respectively.

  6. 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

  7. 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

  8. ISAtx-247 (Isotechnika/Roche).

    PubMed

    Dumont, Francis J

    2004-05-01

    ISAtx-247 is a ciclosporin A analog under development by Isotechnika and Roche as an immunosuppressant for the potential prevention of organ rejection after transplantation, and for the potential treatment of autoimmune diseases such as rheumatoid arthritis, psoriasis and type 1 diabetes. A phase II renal transplantation study had been completed by June 2003. PMID:15202729

  9. 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.

  10. 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.

  11. Comparative study of a modified competitive RT-PCR and Amplicor HCV monitor assays for quantitation of hepatitis C virus RNA in serum.

    PubMed

    Olmedo, E; Costa, J; López-Labrador, F X; Forns, X; Ampurdanés, S; Maluenda, M D; Guilera, M; Sánchez-Tapias, J M; Rodes, J; Jimenez de Anta, M T

    1999-05-01

    A modified competitive RT-PCR (mcRT-PCR) to measure HCV RNA in serum and the Amplicor HCV Monitor assay were compared. For mcRT-PCR, the RNA extracted was retrotranscribed and coamplified in one step with a known amount of a DNA internal control (IC). Digoxigenin-labeled amplified products were hybridized to specific HCV DNA and IC-DNA probes and quantified by colorimetry. HCV RNA concentration was calculated by plotting the ratio of HCV/IC ODs against a calibration curve. Multiple samples were analyzed in the same round and tedious titration of each sample with a competitor was unnecessary. The mcRT-PCR assay was linear from 6 x 10(3) to 6 x 10(7) copies/ml, whereas Amplicor was linear up to 1-2 x 10(6) copies/ml. HCV RNA was measured in samples from 75 carriers. There was agreement between both methods in type 1 infections but not in type 2 or type 3 infections, in which the values measured by Amplicor were, on average, 15 times lower than those measured by the mcRT-PCR. HCV RNA measured by Amplicor was higher in type 1 infections than in type 2 or 3 infections, but no differences were found when viral load was assessed by mcRT-PCR. The binding efficiency of the Amplicor-probe was greater for type 1 than for types 2 or 3, suggesting Amplicor underestimates the viral load in the latter types. In contrast, the mcRT-PCR is not affected by genotype-related variation of HCV. This study suggests that mcRT-PCR assay is reliable for sensitive and accurate measurement of HCV RNA over a broad range of values independently of the HCV genotype.

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

    PubMed Central

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

    2000-01-01

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

  13. Comparison of costs of strategies for measuring levels of human immunodeficiency virus type 1 RNA in plasma by using Amplicor and Ultra Direct assays.

    PubMed

    Raboud, J M; Seminari, E; Rae, S L; Harrigan, P R; Hogg, R S; Conway, B; Sherlock, C; Schechter, M T; O'Shaughnessy, M V; Montaner, J S

    1998-11-01

    The costs of four algorithms for monitoring plasma human immunodeficiency virus type 1 RNA were compared. For patients with strong virologic responses, the use of Ultra Direct exclusively was the cheapest strategy. For patients with weak virologic responses, small savings could be obtained by using Amplicor and retesting only samples with values below 500 copies/ml with Ultra Direct.

  14. Comparison of Costs of Strategies for Measuring Levels of Human Immunodeficiency Virus Type 1 RNA in Plasma by Using Amplicor and Ultra Direct Assays

    PubMed Central

    Raboud, J. M.; Seminari, E.; Rae, S. L.; Harrigan, P. R.; Hogg, R. S.; Conway, B.; Sherlock, C.; Schechter, M. T.; O’Shaughnessy, M. V.; Montaner, J. S. G.

    1998-01-01

    The costs of four algorithms for monitoring plasma human immunodeficiency virus type 1 RNA were compared. For patients with strong virologic responses, the use of Ultra Direct exclusively was the cheapest strategy. For patients with weak virologic responses, small savings could be obtained by using Amplicor and retesting only samples with values below 500 copies/ml with Ultra Direct. PMID:9774597

  15. 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).

  16. 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.

  17. ["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.

  18. ["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

  19. 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

  20. 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.

  1. 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.

  2. Commitment of Roche in malaria and other tropical diseases.

    PubMed

    Stürchler, D; Mittelholzer, M L; Handschin, J

    1993-09-01

    In the absence of a suitable malaria case definition, reliable surveillance data on the impact of malaria are not available. Determinants of case loads, including population movements, environmental changes, lack of political commitment and resources, and resistance to antimalarials and residual insecticides, work towards global deterioration. Some 90% of the Plasmodium falciparum burden is carried by Africa south of the Sahara. There, in 1992, the number of children under five years of age and exposed to high risk was about 106 million. Assuming a malaria attack rate of 0.5-1.5 per child per year, and a case fatality rate of 2%, annual clinical cases and malaria deaths in this population alone come to 53-160 million and 1-3 million, respectively. Roche, a pharmaceutical company with major research efforts in tropical medicine, in collaboration with research centers and international institutions, has recently set up a tropical medicine unit that coordinates and concentrates corporate efforts in this field. The unit aims to make affordable and innovative products available which are effective against major tropical diseases. A commercial product of the unit is Lariam, a major antimalarial used alone or in simultaneous or sequential combinations. The single dose combination of Lariam plus Fansidar (Fansimef) is particularly useful for stand-by or emergency oral therapy. Artemisinine, or its derivatives, followed by one to two doses of Lariam are effective against severe and multiresistant P. falciparum malaria. A new Roche peroxide antimalarial is currently in phase II clinical trials. The unit is also involved in research and development of malaria sporozoite and asexual blood stage vaccine candidates.

  3. Tidal Decay and Roche-Lobe Overflow of Gaseous Exoplanets

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    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, and the distributions of orbital periods and semi-major axes point to non-negligible orbital decay during the main sequence lifetimes of the host stars. Thus, the coupled processes of orbital evolution and RLO likely shape the observed distribution of close-in exoplanets. 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. Applying the Modules for Experiments in Stellar Astrophysics (MESA) suite to model RLO, we find 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 or interior to this orbital period, providing an observational prediction that can corroborate the RLO hypothesis. 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.

  4. 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}.

  5. Performance of the Roche LightCycler real-time PCR assay for diagnosing extrapulmonary tuberculosis.

    PubMed

    Gous, N; Scott, L E; Wong, E; Omar, T; Venter, W D F; Stevens, W

    2012-06-01

    The Roche LightCycler mycobacterium detection molecular assay for Mycobacterium tuberculosis, M. avium, and M. kansasii, was applied to tissue specimens. It performed well on lymph node and cerebrospinal fluid specimens and less well on lung, liver, and bone marrow core biopsy specimens, but used in conjunction with a clinical suspicion of tuberculosis, it could augment patient management.

  6. 75 FR 71135 - Hoffmann-La Roche Inc.; Withdrawal of Approval of a New Drug Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-22

    ..., 2010 (75 FR 39024), FDA issued a notice announcing its determination that ACCUTANE (isotretinoin... Administration (FDA) is withdrawing approval of a new drug application (NDA) for ACCUTANE (isotretinoin) Capsules... INFORMATION: Hoffmann-La Roche Inc. has requested that FDA withdraw approval of NDA 18-662,...

  7. 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.

  8. 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.

  9. 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.

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

    SciTech Connect

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

    2015-11-10

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

  11. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA.

    PubMed

    Alquezar-Planas, David E; Fordyce, Sarah L

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred to as "ancient DNA," using the Roche GS FLX 454 platform.

  12. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA.

    PubMed

    Alquezar-Planas, David E; Fordyce, Sarah L

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred to as "ancient DNA," using the Roche GS FLX 454 platform. PMID:22665278

  13. Roche lobe effects on expanded upper atmospheres of short-periodic giant exoplanets

    NASA Astrophysics Data System (ADS)

    Jaritz, G. F.; Endler, S.; Langmayr, D.; Lammer, H.; Grießmeier, J.-M.; Erkaev, N. V.; Biernat, H. K.

    2005-08-01

    Theoretical studies and recent observational evidence of the expansion of the atmospheres of short-periodic exoplanets show that the atmospheres extend up to several planetary radii. This indicates that the atmospheres experience blow-off conditions. Because of the short orbital distance to their host stars, the expansion of the upper atmosphere is no longer radially symmetric, but depends on the direction to the central body, resulting in a deformation of the expanded atmosphere. We show the connection between atmospheric expansion, tidal forces and effects of the Roche potential and find that HD 209458 b, OGLE-TR-10 b and OGLE-TR-111 b are most likely in a state of classical hydrodynamical blow-off, because the distance where blow-off can occur is less than the distance to the Lagrangian point L1. On the other hand, OGLE-TR-56 b, OGLE-TR-113 b, OGLE-TR-132 b and TreS-1 experience a geometrical blow-off defined by the Roche lobe as proposed by Lecavelier des Etangs et al. (2004, A&A, 418, L1). Our results have important implications for the evolution of short periodic gas giants, because the Roche lobe overflow of the atmosphere can lead to lower mass loss rates over the exoplanets history, compared to gas giants which experience hydrodynamic expansion and loss unaffected by this boundary. Thus, massive exoplanets like OGLE-TR-56 b in very close orbital distances are subject to geometrical blow-off conditions, this results in a total mass loss for this particular exoplanet of the order of about 3 × 10-2 M_pl over the planets age, even if current mass loss rates of about 2 × 1011 g s-1 are calculated. If the exoplanet effected by the geometrical blow-off is more massive, the mass loss rate is even lower. However, giant exoplanets like HD 209458 b, OGLE-TR-10 b and OGLE-TR-111 b at orbital distances of about 0.05 AU may experience classical hydrodynamic blow-off conditions, which can result in higher mass loss rates. Thus, such planets may shrink to their core

  14. Generalized Roche potential for misaligned binary systems - Properties of the critical lobe

    NASA Technical Reports Server (NTRS)

    Avni, Y.; Schiller, N.

    1982-01-01

    The paper considers the Roche potential for binary systems where the stellar rotation axis is not aligned with the orbital revolution axis. It is shown that, as the degree of misalignment varies, internal Lagrangian points and external Lagrangian points may switch their roles. A systematic method to identify the internal Lagrangian point and to calculate the volume of the critical lobe is developed, and numerical results for a wide range of parameters of binary systems with circular orbits are presented. For binary systems with large enough misalignment, discrete changes occur in the topological structure of the equipotential surfaces as the orbital phase varies. The volume of the critical lobe has minima, as a function of orbital phase, at the two instances when the secondary crosses the equatorial plane of the primary. In semidetached systems, mass transfer may be confined to the vicinity of these two instances.

  15. ROCK: the Roche medicinal chemistry knowledge application - design, use and impact.

    PubMed

    Mayweg, Alexander; Hofer, Urs; Schnider, Patrick; Agnetti, Fausto; Galley, Guido; Mattei, Patrizio; Lucas, Matthew; Boehm, Hans-Joachim

    2011-08-01

    Medicinal chemistry is a complex science that lies at the interface of many fields of research and at the very heart of drug discovery, with property relationships based on chemical structure at its core. It is clear that the effective capture and dissemination of medicinal chemistry knowledge and experience will be a key differentiator among pharmaceutical organizations and crucial for the future success in delivering effective and safe drug candidates. Therefore, in 2005 we developed ROCK (Roche medicinal chemistry knowledge), an internal user-friendly and peer-reviewed Wiki-like application to capture, browse and search tacit knowledge, key discoveries and property effects related to chemical structure, which is used as a primary source for addressing challenges faced in drug design.

  16. [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.

  17. Quantitative automated human chorionic gonadotropin measurement in urine using the Modular Analytics E170 module (Roche).

    PubMed

    Ajubi, Nasser E; Nijholt, Nine; Wolthuis, Albert

    2005-01-01

    Ongoing demands on laboratory performance require optimization of processes. An obvious way to achieve this is to reduce manual labor in favor of automated methods. We describe the validation of an automated quantitative urine human chorionic gonadotropin (hCG) analysis on the Roche Modular E170 analyzer to replace the manual qualitative pregnancy test in urine. At urine hCG concentrations of 476, 45 and 11 U/L, we found inter-assay variation of 4.3%, 4.3% and 6.8% and average intra-assay variation of 3.0%, 2.6% and 3.0%, respectively. The analytical detection limit was 0.7 U/L. We did not detect any loss (due to degradation or adsorption) during a storage period of 5 days at 4 degrees C or at -20 degrees C. Recoveries of hCG in urine of a pregnant woman diluted with urine of a pre-menopausal non-pregnant woman (concentration range between 6 and 800 mU/L) were between 93% and 112% (y=0.997x-3.843, r 2 =0.999). Diluting a serum sample (hCG 42,000 U/L) with urine (negative for hCG) up to 8000-fold yielded a completely linear hCG response, indicating that the assay was not affected by the urine matrix. In a correlation study with 60 urine samples (of which 10 were of male origin), we did not find any discrepancies between results for the manual pregnancy test and the hCG test on the Roche Modular E170 (using a cutoff value of 50 U/L).

  18. Robe's restricted problem of 2+2 bodies when the bigger primary is a Roche ellipsoid

    NASA Astrophysics Data System (ADS)

    Kaur, Bhavneet; Aggarwal, Rajiv

    2013-08-01

    In the problem of 2 + 2 bodies in Robe's setup, one of the primaries of mass m1 is a Roche ellipsoid filled with a homogeneous incompressible fluid of density ρ1. The smaller primary of mass m2 is a point mass outside the ellipsoid. The third and the fourth bodies (of mass m3 and m4, respectively), supposed moving inside the ellipsoid, are small solid spheres of density ρ3 and ρ4, respectively, with the assumption that the mass and the radius of the third and the fourth bodies are infinitesimal. We assume that m2 is describing a circle around m1. The masses m3 and m4 mutually attract each other, do not influence the motions of m1 and m2 but are influenced by them. Robe's restricted three body problem is extended to 2 + 2 body problem under the assumption that the fluid body assumes the shape of the Roche ellipsoid (Chandrashekhar [2]). We take 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 m2, and (iii) that arising from the centrifugal force. In this paper, equilibrium solutions of m3 and m4 and their linear stability are analysed. We have proved that there exist only six equilibrium solutions of the system. In a system where the primaries are considered as earth-moon and m3 ,m4 as submarines, the equilibrium solutions thus obtained are unstable.

  19. Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

    PubMed Central

    Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos; Read, Timothy; Konstantinidis, Konstantinos T.

    2012-01-01

    Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ∼90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R2>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ∼1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ∼3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies. PMID:22347999

  20. 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…

  1. 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

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

    2016-02-01

    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.

  2. 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

  3. 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.

  4. 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.

  5. Evaluation of the Roche CoaguChek XS handheld coagulation analyzer in a cardiac outpatient clinic.

    PubMed

    Nam, Myung-Hyun; Roh, Kyoung Ho; Pak, Hui-Nam; Lee, Chang Kyu; Kim, Young-Hoon; Lee, Kap No; Cho, Yunjung

    2008-01-01

    This study evaluated the performance of a handheld coagulation analyzer for measurements of capillary blood specimens of 93 outpatient cardiology patients with atrial fibrillation who were receiving oral anti-coagulant therapy. The international normalized ratio (INR) results of the CoaguChek XS system (Roche Diagnostics) were compared with those obtained in the central laboratory with citrated venous blood specimens using the ACL9000 coagulation analyzer (Instrumentation Laboratory). The INR results for prothrombin time by the CoaguChek XS analyzer were closely correlated with the central laboratory's results in the INR range of 0.96 approximately 8.53 (r = 0.964). A statistically significant difference was noted between 2 lots of test strips, but the difference was miniscule (mean +/- 95% confidence interval: 0.04+/-0.02). The CV of 8 replicate assays with the CoaguChek XS for a blood specimen with high INR value (INR=3.9) was 1.4%; for a blood specimen with medium INR value (INR=1.3), the CV of 8 replicate assays was <0.1%. This study shows that the CoaguChek XS analyzer is precise and reliable for assessment of INR results at clinically significant ranges in cardiac outpatients.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  10. 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.

  11. Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform.

    PubMed

    Chen, Rui; Im, Hogune; Snyder, Michael

    2015-07-01

    Multiple platforms are available for whole-exome enrichment and sequencing (WES). This protocol is based on the Roche NimbleGen SeqCap EZ Exome Library SR platform, which enriches for ∼44 Mb of the human exonic regions. The SeqCap system uses 55- to 105-base DNA probes to capture known coding DNA sequences (CDS) from the NCBI Consensus CDS Database, RefSeq, and Sanger miRBase. The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer.

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

    PubMed

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

    2015-01-01

    The measurement of free immunoglobulin light chains is typically performed on serum; however, the use of alternative specimen types has potential benefits. Using the Freelite™ kappa and lambda free light chains assay on a Roche Diagnostics cobas 8000 c502 analyzer, we compared three specimen types (serum, EDTA-plasma and lithium heparin plasma separator gel-plasma) on 100 patients. Using Deming regression and eliminating outliers (limiting data to light chain concentrations below 400 mg/L), the three specimen types showed comparable results for kappa light chain concentration, lambda light chain concentration, and kappa/lambda ratio with slopes close to 1.0 and y-intercepts close to zero. EDTA-plasma showed slightly more positive bias relative to serum than lithium heparin. Analysis using EDTA-plasma and lithium heparin plasma showed comparable linearity, precision, and temperature stability. A single sample showing hook effect (not in the comparison set) gave comparable results using either plasma specimen type. For the Freelite™ kappa and lambda free light chains assay, both EDTA-plasma or lithium heparin-plasma can serve as acceptable substitutes for serum, at least for the Roche cobas 8000 analyzer. PMID:26682113

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

    PubMed

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

    2015-09-01

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

  14. 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.

  15. 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.

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

    PubMed

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

    2001-04-01

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

  17. 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

  18. 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

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

    PubMed

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

    2014-01-01

    Analytical and stability performances of ten media were compared to PreservCyt medium using the Cobas 4800 HPV test: Easyfix (Labonord SAS, France), Qualicyt (Qualicyt, France), NovaPrep HQ+ (NovaCyt, France), CMDH (SARL Alphapath France), Cyt-All (Cytomega, France), Digene Cervical Sampler (Qiagen, USA), Aptima (Gen-Probe, USA), Multi-Collect (Abbott, Allemagne), M4RT Micro Test (Remel, USA), et PCR-Media (Roche, Suisse). Most of media show a good correlation for all the performance characteristics studied. Cyt-All and NovaPrep HQ+ media are perfectly concordant with PreservCyt all parameters and genotypes considered. CMDH and M4RT have a reduced stability at +25°C (3 and 2 days respectively) and would not be conformed to current shipping practices. Most of media tested show analytical and stability performances equivalent with the reference medium. The prospects of such study are interesting because in the near future, providers would make available media adapted to the problem of cervical smear but also to the conservation, transport of virus or bacteria for performing simultaneous searches of HPV, Chlamydia trachomatis or Neisseria gonorrhea. PMID:24736142

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

    PubMed

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

    2012-05-25

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

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

    PubMed

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

    2012-05-25

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

  2. 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.

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Alton, K. B.; Stępień, K.

    2016-09-01

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

  5. 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.

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

    PubMed

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

    2012-06-01

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

  7. 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

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

    PubMed

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

    2014-08-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2004-09-01

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

  11. 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)

  12. Comparison of the Abbott Architect i2000 assay, the Roche Modular Analytics E170 assay, and an immunoradiometric assay for serum hepatitis B virus markers.

    PubMed

    Kim, Hyunjung; Oh, Eun-Jee; Kang, Mi-Sook; Kim, Sung Hoon; Park, Yeon-Joon

    2007-01-01

    Serum hepatitis B virus (HBV) markers are the most important data for epidemiological screening and clinical diagnosis of HBV infection, especially in endemic areas. We compared the results of the Roche Modular Analytics E170 assay, the Abbott Architect i2000 assay, and an immunoradiometric assay (IRMA) for HBV surface antigen (HBsAg), anti-HBV surface antigen (anti-HBs), HBV e antigen (HBeAg), and anti-HBV e antigen (anti-HBe). A number of serum samples (264, 263, 224, and 202 for HBsAg, anti-HBs, HBeAg, and anti-HBe, respectively) were studied. For samples giving discrepant results for HBeAg between methods, real-time PCR assays were performed. The concordance rates among the three methods were high for HBsAg (100%) and HBeAg (94.6), but low for anti-HBs (91.6%) and anti-HBe (82.2%). For anti-HBs, which could be measured quantitatively by the Modular E170 and Architect i2000 procedures, discrepant results were observed at low levels of anti-HBs. For anti-HBe, the positive rate was highest with Modular E170 (60.9%) followed by the IRMA kit (54.1%) and Architect i2000 (51.0%). This study shows substantial differences between the assay results by the three methods, which should be taken into account in determinations of serum HBV markers.

  13. Influence of the radiation pressure on the planetary exospheres : analytical modeling of density profiles and escape flux, implication for the Three Body problem and the Roche lobe location

    NASA Astrophysics Data System (ADS)

    Beth, A.; Garnier, P.; Toublanc, D.; Dandouras, I.; Mazelle, C.

    2014-04-01

    The uppermost layer of the atmosphere, the exosphere, is not well-known in its global structure since the densities are very low compared to instrument detection capabilities. Because of rare collisions and high Knudsen numbers, the motion of light species (H, H2, ...) in the corona is essentially determined by the external forces : the gravitation from the planet, the radiation pressure, as well the stellar gravity. In this work, we calculate rigorously and analytically, based on the Hamiltonian mechanics and Liouville theorem, the impact of the radiation pressure and gravitation from the planet on the structure of the exosphere. This approach was partially used by [1] but only in the 2D case : we extend it to the 3D case. Assuming a collisionless exosphere and a constant radiation pressure near the planet, we determine the density profiles for ballistic particles (the main contribution for densities in the lower exosphere) for light species as a function of the angle with respect to the Sun direction. We also obtain an analytical formula for the escape flux at the subsolar point, which can be compared with the Jeans' escape flux. Finally, we study the effect of the radiation pressure on the zero velocity curves, position of the Roche lobe and Hill's region for the well-known Three-Body problem especially for Hot Jupiters and discuss about the validity of our model. The goal is to bring some constraints on modelling of exoplanet atmospheres.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2005-07-01

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

  16. Evaluation of the Roche LightCycler: a simple and rapid method for direct detection of factor V Leiden and prothrombin G20210A genotypes from blood samples without the need for DNA extraction.

    PubMed

    Cooper, Peter C; Cooper, Susan M; Smith, Julie M; Kitchen, Steven; Makris, Michael

    2003-07-01

    The Roche LightCycler is a micro-volume thermocycler that combines extremely rapid polymerase chain reaction with fluorescence resonance energy transfer analysis of amplified products. We have evaluated the use of minimally processed blood samples for detection of two point mutations known to increase the risk of venous thromboembolism. Results from the LightCycler using the supernatant of diluted heated blood were compared with those gained by traditional methods based on polymerase chain reaction and restriction enzyme digestion. For factor V Leiden mutation, there was complete agreement between both methods in detection of wild-type (n = 82), heterozygous (n = 100) and homozygous (n = 18) genotypes. Similarly, the prothrombin G20210A mutation showed complete agreement for wild-type (n = 135), heterozygous (n = 63) and homozygous (n = 2) subjects.

  17. [Comparison between the centrifugation on MPA C10 (Roche Diagnostics) and the centrifugation according recommendations of GEHT (Groupe d'étude de l'hémostase et de la thrombose) for the daily hemostasis assays].

    PubMed

    Flamant, Fabrice; Borg, Jeanne-Yvonne; Lenormand, Bernard; Le Cam-Duchez, Véronique

    2014-01-01

    Actually, many laboratories tend to acquire pre analytic automates to prepare specimens for analysis. For haemostasis, these pre analytical modules are not always in agreement with the recommendations from the Groupe d'étude de l'hémostase et de la thrombose (GEHT). For example in the MPA C10 module (Roche Diagnostics) the speed of centrifugation was not rather fast compared with the GEHT recommandations. Then, to be able to use this automate for routine coagulation assays, we compared results of Quick time, activated partial prothombin time, fibrinogen, factor II, factor V, factor VII, factor X and antithrombin levels and unfractioned heparin anti-Xa activity measurement after MPA (1,885 g - 999 sec) or GEHT (2,500 g - 900 sec) protocol of centrifugation. First, we verified platelet counts: in 82% of specimens, the platelet counts were under 10.10(9)/L after centrifugation on MPA module. Moreover, a good correlation was observed in all comparisons. Then we concluded the MPA C10 module was usable for routine coagulation tests.

  18. 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

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

    PubMed

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

    2012-07-01

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

  20. 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…

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

    PubMed

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

    2004-02-01

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

  2. 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

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

    PubMed

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

    2011-01-01

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

  4. Evaluation of six commercial nucleic acid amplification tests for detection of Neisseria gonorrhoeae and other Neisseria species.

    PubMed

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

    2011-10-01

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

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

    PubMed

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

    2006-04-01

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

  6. Clinical Performance of Roche Cobas 4800 HPV Test

    PubMed Central

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

    2014-01-01

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

  7. Detection and identification of mycobacteria by amplification of RNA and DNA in pretreated blood and bone marrow aspirates by a simple lysis method.

    PubMed Central

    Gamboa, F; Manterola, J M; Lonca, J; Matas, L; Viñado, B; Giménez, M; Cardona, P J; Padilla, E; Ausina, V

    1997-01-01

    A sodium dodecyl (lauryl) sulfate method was evaluated for the preparation of blood specimens and bone marrow aspirates for use in two amplification procedures (Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test [AMTDT] and Roche Amplicor M. avium/M. intracellulare [MAI] Test) for the detection and identification of Mycobacterium tuberculosis and M. avium and M. intracellulare, respectively. The AMTDT is based on amplification of rRNA, whereas the Amplicor MAI Test amplifies a specific DNA region of the 16S rRNA gene. The results of amplification techniques were compared with those of standard culture and culture in BACTEC 13A and BACTEC 12B liquid media. A total of 121 blood specimens and 15 bone marrow aspirates were collected from 136 AIDS patients. Mycobacterial growth was recovered for 103 specimens; 35 yielded M. tuberculosis, 62 yielded M. avium, 5 yielded M. genavense, and 1 yielded M. kansasii. The values of sensitivity and specificity in pretreated specimens for detection of M. tuberculosis by the AMTDT were 94.3 and 100%, respectively, and those for detection of M. avium by the Amplicor MAI Test were 91.9 and 100%, respectively. The simple lysis method described in the present work allows the recovery of mycobacteria from blood specimens and bone marrow aspirates and may be used in combination with the AMTDT and the Amplicor MAI Test to detect and identify different members of the genus Mycobacterium. This method might also be applicable for the identification of mycobacteria from blood culture fluids with acridinium-ester-labeled DNA probes. PMID:9230395

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

    PubMed

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

    2007-08-01

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

  9. Can the Swedish new variant of Chlamydia trachomatis (nvCT) be detected by UK NEQAS participants from seventeen European countries and five additional countries/regions in 2009?

    PubMed

    Unemo, M; Rossouw, A; James, V; Jenkins, C

    2009-05-14

    In 2006, a new variant of Chlamydia trachomatis (nvCT) was reported in Sweden. The nvCT contains a deletion that includes the targets for the C. trachomatis genetic diagnostic single-target systems from Roche Diagnostics and Abbott Laboratories. Roche and Abbott have now developed certified dual-target assays that can detect the nvCT. This study examined the nucleic acid amplification tests (NAATs) currently used (in 2009) for C. trachomatis detection in laboratories from 17 European countries and five countries/regions outside Europe that are participating in the United Kingdom (UK) National External Quality Assessment Service (NEQAS). It further examined changes in these laboratories' testing strategy during the period from 2006 to 2009, and their performance regarding nvCT detection. A UK NEQAS blinded nvCT specimen was distributed to all 283 participating laboratories, which were asked to analyse the specimen according to their routine C. trachomatis diagnostic protocols for endocervical swabs. BD ProbeTec was the most commonly used NAAT, followed by Cobas Amplicor, Cobas TaqMan, and Aptima. From 2006 to 2009, the use of Cobas Amplicor, which does not detect the nvCT, decreased, but it was still used by 22% (n=57) of responding participants in 59% of the countries, 54 of these 57 used it as first assay. Virtually all of the other participants detected the nvCT correctly. Laboratories using commercial or in house NAATs that do not detect the nvCT are encouraged to carefully monitor their C. trachomatis incidence, participate in effective internal and external quality assurance and controls schemes, and to consider changing their testing system. PMID:19442398

  10. 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…

  11. 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.

  12. "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

  13. The Swedish new variant of Chlamydia trachomatis (nvCT) remains undetected by many European laboratories as revealed in the recent PCR/NAT ring trial organised by INSTAND e.V., Germany.

    PubMed

    Reischl, U; Straube, E; Unemo, M

    2009-01-01

    The May 2009 round of INSTAND's ring trial "Chlamydia trachomatis detection PCR/NAT" included a sample with high amount of the Swedish new variant of C. trachomatis (nvCT). A spectrum of at least 12 different commercial diagnostic nucleic acid amplification tests (NAATs) and many different in house NAATs were applied by the 128 participating laboratories which reported 152 results. Approximately 80% of the results correctly reported the presence of C. trachomatis in the nvCT specimen. The nvCT sample was mainly missed, as expected, by participants using the Roche COBAS Amplicor CT/NG (15.5% of reported results) but also by several participants using in house NAATs. The trend towards using nvCT-detecting NAATs is obvious and in addition to the new dual-target NAATs from Roche and Abbott, and BD ProbeTec ET, also a number of new CE mark-certified commercial tests from smaller diagnostic companies as well as many different in house NAATs were used. Laboratories using commercial or in house NAATs that do not detect the nvCT are encouraged to carefully monitor their C. trachomatis incidence, participate in appropriate external quality assurance and controls schemes, and consider altering their testing system. The reliable detection of low amounts of the wildtype C. trachomatis strain in other samples of the ring trial set indicates a good diagnostic performance of all applied commercial NAATs while also detecting the nvCT strain. PMID:19679035

  14. 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

  15. 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

  16. Human islet isolation for autologous transplantation: comparison of yield and function using SERVA/Nordmark versus Roche enzymes.

    PubMed

    Anazawa, T; Balamurugan, A N; Bellin, M; Zhang, H J; Matsumoto, S; Yonekawa, Y; Tanaka, T; Loganathan, G; Papas, K K; Beilman, G J; Hering, B J; Sutherland, D E R

    2009-10-01

    Islet autotransplantation (IAT) is used to preserve as much insulin-secretory capacity as possible in patients undergoing total pancreatectomy for painful chronic pancreatitis. The enzyme used to dissociate the pancreas is a critical determinant of islet yield, which is correlated with posttransplant function. Here, we present our experience with IAT procedures to compare islet product data using the new enzyme SERVA/Nordmark (SN group; n = 46) with the standard enzyme Liberase-HI (LH group; n = 40). Total islet yields (mean +/- standard deviation; 216,417 +/- 79,278 islet equivalent [IEQ] in the LH group; 227,958 +/- 58,544 IEQ in the SN group; p = 0.67) were similar. However, the percentage of embedded islets is higher in the SN group compared to the LH group. Significant differences were found in pancreas digestion time, dilution time, and digested pancreas weight between the two groups. Multivariate linear regression analysis showed the two groups differed in portal venous pressure changes. The incidence of graft function and insulin independence was not different between the two groups. The SN and LH enzymes are associated with similar outcomes for IAT. Further optimization of the collagenase/neutral protease ratio is necessary to reduce the number of embedded islets obtained when using the SN enzyme.

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

    PubMed

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

    2014-07-01

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

  18. Challenges of antiretroviral treatment in transient and drug-using populations: the SUN study.

    PubMed

    Sension, M G; Farthing, C; Shaffer, A G; Graham, E; Siemon-Hryczyk, P; Pilson, R S

    2001-03-01

    This is an open-label, single-arm, phase 3b study (part of phase 3 development) to evaluate the efficacy and safety of Fortovase-soft gelatin formulation (saquinavir-SGC), combined with zidovudine (ZDV) and lamivudine (3TC), human immune deficiency virus type 1 in (HIV-1)-positive, antiretroviral-naive individuals. Forty-two HIV-1-positive adults with plasma HIV RNA >10,000 copies per milliliter (Roche Amplicor HIV Monitor assay) and CD4 cell count >100 cells/mm(3) were treated with SQV-SGC, 1200 mg three times per day; ZDV, 300 mg; and 3TC, 150 mg each twice per day for 48 weeks. High proportions were drug users (26%), demonstrated psychiatric disorders (alcohol abuse [14%]/depression [14%]), or were inadequately housed (5%). At 48 weeks, 50% of patients achieved viral suppression <400 copies per milliliter with 43% <20 copies per milliliter using an intent-to-treat analysis (missing values counted as virological failures). Corresponding proportions for patients remaining on therapy at 48 weeks were 91% <400 copies per milliliter and 78% <20 copies per milliliter. Most adverse events were mild. Saquinavir-SGC combined with ZDV and 3TC, achieved potent and durable HIV RNA suppression and was well tolerated over 48 weeks in an antiretroviral-naive population including high proportions of individuals considered difficult to treat, such as drug users, people with psychiatric problems and homeless individuals. PMID:11313025

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

    PubMed

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

    2014-07-01

    The ability to evaluate individual HIV-1 virions from the quasispecies of vertically infected infants was evaluated in a field setting at the Centre for Infectious Disease Research in Zambia. Infant heel-prick blood specimens were spotted onto dried blood spot (DBS) filter paper cards at government health clinics. Nucleic acid was extracted and used as a template for HIV-1 proviral DNA detection by a commercial Amplicor HIV-1 PCR test (Roche, version 1.5). On samples that tested positive by commercial diagnostic assay, amplification of DNA was performed using an in-house assay of the 5' and 3' region of the HIV-1 genome. Additionally, fragments covering 1200 nucleotides within pol (full length protease and partial reverse transcriptase) and 1400 nucleotides within env (variable 1-variable 5 region) were further analyzed by single genome amplification (SGA). In summary, we have demonstrated an in-house assay for amplifying the 5' and 3' proviral HIV-1 DNA as well as pol and env proviral DNA fragments from DBS cards collected and analyzed entirely in Zambia. In conclusion, this study shows the feasibility of utilizing DBS cards to amplify the whole proviral HIV-1 genome as well as perform SGA on key HIV-1 genes. PMID:24667303

  20. 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

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

    PubMed

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

    1996-12-01

    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.

  2. 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

  3. Diagnosis of Neisseria gonorrhoeae using molecular beacon.

    PubMed

    Sachdev, Divya; 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.

  4. A novel RealTime HIV-1 Qualitative assay for the detection of HIV-1 nucleic acids in dried blood spots and plasma.

    PubMed

    Huang, Shihai; Erickson, Brian; Mak, Wai Bing; Salituro, John; Abravaya, Klara

    2011-12-01

    Abbott RealTime HIV-1 Qualitative is an in vitro real-time PCR assay for detecting HIV-1 nucleic acids in human plasma and dried blood spots (DBS). The assay was designed to be used in diagnosis of HIV-1 infections in pediatric and adult patients, with an emphasis on the applicability in resource-limited settings. Use of DBS facilitates specimen collection from remote areas and transportation to testing laboratories. Small sample input requirement facilitates testing of specimens with limited collection volume. The Abbott RealTime HIV-1 Qualitative assay is capable of detecting HIV-1 group M subtypes A-H, group O and group N samples. HIV-1 virus concentrations detected with 95% probability were 80 copies/mL of plasma using the plasma protocol, and 2469 copies/mL of whole blood using the DBS protocol. The assay detected HIV-1 infection in 13 seroconversion panels an average 10.5 days earlier than an HIV-1 antibody test and 4.9 days earlier than a p24 antigen test. For specimens collected from 6 weeks to 18 months old infants born to HIV-1 positive mothers, assay results using both the DBS and plasma protocols agreed well with the Roche Amplicor HIV-1 DNA Test version 1.5 (95.5% agreement for DBS and 97.8% agreement for plasma).

  5. 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.

  6. TaqMan-Based Detection of Trichomonas vaginalis DNA from Female Genital Specimens

    PubMed Central

    Jordan, Jeanne A.; Lowery, Donna; Trucco, Massimo

    2001-01-01

    A double-labeled fluorescent probe was designed and evaluated for detecting Trichomonas vaginalis DNA in a 5′ nuclease (TaqMan) assay. The T. vaginalis-specific probe contains a 5′-fluorescein (5′-FAM) and a 3′-rhodamine (TAMRA) derivative. Female genital secretions were collected on Amplicor (Roche Molecular, Indianapolis, Ind.) swabs and by a transport system used for Chlamydia trachomatis and/or Neisseria gonorrhoeae DNA detection by PCR. Five hundred fifty-two female genital specimens, of which 248 (45%) were vaginal specimens and 304 (55%) were introital, were tested for both T. vaginalis DNA and viable microorganisms using the 5′ nuclease assay and broth culture, respectively. Of these, 304 of 552 (55%) were also evaluated by direct microscopic examination for the characteristic motile organism. After resolving discrepancies, the comparisons produced an analytical sensitivity and specificity for the TaqMan-based PCR assay of 97.8 and 97.4%, respectively. As a result, ΔRQ values (differences in fluorescence due to probe hybridization and resulting 5′-FAM cleavage from the specific PCR product) of ≥2.0 and ≤1.5 were established for T. vaginalis-positive and -negative cutoffs, respectively. ΔRQ values between 1.5 and 2.0 were considered indeterminate. Overall findings revealed a high level of agreement between PCR and culture for detecting T. vaginalis. Potential benefits of the 5′ nuclease assay include a greater sensitivity compared to direct microscopic examination and the ease of testing large numbers of clinical specimens in a significantly shorter turnaround time compared to culture. PMID:11682492

  7. Chlamydia trachomatis infection and sexual behaviour among female students attending higher education in the Republic of Ireland

    PubMed Central

    O'Connell, Emer; Brennan, Wendy; Cormican, Martin; Glacken, Marita; O'Donovan, Diarmuid; Vellinga, Akke; Cahill, Niall; Lysaght, Fionnguala; O'Donnell, Joan

    2009-01-01

    Background There are no prevalence data on Chlamydia trachomatis relating to female students attending higher education available for the Republic of Ireland. This information is required to guide on the necessity for Chlamydia screening programmes in higher education settings. This research aimed to determine the prevalence of and predictive risk factors for Chlamydia trachomatis genital infection among female higher education students in Ireland. Methods All females presenting during one-day periods at Student Health Units in three higher education institutions in two cities in the Republic of Ireland were invited to participate. Participants completed a questionnaire on lifestyle and socio-demographic factors and provided a urine sample. Samples were tested for C. trachomatis DNA by a PCR based technique (Cobas Amplicor, Roche). To examine possible associations between a positive test and demographic and lifestyle risk factors, a univariate analysis was performed. All associations with a p value < 0.05 were included in a multivariate logistic regression analysis. Results Of the 460 sexually active participants 22 tested positive (prevalence 4.8%; 95% CI 3.0 to 7.1%). Variables associated with significantly increased risk were current suggestive symptoms, two or more one-night stands and three or more lifetime sexual partners. The students displayed high-risk sexual behaviour. Conclusion The prevalence of C. trachomatis infection and the lack of awareness of the significance of suggestive symptoms among sexually experienced female students demonstrate the need for a programme to test asymptomatic or non-presenting higher education students. The risk factors identified by multivariate analysis may be useful in identifying those who are most likely to benefit from screening. Alcohol abuse, condom use, sexual behaviour (at home and abroad) and, knowledge of sexually transmitted infections (STIs) (including asymptomatic nature or relevant symptoms) were identified as

  8. 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

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

    NASA Astrophysics Data System (ADS)

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

    2005-07-01

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

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

    PubMed

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

    2012-01-01

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

  11. Émergence de la complexité dans un modèle simple de comportement mécanique des roches

    NASA Astrophysics Data System (ADS)

    Amitrano, David

    2004-04-01

    We propose a mechanical model for the behaviour of rocks based on progressive damage at the elementary scale and elastic interaction. It allows us to simulate several experimental observations: mechanical behaviour ranging from brittle to ductile, fractal structure of the damage, power-law distribution of the damage avalanches. These macroscopic properties are not incorporated at the elementary scale, but are the results of the interaction between elements. This emerging complexity permits us to consider the strain rock process as a complex system characterized by non-linear dynamics. To cite this article: D. Amitrano, C. R. Geoscience 336 (2004).

  12. 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

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

    ERIC Educational Resources Information Center

    Ingvarsson, Einar T.; Morris, Edward K.

    2004-01-01

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

  14. Comparative evaluation of Roche Aurora FLOW, Becton and Dickinson Viper system, and Dynex DS2 for detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis in various clinical specimens.

    PubMed

    Vahidnia, Ali; Costa, Sandra; Veenings, Sanne; Tuin, Hellen; van Loon, Linda; Bliekendaal, Harry

    2014-11-01

    The purpose of this study is to introduce a high-throughput system, Aurora FLOW, for the simultaneous detection of 3 clinically relevant pathogens of sexually transmitted infections. Comparative evaluation with other systems revealed an overall concordance of 97.9% for Chlamydia trachomatis and comparable performance for Neisseria gonorrhoeae and Trichomonas vaginalis.

  15. 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.

  16. 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

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

    PubMed Central

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

    1997-01-01

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

  18. Health care industries' perspective of viral load assays: the VERSANT HIV-1 RNA 3.0 assay.

    PubMed

    Elbeik, Tarek; Loftus, Richard A; Beringer, Scott

    2002-05-01

    This article will compare the VERSANT HIV-1 RNA 3.0 (bDNA 3.0) assay with other HIV-1 viral load assays, particularly the AMPLICOR HIV-1 MONITOR (Amplicor 1.5), the industry standard. The discussion will cover the history of viral load assay development and challenges to the field. It will finish with a description of the evolving markets for viral load assays in the developing world and the impact of variations in the different assays on their ability to reach those markets and patient populations.

  19. Usefulness of in-house PCR methods for hepatitis B virus DNA detection.

    PubMed

    Portilho, Moyra Machado; Baptista, Marcia Leite; da Silva, Messias; de Sousa, Paulo Sérgio Fonseca; Lewis-Ximenez, Lia Laura; Lampe, Elisabeth; Villar, Livia Melo

    2015-10-01

    The aim of the present study was to evaluate the performance of three in-house PCR techniques for HBV DNA detection and compare it with commercial quantitative methods to evaluate the usefulness of in-house methods for HBV diagnosis. Three panels of HBsAg reactive sera samples were evaluated: (i) 50 samples were examined using three methods for in-house qualitative PCR and the Cobas Amplicor HBV Monitor Assay; (ii) 87 samples were assayed using in-house semi-nested PCR and the Cobas TaqMan HBV test; (iii) 11 serial samples obtained from 2 HBV-infected individuals were assayed using the Cobas Amplicor HBV test and semi-nested PCR. In panel I, HBV DNA was detected in 44 samples using the Cobas Amplicor HBV test, 42 samples using semi-nested PCR (90% concordance with Cobas Amplicor), 22 samples using PCR for the core gene (63.6% concordance) and 29 samples using single-round PCR for the pre-S/S gene (75% concordance). In panel II, HBV DNA was quantified in 78 of the 87 HBsAg reactive samples using Cobas TaqMan but 52 samples using semi-nested PCR (67.8% concordance). HBV DNA was detected in serial samples until the 17th and 26th week after first donation using in-house semi-nested PCR and the Cobas Amplicor HBV test, respectively. In-house semi-nested PCR presented adequate concordance with commercial methods as an alternative method for HBV molecular diagnosis in low-resource settings.

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

    PubMed

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

    2006-01-01

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

  1. 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.

  2. Hepatitis B virus markers in anti-HBc only positive individuals.

    PubMed

    Weber, B; Melchior, W; Gehrke, R; Doerr, H W; Berger, A; Rabenau, H

    2001-07-01

    Isolated reactivity to hepatitis B virus (HBV) core antigen (anti-HBc) is observed relatively frequently in immunocompromised individuals, intravenous drug abusers (IVDA), and in the presence of HCV infection. The reason for the lack of HBsAg is not clear. The aim of the present study was to investigate which factors (genetic variability of S gene, low-level HBsAg, and immune complexes may be responsible for the failure of HBsAg detection with commercial HBsAg screening assays. Dilution series of two recombinant HBsAg escape mutants and dilutions of serum samples from chronic HBV carriers with multiple insertions in the a determinant and different HBsAg subtypes were tested with a highly sensitive assay that detects wild-type HBsAg (Elecsys HBsAg, Roche Diagnostics, Penzberg, Germany) and two assays that detect HBV wild-type and escape mutants (Murex HBsAg Version 3, Murex and Enzygnost HBsAg 5.0, Dade Behring, Marburg, Germany). Elecsys HBsAg showed in comparison to Murex HBsAg Version 3 and Enzygnost HBsAg 5.0 a reduced sensitivity for escape mutant detection. On the other hand, the best performance for HBsAg subtype detection was obtained with Elecsys HBsAg. In the second part of the study, a selected panel of isolated anti-HBc reactive (n = 104) serum samples (AxSYM Core) was submitted to testing by Elecsys HBsAg, Murex HBsAg Version 3, Enzygnost HBsAg 5.0, and HBsAg detection after immune complex dissociation (ICD) and anti-HBs determination with two different assays (AxSYM Ausab and Elecsys Anti-HBs). To assess the specificity of anti-HBc test results, all the samples were tested by a second anti-HBc assay (Elecsys Anti-HBc). Quantitative HBV DNA detection was undertaken with a commercially available HBV PCR assay (Amplicor HBV Monitor). HCV infection was present in 65.4% of anti-HBc only reactive individuals. Five AxSYM Core positive samples were negative by Elecsys Anti-HBc. Overall, 15 (14.4%) AxSYM Ausab negative samples gave positive results with Elecsys

  3. Comparison of Three Nucleic Acid Amplification Assays of Cerebrospinal Fluid for Diagnosis of Cytomegalovirus Encephalitis

    PubMed Central

    Bestetti, Arabella; Pierotti, Chiara; Terreni, Mariarosa; Zappa, Alessandra; Vago, Luca; Lazzarin, Adriano; Cinque, Paola

    2001-01-01

    The diagnostic reliabilities of three cytomegalovirus (CMV) nucleic acid amplification assays of cerebrospinal fluid (CSF) were compared by using CSF samples from human immunodeficiency virus-infected patients with a postmortem histopathological diagnosis of CMV encephalitis (n = 15) or other central nervous system conditions (n = 16). By using a nested PCR assay, the quantitative COBAS AMPLICOR CMV MONITOR PCR, and the NucliSens CMV pp67 nucleic acid sequence-based amplification assay, sensitivities were 93.3, 86.6, and 93.3%, respectively, and specificities were 93.7, 93.7, and 87.5%, respectively. The COBAS AMPLICOR assay revealed significantly higher CMV DNA levels in patients with diffuse ventriculoencephalitis than in patients with focal periventricular lesions. PMID:11230445

  4. Is real-time PCR better than conventional PCR for Mycobacterium tuberculosis complex detection in clinical samples?

    PubMed

    Tortoli, Enrico; Urbano, Pasquale; Marcelli, Fiorella; Simonetti, Tullia M; Cirillo, Daniela M

    2012-08-01

    Cobas Amplicor MTB and later Cobas TaqMan MTB were used to test a very large series of consecutive specimens received for tuberculosis diagnosis. Performance parameters were estimated and compared overall and for separate specimen categories. Both systems showed excellent specificity, and that of TaqMan was the higher. The sensitivities were similar but satisfactory only with respiratory specimens and smear-positive samples.

  5. 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

  6. 77 FR 2071 - Medical Devices; Availability of Safety and Effectiveness Summaries for Premarket Approval...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-13

    ... date P100031, FDA-2011-M-0502...... Roche Diagnostics ELECSYS ANTI-HBC IMMUNOASSAY & June 22, 2011. Corp.. ELECSYS PRECICONTROL ANTI-HBC. P100032, FDA-2011-M-0503...... Roche Diagnostics ELECSYS ANTI-HBC IMMUNOASSAY, June 27, 2011. Corp.. ELECSYS PRECICONTROL ANTI-HBC FOR USE ON THE ELECSYS 2010...

  7. 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…

  8. 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…

  9. 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...

  10. The almost contact system RU Eridani

    NASA Astrophysics Data System (ADS)

    Russo, G.

    1982-01-01

    The Wilson and Devinney (1971) method is used to analyze the V and B light curves of the eclipsing binary RU Eridani, in order to obtain a Roche model solution rather than the Russell and Merrill (1952) model used by Sarma and Sanwal (1981). It is found that the system consists of an evolved K1 secondary component which fills its Roche lobe, and an F0 V primary which seems nearly able to fill its own Roche lobe. An estimate of the absolute elements of RU Eri is made on the assumption of a primary component mass corresponding to its spectral type along the lines suggested by Allen (1973).

  11. 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

  12. 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...

  13. 77 FR 42713 - Notice of Intent to Grant an Exclusive License; PadJack, Inc.

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-20

    ... 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...

  14. 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.

  15. 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.

  16. 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... Methadone (9250) II Morphine (9300) II The company plans to import the listed controlled substances for...

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

    NASA Astrophysics Data System (ADS)

    Roman, R.; Szücs-Csillik, I.

    2014-08-01

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

  18. Comparative Study of Two Methods for RNA Extraction Prior to Detection of Resistance to Human Immunodeficiency Virus Type 1 with the Line Probe Assay

    PubMed Central

    Eiros, Jose María; Labayru, Cristina; Hernández, Beatriz; Ortiz de Lejarazu, Raúl; Rodríguez Torres, Antonio

    2002-01-01

    We evaluated two methods from Roche and Promega for RNA extraction prior to the genotypic detection of human immunodeficiency virus type 1 resistance by line probe assay (LiPA). Fifty plasma RNA extracts were processed in parallel by LiPA. Results obtained by the Roche method were superior in the proportion of amplified samples, the percentage of mutated samples, and band intensity. PMID:12037103

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

    NASA Astrophysics Data System (ADS)

    Hyodo, Ryuki; Ohtsuki, Keiji

    2014-11-01

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

  20. Comparison of DNA Amplification, mRNA Amplification, and DNA Hybridization Techniques for Detection of Cytomegalovirus in Bone Marrow Transplant Recipients

    PubMed Central

    Diaz-Mitoma, Francisco; Leger, Chantal; Miller, Helen; Giulivi, Antonio; Frost, Rita; Shaw, Laura; Huebsch, Lothar

    2003-01-01

    A total of 676 specimens from 63 recipients of bone marrow allografts were tested for cytomegalovirus (CMV) by the following assays: CMV pp67 NucliSens (NS), AMPLICOR CMV MONITOR (RA), and the Digene CMV DNA test (DG). In a consensus analysis, the sensitivities and specificities were 60 and 99% (NS), 96 and 98% (RA), and 90 and 76% (DG), respectively; for detection of symptomatic CMV infection, they were 60 and 97% (NS), 65 and 97% (RA), and 95 and 77% (DG), respectively. In multivariate analysis, the major risk factor for symptomatic CMV infection was an increase in the viral load in the DG assay; in univariate analyses, maximum viral loads in both DG and RA assays and a rising viral load in the RA assay were also significant. The earliest detection of CMV replication was provided by the RA assay (mean, 39 days posttransplantation), followed by the DG assay (mean, 48 days) and the NS assay (mean, 58 days). PMID:14605153

  1. Evaluating HPV‐negative CIN2+ in the ATHENA trial

    PubMed Central

    Cox, J. Thomas; Johnson, Kristin; Quint, Wim; Ridder, Ruediger; Sideri, Mario; Wright, Thomas C.; Behrens, Catherine M.

    2016-01-01

    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

  2. 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

  3. 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

  4. [Leo Sternbach, an inventor of benzodiazepines].

    PubMed

    Uchibayashi, Masao

    2007-01-01

    A biography of Leo Sternbach, an inventor of benzodiazepine tranquillizers, is presented. It consists of (1) a societal desire for lifestyle pills, (2) Leo's birth in 1908 and youth, (3) education, (4) in Vienna, (5) in Zurich, (6) at Hoffmann-La Roche, Basel, (7) to the New World, (8) at Roche, Nutley NJ, (9) invention of the new drugs, (10) revolution of people's lifestyle, and (11) reward, retirement and obituary in 2005. This paper may be the first comprehensive biography of this remarkable chemist written in Japanese.

  5. Planetary rings

    NASA Technical Reports Server (NTRS)

    Cook, A. F.

    1980-01-01

    Observations of the Rings of Saturn from the Pioneer spacecraft, discovery of the Ring of Jupiter, ground based polarimetry of the Rings of Saturn and some theoretical studies may be combined to markedly advance our understanding of the Rings of Jupiter, Saturn and Uranus. In particular, narrow rings can be self-gravitatingly stable inside Roche's limit and outside another closer limit. They can be created from a satellite which evolves across its Roche limit either by inward tidal drift or by growth of the planet by accretion. These considerations suggest that Neptune may well be surrounded by one or more narrow rings like those of Uranus.

  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. 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...

  8. Comparison of commercial kits for the detection of antibody to human immunodeficiency virus type 1 (HIV-1) in Nigeria.

    PubMed

    Chikwem, J O; Mohammed, I; Ola, T O

    1990-03-01

    Four commercial kits for the detection of antibodies to HIV-1 were compared with regard to their sensitivity, specificity and positive predictive value. The Wellcozyme competitive enzyme immunoassay was the least sensitive (62.5%), while Roche EIA, was the most sensitive (100%). All the commercial kits gave false negative results except the Roche EIA system. The Serodia particle agglutination test had the least positive predictive value of 26.9% while Roche EIA had the highest (88.9%). Our results show that commercial HIV-I antibody test kits are not equally sensitive in detecting positive sera. The practice of using Wellcozyme EIA alone for screening blood meant for transfusion should be discouraged because it does not detect all positive sera and might therefore increase the chances of transfusing HIV-I positive blood. The Roche EIA system appears to be the most reliable for screening blood. Test systems which detect HIV-2 should also be used for screening blood meant for transfusion.

  9. The determination of the parameters of the W Ser type-eclipsing binary system V367 Cyg.

    NASA Astrophysics Data System (ADS)

    Antokhina, Eh. A.; Menchenkova, E. V.

    Fresa's blue light curve of V367 Cyg was analyzed by the synthesis method in the Roche model and in the model with a geometrically thick disk. The new spectroscopic mass ratio q = M2/M1 = 1.57 was used. The basic parameters and the absolute dimensions of the system were obtained.

  10. Determination of the parameters of the eclipsing binary system V367 CYG by the light-curve synthesis method

    NASA Astrophysics Data System (ADS)

    Antokhina, E. A.; Menchenkova, E. V.

    1990-06-01

    Fresa's (1966) blue light curve of V367 Cyg is analyzed by the synthesis method in the framework of the Roche model and a model with a geometrically thick disk. The new spectroscopic mass ratio q = M2//M1 = 1.57 was used. The fundamental parameters and the absolute dimensions of the system were determined.

  11. 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.…

  12. 1st HPV Test for Use with Preservative Fluid

    MedlinePlus

    ... 159789.html 1st HPV Test for Use With Preservative Fluid Human papillomavirus responsible for 70 percent of ... Roberts Friday, July 8, 2016 FRIDAY, July 8, 2016 (HealthDay News) -- The U.S. Food and Drug Administration has approved Roche's cobas HPV ...

  13. N-body simulations of star clusters

    NASA Astrophysics Data System (ADS)

    Engle, Kimberly Anne

    1999-10-01

    We investigate the structure and evolution of underfilling (i.e. non-Roche-lobe-filling) King model globular star clusters using N-body simulations. We model clusters with various underfilling factors and mass distributions to determine their evolutionary tracks and lifetimes. These models include a self-consistent galactic tidal field, mass loss due to stellar evolution, ejection, and evaporation, and binary evolution. We find that a star cluster that initially does not fill its Roche lobe can live many times longer than one that does initially fill its Roche lobe. After a few relaxation times, the cluster expands to fill its Roche lobe. We also find that the choice of initial mass function significantly affects the lifetime of the cluster. These simulations were performed on the GRAPE-4 (GRAvity PipE) special-purpose hardware with the stellar dynamics package ``Starlab.'' The GRAPE-4 system is a massively-parallel computer designed to calculate the force (and its first time derivative) due to N particles. Starlab's integrator ``kira'' employs a 4th- order Hermite scheme with hierarchical (block) time steps to evolve the stellar system. We discuss, in some detail, the design of the GRAPE-4 system and the manner in which the Hermite integration scheme with block time steps is implemented in the hardware.

  14. 40 CFR 63.62 - Redefinition of glycol ethers listed as hazardous air pollutants.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., diethylene glycol, and triethylene glycol R-(OCH2CH2)n-OR′. Where: n = 1, 2, or 3; R = alkyl C7 or less; or R = phenyl or alkyl substituted phenyl; R′= H or alkyl C7 or less; or OR′ consisting of carboxylic acid...

  15. 40 CFR 63.62 - Redefinition of glycol ethers listed as hazardous air pollutants.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., diethylene glycol, and triethylene glycol R-(OCH2CH2)n-OR′. Where: n = 1, 2, or 3; R = alkyl C7 or less; or R = phenyl or alkyl substituted phenyl; R′= H or alkyl C7 or less; or OR′ consisting of carboxylic acid...

  16. 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

  17. 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...

  18. [Examples of the keeping of drugs during the XVIth, XVIIth and XVIIIth centuries: silenes and drawers].

    PubMed

    Fievet, B

    1998-01-01

    Silenes are wooden boxes with colourful paintings for the keeping of drugs and can be found nowadays in three collections in France: Hotel-Dieu in Troyes (Aube), a pharmacy in Bauge (Maine-et-Loire) and St-Roch museum in Issoudun (Indre). Drawers can be related to silenes but they are more ordinary and less attractive.

  19. Formal synthesis of (+)-discodermolide.

    PubMed

    Francavilla, Charles; Chen, Weichun; Kinder, Frederick R

    2003-04-17

    [structure: see text] Herein we report the formal total synthesis of (+)-discodermolide in 21 steps (longest linear sequence) from commercially available Roche ester. This synthesis features the assembly of C(9-18) and C(19-24) fragments via a metal-chelated aldol coupling reaction.

  20. 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.

  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. 75 FR 27318 - Notice of Intent To Grant an Exclusive License; FIXMO U.S. INC.

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... filed with the National Security Agency 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 6541, Fort George G. Meade, MD 20755-6541, telephone (443)...

  3. 78 FR 34140 - Qualification of Drivers; Exemption Applications; Vision

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-06

    ...) published in the Federal Register on January 17, 2008 (73 FR 3316). FOR FURTHER INFORMATION CONTACT: Elaine.... Brewer (WA) Andre G. Burns (TX) Brett L. Condon (MD) Christopher A. Deadman (MI) William K. Gullett (KY... E. Roche (VA) Luis H. Sanchez (WI) David E. Sanders (NC) David B. Speller (MN) Kenneth C. Steele...

  4. 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...

  5. 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 ...

  6. 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,…

  7. 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.

  8. 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…

  9. Spiral Learning: An Introductory Course on Reading LOTE Online

    ERIC Educational Resources Information Center

    Schuetze, Ulf

    2010-01-01

    In teaching reading, authentic texts with abundant lexical items and complex grammatical structures are typically used (Roche, 1992). Unfortunately, this has been a challenge for students enrolled in reading courses developed for English as a Second Language (ESL) as well as Languages Other Than English (LOTE) students. Students often translate…

  10. A Relational Frame Theory Account of Empathy

    ERIC Educational Resources Information Center

    Vilardaga, Roger

    2009-01-01

    The current paper proposes a Relational Frame Theory (RFT, Hayes, Barnes-Holmes, & Roche, 2001a) conceptualization of empathy and perspective taking that follows previous literature outlining a relationship between those phenomena and general functioning. Deictic framing, a relational operant investigated by RFT researchers, constitutes the…

  11. 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

  12. 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…

  13. 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.

  14. 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....

  15. Michael and Malott's dialog on linguistic productivity.

    PubMed

    Michael, Jack; Malott, Richard W

    2003-01-01

    This is an informal dialog between Jack Michael and Dick Malott inspired by Malott's commentary (In press) on Relational Frame Theory: A Post-Skinnerian Account of Human Language and Cognition (Hayes, Barnes-Holmes, Roche; 2001). Topics range from psychologist Skinner to linguist Hockett and from the Skinner box to verbal behavior (AKA language).

  16. 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.

  17. 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…

  18. 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}.

  19. High-Resolution N-Body Simulation of Lunar Accretion from an Impact-Generated Disk

    NASA Astrophysics Data System (ADS)

    Kokubo, E.; Ida, S.; Makino, J.

    1998-01-01

    We present the high-resolution N-body calculation of the lunar accretion from a circumterrestrial disk of debris generated by a giant impact on Earth. Our calculation is inspired by pioneering work, which was the first published N-body calculation of lunar accretion from an impact-generated disk. They modeled the disk by 1000 1500 particles, which were not enough to see the evolution of the spatial structure of the disk. By using the special-purpose computer for N-body problem HARP, we use 10,000 30,000 particles for the disk. The particle disk is modeled by the power-law surface density distribution and the power-law mass distribution. We use the 4th- order Hermite integrator for time integration. Mutual gravitational interactions among all particles are calculated by HARP. The normal and tangential components of the coefficient of restitution are 0.01-0.1 and 1, respectively. When two particles collide, we merge them if their rebound velocity is less than their surface escape velocity and the sum of their radii is smaller than 70% of their Hill radii, which corresponds to the fact that the two particles are outside their Roche limit. We also perform simulations without artificial accretion in which large bound particle aggregates are formed outside the Roche limit. The aggregates are often deformed or sometimes disrupted by Earth's tidal force. The results of our simulations suggest that the approximate treatment of accretion is generally valid. We follow the evolution of the disk for 1000 TK about 10 months, where TK is the Kepler period at the distance of the classical Roche limit. The typical outcome of the simulation is the formation of one large moon on a nearly circular orbit just outside the Roche limit. The result hardly depends on the initial condition of the disk as long as the disk is compact; in other words, most of the disk's mass exists inside the Roche limit. The evolution of f the dis is summarized as follows: (1) The disk shrinks through the

  20. Frequency and significance of antibodies against hepatitis B core (anti-HBc) antigen as the only serological marker for hepatitis B infection in Lebanese blood donors.

    PubMed Central

    Ramia, S.; Ramlawi, F.; Kanaan, M.; Klayme, S.; Naman, R.

    2005-01-01

    During a 2-year period, blood samples from 2505 Lebanese blood donors were chosen at random, at various periods of time at one blood donation centre (Hotel Dieu de France, Beirut, Lebanon) and were screened for markers of HBV infection (HBsAg, anti-HBc and anti-HBs). The study showed HBsAg positivity of 0.6% and an overall exposure rate to HBV of 10.0%. Out of the 2505 blood donors screened, 56 (22%) were found to be 'anti-HBc alone' positive which is almost four times the HBsAg positivity. The 56 'anti-HBc alone' samples were retested by another ELISA kit commercially available and 54 samples were 'anti-HBc alone' positive by both assays. The 54 samples had no serological markers as evidence of infection with human immunodeficiency virus (HIV) or hepatitis C virus (HCV). Only seven (13%) out of the 54 samples were HBV DNA positive by PCR and all were HBV genotype D. All seven HBV DNA-positive samples had HBV DNA levels below 400 copies/ml. Although any circulating HBV DNA among our 'anti-HBc alone' blood donors was below the detection limit of our Amplicor Monitor assay, some of these samples had circulating virus. A national study, where a larger number of blood donors from different blood donation centres across the country will perhaps determine whether screening for anti-HBc in addition to HBsAg detection is needed in Lebanese blood donors. PMID:16050516

  1. The impact of polymerase chain reaction assays for the detection of hepatitis C virus infection in a hemodialysis unit.

    PubMed

    Hussein, Magdi M; Mooij, Jaap M; Hegazy, Mohamed S; Bamaga, Mohammed S

    2007-03-01

    Hepatitis C virus (HCV) infection is most often diagnosed by detection of antibodies against the virus (HCV Ab). However, it has been reported that some HCV Ab negative patients test positive for HCV-RNA. Over a study period of 30 months, all patients on hemodialysis at the Al Hada Armed Forces Hospital in Taif, Saudi Arabia were tested monthly for HCV Ab and twice per year for HCV-RNA. HCV Ab was tested by a third generation microparticle enzyme immunoassay (MEIA), and HCV-RNA by a qualitative hepatitis-RNA assay, second version (COBAS Amplicor PCR), which was recently introduced in the Molecular Pathology Laboratory of our hospital. Of the 180 patients studied, 34 (18.9%) had positive HCV Ab, and of the 146 HCV Ab negative patients, five patients tested positive for HCV-RNA (3.42%). Our study further finds that, when applying HCV Ab testing only, some patients with HCV viremia may be undetected. For better HCV infection control, routine HCV-RNA testing of dialysis patients should be considered, particularly in areas where the infection is common and in units applying isolation policies.

  2. Real-time PCR assay using molecular beacon for quantitation of hepatitis B virus DNA.

    PubMed

    Sum, Simon Siu-Man; Wong, Danny Ka-Ho; Yuen, Man-Fung; Yuan, He-Jun; Yu, Jian; Lai, Ching-Lung; Ho, David; Zhang, Linqi

    2004-08-01

    Levels of hepatitis B virus (HBV) DNA in the blood serve as an important marker in monitoring the disease progression and treatment efficacy of chronic HBV infection. Several commercial assays are available for accurate measurement of HBV genomic DNA, but many of them are hampered by relatively low sensitivity and limited dynamic range. The aim of this study was to develop a sensitive and accurate assay for measuring HBV genomic DNA using real-time PCR with a molecular beacon (HBV beacon assay). The performance of this assay was validated by testing serial dilutions of the two EUROHEP HBV DNA standards (ad and ay subtypes) of known concentrations. The assay showed low intra-assay (<7%) and interassay (<5%) variations for both subtypes. Its dynamic range was found to be 10(1) to 10(7) copies per reaction (1.0 x 10(2) to 1.0 x 10(9) copies ml(-1)). The assay was further evaluated clinically using serum samples from 175 individuals with chronic hepatitis B. The HBV DNA level measured by this assay showed good correlation with that measured by the commercially available COBAS AMPLICOR HBV Monitor test (r = 0.901; P < 0.001). The higher sensitivity and broader dynamic range of this assay compared to the existing commercial assays will provide an ideal tool for monitoring disease progression and treatment efficacy in HBV-infected patients, in particular for those with low levels of HBV viremia.

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

    PubMed

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

    2006-02-01

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

  4. How the field of thyroid endocrinology developed in France after World War II.

    PubMed

    Fragu, Philippe

    2003-01-01

    This microhistory analyzes the transformation of French medical practice after World War II. Before the 1940s, coordinated clinical and experimental studies on a patient with thyroid disease were nonexistent. Starting in 1945, thyroid endocrinology was pushed forward by the use of radioiodine, which led pediatricians to rethink the hereditary transmission of thyroid diseases, stimulated by the school of biochemistry headed by Jean Roche, who participated in the elucidation of thyroid-hormone metabolism. Roche knew how to listen to hospital clinicians, who, in return, gave him free access to patients to conduct investigations on thyroid metabolism. Radioiodine proved to be sufficiently flexible to respond to the respective information needs of clinicians and biochemists, and was also responsible for the profound transformation of scientific reasoning: the chemical framework that had dominated thyroid studies since the discovery of thyroid iodine (1896) was replaced by the hormone paradigm. PMID:12955965

  5. An improved photometric analysis of SX Aurigae

    NASA Technical Reports Server (NTRS)

    Linnel, Albert P.; Peters, Geraldine J.; Polidan, Ronald S.

    1988-01-01

    A new analysis of existing photometric data on SX Aurigae is presented which changes current conclusions in the literature concerning the star. It is concluded, based on fitting of the continuous spectrum to Kurucz model atmospheres and simplex optimization procedure utilized, that the system consists of two normal main-sequence stars of spectral types B2 and slightly earlier than B5. The components are very close to the inner Roche limiting surface. The secondary component is unevolved, and the primary component is extremely close to contact with its inner Roche lobe. The evidence indicates that mass flow from the primary to the secondary has not yet begun. Allowing the bolometric albedo of the secondary to be a free parameter produces a solution with an excellent fit to the B, V data. The derived value, A2 = 0.40, disagrees with the theoretical value for radiative atmospheres and agrees with the value for convective equilibrium.

  6. 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).

  7. Tidal disruption and the origin of the Moon

    NASA Technical Reports Server (NTRS)

    Mizuno, H.; Boss, A. P.

    1984-01-01

    The dynamic problem of the tidal disruption of a rocky planetismal was solved by a direct integration of the fully three-dimensional, nonlinear equations of motion. The hypothesis that any object that passes within the Roche limit is disrupted was disproven. A time dependent solution was performed numerically, treating the planetismal as a fluid with a Murnaghan equation of state in the solid regions and zero pressure otherwise. Calculations show that a rocky body which passes by the Earth on a parabolic orbit with a perigee within the Roche limit is not tidally disrupted. Objects on hyperbolic orbits would experience even less tidal disruption. The results herein do not apply to bodies with very low viscosity. It is shown, however, that tidal disruption can be ruled out as a mechanism for reducing planetismal masses. Mechanisms for forming the Moon which rely upon tidal disruption are unlikely to be correct.

  8. Fiber-optic-echelle-CCD spectral monitoring of UX Arietis

    SciTech Connect

    Huenemoerder, D.P.; Buzasi, D.L.; Ramsey, L.W. )

    1989-10-01

    Results are presented on 30 fiber-optic-echelle-CCD spectra for the UX Ari system, covering one orbit in the spring and two orbits in the fall of 1987. The spectra obtained have a resolution of about 12,000 over the range of the Ca II H lines in the near UV to the Ca II triplet in the near IR, covering several activity sensitive lines. The most striking features observed were strong H-alpha and H-beta absorption near phase 0.8, which were present at epochs eight months apart. The geometry of the system, as determined from the mass ratio, rotational velocities, and the assumption of synchronous rotation, gives a radius for the K star that is approximately filling its Roche lobe. It is suggested that the excess absorption seen is due to mass-transfer activity resulting from Roche lobe overflow of the K star and accretion onto the G star. 30 refs.

  9. On the behavior of double degenerate binaries associated with Type I supernovae

    NASA Technical Reports Server (NTRS)

    Cameron, A. G. W.; Iben, I., Jr.

    1986-01-01

    An analytical investigation is performed of the evolution of double degenerate dwarf binary systems into Type I supernovae. The discussion is limited to systems consisting of carbon-oxygen and oxygen-neon-magnesium dwarfs and those composed of two carbon-oxygen dwarfs. The companions spiral together and the secondary, with a mass more than about 0.6 solar mass, fills its Roche lobe. The radius of the secondary increases faster than the Roche lobe due to mass overflow, which becomes unstable. The instability can lead to a Type I explosion and may or may not cause the formation of a neutron star. If a neutron star forms, the secondary, reduced to below 0.6 solar mass, will spiral inward to the primary and eventually be absorbed by the neutron star. If a white dwarf remnant remains after the supernova explosion of the overflow radius, then a second supernova explosion can occur.

  10. B and V photoelectric photometry and light curve solution of the interacting binary systems HI Puppis,Bl Eridani and SY Horologii

    NASA Astrophysics Data System (ADS)

    Kern, J. R.

    The first photoelectric observations of the eclipsing binary systems HI Puppis, BL Eridani and SY Horologii were obtained and complete B and V lights curves are presented. Improved light elements were derived for all three systems. The light curves of HI Puppis were analyzed by the computer models of Wilson and Devinney, Binnendijk and Wood to get the geometrical and photometric elements of the system. HI Puppis is shown to be a classic A type W Ursae Majoris system. The BL Eridani system is found to be a near contact system with the primary component filling its Roche lobe and the secondary nearly filling its lobe with a fill out ratio of approximately 1.0. The SY Horologii system is a near contact system with the secondary component filling its Roche lobe and the primary nearly filling its lobe with a fill out ratio of approximately 1.0.

  11. Formation of regular satellites from ancient massive rings in the solar system.

    PubMed

    Crida, A; Charnoz, S

    2012-11-30

    When a planetary tidal disk--like Saturn's rings--spreads beyond the Roche radius (inside which planetary tides prevent aggregation), satellites form and migrate away. Here, we show that most regular satellites in the solar system probably formed in this way. According to our analytical model, when the spreading is slow, a retinue of satellites appear with masses increasing with distance to the Roche radius, in excellent agreement with Saturn's, Uranus', and Neptune's satellite systems. This suggests that Uranus and Neptune used to have massive rings that disappeared to give birth to most of their regular satellites. When the spreading is fast, only one large satellite forms, as was the case for Pluto and Earth. This conceptually bridges the gap between terrestrial and giant planet systems. PMID:23197530

  12. 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.

  13. 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

  14. [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.

  15. Ranibizumab (Lucentis) versus Bevacizumab (Avastin) for the Treatment of Age-Related Macular Degeneration: An Economic Disparity of Eye Health.

    PubMed

    Moreno, Tomas A; Kim, Stephen J

    2016-01-01

    Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, and the advent of anti-vascular endothelial growth factor agents (VEGF) has revolutionized treatment for neovascular AMD. Two of the most popular anti-VEGF agents, ranibizumab (Lucentis; Genentech/Roche) and bevacizumab (Avastin; Genentech/Roche), effectively treat neovascular AMD but have a substantial difference in price. Multiple level 1 trials have demonstrated that bevacizumab is noninferior to ranibizumab in the treatment of neovascular AMD and that both have similar safety profiles. The decision to use one drug over the other is multifactorial with influences from industry as well as individual physician biases. However, the additional billions spent on ranibizumab result in a large economic disparity that is not rationalized by cost effectiveness models.

  16. Human Papillomavirus Genotyping Using Archival Vulval Dysplastic or Neoplastic Biopsy Tissues: Comparison between the INNO-LiPA and Linear Array Assays▿

    PubMed Central

    Tan, Sarah E.; Garland, Suzanne M.; Rumbold, Alice R.; Tabrizi, Sepehr N.

    2010-01-01

    The Roche Linear Array (LA) and Innogenetics INNO-LiPA human papillomavirus (HPV) genotyping assays were compared for paraffin-embedded vulval tissues. The LA detected amplifiable DNA in 28 (57%) out of 49 biopsy specimens, 20 (40%) being HPV genotyped, compared to 49 (100%) and 41 (83%), respectively, detected by the INNO-LiPA. The INNO-LiPA provides greater sensitivity for HPV genotyping in archival tissue. PMID:20181920

  17. Studies of an x ray selected sample of cataclysmic variables. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Silber, Andrew D.

    1986-01-01

    Just prior to the thesis research, an all-sky survey in hard x rays with the HEAO-1 satellite and further observations in the optical resulted in a catalog of about 700 x-ray sources with known optical counterparts. This sample includes 43 cataclysmic variables, which are binaries consisting of a detached white-dwarf and a Roche lobe filling companion star. This thesis consists of studies of the x-ray selected sample of catalcysmic variables.

  18. RZ Cas, KO Aql and S Equ: a Piece of Cake of Case A RLOF?

    NASA Astrophysics Data System (ADS)

    De Greve, J. P.; Mennekens, N.; Rensbergen, W. V.; Yungelson, L.

    2009-08-01

    We determine the present evolutionary state and the restrictions on the initial mass ratios of RZ Cas, KO Aql and S Equ. The gainers are in an early main sequence stage (X_c > 0.5), with KO Aql being almost unevolved. The initial donor/gainer mass ratios Mdi /Mgi must be larger than three to obtain the present mass and luminosity of the gainers. However, conservative mass transfer leads to considerable overflow of the gainer's radius over the Roche radius.

  19. SS433 Trek 2: light curve analysis.

    NASA Astrophysics Data System (ADS)

    Fukue, J.; Obana, Y.; Okugami, M.

    The authors have calculated theoretical light curves of SS433 during eclipse and precession, using a model in which SS433 consists of a geometrically thick torus around a compact star and a companion star filling the Roche lobe. The favorite combination is that the mass ratio is about 2 (a compact star is a black hole) and the surface temperature of the companion is around 17000K.

  20. [Next-generation sequencing technologies and the application in microbiology--a review].

    PubMed

    Qin, Nan; Li, Dongfang; Yang, Ruifu

    2011-04-01

    Since its invention in 1970s, nucleic acid sequencing technology has contributed tremendously to the genomics advances. The next-generation sequencing technologies, represented by HiSeq 2000 from Illumina, SOLiD from Applied Biosystems and 454 from Roche, re-energized the application of genomics. In this review, we first introduced the next-generation sequencing technologies, then, described their potential applications in the field of microbiology.

  1. Performance comparison of Next Generation sequencing platforms.

    PubMed

    Erguner, Bekir; Ustek, Duran; Sagiroglu, Mahmut S

    2015-01-01

    Next Generation DNA Sequencing technologies offer ultra high sequencing throughput for very low prices. The increase in throughput and diminished costs open up new research areas. Moreover, number of clinicians utilizing DNA sequencing keeps growing. One of the main concern for researchers and clinicians who are adopting these platforms is their sequencing accuracy. We compared three of the most commonly used Next Generation Sequencing platforms; Ion Torrent from Life Technologies, GS FLX+ from Roche and HiSeq 2000 from Illumina.

  2. Performance of two real-time PCR assays for hepatitis B virus DNA detection and quantitation.

    PubMed

    Kania, Dramane; Ottomani, Laure; Meda, Nicolas; Peries, Marianne; Dujols, Pierre; Bolloré, Karine; Rénier, Wendy; Viljoen, Johannes; Ducos, Jacques; Van de Perre, Philippe; Tuaillon, Edouard

    2014-06-01

    In-house developed real-time PCR (qPCR) techniques could be useful conjunctives to the management of hepatitis B virus (HBV) infection in resource-limited settings with high prevalence. Two qPCR assays (qPCR1 and qPCR2), based on primers/probes targeting conserved regions of the X and S genes of HBV respectively, were evaluated using clinical samples of varying HBV genotypes, and compared to the commercial Roche Cobas AmpliPrep/Cobas TaqMan HBV Test v2.0. The lower detection limit (LDL) was established at 104 IU/ml for qPCR1, and 91 IU/ml for qPCR2. Good agreement and correlation were obtained between the Roche assay and both qPCR assays (r = 0.834 for qPCR1; and r = 0.870 for qPCR2). Differences in HBV DNA load of > 0.5 Log10 IU/ml between the Roche and the qPCR assays were found in 49/122 samples of qPCR1, and 35/122 samples of qPCR2. qPCR1 tended to underestimate HBV DNA quantity in samples with a low viral load and overestimate HBV DNA concentration in samples with a high viral load when compared to the Roche test. Both molecular tools that were developed, used on an open real-time PCR system, were reliable for HBV DNA detection and quantitation. The qPCR2 performed better than the qPCR1 and had the additional advantage of various HBV genotype detection and quantitation. This low cost quantitative HBV DNA PCR assay may be an alternative solution when implementing national programmes to diagnose, monitor and treat HBV infection in low- to middle-income countries where testing for HBV DNA is not available in governmental health programmes.

  3. 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.

  4. Transcriptome analysis of gill tissue of Atlantic cod Gadus morhua L. from the Baltic Sea.

    PubMed

    Małachowicz, Magdalena; Kijewska, Agnieszka; Wenne, Roman

    2015-10-01

    The Atlantic cod (Gadus morhua L.) is one of the most ecologically and economically important marine fish species in the North Atlantic Ocean. Using Roche GS-FLX 454 pyrosequencing technique 962,516 reads, representing 379Mbp of the Baltic cod transcriptome, were obtained. Data was assembled into 14,029 contigs of which 100% displayed homology to the Atlantic cod transcriptome. Despite a high similarity between transcripts, evidence for significant differences between Baltic and Atlantic cod was found.

  5. 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.

  6. 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.

  7. 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.

  8. Comparison of six real-time PCR assays for qualitative detection of cytomegalovirus in clinical specimens.

    PubMed

    Binnicker, M J; Espy, M E

    2013-11-01

    In this study, we compared the performance of six real-time PCR assays for the qualitative detection of cytomegalovirus (CMV) in clinical samples other than plasma. Two hundred specimens (respiratory [n = 72], urine [n = 67], cerebrospinal fluid [CSF] [n = 25], tissue [n = 18], amniotic fluid [n = 10], and bone marrow [n = 8]) submitted for routine testing by CMV real-time PCR analyte-specific reagents (ASR) (Roche Diagnostics, Indianapolis, IN) were also tested by a laboratory-developed test (LDT) and 4 commercially available PCR assays: EraGen Multicode (Luminex, Austin, TX), Focus Simplexa (Focus Diagnostics, Cypress, CA), Elitech MGB Alert CMV (Fisher Scientific, Hanover Park, IL), and Abbott CMV (Abbott Park, IL). Nucleic acid was extracted using the MagNA Pure system (Roche Diagnostics) and subsequently tested by each PCR method. Results were analyzed by comparing each assay to a "consensus result," which was defined as the result obtained from at least 4 of the 6 assays. In addition to the prospective samples, 13 lower respiratory samples with known positive results by CMV shell vial were tested by each PCR method. Following testing of the 200 prospective specimens, the Abbott, Elitech, EraGen, and Focus PCR assays demonstrated a sensitivity of 100% (46/46), while the Roche analyte-specific reagents (ASR) and LDT showed sensitivities of 89% (41/46) and 98% (45/46), respectively. Percent specificities ranged from 97% (149/154) by Elitech to 100% (154/154) by the LDT. Among the 13 shell vial-positive lower respiratory samples, the percent sensitivities ranged from 69% (9/13) by Elitech to 92% (12/13) by the LDT. The Abbott, EraGen, Elitech, Focus, and LDT PCR assays performed similarly (κ ≥ 0.89) for the detection of CMV in clinical specimens and demonstrated increased sensitivity compared to the Roche ASR.

  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. 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.

  11. Evaluation of the Cepheid herpes simplex virus typing real-time PCR assay using dermal and genital specimens.

    PubMed

    Podzorski, Raymond P

    2006-10-01

    The Cepheid herpes simplex virus (HSV) (Cepheid, Sunnyvale, CA) typing multiplex real-time polymerase chain reaction (PCR) assay was evaluated for its ability to detect HSV in dermal and genital specimens stored in M5 media. Swab specimens (n = 114) for HSV testing were placed in M5 media and split between our laboratory and a highly experienced reference laboratory. Aliquots for testing with the Cepheid assay were processed using a simple boil-and-go procedure and then run in a SmartCycler II (Cepheid). Aliquots tested at the reference laboratory were processed using a MagNA Pure LC DNA extractor (Roche Molecular Systems, Alameda, CA) and tested by the Roche HSV real-time PCR assay. Both laboratories detected 35 positives. Of the positive specimens, the Cepheid assay typed 16 as HSV 1 and 19 as HSV 2; the reference laboratory typed 15 as HSV 1, 19 as HSV 2, and 1 as HSV indeterminate. Our results demonstrate that the Cepheid real-time PCR assay, using specimens subjected to minimal specimen processing, performed as well as the Roche real-time PCR assay, using DNA extracts, for the detection of HSV DNA in genital and dermal specimens.

  12. 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.

  13. 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.

  14. 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

  15. Formation of Janus and Epimetheus from Saturn's rings as coorbitals, thanks to Mimas' 2:3 inner Mean Motion Resonances

    NASA Astrophysics Data System (ADS)

    Crida, Aurelien; El Moutamid, Maryame

    2016-10-01

    Janus and Epimetheus orbit Saturn at 151461 km on average, on mutual horseshoe orbits with orbital separation 50 km, exchanging position every 4 years. This configuration is unique and intriguing : Lissauer et al. (1985) have shown that their orbital separation should converge to zero in about 20 Myrs only, and no satisfactory model for the origin of this co-orbital resonance exists yet.Charnoz et al. (2010) have shown that Janus and Epimetheus probably formed from the spreading of the rings beyond the Roche radius. Here, we show that this happened when Mimas' 2:3 Lindblad Resonance, which used to confine the rings, receded past the Roche radius. This first explains the gap in mass and distance between Janus and Mimas, which is unexpected in the pyramidal regime of the ring spreading model (Crida & Charnoz 2012). Furthermore, at this time, the two capture sites of Mimas's 2:3 Corotation Resonance were full of ring material. We suggest that as the two capture sites were brought beyond the Roche radius, the captured material agglomerated into two bodies of ~1015 kg on the exact same orbit. These bodies then migrated outwards together due to their interaction with the rings, in mutual horseshoe orbits. The rings then spawn new small satellites, eventually accreted by the proto-Janus and the proto-Epimetheus. This excites their orbital separation, leading to today's configuration.

  16. 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.

  17. Overview of existing research and information linking isotretinoin (accutane), depression, psychosis, and suicide.

    PubMed

    O'Donnell, James

    2003-01-01

    Isotretinoin (Accutane; Hoffmann-La Roche, Nutley, NJ) is a drug closely related to the chemical structure of vitamin A. The pharmacology and toxicology of these two retinoids are similar enough to warrant comparison. Accutane is a powerful drug that its manufacturer, Roche, indicates is limited for severe recalcitrant nodular acne. This potency is also reflected in Accutane's well-known ability to produce severe birth defects if taken during pregnancy. Less well known is the risk of this lipid-soluble chemical to affect the central nervous system. Reports of intracranial hypertension, depression, and suicidal ideation with Accutane use have prompted an examination of its serious and life-threatening potential. Although Roche has added a warning to its product label for signs of depression, and suicidal ideation, this product is overprescribed for all forms of acne, including mild and moderate cases that have not been treated with alternative medications with less risk of depression and suicide. There is no contesting that this drug is effective at clearing up the most severe forms of acne, but the public must be informed of the proper limited indication for its use, because depression and suicide can follow in patients with no prior history of psychiatric symptoms or suicide attempts.

  18. 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.

  19. Use of PCR and direct immunofluorescence microscopy for confirmation of results obtained by Syva MicroTrak Chlamydia enzyme immunoassay.

    PubMed Central

    Ostergaard, L; Møller, J K

    1995-01-01

    A procedure for use of the Amplicor Chlamydia PCR with the Syva MicroTrak enzyme immunoassay (EIA) medium was developed, and the performance of the Syva MicroTrak EIA was evaluated by use of PCR and the Syva MicroTrak direct immunofluorescence assay (DFA) as confirmatory methods. PCR detected Chlamydia organisms at a 10-fold greater dilution than did DFA. Of 366 specimens, 119 specimens were positive by both PCR and DFA, 6 specimens were positive only by PCR, and 241 specimens were negative by both PCR and DFA. Subsequently, DFA and the developed PCR procedure were used prospectively for confirmation of EIA results in a defined negative gray zone between the cutoff value and 30% of the cutoff value (70% below the cutoff value). All specimens with results above the EIA cutoff value were also subjected to confirmation with DFA and PCR. EIA was performed on 7,748 endocervical swab specimens, of which 494 (6.4%) were subjected to confirmation, and on 968 male urethral swab specimens, of which 185 (19.1%) were subjected to confirmation. A "gold standard" was based on the findings by DFA and PCR, and divergent results were resolved by a major outer membrane protein-based PCR. Forty-five of 160 female specimens (28.1%) and 11 of 93 male specimens (11.8%) within the defined negative gray zone were found to be positive. Of 334 female specimens having absorbance unit (AU) values above the EIA cutoff value, 258 could be confirmed, thereby giving a positive predictive value of 77% (258/334). Accordingly, the positive predictive value with male specimens was 95% (87/92). The prevalence of Chlamydia trachomatis-positive specimens was 3.9% (303/7,748) in females and 10.1% (98/968) in males.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8567894

  20. Quantification of human immunodeficiency virus type 1 RNA from dried plasma spots collected on filter paper.

    PubMed Central

    Cassol, S; Gill, M J; Pilon, R; Cormier, M; Voigt, R F; Willoughby, B; Forbes, J

    1997-01-01

    To assess dried plasma spots (DPSs) as a source of material for virus quantification, human immunodeficiency virus type 1 (HIV-1) RNA levels were quantified in matched DPS and liquid plasma samples from 73 infected patients, including 5 neonates and 4 adult patients with acute HIV-1 infection. Quantifications were performed by commercially available assays (NASBA [nucleic acid sequence-based amplification] or Amplicor, or both). There was a strong correlation between HIV-1 RNA levels in plasma and DPSs. More importantly, there was no decline in HIV-1 RNA levels in DPSs stored for as long as 2 weeks at 20 degrees C. Similarly, storage of DPSs for 3 days at 37 degrees C resulted in no decrease in viral RNA levels. For patients with primary infection, the DPS method allowed for the measurement of RNA levels in plasma during the initial spike in the level of viremia and in the subsequent period of suppressed viral replication. DPS quantification was equally informative in the neonatal setting, with all five newborns showing HIV-1 RNA loads of greater than 4.991 log10 copies/ml. We conclude that the viral RNA levels in DPSs are equivalent to those measured in fresh-frozen plasma. The ease and economy of DPS sampling, the minute volumes required, and the unexpected stability of dried RNA suggest that the use of DPSs will be particularly valuable for small-volume neonatal samples and large, population-based studies in which cold storage and transportation present special problems, as is often the case in developing countries. The ability to measure viral changes during primary infection suggests that the method will be useful for assessing vaccine efficacy in large field trials. PMID:9350736

  1. 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

  2. Performance Characteristics of the TRUGENE HIV-1 Genotyping Kit and the Opengene DNA Sequencing System

    PubMed Central

    Kuritzkes, Daniel R.; Grant, Robert M.; Feorino, Paul; Griswold, Marshal; Hoover, Marie; Young, Russell; Day, Stephen; Lloyd, Jr., Robert M.; Reid, Caroline; Morgan, Gillian F.; Winslow, Dean L.

    2003-01-01

    The TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System are designed to sequence the protease (PR)- and reverse transcriptase (RT)-coding regions of human immunodeficiency virus type 1 (HIV-1) pol. Studies were undertaken to determine the accuracy of this assay system in detecting resistance-associated mutations and to determine the effects of RNA extraction methods, anticoagulants, specimen handling, and potentially interfering substances. Samples were plasma obtained from HIV-infected subjects or seronegative plasma to which viruses derived from wild-type and mutant infectious molecular clones (IMC) of HIV-1 were added. Extraction methods tested included standard and UltraSensitive AMPLICOR HIV-1 MONITOR, QIAGEN viral RNA extraction mini kit, and QIAGEN Ultra HIV extraction kit, and NASBA manual HIV-1 quantitative NucliSens. Sequence data from test sites were compared to a “gold standard” reference sequence to determine the percent agreement. Comparisons between test and reference sequences at the nucleotide level showed 97.5 to 100% agreement. Similar results were obtained regardless of extraction method, regardless of use of EDTA or acid citrate dextrose as anticoagulant, and despite the presence of triglycerides, bilirubin, hemoglobin, antiretroviral drugs, HIV-2, hepatitis C virus (HCV), HBV, cytomegalovirus, human T-cell leukemia virus type 1 (HTLV-1), or HTLV-2. Samples with HIV-1 RNA titers of ≥1,000 copies/ml gave consistent results. The TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System consistently generate highly accurate sequence data when tested with IMC-derived HIV and patient samples. PMID:12682150

  3. 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

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

    PubMed

    Anderson, Olin D; Huo, Naxin; Gu, Yong Q

    2013-06-01

    The complete set of unique γ-gliadin genes is described for the wheat cultivar Chinese Spring using a combination of expressed sequence tag (EST) and Roche 454 DNA sequences. Assemblies of Chinese Spring ESTs yielded 11 different γ-gliadin gene sequences. Two of the sequences encode identical polypeptides and are assumed to be the result of a recent gene duplication. One gene has a 3' coding mutation that changes the reading frame in the final eight codons. A second assembly of Chinese Spring γ-gliadin sequences was generated using Roche 454 total genomic DNA sequences. The 454 assembly confirmed the same 11 active genes as the EST assembly plus two pseudogenes not represented by ESTs. These 13 γ-gliadin sequences represent the complete unique set of γ-gliadin genes for cv Chinese Spring, although not ruled out are additional genes that are exact duplications of these 13 genes. A comparison with the ESTs of two other hexaploid cultivars (Butte 86 and Recital) finds that the most active genes are present in all three cultivars, with exceptions likely due to too few ESTs for detection in Butte 86 and Recital. A comparison of the numbers of ESTs per gene indicates differential levels of expression within the γ-gliadin gene family. Genome assignments were made for 6 of the 13 Chinese Spring γ-gliadin genes, i.e., one assignment from a match to two γ-gliadin genes found within a tetraploid wheat A genome BAC and four genes that match four distinct γ-gliadin sequences assembled from Roche 454 sequences from Aegilops tauschii, the hexaploid wheat D-genome ancestor.

  5. 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

  6. On the Evolution of Low-Mass X-Ray Binaries under the Influence of a Donor Stellar Wind Induced by X-Rays from the Accretor

    NASA Astrophysics Data System (ADS)

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

    1997-09-01

    In a low-mass X-ray binary (LMXB), an intense stellar wind from the mass donor may be a consequence of the absorption of X-rays from the mass-accreting neutron star or black hole, and such a wind could change the evolution of these binaries dramatically compared with the evolution of cataclysmic variables (CVs), which are close binaries in which the accretor is a white dwarf. An analytical study and numerical models show that, in the closest and brightest LMXBs, a relativistic companion can capture up to ~10% of the mass lost in the induced stellar wind (ISW) from the main-sequence or subgiant donor, and this is enough to keep the X-ray luminosity of a typical LMXB on the level of LX ~ 5000 L⊙ and to accelerate the rotation of an old neutron star with a low magnetic field into the millisecond-period range. A self-sustained ISW may exist even if the donor does not fill its Roche lobe, but the system can be bright (LX > 100 L⊙) only if the radius of the donor is a substantial fraction (>~0.8) of the Roche lobe radius. A lower limit on the Roche lobe filling factor follows from the circumstance that both the rate Ėwind at which work must be done to lift wind matter off the donor and the rate Ėabs at which the donor absorbs X-ray energy are proportional to ṀISW (the ISW mass-loss rate) and from the requirement that Ėwind<Ėabs in order for energy to be conserved. The observed number (~100) of bright LMXBs in our Galaxy can be understood as the product of a relatively short lifetime (a few × 107 yr) and a small theoretical birthrate (~2 × 10-6-8 × 10-6 yr-1), which is comparable to semiempirical estimates of the birthrate of LMXBs and millisecond pulsars (~2 × 10-6 yr-1). The theoretical lifetime is ~10-60 times shorter than when the ISW is not taken into account, and the theoretical birthrate is ~3-6 times smaller, because of the fact that the ISW acts to expand the orbit and reduce the number of systems that can evolve through an X-ray bright stage under

  7. 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.

  8. Recovery of spiked troponin I in four routine assays

    PubMed Central

    Loh, Tze Ping; Lim, Xiong Chang; Kieu, Karize; Sajiir, Haressh; Neo, Siew Fong; Cheng, Wan Ling; Sethi, Sunil Kumar

    2016-01-01

    Introduction This study aimed to examine the recovery of spiked human cardiac troponin I (cTnI) results measured by four routine assays, and investigate possible interference from microclots. Materials and methods 457 consecutive samples with cTnI concentration below limit of quantitation (12 ng/L), declared by the Vitros TnI ES assay (reference assay), were measured on Beckman Coulter Accu TnI+3, Siemens TnI-Ultra and Roche TnI STAT assays. These samples were enriched with native full-length cTnI to a concentration of 100 ng/L and retested. A post-spiking result that exceeded the critical difference at a predefined probability of 0.0005 of the target concentration (the median post-spiking result for each individual assay) was considered as outlier. To determine whether microclots were a significant cause of critically discrepant outlier results, a separate 50 samples were centrifuged twice between two post-spiking measurements using the Vitros TnI ES assay. Results The median recovery of the enriched cTnI was highest with the Roche assay (271 ng/L) and lowest with the Vitros assay (29 ng/L). The Vitros assay had the highest percentage of results that exceeded the critical difference (49%), followed by the Siemens (38%), Roche (18%) and Beckman Coulter (7%) assays. None of the 50 additional samples produced a critically lower cTnI result after re-centrifugation. Conclusions Our findings underscored the variability of cTnI assays in measuring native cTnI. The lack of cTnI results that became significantly lower after re-centrifugation suggested that microclots are unlikely to be a major cause of the outlier results. PMID:27346968

  9. Performance of an Early Infant Diagnostic Test, AmpliSens DNA-HIV-FRT, Using Dried Blood Spots Collected from Children Born to Human Immunodeficiency Virus-Infected Mothers in Ukraine

    PubMed Central

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

    2015-01-01

    An accurate accessible test for early infant diagnosis (EID) is crucial for identifying HIV-infected infants and linking them to treatment. To improve EID services in Ukraine, dried blood spot (DBS) samples obtained from 237 HIV-exposed children (≤18 months of age) in six regions in Ukraine in 2012 to 2013 were tested with the AmpliSens DNA-HIV-FRT assay, the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 Qual test, and the Abbott RealTime HIV-1 Qualitative assay. In comparison with the paired whole-blood results generated from AmpliSens testing at the oblast HIV reference laboratories in Ukraine, the sensitivity was 0.99 (95% confidence interval [CI], 0.95 to 1.00) for the AmpliSens and Roche CAP/CTM Qual assays and 0.96 (95% CI, 0.90 to 0.98) for the Abbott Qualitative assay. The specificity was 1.00 (95% CI, 0.97 to 1.00) for the AmpliSens and Abbott Qualitative assays and 0.99 (95% CI, 0.96 to 1.00) for the Roche CAP/CTM Qual assay. McNemar analysis indicated that the proportions of positive results for the tests were not significantly different (P > 0.05). Cohen's kappa (0.97 to 0.99) indicated almost perfect agreement among the three tests. These results indicated that the AmpliSens DBS and whole-blood tests performed equally well and were comparable to the two commercially available EID tests. More importantly, the performance characteristics of the AmpliSens DBS test meets the World Health Organization EID test requirements; implementing AmpliSens DBS testing might improve EID services in resource-limited settings. PMID:26447114

  10. Multicenter evaluation of Seegene Anyplex TB PCR for the detection of Mycobacterium tuberculosis in respiratory specimens.

    PubMed

    Lim, Jinsook; Kim, Jimyung; Kim, Jong Wan; Ihm, Chunhwa; Sohn, Yong-Hak; Cho, Hyun-Jung; Kim, Jayoung; Koo, Sun Hoe

    2014-07-01

    Culture is the gold standard for diagnosis of tuberculosis, but it takes 6 to 8 weeks to confirm the result. This issue is complemented by the detection method using polymerase chain reaction, which is now widely used in a routine microbiology laboratory. In this study, we evaluated the performance of the Seegene Anyplex TB PCR to assess its diagnostic sensitivity and specificity, and compared its results with the Roche Cobas TaqMan MTB PCR, one of the most widely used assays in the world. Five university hospitals located in the Chungcheong area in South Korea participated in the study. A total of 1,167 respiratory specimens ordered for acid-fast bacilli staining and culture were collected for four months, analyzed via the Seegene Anyplex TB PCR, and its results were compared with the Roche Cobas TaqMan MTB PCR. For detection of Mycobacterium tuberculosis, the diagnostic sensitivity and specificity of the Anyplex TB PCR were 87.5% and 98.2% respectively, whereas those of the Cobas TaqMan were 92.0% and 98.0% respectively (p value > 0.05). For smear-positive specimens, the sensitivity of the Anyplex TB PCR was 95.2%, which was exactly the same as that of the Cobas TaqMan. For smear-negative specimens, the sensitivity of the Anyplex TB PCR was 69.2%, whereas that of the Cobas TaqMan TB PCR was 84.6%. For detection of MTB, the Seegene Anyplex TB PCR showed excellent diagnostic performance, and high sensitivity and specificity, which were comparable to the Roche Cobas TaqMan MTB PCR. In conclusion, the Anyplex TB PCR can be a useful diagnostic tool for the early detection of tuberculosis in clinical laboratories.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. The continuous measurement of tissue pH in the human fetus during labour using a new application technique.

    PubMed

    Flynn, A M; Kelly, J

    1980-08-01

    The subcutaneous tissue pH (tpH) of 61 fetuses has been measured continuously during labour using the tissue pH electrode designed by Stamm (Stamm et al, 1976) and adapted for use by Roche Medical and Laboratory Systems. These 61 fetuses fell chronologically into two groups: Group 1 comprised 31 fetuses in whom the original method of fixation to the fetal scalp was used, and Group 2 comprised 30 fetuses in whom the fixation apparatus incorporated the latest technical developments of the double spiral electrocardiograph (ECG) electrode and the fetal tpH Applicator Tool Set Model 678449. Better results were obtained with Model 678449.

  16. Slim accretion disks

    SciTech Connect

    Abramowicz, M.A.; Czerny, B.; Lasota, J.P.; Szuszkiewicz, E.

    1988-09-01

    A new branch of equilibrium solutions for stationary accretion disks around black holes is found. These solutions correspond to moderately super-Eddington accretion rates. The existence of the new branch is a consequence of an additional cooling due to general relativistic Roche lobe overflow and horizontal advection of heat. On an accretion rate versus surface density plane the new branch forms, together with the two standard branches (corresponding to the Shakura-Sunyaev accretion disk models) a characteristically S-shaped curve. This could imply a limit cycle-type behavior for black hole accretion flows with accretion rates close ot the Eddington one. 29 references.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  18. [Choice of respirators for anesthesia].

    PubMed

    Neidhardt, A; Bachour, K; Costes, Y

    1992-01-01

    Criteria of quality of gases and vapours supply, ventilator, patient's circle circuit and monitoring devices are recalled to help the anesthetist to choose his anesthesia machine. Advantages of compact or modular apparatus are discussed. Four, now wellknown, anesthesia machines (modulus II+, Siemens 900 D+SAC985, Roche Kontron 4300 and Engstrom Elsa) were analysed in clinical controlled ventilation and in simulated spontaneous ventilation to study the imposed work of breathing. Results are discussed with regard to safety rules and to ergonomics, bearing in mind their respective prices. Comparison is made with an original "bisontin" prototype.

  19. 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.

  20. 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.

  1. Holocene collapse of a mountain summit in the Belledonne massif (France): evidence from geomorphological mapping

    NASA Astrophysics Data System (ADS)

    Ravanel, L.; Allignol, F.; Deline, P.

    2009-04-01

    Rock avalanching is a high magnitude / low frequency process in mountain environment. It is an extremely rapid flow of fragmenting rock particles, with a volume > 1 M m3, involving a large amount of energy and travelling farther than expected with a normal sliding friction law. Rock avalanches are not uncommon in the Alps, in particular because of debuttressing of rock slopes due to glacier retreat and downwasting since the last Glacial maximum. The upper Vorz catchment basin is one of the few still glaciarized basins in the Belledonne massif (French external crystalline massif, peaking at 2977 m a.s.l.). A deposit related to a rock avalanche lies at the Habert du Mousset (1680 m a.s.l.), covering an area of 95 000 m2, tens of meters-thick and with a volume exceeding 1 M of m3. A geomorphological study suggests that the deposit should result from the collapse of the palaeo-summit of Roche Rousse (2753 m a.s.l. at present). The main part of the collapsed volume fell on the east side of the mountain ridge, but a smaller part probably travelled along the west side to form the deposit of the Habert du Mousset. Vertical and horizontal travel distances would have been 1100 m and 2750 m, respectively. The apparent coefficient of friction (height-over-length H/L ratio) is 0.4, indicating a highly mobile rock avalanche (H/L ratio is 0.62 with a ‘normal' coefficient of friction). Two elements support the hypothesis of a Holocene collapse: (i) glacial striations, rat tails, chattermarks and grooves are present on roches moutonnées up to 20 m to the crest. Those inherited glacial forms required a glacier thick enough to erode the bedrock. Because the surface of the Last Glacial Maximum glacier was standing well below this site (> 1000 m), only a local glacier could have form, which would have been impossible with the present topography. Thus, the palaeo-summit of Roche Rousse collapsed not before the Lateglacial. As suggested by (ii) the very steep, sometimes overhanging

  2. 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

  3. [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

  4. 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.

  5. Stellar Coronal Physics with VLBI Imaging

    NASA Astrophysics Data System (ADS)

    Peterson, William; Mutel, Robert

    2009-11-01

    We present the results of synoptic high-resolution imaging studies of two active binary star systems. Both were conducted using the VLBA-HSA at 15 GHz, making them the first images of extrasolar stars capable of discerning structure at scales smaller than a stellar diameter. Images revealed a giant coronal loop on Algol, filled with gyrosynchrotron flux at high activity levels and emitting from only the feet of the loop during quiescent epochs. UX Ari displays similar activity levels to Algol, but the components do not fill their Roche Lobes, making it an optimal comparison case for the role of mass transfer in the formation of global magnetic fields.

  6. 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.

  7. Evolution of vaporizing pulsars

    NASA Technical Reports Server (NTRS)

    Mccormick, P.

    1994-01-01

    We construct evolutional scenarios for LMXB's using a simplified stellar model. We discuss the origin and evolution of short-period, low mass binary pulsars with evaporating companions. We suggest that these systems descend from low-mass X-ray binaries and that angular momentum loss mainly due to evaporative wind drives their evolution. We derive limits on the energy and angular momentum carried away by the wind based on the observed low eccentricity. In our model the companion remains near contact, and its quasiadiabatic expansion causes the binary to expand. Short-term oscillations of the orbital period may occur if the Roche-lobe overflow forms an evaporating disk.

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

    PubMed Central

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

    2016-01-01

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

  9. Determination of renal clearances of amylase/creatinine with chromogenic and enzymatic methods.

    PubMed

    Hohenwallner, W; Wimmer, E; Sommer, R

    1979-12-01

    Urinary amylase was estimated by chromogenic (amylochrome Roche) as well as enzymatic methods (SKI and Beckman: substrate starch and substrate maltotetraose respectively). Random and timed urines (24 hour collections) were analysed. Clearances of amylase gave different results dependent upon the amylase-test used and the glomerular filtration rate. Correlation between chromogenic and enzymatic methods (starch as substrate) was poor. The ratio of amylase and creatinine clearance was used to test different methods. Reference values for this ratio for the amylochrome method (N = 106) were 2.85 +/- 0.99% and for the Beckman-DS method (N = 60) 2.82 +/- 0.87%.

  10. 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

  11. [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.

  12. 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.

  13. Methaqualone RIA structure versus reactivity.

    PubMed

    Budd, R D

    1980-04-01

    Fourteen different methaqualone-related substances (substituted 2-methyl-3-phenyl-4-quinazolinones) were analyzed by radioimmunoassay (RIA) at several different concentrations. An attempt is made to relate structural differences to the affinity of the compounds for the Roche RIA methaqualone antibody. The effects of substituent placement on the 2-methyl-3-phenyl-4-quinazolinone molecule are studied. Addition of a group to the para-position of the 3-phenyl group increased affinity, but alteration of other key functional groups had a reverse effect.

  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. 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.

  16. 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]. [....

  17. O'Connell Effect in Early-Type Contact(?) Binaries: du Boo and AG Vir

    NASA Astrophysics Data System (ADS)

    Pribulla, Theodor; Vaňko, Martin; Chochol, Drahomír; Hambálek, L'ubomıır; Parimucha, Štefan

    2010-12-01

    O'Connell effect in early-type close eclipsing binaries is not caused by solar-type spots. In most early-type contact binaries it has the same sign: maximum following the primary minimum being the brighter of the two. Broadening functions of two early-type systems, DU Boo and AG Vir, do not show presence of dark solar-type spots in spite of strong light-curve asymmetry but indicate departures from the Roche model and/or possibly additional structures (stream, disc, etc.).

  18. Mass loss from “Hot Jupiters”—Implications for CoRoT discoveries, Part II: Long time thermal atmospheric evaporation modeling

    NASA Astrophysics Data System (ADS)

    Penz, T.; Erkaev, N. V.; Kulikov, Yu. N.; Langmayr, D.; Lammer, H.; Micela, G.; Cecchi-Pestellini, C.; Biernat, H. K.; Selsis, F.; Barge, P.; Deleuil, M.; Léger, A.

    2008-07-01

    We investigate the efficiency of the atmospheric mass loss due to hydrodynamic blow-off over the lifetime of the exoplanet HD209458b by studying numerically its hydrogen wind for host star X-ray and EUV (XUV) fluxes between 1 and 100 times that of the present Sun. We apply a time-dependent numerical algorithm which is able to solve the system of hydrodynamic equations straight through the transonic point of the flow including Roche lobe effects. The mass loss rates are calculated as functions of the absorbed energy in the thermosphere. Depending on the heating efficiency for a hydrogen-rich thermosphere the maximum temperature obtained in our study at 1.5Rpl by neglecting IR cooling is about 5000-10,000 K for heating efficiencies of 10% and 60%, respectively. We find that the upper atmosphere of HD209458b experiences hydrodynamic blow-off even at such low temperatures if one does not neglect gravitational effects caused by the proximity of the planet to its Roche lobe boundary. Depending on the heating efficiency, we find from the solution of the hydrodynamic equations of mass, momentum, and energy balance that energy-limited mass loss rate estimations overestimate the realistic mass loss rate at present time for HD209458b by several times. Using the maximum heating efficiency for hydrogen-rich atmospheres of 60% we find that HD209458b may experience an atmospheric mass loss rate at present time of about 3.5×1010gs-1. The mass loss rate evolves to higher values for higher XUV fluxes expected during the early period of the planet's host star evolution, reaching values of several times 1012gs-1. The integrated mass loss is found to be between 1.8% and 4.4% of the present mass of HD209458b. We found that the influence of the stellar tidal forces on atmospheric loss (the Roche lobe effect) is not significant at 0.045 AU. For a similar exoplanet, but at closer orbital distances ⩽0.02AU, the combined effect of the Roche lobe and the high XUV radiation result in much

  19. 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

  20. Analytical performance specifications: relating laboratory performance to quality required for intended clinical use.

    PubMed

    Dalenberg, Daniel A; Schryver, Patricia G; Klee, George G

    2013-03-01

    This article proposes analytic performance goals for five quality indicators: precision, trueness, linearity, detection limits, and consistency across instruments and time. We defined our goals using methods linked to clinical practice data. Goals for desirable precision and trueness are based on biological variation. Linearity goals are related to total error recommendations. Detection limit goals are derived from 0.1 percentile of patient values. Goals for consistency are derived from the variability of distributions of patient test values. Data were collected and evaluated for each of these quality indicators for 46 chemistry tests measured on the Roche cobas 8000 analyzer.

  1. [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

  2. 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

  3. Are most regular satellites of the Solar System born from massive rings ?

    NASA Astrophysics Data System (ADS)

    Crida, A.; Charnoz, S.

    2012-09-01

    We analytically describe satellite formation from the spreading of a massive ring of solid particles ; beyond the Roche radius, new moons coagulate and migrate outwards because of gravitational instability and the disk's tides. We show that it naturally produces either a satellite system with a specific orbital architecture (that matches the Saturnian, Uranian and Neptunian systems) or only one massive satellite (in the Earth's case). We conclude that Uranus and Neptune, like Saturn, had massive rings in the past, from which their regular satellites formed, and that satellite formation from the spreading of a tidal disk is thus a generic mechanism in the whole Solar System.

  4. Are we underdosing acne patients with generic isotretinoin?

    PubMed

    Mutizwa, Misha M; Sheinbein, David M

    2013-01-15

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

  5. Accretion Disks in Massive Binary Systems

    NASA Astrophysics Data System (ADS)

    Djurašević, G. R.; Vince, I.; Atanacković, O.

    2010-12-01

    The results of our investigations of some massive close binaries (CB) (RY Sct, V448 Cyg, UU Cas and V455 Cyg), based on the photometric and spectroscopic observations indicate the existance of the accretion disk around the more massive component, located deep inside the Roche lobe. The light curve shapes of some of this systems are similar to the ones of the overcontact systems like W UMa, but the nature of these massive CBs is completely different. Here we present the models of these systems and their basic elements.

  6. 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.

  7. Performance evaluation of new automated hepatitis B viral markers in the clinical laboratory: two quantitative hepatitis B surface antigen assays and an HBV core-related antigen assay.

    PubMed

    Park, Yongjung; Hong, Duck Jin; Shin, Saeam; Cho, Yonggeun; Kim, Hyon-Suk

    2012-05-01

    We evaluated quantitative hepatitis B surface antigen (qHBsAg) assays and a hepatitis B virus (HBV) core-related antigen (HBcrAg) assay. A total of 529 serum samples from patients with hepatitis B were tested. HBsAg levels were determined by using the Elecsys (Roche Diagnostics, Indianapolis, IN) and Architect (Abbott Laboratories, Abbott Park, IL) qHBsAg assays. HBcrAg was measured by using Lumipulse HBcrAg assay (Fujirebio, Tokyo, Japan). Serum aminotransferases and HBV DNA were respectively quantified by using the Hitachi 7600 analyzer (Hitachi High-Technologies, Tokyo, Japan) and the Cobas AmpliPrep/Cobas TaqMan test (Roche). Precision of the qHBsAg and HBcrAg assays was assessed, and linearity of the qHBsAg assays was verified. All assays showed good precision performance with coefficients of variation between 4.5% and 5.3% except for some levels. Both qHBsAg assays showed linearity from 0.1 to 12,000.0 IU/mL and correlated well (r = 0.9934). HBsAg levels correlated with HBV DNA (r = 0.3373) and with HBcrAg (r = 0.5164), and HBcrAg also correlated with HBV DNA (r = 0.5198; P < .0001). This observation could provide impetus for further research to elucidate the clinical usefulness of the qHBsAg and HBcrAg assays.

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

    PubMed Central

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

    2016-01-01

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

  9. Obinutuzumab: first global approval.

    PubMed

    Cameron, Fiona; McCormack, Paul L

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  11. 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.

  12. 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.

  13. A comprehensive photometric study of the eclipsing binary EP Aurigae

    NASA Astrophysics Data System (ADS)

    Li, H.-L.; Wei, J.-Y.; Yang, Y.-G.; Li, K.; Zhang, X.-B.

    2015-02-01

    We present new observations for the eclipsing binary EP Aurigae, which were performed by using three small telescopes in China from 2003 December to 2014 January. With the updated 2003 version of the Wilson-Devinney code, the photometric elements were deduced from three sets of light curves. Based on all available eclipsing times, the orbital period changes were investigated. It is discovered that the (O-C) curve may show an existence of light-time effect due to an unseen third body, which was weakly identified by the photometric solution. The modulated period and amplitude of the cyclic variation are P3=71.2(±8.0) yr and A=0.0101(±0.0008) day, respectively. In the co-planar orbit with the binary system, the mass of the third body is M3=0.18(±0.02) M⊙. The photometric results imply that EP Aur is an Algol-type binary with a mass ratio of q=0.831(±0.004). Its primary component almost fills its Roche lobe. Therefore, EP Aur may consist of a normal main-sequence star and a cool Roche-lobe filling subgiant, which may be undergoing rapid mass transfer.

  14. Automated Extraction Improves Multiplex Molecular Detection of Infection in Septic Patients

    PubMed Central

    Regueiro, Benito J.; Varela-Ledo, Eduardo; Martinez-Lamas, Lucia; Rodriguez-Calviño, Javier; Aguilera, Antonio; Santos, Antonio; Gomez-Tato, Antonio; Alvarez-Escudero, Julian

    2010-01-01

    Sepsis is one of the leading causes of morbidity and mortality in hospitalized patients worldwide. Molecular technologies for rapid detection of microorganisms in patients with sepsis have only recently become available. LightCycler SeptiFast test Mgrade (Roche Diagnostics GmbH) is a multiplex PCR analysis able to detect DNA of the 25 most frequent pathogens in bloodstream infections. The time and labor saved while avoiding excessive laboratory manipulation is the rationale for selecting the automated MagNA Pure compact nucleic acid isolation kit-I (Roche Applied Science, GmbH) as an alternative to conventional SeptiFast extraction. For the purposes of this study, we evaluate extraction in order to demonstrate the feasibility of automation. Finally, a prospective observational study was done using 106 clinical samples obtained from 76 patients in our ICU. Both extraction methods were used in parallel to test the samples. When molecular detection test results using both manual and automated extraction were compared with the data from blood cultures obtained at the same time, the results show that SeptiFast with the alternative MagNA Pure compact extraction not only shortens the complete workflow to 3.57 hrs., but also increases sensitivity of the molecular assay for detecting infection as defined by positive blood culture confirmation. PMID:20967222

  15. 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.

  16. 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.

  17. 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.

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

    NASA Technical Reports Server (NTRS)

    Conway, B. A.

    1984-01-01

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

  19. 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.

  20. Read length versus depth of coverage for viral quasispecies reconstruction.

    PubMed

    Zagordi, Osvaldo; Däumer, Martin; Beisel, Christian; Beerenwinkel, Niko

    2012-01-01

    Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different underlying technologies and performance characteristics are available for viral diversity studies. Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes. Using a mixture of ten HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also be sufficient to assess the diversity of the sample if sequences are dissimilar enough, but, in general, assembly of full-length haplotypes is feasible only with the longer 454/Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidance for the design of viral diversity studies.

  1. 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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Gohau, , G.

    1998-05-01

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

  4. 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

  5. Comparison of commercial DNA preparation kits for the detection of Brucellae in tissue using quantitative real-time PCR

    PubMed Central

    2010-01-01

    Background The detection of Brucellae in tissue specimens using PCR assays is difficult because the amount of bacteria is usually low. Therefore, optimised DNA extraction methods are critical. The aim of this study was to assess the performance of commercial kits for the extraction of Brucella DNA. Methods Five kits were evaluated using clinical specimens: QIAamp™ DNA Mini Kit (QIAGEN), peqGold™ Tissue DNA Mini Kit (PeqLab), UltraClean™ Tissue and Cells DNA Isolation Kit (MoBio), DNA Isolation Kit for Cells and Tissues (Roche), and NucleoSpin™ Tissue (Macherey-Nagel). DNA yield was determined using a quantitative real-time PCR assay targeting IS711 that included an internal amplification control. Results Kits of QIAGEN and Roche provided the highest amount of DNA, Macherey-Nagel and Peqlab products were intermediate whereas MoBio yielded the lowest amount of DNA. Differences were significant (p < 0.05) and of diagnostic relevance. Sample volume, elution volume, and processing time were also compared. Conclusions We observed differences in DNA yield as high as two orders of magnitude for some samples between the best and the worst DNA extraction kits and inhibition was observed occasionally. This indicates that DNA purification may be more relevant than expected when the amount of DNA in tissue is very low. PMID:20403208

  6. [Isolation and characterization of 27 polymorphic microsatellite markers in Armillaria luteo-virens ( Physalacriaceae)].

    PubMed

    Xing, Rui; Gao, Qingbo; Zhang, Faqi; Li, Yinhu; Ful, Pengcheng; Zhang, Jinhua; Wang, Jiuli; Chen, Shilong

    2014-09-01

    [OBJECTIVE] The objectives of this study were to use Roche 454 GS FLX system to develop SSR markers for Armillaria luteo-virens. These datasets will be valuable for detecting genetic diversity and population structure of this species. [METHODS] We collected Armillaria luteo-virens samples from Yushu in Qinghai province, China. Total RNA was isolated by using the TRIzol reagent, after that we constructed cDNA library and performed one quarter plate of the whole run 454 pyrosequencing. We selected 98 primer pairs randomly from the 321 SSRs to evaluate their application and the polymorphism across 66 individuals (Armillaria luteo-virens) representing 3 wild populations. [RESULTS] Roche 454 sequencing yielded 197,121 reads with a total nucleotide size of 88,585,965bp. 27 of 98 SSRs loci were polymorphic. Numbers of alleles (Na) ranged from 2 to 8. Expected heterozygosity (HE) ranged from less than 0. 001 to 0. 810 at locus ALV65, while observed heterozygosity (Ho) from 0 at loci AIV64 and AIV92 to 0. 900 at loci ALV8. We found no evidence of linkage disequiliburium, however 10 of 27 SSR markers showed significant deviation from Hardy-weinberg equilibrium. [CONCLUSION] These remaining 17 pairs of Armillaria luteo-virens SSR markers will be valuable for future research on detecting population structure and conservation of this species.

  7. 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

  8. 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

  9. 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.

  10. Computer vision-based sorting of Atlantic salmon (Salmo salar) fillets according to their color level.

    PubMed

    Misimi, E; Mathiassen, J R; Erikson, U

    2007-01-01

    Computer vision method was used to evaluate the color of Atlantic salmon (Salmo salar) fillets. Computer vision-based sorting of fillets according to their color was studied on 2 separate groups of salmon fillets. The images of fillets were captured using a digital camera of high resolution. Images of salmon fillets were then segmented in the regions of interest and analyzed in red, green, and blue (RGB) and CIE Lightness, redness, and yellowness (Lab) color spaces, and classified according to the Roche color card industrial standard. Comparisons of fillet color between visual evaluations were made by a panel of human inspectors, according to the Roche SalmoFan lineal standard, and the color scores generated from computer vision algorithm showed that there were no significant differences between the methods. Overall, computer vision can be used as a powerful tool to sort fillets by color in a fast and nondestructive manner. The low cost of implementing computer vision solutions creates the potential to replace manual labor in fish processing plants with automation.

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

    PubMed

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

    2006-06-01

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

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

    SciTech Connect

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

    2015-06-10

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

  13. 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.

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

    PubMed

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

    2002-01-01

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

  15. 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.

  16. 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.

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

    PubMed Central

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

    2011-01-01

    Methods of genomic selection that combine high-density oligonucleotide microarrays with next-generation DNA sequencing allow investigators to characterize genomic variation in selected portions of complex eukaryotic genomes. Yet choosing which specific oligonucleotides to be use can pose a major technical challenge. To address this issue, we have developed a software package called MOPeD (Microarray Oligonucleotide Probe Designer), which automates the process of designing genomic selection microarrays. This web-based software allows individual investigators to design custom genomic selection microarrays optimized for synthesis with Roche NimbleGen’s maskless photolithography. Design parameters include uniqueness of the probe sequences, melting temperature, hairpin formation, and the presence of single nucleotide polymorphisms. We generated probe databases for the human, mouse, and rhesus macaque genomes and conducted experimental validation of MOPeD-designed microarrays in human samples by sequencing the human X chromosome exome, where relevant sequence metrics indicated superior performance relative to a microarray designed by the Roche NimbleGen proprietary algorithm. We also performed validation in the mouse to identify known mutations contained within a 487-kb region from mouse chromosome 16, the mouse chromosome 16 exome (1.7 Mb), and the mouse chromosome 12 exome (3.3 Mb). Our results suggest that the open source MOPeD software package and website (http://moped.genetics.emory.edu/) will make a valuable resource for investigators in their sequence-based studies of complex eukaryotic genomes. PMID:21379402

  18. Biomineral proteins from Mytilus edulis mantle tissue transcriptome.

    PubMed

    Freer, Andy; Bridgett, Stephen; Jiang, Jiahong; Cusack, Maggie

    2014-02-01

    The common blue mussel, Mytilus edulis, has a bimineralic shell composed of approximately equal proportions of the two major polymorphs of calcium carbonate: calcite and aragonite. The exquisite biological control of polymorph production is the focus of research interest in terms of understanding the details of biomineralisation and the proteins involved in the process of complex shell formation. Recent advances in ease and availability of pyrosequencing and assembly have resulted in a sharp increase in transcriptome data for invertebrate biominerals. We have applied Roche 454 pyrosequencing technology to profile the transcriptome for the mantle tissue of the bivalve M. edulis. A comparison was made between the results of several assembly programs: Roche Newbler assembler versions 2.3, 2.5.2 and 2.6 and MIRA 3.2.1 and 3.4.0. The Newbler and MIRA assemblies were subsequently merged using the CAP3 assembler to give a higher consensus in alignments and a more accurate estimate of the true size of the M. edulis transcriptome. Comparison sequence searches show that the mantle transcripts for M. edulis encode putative proteins exhibiting sequence similarities with previously characterised shell proteins of other species of Mytilus, the Bivalvia Pinctada and haliotid gastropods. Importantly, this enhanced transcriptome has detected several transcripts that encode proteins with sequence similarity with previously described shell biomineral proteins including Shematrins and lysine-rich matrix proteins (KRMPs) not previously found in Mytilus.

  19. 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

  20. 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.

  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. Accuracy of capillary whole blood international normalized ratio on the CoaguChek S, CoaguChek XS, and i-STAT 1 point-of-care analyzers.

    PubMed

    Karon, Brad S; McBane, Robert D; Chaudhry, Rajeev; Beyer, Lisa K; Santrach, Paula J

    2008-07-01

    We evaluated the accuracy of capillary whole blood international normalized ratio (INR) on the CoaguChek S (Roche Diagnostics, Indianapolis, IN), CoaguChek XS (Roche Diagnostics), and i-STAT 1 (i-STAT, East Windsor, NJ) point-of-care (POC) analyzers compared with venous plasma INRs determined by a reference laboratory method. Overall agreement between POC and laboratory plasma INR was very good, with median bias between capillary whole blood and laboratory plasma INRs varying from 0.0 to -0.2 INR units on all devices. More than 90% of results on the CoaguChek XS and i-STAT 1 and 88% of CoaguChek S results were within 0.4 INR units of the reference laboratory method. The CoaguChek XS and i-STAT 1 demonstrated greater accuracy than the CoaguChek S as measured by the number of results that differed by more than 0.5 INR units from the reference method. Median bias between CoaguChek S capillary whole blood and laboratory plasma INRs changed over time, demonstrating the need for ongoing quality assurance measures for POC INR programs.

  3. 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.

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

    PubMed

    Oberhofer, T R

    1981-03-01

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

  5. The Cyclic Nature of Martian Satellites

    NASA Astrophysics Data System (ADS)

    Hesselbrock, Andrew; Minton, David A.

    2016-10-01

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

  6. 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

  7. 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.

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

    PubMed

    Metcalf, Devon; Weese, J Scott

    2012-12-01

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

  9. 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.

  10. 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

  11. [Practical evaluation of rapid diagnostic tests for mycobacteriosis and virus infection].

    PubMed

    Nakamura, Hisako

    2002-01-01

    Because cultures of mycobacteria and viruses take a great number of days, the results are delayed in these clinical laboratory tests. For this reason, rapid diagnostic tests without these cultures are required. Among the laboratory tests of mycobacteria, acid-fast stain as a rapid diagnostic test is the first to give significant information to laboratory staffs and physicians. There are mainly two procedures, directly smearing clinical specimens and smearing concentrated specimens treated with NALC-NaOH on slide glass. The former is performed for specimens from emergency patients. When a patient is suspected of tuberculosis, a DNA-amplification test such as COBAS AMPLICOR TEST (PCR test) is performed for directly detecting Mycobacterium tuberculosis in clinical specimens, regardless of whether the specimens show positive or negative by acid-fast stain. Sixty-one of 1,023 specimens tested in Showa University Fujigaoka Hospital in February 2000-May 2002 were found positive by both PCR and culture tests. Fourteen were found negative by PCR test and positive by culture test. Five were found positive by PCR test and negative by culture test. Alternatively, MTB-64 (Capilia TB) is a kit for rapidly identifying M. tuberculosis using colonies. The time necessary for completion of the test was approximately 15 minutes per sample. In our study, the identification test showed weak-positive for 2 strains of M. marinum (ATCC927 and one clinical isolate), compared with positive for 28 clinical isolates and strain H37Ra of M. tuberculosis. Recently, rapid diagnostic kits for detecting various pathogenic viruses have been developed. The kits for detecting influenza virus are in especially great demand with the spread of newly-developed antiviral agents. There was an epidemic of the type A virus in the winters 2001-2002. 101 (32%) of 316 clinical specimens tested in the hospital were found positive with InfluA. B-Quick [SEIKEN] (Denka) or Directigen Flu A (Becton Dickinson). These

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

    PubMed Central

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

    2000-01-01

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

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

    PubMed Central

    2013-01-01

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

  14. 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

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

    PubMed Central

    2010-01-01

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

  16. Photometric Properties for Selected Algol-type Binaries. II. AO Serpentis and V338 Herculis

    NASA Astrophysics Data System (ADS)

    Yang, Y.-G.; Hu, S.-M.; Guo, D.-F.; Wei, J.-Y.; Dai, H.-F.

    2010-04-01

    We present the first multiband photometry for the semidetached eclipsing binary AO Serpentis, observed on seven nights between 2009 April and July at the Weihai Observatory of Shandong University. By using the 2003 version of the Wilson-Devinney code, the photometric solutions of AO Ser and a similar object V338 Her were (re)deduced. The spectral types and orbital periods are A2 and P = 0.8793 days for AO Ser, F1V and P = 1.3057 days for V338 Her. The results reveal that two binaries are low mass ratio systems, whose secondary components fill their Roche lobes. The fill-out factors of the primary components are f = 58.6% for AO Ser and f = 54.2% for V338 Her, respectively. From the O - C curves of AO Ser and V338 Her, it is discovered that secular period changes with cyclic variations exist. The periods and semiamplitudes are 17.32(±0.01) yr and 0.0051(±0.0001) days for AO Ser, 29.07(±0.04) yr and 0.0116(±0.0015) days for V338 Her, respectively. This kind of cyclic oscillation may be attributed to either the light-time effect via an assumed third body or perhaps cyclic magnetic activity on the secondary component. For AO Ser, the long-term period decreases at a rate of dP/dt = -5.35(±0.03) × 10-7 days yr-1, which may be caused by mass and angular momentum loss from the system. Considering the period decreasing, the fill-out factor of the primary for AO Ser will increase and it will finally fill its Roche lobe. Meanwhile, the secular period increase rate for V338 Her is dP/dt = +1.44(±0.24) × 10-7 days yr-1, indicating that mass transfers from the less massive component to the more massive component. This will also cause the fill-out factor of the primary to increase. When the primaries fill their Roche lobes, AO Ser and V338 Her may evolve into contact stars, as predicted by the theory of thermal relaxation oscillations.

  17. 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

  18. 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

  19. Comparison of Serum HBsAg Quantitation by Four Immunoassays, and Relationships of HBsAg Level with HBV Replication and HBV Genotypes

    PubMed Central

    Tuaillon, Edouard; Mondain, Anne-Marie; Nagot, Nicolas; Ottomani, Laure; Kania, Dramane; Nogue, Erika; Rubbo, Pierre-Alain; Pageaux, Georges-Philippe; Van de Perre, Philippe; Ducos, Jacques

    2012-01-01

    Background The decline in hepatitis B virus surface antigen (HBsAg) may be an early predictor of the viral efficacy of Hepatitis B virus (HBV) therapy. The HBsAg levels obtained by different immunoassays now need comparing and the relationships between levels of HBsAg and HBV DNA alongside HBsAg and genotype must be evaluated. Methodology/Principal Findings HBsAg levels were compared among 80 patients using the Abbott Architect assay, a commercial immunoassay approved for HBsAg detection and quantitation, and three other assays derived from immunoassays approved for HBsAg detection (manufactured by Diasorin, Bio-Rad and Roche). Good correlation was found between the Abbot vs. Diasorin, Bio-Rad and Roche assays with narrow 95% limits of agreement and small mean differences: −0.06 to 0.11, −0.09 log10 IU/mL; −0.57 to 0.64, −0.04 log10 IU/mL; −0.09 to 0.45, −0.27 log10 IU/mL, respectively. These agreements were not affected by genotypes A or D. HBsAg was weakly correlated with HBV DNA, whatever the HBsAg assay used: Abbott, ρ = 0.36 p = 0.001, Diasorin ρ = 0.34, p = 0.002; Bio-Rad ρ = 0.37, p<0.001; or Roche ρ = 0.41, p<0.001. This relationship between levels of HBsAg and HBV DNA seemed to depend on genotypes. Whereas HBsAg (Abbott assay) tended to correlate with HBV DNA for genotype A (ρ = 0.44, p = 0.02), no such correlation was significant for genotypes D (ρ = 0.29, p = 0.15). Conclusion/Significance The quantitation of HBsAg in routine clinical samples is comparable between the reference assay and the adapted assays with acceptable accuracy limits, low levels of variability and minimum discrepancy. While HBsAg quantitation is not affected by HBV genotype, the observed association between levels of HBsAg and HBV DNA seems genotype dependent. PMID:22403628

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

    PubMed

    Müller, Klaus

    2014-01-01

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

  1. 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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    La Dous, Constanze

    1993-09-01

    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

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. On the nature and evolution of the windy binary pulsar PSR 1744 - 24A

    NASA Astrophysics Data System (ADS)

    Shaham, Jacob; Tavani, Marco

    1991-08-01

    It is suggested that the companion of the pulsar PSR 1744 - 24A is an approximately 0.1 solar mass main-sequence star that slightly underfills its Roche lobe and is sending off a cool wind due to excitation by radiation from the pulsar. Unlike in the similarly excited system of pulsar PSR 1957 + 20, pulsar radiation pressure here almost balances wind pressure at the companion distance, leading to vastly fluctuating eclipse patterns and to occasional attempted accretion episodes that are aborted by the propeller effect and result in X-ray bursts. If this picture is correct, multiwavelength continuous observations of PSR 1744 - 24A will give valuable information about the accretion process onto neutron stars rotating with millisecond periods.

  10. 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.

  11. 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

  12. 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

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

    PubMed

    Nayak, M; Asphaug, E

    2016-08-30

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

  14. Hypothesis on interferences in kinetic interaction of microparticles in solution (KIMS) technology.

    PubMed

    De Giovanni, Nadia; Fucci, Nadia

    2006-01-01

    The present paper describes an evaluation of the interferences found with an immunochemical drug test performed during a workplace control. During the period 1993-2003 more than 200,000 urine samples from workers were examined by the Italian Air Force. Samples were screened for drugs of abuse (opiates, cocaine, cannabinoids, amphetamines, methadone) using an immunochemical technique (Roche, kinetic interaction of microparticles in solution, KIMS). A total of 520 positive samples were sent to the Forensic Toxicology Laboratory for confirmation by gas chromatography/mass spectrometry (GC/MS). Approximately 39% of these were found to be true positives. For the remaining samples, pharmacological therapy in subjects was estimated to evaluate possible interferences due to medicine intake. Our study showed a high frequency of false-positive results with this immunochemical technique, mainly for the cannabinoid and amphetamine groups. Recurrent references to some medicines during subject anamnesis were noted.

  15. Recent advances in nanopore sequencing

    PubMed Central

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

    2013-01-01

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

  16. 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.

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

    PubMed

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

    2016-01-27

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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. On the potentially dramatic history of the super-Earth ρ 55 Cancri e

    NASA Astrophysics Data System (ADS)

    Hansen, Bradley M. S.; Zink, Jonathon

    2015-07-01

    We demonstrate that tidal evolution of the inner planet (`e') of the system orbiting the star ρ 55 Cancri could have led to passage through two secular resonances with other planets in the system. The consequence of this evolution is excitation of both the planetary eccentricity and inclination relative to the original orbital plane. The large mass ratio between the innermost planet and the others means that these excitations can be of substantial amplitude and can have dramatic consequences for the system organization. Such evolution can potentially explain the large observed mutual inclination between the innermost and outermost planets in the system, and implies that tidal heating could have substantially modified the structure of planet e, and possibly reduced its mass by Roche lobe overflow. Similar inner secular resonances may be found in many multiple planet systems and suggest that many of the innermost planets in these systems could have suffered similar evolutions.

  3. 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.

  4. [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

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. Assessment of liver hydatid cyst cases--10 years experience in Turkey.

    PubMed

    Mergen, Haluk; Genç, Hüdai; Tavusbay, Cengiz

    2007-01-01

    We analysed 73 hydatid cyst patients according to their age, gender, localization, number of cysts, infectivity, symptoms, physical examination findings, presence of accompanying diseases, and diagnostic methods. Female/male ratio was 1.6/1. In total, 69% of cases had a single cyst and 31% multiple cysts. Of the cysts, 61% were in form of "eau de roche" and the rest infective. The mean age was 42.3 years, ranging from 18 to 85 years. The most common symptom was abdominal pain in 74% of patients. Right lobe involvement was encountered in 65% of cases, left lobe in 13%, and left and right in 8%. In 27% of patients, cholelithiasis was the most common accompanying disease. As an imaging technique ultrasound was the most commonly used diagnostic technique. PMID:17326896

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

    PubMed

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

    2015-12-01

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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  18. 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.

  19. 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.

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

    PubMed

    Lee, Tong Geon; Seo, Yong Weon

    2015-09-01

    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.

  1. [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

  2. 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.

  3. 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.

  4. 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

  5. Massively parallel sequencing approaches for characterization of structural variation.

    PubMed

    Koboldt, Daniel C; Larson, David E; Chen, Ken; Ding, Li; Wilson, Richard K

    2012-01-01

    The emergence of next-generation sequencing (NGS) technologies offers an incredible opportunity to comprehensively study DNA sequence variation in human genomes. Commercially available platforms from Roche (454), Illumina (Genome Analyzer and Hiseq 2000), and Applied Biosystems (SOLiD) have the capability to completely sequence individual genomes to high levels of coverage. NGS data is particularly advantageous for the study of structural variation (SV) because it offers the sensitivity to detect variants of various sizes and types, as well as the precision to characterize their breakpoints at base pair resolution. In this chapter, we present methods and software algorithms that have been developed to detect SVs and copy number changes using massively parallel sequencing data. We describe visualization and de novo assembly strategies for characterizing SV breakpoints and removing false positives.

  6. The 1983 June 15 occultation by Neptune. I - Limits on a possible ring system

    NASA Technical Reports Server (NTRS)

    Elliot, J. L.; Baron, R. L.; Dunham, E. W.; French, R. G.; Meech, K. J.; Mink, D. J.; Erickson, E. F.

    1985-01-01

    Observations on 15 June 1983 of an occultation of a star by Neptune from Mauna Kea, Mount Stromlo, Siding Spring, and the Kuiper Airborne Observatory show no evidence for equatorial rings between 25,300 and 200,000 km (R/N/ = 25,269 km). Within most of this region, the upper limit on the optical depth along the line of sight, for rings broader than 6 km , is 0.04, which corresponds to a normal optical depth of 0.016. These results rule out a Neptunian ring system similar to that of Saturn or Uranus, but not a system of low optical depth similar to the Jovian rings. The data show no features that appear likely to have been caused by material in the equatorial plane of Neptune near the Roche limit.

  7. A Search for Planetary Eclipses of White Dwarfs in the Pan-STARRS1 Medium-deep Fields

    NASA Astrophysics Data System (ADS)

    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 ⊕. 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.

  8. 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.

  9. 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.

  10. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  12. 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

  13. 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

  14. Computational methods for the analysis of tag sequences in metagenomics studies.

    PubMed

    Chang, Qin; Luan, Yihui; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

    2012-06-01

    Metagenomics commonly refers to the study of genetic materials directly derived from environments without culturing. Several ongoing large-scale metagenomics projects related to human and marine life, as well as pedology studies, have generated enormous amounts of data, posing a key challenge for efficient analysis, as we try to 1) understand microbial organism assemblage under different conditions, 2) compare different communities, and 3) understand how microbial organisms associate with each other and the environment.To address such questions, investigators are using new sequencing technologies, including Sanger, Illumina Solexa, and Roche 454, to sequence either particular genes, called tag sequences, mostly 16S or 18S ribosomal RNA sequences or other conserved genes, or whole metagenome shotgun sequences of all the genetic materials in a given community. In this paper, we review computational methods used for the analysis of tag sequences.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Challenges and Rewards in Medicinal Chemistry Targeting Cardiovascular and Metabolic Diseases.

    PubMed

    Neidhart, Werner; Ackermann, Jean; Amrein, Kurt; Conte, Aurelia; Hunziker, Daniel; Kuhn, Bernd; Märki, Hans Peter; Nettekoven, Matthias; Ruf, Armin; Schulz-Gasch, Tanja; Mayweg, Alexander V

    2015-01-01

    Medicinal chemistry has been transformed by major technological and conceptual innovations over the last three decades: structural biology and bioinformatics, structure and property based molecular design, the concepts of multidimensional optimization (MDO), in silico and experimental high-throughput molecular property analysis. The novel technologies advanced gradually and in synergy with biology and Roche has been at the forefront. Applications in drug discovery programs towards new medicines in cardiovascular and metabolic diseases are highlighted to show impact and advancement: the early discovery of endothelin antagonists for endothelial dysfunction (Bosentan), 11-beta hydroxysteroid dehydrogenase (11β-HSD1) inhibitors for dysregulated cellular glucocorticoid tonus (type 2 diabetes and metabolic syndrome) and non-covalent hormone sensitive lipase (HSL) inhibitors to study the scope of direct inhibition of lipolysis in the conceptual frame of lipotoxicity and type 2 diabetes. PMID:26507592

  20. 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

  1. 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.

  2. New, faster blood test may make blood supply safer.

    PubMed

    1999-11-01

    Major blood suppliers in the United States are investigating a new HIV test that could move the country closer to a zero percent transmission rate. The Milwaukee Blood Center was the first in the nation to use the test, which identifies HIV infection two weeks earlier than standard tests. The test reduces the time period during which HIV infection is undetectable from 22 days to 10. The new test called nucleic acid amplification technology (NAT) was developed by Roche Molecular Systems and Chiron Corp. It identifies HIV genetic material circulating in the blood stream. America's Blood Centers has been testing NAT in 16 facilities. The procedure was initially developed to reduce the risk of transmitting hepatitis C, and a single sample can be used for testing both hepatitis C and HIV. The cost of using the new test would be an additional $5 to $7 per blood donation. NAT has not yet been licensed by the Food and Drug Administration.

  3. 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

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

    PubMed

    Lee, Tong Geon; Seo, Yong Weon

    2015-09-01

    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

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

    PubMed

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

    2015-06-03

    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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Karino, S.; Miller, J. C.

    2016-11-01

    Periodic pulsations have been found in emission from the ultraluminous X-ray source 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. Multicentre physiological reference values for some urinary component-to-creatinine (creatininium) concentration ratios.

    PubMed

    Fuentes-Arderiu, Xavier; Mas-Serra, Roser; de-Nó-Lengaran, Carmen; Espejo-López, Francisco; Filgueiras-Martínez, Paula; Gassiot-Cordomí, Paula; Idoate-Cervantes, Isabel; Poncela-García, María Victoria; Porras-Gracia, Juan; Sanz-Lobo, Irene; Viloria-Peñas, María del Mar; Juvé-Cuxart, Santiago

    2005-01-01

    Nine clinical laboratories in different regions of Spain have shared the search for reference individuals and the production of reference values for urinary component-to-creatininium concentration ratios measured in first morning urine samples using RD/Hitachi analysers. These urinary quantities include albumin, calcium(II), chloride, magnesium(II), phosphate, potassium ion, protein, sodium ion, urate and urea. All the logistic work was done in co-operation with the reagents' and analysers' supplier (Roche Diagnostics España, S.L., Sant Cugat del Vallès, Catalonia, Spain). From the blend of reference values obtained by each laboratory, the multicentre reference limits were estimated parametrically after mathematical transformation of original data.

  9. [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

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

    PubMed

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

    2010-09-01

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

  11. Saturn ring particles as dynamic ephemeral bodies

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

    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.

  12. U.N. drug initiative hits the ground.

    PubMed

    Cadman, J

    1998-06-01

    The Joint United Nations Programme on HIV/AIDS (UNAIDS) announced its HIV Drug Access Initiative in November 1997. Advisory boards oversee the Initiative, set national policy, and determine criteria for eligible participants. The program also provides drugs for opportunistic infections and sexually transmitted diseases. The initial phase of the program includes Uganda, the Ivory Coast, Chile, and Vietnam, although funding remains a problem. UNAIDS is helping with medical training in each country, and uses a computerized system to track participants and drug distribution. UNAIDS is also negotiating with pharmaceutical companies to provide drugs at subsidized costs. Glaxo Wellcome and Hoffman-LaRoche have committed to making their drugs and diagnostic kits available via the program; others are considering joining the effort. A major effort is underway by the program to reduce vertical transmission of HIV.

  13. 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.

  14. 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.

  15. 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.

  16. Analysis of the eclipsing binary ST Carinae using the SIMPLEX algorithm

    SciTech Connect

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

    1990-07-01

    This work presents the analyses of two UBV data sets for the Algol binary ST Carinae, presenting a homogeneous study of all the data. The light-curve parameters for the system are derived using the Wilson-Devinney model (1917), with the SIMPLEX algorithm as an optimization procedure, and a mass ratio of q=0.54 is obtained. The primary has colors consistent with a B9.5 V primary, and the solution indicates that the secondary is an F subgiant (Te=6200 K) that fills its Roche lobe. The application of Kepler's law (using the observed period and the mass ratio determined in this investigation) indicates that the absolute dimensions for the components are normal for their respective classes. A description of SIMPLEX is given, and its advantages for the solution of eclipsing binary parameters are discussed. 19 refs.

  17. Hα Variability in PTFO8-8695 and the Possible Direct Detection of Emission from a 2 Million Year Old Evaporating Hot Jupiter

    NASA Astrophysics Data System (ADS)

    Johns-Krull, Christopher M.; Prato, Lisa; McLane, Jacob N.; Ciardi, David R.; van Eyken, Julian C.; Chen, Wei; Stauffer, John R.; Beichman, Charles A.; Frazier, Sarah A.; Boden, Andrew F.; Morales-Calderón, Maria; Rebull, Luisa M.

    2016-10-01

    We use high time cadence, high spectral resolution optical observations to detect excess Hα emission from the 2–3 Myr old weak-lined T Tauri star PTFO 8-8695. This excess emission appears to move in velocity as expected if it were produced by the suspected planetary companion to this young star. The excess emission is not always present, but when it is, the predicted velocity motion is often observed. We have considered the possibility that the observed excess emission is produced by stellar activity (flares), accretion from a disk, or a planetary companion; we find the planetary companion to be the most likely explanation. If this is the case, the strength of the Hα line indicates that the emission comes from an extended volume around the planet, likely fed by mass loss from the planet which is expected to be overflowing its Roche lobe.

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

    PubMed

    Lanevschi, Anne; Kramer, John W.

    1996-01-01

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

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

    PubMed

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

    2015-04-28

    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. PMID:25815711

  20. Over-Contact Binary GR Tauri

    NASA Astrophysics Data System (ADS)

    Snyder, Lee

    2009-05-01

    New times of minima and ephemeredes are presented on the over-contact system GR Tauri. An observed minus calculated (O-C), times of minimum chart was constructed and based on statistical analysis the orbital period of the system is found to be decreasing with a rate of dP/dE = 3.33^-4 seconds Yr^-1 since 1931. Both components are filling their respective critical Roche lobes with fillouts f = 0.11 and 0.95. The light curve displays the O'Connell effect which is discussed on the assumption mass is going from the primary to the secondary creating a hot spot. The TRO, thermal relaxation oscillations (Lucy & Wilson 1979), theory is discussed as an explanation.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. [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

  6. 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.

  7. 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.

  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

    2014-05-20

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

  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. Photometric study of the eclipsing binary RR Leporis

    NASA Astrophysics Data System (ADS)

    Vyas, M. L.; Abhyankar, K. D.

    1989-11-01

    The eclipsing binary RR Leporis has been observed on 42 nights during 1982-1987 in standard U, B and V passbands. The complete light curves and photometric solutions for this binary system are presented. The preliminary elements derived by Russell-Merrill method were used as inputs in Wilson-Devinney's Differential Corrections Program. All the three light curves in UBV were treated simultaneously. Two different Mode 5 solutions, in which the secondary fills its roche lobe, fitted the light curves equally well. On comparing these photometric elements with those given by Samec et al. (1988), it was found that the solution is indeterminate because i and q are strongly correlated. In the absence of any accurate spectroscopic data, it is premature to derive absolute dimensions of the system. The most likely parameters are given.

  11. Challenges and Rewards in Medicinal Chemistry Targeting Cardiovascular and Metabolic Diseases.

    PubMed

    Neidhart, Werner; Ackermann, Jean; Amrein, Kurt; Conte, Aurelia; Hunziker, Daniel; Kuhn, Bernd; Märki, Hans Peter; Nettekoven, Matthias; Ruf, Armin; Schulz-Gasch, Tanja; Mayweg, Alexander V

    2015-01-01

    Medicinal chemistry has been transformed by major technological and conceptual innovations over the last three decades: structural biology and bioinformatics, structure and property based molecular design, the concepts of multidimensional optimization (MDO), in silico and experimental high-throughput molecular property analysis. The novel technologies advanced gradually and in synergy with biology and Roche has been at the forefront. Applications in drug discovery programs towards new medicines in cardiovascular and metabolic diseases are highlighted to show impact and advancement: the early discovery of endothelin antagonists for endothelial dysfunction (Bosentan), 11-beta hydroxysteroid dehydrogenase (11β-HSD1) inhibitors for dysregulated cellular glucocorticoid tonus (type 2 diabetes and metabolic syndrome) and non-covalent hormone sensitive lipase (HSL) inhibitors to study the scope of direct inhibition of lipolysis in the conceptual frame of lipotoxicity and type 2 diabetes.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. Comparison of next-generation sequencing systems.

    PubMed

    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.

  18. 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.

  19. 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

  20. 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.

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Nayak, M.; Asphaug, E.

    2016-08-01

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

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

    PubMed Central

    Nayak, M.; Asphaug, E.

    2016-01-01

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

  5. 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.

  6. 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.

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

    NASA Technical Reports Server (NTRS)

    Eaton, J. A.

    1978-01-01

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

  8. 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.

  9. Rapid laser nephelometric determination of amylase activity in serum and urine.

    PubMed

    Liu, T Z; Wei, J S

    1991-03-01

    We describe herein a rapid and sensitive laser nephelometric method for the determination of serum and urinary amylase activities. Our data showed that the change in relative light scattering (RLS) of an amylopectin substrate measured by a laser nephelometer related directly with amylolytic activity of amylase from 50 to 600 IU/L. Within-run variations at 293 and 769 IU/L sera showed CV's of 5.0% and 3.1%, respectively. Day-to-day variation for the same sera showed CV's of 7.2% and 4.7%, respectively. Correlation studies using the manual Phadebas dye-starch complex method and with the Roche amylochrome method showed correlation coefficients of 0.99 and 0.95, respectively. Using urine specimens, the correlation studies also showed a correlation coefficient of 0.98. These studies indicated that the proposed method was sensitive, fast, economical and easily adaptable to emergency and routine applications.

  10. 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

  11. A simple and sensitive method to extract bacterial, yeast and fungal DNA from blood culture material.

    PubMed

    Millar, B C; Jiru, X; Moore, J E; Earle, J A

    2000-10-01

    This study investigated the various commercially available kits and 'in-house' methods to extract DNA from Gram-negative and Gram-positive bacteria, yeast and fungal agents in commonly employed blood culture material. The main methods investigated were as follows; Qiagen QIAmp Blood kit, Roche high PCR template preparation kit, Puregene DNA extraction kit, boiling, glass beads/sonication and wash/alkali/heat lysis. The results indicated that a simple wash/alkali/heat lysis method was the most sensitive, reproducible, simple and cost-effective extraction method. This was the only method which removed any PCR inhibitors and inherent DNA which existed in virgin BacT/Alert aerobic, anaerobic and paediatric blood culture material. Contaminating microbial DNA from Lactococcus lactis or Bacillus coagulans was identified in all batches of BacT/Alert FAN aerobic blood culture material examined.

  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. [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.

  14. The coupled effect of tides and stellar winds on the evolution of compact binaries

    NASA Astrophysics Data System (ADS)

    Repetto, Serena; Nelemans, Gijs

    2014-10-01

    We follow the evolution of compact binaries under the coupled effect of tides and stellar winds until the onset of Roche lobe overflow. These binaries contain a compact object (either a black hole, a neutron star or a planet) and a stellar component. We integrate the full set of tidal equations, which are based on Hut's model for tidal evolution, and we couple them with the angular momentum loss in a stellar wind. Our aim is twofold. First, we wish to highlight some interesting evolutionary outcomes of the coupling. When tides are coupled with a non-massive stellar wind, one interesting outcome is that in certain types of binaries, the stellar spin tends to reach a quasi-equilibrium state, where the effects of tides and wind are counteracting each other. When tides are coupled with a massive wind, we parametrize the evolution in terms of the decoupling radius, at which the wind decouples from the star. Even for small decoupling radii, this wind braking can drive systems on the main sequence to Roche lobe overflow that otherwise would fail to do so. Our second aim is to inspect whether simple time-scale considerations are a good description of the evolution of the systems. We find that simple time-scale considerations, which rely on neglecting the coupling between tides and stellar winds, do not accurately represent the true evolution of compact binaries. The outcome of the coupled evolution of the rotational and orbital elements can strongly differ from simple time-scale considerations, as already pointed out by Barker and Ogilvie in the case of short-period planetary systems.

  15. High accuracy mutation detection in leukemia on a selected panel of cancer genes.

    PubMed

    Kalender Atak, Zeynep; De Keersmaecker, Kim; Gianfelici, Valentina; Geerdens, Ellen; Vandepoel, Roel; Pauwels, Daphnie; Porcu, Michaël; Lahortiga, Idoya; Brys, Vanessa; Dirks, Willy G; Quentmeier, Hilmar; Cloos, Jacqueline; Cuppens, Harry; Uyttebroeck, Anne; Vandenberghe, Peter; Cools, Jan; Aerts, Stein

    2012-01-01

    With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely BWA-SW and SSAHA2, coupled with the variant calling algorithm Atlas-SNP2 yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations.

  16. Continuous glucose monitoring in newborn infants: how do errors in calibration measurements affect detected hypoglycemia?

    PubMed

    Thomas, Felicity; Signal, Mathew; Harris, Deborah L; Weston, Philip J; Harding, Jane E; Shaw, Geoffrey M; Chase, J Geoffrey

    2014-05-01

    Neonatal hypoglycemia is common and can cause serious brain injury. Continuous glucose monitoring (CGM) could improve hypoglycemia detection, while reducing blood glucose (BG) measurements. Calibration algorithms use BG measurements to convert sensor signals into CGM data. Thus, inaccuracies in calibration BG measurements directly affect CGM values and any metrics calculated from them. The aim was to quantify the effect of timing delays and calibration BG measurement errors on hypoglycemia metrics in newborn infants. Data from 155 babies were used. Two timing and 3 BG meter error models (Abbott Optium Xceed, Roche Accu-Chek Inform II, Nova Statstrip) were created using empirical data. Monte-Carlo methods were employed, and each simulation was run 1000 times. Each set of patient data in each simulation had randomly selected timing and/or measurement error added to BG measurements before CGM data were calibrated. The number of hypoglycemic events, duration of hypoglycemia, and hypoglycemic index were then calculated using the CGM data and compared to baseline values. Timing error alone had little effect on hypoglycemia metrics, but measurement error caused substantial variation. Abbott results underreported the number of hypoglycemic events by up to 8 and Roche overreported by up to 4 where the original number reported was 2. Nova results were closest to baseline. Similar trends were observed in the other hypoglycemia metrics. Errors in blood glucose concentration measurements used for calibration of CGM devices can have a clinically important impact on detection of hypoglycemia. If CGM devices are going to be used for assessing hypoglycemia it is important to understand of the impact of these errors on CGM data.

  17. Carbon-Oxygen White Dwarfs Accreting CO-rich Matter. I. A Comparison between Rotating and Nonrotating Models

    NASA Astrophysics Data System (ADS)

    Piersanti, Luciano; Gagliardi, Simona; Iben, Icko, Jr.; Tornambé, Amedeo

    2003-02-01

    We investigate the lifting effect of rotation on the thermal evolution of CO white dwarfs accreting CO-rich matter. We find that rotation induces the cooling of the accreting structure so that the delivered gravitational energy causes a greater expansion with respect to the standard nonrotating case. The increase in the surface radius produces a decrease in the surface value of the critical angular velocity and, therefore, the accreting white dwarf becomes gravitationally unbound (Roche instability). This occurrence is due to an increase in the total angular momentum of the accreting white dwarf and depends critically on the amount of specific angular momentum deposited by the accreted matter. If the specific angular momentum of the accreted matter is equal to that of the outer layers of the accreting structure, the Roche instability occurs well before the accreting white dwarf can attain the physical conditions for carbon burning. If the values of both initial angular velocity and accretion rate are small, we find that the accreting white dwarf undergoes a secular instability when its total mass approaches 1.4 Msolar. At this stage, the ratio between the rotational energy and the gravitational binding energy of the white dwarf becomes of the order of 0.1, so that the star must deform by adopting an elliptical shape. In this case, since the angular velocity of the white dwarf is as large as ~1 rad s-1, the anisotropic mass distribution induces the loss of rotational energy and angular momentum via gravitational wave radiation. We find that, independent of the braking efficiency, the white dwarf contracts and achieves the physical conditions suitable for explosive carbon burning at the center so that a Type Ia supernova event is produced.

  18. Habitable Evaporated Cores: Converting Mini-Neptunes into Super- Earths in the Habitable Zone of M Dwarfs

    NASA Astrophysics Data System (ADS)

    Luger, R.; Barnes, R.; Lopez, E.; Fortney, J.; Jackson, B.; Meadows, V.

    2014-03-01

    The low masses and luminosities of M dwarfs make them ideal targets for thedetection of terrestrial planets in the habitable zone (HZ). However, studies suggest that planets formed only from material in the HZs of these stars are likely to be small and dry (e.g., Raymond et al. 2007). As a result, many of the planets that will be detected in the HZ by upcoming missions are probably the result of migration from beyond the snow line, and may have formed with large H/He envelopes (so-called mini-Neptunes). Here we show that photoevaporation and Roche lobe overflow of these planets can lead to the complete loss of their gaseous envelopes, transforming them into potentially habitable worlds, which we call “habitable evaporated cores”. We couple the planet structure models of Lopez et al. (2012) with a simple Roche lobe overflow scheme and the X-ray/extreme ultraviolet (XUV)-induced mass loss model of Erkaev et al. (2007). We also couple the orbital effects of anisotropic mass loss with tidal evolution and show that this coupling can lead to orbital changes that significantly enhance the mass loss rate.Habitable evaporated cores are most likely to form from small mini-Neptunes (≲4 M⊕) with large (≲50%) initial hydrogen fractions orbiting M4 stars and later. Given the steep decrease in stellar XUV flux with time (Ribas et al. 2005), mass loss is negligible after ~1 Gyr, at which point a habitable evaporated core is capable of degassing and maintaining a secondary atmosphere. This process may be the dominant formation mechanism for habitable planets around M dwarfs, and may be discovered by missions such as TESS and PLATO.

  19. 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

  20. MODULAR ANALYTICS: A New Approach to Automation in the Clinical Laboratory.

    PubMed

    Horowitz, Gary L; Zaman, Zahur; Blanckaert, Norbert J C; Chan, Daniel W; Dubois, Jeffrey A; Golaz, Olivier; Mensi, Noury; Keller, Franz; Stolz, Herbert; Klingler, Karl; Marocchi, Alessandro; Prencipe, Lorenzo; McLawhon, Ronald W; Nilsen, Olaug L; Oellerich, Michael; Luthe, Hilmar; Orsonneau, Jean-Luc; Richeux, Gérard; Recio, Fernando; Roldan, Esther; Rymo, Lars; Wicktorsson, Anne-Charlotte; Welch, Shirley L; Wieland, Heinrich; Grawitz, Andrea Busse; Mitsumaki, Hiroshi; McGovern, Margaret; Ng, Katherine; Stockmann, Wolfgang

    2005-01-01

    MODULAR ANALYTICS (Roche Diagnostics) (MODULAR ANALYTICS, Elecsys and Cobas Integra are trademarks of a member of the Roche Group) represents a new approach to automation for the clinical chemistry laboratory. It consists of a control unit, a core unit with a bidirectional multitrack rack transportation system, and three distinct kinds of analytical modules: an ISE module, a P800 module (44 photometric tests, throughput of up to 800 tests/h), and a D2400 module (16 photometric tests, throughput up to 2400 tests/h). MODULAR ANALYTICS allows customised configurations for various laboratory workloads. The performance and practicability of MODULAR ANALYTICS were evaluated in an international multicentre study at 16 sites. Studies included precision, accuracy, analytical range, carry-over, and workflow assessment. More than 700 000 results were obtained during the course of the study. Median between-day CVs were typically less than 3% for clinical chemistries and less than 6% for homogeneous immunoassays. Median recoveries for nearly all standardised reference materials were within 5% of assigned values. Method comparisons versus current existing routine instrumentation were clinically acceptable in all cases. During the workflow studies, the work from three to four single workstations was transferred to MODULAR ANALYTICS, which offered over 100 possible methods, with reduction in sample splitting, handling errors, and turnaround time. Typical sample processing time on MODULAR ANALYTICS was less than 30 minutes, an improvement from the current laboratory systems. By combining multiple analytic units in flexible ways, MODULAR ANALYTICS met diverse laboratory needs and offered improvement in workflow over current laboratory situations. It increased overall efficiency while maintaining (or improving) quality.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. The K2-ESPRINT Project I: Discovery of the Disintegrating Rocky Planet K2-22b with a Cometary Head and Leading Tail

    NASA Astrophysics Data System (ADS)

    Sanchis-Ojeda, R.; Rappaport, S.; Pallè, E.; Delrez, L.; DeVore, J.; Gandolfi, D.; Fukui, A.; Ribas, I.; Stassun, K. G.; Albrecht, S.; Dai, F.; Gaidos, E.; Gillon, M.; Hirano, T.; Holman, M.; Howard, A. W.; Isaacson, H.; Jehin, E.; Kuzuhara, M.; Mann, A. W.; Marcy, G. W.; Miles-Páez, P. A.; Montañés-Rodríguez, P.; Murgas, F.; Narita, N.; Nowak, G.; Onitsuka, M.; Paegert, M.; Van Eylen, V.; Winn, J. N.; Yu, L.

    2015-10-01

    We present the discovery of a transiting exoplanet candidate in the K2 Field-1 with an orbital period of 9.1457 hr: K2-22b. The highly variable transit depths, ranging from ∼0% to 1.3%, are suggestive of a planet that is disintegrating via the emission of dusty effluents. We characterize the host star as an M-dwarf with Teff ≃ 3800 K. We have obtained ground-based transit measurements with several 1-m class telescopes and with the GTC. These observations (1) improve the transit ephemeris; (2) confirm the variable nature of the transit depths; (3) indicate variations in the transit shapes; and (4) demonstrate clearly that at least on one occasion the transit depths were significantly wavelength dependent. The latter three effects tend to indicate extinction of starlight by dust rather than by any combination of solid bodies. The K2 observations yield a folded light curve with lower time resolution but with substantially better statistical precision compared with the ground-based observations. We detect a significant “bump” just after the transit egress, and a less significant bump just prior to transit ingress. We interpret these bumps in the context of a planet that is not only likely streaming a dust tail behind it, but also has a more prominent leading dust trail that precedes it. This effect is modeled in terms of dust grains that can escape to beyond the planet's Hill sphere and effectively undergo “Roche lobe overflow,” even though the planet's surface is likely underfilling its Roche lobe by a factor of 2.

  6. 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.

  7. On the Origin of Subdwarf B Stars and Related Metal-Rich Binaries

    NASA Astrophysics Data System (ADS)

    Green, E. M.; Liebert, J.; Saffer, R. A.

    2000-12-01

    Mounting evidence from subdwarf B (sdB) stars in the galactic field and their recently discovered counterparts in old open clusters indicates that at least two thirds of local disk sdB stars are binaries. Our recent radial velocity survey showed that binary sdB stars naturally divide into two groups with contrasting spectroscopic and kinematic properties. Those with detectable spectral lines from a cooler companion invariably have periods longer than a year. A larger number with periods on the order of hours or a few days have essentially invisible companions. We suggest that the long period sdB binaries must have been produced by Roche lobe overflow/mass transfer from low mass, metal-rich giants near the first red giant branch tip, without forming a common envelope. The same process should also occur at slightly lower red giant luminosities, producing a wide binary with a helium white dwarf instead of an sdB star. We present new evidence that most short period sdB's result from a common envelope following subsequent Roche lobe overflow of the initial secondary onto one of these white dwarfs. Rare post-common envelope sdB + main sequence (MS) binaries also exist, but available data suggest that most such systems involving lower MS companions probably merge. The two known MS survivors in short period sdB binaries have small and nearly identical masses, implying that the MS secondary must have lost a large fraction of its initial mass along with the envelope of the red giant sdB progenitor. This work was supported by NSF grant AST97-31655.

  8. 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%.

  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. HIV Viral Load Trends in Six Eastern Caribbean Countries Utilizing a Regional Laboratory Referral Service: Implications for Treatment as Prevention

    PubMed Central

    Landis, R. Clive; Carmichael-Simmons, Kelly; Hambleton, Ian R.; Best, Anton

    2015-01-01

    Objective Since 2009, seven countries in the Organization of Eastern Caribbean States (OECS), Antigua & Barbuda, Dominica, Grenada, Montserrat, St. Kitts & Nevis, Saint Lucia, and St. Vincent & the Grenadines, have been utilizing a laboratory referral service for HIV-1 viral load (VL) offered by The Ladymeade Reference Unit (LRU) Laboratory, Barbados. The objective of this study was to evaluate 5 year VL trends in the six larger OECS countries participating in this regional referral service. Methods Blood samples were collected in source countries and transported to Barbados as frozen plasma according to a standardized protocol. Plasma specimens were amplified by RT PCR on a Roche TaqMan 48 analyser (Roche Diagnostics, Panama City, Panama). VL was considered optimally suppressed below a threshold level of < 200 HIV-1 copies/mL of blood. The same threshold was used as a binary indicator in an analysis of the secular change in VL suppression. Montserrat was excluded due to insufficient number of samples. Results A steady rise in VL referrals from OECS countries was recorded, rising from 312 samples in 2009 to 1,060 samples in 2013. A total of 3,543 samples were tested, with a sample rejection rate (9.2%) mostly due to breaks in the cold chain. Aggregate VL data showed the odds of VL suppression in the Eastern Caribbean improved by 66% for each additional year after 2009 (Odds Ratio 1.66 [95% CI 1.46 to 1.88]; p<0.001). Conclusion We demonstrate the feasibility of establishing a regional laboratory referral service for HIV VL monitoring in the Eastern Caribbean. Aggregate VL trends showed a significant year-on-year improvement in VL suppression, implying public health benefits through treatment as prevention in the OECS. VL provides a powerful monitoring & evaluation tool for strengthening HIV programs at country level among the small island states participating in this regional referral network. PMID:25923741

  11. 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.

  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.

  13. 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.

  14. Are Young Hot Jupiters Tidally Disrupted And "downsized" To Super-Earths?

    NASA Astrophysics Data System (ADS)

    Nayakshin, Sergei

    2011-09-01

    Boley, Nayakshin and others have recently suggested that young massive gaseous proto-planets migrate faster than they contract and are therefore tidally disrupted. The disruption may "downside" the planets into Neptunes or Earth-sized planets. However, this potentially interesting scenario for planet formation has not yet been detailed. We present detailed calculations that may shed unbiased light on the utility of these ideas. In particular, we (Nayakshin and Lodato, in prep.) model numerically the viscous gas disc evolution together with the radial migration of the giant gaseous planet embedded in the disc. The planet typically fills its Roche lobe at the planet-star separation of about 0.05 to 0.1 AU. The material overflowing the Roche lobe is deposited in the disc interior of the planet, which fuels a major protostellar accretion outburst rising on the time-scales of years. The result of the planet's disruption depends on the radius-mass relation for the planet and whether the gap in the disc remains opened or not. If planet does not expand as it looses mass, or does so slowly, then there is a quasi-steady regime. This regime is well known from stellar binaries. The secondary (the planet here) looses mass to the primary and moves OUTWARD due to the conservation of angular momentum (overpowering the outer disc torques). When the gap is partially closed, the planet's steady-state outward migration< falters, and the gaseous envelope can be destroyed very rapidly. Only solid cores survive such disruptions. However, if the partially disrupted giant contracts faster than it migrates, the result is a solid core surrounded by smaller (than the original) gaseous envelope, e.g. Neptune or Saturn-type planets. We plan to include detailed theoretical planet models (a la Baraffe et al) for detailed comparisons of our calculations with observations of "hot" exoplanets and the FU Ori outburst lightcurves.

  15. Late-Type Near-Contact Eclipsing Binary [HH97] FS Aur-79

    NASA Astrophysics Data System (ADS)

    Austin, S. J.; Robertson, J. W.; Tycner, C.; Campbell, T.; Honeycutt, R. K.

    2007-05-01

    The secondary photometric standard star number 79 for the FS Aur field (Henden & Honeycutt 1997), designated as [HH97] FS Aur-79 (GSC 1874-399), is a short-period (0.2508 days) eclipsing binary whose light curve is a combination of the β Lyr and BY Dra type variables. High signal-to-noise ratio multicolor photometry was obtained using the US Naval Observatory 1 m telescope. These light curves show asymmetry at quadrature phases (the O'Connell effect), which can be modeled with the presence of starspots. A low-resolution spectrum obtained with the 3.5 m Wisconsin-Indiana-Yale-NOAO telescope at orbital phase 0.76 is consistent with a spectral type of dK7e and dM3e. A radial velocity curve for the primary star was constructed using 24 high-resolution spectra from the 9.2 m Hobby-Eberly Telescope. Spectra show Hα and Hβ in emission confirming chromospheric activity and possibly the presence of circumstellar material. Binary star models that simultaneously fit the U, B, V, R, and radial velocity curves are those with a primary star of mass 0.59+/-0.02 Msolar, temperature 4100+/-25 K, and mean radius 0.67 Rsolar, just filling its Roche lobe, and a secondary star of mass 0.31+/-0.09 Msolar, temperature 3425+/-25 K, and mean radius 0.48 Rsolar, just within its Roche lobe. An inclination angle of 83deg+/-2deg with a center-of-mass separation of 1.62 Rsolar is also derived. Starspots, expected for a rotation period of less than 1 day, had to be included in the modeling to fit the O'Connell effect.

  16. Formation of redbacks via accretion-induced collapse

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    We examine the growing class of binary millisecond pulsars known as redbacks. In these systems, the pulsar's companion has a mass between 0.1 and about 0.5 M⊙ in an orbital period of less than 1.5 d. All show extended radio eclipses associated with circumbinary material. They do not lie on the period-companion mass relation expected from the canonical intermediate-mass X-ray binary evolution in which the companion filled its Roche lobe as a red giant and has now lost its envelope and cooled as a white dwarf. The redbacks lie closer to, but usually at higher period than, the period-companion mass relation followed by cataclysmic variables and low-mass X-ray binaries. In order to turn on as a pulsar mass accretion on to a neutron star must be sufficiently weak, considerably weaker than expected in systems with low-mass main-sequence companions driven together by magnetic braking or gravitational radiation. If a neutron star is formed by accretion-induced collapse of a white dwarf as it approaches the Chandrasekhar limit some baryonic mass is abruptly lost to its binding energy so that its effective gravitational mass falls. We propose that redbacks form when accretion-induced collapse of a white dwarf takes place during cataclysmic variable binary evolution because the loss of gravitational mass makes the orbit expand suddenly so that the companion no longer fills its Roche lobe. Once activated, the pulsar can ablate its companion and so further expand the orbit and also account for the extended eclipses in the radio emission of the pulsar that are characteristic of these systems. The whole period-companion mass space occupied by the redbacks can be populated in this way.

  17. 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.

  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. The effect of tides on the population of PN from interacting binaries

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    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 planetary nebula (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 overabundance of post-interaction central stars of PN cannot be easily explained considering the uncertainties. We examine a range of explanations for this discrepancy.

  20. Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa.

    PubMed

    Hiremath, Pavana J; Farmer, Andrew; Cannon, Steven B; Woodward, Jimmy; Kudapa, Himabindu; Tuteja, Reetu; Kumar, Ashish; Bhanuprakash, Amindala; Mulaosmanovic, Benjamin; Gujaria, Neha; Krishnamurthy, Laxmanan; Gaur, Pooran M; Kavikishor, Polavarapu B; Shah, Trushar; Srinivasan, Ramamurthy; Lohse, Marc; Xiao, Yongli; Town, Christopher D; Cook, Douglas R; May, Gregory D; Varshney, Rajeev K

    2011-10-01

    Chickpea (Cicer arietinum L.) is an important legume crop in the semi-arid regions of Asia and Africa. Gains in crop productivity have been low however, particularly because of biotic and abiotic stresses. To help enhance crop productivity using molecular breeding techniques, next generation sequencing technologies such as Roche/454 and Illumina/Solexa were used to determine the sequence of most gene transcripts and to identify drought-responsive genes and gene-based molecular markers. A total of 103,215 tentative unique sequences (TUSs) have been produced from 435,018 Roche/454 reads and 21,491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49,437 (47.8%) of the TUSs, and gene ontology assignments were determined for 20,634 (41.7%) of the TUSs. Comparison of the chickpea TUSs with the Medicago truncatula genome assembly (Mt 3.5.1 build) resulted in 42,141 aligned TUSs with putative gene structures (including 39,281 predicted intron/splice junctions). Alignment of ∼37 million Illumina/Solexa tags generated from drought-challenged root tissues of two chickpea genotypes against the TUSs identified 44,639 differentially expressed TUSs. The TUSs were also used to identify a diverse set of markers, including 728 simple sequence repeats (SSRs), 495 single nucleotide polymorphisms (SNPs), 387 conserved orthologous sequence (COS) markers, and 2088 intron-spanning region (ISR) markers. This resource will be useful for basic and applied research for genome analysis and crop improvement in chickpea.

  1. Novel Degenerate PCR Method for Whole-Genome Amplification Applied to Peru Margin (ODP Leg 201) Subsurface Samples.

    PubMed

    Martino, Amanda J; Rhodes, Matthew E; Biddle, Jennifer F; Brandt, Leah D; Tomsho, Lynn P; House, Christopher H

    2012-01-01

    A degenerate polymerase chain reaction (PCR)-based method of whole-genome amplification, designed to work fluidly with 454 sequencing technology, was developed and tested for use on deep marine subsurface DNA samples. While optimized here for use with Roche 454 technology, the general framework presented may be applicable to other next generation sequencing systems as well (e.g., Illumina, Ion Torrent). The method, which we have called random amplification metagenomic PCR (RAMP), involves the use of specific primers from Roche 454 amplicon sequencing, modified by the addition of a degenerate region at the 3' end. It utilizes a PCR reaction, which resulted in no amplification from blanks, even after 50 cycles of PCR. After efforts to optimize experimental conditions, the method was tested with DNA extracted from cultured E. coli cells, and genome coverage was estimated after sequencing on three different occasions. Coverage did not vary greatly with the different experimental conditions tested, and was around 62% with a sequencing effort equivalent to a theoretical genome coverage of 14.10×. The GC content of the sequenced amplification product was within 2% of the predicted values for this strain of E. coli. The method was also applied to DNA extracted from marine subsurface samples from ODP Leg 201 site 1229 (Peru Margin), and results of a taxonomic analysis revealed microbial communities dominated by Proteobacteria, Chloroflexi, Firmicutes, Euryarchaeota, and Crenarchaeota, among others. These results were similar to those obtained previously for those samples; however, variations in the proportions of taxa identified illustrates well the generally accepted view that community analysis is sensitive to both the amplification technique used and the method of assigning sequences to taxonomic groups. Overall, we find that RAMP represents a valid methodology for amplifying metagenomes from low-biomass samples.

  2. 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

  3. 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

  4. [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

  5. Variation in Methods of Predicting Adult Height in Children with Idiopathic Short Stature

    PubMed Central

    Topor, Lisa Swartz; Feldman, Henry A.; Bauchner, Howard; Cohen, Laurie E.

    2013-01-01

    Objective Recombinant human growth hormone (GH) is approved for treatment of children with idiopathic short stature (ISS). Endocrinologists often depend on algorithms to predict adult height. As algorithm performance is often included in treatment decision, we sought to evaluate agreement among height prediction formulas. Methods We identified 3 commonly used algorithms for height prediction: Bayley-Pinneau (BP), Roche-Wainer-Thissen (RWT), and Khamis-Roche (KR). We constructed simulated samples of children with typical distributions of ages, heights, weights, bone ages, and parental heights seen in patients with ISS, and applied the algorithms to the simulated children to determine if predicted adult height was <160 cm for boys or <150 cm for girls, the 1.2nd height percentiles for adults. Results We found substantial disagreement amongst algorithms in the percentage of simulated children with predicted adult height < 1.2nd percentile, a cut-off that may influence GH treatment decisions. Using the BP formula, 43% of boys and 81% of girls had predicted adult height below this threshold, whereas only 3% of boys and 0.2% of girls had predicted heights < 1.2nd percentile using the KR method. RWT predictions fell in between. Overall agreement of the methods was poor (kappa = 0.21) in boys and negative in girls. Conclusions Wide variation exists among formulas used to predict adult height. As these algorithms may be used in decisions about whether to initiate GH treatment and to assess GH’s efficacy in research trials, it is important for parents, pediatricians, and investigators to recognize the considerable variation involved in height prediction. PMID:20974789

  6. [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.

  7. A possible scenario of the flaring activity in AE Aqr

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    The flow structure in magnetic cataclysmic variables with strong magnetic field and fast rotation of the white dwarf was investigated. We model the AE Aqr system as a representative observational object whose spin period of the white dwarf is about 1000 times shorter than the orbital period of the system. Observations show that in spite of the fast rotation some part of the material from the inner Lagrangian point is present in the Roche lobe of the white dwarf. We analyze the possible physical mechanisms that can lead to the less effective angular momentum transfer from the rotating magnetosphere to the inflowing material. Among these mechanisms are the ambipolar diffusion, the pressure of the magneto-dipole radiation, the relativistic retard of magnetic field lines and the incomplete penetration of the magnetic field to plasma. Results of our analysis show that the last mechanism is the most effective. Taking this effect into account we can find the flow structure that is in an agreement with observations. The unique flaring activity is the most prominent property of the AE Aqr system. In this system, the active and quiescent phases alternate. The flaring activity may be caused by the transitions between the laminar and turbulent regimes. In the laminar regime, the flow goes around the star and collides with the material flowing from the inner Lagrangian point. As a result the shock occurs which produces the flow turbulence. In the turbulent regime, the magnetosphere pushes the material away from the Roche lobe of the white dwarf and the flow becomes quickly laminar again.

  8. 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).

  9. 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

  10. THE K2-ESPRINT PROJECT. I. DISCOVERY OF THE DISINTEGRATING ROCKY PLANET K2-22b WITH A COMETARY HEAD AND LEADING TAIL

    SciTech Connect

    Sanchis-Ojeda, R.; Rappaport, S.; Dai, F.; Pallè, E.; Delrez, L.; DeVore, J.; Gandolfi, D.; Fukui, A.; Ribas, I.; Stassun, K. G.; Albrecht, S.; Gaidos, E.; Gillon, M.; Hirano, T.; and others

    2015-10-20

    We present the discovery of a transiting exoplanet candidate in the K2 Field-1 with an orbital period of 9.1457 hr: K2-22b. The highly variable transit depths, ranging from ∼0% to 1.3%, are suggestive of a planet that is disintegrating via the emission of dusty effluents. We characterize the host star as an M-dwarf with T{sub eff} ≃ 3800 K. We have obtained ground-based transit measurements with several 1-m class telescopes and with the GTC. These observations (1) improve the transit ephemeris; (2) confirm the variable nature of the transit depths; (3) indicate variations in the transit shapes; and (4) demonstrate clearly that at least on one occasion the transit depths were significantly wavelength dependent. The latter three effects tend to indicate extinction of starlight by dust rather than by any combination of solid bodies. The K2 observations yield a folded light curve with lower time resolution but with substantially better statistical precision compared with the ground-based observations. We detect a significant “bump” just after the transit egress, and a less significant bump just prior to transit ingress. We interpret these bumps in the context of a planet that is not only likely streaming a dust tail behind it, but also has a more prominent leading dust trail that precedes it. This effect is modeled in terms of dust grains that can escape to beyond the planet's Hill sphere and effectively undergo “Roche lobe overflow,” even though the planet's surface is likely underfilling its Roche lobe by a factor of 2.

  11. Formation of Multiple-satellite Systems From Low-mass Circumplanetary Particle Disks

    NASA Astrophysics Data System (ADS)

    Hyodo, Ryuki; Ohtsuki, Keiji; Takeda, Takaaki

    2015-01-01

    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.

  12. Characterization of a new highly sensitive immunometric assay for thyroglobulin with reduced interference from autoantibodies.

    PubMed

    Broughton, Marianne Nordlund; Nome, Ragnhild; Sandven, Ingvill; Paus, Elisabeth; Bjøro, Trine

    2016-06-01

    Measurements of serum thyroglobulin (Tg) with sensitive immunoassays are of great importance for the management of patients with differentiated thyroid carcinomas. However, interference of circulating autoantibodies to Tg (hTgAb) hampers the usefulness of most assays. We have produced a panel of monoclonal antibodies (mAbs) selected to bind Tg in the presence of Tg autoantibodies and developed a sensitive immunoassay for Tg with minor interference by hTgAbs. The antibodies were characterized by cross-inhibition and immunoassay combination studies, as well as affinity estimation. The within-run and total imprecision of the assay were determined with 2664 samples in 60 separate runs. The most sensitive assay combination with superior protection against autoantibodies consisted of two solid phase mAbs and two tracer mAbs with distinct binding sites. The assay was linear and displayed a wide dynamic range up to 1342 μg/l with a functional sensitivity of 0.1 μg/l and a total imprecision of less than 10 %. There was good agreement between the new high sensitive immunofluorometric assay (IFMA) and two well-established Tg assays from Brahms Kryptor and Roche Diagnostics. Mean difference between the new IFMA and the Kryptor assay was 0.059 μg/l with a 95 % confidence interval of -0.032 to 0.151 μg/l, whereas the mean difference between the new IFMA and the Roche assay was -0.80 μg/l with a 95 % confidence interval of -1.24 to -0.35 μg/l.

  13. Comparison of real-time multiplex human papillomavirus (HPV) PCR assays with the linear array HPV genotyping PCR assay and influence of DNA extraction method on HPV detection.

    PubMed

    Roberts, Christine C; Swoyer, Ryan; Bryan, Janine T; Taddeo, Frank J

    2011-05-01

    Real-time human papillomavirus (HPV) type-specific multiplex PCR assays were developed to detect HPV DNA in specimens collected for the efficacy determination of the quadrivalent HPV (type 6, 11, 16, and 18) L1 virus-like particle (VLP) vaccine (Gardasil). We evaluated the concordance between type-specific multiplex HPV PCR and the widely used, commercially available Roche Linear Array genotyping PCR assay. Female genital swab specimens were tested for the presence of L1, E6, and E7 sequences of HPV type 6 (HPV6), HPV11, HPV16, HPV18, HPV31, HPV45, HPV52, and HPV58 and E6 and E7 sequences of HPV33, HPV35, HPV39, HPV51, HPV56, and HPV59 in type- and gene-specific real-time multiplex PCR assays. Specimens were also tested for the presence of L1 sequences using two versions of the Roche Linear Array genotyping assay. Measures of concordance of a modified version of the Linear Array and the standard Linear Array PCR assay were evaluated. With specimen DNA extraction using the Qiagen Spin blood kit held as the constant, multiplex PCR assays detect more HPV-positive specimens for the 14 HPV types common to both than either version of the Linear Array HPV genotyping assay. Type-specific agreements between the assays were good, at least 0.838, but were often driven by negative agreement in HPV types with low prevalence, as evidenced by reduced proportions of positive agreement. Overall HPV status agreements ranged from 0.615 for multiplex PCR and standard Linear Array to 0.881 for multiplex PCR and modified Linear Array. An alternate DNA extraction technique, that used by the Qiagen MinElute kit, impacted subsequent HPV detection in both the multiplex PCR and Linear Array assays.

  14. [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

  15. On the evolution of the nova-like variable AE Aquarii

    NASA Astrophysics Data System (ADS)

    Meintjes, P. J.

    2002-10-01

    A possible evolution for the enigmatic cataclysmic variable AE Aquarii is considered that may put into context the long orbital period and short white dwarf rotation period compared with other DQ Her systems. It has been shown that mass transfer could have been initiated when the secondary KIV-V star was already somewhat evolved when it established Roche lobe contact. In this initial phase the orbital period of the system was probably Porb,i~ 8.5 h, and the white dwarf rotation period P*,i > 1 h. Mass transfer in the form of diamagnetic gas blobs will result in an initial discless accretion process, resulting in an efficient drain of the binary orbital angular momentum. Since the initial mass ratio of the binary was probably qi~ 0.8, a high mass transfer rate and a slow expansion of the Roche lobe of the secondary star followed, accompanied by a fast expanding secondary following the mass loss. This could have resulted in the KIV-V secondary flooding its Roche surface, causing a run-away mass transfer of that lasted for approximately , during which time the binary expanded to an orbital period of approximately Porb~ 11 h. During this phase the mass accretion rate on to the surface of the white dwarf most probably exceeded the critical value for stable nuclear burning , which could have resulted in AE Aqr turning into an ultrasoft X-ray source. The high mass transfer terminated when a critical mass ratio of qcrit= 0.73 was reached. Disc torques spun-up the white dwarf to a period close to 33 s within the time-scale before the high mass transfer shut down when qcrit was reached. The decrease in the mass loss of the secondary allowed it to re-establish hydrostatic equilibrium on the dynamical time-scale (fraction of a day). From this point when qcrit is reached the mass transfer and binary evolution proceed at a slower rate since mass transfer from the secondary star is driven by magnetic braking of the secondary on a time-scale , which is the same as the thermal time

  16. [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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. The x-ray and spectropolarimetric view of mass loss and transfer in massive binary stars

    NASA Astrophysics Data System (ADS)

    Lomax, Jamie R.

    2013-03-01

    The majority of massive stars are members of binary systems. In order to have a better understanding of their evolutionary pathways, the mass and angular momentum loss from massive binaries needs to be well understood. Self consistent explanations for their behavior need to be valid across many wavelength regimes in order to illuminate key phases of mass loss to completely determine how it affects their evolution. In this dissertation I present the results of X-ray and specropolarimetric studies on one Roche-lobe overflow binary (beta Lyr) and two colliding wind binaries (V444 Cyg and WR 140). In beta Lyr a repeatable discrepancy between the secondary eclipse in total and polarized light indicates that an accretion hot spot has formed on the edge of the disk in the system. This hot spot may also be the source of the bipolar outflows within the system. The existence of a hot spot and its relationship to bipolar outflows is important in understanding the mass transfer dynamics of Roche-lobe overflow binaries. The absorption of the 2.0 keV spectral fit component in V444 Cyg suggests that the shock has a large opening angle while analysis of the X-ray light curves places the stagnation point farther away from the O star than theoretically expected. Combining this with evidence of polarimetric variability in V444 Cyg's optical emission lines shows that the effects of radiative inhibition or braking are significant for this close binary and may be important in other colliding wind systems. Long term X-ray monitoring of the shock formed by the winds in WR 140 shows conflicting evidence for unexpected intrinsic hard X-ray emission. Spectral analysis shows that the low energy thermal tail is causing the observed higher energy emission. On the other hand, light curve analysis of the absorption feature near periastron passage suggests that there may be intrinsic hard X-ray emission from the system. WR 140's polarimetric behavior is consistent with the formation of dust near

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Diagnostic accuracy of sensitive or high-sensitive troponin on presentation for myocardial infarction: a meta-analysis and systematic review

    PubMed Central

    Sethi, Ankur; Bajaj, Anurag; Malhotra, Gurveen; Arora, Rohit R; Khosla, Sandeep

    2014-01-01

    Background Recently, high-sensitive troponin (hsTrop) assays consistent with professional societies’ recommendations became available. We aimed to summarize the evidence on the diagnostic accuracy of hsTrop on presentation. Methods We searched electronic databases for studies evaluating the diagnostic accuracy of hsTrop in suspected acute coronary syndrome (ACS) patients. Random effect meta-analyses and meta-regression were performed. Primary and secondary analyses were restricted to studies using conventional Trop and hsTrop in the reference standard, respectively. Results Fifteen studies with a total of 8,628 patients met the inclusion criteria for the primary analysis. hsTrop T (Hoffman-La Roche Ltd) and hsTrop I (Siemens) had sensitivities of 0.89 (95% confidence interval [CI]: 0.86–0.91) and 0.90 (95% CI: 0.87–0.92) and specificities of 0.79 (95% CI: 0.77–0.80) and 0.89 (95% CI: 0.87–0.90), respectively. There was no statistically significant difference in the area under the curve between hsTrop (95% CI: 0.920) and conventional Trop (95% CI: 0.929) at the 99th percentile (P=0.62). hsTrop at the level of detection had a sensitivity of 0.97 (95% CI: 0.96–0.98) and a specificity of 0.41 (95% CI: 0.40–0.42). The studies using a cut-off at coefficient of variance <10% as opposed to the 99th percentile for the conventional assay used for diagnosis reported higher diagnostic accuracy (relative diagnostic odds ratio =2.13, P=0.02). Five studies were included in the secondary analysis; hsTrop T (Hoffman-La Roche Ltd) had a sensitivity of 0.91 (95% CI: 0.89–0.93) and a specificity of 0.67 (95% CI: 0.63–0.70). There was significant heterogeneity among the studies. Conclusion hsTrop have excellent diagnostic accuracy for myocardial infarction on presentation, but may not outperform conventional Trop assays. The variation among the studies can be explained, in part, by the cut-off used for conventional Trop assays. PMID:25092986

  12. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood

    PubMed Central

    2014-01-01

    Background The introduction of benchtop sequencers has made adoption of whole genome sequencing possible for a broader community of researchers than ever before. Concurrently, metagenomic sequencing (MGS) is rapidly emerging as a tool for interrogating complex samples that defy conventional analyses. In addition, next-generation sequencers are increasingly being used in clinical or related settings, for instance to track outbreaks. However, information regarding the analytical sensitivity or limit of detection (LoD) of benchtop sequencers is currently lacking. Furthermore, the specificity of sequence information at or near the LoD is unknown. Results In the present study, we assess the ability of three next-generation sequencing platforms to identify a pathogen (viral or bacterial) present in low titers in a clinically relevant sample (blood). Our results indicate that the Roche-454 Titanium platform is capable of detecting Dengue virus at titers as low as 1X102.5 pfu/mL, corresponding to an estimated 5.4X104 genome copies/ml maximum. The increased throughput of the benchtop sequencers, the Ion Torrent PGM and Illumina MiSeq platforms, enabled detection of viral genomes at concentrations as low as 1X104 genome copies/mL. Platform-specific biases were evident in sequence read distributions as well as viral genome coverage. For bacterial samples, only the MiSeq platform was able to provide sequencing reads that could be unambiguously classified as originating from Bacillus anthracis. Conclusion The analytical sensitivity of all three platforms approaches that of standard qPCR assays. Although all platforms were able to detect pathogens at the levels tested, there were several noteworthy differences. The Roche-454 Titanium platform produced consistently longer reads, even when compared with the latest chemistry updates for the PGM platform. The MiSeq platform produced consistently greater depth and breadth of coverage, while the Ion Torrent was unequaled for speed of

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. The formation of the light-ion trough and peeling off the plasmasphere

    NASA Astrophysics Data System (ADS)

    Lemaire, J. F.

    2001-07-01

    The plasma density gradients in the outer drift shells of the plasmasphere are generally stable with respect to convective instability during quiet geomagnetic-geoelectric conditions. When the IMF turns southward before the onset of a magnetic substorm, this situation gradually changes: the magnetospheric convection electric field is then enhanced and penetrates deeper in the nightside plasmasphere. The sunward and eastward magnetospheric convection velocity is enhanced in the post-midnight local time sector at /L>4, and occasionally down to /L=2.5. As a result of this enhancement of the azimuthal component of the convection velocity, centrifugal effects are augmented in the distant region of the magnetosphere; the field-aligned potential energy of ions and electrons is reduced along the equatorial portion of magnetic field lines; the field-aligned plasma density distribution, initially in mechanical equilibrium, is accelerated and becomes convectively unstable. As a consequence, a field-aligned polar-wind-like flow of H+-ions (and He+-ions) is driven upward and the mid-latitude ionosphere gets depleted of its light ions. The plasma density at high altitudes diminishes in all flux tubes whose angular speed has been enhanced. It does not change significantly, however, on lower L-shells where the convection velocity has not changed. As a result of the shear in the upward ionization flow, a ``knee'' develops in the cross-L plasma density distribution along the drift shell which is tangent to a surface which has been called the Roche limit surface or zero-parallel-force surface. As a result of Coulomb collisions and wave-particle interaction, the upflowing particles that are able to overcome the reduced potential barrier may become trapped, and will tend to accumulate in the equatorial potential well beyond this zero-parallel-force surface. But, quasi-interchange - a type of ballooning instability driven by gravitational force or centrifugal effects - prevents this

  19. 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

  20. SAMBA HIV Semiquantitative Test, a New Point-of-Care Viral-Load-Monitoring Assay for Resource-Limited Settings

    PubMed Central

    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

    2014-01-01

    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