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Sample records for cobas taqscreen mpx

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

    PubMed

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

    2008-09-01

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

  2. A significantly lower potency observed for the 3rd WHO International Standard for Parvovirus B19V DNA with the cobas TaqScreen DPX test.

    PubMed

    Pisani, G; Cristiano, K; Fabi, S; Simeoni, M; Marino, F; Gaggioli, A

    2016-08-01

    In the context of the Official Medicines Control Laboratories plasma pool testing for Parvovirus B19 DNA, we use the cobas TaqScreen DPX test. When we re-evaluated this method using the 3rd B19 DNA WHO IS at the final concentration of 4 log IU/mL, we observed a titre lower than expected, i.e. 3.79 log IU/mL. Therefore, we further investigated the accuracy of the DPX test. The following B19V DNA materials were tested by using both the DPX test and an in-house real-time PCR: The 1st, 2nd and 3rd WHO ISs for B19V DNA The Non WHO B19V DNA Reference Material for NAT The Biological Reference Preparation B19 virus DNA for NAT testing, batch 1 . The DPX test showed a good accuracy for all B19V DNA materials with the exception of the 3rd WHO IS for B19V DNA. In fact, an underestimation of about 38% was observed for all dilutions of this standard with respect to the nominal titre. With the B19V in-house real-time PCR, all four materials proved to be well calibrated against the 1(st) WHO IS for B19V DNA, used as external standard curve. In this study, we demonstrated that the DPX test underestimates the B19V DNA content of the 3rd WHO IS for B19V DNA and that this is not due to an incorrect potency assigned to the standard but, most probably, to a mismatch between the primers/probe and the sequence of the target region in the 3rd WHO IS for B19V DNA. © 2016 International Society of Blood Transfusion.

  3. Detection and identification of occult HBV in blood donors in Taiwan using a commercial, multiplex, multi-dye nucleic acid amplification technology screening test.

    PubMed

    Lin, K T; Chang, C L; Tsai, M H; Lin, K S; Saldanha, J; Hung, C M

    2014-02-01

    The ability of a new generation commercial, multiplex, multi-dye test from Roche, the cobas TaqScreen MPX test, version 2.0, to detect and identify occult HBV infections was evaluated using routine donor samples from Kaohsiung Blood Bank, Taiwan. A total of 5973 samples were tested by nucleic acid amplification technology (NAT); 5898 in pools of six, 66 in pools of less than six and nine samples individually. NAT-reactive samples were retested with alternative NAT tests, and follow-up samples from the donors were tested individually by NAT and for all the HBV serological markers. Eight NAT-only-reactive donors were identified, and follow-up samples were obtained from six of the donors. The results indicated that all eight donors had an occult HBV infection with viral loads <12 IU/ml. The cobas(®) TaqScreen MPX test, version 2.0, has an advantage over the current Roche blood screening test, the cobas TaqScreen MPX test, for screening donations in countries with a high prevalence of occult HBV infections since the uncertainty associated with identifying samples with very low viremia is removed by the ability of the test to identify the viral target in samples that are reactive with the cobas TaqScreen MPX test, version 2.0. © 2013 International Society of Blood Transfusion.

  4. Comparison of telogen hair analyses: genRES MPX-2SP kit versus genRES MPX-SP1 and genRES MPX-SP2 kits.

    PubMed

    Schmid, D; Bayer, B; Anslinger, K

    2008-12-01

    STR investigations of telogen hair are invariably difficult due to the small amounts of nuclear DNA and its degradation products. However, in recent years there has been a considerable improvement. This study examined the suitability of a new STR kit with shortened amplicons for the investigation of hair in routine casework. This kit allows the simultaneous amplification of the eight STR-loci D3S1358, VWA, FGA, TH01, SE33, D8S1179, D18S51, and D21S11, and the sex-determining amelogenin system. It was tested against the genRES MPX-SP1 and genRES MPX-SP2 kits. The sensitivity of the new genRES MPX-2SP kit was demonstrated to be inferior to that of the genRES MPX-SP1, but almost equal to that of the genRES MPX-SP2 kit.

  5. Photoelectrochemical response of some layered chalcogenophosphate compounds /MPX3/

    NASA Technical Reports Server (NTRS)

    Byvik, C. E.; Reichman, B.; Coleman, D. W.

    1982-01-01

    New photoelectrochemical results for the layered chalcogenophosphate compounds MPX3, FePS3, NiPS3, and SnPS3 are presented. The compounds were grown by iodine vapor transport in quartz ampules from a stoichiometric amount of the elements. Crystals of the layered type up to 10 mm x 10 mm x 0.1 mm were grown. The results of the layered compounds from the MPX3 series show good stability in acid solutions under photoelectrolysis condition. The relatively slow increase in the photocurrent with increasing electrode potential suggests high recombination rates for the photogenerated carriers in these layered materials. It is noted that improvements may be possible by, for example, optimizing the preparation of the crystals and the electrode surfaces.

  6. MPX-004 and MPX-007: New Pharmacological Tools to Study the Physiology of NMDA Receptors Containing the GluN2A Subunit.

    PubMed

    Volkmann, Robert A; Fanger, Christopher M; Anderson, David R; Sirivolu, Venkata Ramana; Paschetto, Kathy; Gordon, Earl; Virginio, Caterina; Gleyzes, Melanie; Buisson, Bruno; Steidl, Esther; Mierau, Susanna B; Fagiolini, Michela; Menniti, Frank S

    2016-01-01

    GluN2A is the most abundant of the GluN2 NMDA receptor subunits in the mammalian CNS. Physiological and genetic evidence implicate GluN2A-containing receptors in susceptibility to autism, schizophrenia, childhood epilepsy and neurodevelopmental disorders such as Rett Syndrome. However, GluN2A-selective pharmacological probes to explore the therapeutic potential of targeting these receptors have been lacking. Here we disclose a novel series of pyrazine-containing GluN2A antagonists exemplified by MPX-004 (5-(((3-chloro-4-fluorophenyl)sulfonamido)methyl)-N-((2-methylthiazol-5-yl)methyl)pyrazine-2-carboxamide) and MPX-007 (5-(((3-fluoro-4-fluorophenyl)sulfonamido)methyl)-N-((2-methylthiazol-5-yl)methyl)methylpyrazine-2-carboxamide). MPX-004 and MPX-007 inhibit GluN2A-containing NMDA receptors expressed in HEK cells with IC50s of 79 nM and 27 nM, respectively. In contrast, at concentrations that completely inhibited GluN2A activity these compounds have no inhibitory effect on GluN2B or GluN2D receptor-mediated responses in similar HEK cell-based assays. Potency and selectivity were confirmed in electrophysiology assays in Xenopus oocytes expressing GluN2A-D receptor subtypes. Maximal concentrations of MPX-004 and MPX-007 inhibited ~30% of the whole-cell current in rat pyramidal neurons in primary culture and MPX-004 inhibited ~60% of the total NMDA receptor-mediated EPSP in rat hippocampal slices. GluN2A-selectivity at native receptors was confirmed by the finding that MPX-004 had no inhibitory effect on NMDA receptor mediated synaptic currents in cortical slices from GRIN2A knock out mice. Thus, MPX-004 and MPX-007 offer highly selective pharmacological tools to probe GluN2A physiology and involvement in neuropsychiatric and developmental disorders.

  7. MPX-004 and MPX-007: New Pharmacological Tools to Study the Physiology of NMDA Receptors Containing the GluN2A Subunit

    PubMed Central

    Volkmann, Robert A.; Fanger, Christopher M.; Anderson, David R.; Sirivolu, Venkata Ramana; Paschetto, Kathy; Gordon, Earl; Virginio, Caterina; Gleyzes, Melanie; Buisson, Bruno; Steidl, Esther; Mierau, Susanna B.; Fagiolini, Michela; Menniti, Frank S.

    2016-01-01

    GluN2A is the most abundant of the GluN2 NMDA receptor subunits in the mammalian CNS. Physiological and genetic evidence implicate GluN2A-containing receptors in susceptibility to autism, schizophrenia, childhood epilepsy and neurodevelopmental disorders such as Rett Syndrome. However, GluN2A-selective pharmacological probes to explore the therapeutic potential of targeting these receptors have been lacking. Here we disclose a novel series of pyrazine-containing GluN2A antagonists exemplified by MPX-004 (5-(((3-chloro-4-fluorophenyl)sulfonamido)methyl)-N-((2-methylthiazol-5-yl)methyl)pyrazine-2-carboxamide) and MPX-007 (5-(((3-fluoro-4-fluorophenyl)sulfonamido)methyl)-N-((2-methylthiazol-5-yl)methyl)methylpyrazine-2-carboxamide). MPX-004 and MPX-007 inhibit GluN2A-containing NMDA receptors expressed in HEK cells with IC50s of 79 nM and 27 nM, respectively. In contrast, at concentrations that completely inhibited GluN2A activity these compounds have no inhibitory effect on GluN2B or GluN2D receptor-mediated responses in similar HEK cell-based assays. Potency and selectivity were confirmed in electrophysiology assays in Xenopus oocytes expressing GluN2A-D receptor subtypes. Maximal concentrations of MPX-004 and MPX-007 inhibited ~30% of the whole-cell current in rat pyramidal neurons in primary culture and MPX-004 inhibited ~60% of the total NMDA receptor-mediated EPSP in rat hippocampal slices. GluN2A-selectivity at native receptors was confirmed by the finding that MPX-004 had no inhibitory effect on NMDA receptor mediated synaptic currents in cortical slices from GRIN2A knock out mice. Thus, MPX-004 and MPX-007 offer highly selective pharmacological tools to probe GluN2A physiology and involvement in neuropsychiatric and developmental disorders. PMID:26829109

  8. Estimate of the neutron fields in ATLAS based on ATLAS-MPX detectors data

    NASA Astrophysics Data System (ADS)

    Bouchami, J.; Dallaire, F.; Gutiérrez, A.; Idarraga, J.; Král, V.; Leroy, C.; Picard, S.; Pospíšil, S.; Scallon, O.; Solc, J.; Suk, M.; Turecek, D.; Vykydal, Z.; Žemlièka, J.

    2011-01-01

    The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are covered with converting layers of 6LiF and polyethylene (PE) to increase their sensitivity to thermal and fast neutrons, respectively. These devices allow the measurement of the composition and spectroscopic characteristics of the radiation field in ATLAS, particularly of neutrons. These detectors can operate in low or high preset energy threshold mode. The signature of particles interacting in a ATLAS-MPX detector at low threshold are clusters of adjacent pixels with different size and form depending on their type, energy and incidence angle. The classification of particles into different categories can be done using the geometrical parameters of these clusters. The Medipix analysis framework (MAFalda) — based on the ROOT application — allows the recognition of particle tracks left in ATLAS-MPX devices located at various positions in the ATLAS detector and cavern. The pattern recognition obtained from the application of MAFalda was configured to distinguish the response of neutrons from other radiation. The neutron response at low threshold is characterized by clusters of adjoining pixels (heavy tracks and heavy blobs) left by protons and heavy ions resulting from neutron interactions in the converting layers of the ATLAS-MPX devices. The neutron detection efficiency of ATLAS-MPX devices has been determined by the exposure of two detectors of reference to radionuclide sources of neutrons (252Cf and 241AmBe). With these results, an estimate of the neutrons fields produced at the devices locations during ATLAS operation was done.

  9. Ab initio study of magnetic single layer MPX3 metal-phosphorous-trichalcogenides

    NASA Astrophysics Data System (ADS)

    Chittari, Bheema Lingam; Hwang, Euyheon; Jung, Jeil; MacDonald, Allan H.

    We analyze the electronic structure of two dimensional (2D) MPX3 (M= V, Cr, Mn, Fe, Co, Ni, Cu, Zn, and X = S, Se, Te) transition metal thiophosphates, viewing them as single layer van der Waals materials that can exhibit magnetic order. Our ab initio calculations for MPX3 single layer compounds predict both semiconducting phases with variable band gap sizes and metallic phases, and an intimate interplay between magnetic order and the presence of a gap. A systematic trend of decreasing band gaps in antiferromagnetic states is observed as the chalcogen atoms S, Se, and Te change from smaller to larger atomic number, Ferromagnetic, antiferromagnetic, and nonmagnetic phases, and lattice constant changes accompanied by distortions in crystal symmetry, occur as the metal atom is varied. The sensitive interdependence between magnetic, structural, and electronic properties suggests the important potential of this class of 2D magnetic van der Waals materials for strain and field-effect carrier tunable spintronics.

  10. 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

  11. Luminosity from thermal neutron counting with MPX detectors and relation to ATLAS reference luminosity at √s= 8 TeV proton-proton collisions

    NASA Astrophysics Data System (ADS)

    Sopczak, A.; Ali, B.; Asbah, N.; Bergmann, B.; Bekhouche, K.; Caforio, D.; Campbell, M.; Heijne, E.; Leroy, C.; Lipniacka, A.; Nessi, M.; Pospíšil, S.; Seifert, F.; Şolc, J.; Soueid, P.; Suk, M.; Tureček, D.; Vykydal, Z.

    2017-09-01

    A luminosity determination based on thermal neutron counting with six MPX silicon pixel devices installed in the ATLAS cavern is presented. Recently, the ATLAS Collaboration published final √s=8 TeV luminosity results. This made possible to perform a detailed comparison and verify the potential of the thermal neutron counting as a novel method for luminosity measurements to supplement the well-established presently used procedures. This measurement is unique to the MPX network and has the advantage that the neutrons, which pass the MPX devices, cannot result from activation processes of material nearby. Good agreement is found between the MPX neutron counting results and the ATLAS reference luminosity. The differences between the ATLAS and MPX luminosity measurements are described by a Gaussian distribution with width of 1.5%.

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

    PubMed

    Kessler, Harald H; Stelzl, Evelyn

    2017-04-01

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

  13. Deceased tissue donor serology and molecular testing for HIV, hepatitis B and hepatitis C viruses: a lack of cadaveric validated tests.

    PubMed

    Victer, Thayssa Neiva da Fonseca; Dos Santos, Cris Stéphany Rodrigues; Báo, Sônia Nair; Sampaio, Thatiane Lima

    2016-12-01

    Vital to patient safety is the accurate assessment and minimization of risk for human immunodeficiency virus (HIV), Hepatitis C (HCV), and Hepatitis B (HBV) virus transmission by deceased donor organ and tissue transplantation. The pathogens are tested by serological kits based on enzyme-linked immunosorbent assay (ELISA), chemiluminescence (CLIA) and eletrochemiluminescence (ECLIA) immunoassays. Organ transplantation is a highly successful life-saving treatment in Brazil, but the Brazilian Health Surveillance Agency currently mandates that all deceased organ donors are screened for HIV, HCV and HBV following living donor policies. In this review, six ELISA (Wama(®), Bio-Rad(®), Biomerieux(®), DiaSorin(®), Acon Biotech(®) and Biokit(®)), three CLIA (Abbott(®), Siemens(®), Diasorin(®)) and one ECLIA (Roche(®)) were utilized for evaluating the effectiveness of those serological tests for deceased donors in Brazil according to manufacturer's guidelines. NAT for HIV, HCV and HBV can assist with detection of pre-seroconversion for those infections, and only Cobas(®) TaqScreen MPX(®) test, the Tigris System(®) Procleix Ultrio Assay(®) and the Bio-Manguinhos(®) HIV/HCV/HBV NAT are commercially available. Between all the tests, only the manufacturer Abbott(®) and Cobas(®) TaqScreen MPX(®) test are currently validated for cadaver samples.

  14. Routine screening of blood donations at Qingdao central blood bank, China, for hepatitis B virus (HBV) DNA with a real-time, multiplex nucleic acid test for HBV, hepatitis C virus, and human immunodeficiency virus Types 1 and 2.

    PubMed

    Yang, Zhongsi; Xu, Lei; Liu, Li; Feng, Qiuxia; Zhang, Longmu; Ma, Weijuan; Saldanha, John; Wang, Mingmin; Zhao, Lin

    2013-10-01

    The Roche cobas TaqScreen MPX test was used to evaluate the rate of hepatitis B surface antigen (HBsAg)-negative donations that were hepatitis B virus (HBV) DNA reactive from June 2010 to January 2011 in Qingdao, China. HBsAg-negative samples from 65,800 voluntary blood donors were tested with the cobas TaqScreen MPX test in pools of 6 on the Roche cobas s 201 blood screening platform. Samples positive for HBV DNA and negative for HBsAg were quantitated with the Roche COBAS AmpliPrep/COBAS TaqMan HBV test. In addition, serologic tests for HBsAg, hepatitis B surface antibody, anti-hepatitis B core antigen (anti-HBc), anti-hepatitis B e antigen (anti-HBe), and hepatitis B e antigen (HBe) were done using the Roche electrochemiluminescence immunoassay. A total of 80 nucleic acid amplification technology (NAT) test-reactive pools were identified and 59 pools (74%) resolved to a reactive sample. All samples were HBV DNA reactive and the viral load in each sample was quantitated. The viral loads of the samples ranged from less than 20 to 34,600 IU/mL; 13 samples (22%) had viral loads of more than 20 IU/mL, 27 samples (45.8%) had viral loads of less than 20 IU/mL, and 19 samples (32.2%) had undetectable viral loads. Of the 59 NAT-reactive samples, 40 (67.8%) were anti-HBc positive. Fifteen of the 59 samples could not be confirmed as NAT reactive either by an alternative NAT test or by serology. The HBV NAT yield in blood donors in Qingdao is 0.06% (38/65,800). This study confirmed the value of NAT for interdicting HBV-positive donations and preventing transfusion-transmitted HBV infections. © 2013 American Association of Blood Banks.

  15. Use of the cobas 4800 system for the rapid detection of toxigenic Clostridium difficile and methicillin-resistant Staphylococcus aureus.

    PubMed

    Moure, Raquel; Cañizares, Ángeles; Muíño, María; Lobato, Margarita; Fernández, Ana; Rodríguez, María; Gude, Maria José; Tomás, Maria; Bou, Germán

    2016-01-01

    The new cobas® Cdiff and cobas® MRSA/SA tests were compared with conventional methods for the rapid detection of toxigenic Clostridium difficile and methicillin-resistant Staphylococcus aureus. The final concordance between cobas Cdiff Test and GDH/toxin gene screening was 97.62% and between cobas MRSA/SA Test and chromogenic culture, 91.30%, respectively.

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

    PubMed

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

    2013-07-01

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

  17. RTK-GPS positioning by TV audio-MPX-data broadcast in Japan

    NASA Astrophysics Data System (ADS)

    Namie, Hiromune; Yasuda, Akio; Sasano, Koji

    2000-10-01

    RTK-GPS is a satellite positioning system which provides instant and accurate positions. The ranging error to the satellite from a user GPS antenna determined by the phase measurement of the carrier waves from the GPS satellites is of the order of mms. Thus an accuracy of a few cm can be easily obtained. The system is easier to operate than a traditional survey system such as the `Total Station'. Hence it has been used for many applications in Japan. It is necessary, however, to provide a fast data communication link for the transmission of carrier phase data from a reference station located at a known position, to a user receiver. A radio communication device with low power, is commonly used because it requires no license. However the data transmission area is generally limited to just several hundred meters in radius from the reference station. The authors have investigated RTK-GPS positioning with several different lengths of baseline using data transmission via TV audio-MPX-data broadcast, and evaluated its validity. The carrier phase data is transmitted from the reference receiver at the Tokyo University of Mercantile Marine, to the experimental station of the Asahi National Broadcasting Company, by public phone line with data rate 9,600 bps. The data, which when multiplexed into TV audio, was then disseminated with the rate of about 8 kbps from the Tokyo Tower. The data transmission delay in this system appeared random between 0.740 and 1.317 s, of which the difference (0.577 s) corresponds to the transmission time of 32 blocks of multiplexed data. Positioning was tried at several fixed points with different lengths of baseline (0-21 km). Tests proved that the accuracy became worse as the length of baselines became longer. The 2drms height are less than the 2.5 cm, and `Fix' solution success rates are more than 98%, for shorter baselines less than 10 km in length.

  18. Mesure des champs de radiation dans le detecteur ATLAS et sa caverne avec les detecteurs au silicium a pixels ATLAS-MPX

    NASA Astrophysics Data System (ADS)

    Bouchami, Jihene

    The LHC proton-proton collisions create a hard radiation environment in the ATLAS detector. In order to quantify the effects of this environment on the detector performance and human safety, several Monte Carlo simulations have been performed. However, direct measurement is indispensable to monitor radiation levels in ATLAS and also to verify the simulation predictions. For this purpose, sixteen ATLAS-MPX devices have been installed at various positions in the ATLAS experimental and technical areas. They are composed of a pixelated silicon detector called MPX whose active surface is partially covered with converter layers for the detection of thermal, slow and fast neutrons. The ATLAS-MPX devices perform real-time measurement of radiation fields by recording the detected particle tracks as raster images. The analysis of the acquired images allows the identification of the detected particle types by the shapes of their tracks. For this aim, a pattern recognition software called MAFalda has been conceived. Since the tracks of strongly ionizing particles are influenced by charge sharing between adjacent pixels, a semi-empirical model describing this effect has been developed. Using this model, the energy of strongly ionizing particles can be estimated from the size of their tracks. The converter layers covering each ATLAS-MPX device form six different regions. The efficiency of each region to detect thermal, slow and fast neutrons has been determined by calibration measurements with known sources. The study of the ATLAS-MPX devices response to the radiation produced by proton-proton collisions at a center of mass energy of 7 TeV has demonstrated that the number of recorded tracks is proportional to the LHC luminosity. This result allows the ATLAS-MPX devices to be employed as luminosity monitors. To perform an absolute luminosity measurement and calibration with these devices, the van der Meer method based on the LHC beam parameters has been proposed. Since the ATLAS-MPX

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

    PubMed

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

    2013-01-01

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

  20. Development of a Second Version of the Cobas AmpliPrep/Cobas TaqMan Hepatitis C Virus Quantitative Test with Improved Genotype Inclusivity▿

    PubMed Central

    Vermehren, Johannes; Colucci, Giuseppe; Gohl, Peter; Hamdi, Nabila; Abdelaziz, Ahmed Ihab; Karey, Ursula; Thamke, Diana; Zitzer, Heike; Zeuzem, Stefan; Sarrazin, Christoph

    2011-01-01

    Hepatitis C virus (HCV) RNA measurement has been facilitated by the introduction of real-time PCR-based assays with low limits of detection and broad dynamic ranges for quantification. In the present study, the performance of two second-version prototypes of the Cobas AmpliPrep/Cobas TaqMan HCV Quantitative Test (CAP/CTM v2) with decreased sample input volume and improved genotype inclusivity was investigated. A total of 232 serum and plasma samples derived from patients with chronic hepatitis C (genotype 1 [GT1], n = 108; GT2, n = 8; GT3, n = 24; GT4, n = 87; GT5, n = 3; and GT6, n = 2) were processed in parallel with the Cobas AmpliPrep/Cobas TaqMan HCV Test (CAP/CTM), Cobas Amplicor HCV Monitor Test v2.0 (CAM), and two second-version prototype formulations of CAP/CTM, Mastermix 1 (MMx1) and MMx2. In addition, three GT4 transcripts containing rare variant sequences were tested. The mean log10 HCV RNA differences for the best-performing CAP/CTM v2/MMx2 formulation in comparison to CAM were −0.05, 0.05, −0.12, −0.10, −0.44, and −0.29 for patients with GT1, GT2, GT3, GT4, GT5, and GT6 infections, respectively. GT1, GT2, and GT4 samples including isolates with known variants within the 5′ untranslated region (G145A, A165T) that were underquantified with CAP/CTM were correctly quantified with the second-version prototype. In addition, CAP/CTM v2 was able to accurately quantify the three transcripts with rare variant sequences. In conclusion, CAP/CTM v2 accurately quantifies HCV RNA across all HCV genotypes, including specimens with rare polymorphisms previously associated with underquantification. PMID:21752967

  1. Development of a second version of the Cobas AmpliPrep/Cobas TaqMan hepatitis C virus quantitative test with improved genotype inclusivity.

    PubMed

    Vermehren, Johannes; Colucci, Giuseppe; Gohl, Peter; Hamdi, Nabila; Abdelaziz, Ahmed Ihab; Karey, Ursula; Thamke, Diana; Zitzer, Heike; Zeuzem, Stefan; Sarrazin, Christoph

    2011-09-01

    Hepatitis C virus (HCV) RNA measurement has been facilitated by the introduction of real-time PCR-based assays with low limits of detection and broad dynamic ranges for quantification. In the present study, the performance of two second-version prototypes of the Cobas AmpliPrep/Cobas TaqMan HCV Quantitative Test (CAP/CTM v2) with decreased sample input volume and improved genotype inclusivity was investigated. A total of 232 serum and plasma samples derived from patients with chronic hepatitis C (genotype 1 [GT1], n = 108; GT2, n = 8; GT3, n = 24; GT4, n = 87; GT5, n = 3; and GT6, n = 2) were processed in parallel with the Cobas AmpliPrep/Cobas TaqMan HCV Test (CAP/CTM), Cobas Amplicor HCV Monitor Test v2.0 (CAM), and two second-version prototype formulations of CAP/CTM, Mastermix 1 (MMx1) and MMx2. In addition, three GT4 transcripts containing rare variant sequences were tested. The mean log(10) HCV RNA differences for the best-performing CAP/CTM v2/MMx2 formulation in comparison to CAM were -0.05, 0.05, -0.12, -0.10, -0.44, and -0.29 for patients with GT1, GT2, GT3, GT4, GT5, and GT6 infections, respectively. GT1, GT2, and GT4 samples including isolates with known variants within the 5' untranslated region (G145A, A165T) that were underquantified with CAP/CTM were correctly quantified with the second-version prototype. In addition, CAP/CTM v2 was able to accurately quantify the three transcripts with rare variant sequences. In conclusion, CAP/CTM v2 accurately quantifies HCV RNA across all HCV genotypes, including specimens with rare polymorphisms previously associated with underquantification.

  2. Novel Approach for Clinical Validation of the cobas KRAS Mutation Test in Advanced Colorectal Cancer.

    PubMed

    Sharma, Abha; Zhang, Guili; Aslam, Shagufta; Yu, Karen; Chee, Melody; Palma, John F

    2016-06-01

    Our objective was to assess the performance of the cobas test versus comparators for KRAS mutation status and predicting clinical response to anti-epidermal growth factor receptor (EGFR) therapy in patients with metastatic colorectal cancer (mCRC). mCRC samples from 398 patients from Roche study NO16968 (XELOXA) and 82 supplemental samples were tested with the cobas(®) KRAS mutation test (cobas test), the therascreen(®) KRAS RGQ PCR kit test (therascreen test), and Sanger sequencing as the reference method for detecting mutations in codons 12/13. For 461 eligible samples, the cobas test, therascreen test, and sequencing had invalid results for 5.2, 10.8, and 2.6 % of specimens, respectively. Valid cobas and therascreen test results had similar KRAS mutation-positive rates (37.3 vs. 36.3 %, respectively); sequencing was 28.5 %. Positive and negative percent agreement (PPA/NPA) between the cobas test and sequencing was 96.9 % (95 % confidence interval [CI] 92.2-98.8), and 88.7 % (95 % CI 84.7-91.8), respectively. PPA/NPA between the cobas and therascreen tests was 93.3 % (95 % CI 88.1-96.3) and 96.5 % (95 % CI 93.5-98.1), respectively. Bridging analysis from NCIC-CO.17 and NCT00113763 using the cobas test yielded modeled hazard ratios for overall survival and progression-free survival (PFS) of 0.558 (95 % CI 0.422-0.752) and 0.413 (95 % CI 0.304-0.550), respectively, for cetuximab and 0.989 (95 % CI 0.778-1.299) and 0.471 (95 % CI 0.360-0.626), respectively, for panitumumab, demonstrating significant efficacy in the KRAS-negative population for PFS. The cobas test showed similar accuracy to the therascreen test for detecting KRAS mutations and could appropriately identify mCRC patients ineligible for anti-EGFR therapy as demonstrated by bridging analysis results.

  3. Performance Evaluation and Comparison of the Fully Automated Urinalysis Analyzers UX-2000 and Cobas 6500.

    PubMed

    Wesarachkitti, Bongkot; Khejonnit, Varanya; Pratumvinit, Busadee; Reesukumal, Kanit; Meepanya, Suriya; Pattanavin, Chanutchaya; Wongkrajang, Preechaya

    2016-05-01

    To evaluate and compare the performances of the automated urinalysis devices UX-2000 and Cobas 6500. A total of 258 urine specimens were collected from the routine specimen workload. We analyzed all specimens on both automated instruments and recorded the turnaround time from each method. Physical, chemical, and sedimentary urine components were compared between the automated and the manual method for each analyzer. The correlation of urine physical/chemical properties between the 2 instruments was excellent. The Cobas 6500 instrument demonstrated a higher level of agreement for red blood cells (Cobas 6500:R= 0.94; UX-2000:R= 0.78) and white blood cells (Cobas 6500:R= 0.95; UX-2000:R= 0.85). The UX-2000 demonstrated higher sensitivity for small round cells, hyaline casts, pathological casts, and bacteria. The median turnaround time was 1.5 minutes and 8.5 minutes for the Cobas 6500 and UX-2000, respectively. The 2 devices showed similar performance in technical evaluation; they each reduce workload and increase time saving. However, manual examination by technicians is recommended for pathological specimens. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. 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

  5. Evaluation of the clinical performance of the cobas 4800 HPV test in patients referred for colposcopy.

    PubMed

    White, Christine; Keegan, Helen; Pilkington, Loretto; Ruttle, Carmel; Kerr, Patrick; Sharp, Linda; O'Toole, Sharon; Turner, Michael; Prendiville, Walter; D'Arcy, Tom; Fitzpatrick, Myra; Lenehan, Peter; Flannelly, Grainne; O'Leary, John J; Martin, Cara M

    2013-10-01

    The clinical performance of the cobas human papillomavirus (HPV) test for detection of high-grade disease in a colposcopy-referred population was compared with that of Hybrid Capture 2 (HC2). The overall agreement between the tests was 92.3%. Clinical sensitivity and specificity for detection of cervical intraepithelial neoplasia grade 2 or greater (CIN2+) were 90.0% and 55.5% for cobas and 90.5% and 50.2% for HC2, respectively. In conclusion, both tests showed comparable performance for detection of CIN2+.

  6. Second-generation Cobas AmpliPrep/Cobas TaqMan HCV quantitative test for viral load monitoring: a novel dual-probe assay design.

    PubMed

    Zitzer, Heike; Heilek, Gabrielle; Truchon, Karine; Susser, Simone; Vermehren, Johannes; Sizmann, Dorothea; Cobb, Bryan; Sarrazin, Christoph

    2013-02-01

    Hepatitis C virus (HCV) RNA viral load (VL) monitoring is a well-established diagnostic tool for the management of chronic hepatitis C patients. HCV RNA VL results are used to make treatment decisions with the goal of therapy to achieve an undetectable VL result. Therefore, a sensitive assay with high specificity in detecting and accurately quantifying HCV RNA across genotypes is critical. Additionally, a lower sample volume requirement is desirable for the laboratory and the patient. This study evaluated the performance characteristics of a second-generation real-time PCR assay, the Cobas AmpliPrep/Cobas TaqMan HCV quantitative test, version 2.0 (CAP/CTM HCV test, v2.0), designed with a novel dual-probe approach and an optimized automated extraction and amplification procedure. The new assay demonstrated a limit of detection and lower limit of quantification of 15 IU/ml across all HCV genotypes and was linear from 15 to 100,000,000 IU/ml with high accuracy (<0.2-log(10) difference) and precision (standard deviation of 0.04 to 0.22 log(10)). A specificity of 100% was demonstrated with 600 HCV-seronegative specimens without cross-reactivity or interference. Correlation to the Cobas AmpliPrep/Cobas TaqMan HCV test (version 1) was good (n = 412 genotype 1 to 6 samples, R(2) = 0.88; R(2) = 0.94 without 105 genotype 4 samples). Paired plasma and serum samples showed similar performance (n = 25, R(2) = 0.99). The sample input volume was reduced from 1 to 0.65 ml in the second version. The CAP/CTM HCV test, v2.0, demonstrated excellent performance and sensitivity across all HCV genotypes with a smaller sample volume. The new HCV RNA VL assay has performance characteristics that make it suitable for use with currently available direct-acting antiviral agents.

  7. Second-Generation Cobas AmpliPrep/Cobas TaqMan HCV Quantitative Test for Viral Load Monitoring: a Novel Dual-Probe Assay Design

    PubMed Central

    Zitzer, Heike; Heilek, Gabrielle; Truchon, Karine; Susser, Simone; Vermehren, Johannes; Sizmann, Dorothea; Cobb, Bryan

    2013-01-01

    Hepatitis C virus (HCV) RNA viral load (VL) monitoring is a well-established diagnostic tool for the management of chronic hepatitis C patients. HCV RNA VL results are used to make treatment decisions with the goal of therapy to achieve an undetectable VL result. Therefore, a sensitive assay with high specificity in detecting and accurately quantifying HCV RNA across genotypes is critical. Additionally, a lower sample volume requirement is desirable for the laboratory and the patient. This study evaluated the performance characteristics of a second-generation real-time PCR assay, the Cobas AmpliPrep/Cobas TaqMan HCV quantitative test, version 2.0 (CAP/CTM HCV test, v2.0), designed with a novel dual-probe approach and an optimized automated extraction and amplification procedure. The new assay demonstrated a limit of detection and lower limit of quantification of 15 IU/ml across all HCV genotypes and was linear from 15 to 100,000,000 IU/ml with high accuracy (<0.2-log10 difference) and precision (standard deviation of 0.04 to 0.22 log10). A specificity of 100% was demonstrated with 600 HCV-seronegative specimens without cross-reactivity or interference. Correlation to the Cobas AmpliPrep/Cobas TaqMan HCV test (version 1) was good (n = 412 genotype 1 to 6 samples, R2 = 0.88; R2 = 0.94 without 105 genotype 4 samples). Paired plasma and serum samples showed similar performance (n = 25, R2 = 0.99). The sample input volume was reduced from 1 to 0.65 ml in the second version. The CAP/CTM HCV test, v2.0, demonstrated excellent performance and sensitivity across all HCV genotypes with a smaller sample volume. The new HCV RNA VL assay has performance characteristics that make it suitable for use with currently available direct-acting antiviral agents. PMID:23241371

  8. The cobas® HCV GT is a new tool that accurately identifies Hepatitis C virus genotypes for clinical practice.

    PubMed

    Fernández-Caballero, J A; Alvarez, M; Chueca, N; Pérez, A B; García, F

    2017-01-01

    We aimed to evaluate the correct assignment of HCV genotype/subtypes 1a and 1b by cobas® HCV genotyping (GT) assay (Roche Molecular Diagnostics) compared with nonstructural protein 5B (NS5B) sequencing. Clinical samples from 153 patients submitted for HCV genotyping were studied. After genotyping with the cobas® HCV GT, sequencing of a 387 bp fragment in the NS5B gene and phylogenetic analysis was employed to compare genotyping results. Major discrepancies were defined as differences in the assigned genotype by cobas® HCV GT and NS5B sequencing (including genotype 1 subtypes 1a and 1b misclassification). Overall agreement between the cobas® HCV GT and NS5B sequencing was 98%; all the 1a, 1b, 2, 3 and 4 genotypes identified by cobas® HCV GT were concordant with NS5B sequencing. Three samples tested "indetermined" by cobas® HCV GT assay and were genotyped as 1a, 3a, and 4d by NS5B sequencing. These results indicate that the cobas® HCV GT assay correctly identifies HCV genotypes, and points out the importance of additional methods based on DNA sequencing for resolving indeterminate results.

  9. 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.

  10. Analytical performances of the Diazyme ADA assay on the Cobas® 6000 system.

    PubMed

    Delacour, Hervé; Sauvanet, Christophe; Ceppa, Franck; Burnat, Pascal

    2010-12-01

    To evaluate the analytical performance of the Diazyme ADA assay on the Cobas® 6000 system for pleural fluid samples analysis. Imprecision, linearity, calibration curve stability, interference, and correlation studies were completed. The Diazyme ADA assay demonstrated excellent precision (CV<4%) over the analytical measurement range (0.5-117 U/L). Bilirubin above 50 μmol/L and haemoglobin above 177 μmol/L interfered with the test, inducing a negative and a positive interference respectively. The Diazyme ADA assay correlated well with the Giusti method (r(2)=0.93) but exhibited a negative bias (~ -30%). The Diazyme ADA assay on the Cobas® 6000 system represents a rapid, accurate, precise and reliable method for determination of ADA activity in pleural fluid samples. Copyright © 2010 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  11. Evaluation of the ABX Cobas Vega automated hematology analyzer and comparison with the Coulter STKS.

    PubMed

    Ferrero-Vacher, C; Sudaka, I; Jambou, D; Vanhaeke, D; Fischer, F; Bayle, J

    1997-06-01

    An evaluation of the new automated hematology analyzer was performed in comparison with the Coulter STKS on 1,694 blood samples coming from the different departments of Nice University Hospital. The Cobas Vega showed very satisfactory results in terms of repeatability, reproducibility and linearity. Correlation with the STKS was excellent with the exception of the following parameters: red blood cell distribution index and the absolute values for eosinophils and basophils. Two qualities were particularly appreciable: absence of leukocyte carryover, and stability of the complete blood count and leukocyte differential count over a long period. Analysis of qualitative flags showed that the overall blood smear review rate was 47% for the Cobas Vega, not forgetting that optical microscopy detects 37% of all abnormalities. The STKS's review rate was 49.5%. Flags commonly concerned the granulocytic lineage, 61% for the STKS and 48% for the Vega, with a false positive rate of 43.4% for the STKS compared with 22% for the Vega. The opposite phenomenon was observed with the flag for atypical lymphocytes which represented 11% of flags for the STKS and 25.6% for the Vega, with a false positive rate of 25.5% for the STKS and 34% for the Cobas Vega. This may be explained by the fact that lymphocyte abnormalities sometimes generated "granulocytic" flags on the STKS. Studies of the false negative rate carried out using light microscopy on 505 blood samples without flags on either system, detected the presence of a slight myelemia, and a few hyperbasophilic lymphocytes or plasmocytes in 18.6% of all cases. Finally, the Cobas Vega's practicality was greatly appreciated and there was no trouble with breakdowns throughout the whole period of its use.

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

    PubMed

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

    2013-04-01

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

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

    PubMed Central

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

    2013-01-01

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

  14. Performance of Aptima and Cobas HPV testing platforms in detecting high-grade cervical dysplasia and cancer.

    PubMed

    Ge, Yimin; Christensen, Paul; Luna, Eric; Armylagos, Donna; Schwartz, Mary R; Mody, Dina R

    2017-08-01

    Human papillomavirus (HPV) tests and genotyping have been used in clinical risk assessment. The purpose of this study was to analyze the performance of 2 common HPV testing platforms in detecting high-grade cervical lesions (high-grade squamous intraepithelial lesion [HSIL] or worse [≥HSIL]). Between January 1 and December 31, 2015, 2041 Papanicolaou (Pap) tests with biopsy confirmation were analyzed along with HPV tests performed on Cobas or Aptima platforms. A biopsy diagnosis of grade 2 cervical intraepithelial neoplasia was confirmed with p16/Ki-67 immunohistochemistry. In total, 1866 and 175 Pap cases were tested on Cobas and Aptima platforms, respectively. Both platforms were highly sensitive (97% for both) for biopsy-confirmed ≥HSIL. Cobas HPV testing had higher positive rates for the diagnosis of benign lesions (84% vs 51%) and low-grade squamous intraepithelial lesions (89% vs 63%) on biopsy compared with Aptima. Aptima testing had significantly higher specificity for ≥HSIL than Cobas (41% vs 13%; P < .0001). Overall, performance of the Aptima platform was superior to that of the Cobas platform in detecting biopsy-confirmed ≥HSIL, resulting from its significantly higher positive predictive value (25% vs 16%; P < .03) and overall accuracy (50% vs 26%; P < .0001). Although both the Cobas and Aptima platforms offer highly sensitive tests for high-grade cervical lesions, Aptima HPV testing demonstrated significantly higher specificity and positive predictive value than Cobas testing for biopsy-confirmed ≥HSIL. The considerable difference may be related to the significant increase in E6/E7 expression after HPV DNA integration. The significantly higher specificity and overall accuracy of Aptima testing for ≥HSIL, resulting in the identification of high-risk populations that require immediate treatment and close follow-up, may prove useful in clinical risk stratification. Cancer Cytopathol 2017;125:652-7. © 2017 American Cancer Society. © 2017

  15. Performance of Version 2.0 of the Cobas AmpliPrep/Cobas TaqMan Real-Time PCR Assay for Hepatitis B Virus DNA Quantification ▿

    PubMed Central

    Chevaliez, Stéphane; Bouvier-Alias, Magali; Laperche, Syria; Hézode, Christophe; Pawlotsky, Jean-Michel

    2010-01-01

    The detection and quantification of hepatitis B virus (HBV) DNA are essential for the diagnosis and treatment of chronic HBV infection. The use of real-time PCR assays for HBV DNA quantification is strongly recommended. The goal of this study was to evaluate the intrinsic characteristics and clinical performance of version 2.0 (v2.0) of the Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) assay, a fully automated platform for HBV DNA quantification in serum or in plasma with a claimed lower limit of detection of 20 IU/ml and a claimed upper limit of quantification of 1.7 × 108 IU/ml. The specificity of the assay was 99% (95% confidence interval, 94.7 to 100%). Intra-assay and interassay coefficients of variation ranged from 0.21% to 2.67% and from 0.65% to 2.25%, respectively. The calibration of the assay was found to be satisfactory. Study of blood specimens from patients infected with HBV genotypes A to F showed good correspondence between HBV DNA levels measured by the CAP/CTM v2.0 assay, version 1.0 of the same assay, and the third-generation “branched DNA” assay. The CAP/CTM v2.0 assay quantified HBV DNA levels in serum or plasma from the same patients equally. In conclusion, the new version of the CAP/CTM assay is sensitive, specific, and reproducible. It accurately quantifies HBV DNA levels in patients chronically infected with HBV genotypes A to F. Improvements made to ensure equal quantification of HBV DNA in serum and plasma have been successful. Overall, the CAP/CTM assay, version 2.0, is well suited to monitoring clinical HBV DNA levels according to current clinical practice guidelines. PMID:20720031

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

    PubMed

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

    2001-11-01

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

  17. Evaluation of the cobas® Cdiff test for the Detection of Toxigenic Clostridium difficile in Stool Samples.

    PubMed

    Peterson, Lance R; Young, Stephen A; Davis, Thomas E; Wang, Zi-Xuam; Duncan, John; Noutsios, Christopher; Liesenfeld, Oliver; Osiecki, John C; Lewinski, Michael A

    2017-09-27

    Nucleic acid amplification tests are reliable tools for the detection of toxigenic Clostridium difficile from unformed (liquid or soft) stool samples. The objective of this study was to evaluate performance of the cobas® Cdiff Test on the cobas® 4800 System using prospectively collected stool specimens from patients suspected of C. difficile infection (CDI). Performance of the cobas® Cdiff Test was compared to the combined results of direct and broth enriched toxigenic culture in a large, multicenter clinical trial. Additional discrepant analysis was performed using the Xpert® C. difficile Epi Test. Sample storage was evaluated on contrived and fresh samples before and after storage at -20°C. Testing was from 683 subjects (306 males and 377 females); 113 (16.5%) of 683 were positive for toxigenic C. difficile by direct toxigenic culture and 141 of 682 were positive using the combined direct and enriched toxigenic culture (reference method), for a prevalence rate of 20.7%. The sensitivity and specificity of the cobas® Cdiff Test compared to combined direct and enriched culture was 92.9% (131/141; 95% CI: 87.4% to 96.1%) and 98.7% (534/541; 95% CI: 97.4% to 99.4%), respectively. Discrepancy analysis using a retested sample results from a second NAAT (Xpert® C. difficile/Epi test (Cepheid, Sunnyvale, CA) found no false negative and 4 false positive cobas® Cdiff Test results. There was no difference in positive and negative results when comparing fresh and stored samples. These results support the use of the cobas® Cdiff Test as a robust aid in the diagnosis of CDI. Copyright © 2017 American Society for Microbiology.

  18. Comparison of Cobas® HPV and Anyplex™ II HPV28 assays for detecting and genotyping human papillomavirus.

    PubMed

    Pasquier, Christophe; Sauné, Karine; Raymond, Stéphanie; Boisneau, Jérôme; Courtade, Monique; Izopet, Jacques

    2017-01-01

    Persistent infection with high-risk human papillomavirus (HPV-HR) is a recognized cause of cervical cancer. The aim of this study was to compare analytical and clinical performances of the Cobas® HPV and Anyplex™ II HPV28 assays for HPV detection and genotyping. A total of 94 cervical samples were tested. For HPV-HR, the results agreed very well (94.68%), with 100% agreement when detecting CIN2+. The Anyplex™ II HPV28 assay detected more genotypes than the Cobas® HPV Test, but their clinical performances were similar. Copyright © 2016. Published by Elsevier Inc.

  19. Comparison of Assurance GDS(®) MPX ID for Top STEC with Reference Culture Methods for the Detection of E. coli Top 6 STEC; Direct Confirmation of Top 6 STEC from Isolation Plates and Determination of Equivalence of PickPen(®) and FSIS OctoMACS™ Concentration Protocols.

    PubMed

    Feldsine, Philip; Lienau, Andrew H; Shah, Khyati; Immermann, Amy; Soliven, Khanh; Kaur, Mandeep; Kerr, David E; Jucker, Markus; Hammack, Tom; Brodsky, Michael; Agin, James

    2016-01-01

    Assurance GDS(®) MPX ID for Top Shiga toxin-producing Escherichia coli (STEC; MPX ID) was validated according to the AOAC INTERNATIONAL Methods Committee Guidelines for Validation of Microbiological Methods for Foods and Environmental Surfaces as (1) a secondary screening method for specific detection of the Top 6 STEC serogroups (O26, O45, O103, O111, O121, and O145) in raw beef trim, raw ground beef, raw spinach, and on stainless steel; and (2) as a confirmatory method for the identification of pure culture isolates as Top 6 STEC. MPX ID is used in conjunction with the upfront BCS Assurance GDS MPX Top 7 STEC assay. This Performance Tested Method(SM) validation has two main parts: Method Developer studies and the Independent Laboratory study. A total of 180 samples and controls were analyzed. Results showed that MPX ID had no statistically significant differences with the reference culture methods for the detection of Top 6 STEC in the food matrixes (raw beef trim, raw ground beef, and raw spinach) and environmental sponges (stainless steel) studied. Inclusivity/exclusivity studies were also conducted. One hundred percent inclusivity among the 50 Top 6 STEC serovars tested and 100% exclusivity for the 30 non-Top 6 STEC organisms tested were demonstrated. For validation of MPX ID as a confirmatory method for isolated colonies, all inclusivity and exclusivity organisms were streaked for isolation onto five STEC plating media: modified rainbow agar, Levine's eosin-methylene blue (L-EMB) agar, rainbow agar with novobiocin and cefixime, and enterohemolysin agar with selective agents as well as trypticase soy agar with yeast extract. These isolated colonies were suspended and analyzed by Assurance GDS MPX Top 7 STEC and MPX ID. MPX ID was able to correctly confirm all inclusivity organisms from all plate types, except two STEC isolates from L-EMB agar plates only in the Independent Laboratory study. All exclusivity organisms were correctly determined by MPX ID as non

  20. Evaluation of two, commercial, multi-dye, nucleic acid amplification technology tests, for HBV/HCV/HIV-1/HIV-2 and B19V/HAV, for screening blood and plasma for further manufacture.

    PubMed

    Müller, M M; Fraile, M I G; Hourfar, M K; Peris, L B; Sireis, W; Rubin, M G; López, E M; Rodriguez, G T; Seifried, E; Saldanha, J; Schmidt, M

    2013-01-01

    The cobas TaqScreen MPX Test, version 2.0, a multiplex, multi-dye nucleic acid amplification technology (NAT) test from Roche was evaluated by two European Blood Banks, the German Red Cross Blood Donor Service, Frankfurt, Germany and Centro de Hemoterapia y Hemodonación de Castilla y León, Valladolid, Spain. In addition, the cobas TaqScreen DPX Test was evaluated for the simultaneous detection and quantitation of parvovirus B19 and the detection of hepatitis A virus (HAV). The performances of the two tests were evaluated regarding the analytical sensitivity, the reproducibility of the tests using samples containing low concentrations of each virus and cross-contamination using samples containing high titres of virus. The analytical sensitivity of the MPX Test, version 2.0, obtained by the German Red Cross Blood Donor Service was 1·1, 3·9 and 43·3 IU/ml for HBV, HCV and HIV-1, respectively. The comparable analytical sensitivity at Centro de Hemoterapia y Hemodonación de Castilla y León was 3·5, 17·6 and 50·6 IU/ml for HBV, HCV and HIV-1, respectively. The analytical sensitivity of the DPX test determined by the German Red Cross Blood Donor Service was 0·6 and 3·8 IU/ml for HAV and B19. These multiplex and multi-dye blood screening assays represent a flexible NAT screening system for mini-pools between 6 and 96 samples per pool and fulfil all requirements of the European Pharmacopoeia for HCV and B19V testing of plasma for fractionation. The inclusion of a new multi-dye technology means discriminatory assays are no longer required for either test thus improving workflow, turn-around time and minimize the risk of obtaining a reactive result for which the virus cannot be identified. © 2012 The Author(s). Vox Sanguinis © 2012 International Society of Blood Transfusion.

  1. [Implementation of the COBAS Taqman HIV-1 Test, v1.0 for vertical transmission diagnosis].

    PubMed

    Castro, Gonzalo M; Sosa, María P; Gallego, Sandra V; Sicilia, Paola; Marin, Ángeles L; Altamirano, Natalia; Kademian, Silvia; Barbás, María G; Cudolá, Analía

    2015-01-01

    Vertical transmission is the main route of HIV infection in childhood. Because of the persistence of maternal HIV antibodies, virologic assays that directly detect HIV are required to diagnose HIV infection in infants younger than 18 months of age. The sensitivity of HIV RNA/DNA assays increases as the child becomes older. These tests have specificity values greater than 95%. The aim of this study was to evaluate the performance of the COBAS Taqman HIV-1 Test, v1.0 assay (Roche) and its concordance with a Multiplex Nested-PCR. Of 341 samples processed, 15 were positive and 326 negative by both methods. Sensitivity and specificity overall values for the viral load assay were 88.2% and 100%, respectively. Our results indicate that the COBAS Taqman assay evaluated could be used as an alternative method to diagnose HIV congenital infection. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

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

    PubMed

    Manavi, Kaveh

    2008-01-01

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

  3. 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

  4. Detection of Epidermal Growth Factor Receptor Mutations in Lung Adenocarcinoma: Comparing Cobas 4800 EGFR Assay With Sanger Bidirectional Sequencing.

    PubMed

    Ardakani, Nima Mesbah; Giardina, Tindaro; Grieu-Iacopetta, Fabienne; Tesfai, Yordanos; Carrello, Amerigo; Taylor, Jeremy; Robinson, Cleo; Spagnolo, Dominic; Amanuel, Benhur

    2016-09-01

    Accurate detection of epidermal growth factor receptor (EGFR) mutations has a crucial role in the current treatment of patients with lung adenocarcinoma, and identification of clinically relevant mutations would qualify patients for treatment with tyrosine kinase inhibitors. Historically, Sanger sequencing has been used as the reference standard assay for EGFR mutational analysis; however, Cobas 4800 is a relatively new method. In the present study, we compared the performance of the Cobas assay against that of Sanger sequencing. A total of 493 consecutive formalin-fixed paraffin-embedded samples of lung adenocarcinoma were simultaneously tested for EGFR mutations using both methods. After exclusion of the invalid results (n = 19), 474 samples from 455 patients were analyzed. The Cobas assay showed a mutation detection rate comparable to that of Sanger sequencing (18.1% vs. 17.9%, respectively; P < .05). Excellent agreement of 98.9% (κ, 0.964) was observed between the 2 methods. The Cobas assay is a fast and diagnostically robust platform with high analytical sensitivity; however, it is limited by its detection range and low tolerance to low DNA quality. Sanger sequencing is mostly affected by its lower analytic sensitivity. Ultimately, a dual testing strategy will be justified to increase the detection of novel mutations and reduce the false-negative results within an acceptable turnaround time. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  5. Analytic and clinical performance of cobas HPV testing in anal specimens from HIV-positive men who have sex with men.

    PubMed

    Wentzensen, Nicolas; Follansbee, Stephen; Borgonovo, Sylvia; Tokugawa, Diane; Sahasrabuddhe, Vikrant V; Chen, Jie; Lorey, Thomas S; Gage, Julia C; Fetterman, Barbara; Boyle, Sean; Sadorra, Mark; Tang, Scott Dahai; Darragh, Teresa M; Castle, Philip E

    2014-08-01

    Anal human papillomavirus (HPV) infections are common, and the incidence of anal cancer is high in HIV-infected men who have sex with men (MSM). To evaluate the performance of HPV assays in anal samples, we compared the cobas HPV test (cobas) to the Roche Linear Array HPV genotyping assay (LA) and cytology in HIV-infected MSM. Cytology and cobas and LA HPV testing were conducted for 342 subjects. We calculated agreement between the HPV assays and the clinical performance of HPV testing and HPV genotyping alone and in combination with anal cytology. We observed high agreement between cobas and LA, with cobas more likely than LA to show positive results for HPV16, HPV18, and other carcinogenic types. Specimens testing positive in cobas but not in LA were more likely to be positive for other markers of HPV-related disease compared to those testing negative in both assays, suggesting that at least some of these were true positives for HPV. cobas and LA showed high sensitivities but low specificities for the detection of anal intraepithelial neoplasia grade 2/3 (AIN2/3) in this population (100% sensitivity and 26% specificity for cobas versus 98.4% sensitivity and 28.9% specificity for LA). A combination of anal cytology and HPV genotyping provided the highest accuracy for detecting anal precancer. A higher HPV load was associated with a higher risk of AIN2/3 with HPV16 (P(trend) < 0.001), HPV18 (P(trend) = 0.07), and other carcinogenic types (P(trend) < 0.001). We demonstrate that cobas can be used for HPV detection in anal cytology specimens. Additional tests are necessary to identify men at the highest risk of anal cancer among those infected with high-risk HPV. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  6. Lab-in-a-tube: Real-time molecular point-of-care diagnostics for influenza A and B using the cobas® Liat® system.

    PubMed

    Melchers, Willem J G; Kuijpers, Judith; Sickler, Joanna Jackson; Rahamat-Langendoen, Janette

    2017-02-18

    Rapid diagnosis of influenza A and B is important for direct treatment decisions in patient care and for the reduction of in-hospital transmissions. The new real-time PCR based molecular point-of-care (POC) assay, the cobas(®) Influenza A/B test on the cobas(®) Liat(®) System (cobas(®) Liat(®) Influenza A/B assay), generated a PCR result in less than 20 min, was evaluated for the detection of influenza A and B. One hundred twenty-one retrospectively collected respiratory specimens, previously analyzed with a routine influenza A/B test (Diagenode) were tested using the cobas(®) Liat(®) Influenza A/B assay. The cobas(®) Liat(®) Influenza A/B assay allows influenza A and B testing by RT-PCR within 20 min. This assay detected influenza A in 51 of 56 samples positive by the Diagenode test. The five discrepant results were retested with the Cepheid Influenza A/B test, confirming two positive cases. All 30 influenza B Diagenode positive samples were found positive by the cobas(®) Liat(®) Influenza A/B assay. Control samples (viral negative and non-influenza pathogens) were all negative by the cobas(®) Liat(®) Influenza A/B assay. The cobas(®) Liat(®) Influenza A/B assay showed a sensitivity for influenza A/B of 96% and 100%, respectively, and 100% specificity for both targets. The cobas(®) Liat(®) Influenza A/B assay is a useful tool for accurate, rapid, and sensitive detection of influenza A and B, offering timely and personalized patient management and infection control when implemented at the point-of-care.

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

    PubMed

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

    2013-01-01

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

  8. Performance of the Cobas® Influenza A/B Assay for Rapid Pcr-Based Detection of Influenza Compared to Prodesse ProFlu+ and Viral Culture

    PubMed Central

    Chen, L.; Tian, Y.; Chen, S.; Liesenfeld, O.

    2015-01-01

    Rapid and accurate diagnosis of influenza is important for patient management and infection control. We determined the performance of the cobas® Influenza A/B assay, a rapid automated nucleic acid assay performed on the cobas® Liat System for qualitative detection of influenza A and influenza B from nasopharyngeal (NP) swab specimens. Retrospective frozen and prospectively collected NP swabs from patients with signs and symptoms of influenza collected in universal transport medium (UTM) were tested at multiple sites including CLIA-waived sites using the cobas® Influenza A/B assay. Results were compared to the Prodesse Pro-Flu+ assay and to viral culture. Compared to the Prodesse ProFlu+ Assay, sensitivities of the cobas® Influenza A/B assay for influenza A and B were 97.7 and 98.6%, respectively; specificity was 99.2 and 99.4%. Compared to viral culture, the cobas® Influenza A/B assay showed sensitivities of 97.5 and 96.9% for influenza virus A and B, respectively; specificities were 97.9% for both viruses. Polymerase chain reaction (PCR)/sequencing showed that the majority of viral culture negative but cobas® Influenza A/B positive results were true positive results, indicating that the cobas® Influenza A/B assay has higher sensitivity compared to viral culture. In conclusion, the excellent accuracy, rapid time to result, and remarkable ease of use make the cobas® Influenza A/B nucleic acid assay for use on the cobas® Liat System a highly suitable point-of-care solution for the management of patients with suspected influenza A and B infection. PMID:26716012

  9. Comparison of Architect i2000sr and Cobas e601 Systems for Determining Serum Human Chorionic Gonadotropin-Beta.

    PubMed

    Guan, Xiaoyong; Sun, Yifan; Zhang, Hongyu; Liang, Ka; Long, Kang; Li, Jin; Tang, Shifu; Liu, Chunming

    2016-09-01

    Human chorionic gonadotropin-beta (β-hCG) is an important index used to monitor embryonic development following embryo transfer. Architect i2000sr and Cobas e601 are widely used automated immunoassay systems used to measure serum β-hCG concentrations; however, the correlations between serum β-hCG levels measured with these two immunoassays and the accuracy of the immunoassays have not been fully evaluated. Serum β-hCG levels were measured in 133 serum samples using the Architect i2000sr and Cobas e601 automated immunoassay systems. Passing-Bablok regression analysis was used to compare the correlation in serum β-hCG levels obtained using the two immunoassays. A Bland-Altman plot analysis was used to identify mean ratios and 95% CIs of the mean ratios of the β-hCG results between the two immunoassays. In this graphical method the mean ratios between the two techniques were plotted against the averages of the two techniques. The total coefficients of variations (CVs) of serum β-hCG ranged from 3.12 - 4.66% for Cobas e601 and 3.18 - 4.99% for Architect i2000sr. The measured value of serum β-hCG detected by the two immunoassays was statistically significant (p < 0.001). The Passing-Bablok regression analysis showed good correlation between the serum β-hCG values measured using the two systems. At a low concentration of serum β-hCG (< 10000 IU/L, n = 52), the correlation coefficient r was 0.9628. At a high concentration of serum β-hCG (> 10000 IU/L, n = 81), the correlation coefficient r was 0.8076. The Bland-Altman plot analysis showed that the measured value of serum β-hCG detected by Architect i2000sr was about 1.25 times higher than that of Cobas e601. The mean ratio was 1.12 at a low concentration of serum β-hCG, and it was 1.33 at a high concentration. Architect i2000sr and Cobas e601 have good concordance for determining serum β-hCG. However, the β-hCG values measured with Architect i2000sr were 25% higher than those obtained using Cobas e601.

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

    PubMed

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

    2014-03-01

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

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

    PubMed

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

    2016-07-01

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

  12. Evaluation of the Cobas TaqMan MTB real-time PCR assay for direct detection of Mycobacterium tuberculosis in respiratory specimens.

    PubMed

    Lee, Meng-Rui; Chung, Kuei-Pin; Wang, Hao-Chien; Lin, Chih-Bin; Yu, Chong-Jen; Lee, Jen-Jyh; Hsueh, Po-Ren

    2013-08-01

    The Cobas TaqMan MTB assay is a real-time PCR (qPCR) kit for rapid detection of Mycobacterium tuberculosis from clinical specimens. There are, however, limited studies validating its performance. We performed a prospective study in two hospitals in Taiwan on 586 respiratory specimens. By using culture as the reference method, the sensitivity and specificity of the Cobas TaqMan MTB assay were found to be 82.7 and 96.5 %, respectively. The sensitivity of the Cobas TaqMan MTB assay in acid-fast stain-negative respiratory specimens was only 34.9 %. Five specimens from five patients were positive for M. tuberculosis by the Cobas TaqMan MTB assay but were negative for M. tuberculosis by conventional culture methods. A diagnosis of pulmonary tuberculosis (TB) was made based on clinical and radiological findings as well as the response to anti-TB treatment in these five patients. Addition of data from these five specimens with discrepant results (PCR vs culture) from patients with symptoms clinically compatible with TB increased the sensitivity of the Cobas TaqMan MTB assay to 83.1 %. The Cobas TaqMan MTB assay is a rapid identification tool with a high degree of specificity for the direct detection of M. tuberculosis in respiratory specimens. The sensitivity for detecting acid-fast smear-negative respiratory specimens, however, is low.

  13. Performance of the COBAS® AmpliPrep/COBAS TaqMan® automated system for hepatitis C virus (HCV) quantification in a multi-center comparison.

    PubMed

    Bossler, Aaron; Gunsolly, Cynthia; Pyne, Michael T; Rendo, Angela; Rachel, Jane; Mills, Ray; Miller, Marjorie; Sipley, John; Hillyard, David; Jenkins, Stephen; Essmyer, Cynthia; Young, Steve; Lewinski, Michael; Rennert, Hanna

    2011-02-01

    Quantitative HCV RNA testing is considered standard of care for monitoring during treatment of patients infected with HCV. The COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HCV Test fully automates specimen processing and reaction assembly for HCV viral load testing using reverse transcription and real-time PCR amplification. The performance of the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HCV Test was evaluated in a multi-center study. Typical plasma based specimens were tested for accuracy, analytic range of measurement, reproducibility and genotype specific quantitation. Linear regression analysis of the quantitative results demonstrated a linear range of detection from 50 to 5 million (1.7-6.7 log(10))IU/mL and a coefficient of determination (R(2)) of 0.9948. The precision of the assay was highly reproducible within and between runs and among laboratories with coefficients of variance (CV) ranging from 6.7% to 40.0% across the seven laboratories. A representative sample for each of the six major HCV genotypes demonstrated reproducible quantitation between the seven laboratories. The COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HCV Test is a reliable and sensitive assay for HCV RNA quantitation. Copyright © 2010 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2015-04-01

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

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

    PubMed

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

    2013-01-01

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

  16. Quantification of intrahepatic total HBV DNA in liver biopsies of HBV-infected patients by a modified version of COBAS(®) Ampliprep/COBAS(®)TaqMan HBV test v2.0.

    PubMed

    Salpini, Romina; Piermatteo, Lorenzo; Gill, Upkar; Battisti, Arianna; Stazi, Francesca; Guenci, Tania; Giannella, Sara; Serafini, Valentina; Kennedy, Patrick T F; Perno, Carlo Federico; Svicher, Valentina; Ciotti, Marco

    2017-04-11

    Intrahepatic total HBV DNA (it-HBV DNA) level might reflect the size of virus reservoir and correlate with the histological status of the liver. To quantitate it-HBV DNA in a series of 70 liver biopsies obtained from hepatitis B chronic patients, a modified version of the COBAS(®)Ampliprep/COBAS(®)TaqMan HBV test v2.0 was used for this purpose. The linearity and reproducibility of the modified protocol was tested by quantifying serial dilutions of a full-length HBV containing plasmid and it-HBV DNA from a reference patient. A good linear trend between the expected values and those generated by the assay was observed at different concentrations of both plasmid and reference patient (R (2) = 0.994 and 0.962, respectively). Differences between the values obtained in two independent runs were ≤0.3 log IU for the plasmid and ≤0.6 log IU/mg for the reference patient, showing a high inter-run reproducibility. In the 70 liver biopsies, it-HBV DNA level ranged from 1.4 to 5.4 log IU/mg, with a good linearity and reproducibility between the values obtained in two runs [R (2) = 0.981; median (IQR) difference of it-HBV DNA 0.05 (0.02-0.09) IU/mg]. The modified COBAS(®)Ampliprep/COBAS(®)TaqMan HBV test v2.0 allows an accurate quantitation of it-HBV DNA. Its determination may have prognostic value and may be a useful tool for the new therapeutic strategies aimed at eradicating the HBV infection.

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2010-07-01

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

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

    PubMed Central

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

    2007-01-01

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

  20. The cobas p 630 instrument: a dedicated pre-analytic solution to optimize COBAS® AmpliPrep/COBAS® TaqMan® system workflow and turn-around-time.

    PubMed

    Vallefuoco, L; Sorrentino, R; Spalletti Cernia, D; Colucci, G; Portella, G

    2012-12-01

    The cobas p 630, a fully automated pre-analytical instrument for primary tube handling recently introduced to complete the Cobas(®) TaqMan systems portfolio, was evaluated in conjunction with: the COBAS(®) AmpliPrep/COBAS(®) TaqMan HBV Test, v2.0, COBAS(®) AmpliPrep/COBAS(®) TaqMan HCV Test, v1.0 and COBAS(®) AmpliPrep/COBAS(®) TaqMan HIV Test, v2.0. The instrument performance in transferring samples from primary to secondary tubes, its impact in improving COBAS(®) AmpliPrep/COBAS(®) TaqMan workflow and hands-on reduction and the risk of possible cross-contamination were assessed. Samples from 42 HBsAg positive, 42 HCV and 42 HIV antibody (Ab) positive patients as well as 21 healthy blood donors were processed with or without automated primary tubes. HIV, HCV and HBsAg positive samples showed a correlation index of 0.999, 0.987 and of 0.994, respectively. To assess for cross-contamination, high titer HBV DNA positive samples, HCV RNA and HIV RNA positive samples were distributed in the cobas p 630 in alternate tube positions, adjacent to negative control samples within the same rack. None of the healthy donor samples showed any reactivity. Based on these results, the cobas p 630 can improve workflow and sample tracing in laboratories performing molecular tests, and reduce turnaround time, errors, and risks.

  1. CLSI-Based Validation of Manufacturer-Derived Reference Intervals on the Cobas 8000 Platform.

    PubMed

    Leitner-Ferenc, Veronika; Atamaniuk, Johanna; Jansen-Skoupy, Sonja; Stöckelmeier, Brigitta; Grohs, Katharina; Födinger, Manuela

    2017-05-01

    Reference intervals provided by diagnostic test manufacturers should be transferred to clinical laboratories after validation. Although protocols exist, laboratories rarely perform and report on results of validation studies. We validated reference intervals (RIs) of 87 analytes on a Cobas 8000 platform according to standards published by the Clinical and Laboratory Standards Institute (CLSI). For 8 analytes, decision limits were provided in the package inserts. Among the 79 RIs subjected to transference validation, 8 were found not valid for transference, including lactate dehydrogenase (LDH) among women, and the following among both sexes: potassium, homocysteine, immunoglobulin E (IgE), free lambda light chain (FLC λ), C3 complement (C3c), folate, and 25-hydroxy vitamin D (25[(OH]D). For LDH, potassium, homocysteine, C3c, folate, and 25(OH)D, RIs or thresholds suitable for transference were available in the literature; however, this was not the case for IgE and FLC λ. The present study demonstrates that validation of RIs provided in the manufacturer provided package inserts is indispensable.

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

    PubMed

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

    2016-02-01

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

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

    PubMed Central

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

    2009-01-01

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

  4. Validation of methods performance for routine biochemistry analytes at Cobas 6000 analyzer series module c501.

    PubMed

    Supak Smolcic, Vesna; Bilic-Zulle, Lidija; Fisic, Elizabeta

    2011-01-01

    Cobas 6000 (Roche, Germany) is biochemistry analyzer for spectrophotometric, immunoturbidimetric and ion-selective determination of biochemical analytes. Hereby we present analytical validation with emphasis on method performance judgment for routine operation. Validation was made for 30 analytes (metabolites, enzymes, trace elements, specific proteins and electrolytes). Research included determination of within-run (N = 20) and between-run imprecision (N = 30), inaccuracy (N = 30) and method comparison with routine analyzer (Beckman Coulter AU640) (N = 50). For validation of complete analytical process we calculated total error (TE). Results were judged according to quality specification criteria given by European Working Group. Within-run imprecision CVs were all below 5% except for cholesterol, triglycerides, IgA and IgM. Between-run CVs for all analytes were below 10%. Analytes that did not meet the required specifications for imprecision were: total protein, albumin, calcium, sodium, chloride, immunoglobulins and HDL cholesterol. Analytes that did not fulfill requirements for inaccuracy were: total protein, calcium, sodium and chloride. Analytes that deviated from quality specifications for total error were: total protein, albumin, calcium, sodium, chloride and IgM. Passing-Bablok regression analysis provided linear equation and 95% confidence interval for intercept and slope. Complete accordance with routine analyzer Beckman Coulter AU640 showed small number of analytes. Other analytes showed small proportional and/or small constant difference and therefore need to be adjusted for routine operation. Regarding low CV values, tested analyzer has satisfactory accuracy and precision and is extremely stable. Except for analytes that are coherent on both analyzers, some analytes require adjustments of slope and intercept for complete accordance.

  5. Development and Validation of a Preanalytic Procedure for Performing the cobas HPV Test in SurePath Preservative Fluid.

    PubMed

    Krevolin, Mark D; Hardy, David; Pane, Jim; Aslam, Shagufta; Behrens, Catherine M

    2017-03-01

    The formation of chemical cross-links between nucleic acids and proteins in formalin-containing media presents challenges for human papillomavirus (HPV) testing of cervical samples collected in SurePath Preservative Fluid. A preanalytic process involving addition of a nucleophilic buffer and heating the sample to 120°C was developed to reverse the effects of cross-linking and improve nucleic acid accessibility for the cobas HPV Test in SurePath. Cycle threshold (CT) values for cobas HPV detection were evaluated over time and various temperatures, and mean CT differences between pretreated and both untreated SurePath samples and those collected in PreservCyt were assessed. Without pretreatment, low viral levels (1 × limit of detection) of HPV were no longer detectable by 7 days. For prospectively collected specimens, mean (95% CI) CT differences between pretreated and untreated samples indicated enhanced HPV DNA recovery in all categories of treated samples: -2.58 (-3.16 to -2.01), -2.63 (-3.62 to -1.64), and -3.39 (-4.95 to -1.82), respectively, for other 12 high-risk HPV types, HPV16, and HPV18. Furthermore, mean (95% CI) CT differences of pretreated SurePath samples were comparable to simultaneously collected PreservCyt samples: -0.48 (-0.98 to 0.02) and -0.23 (-0.93 to 0.46), respectively, for HPV16 and HPV18; a borderline significant difference [-0.35 (-0.57 to -0.13)] was observed for other 12 high-risk HPV types. This preanalytic procedure therefore ensures a validated, safe, and accurate method for cobas HPV testing in SurePath.

  6. Comparison of on-treatment HCV RNA during direct antiviral therapy using two different COBAS TaqMan HCV assays.

    PubMed

    Vermehren, Johannes; Bourlière, Marc; Pol, Stanislas; Marcellin, Patrick; Hyland, Robert H; Jiang, Deyuan; Brainard, Diana M; Zeuzem, Stefan; Welzel, Tania M

    2017-04-01

    Repeated measurements of hepatitis C virus (HCV) RNA levels during antiviral therapy are recommended to monitor treatment efficacy and adherence. Throughout most direct antiviral agent (DAA) approval studies, HCV RNA cutoffs and endpoints were established with the COBAS TaqMan assay for use with the High Pure System (HPS/CTM). Different assays used in clinical practice may yield different quantitative results and possibly impact treatment decisions. The concordance of the fully-automated COBAS AmpliPrep/COBAS TaqMan assay (CAP/CTM) with HPS/CTM and its ability to predict response to DAA-treatment with ledipasvir/sofosbuvir was assessed in cirrhotic patients with HCV genotype-1-infection who had failed prior treatment with protease inhibitor-based regimens. Serum samples from patients (n=154) treated in the phase-2 SIRIUS-study were collected at baseline and during antiviral therapy (weeks 1-8), and were tested in parallel by both assays. The mean difference between HPS/CTM and CAP/CTM at baseline (n=153) was 0.32 log10 IU/mL HCV RNA. Discordant results were observed in 12% of samples collected at treatment weeks 1-8, with the greatest differences observed at weeks 2 and 4 (14% and 29%, respectively, for undetectable HCV RNA). SVR rates were 96%-97% in the study and were not significantly different between patients with detectable vs. undetectable HCV RNA according to both assays at weeks 1-4 of antiviral therapy. CAP/CTM and HPS/CTM showed significantly different response rates during the early stages of ledipasvir/sofosbuvir treatment. However, on-treatment response was not predictive of SVR with either assay, indicating that determination of on-treatment HCV RNA levels may not be useful to guide treatment decisions. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Comparison of AdvanSure TB/NTM PCR and COBAS TaqMan MTB PCR for Detection of Mycobacterium tuberculosis Complex in Routine Clinical Practice.

    PubMed

    Cho, Won-Hyung; Won, Eun-Jeong; Choi, Hyun-Jung; Kee, Seung-Jung; Shin, Jong-Hee; Ryang, Dong-Wook; Suh, Soon-Pal

    2015-05-01

    The AdvanSure tuberculosis/non-tuberculous mycobacterium (TB/NTM) PCR (LG Life Science, Korea) and COBAS TaqMan Mycobacterium tuberculosis (MTB) PCR (Roche Diagnostics, USA) are commonly used in clinical microbiology laboratories. We aimed to evaluate these two commercial real-time PCR assays for detection of MTB in a large set of clinical samples over a two-year period. AdvanSure TB/NTM PCR and COBAS TaqMan MTB PCR were performed on 9,119 (75.2%) and 3,010 (24.8%) of 12,129 (9,728 respiratory and 2,401 non-respiratory) MTB specimens, with 361 (4.0%) and 102 (3.4%) acid-fast bacilli (AFB)-positive results, respectively. In MTB culture, 788 (6.5%) MTB and 514 (4.2%) NTM were identified. The total sensitivity and specificity of the AdvanSure assay were 67.8% (95% confidence interval [CI], 63.9-71.6) and 98.3% (95% CI, 98.0-98.6), while those of the COBAS TaqMan assay were 67.2% (95% CI, 60.0-73.8) and 98.4% (95% CI, 97.9-98.9), respectively. The sensitivities and specificities of the AdvanSure and COBAS TaqMan assays for AFB-positive and AFB-negative samples were comparable. Furthermore, the AdvanSure assay showed fewer invalid results compared with the COBAS TaqMan assay (5.0 vs. 20.4 invalid results/1,000 tests, P<0.001). AdvanSure assay represents a comparable yet more reliable method than COBAS TaqMan for the identification of mycobacteria in routine clinical microbiology.

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

    PubMed

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

    2015-09-01

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

  9. Comparison of Cobas 6500 and Iris IQ200 fully-automated urine analyzers to manual urine microscopy.

    PubMed

    Bakan, Ebubekir; Ozturk, Nurinnisa; Baygutalp, Nurcan Kilic; Polat, Elif; Akpinar, Kadriye; Dorman, Emrullah; Polat, Harun; Bakan, Nuri

    2016-10-15

    Urine screening is achieved by either automated or manual microscopic analysis. The aim of the study was to compare Cobas 6500 and Iris IQ200 urine analyzers, and manual urine microscopic analysis. A total of 540 urine samples sent to the laboratory for chemical and sediment analysis were analyzed on Cobas 6500 and Iris IQ200 within 1 hour from sampling. One hundred and fifty three samples were found to have pathological sediment results and were subjected to manual microscopic analysis performed by laboratory staff blinded to the study. Spearman's and Gamma statistics were used for correlation analyses, and the McNemar test for the comparison of the two automated analyzers. The comparison of Cobas u701 to the manual method yielded the following regression equations: y = - 0.12 (95% CI: - 1.09 to 0.67) + 0.78 (95% CI: 0.65 to 0.95) x for WBC and y = 0.06 (95% CI: - 0.09 to 0.25) + 0.66 (95% CI: 0.57 to 0.73) x for RBC. The comparison of IQ200 Elite to manual method the following equations: y = 0.03 (95% CI: - 1.00 to 1.00) + 0.88 (95% CI: 0.66 to 1.00) x for WBC and y = - 0.22 (95% CI: - 0.80 to 0.20) + 0.40 (95% CI: 0.32 to 0.50) x for RBC. IQ200 Elite compared to Cobas u701 yielded the following equations: y = - 0.95 (95% CI: - 2.13 to 0.11) + 1.25 (95% CI: 1.08 to 1.44) x for WBC and y = - 1.20 (95% CI: - 1.80 to -0.30) + 0. 80 (95% CI: 0.55 to 1.00) x for RBC. The two analyzers showed similar performances and good compatibility to manual microscopy. However, they are still inadequate in the determination of WBC, RBC, and EC in highly-pathological samples. Thus, confirmation by manual microscopic analysis may be useful.

  10. Comparison of Cobas 6500 and Iris IQ200 fully-automated urine analyzers to manual urine microscopy

    PubMed Central

    Bakan, Ebubekir; Ozturk, Nurinnisa; Baygutalp, Nurcan Kilic; Polat, Elif; Akpinar, Kadriye; Dorman, Emrullah; Polat, Harun; Bakan, Nuri

    2016-01-01

    Introduction Urine screening is achieved by either automated or manual microscopic analysis. The aim of the study was to compare Cobas 6500 and Iris IQ200 urine analyzers, and manual urine microscopic analysis. Materials and methods A total of 540 urine samples sent to the laboratory for chemical and sediment analysis were analyzed on Cobas 6500 and Iris IQ200 within 1 hour from sampling. One hundred and fifty three samples were found to have pathological sediment results and were subjected to manual microscopic analysis performed by laboratory staff blinded to the study. Spearman’s and Gamma statistics were used for correlation analyses, and the McNemar test for the comparison of the two automated analyzers. Results The comparison of Cobas u701 to the manual method yielded the following regression equations: y = - 0.12 (95% CI: - 1.09 to 0.67) + 0.78 (95% CI: 0.65 to 0.95) x for WBC and y = 0.06 (95% CI: - 0.09 to 0.25) + 0.66 (95% CI: 0.57 to 0.73) x for RBC. The comparison of IQ200 Elite to manual method the following equations: y = 0.03 (95% CI: - 1.00 to 1.00) + 0.88 (95% CI: 0.66 to 1.00) x for WBC and y = - 0.22 (95% CI: - 0.80 to 0.20) + 0.40 (95% CI: 0.32 to 0.50) x for RBC. IQ200 Elite compared to Cobas u701 yielded the following equations: y = - 0.95 (95% CI: - 2.13 to 0.11) + 1.25 (95% CI: 1.08 to 1.44) x for WBC and y = - 1.20 (95% CI: - 1.80 to -0.30) + 0. 80 (95% CI: 0.55 to 1.00) x for RBC. Conclusions The two analyzers showed similar performances and good compatibility to manual microscopy. However, they are still inadequate in the determination of WBC, RBC, and EC in highly-pathological samples. Thus, confirmation by manual microscopic analysis may be useful. PMID:27812305

  11. PRISM hepatitis B surface antigen detection of hepatits B virus minipool nucleic acid testing yield samples.

    PubMed

    Linauts, Sandy; Saldanha, John; Strong, D Michael

    2008-07-01

    Hepatitis B virus (HBV) residual risk has been estimated at 1:63,000-1:205,000 and introduction of more sensitive serological tests and nucleic acid testing (NAT) would reduce that risk. Sensitivity of the recently licensed Abbott PRISM hepatitis B surface antigen (HBsAg) CLIA and minipool (MP) HBV NAT has been described as comparable and thus the need for HBV NAT has not been compelling. In this study, eight samples identified as yield samples with MP HBV NAT were tested using the PRISM test. Seven samples were identified using the Roche COBAS AmpliScreen HBV test and one additional sample was obtained from the clinical trial for the Roche cobas TaqScreen MPX test. Each of these samples was reactive by MP HBV NAT and nonreactive for HBsAg using one of three licensed enzyme immunoassay (EIA) tests. After licensure of the PRISM HBsAg, aliquots were tested with this assay, and DNA quantitation and genotyping were repeated where sample volume permitted. Three samples (2000, 2300, and 61,000 copies/mL) produced reactive results with PRISM. Four samples with viral loads less than 300 copies per mL produced nonreactive results. One sample, originally quantitated at 37,000 copies per mL (but 3850 copies/mL in repeat testing) was also nonreactive by PRISM. Genotyping of this sample indicated a type C genotype with no mutations. Adding serological sensitivity of PRISM CLIA reduced the NAT yield from the original 1: 385,555 to 1:610,488. However, MP HBV NAT still provides additional sensitivity over CLIA, even for a donation with a viral load of almost 4000 copies per mL.

  12. 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.

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

    PubMed Central

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

    2016-01-01

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

  14. Evaluation of the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HCV Test v2.0 for HCV viral load monitoring using dried blood spot specimens.

    PubMed

    Marins, Ed G; Bodinaidu, Keerthi; Lin, Matthew; Deforest, Alison

    2017-09-01

    This study evaluated the use of dried blood spot (DBS) for HCV viral load quantification using the COBAS(®) AmpliPrep/COBAS(®) Taqman(®) HCV Quantitative Test v2.0 (CAP/CTM HCV v2), and compared two different procedures for preparation of DBS samples with a Specimen Pre-Extraction (SPEX) reagent (either heated [SPEX with SH] for 10min at 56°C on a thermomixer, or incubated for 1h at room temperature [SPEX at RT]) against the standard plasma input. Whole blood specimens from 48 patients with chronic HCV infection and Whatman(®) 903 Protein Saver Cards were used to prepare 35μL DBS. An aliquot of plasma was spun and frozen from each draw. Mean DBS viral load results were compared to the corresponding results from plasma. Correlation between DBS to plasma was linear for both SPEX with SH (R(2)=0.96) and SPEX at RT (R(2)=0.97) procedures, with a constant negative offset of approximately 2.0log10IU/mL between whole blood DBS without any adjustments and plasma results. After volume corrections, the mean offset to plasma decreased to -0.39 and -0.36 for the two procedures, respectively. The study demonstrated the use of DBS for HCV viral load correlates well with plasma with a constant offset. Copyright © 2017 Roche Molecular Systems, Inc. Published by Elsevier B.V. All rights reserved.

  15. 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.

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

    PubMed

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

    2017-03-01

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

  17. [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. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España. All rights reserved.

  18. Detection of BRAF V600 mutations in melanoma: evaluation of concordance between the Cobas® 4800 BRAF V600 mutation test and the methods used in French National Cancer Institute (INCa) platforms in a real-life setting.

    PubMed

    Mourah, Samia; Denis, Marc G; Narducci, Fabienne Escande; Solassol, Jérôme; Merlin, Jean-Louis; Sabourin, Jean-Christophe; Scoazec, Jean-Yves; Ouafik, L'Houcine; Emile, Jean-François; Heller, Remy; Souvignet, Claude; Bergougnoux, Loïc; Merlio, Jean-Philippe

    2015-01-01

    Vemurafenib is approved for the treatment of metastatic melanoma in patients with BRAF V600 mutation. In pivotal clinical trials, BRAF testing has always been done with the approved cobas 4800 BRAF test. In routine practice, several methods are available and are used according to the laboratories usual procedures. A national, multicenter, non-interventional study was conducted with prospective and consecutive collection of tumor samples. A parallel evaluation was performed in routine practice between the cobas 4800 BRAF V600 mutation test and home brew methods (HBMs) of 12 national laboratories, labelled and funded by the French National Cancer Institute (INCa). For 420 melanoma samples tested, the cobas method versus HBM showed a high concordance (93.3%; kappa = 0.86) in BRAF V600 genotyping with similar mutation rates (34.0% versus 35.7%, respectively). Overall, 97.4% and 98.6% of samples gave valid results using the cobas and HBM, respectively. Of the 185 samples strictly fulfilling the cobas guidelines, the concordance rate was even higher (95.7%; kappa = 0.91; 95%CI [0.85; 0.97]). Out of the 420 samples tested, 28 (6.7%) showed discordance between HBM and cobas. This prospective study shows a high concordance rate between the cobas 4800 BRAF V600 test and home brew methods in the routine detection of BRAF V600E mutations.

  19. Comparison of a highly automated 5-h susceptibility testing system, the Cobas-Bact, with two reference methods: Kirby-Bauer disk diffusion and broth microdilution.

    PubMed

    Murray, P R; Niles, A C; Heeren, R L

    1987-12-01

    The results of susceptibility tests performed with the Cobas-Bact system were compared with those of the Kirby-Bauer disk diffusion and the broth microdilution methods. The evaluation included tests with 24 antibiotics against 250 isolates of the family Enterobacteriaceae and 13 antibiotics against 100 gram-positive cocci. Complete agreements between the Cobas-Bact and Kirby-Bauer methods were 82.8 and 84.5% for gram-positive cocci and gram-negative bacilli, respectively. Agreements between the Cobas-Bact and broth microdilution methods were 76.7% for gram-positive cocci and 84.8% for gram-negative bacilli. Complete agreements between the Kirby-Bauer and broth microdilution methods were 87.0% for gram-positive cocci and 92.2% for gram-negative bacilli. Despite generally satisfactory results with most organism-antibiotic combinations tested, additional modifications of the Cobas-Bact system are required to reduce the number of major and very major discrepancies, as well as to permit testing of Pseudomonas spp. and other gram-negative nonfermentative bacilli.

  20. Comparison of a highly automated 5-h susceptibility testing system, the Cobas-Bact, with two reference methods: Kirby-Bauer disk diffusion and broth microdilution.

    PubMed Central

    Murray, P R; Niles, A C; Heeren, R L

    1987-01-01

    The results of susceptibility tests performed with the Cobas-Bact system were compared with those of the Kirby-Bauer disk diffusion and the broth microdilution methods. The evaluation included tests with 24 antibiotics against 250 isolates of the family Enterobacteriaceae and 13 antibiotics against 100 gram-positive cocci. Complete agreements between the Cobas-Bact and Kirby-Bauer methods were 82.8 and 84.5% for gram-positive cocci and gram-negative bacilli, respectively. Agreements between the Cobas-Bact and broth microdilution methods were 76.7% for gram-positive cocci and 84.8% for gram-negative bacilli. Complete agreements between the Kirby-Bauer and broth microdilution methods were 87.0% for gram-positive cocci and 92.2% for gram-negative bacilli. Despite generally satisfactory results with most organism-antibiotic combinations tested, additional modifications of the Cobas-Bact system are required to reduce the number of major and very major discrepancies, as well as to permit testing of Pseudomonas spp. and other gram-negative nonfermentative bacilli. PMID:3429627

  1. Quantification of hepatitis C virus in patients treated with peginterferon-alfa 2a plus ribavirin treatment by COBAS TaqMan HCV test.

    PubMed

    Kanda, T; Imazeki, F; Yonemitsu, Y; Mikami, S; Takada, N; Nishino, T; Takashi, M; Tsubota, A; Kato, K; Sugiura, N; Tawada, A; Wu, S; Tanaka, T; Nakamoto, S; Mikata, R; Tada, M; Chiba, T; Kurihara, T; Arai, M; Fujiwara, K; Kanai, F; Yokosuka, O

    2011-07-01

    Extremely low levels of serum hepatitis C virus (HCV) RNA can be detected by COBAS TaqMan HCV test. To investigate whether the COBAS TaqMan HCV test is useful for measuring rapid virological response (RVR) and early virological response (EVR) to predict sustained virological response (SVR), we compared the virological response to PEG-IFN-alfa 2a plus RBV in 76 patients infected with HCV genotype 1 when undetectable HCV RNA by the COBAS TaqMan HCV test was used, with those when below 1.7 log IU/mL HCV RNA by COBAS TaqMan HCV test was used, which corresponded to the use of traditional methods. Among the 76 patients, 28 (36.8%) had SVR, 13 (17.1%) relapsed, 19 (25.0%) did not respond, and 16 (21.0%) discontinued the treatment due to side effects. The positive predictive values for SVR based on undetectable HCV RNA by COBAS TaqMan HCV test at 24 weeks after the end of treatment [10/10 (100%) at week 4, 21/23 (91.3%) at week 8 and 26/33 (78.7%) at week 12] were superior to those based on <1.7 log IU/mL HCV RNA [17/19 (89.4%) at week 4, 27/38 (71.0%) at week 8, and 27/43 (62.7%) at week 12]. The negative predictive values for SVR based on <1.7 log IU/mL HCV RNA by COBAS TaqMan HCV test [46/57 (80.7%) at week 4, 37/38 (97.3%) at week 8, and 32/33 (96.9%) at week 12] were superior to those based on undetectable HCV RNA [48/66 (72.7%) at week 4, 46/53 (86.7%) at week 8, and 41/43 (95.3%) at week 12]. The utilization of both undetectable RNA and <1.7 log IU/mL HCV RNA by COBAS TaqMan HCV test is useful and could predict SVR and non-SVR patients with greater accuracy.

  2. Comparison of COBAS 4800 KRAS, TaqMan PCR and high resolution melting PCR assays for the detection of KRAS somatic mutations in formalin-fixed paraffin embedded colorectal carcinomas.

    PubMed

    Harlé, Alexandre; Busser, Benoit; Rouyer, Marie; Harter, Valentin; Genin, Pascal; Leroux, Agnès; Merlin, Jean-Louis

    2013-03-01

    Many studies documented the influence of KRAS mutation status on the response of patients with metastatic colorectal cancer (mCRC) to anti-EGFR monoclonal antibodies. The COBAS 4800 KRAS is an assay using real time PCR and TaqMelt technology, CE-IVD validated, for the detection of 19 KRAS somatic mutations in exons 2 and 3. We compared COBAS with previously validated PCR TaqMan and High Resolution Melting (HRM) assays on 156 formalin-fixed paraffin embedded (FFPE) specimens of colorectal carcinoma. DNA extraction procedures, using the Qiagen QiAMP kit and the Roche COBAS DNA kit, were also compared. Of the 156 samples, 132 were interpretable using COBAS and TaqMan and 92 using COBAS and HRM. No statistically significant difference was found between COBAS/TaqMan and COBAS/HRM (k = 0.937; p < 0.001 - four discordant cases were found, mostly concerning codon 61 mutations and k = 0.891; p < 0.001 - five discordant cases were found, three regarding codon 61 and two on codon 12/13, respectively). No difference was found between the two DNA extraction methods (t = 1.7185; dol = 39; α = 5 %). The three assays were found suitable to detect accurately KRAS mutations in colon FFPE specimens. COBAS and TaqMan were found to be more robust than HRM, as they yielded fewer non-interpretable results. DNA extraction kits were found to provide equivalent results. The present study shows that pre-screening using COBAS with further TaqMan mutation characterization constitutes an easy and reliable approach for routine diagnostic purposes.

  3. Multi-center evaluation of the cobas(®) Liat(®) Influenza A/B & RSV assay for rapid point of care diagnosis.

    PubMed

    Gibson, Jane; Schechter-Perkins, Elissa M; Mitchell, Patricia; Mace, Sharon; Tian, Yu; Williams, Kemi; Luo, Robert; Yen-Lieberman, Belinda

    2017-10-01

    Point of Care Testing (POCT) provides the capability for rapid laboratory test results in patient care environments where a traditional clinical laboratory is not available. POCTs have shorter turn-around times (TATs), they may be performed by non-laboratory personnel, and the need for transport time is eliminated. The Food and Drug Administration (FDA) recently granted Clinical Laboratory Improvements Amendment (CLIA) waiver status to the cobas(®) Influenza A/B & RSV assay, a rapid, accurate point-of-care test for Influenza and respiratory syncytial virus (RSV) performed on the Liat(®) System. The performance characteristics of this test were determined though a multi-site study consisting of different point of care testing environments. Prospectively collected Nasopharyngeal (NP) swabs from 1361 patients seen at 8 primary care clinics and 4 emergency departments (EDs) and 295 retrospectively identified specimens were tested for Influenza A/B and RSV on the cobas(®) Liat(®) platform. Performance characteristics were determined through comparison to ProFlu+, a laboratory-based PCR test for Influenza A/B and RSV (reference test). Discordant specimens were adjudicated following bi-directional sequencing. The cobas(®) Influenza A/B and RSV assay showed sensitivities of 99.6%, 99.3%, and 96.8% for Influenza A, Influenza B, and RSV, respectively as determined from percent positive agreement (PPA) following comparison to the reference test. Sequencing confirmed cobas(®) Influenza A/B and RSV results in 49.2% of reference test discordant specimens, while crossing threshold data suggest increased sensitivity compared to the reference test. The cobas(®) Influenza A/B and RSV assay was found to be a rapid, sensitive POCT for the detection of these viruses, and provides laboratory-quality PCR-based diagnostic results in point of care settings. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2015-11-01

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

  5. Detection and quantitation of HBV DNA in miniaturized samples: multi centre study to evaluate the performance of the COBAS ® AmpliPrep/COBAS ® TaqMan ® hepatitis B virus (HBV) test v2.0 by the use of plasma or serum specimens.

    PubMed

    Berger, Annemarie; Gohl, Peter; Stürmer, Martin; Rabenau, Holger Felix; Nauck, Markus; Doerr, Hans Wilhelm

    2010-11-01

    Laboratory analysis of blood specimens is an increasingly important tool for rapid diagnosis and control of therapy. So, miniaturization of test systems is needed, but reduced specimens might impair test quality. For rapid detection and quantitation of HBV DNA, the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV test has proved a robust instrument in routine diagnostic services. The test system has been modified recently for application of reduced samples of blood plasma and for blood serum, too. The performance of this modified COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV v2.0 (HBV v2.0 (this test is currently not available in the USA)) test was evaluated by comparison with the former COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV v1.0 (HBV v1.0) test. In this study a platform correlation of both assay versions was done including 275 HBV DNA positive EDTA plasma samples. Comparable results were obtained (R(2)=0.97, mean difference -0.03 log(10)IU/ml). The verification of equivalency of the sample matrix (plasma vs. serum samples tested in HBV v2.0 in the same run) showed comparable results for all 278 samples with a R(2)=0.99 and a mean difference of 0.06 log(10)IU/ml. In conclusion, the new test version HBV v2.0 is highly specific and reproducible and quantifies accurately HBV DNA in EDTA plasma and serum samples from patients with chronic HBV infection.

  6. Cloning, sequencing, and expression of the uroporphyrinogen III methyltransferase cobA gene of Propionibacterium freudenreichii (shermanii).

    PubMed

    Sattler, I; Roessner, C A; Stolowich, N J; Hardin, S H; Harris-Haller, L W; Yokubaitis, N T; Murooka, Y; Hashimoto, Y; Scott, A I

    1995-03-01

    We cloned, sequenced, and overexpressed cobA, the gene encoding uroporphyrinogen III methyltransferase in Propionibacterium freudenreichii, and examined the catalytic properties of the enzyme. The methyltransferase is similar in mass (27 kDa) and homologous to the one isolated from Pseudomonas denitrificans. In contrast to the much larger isoenzyme encoded by the cysG gene of Escherichia coli (52 kDa), the P. freudenreichii enzyme does not contain the additional 22-kDa peptide moiety at its N-terminal end bearing the oxidase-ferrochelatase activity responsible for the conversion of dihydrosirohydrochlorin (precorrin-2) to siroheme. Since it does not contain this moiety, it is not a likely candidate for synthesis of a cobalt-containing early intermediate that has been proposed for the vitamin B12 biosynthetic pathway in P. freudenreichii. Uroporphyrinogen III methyltransferase of P. freudenreichii not only catalyzes the addition of two methyl groups to uroporphyrinogen III to afford the early vitamin B12 intermediate, precorrin-2, but also has an overmethylation property that catalyzes the synthesis of several tri- and tetra-methylated compounds that are not part of the vitamin B12 pathway. The enzyme catalyzes the addition of three methyl groups to uroporphyrinogen I to form trimethylpyrrocorphin, the intermediate necessary for biosynthesis of the natural products, factors S1 and S3, previously isolated from this organism. A second gene found upstream from the cobA gene encodes a protein homologous to CbiO of Salmonella typhimurium, a membrane-bound, ATP-dependent transport protein thought to be part of the cobalt transport system involved in vitamin B12 synthesis. These two genes do not appear to constitute part of an extensive cobalamin operon.

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

    PubMed

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

    2009-12-01

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

  8. The role of human papillomavirus (HPV) genotyping in cervical cancer screening: A large-scale evaluation of the cobas HPV test

    PubMed Central

    Schiffman, Mark; Boyle, Sean; Raine-Bennett, Tina; Katki, Hormuzd A.; Gage, Julia C.; Wentzensen, Nicolas; Kornegay, Janet R; Apple, Raymond; Aldrich, Carrie; Erlich, Henry A.; Tam, Thanh; Befano, Brian; Burk, Robert D.; Castle, Philip E.

    2015-01-01

    Background The cobas® HPV Test (“cobas”, Roche Molecular Systems) detects HPV16 and HPV18 individually, and a pool of 12 other high-risk (HR) HPV types. The test is approved for 1) ASC-US triage to determine need for colposcopy, 2) combined screening with cytology (“co-testing”), and 3) primary HPV screening. Methods To assess the possible value of HPV16/18 typing, >17,000 specimens from a longitudinal cohort study of initially HPV-positive women (HC2, Qiagen) were retested with cobas. To study accuracy, cobas genotyping results were compared to those of an established method, the LINEAR ARRAY HPV Genotyping Test (LA, Roche Molecular Systems). Clinical value of the typing strategy was evaluated by linking the cobas results (supplemented by other available typing results) to 3-year cumulative risks of CIN3+. Results Grouped hierarchically (HPV16, else HPV18, else other HR types, else negative), the kappa statistic for agreement between cobas and LA was 0.86 (95%CI=0.86-0.87). In all 3 scenarios, HPV16-positive women were at much higher 3-year risk of CIN3+ than HPV16-negative women: women aged 21 and older with ASC-US (14.5%, 95%CI=13.5%-15.5% versus 3.5%, 95%CI=3.3%-3.6%); women aged 30 and older that were HPV-positive cytology-negative (10.3%, 95%CI=9.6%-11.1% versus 2.3%, 95%CI=2.2%-2.4%); and all women 25 and older that were HPV-positive (18.5%, 95%CI=17.8%-19.2% versus 4.3%, 95%CI=4.2%-4.4%). Conclusion The cobas and LA results show excellent agreement. The data support HPV16 typing. Impact HPV16 typing is useful in the management of HPV- positive/cytology-negative women in co-testing, of all HPV-positive women in primary HPV testing, and perhaps in the management of HPV-positive women with ASC-US. PMID:26088703

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

    PubMed

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

    2016-08-01

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

  10. A European multicentre study on the comparison of HCV viral loads between VERIS HCV assay and COBAS(®) TaqMan(®) HCV Test and RealTime HCV Assay.

    PubMed

    Braun, Patrick; Drago, Monica; Fanti, Diana; Fleury, Hervé; Hofmann, Jörg; Izopet, Jacques; Kühn, Sebastian; Lombardi, Alessandra; Micheli, Valeria; Sauné, Karine; Trimoulet, Pascale; Whittaker, Duncan; Artus, Alain; Rhodes, Daniel

    2017-05-01

    Beckman Coulter has developed the VERIS HCV Assay for use on the new fully automated DxN VERIS Molecular Diagnostic System(¥) for HCV viral load monitoring. Evaluate the clinical performance of the new quantitative VERIS HCV Assay. Comparison was performed on 279 plasma specimens from HCV infected patients tested with the VERIS HCV Assay and COBAS(®) Ampliprep/COBAS(®) Taqman(®) HCV Test and 369 specimens tested with the VERIS HCV Assay and RealTime HCV Assay. Patient monitoring sample results from four time points were also compared. The average bias between the VERIS HCV Assay and the COBAS(®) Ampliprep/COBAS(®) Taqman(®) HCV Test was 0.04 log10IU/mL, while between the VERIS HCV Assay and the RealTime HCV Assay average bias was 0.21 log10IU/mL. Bias, however, was not consistent across the measuring range. Analysis at the lower end of quantification levels 50, 100, and 1000IU/mL showed a predicted bias for VERIS HCV Assay versus COBAS(®) Ampliprep/COBAS(®) Taqman(®) HCV Test between -0.42 and -0.22 log10IU/mL and for VERIS HCV Assay versus RealTime HCV Assay between 0.00 and 0.13 log10IU/mL. Patient monitoring of HCV viral load over time demonstrated similar levels between VERIS HCV Assay results and COBAS(®) Ampliprep/COBAS(®) Taqman(®) HCV Test (52 samples from 13 patients) and RealTime HCV Assay (112 samples from 28 patients). VERIS HCV Assay for use on the DxN VERIS Molecular Diagnostic System represents a reliable new tool for easy sample to result HCV RNA viral load monitoring. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2013-01-01

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

  13. 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

  14. Detection of epidermal growth factor receptor gene T790M mutation in cytology samples using the cobas(®) EGFR mutation test.

    PubMed

    Satouchi, Miyako; Tanaka, Hiroshi; Yoshioka, Hiroshige; Shimokawaji, Tadasuke; Mizuno, Keiko; Takeda, Koji; Yoshino, Ichiro; Seto, Takashi; Kurata, Takayasu; Tashiro, Naoki; Hagiwara, Koichi

    2017-09-01

    Detection of epidermal growth factor receptor (EGFR) gene mutations is essential in deciding therapeutic strategy in non-small cell lung cancer (NSCLC) patients at initial diagnosis. Moreover, in EGFR mutation-positive (EGFRm) NSCLC patients, re-biopsy at disease progression to clarify resistance mechanisms is also important. However, collecting histology samples is often difficult because of inaccessibility and invasiveness. In some cases, only cytology samples can be collected, and studies have reported that cytology samples are appropriate for EGFR gene mutation testing. The cobas(®) EGFR Mutation Test (Roche Molecular Systems Inc., Branchburg, New Jersey, USA) is approved as a companion diagnostic for osimertinib, a third-generation EGFR-tyrosine kinase inhibitor approved in Japan. However, it is not clear whether the EGFR T790M mutation can be detected in cytology samples using this test. The primary objective of this study was to assess concordance of EGFR T790M gene mutation detection between histology and matched cytology samples using the cobas(®) EGFR Mutation Test. We conducted a multicenter, observational study in Japan. Overall, 41 EGFRm NSCLC patients who had both histology and cytology samples collected at the same time at re-biopsy and with the results of EGFR mutation test using histology samples were enrolled. The EGFR mutation status of both sample types was tested using the cobas(®) EGFR Mutation Test and the concordance rates were calculated. The EGFR T790M mutation detection rate in histology and cytology samples was 42.5% and 37.5%, respectively. The overall percent agreement between the histology and cytology samples was 91.7%. These data demonstrate that the cobas(®) EGFR Mutation Test can detect the EGFR T790M mutation in both cytology and histology samples. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  15. Differences between quantification of genotype 3 hepatitis C virus RNA by Versions 1.0 and 2.0 of the COBAS AmpliPrep/COBAS TaqMan HCV Test.

    PubMed

    Pierce, Virginia M; Eversley, Jacqueline S; Tran, Thuy K; Rosenberg, Eric S

    2017-06-27

    Differences between the designs of hepatitis C virus (HCV) viral load assays can result in genotype-related variability in RNA quantification. We tested paired aliquots of plasma specimens from HCV-infected individuals using two versions (v1.0 and v2.0) of the Roche COBAS AmpliPrep/COBAS TaqMan HCV Test (CAP/CTM HCV) and noted variability between results for a subset of specimens; we then sought to determine whether discrepant results were more prevalent among specific HCV genotypes. Archived and prospectively-collected plasma samples from 114 unique patients were tested using CAP/CTM HCV v1.0 and v2.0. The HCV genotype result for each patient was determined by retrospectively reviewing laboratory records. All (46/46) specimens with quantifiable viral loads from patients with genotype 1 or 2 infection had CAP/CTM HCV v1.0 and v2.0 results that were within 0.5 log10 IU/mL; in contrast, only 3/11 (27.3%) from patients with HCV genotype 3 (mean difference, 0.56 log10 IU/mL higher with v2.0) and 0/3 (0%) from patients with HCV genotype 4 (mean difference, 0.91 log10 IU/mL higher with v2.0) had results within 0.5 log10 IU/mL. Among specimens with detectable HCV RNA below the lower limit of quantification with v1.0, greater proportions of genotype 3 (4/7, 57.1%) and genotype 4 (3/4, 75.0%) specimens than genotype 1 or 2 specimens (6/30, 20.0%) had v2.0 results within the quantifiable range. In patients infected with HCV genotype 3, sequential CAP/CTM HCV viral load results should be compared with caution and interpreted in the context of the specific assay version used.

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

    PubMed

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

    2017-02-01

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

  17. Performance of the cobas MRSA/SA Test for Simultaneous Detection of Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus From Nasal Swabs.

    PubMed

    Peterson, Lance R; Woods, Christopher W; Davis, Thomas E; Wang, Zi-Xuam; Young, Stephen A; Osiecki, John C; Lewinski, Michael A; Liesenfeld, Oliver

    2017-08-01

    Health care-associated methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus aureus (SA) infections are continuing problems. Rapidly determining the MRSA colonization status of a patient facilitates practice to reduce spread of MRSA clinical disease. Sensitive detection of all SA prior to surgery, followed by decolonization, can significantly reduce postoperative infection from this pathogen. Our goal was to validate a new automated assay for this testing. We compared performance of the cobas MRSA/SA Test on the cobas 4800 System to direct and enriched chromogenic culture using nasal swabs collected from patients at six United States sites. Compared to direct and enriched culture, the sensitivity for MRSA and SA was 93.1% and 93.9%, and the specificity was 97.5% and 94.2%, respectively. After discrepancy analysis, the sensitivity for MRSA and SA was 97.1% and 98.6%, and the specificity was 98.3% and 95.5%, respectively. Compared to direct culture, sensitivity for detecting any SA was 99.6%. The cobas MRSA/SA Test is an effective tool to simultaneously perform surveillance testing for nasal colonization of both MRSA and MSSA.

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

    PubMed

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

    2015-12-16

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

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

    PubMed

    Forman, Michael Stuart; Valsamakis, Alexandra

    2004-08-01

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

  20. [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.

  1. Development of a photometric assay for activated partial thromboplastin time and its application to the Cobas Bio centrifugal analyzer.

    PubMed

    Becker, U; Bartl, K; Lill, H; Wahlefeld, A W

    1985-12-15

    We describe a two-step procedure for APTT that can be performed on photometric devices. It includes preincubation of diluted plasma with ellagic acid and phospholipids and a starting reagent that contains calcium and a chromogenic peptide substrate for thrombin, Tos-Gly-Pro-Arg-pNA. Reaction time is recorded from addition of the starting reagent until thrombin formation occurs, and a prefixed amount of substrate is cleaved. The pattern of sensitivity to clotting factors and heparin was similar to clotting assays and the substrate used did not interfere with the activity of factor Xa. An application of the method was made for the Cobas(R) Bio centrifugal analyzer. Absorbance readings were sent to an external computer and were transformed into reaction times by a computer program. Although the results are independent on fibrinogen concentrations, from kinetic data of the reaction curve fibrinogen concentrations can be estimated. Correlation studies showed good correspondence to clotting methods (r = 0.92, n = 53) as well as an excellent precision (CV 3% for inter-assays, n = 15) and high throughput of samples (greater than 100/h) in the automated assay.

  2. A clinical evaluation of the Cobas Fara clinical chemistry analyzer for some routine serum enzymes and glucose.

    PubMed

    Moses, G C; Lightle, G O; Tuckerman, J F; Henderson, A R

    1987-11-01

    The authors evaluated the Cobas FARA centrifugal analyzer with respect to pipetting precision and accuracy, instrument temperature, spectrophotometric response, and analytic performance for the assay of five serum enzymes and glucose. Spectrophotometric response, temperature response, pipetting precision, and accuracy were satisfactory. However, sufficient time must be allowed for cuvet contents to reach a stable temperature before measurements are made. Total day-to-day imprecision (within plus between run) was less than 5% (coefficient of variation) for aspartate and alanine aminotransferases (AST; Enzyme Commission classification number [EC] EC 2.6.1.1; and ALT; EC 2.6.1.2); alkaline phosphatase (AP; EC 3.1.3.1); gamma-glutamyltransferase (GGT; EC 2.3.1.2); lactate dehydrogenase (LD; EC 1.1.1.17); creatine kinase (CK; EC 2.7.3.1); and glucose assays. Results compare well with those obtained with other current clinical chemistry analyzers; correlation coefficients were greater than 0.993. Sample-to-sample carryover was negligible, and method linearity was satisfactory for all tests.

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2012-03-01

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

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

    PubMed Central

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

    1996-01-01

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

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

    PubMed

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

    1996-11-01

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

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

    PubMed

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

    2005-12-01

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

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

    PubMed

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

    2015-03-01

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

  9. Effect of glacial acetic acid treatment of cervical ThinPrep specimens on HPV DNA detection with the cobas 4800 HPV test.

    PubMed

    McMenamin, M; McKenna, M

    2013-10-01

    Cytology laboratories in the UK routinely treat unsatisfactory cervical liquid-based cytology (LBC) specimens with glacial acetic acid (GAA) to reduce the unsatisfactory rate. However, there is limited published data on the effect of GAA reprocessing on the molecular detection of human papillomavirus (HPV). The aim of this study was to assess the impact of GAA treatment of cervical ThinPrep(®) samples on HPV detection with the cobas(®) 4800 HPV Test (Roche Molecular Systems, Pleasanton, CA, USA). Residual ThinPrep samples (n = 121) were selected to provide a range of typical cytology results and enrich the study samples for HPV positivity. Specimens were equally split into two fractions: one part treated with 10% GAA and the other part left untreated. All samples were HPV tested using the cobas 4800 HPV Test, which simultaneously detects a total of 14 high-risk HPV (hrHPV) genotypes and individually identifies HPV16 and HPV18. The HPV positive/negative status of tested samples determined the level of agreement between treated and untreated fractions; one sample failed owing to detection of a clot by the instrument during pipetting, leaving 120 samples in the study. Statistical analysis was performed using an unweighted kappa. Analysis of overall HPV positivity showed 97.5% (117/120) agreement between the treated and untreated fractions with a kappa value of 0.95. There were 63/65 (96.9%) concordant HPV positive and 54/55 (98.2%) concordant HPV negative results. In addition to the three discordant results for overall HPV positivity, there were three HPV type-specific discrepancies giving a total of 114/120 concordant HPV results (95% agreement). Glacial acetic acid (GAA) treatment of cervical ThinPrep specimens does not have significant adverse affects on HPV detection with the cobas 4800 HPV Test. © 2013 John Wiley & Sons Ltd.

  10. Stability Study of Cervical Specimens Collected by Swab and Stored Dry Followed by Human Papillomavirus DNA Detection Using the cobas 4800 Test.

    PubMed

    Lin, Chun-Qing; Zeng, Xi; Cui, Jian-Feng; Liao, Guang-Dong; Wu, Ze-Ni; Gao, Qian-Qian; Zhang, Xun; Yu, Xiu-Zhang; Chen, Wen; Xi, Ming-Rong; Qiao, You-Lin

    2017-02-01

    Safer, more convenient methods for cervical sample collection and storage are necessary to facilitate human papillomavirus (HPV) DNA testing in low-resource settings. Our study aimed to evaluate the stability of cervical specimens collected with dry swabs and stored dry, compared to liquid-based cytology (LBC) samples, as detected by HPV DNA testing. Women with abnormal cytological findings or HPV-positive results at colposcopy were recruited from the West China Second University Hospital, Sichuan University, between October 2013 and March 2014. From each woman, physicians collected cervical specimens with a swab placed into a Sarstedt tube and a CytoBrush placed into LBC medium. Samples were randomly assigned to be stored at uncontrolled ambient temperature for 2, 7, 14, or 28 days and then were tested for 14 high-risk HPV (HR-HPV) types using the cobas HPV test. The rates of agreement between dry swab and LBC samples for any HR-HPV type, HPV16, HPV18, and the 12 pooled HR-HPV types were 93.8%, 97.8%, 99.4%, and 93.2%, respectively, with kappa values of 0.87 (95% confidence interval [CI], 0.83 to 0.91), 0.94 (95% CI, 0.91 to 0.97), 0.94 (95% CI, 0.87 to 1.00), and 0.86 (95% CI, 0.82 to 0.90). The performance of swab samples for detection of cervical precancerous lesions by means of cobas HPV testing was equal to that of LBC samples, even with stratification by storage time. Dry storage of swab-collected cervical samples can last for 1 month without loss of test performance by cobas HPV testing, compared to LBC samples, which may offer a simple inexpensive approach for cervical cancer screening in low-resource settings.

  11. Therapeutic drug monitoring and drugs of abuse testing on the cobas 6000 analyzer series: analytical performance under routine-like conditions.

    PubMed

    Brandhorst, Gunnar; Luthe, Hilmar; Domke, Ingrid; Knoke, Christiane; Rhode, Karl-Heinz; Sauter, Heike; Oellerich, Michael

    2009-01-01

    The analytical performance of the clinical chemistry module c 501 (cobas 6000 analyzer series) was evaluated for therapeutic drug monitoring and drugs of abuse testing using a spectrum of representative assays. Particular attention was paid to potential interactions between reagents using a simulated routine workload. Within-run and total imprecision were assessed using a selection of representative reagents. Deviation from a consensus mean was tested using samples from a proficiency testing scheme. Method comparison using routine samples was carried out against the MODULAR ANALYTICS SWA and COBAS INTEGRA 800 analysis systems. Total coefficients of variation (CV) ranged from 1.9% to 7.8% for individual drugs, and from 3.2% to 8.6% for drugs of abuse testing. Results from proficiency test samples were between 81% and 125% of the consensus mean for therapeutic drugs. Method comparisons (Passing-Bablok regression) showed overall good comparability to MODULAR ANALYTICS SWA and COBAS INTEGRA 800 systems, with slopes from 0.93 to 1.17 and correlation coefficients r > 0.98. Imprecision in a simulated routine run was tested using a total of 42 methods (10 therapeutic drug monitoring, 9 drugs of abuse testing, 3 enzymes, 12 substrates, 8 specific protein assays). Imprecision in the reference batch run ranged from 0.7% to 5.0% CV for therapeutic drug monitoring assays, except for digoxin (DIG) (7.3%), and from 0.9% to 7.7% for drugs of abuse testing. The CVs of general clinical chemistry and specific protein tests were within the expected limits of 2% and 4%. CV changes in the simulated routine run were within the expected limits for most assays. Negative DeltaCVs (> or = 2%) for DIG, digitoxin (DIGIT), cannabinoids (THC), and phencyclidine (PCP) may indicate improved performance when running these assays in a simulated routine operation. A positive DeltaCV (> or = 3%) was found for amphetamines (AMPHs). In conclusion, the cobas c 501 module seems to be well-suited for

  12. Evaluation of KIMS immunoassays on a cobas c 501 analyzer for drugs of abuse and ethyl glucuronide testing in urine for forensic abstinence control.

    PubMed

    Neukamm, Merja A; Bahrami, Arsham; Auwärter, Volker; Mehne, Felix M P; Höss, Eva

    2017-08-01

    For the medico-psychological assessment (MPA) during driving licence re-granting in Germany, abstinence control including urine samples is required. In these programmes, even small amounts of markers for drug or alcohol abuse have to be detected. Thus, the concentrations of the target compounds are very low, and, in consequence, the sensitivity of the applied screening method has to be much higher than for clinical use. Modified drugs of abuse and ethyl glucuronide immunoassays on a Roche cobas c 501 analyzer were evaluated for precision, accuracy, onboard calibration stability, cross reactivity, sensitivity, and specificity using authentic urine samples. Precision (intra-day and inter-day relative standard deviation (RSD) and accuracy (bias) at three concentrations were 12% or lower for all parameters. The calibrations remained stable (deviations <25%) for at least 28 days for all assays except amphetamines (21 days). Satisfactory cross reactivity was determined for the relevant analytes and also for several new psychoactive substances (NPS). The sensitivity was 100% for all parameters except methadone metabolite EDDP (92%) and fully met the sensitivity criteria for MPA urine testing. The presented kinetic interaction of microparticles in a solution (KIMS) immunoassays on a cobas c 501 thus provide a new method to reliably detect drug or alcohol consumption in abstinence control programmes requiring high sensitivity. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  13. Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD-PA1779-cobA operon.

    PubMed

    Romeo, Alessandra; Sonnleitner, Elisabeth; Sorger-Domenigg, Theresa; Nakano, Masayuki; Eisenhaber, Birgit; Bläsi, Udo

    2012-06-01

    Bioinformatic approaches employed to analyse intergenic regions of Pseudomonas aeruginosa O1 (PAO1) for small RNAs (sRNAs) revealed a putative RNA gene encoded upstream of the nitrate assimilation operon nirBD-PA1779-cobA. Here, we show that this RNA, termed nitrogen assimilation leader A (NalA), represents the leader RNA of the nirBD-PA1779-cobA operon, and that nalA transcription is σ(54)- and NtrC-dependent. A PAO1 nalA deletion strain and a strain bearing a deletion in ORF PA1785 failed to grow on nitrate. PA1785 was identified as a homologue of the Azotobacter vinelandii nasT gene, the product of which is required for transcription of the A. vinelandii nitrite/nitrate reductase operon. Collectively, these studies reveal that transcriptional antitermination of the leader RNA NalA is required for expression of the PAO1 nitrate assimilation operon, and that this process is governed by conserved functions in PAO1 and A. vinelandii.

  14. Human Papillomavirus (HPV) DNA Triage of Women with Atypical Squamous Cells of Undetermined Significance with cobas 4800 HPV and Hybrid Capture 2 Tests for Detection of High-Grade Lesions of the Uterine Cervix

    PubMed Central

    Lapierre, Simon Grandjean; Sauthier, Philippe; Mayrand, Marie-Hélène; Dufresne, Simon; Petignat, Patrick; Provencher, Diane; Drouin, Pierre; Gauthier, Philippe; Dupuis, Marie-Josée; Michon, Bertrand; Ouellet, Stéphan; Hadjeres, Rachid; Ferenczy, Alex; Franco, Eduardo L.

    2012-01-01

    The triage of women with high-risk (HR) human papillomavirus (HPV)-positive smears for atypical squamous cells of undetermined significance (ASC-US) to colposcopy is now an integrated option in clinical guidelines. The performance of cobas 4800 HPV and that of Hybrid Capture 2 (HC2) for HR HPV DNA detection in cervical samples in PreservCyt were compared in 396 women referred to colposcopy for ASC-US. Of these, 316 did not have cervical intraepithelial neoplasia (CIN), 47 had CIN1, 29 had CIN2 or CIN3 (CIN2+), and 4 had CIN of unknown grade. HR HPV was detected in 129 (32.6%) and 149 (37.6%) samples with HC2 and cobas 4800 HPV, respectively (P = 0.15). The clinical sensitivities and specificities for detecting CIN2+ were 89.7% (95% confidence interval [CI], 72.8 to 97.2%) and 66.7% (95% CI, 61.7 to 71.3%) with cobas 4800 HPV and 93.1% (95% CI, 77.0 to 99.2%) and 72.2% (95% CI 67.4 to 76.5%) with HC2. The performance of cobas 4800 HPV was similar to that of HC2 for identifying women with ASC-US who would benefit the most from colposcopy. PMID:22301023

  15. Analytical characteristics and comparative evaluation of Aptima HCV quant Dx assay with the Abbott RealTime HCV assay and Roche COBAS AmpliPrep/COBAS TaqMan HCV quantitative test v2.0.

    PubMed

    Worlock, A; Blair, D; Hunsicker, M; Le-Nguyen, T; Motta, C; Nguyen, C; Papachristou, E; Pham, J; Williams, A; Vi, M; Vinluan, B; Hatzakis, A

    2017-04-04

    The Aptima HCV Quant Dx assay (Aptima assay) is a fully automated quantitative assay on the Panther® system. This assay is intended for confirmation of diagnosis and monitoring of HCV RNA in plasma and serum specimens. The purpose of the testing described in this paper was to evaluate the performance of the Aptima assay. The analytical sensitivity, analytical specificity, precision, and linearity of the Aptima assay were assessed. The performance of the Aptima assay was compared to two commercially available HCV assays; the Abbott RealTime HCV assay (Abbott assay, Abbott Labs Illinois, USA) and the Roche COBAS Ampliprep/COBAS Taqman HCV Quantitative Test v2.0 (Roche Assay, Roche Molecular Systems, Pleasanton CA, USA). The 95% Lower Limit of Detection (LoD) of the assay was determined from dilutions of the 2nd HCV WHO International Standard (NIBSC 96/798 genotype 1) and HCV positive clinical specimens in HCV negative human plasma and serum. Probit analysis was performed to generate the 95% predicted detection limits. The Lower Limit of Quantitation (LLoQ) was established for each genotype by diluting clinical specimens and the 2nd HCV WHO International Standard (NIBSC 96/798 genotype 1) in HCV negative human plasma and serum. Specificity was determined using 200 fresh and 536 frozen HCV RNA negative clinical specimens including 370 plasma specimens and 366 serum specimens. Linearity for genotypes 1 to 6 was established by diluting armored RNA or HCV positive clinical specimens in HCV negative serum or plasma from 8.08 log IU/mL to below 1 log IU/mL. Precision was tested using a 10 member panel made by diluting HCV positive clinical specimens or spiking armored RNA into HCV negative plasma and serum. A method comparison was conducted against the Abbott assay using 1058 clinical specimens and against the Roche assay using 608 clinical specimens from HCV infected patients. In addition, agreement between the Roche assay and the Aptima assay using specimens with low

  16. Validation of dilution of plasma samples with phosphate buffered saline to eliminate the problem of small volumes associated with children infected with HIV-1 for viral load testing using Cobas AmpliPrep/COBAS TaqMan HIV-1 test, version 2.0 (CAP CTM HIV v2.0).

    PubMed

    Mine, Madisa; Nkoane, Tapologo; Sebetso, Gaseene; Sakyi, Bright; Makhaola, Kgomotso; Gaolathe, Tendani

    2013-12-01

    The sample requirement of 1 mL for the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 test, version 2.0 (CAP CTM HIV v2.0) limits its utility in measuring plasma HIV-1 RNA levels for small volume samples from children infected with HIV-1. Viral load monitoring is the standard of care for HIV-1-infected patients on antiretroviral therapy in Botswana. The study aimed to validate the dilution of small volume samples with phosphate buffered saline (1× PBS) when quantifying HIV-1 RNA in patient plasma. HIV RNA concentrations were determined in undiluted and diluted pairs of samples comprising panels of quality assessment standards (n=52) as well as patient samples (n=325). There was strong correlation (R(2)) of 0.98 and 0.95 within the dynamic range of the CAP CTM HIV v2.0 test between undiluted and diluted samples from quality assessment standards and patients, respectively. The difference between viral load measurements of diluted and undiluted pairs of quality assessment standards and patient samples using the Altman-Bland test showed that the 95% limits of agreement were between -0.40 Log 10 and 0.49 Log 10. This difference was within the 0.5 Log 10 which is generally considered as normal assay variation of plasma RNA levels. Dilution of samples with 1× PBS produced comparable viral load measurements to undiluted samples.

  17. Blood donor screening for West Nile virus (WNV) revealed acute Usutu virus (USUV) infection, Germany, September 2016

    PubMed Central

    Cadar, Daniel; Maier, Philipp; Müller, Susanne; Kress, Julia; Chudy, Michael; Bialonski, Alexandra; Schlaphof, Alexander; Jansen, Stephanie; Jöst, Hanna; Tannich, Egbert; Runkel, Stefan; Hitzler, Walter E; Hutschenreuter, Gabriele; Wessiepe, Martina; Schmidt-Chanasit, Jonas

    2017-01-01

    Between 1 June and 31 December 2016, 13,023 blood donations from the University Hospital Aachen in Germany were routinely screened for West Nile virus (WNV) RNA using the cobas TaqScreen WNV Test. On 28 September 2016, one blood donor was tested positive. Subsequent analysis revealed an acute Usutu virus (USUV) infection. During the ongoing USUV epizootics in Germany, blood transfusion services, public health authorities and clinicians should be aware of increased human USUV infections. PMID:28422005

  18. Improved COBAS TaqMan hepatitis C virus test (Version 2.0) for use with the High Pure system: enhanced genotype inclusivity and performance characteristics in a multisite study.

    PubMed

    Colucci, G; Ferguson, J; Harkleroad, C; Lee, S; Romo, D; Soviero, S; Thompson, J; Velez, M; Wang, A; Miyahara, Y; Young, S; Sarrazin, C

    2007-11-01

    We have evaluated the COBAS TaqMan hepatitis C virus (HCV) test (version 2.0) for use with the High Pure system (HCVHPS V2), a new, revised real-time reverse transcription-PCR assay developed to improve the genotype quantitation of version 1.0 (HCVHPS V1). Revisions were made in the wash buffer and in the reverse transcription temperature. The genotype inclusivity of HCVHPS V2 was evaluated at three different sites, using HCVHPS V2, HCVHPS V1, and the COBAS AMPLICOR HCV MONITOR test (version 2.0) (CAHCM). The fully automated COBAS Ampliprep/COBAS TaqMan HCV test was also used in one of the participating laboratories. The mean differences in HCV RNA values between HCVHPS V2 and CAHCM and between HCVHPS V2 and HCVHPS V1 ranged from -0.21 to 0.13 log and from 0.24 to 1.27 log, respectively, with >0.5-log differences for genotypes 2, 3, 4, and 5. With a NIBSC panel of HCV genotypes 1 through 6, the measured HCVHPS V2 values were within 0.25 log of the nominal values for all 6 genotypes. When serial dilutions of genotype-specific clinical HCV specimens were tested, the assay showed a limit of detection between 10 and 20 IU/ml and a linear range of 25 IU/ml to 3.91 x 10(8) IU/ml. Clinical and analytical specificities of 100% were demonstrated with 100 HCV-seronegative specimens as well as with 12 non-HCV members of Flaviviridae and 22 additional microorganisms. These data indicate that HCVHPS V2 is a robust and accurate test for the quantitation of all six HCV genotypes and useful in monitoring viral load in all clinical HCV specimens.

  19. Comparison of the Cobas 4800 HPV and HPV 9G DNA Chip Tests for Detection of High-Risk Human Papillomavirus in Cervical Specimens of Women with Consecutive Positive HPV Tests But Negative Pap Smears.

    PubMed

    Jun, Sun-Young; Park, Eun Su; Kim, Jiyoung; Kang, Jun; Lee, Jae Jun; Bae, Yoonjin; Kim, Sang-Il; Maeng, Lee-So

    2015-01-01

    Detecting high-risk (HR) HPV is important for clinical management of women with persistent HPV-positive and Pap-negative results. The Cobas 4800 HPV test is the first FDA-approved HPV DNA test that can be used alone as a first-line screening tool. The HPV 9G DNA chip test is a PCR-based DNA microarray assay. We evaluated the patients of consecutive HPV-positivity on HPV 9G DNA chip test without cytologic abnormalities. We then compared the performances of HPV 9G DNA chip and the Cobas 4800 HPV tests for detecting HR HPV with each other and confirmed HPV genotyping using direct sequencing. All 214 liquid-based cytology specimens were collected from 100 women with consecutive HPV-positive and Pap-negative results on the HPV 9G DNA chip test between May 2012 and Dec 2013, but only 180 specimens were available for comparing HPV test results. The HPV 9G DNA chip and the Cobas 4800 HPV tests agreed with each other in 81.7% of the samples, and the concordance rate was greater than 97.2% for detecting HPV-16 or -18. For HR genotypes other than HPV types 16 and 18, the two tests agreed for 81.1% of the samples. The sensitivity of both assays for detecting HR HPV was 100%, regardless of HR genotypes. The HPV 9G DNA chip test may be as effective as the Cobas 4800 HPV test in detecting HR HPV, and has a similar ability to identify HPV-16 and -18.

  20. Comparison of the Cobas 4800 HPV and HPV 9G DNA Chip Tests for Detection of High-Risk Human Papillomavirus in Cervical Specimens of Women with Consecutive Positive HPV Tests But Negative Pap Smears

    PubMed Central

    Jun, Sun-Young; Park, Eun Su; Kim, Jiyoung; Kang, Jun; Lee, Jae Jun; Bae, Yoonjin; Kim, Sang-Il; Maeng, Lee-So

    2015-01-01

    Detecting high-risk (HR) HPV is important for clinical management of women with persistent HPV-positive and Pap-negative results. The Cobas 4800 HPV test is the first FDA-approved HPV DNA test that can be used alone as a first-line screening tool. The HPV 9G DNA chip test is a PCR-based DNA microarray assay. We evaluated the patients of consecutive HPV-positivity on HPV 9G DNA chip test without cytologic abnormalities. We then compared the performances of HPV 9G DNA chip and the Cobas 4800 HPV tests for detecting HR HPV with each other and confirmed HPV genotyping using direct sequencing. All 214 liquid-based cytology specimens were collected from 100 women with consecutive HPV-positive and Pap-negative results on the HPV 9G DNA chip test between May 2012 and Dec 2013, but only 180 specimens were available for comparing HPV test results. The HPV 9G DNA chip and the Cobas 4800 HPV tests agreed with each other in 81.7% of the samples, and the concordance rate was greater than 97.2% for detecting HPV-16 or -18. For HR genotypes other than HPV types 16 and 18, the two tests agreed for 81.1% of the samples. The sensitivity of both assays for detecting HR HPV was 100%, regardless of HR genotypes. The HPV 9G DNA chip test may be as effective as the Cobas 4800 HPV test in detecting HR HPV, and has a similar ability to identify HPV-16 and -18. PMID:26469982

  1. SurePath Specimens Versus ThinPrep Specimen Types on the COBAS 4800 Platform: High-Risk HPV Status and Cytology Correlation in an Ethnically Diverse Bronx Population.

    PubMed

    Naeem, R C; Goldstein, D Y; Einstein, Mark H; Ramos Rivera, G; Schlesinger, K; Khader, S N; Suhrland, M; Fox, A S

    2017-08-01

    To compare the cytologic preparations of 130 cervical specimens (from women of various ethnicities at high risk for human papillomavirus [HPV] infection) using the SurePath (SP) collection system with specimens gathered using the ThinPrep (TP) system, as processed on the Cobas 4800 analyzer, to determine which collection method more accurately identifies HPV infection. In our prospective study, specimens were collected from 130 women of various ethnicities residing in or near Bronx County, NY. The SP-collected specimen was first processed for cytologic findings; if clinical HPV testing was requested on that specimen, it was tested using Hybrid Capture II (HC2) methodology. We tested the remnant SP-collected cell concentrate using the Cobas analyzer. Then, the TP-collected and SP-collected specimens were tested in the same run on that analyzer, and the results were compared. We also compared the results with the concurrent cytologic findings. The results were concordant for overall HR-HPV status in 93.8% of cases. Also, a statistically significant lower cycle threshold value was observed with Cobas testing of specimen concentrates tested via the BD SurePath Pap Test (P = .001), suggesting higher sensitivity compared with specimens tested via the ThinPrep Pap Test. Cobas 4800 HPV testing of SP-collected specimen concentrates yields comparable results to TP-collected specimen concentrates. Based on the limited data that we derived, SP collection may be a more favorable methodology than TP collection for HPV testing of individuals at high risk in our ethnically diverse, urban patient population.

  2. Improved COBAS TaqMan Hepatitis C Virus Test (Version 2.0) for Use with the High Pure System: Enhanced Genotype Inclusivity and Performance Characteristics in a Multisite Study▿

    PubMed Central

    Colucci, G.; Ferguson, J.; Harkleroad, C.; Lee, S.; Romo, D.; Soviero, S.; Thompson, J.; Velez, M.; Wang, A.; Miyahara, Y.; Young, S.; Sarrazin, C.

    2007-01-01

    We have evaluated the COBAS TaqMan hepatitis C virus (HCV) test (version 2.0) for use with the High Pure system (HCVHPS V2), a new, revised real-time reverse transcription-PCR assay developed to improve the genotype quantitation of version 1.0 (HCVHPS V1). Revisions were made in the wash buffer and in the reverse transcription temperature. The genotype inclusivity of HCVHPS V2 was evaluated at three different sites, using HCVHPS V2, HCVHPS V1, and the COBAS AMPLICOR HCV MONITOR test (version 2.0) (CAHCM). The fully automated COBAS Ampliprep/COBAS TaqMan HCV test was also used in one of the participating laboratories. The mean differences in HCV RNA values between HCVHPS V2 and CAHCM and between HCVHPS V2 and HCVHPS V1 ranged from −0.21 to 0.13 log and from 0.24 to 1.27 log, respectively, with >0.5-log differences for genotypes 2, 3, 4, and 5. With a NIBSC panel of HCV genotypes 1 through 6, the measured HCVHPS V2 values were within 0.25 log of the nominal values for all 6 genotypes. When serial dilutions of genotype-specific clinical HCV specimens were tested, the assay showed a limit of detection between 10 and 20 IU/ml and a linear range of 25 IU/ml to 3.91 × 108 IU/ml. Clinical and analytical specificities of 100% were demonstrated with 100 HCV-seronegative specimens as well as with 12 non-HCV members of Flaviviridae and 22 additional microorganisms. These data indicate that HCVHPS V2 is a robust and accurate test for the quantitation of all six HCV genotypes and useful in monitoring viral load in all clinical HCV specimens. PMID:17898157

  3. Comparison of the cobas 4800 CT/NG Test with Culture for Detecting Neisseria gonorrhoeae in Genital and Nongenital Specimens in a Low-Prevalence Population in New Zealand

    PubMed Central

    Miller, Amanda; Jones, Mark; Whiley, David

    2013-01-01

    To assess the clinical utility of replacing microbial culture for Neisseria gonorrhoeae with a nucleic acid amplification test (NAAT), we compared N. gonorrhoeae culture with the cobas 4800 CT/NG test for 18,247 urogenital and 666 nongenital samples. For urogenital specimens, the sensitivity, specificity, and positive and negative predictive values of the cobas N. gonorrhoeae PCR were 98.7%, 100%, 95.6%, and 100%, respectively, and for nongenital specimens, the values were 100%, 99.8%, 92.9%, and 100%, respectively. In our test population, 37% (10,185) of patients tested over the study period were screened for C. trachomatis by PCR but were not screened for gonorrhea by culture. Of these, 43 were N. gonorrhoeae positive by PCR and therefore went undiagnosed. The cobas 4800 CT/NG test diagnosed 33% (n = 30) more urogenital and 25% (n = 3) more rectal gonorrhea infections than culture and, based on the above performance indicators, does not require supplementary testing for urogenital or rectal specimens. The ability to test noninvasive specimens (such as urine and self-taken vulvovaginal swabs) for N. gonorrhoeae will enable more patients to be screened for infection, thus offering significant positive public health benefits. PMID:23467604

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

    PubMed

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

    2011-12-01

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

  5. Limited utility of dried-blood- and plasma spot-based screening for antiretroviral treatment failure with Cobas Ampliprep/TaqMan HIV-1 version 2.0.

    PubMed

    Sawadogo, Souleymane; Shiningavamwe, Andreas; Chang, Joy; Maher, Andrew D; Zhang, Guoqing; Yang, Chunfu; Gaeb, Esegiel; Kaura, Harold; Ellenberger, Dennis; Lowrance, David W

    2014-11-01

    The 2013 WHO antiretroviral therapy (ART) guidelines recommend dried blood spots (DBS) as an alternative specimen type for viral load (VL) monitoring. We assessed the programmatic utility of screening for antiretroviral (ARV) treatment failure (TF) at 5,000 and 1,000 copies/ml using DBS and dried plasma spots (DPS) with a commonly used VL assay, the Roche Cobas Ampliprep/Cobas TaqMan V.2.0 (CAP/CTM). Plasma, DBS, and DPS were prepared from 839 whole-blood specimens collected from patients on ART for ≥ 6 months at three public facilities in Namibia. Using the CAP/CTM test, VL were measured in plasma, DBS, and DPS, and the results were compared using the plasma VL as the reference standard. The clinical sensitivities, specificities, and positive (PPV) and negative predictive values (NPV) of DBS at ARV TF diagnostic thresholds of 5,000 copies/ml and 1,000 copies/ml were 0.99, 0.55, 0.33, and 0.99 and 0.99, 0.26, 0.29, and 0.99, respectively, and for DPS at TF diagnostic thresholds of 5,000 copies/ml and 1,000 copies/ml, they were 0.88, 0.98, 0.92, and 0.97 and 0.91, 0.96, 0.89, and 0.97, respectively. The prevalences of TF were overestimated in DBS by 33% and 57% at these two thresholds, respectively. A high rate of false-positive results would occur if the CAP/CTM with DBS were to be used to screen for ARV TF. WHO recommendations for DBS-based VL monitoring should be specific to the VL assay version and type. Despite the better performance of DPS, the programmatic utility for TF screening may be limited by requirements for processing the whole blood at the collection site. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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

    PubMed

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

    2007-03-01

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

  8. An evaluation of clinical performance of FTA cards for HPV 16/18 detection using cobas 4800 HPV Test compared to dry swab and liquid medium.

    PubMed

    Dong, Li; Lin, Chunqing; Li, Li; Wang, Margaret; Cui, Jianfeng; Feng, Ruimei; Liu, Bin; Wu, Zeni; Lian, Jia; Liao, Guangdong; Chen, Wen; Qiao, Youlin

    2017-09-01

    Effective dry storage and transport media as an alternative to conventional liquid-based medium would facilitate the accessibility of women in the low-resource settings to human papillomavirus (HPV)- based cervical cancer screening. To evaluate analytical and clinical performance of indicating FTA™ Elute Cartridge (FTA card) for the detection of HPV16/18 and cervical precancerous lesions and cancer compared to dry swab and liquid medium. Ninety patients with abnormal cytology and/or HPV infection were included for analysis. Three specimens of cervical exfoliated cells from each woman were randomly collected by FTA card, dry swab or liquid-based medium prior to colposcopy examination. The subsequent HPV DNA tests were performed on cobas 4800 HPV platform. High-risk HPV (hrHPV) positivity rate was 63.3%, 62.2% and 65.6% for samples collected by FTA card, dry swab and liquid medium, respectively. The overall agreements and kappa values for the detection of hrHPV, HPV 16 and HPV 18 between FTA card and liquid-based medium were 88.9% (κ=0.76), 97.8% (κ=0.94) and 100% (κ=1.0),respectively; between FTA card and dry swab were 92.1% (κ=0.83), 94.5% (κ=0.87) and 100% (κ=1.0), respectively. The performances of hrHPV tested by FTA card, dry swab, and liquid-based medium for detecting CIN2+ were comparable in terms of the sensitivity and specificity. The specificity of detection of CIN2+ by HPV16/18 increased by approximately 40% compared to hrHPV for any medium albeit at cost of a moderate loss of sensitivity. Dry medium might offer an alternative to conventional liquid-based medium in the HPV-based cervical cancer screening program especially in low-resource settings but still needs further evaluation. Copyright © 2017. Published by Elsevier B.V.

  9. Serum ASAT, ALAT, ALP, LD, GT, and CK determined in the Cobas-Bio centrifugal analyser by the methods of the Scandinavian Committee on Enzymes.

    PubMed

    Izquierdo, J M; Sotorrío, P; Alvarez-Uría, J; Estrada, J M; Quirós, A

    1982-04-01

    The recommended methods of the Scandinavian Committee on Enzymes [4, 5, 6, 7, 8] have been applied to the Cobas-Bio centrifugal analyser. Reagents and serum volumes were scaled down and final molarities were kept equal. Serum volumes in microliters were as follows: ASAT 30, ALAT 30, ALP 3, LD 5, GT 20, and CK 10. Including the dead space of the sample cup, the volume needed to perform all six tests was 113 microliter. Within-run and between-run precision (CV%) were as follows: ASAT 1.32 and 1.95, ALAT 1.68 and 2.93, ALP 1.56 and 3.10, LD 1.63 and 4.44, GT 0.81 and 2.23, and CK 1.02 and 1.94. Mean deviations (%) from target values of two commercial sera were as follows: ASAT -0.3 and -0.4, ALAT -0.4 and -2.2, ALP -1.8 and -7.3, LD 0.4 and -6.2, GT 13.9 and -10.7, and CK -4.9 and -1.3. Results of all the methods correlated well with those obtained with their respective manual methods. Analytical time for 28 samples of each analyte was 10 min, apart from CK which was 14 min. Reagent cost per sample was 0.6, 0.9, 0.1, 0.3, 0.9, and 26 US cents respectively. All reagents were prepared in the laboratory, except those for CK which were bought from J.T. Baker (Phillipsburgh, NJ, USA). In conclusion, the methods keep the features of the manual methods but they are more precise and practicable, much faster and cheaper, and use minimal amounts of sera more convenient for paediatric work.

  10. Effect of the hemoglobin-based oxygen carrier HBOC-201 on laboratory instrumentation: cobas integra, chiron blood gas analyzer 840, Sysmex SE-9000 and BCT.

    PubMed

    Wolthuis, A; Peek, D; Scholten, R; Moreira, P; Gawryl, M; Clark, T; Westerhuis, L

    1999-01-01

    As part of a clinical trial, we evaluated the effects of the hemoglobin-based oxygen-carrier (HBOC) HBOC-201 (an ultrapurified, stroma-free bovine hemoglobin product, Biopure, Cambridge, MA, USA) on our routine clinical chemistry analyzer (Cobas Integra, F. Hoffmann-La Roche Ltd, Basel, Switzerland ), blood gas analyzer (Chiron 840, Chiron Diagnostics Corporation, East Walpole, MA, USA), routine hemocytometry analyzer (Sysmex SE-9000, TOA Medical Electronics Co Ltd., Kobe, Japan), hemostasis analyzer (BCT, Dade-Behring, Marburg, Germany) and bloodbanking system (Dia-Med-ID Micro Typing System, DiaMed AG, Cressier, Switzerland). The maximum tested concentration of HBOC-201 was 65 g/l. Of the 27 routine clinical chemistry tests challenged with HBOC-201, bilirubin-direct, creatine kinase MB-fraction (CK-MB), creatine kinase (CK), gamma-glutamyltransferase (GGT), magnesium and uric acid were influenced by even low concentrations of HBOC-201. These tests were excluded from use on the plasma of patients treated with HBOC-201. Since the non-availability of the cardiac marker CK-MB may lead to problems in acute situations, we introduced the qualitative Trop T-test (Boehringer Mannheim), which was not influenced. The applicability of another nine tests was limited by the concentration of the HBOC-201 in the patients' plasma. No interference of HBOC-201 in routine hemocytometry, hemostasis-analysis and red-blood cell agglutination detection (blood-bank tests) was observed. Although immediate patient-care was not compromised, routine use of hemoglobin-based oxygen carriers will have a strong impact on logistical management. The development of robust laboratory tests free from the interference of the pigmented oxygen carriers should therefore precede its introduction into routine transfusion medicine.

  11. 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.

  12. Comparative investigation of hair with the genRES(®) MPX-SP1, genRES MPX-SP2, and genRES MPX-2 kits.

    PubMed

    Anslinger, K; Bayer, B; Rolf, B

    2007-03-01

    In recent years there has been considerable improvement in short-tandem repeat (STR) investigations of hair, which were previously marred by small amounts of nuclear DNA and its degradation. This study examined the suitability of two STR kits with shortened amplicons for the investigation of hairs from routine casework. The overall sucess rate was more than 20%. Furthermore, the usefulness of quantification with real-time ploymerase chain reaction as a screening method was demonstrated.

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

    PubMed

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

    2000-07-01

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

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

    PubMed

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

    2009-01-01

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

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

    PubMed

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

    2016-04-01

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

  16. Differences between two real-time PCR-based hepatitis C virus (HCV) assays (RealTime HCV and Cobas AmpliPrep/Cobas TaqMan) and one signal amplification assay (Versant HCV RNA 3.0) for RNA detection and quantification.

    PubMed

    Vermehren, Johannes; Kau, Annika; Gärtner, Barbara C; Göbel, Reinhild; Zeuzem, Stefan; Sarrazin, Christoph

    2008-12-01

    Hepatitis C virus (HCV) RNA detection and quantification are the key diagnostic tools for the management of hepatitis C. Commercially available HCV RNA assays are calibrated to the HCV genotype 1 (gt1)-based WHO standard. Significant differences between assays have been reported. However, it is unknown which assay matches the WHO standard best, and little is known about the sensitivity and linear quantification of the assays for non-gt1 specimens. Two real-time reverse transcriptase PCR-based assays (RealTime HCV and Cobas Ampliprep/Cobas TaqMan HCV [CAP/CTM]) and one signal amplification-based assay (the Versant HCV RNA, version 3.0, branched DNA [bDNA] assay) were compared for their abilities to quantify HCV RNA in clinical specimens (n = 65) harboring HCV isolates of gt1 to g5. The mean differences in the amounts detected by RealTime HCV in comparison to those detected by the bDNA assay and CAP/CTM were -0.02 and 0.72 log(10) IU/ml HCV RNA, respectively, for gt1; -0.22 and 0.03 log(10) IU/ml HCV RNA, respectively, for gt2; -0.27 and -0.22 log(10) IU/ml HCV RNA, respectively, for gt3; -0.19 and -1.27 log(10) IU/ml HCV RNA, respectively, for gt4; and -0.03 and 0.09 log(10) IU/ml HCV RNA, respectively, for gt5. The lower limits of detection for RealTime HCV and CAP/CTM were 16.8 and 10.3 IU/ml, respectively, for the WHO standard and in the range of 4.7 to 9.0 and 3.4 to 44.4 IU/ml, respectively, for clinical specimens harboring gt1 to gt6. Direct comparison of the two assays with samples of the WHO standard (code 96/798) with high titers yielded slightly smaller amounts by RealTime HCV (-0.2 log(10) at 1,500 IU/ml and -0.3 log(10) at 25,000 IU/ml) and larger amounts by CAP/CTM (0.3 log(10) at 1,500 IU/ml and 0.2 log(10) at 25,000 IU/ml). Finally, all three tests were linear between 4.0 x 10(3) and 1.0 x 10(6) IU/ml (correlation coefficient, >or=0.99). In conclusion, the real-time PCR based assays sensitively detected all genotypes and showed comparable linearities

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

    PubMed Central

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

    2002-01-01

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

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

    PubMed

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

    2002-05-01

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

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

    PubMed

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

    2014-06-01

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

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

    PubMed

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

    2017-10-01

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

  1. COBA-Cohort: a prospective cohort of HIV-negative men who have sex with men, attending community-based HIV testing services in five European countries (a study protocol)

    PubMed Central

    Fernàndez-López, Laura; Fuertes, Ricardo; Rojas Castro, Daniela; Pichon, François; Cigan, Bojan; Chanos, Sophocles; Meireles, Paula; Morel, Stéphane; Slaaen Kaye, Per; Agustí, Cristina; Klavs, Irena; Casabona, Jordi

    2016-01-01

    Introduction Community-based voluntary counselling and testing (CBVCT) services for men who have sex with men (MSM) can reach those most-at-risk and provide an environment for gay men that is likely to be non-stigmatising. Longitudinal data on the behaviour of HIV-negative MSM are scarce in Europe. The aim of this protocol, developed during the Euro HIV Early Diagnosis And Treatment (EDAT) project, is to implement a multicentre community-based cohort of HIV-negative MSM attending 15 CBVCT services in 5 European countries. Research objectives (1) To describe the patterns of CBVCT use, (2) to estimate HIV incidence, and to identify determinants of (3) HIV seroconversion and (4) HIV and/or sexually transmitted infection (STI) test-seeking behaviour. Methods and analysis All MSM aged 18 years or over and who had a negative HIV test result are invited to participate in the COmmunity-BAsed Cohort (COBA-Cohort). Study enrolment started in February 2015, and is due to continue for at least 12 months at each study site. Follow-up frequency depends on the testing recommendations in each country (at least 1 test per year). Sociodemographic data are collected at baseline; baseline and follow-up questionnaires both gather data on attitudes and perceptions, discrimination, HIV/STI testing history, sexual behaviour, condom use, and pre- and post-exposure prophylaxis. Descriptive, exploratory and multivariate analyses will be performed to address the main research objectives of this study, using appropriate statistical tests and models. These analyses will be performed on the whole cohort data and stratified by study site or country. Ethics and dissemination The study was approved by the Public Health authorities of each country where the study is being implemented. Findings from the COBA-Cohort study will be summarised in a report to the European Commission, and in leaflets to be distributed to study participants. Articles and conference abstracts will be submitted to peer

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

    PubMed

    Koch, Carmo; Araújo, Fernando

    2013-01-01

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

  3. Sensitivity and specificity of Cobas TaqMan MTB real-time polymerase chain reaction for culture-proven Mycobacterium tuberculosis: meta-analysis of 26999 specimens from 17 Studies.

    PubMed

    Horita, Nobuyuki; Yamamoto, Masaki; Sato, Takashi; Tsukahara, Toshinori; Nagakura, Hideyuki; Tashiro, Ken; Shibata, Yuji; Watanabe, Hiroki; Nagai, Kenjiro; Nakashima, Kentaro; Ushio, Ryota; Ikeda, Misako; Sakamaki, Kentaro; Yoshiyama, Takashi; Kaneko, Takeshi

    2015-12-09

    Since 2010, studies on the diagnostic accuracy of COBAS TaqMan MTB (CTM) have been frequently reported with an unignorable discrepancy. The key inclusion criterion for this systematic review was original studies that could provide sufficient data for calculating the sensitivity and the specificity of CTM for M tuberculosis (TB) or M tuberculosis complex. The reference test was Mycobacterium culture. We used bivariate model for meta-analyses. Of the 201 candidate articles, we finally identified 17 eligible articles.Concerning the respiratory specimens, 1900 culture positive specimens and 20983 culture negative specimens from 15 studies were assessed. This provided the summary estimate sensitivity of 0.808 (95% CI 0.758-0.850) and the summary estimate specificity of 0.990 (95% CI 0.981-0.994). The area under curve was 0.956. The diagnostic odds ratio was 459 (95% CI 261-805, I(2) 26%). For the smear positive respiratory specimens, the sensitivity was 0.952 (95% CI 0.926-0.969) and the specificity was 0.916 (95% CI 0.797-0.968). For the smear negative respiratory specimens, the sensitivity and the specificity were 0.600 (95% CI 0.459-0.726) and 0.989 (95% CI 0.981-0.993), respectively. The diagnostic accuracy was poorer for the non-respiratory specimens, than for the respiratory specimens, but was acceptable. We believe that the information obtained from this study will aid physicians' decision making.

  4. Performance of the New Aptima HCV Quant Dx Assay in Comparison to the Cobas TaqMan HCV2 Test for Use with the High Pure System in Detection and Quantification of Hepatitis C Virus RNA in Plasma or Serum.

    PubMed

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

    2016-04-01

    Quantitating the level of hepatitis C virus (HCV) RNA is the standard of care for monitoring HCV-infected patients during treatment. The performances of commercially available assays differ for precision, limit of detection, and limit of quantitation (LOQ). Here, we compare the performance of the Hologic Aptima HCV Quant Dx assay (Aptima) to that of the Roche Cobas TaqMan HCV test, version 2.0, using the High Pure system (HPS/CTM), considered a reference assay since it has been used in trials defining clinical decision points in patient care. The assays' performance characteristics were assessed using HCV RNA reference panels and plasma/serum from chronically HCV-infected patients. The agreement between the assays for the 3 reference panels was good, with a difference in quantitation values of <0.5 log. High concordance was demonstrated between the assays for 245 clinical samples (kappa = 0.80; 95% confidence interval [CI], 0.720 to 0.881); however, Aptima detected and/or quantitated 20 samples that HPS/CTM did not detect, while Aptima did not detect 1 sample that was quantitated by HPS/CTM. For the 165 samples quantitated by both assays, the values were highly correlated (R= 0.98;P< 0.0001). The linearity of quantitation from concentrations of 1.4 to 6 log was excellent for both assays for all HCV genotypes (GT) tested (GT 1a, 1b, 2b, and 3a) (R(2)> 0.99). The assays had similar levels of total and intra-assay variability across all genotypes at concentrations from 1,000 to 25 IU/ml. Aptima had a greater analytical sensitivity, quantitating more than 50% of replicates at 25-IU/ml target. Aptima showed performance characteristics comparable to those of HPS/CTM and increased sensitivity, making it suitable for use as a clinical diagnostic tool on the fully automated Panther platform.

  5. Performance of the New Aptima HCV Quant Dx Assay in Comparison to the Cobas TaqMan HCV2 Test for Use with the High Pure System in Detection and Quantification of Hepatitis C Virus RNA in Plasma or Serum

    PubMed Central

    Speicher, Andrea; Börner, Anna; Enders, Martin

    2016-01-01

    Quantitating the level of hepatitis C virus (HCV) RNA is the standard of care for monitoring HCV-infected patients during treatment. The performances of commercially available assays differ for precision, limit of detection, and limit of quantitation (LOQ). Here, we compare the performance of the Hologic Aptima HCV Quant Dx assay (Aptima) to that of the Roche Cobas TaqMan HCV test, version 2.0, using the High Pure system (HPS/CTM), considered a reference assay since it has been used in trials defining clinical decision points in patient care. The assays' performance characteristics were assessed using HCV RNA reference panels and plasma/serum from chronically HCV-infected patients. The agreement between the assays for the 3 reference panels was good, with a difference in quantitation values of <0.5 log. High concordance was demonstrated between the assays for 245 clinical samples (kappa = 0.80; 95% confidence interval [CI], 0.720 to 0.881); however, Aptima detected and/or quantitated 20 samples that HPS/CTM did not detect, while Aptima did not detect 1 sample that was quantitated by HPS/CTM. For the 165 samples quantitated by both assays, the values were highly correlated (R = 0.98; P < 0.0001). The linearity of quantitation from concentrations of 1.4 to 6 log was excellent for both assays for all HCV genotypes (GT) tested (GT 1a, 1b, 2b, and 3a) (R2 > 0.99). The assays had similar levels of total and intra-assay variability across all genotypes at concentrations from 1,000 to 25 IU/ml. Aptima had a greater analytical sensitivity, quantitating more than 50% of replicates at 25-IU/ml target. Aptima showed performance characteristics comparable to those of HPS/CTM and increased sensitivity, making it suitable for use as a clinical diagnostic tool on the fully automated Panther platform. PMID:26865682

  6. 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

  7. Diagnostic accuracy of the real-time PCR cobas(®) Liat(®) Influenza A/B assay and the Alere i Influenza A&B NEAR isothermal nucleic acid amplification assay for the detection of influenza using adult nasopharyngeal specimens.

    PubMed

    Young, Stephen; Illescas, Patrick; Nicasio, Joclin; Sickler, Joanna Jackson

    2017-09-01

    Accurate detection of influenza requires diagnostic testing; however, methods such as RADTs and central laboratory-based tests are limited by low sensitivity and time constraints, respectively. To compare the performances of the cobas(®) Liat(®) Influenza A/B and Alere™ i Influenza A&B point-of-care (POC) assays for detecting influenza A and B viruses using fresh nasopharyngeal specimens with the GenMark Dx(®) Respiratory Viral Panel as the reference method, a FDA cleared IVD PCR test. A total of 87 samples collected in viral transport medium from adults ≥18 years of age were re-tested on both POC assays (based on the reference PCR method, 29 were influenza A and 18 were influenza B virus positive). The overall sensitivity and specificity of the cobas Influenza A/B for the detection of influenza A and B relative to reference PCR was 97.9% (95% confidence interval [CI] 88.9%, 99.6%) and 97.5% (95% CI: 87.1%, 99.6%), respectively, while the sensitivity of the Alere i Influenza A&B assay relative to the reference PCR method was 63.8% (95% CI: 49.5%, 76.0%) and the specificity was 97.5% (95% CI: 87.1%, 99.6%). The individual sensitivities and specificities of the cobas Influenza A/B assay for influenza A alone and influenza B alone were comparable to those of the reference PCR method (influenza A: sensitivity of 100% [95% CI: 88.3%, 100.0%] and specificity of 98.3% [95% CI: 90.9%, 99.7%]; influenza B: sensitivity of 94.4% [95% CI: 74.2%, 99.0%] and specificity of 100% [95% CI: 94.7%, 100.0%]). For the Alere i Influenza A&B assay, the individual specificities for influenza A and B were comparable to those of the reference PCR method (98.3% [95% CI: 90.9%, 99.7%] and 97.1% [95% CI: 90.0%, 99.2%], respectively), while the individual sensitivities were low relative to reference PCR (55.2% [95% CI: 37.5%, 71.6%] and 72.2% [95% CI: 49.1%, 87.5%], respectively). The cobas Influenza A/B assay demonstrated performance equivalent to laboratory-based PCR, and could replace

  8. 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.

  9. Assessment of a Novel Automatic Real-Time PCR Assay on the Cobas 4800 Analyzer as a Screening Platform for Hepatitis C Virus Genotyping in Clinical Practice: Comparison with Massive Sequencing

    PubMed Central

    Nieto-Aponte, Leonardo; Ruiz-Ripa, Alicia; Tabernero, David; Gonzalez, Carolina; Gregori, Josep; Vila, Marta; Asensio, Miriam; Garcia-Cehic, Damir; Ruiz, Gerardo; Chen, Qian; Ordeig, Laura; Llorens, Meritxell; Saez, Montserrat; Esteban, Juan I.; Esteban, Rafael; Buti, Maria; Pumarola, Tomas

    2016-01-01

    ABSTRACT The unequivocal identification of hepatitis C virus (HCV) subtypes 1a/1b and genotypes 2 to 6 is required for optimizing the effectiveness of interferon-free, direct-acting antiviral therapies. We compared the performance of a new real-time HCV genotyping assay used on the Cobas 4800 system (C4800) with that of high-resolution HCV subtyping (HRCS). In total, 502 samples were used, including 184 samples from chronic HCV patients (from routine laboratory activity during April 2016), 5 stored samples with double HCV genotype infections for testing the limitations of the method, and 313 samples from a screening protocol implemented in our hospital (from May to August 2016) based on the new method to further determine its genotyping accuracy. A total of 282 samples, including 171 from April 2016 (the 13 remaining had too low of a viral load for HRCS), 5 selected with double infections, and 106 from screening, were analyzed by both methods, and 220 were analyzed only by the C4800. The C4800 correctly subtyped 125 of 126 1a/1b samples, and the 1 remaining sample was reported as genotype 1. The C4800 correctly genotyped 38 of 45 non-1a/1b samples (classified by HRCS), and it reported the remaining 7 samples as indeterminate. One hundred two of 106 non-1a/1b genotype samples that were identified using the C4800 for screening were confirmed by HRCS. In the 4 remaining samples, 3 were correctly reported as genotype 1 (without defining the subtype) and 1 was reported as indeterminate. None of the samples were misgenotyped. Four of 7 samples with double HCV infections were correctly genotyped by the C4800. Excluding the 5 selected double-infected samples, the C4800 showed 95.7% concordant results for genotyping HCVs 2 to 6 and 1a/1b subtyping, and 99.2% concordance for subtyping 1a/1b single infections in clinical samples. To improve laboratory workflow, we propose using the C4800 as a first-line test for HCV genotyping and 1a/1b classification, followed by

  10. Assessment of a Novel Automatic Real-Time PCR Assay on the Cobas 4800 Analyzer as a Screening Platform for Hepatitis C Virus Genotyping in Clinical Practice: Comparison with Massive Sequencing.

    PubMed

    Nieto-Aponte, Leonardo; Quer, Josep; Ruiz-Ripa, Alicia; Tabernero, David; Gonzalez, Carolina; Gregori, Josep; Vila, Marta; Asensio, Miriam; Garcia-Cehic, Damir; Ruiz, Gerardo; Chen, Qian; Ordeig, Laura; Llorens, Meritxell; Saez, Montserrat; Esteban, Juan I; Esteban, Rafael; Buti, Maria; Pumarola, Tomas; Rodriguez-Frias, Francisco

    2017-02-01

    The unequivocal identification of hepatitis C virus (HCV) subtypes 1a/1b and genotypes 2 to 6 is required for optimizing the effectiveness of interferon-free, direct-acting antiviral therapies. We compared the performance of a new real-time HCV genotyping assay used on the Cobas 4800 system (C4800) with that of high-resolution HCV subtyping (HRCS). In total, 502 samples were used, including 184 samples from chronic HCV patients (from routine laboratory activity during April 2016), 5 stored samples with double HCV genotype infections for testing the limitations of the method, and 313 samples from a screening protocol implemented in our hospital (from May to August 2016) based on the new method to further determine its genotyping accuracy. A total of 282 samples, including 171 from April 2016 (the 13 remaining had too low of a viral load for HRCS), 5 selected with double infections, and 106 from screening, were analyzed by both methods, and 220 were analyzed only by the C4800. The C4800 correctly subtyped 125 of 126 1a/1b samples, and the 1 remaining sample was reported as genotype 1. The C4800 correctly genotyped 38 of 45 non-1a/1b samples (classified by HRCS), and it reported the remaining 7 samples as indeterminate. One hundred two of 106 non-1a/1b genotype samples that were identified using the C4800 for screening were confirmed by HRCS. In the 4 remaining samples, 3 were correctly reported as genotype 1 (without defining the subtype) and 1 was reported as indeterminate. None of the samples were misgenotyped. Four of 7 samples with double HCV infections were correctly genotyped by the C4800. Excluding the 5 selected double-infected samples, the C4800 showed 95.7% concordant results for genotyping HCVs 2 to 6 and 1a/1b subtyping, and 99.2% concordance for subtyping 1a/1b single infections in clinical samples. To improve laboratory workflow, we propose using the C4800 as a first-line test for HCV genotyping and 1a/1b classification, followed by transferring non-1a

  11. Cost effective CD control for DUV implant layers using the Archer MPX focus-exposure monitor

    NASA Astrophysics Data System (ADS)

    Hannon, Sean; Eichelberger, Brad; Nelson, Chris; Dinu, Berta; Kennemer, Harold; Monahan, Kevin

    2005-05-01

    CD control is one of the main parameters for IC product performances and a major contributor to yield performance. Traditional SEM metrology can be a challenge on particular layers due to normal process variation and has not proven to provide sufficient focus monitoring ability. This in turn causes false positives resulting in unnecessary rework, but more importantly missed focus excursions resulting in yield loss. Alexander Starikov, Intel Corporation, alludes to the fact that focus and exposure "knobs" account for greater than 80% of CD correctible variance1. Spansion F25 is evaluating an alternative technology using an optical method for the indirect monitoring of the CD on the implant layer. The optical method utilizes a dual tone line-end-shortening (LES) target which is measured on a standard optical overlay tool. The dual tone technology enables the ability to separate the contributions of the focus and exposure resulting in a more accurate characterization of the two parameters on standard production wafers. Ultimately by keeping focus and exposure within acceptable limits it can be assumed that the CD will be within acceptable limits as well without the unnecessary rework caused by process variation. By using designed experiments this paper will provide characterization of the LES technique on the implant layer showing its ability to separate focus-exposure errors vs. the traditional SEM metrology. Actual high volume production data will be used to compare the robustness and sensitivity of the two technologies in a real life production environment. An overall outline of the production implementation will be documented as well.

  12. Layered transition metal thiophosphates /MPX3/ as photoelectrodes in photoelectrochemical cells

    NASA Technical Reports Server (NTRS)

    Byvik, C. E.; Smith, B. T.; Reichman, B.

    1982-01-01

    Layered crystals of the transition metal thiophosphates were synthesized and characterized for use as photoelectrodes in photoelectrochemical cells. Crystals incorporating tin and manganese show n-type response while those with iron and nickel show p-type response. These materials have a measured indirect bandgap of about 2.1 eV. They show ability to photoelectrolyze water in acid solutions with onset potentials which change in a Nernstian way as the PH of the solution changes. The onset potential is near zero volts versus a saturated calomel electrode at pH 2. At n-type crystals, oxygen could be evolved upon irradiation at underpotentials of 850 mV and at p-type crystals, hydrogen could be evolved at underpotentials of 400 mV, indicating a net gain in energy conversion. All crystals were unstable in basic solution. Liquid junction photovoltaic cells in iodide-triiodide acid solution using these layered materials were also constructed and found to have low efficiences.

  13. 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.

  14. One window-period donation in two years of individual donor-nucleic acid test screening for hepatitis B, hepatitis C and human immunodeficiency virus

    PubMed Central

    Levi, José Eduardo; Pereira, Ricardo Antonio D'Almeida; Polite, Márcia Bernardino de Carvalho; Mota, Mariza Aparecida; Nunez, Silvia Patricia; Pinho, João Renato Rebello; Kutner, José Mauro

    2013-01-01

    Objective To describe general data on nucleic acid/serology testing and report the first hepatitis B-nucleic acid testing yield case of an immunized donor in Brazil. Methods A total of 24,441 donations collected in 2010 and 2011 were submitted to individual nucleic acid testing for hepatitis B, hepatitis C and human immunodeficiency virus using the TaqMan(r) MPX kit (Roche) on the Cobas s201 platform, in addition to routine screening for serological markers. Nucleic acid testing-reactive donations were further evaluated by real-time polymerase chain reaction using Cobas AmpliPrep/Cobas TaqMan hepatitis B virus, hepatitis C virus and human immunodeficiency virus tests. Results Thirty-two donations were reactive by nucleic acid testing, 31 were also serologically reactive and one first-time donor was identified as having hepatitis B in the window period. Follow-up samples showed increasing titers of anti-HBs rising from 19 UI/mL in the index donation to 109 IU/mL seven months later attributable to his vaccination history. Curiously, this donor was never reactive for HbsAg nor for anti-HBc. In the yield donation, he was concomitantly reactive for syphilis (enzyme immunoassay and fluorescent treponemal antibody-absorption; venereal disease research laboratory non-reactive). Overall, six donors (0.02%) were characterized as occult hepatitis B. A total of 35% of the confirmed (recombinant immunoblot assay positive) hepatitis C donations were nucleic acid testing non-reactive and no human immunodeficiency virus "elite controller" was identified. Conclusion The yield rate (1:24,441; 95% confidence interval: 1:9,537 - 1:89,717) contrasts to the North American rate (1:410,540 donations) and strongly advocates the adoption of nucleic acid testing for hepatitis B in Brazil despite the increasing rate of anti-HBs reactive subjects due to the successful immunization program. PMID:23904804

  15. Communications Data Base Analysis for Military Operations in a Built-Up Area (MOBA/COBA).

    DTIC Science & Technology

    1979-08-09

    34. The objectives of this study were, broadly, (i) to a sess the state-of-the- art for radio communications in built- up areas; (ii) to determine the...assess the state-of-the- art for communications in built-up areas; (ii) determine the capabilities of the military to maintain reliable communications in...antenna, 0 namely its low profile (much , than a ,-.ar: i ,ve antenna) d small size and weight. 4.1 MOBA Communications Meeti,,,is with Europea

  16. On Coba and Cocok: youth-led drug-experimentation in Eastern Indonesia.

    PubMed

    Hardon, Anita; Idrus, Nurul Ilmi

    2014-01-01

    The everyday lives of contemporary youths are awash with drugs to boost pleasure, moods, sexual performance, vitality, appearance and health. This paper examines pervasive practices of chemical 'self-maximization' from the perspectives of youths themselves. The research for this paper was conducted among male, female and transgender (male to female, so-called waria) sex workers in Makassar, Indonesia. It presents the authors' ethnographic findings on how these youths experiment with drugs to achieve their desired mental and bodily states: with the painkiller Somadril to feel happy, confident and less reluctant to engage in sex with clients, and contraceptive pills and injectable hormones to feminize their male bodies and to attract customers. Youths are extremely creative in adjusting dosages and mixing substances, with knowledge of the (mostly positive) 'lived effects' of drugs spreading through collective experimentation and word of mouth. The paper outlines how these experimental practices differ from those that have become the gold standard in biomedicine.

  17. On Coba and Cocok: youth-led drug-experimentation in Eastern Indonesia

    PubMed Central

    Hardon, Anita; Idrus, Nurul Ilmi

    2014-01-01

    The everyday lives of contemporary youths are awash with drugs to boost pleasure, moods, sexual performance, vitality, appearance and health. This paper examines pervasive practices of chemical ‘self-maximization’ from the perspectives of youths themselves. The research for this paper was conducted among male, female and transgender (male to female, so-called waria) sex workers in Makassar, Indonesia. It presents the authors’ ethnographic findings on how these youths experiment with drugs to achieve their desired mental and bodily states: with the painkiller Somadril to feel happy, confident and less reluctant to engage in sex with clients, and contraceptive pills and injectable hormones to feminize their male bodies and to attract customers. Youths are extremely creative in adjusting dosages and mixing substances, with knowledge of the (mostly positive) ‘lived effects’ of drugs spreading through collective experimentation and word of mouth. The paper outlines how these experimental practices differ from those that have become the gold standard in biomedicine. PMID:25175296

  18. Ada (Trade Name) Compiler Validation Summary Report: TeleSoft, Inc. TeleSoft Ada Compiler, Version 2.3C3 for the Gould CONCEPT/32 (Trade Name) Model 9750 under MPX, Version 3.2.

    DTIC Science & Technology

    1985-12-06

    ACCESSION NO .I 1 RE.CIP)IErN-S C-A A-INJBIE I; A~ -- .T .’.. a TTLE ivdS.1" h I YPL OF REPORT b PERIOD COVERED Ada Compiler Validation Summary Report...3 2-, . . h ~ .. " ." ~~.* .*..2. TEST RESULTS 2.1.7 Support Units Three units (REPORT package, CHECKFILE procedure, and VARSTRINGS package) support...needed to complete the block for case H beginning at line 389. 2-9 2-9 "’ II . .- .... > ....-. .i + -.. ’-.- .i

  19. Blood donors screening for blood born viruses in Poland.

    PubMed

    Grabarczyk, Piotr; Kopacz, Aneta; Sulkowska, Ewa; Kubicka-Russel, Dorota; Mikulska, Maria; Brojer, Ewa; Łętowska, Magdalena

    2015-01-01

    Blood donor screening of viral markers in Poland is based on serologic testing for anti-HCV, HBsAg, anti-HIV1/2 (chemiluminescence tests) and on nucleic acid testing (NAT) for RNA HCV, RNA HIV-1 and DNA HBV performed in minipools of 6 with real-time PCR (MPX 2.0 test on cobas s201) or with TMA in individual donations (Ultrio Plus or Ultrio Elite). Donors of plasma for anti-D and anti-HBs production are tested for parvovirus B19 DNA. Before implementation tests and equipment are evaluated at the Institute of Hematology and Transfusion Medicine (IHTM). The last 20 years witnessed a decreasing trend for HBsAg in both first time and repeat donors (1%-0.3% and 0.1%-0.02% respectively). Prevalence of anti-HCV repeat reactive results was stable and oscillated around 0.8% for first time donors and 0.2% for repeat donors. Elevated prevalence of seropositive HIV infected donors was recently observed (7.5-9 cases/100,000 donors). Since respective molecular markers implementation HCV RNA was detected on average in 1/119,235 seronegative donations, HIV RNA in 1/783,821 and HBV DNA in 1/61,047. HBV NAT yields were mostly occult hepatitis B (1/80,248); window period cases were less frequent (1/255,146). The efficiency of HBV DNA detection depends on the sensitivity of the HBV DNA screening system.

  20. Adaptation of an enzymatic cycling assay for NADP(H) measurement to the COBAS-FARA centrifugal analyzer.

    PubMed

    Lewis, B L; McGuinness, E T

    1990-01-01

    NADP(H) measurements by enzymatic amplification are described in which the interface step between cycling (glucose-6-phosphate and glutamic dehydrogenases) and indicator (6-phosphogluconic dehydrogenase) enzymes has been reconfigured, permitting the entire operation to run as a continuous assay on a centrifugal fast analyzer. This is accomplished by using the sequential load feature of the analyzer and incorporating either sodium dodecyl sulfate (SDS) or SDS and hydrogen peroxide as kill reagents to replace the thermal step (destruction of cycle enzymes by boiling). The ability of SDS to render a cycle inoperative during the run time of the indicator enzyme depends on the inherent resistivity and absolute amount of its enzyme proteins to this surfactant. Criteria used to judge the efficacy of a potential kill reagent are based on the sample blank time-response curve and the cycle product recovery by the indicator enzyme. Various other enzyme cycling systems which can be fitted to the centrifugal fast analyzer are highlighted.

  1. Heteronuclear (Co-Ca, Co-Ba) 2,3-pyridinedicarboxylate complexes: synthesis, structure and physico-chemical properties.

    PubMed

    Lazarescu, Ana; Shova, Sergiu; Bartolome, Juan; Alonso, Pablo; Arauzo, Ana; Balu, Alina M; Simonov, Yuri A; Gdaniec, Maria; Turta, Constantin; Filoti, George; Luque, Rafael

    2011-01-14

    Three pyridine 2,3-dicarboxylate complexes have been synthesized and characterized by IR spectroscopy, thermal analysis and single crystal X-ray diffractometry. Their magnetic properties have also been studied by EPR and magnetisation measurements. The decomposition of such complexes in air leads to the generation of mixed metal oxides, as confirmed by powder X-ray diffraction.

  2. Quantification of Viral Loads Lower than 50 Copies per Milliliter by Use of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test, Version 2.0, Can Predict the Likelihood of Subsequent Virological Rebound to >50 Copies per Milliliter

    PubMed Central

    Álvarez Estévez, Marta; Chueca Porcuna, Natalia; Guillot Suay, Vicente; Peña Monge, Alejandro; García García, Fernando; Muñoz Medina, Leopoldo; Vinuesa García, David; Parra Ruiz, Jorge; Hernández-Quero, Jose

    2013-01-01

    After 1 year of follow-up, patients on HAART with a baseline viral load (VL) of <20 copies/ml showed significantly lower odds of virological rebound to two consecutive VLs of >50 copies/ml than those with baseline VLs of 20 to 39 and 40 to 49 (P < 0.001). The time to virological rebound was also significantly shorter (P < 0.001) for the groups with baseline VLs of 20 to 39 and 40 to 49. PMID:23390288

  3. Evaluation of the GeneXpert for Human Monkeypox Diagnosis

    PubMed Central

    Li, Daniel; Wilkins, Kimberly; McCollum, Andrea M.; Osadebe, Lynda; Kabamba, Joelle; Nguete, Beatrice; Likafi, Toutou; Balilo, Marcel Pie; Lushima, Robert Shongo; Malekani, Jean; Damon, Inger K.; Vickery, Michael C. L.; Pukuta, Elisabeth; Nkawa, Frida; Karhemere, Stomy; Tamfum, Jean-Jacques Muyembe; Okitolonda, Emile Wemakoy; Li, Yu; Reynolds, Mary G.

    2017-01-01

    Monkeypox virus (MPXV), a zoonotic orthopoxvirus (OPX), is endemic in the Democratic Republic of Congo (DRC). Currently, diagnostic assays for human monkeypox (MPX) focus on real-time quantitative polymerase chain reaction (PCR) assays, which are typically performed in sophisticated laboratory settings. Herein, we evaluated the accuracy and utility of a multiplex MPX assay using the GeneXpert platform, a portable rapid diagnostic device that may serve as a point-of-care test to diagnose infections in endemic areas. The multiplex MPX/OPX assay includes a MPX-specific PCR test, OPX-generic PCR test, and an internal control PCR test. In total, 164 diagnostic specimens (50 crusts and 114 vesicular swabs) were collected from suspected MPX cases in Tshuapa Province, DRC, under national surveillance guidelines. The specimens were tested with the GeneXpert MPX/OPX assay and an OPX PCR assay at the Institut National de Recherche Biomedicale (INRB) in Kinshasa. Aliquots of each specimen were tested in parallel with a MPX-specific PCR assay at the Centers for Disease Control and Prevention. The results of the MPX PCR were used as the gold standard for all analyses. The GeneXpert MPX/OPX assay performed at INRB had a sensitivity of 98.8% and specificity of 100%. The GeneXpert assay performed well with both crust and vesicle samples. The GeneXpert MPX/OPX test incorporates a simple methodology that performs well in both laboratory and field conditions, suggesting its viability as a diagnostic platform that may expand and expedite current MPX detection capabilities. PMID:27994107

  4. Ada (Trade name) Validation Summary Report: TeleSoft, Inc., TeleSoft Ada Compiler, Version 2.3C3 for the Gould CONCEPT/32 (Trade name) Model 6750 under MPX, Version 3.2. Completion of On-Site Validation.

    DTIC Science & Technology

    1985-12-06

    B.ADA P B62001E-B.ADA P C62003B-B.ADA P C65003A-B.ADA P B63006P-B.ADA P c63004A-AB.ADA P C65003B-B.ADA P B63005A- ABADA P C62006A-B.ADA P C66002DA...B.ADA P B63005B-AB.ADA P C63004A-AB.ADA P C66002C-AB.ADA P B63005A-AB.ADA P c6�B-B.ADA P C66002D- ABADA P% B63005B-AB.ADA P C64OO0IG-B.ADA P C66002E

  5. Cognitive Impairments Are Different in Single-Incidence and Multi-Incidence ADHD Families

    ERIC Educational Resources Information Center

    Oerlemans, Anoek M.; Hartman, Catharina A.; Bruijn, Yvette G. E.; Franke, Barbara; Buitelaar, Jan K.; Rommelse, Nanda N. J.

    2015-01-01

    Background: We may improve our understanding of the role of common versus unique risk factors in attention-deficit/hyperactivity disorder (ADHD) by examining ADHD-related cognitive deficits in single- (SPX), and multi-incidence (MPX) families. Given that individuals from multiplex (MPX) families are likely to share genetic vulnerability for the…

  6. Does the Cognitive Architecture of Simplex and Multiplex ASD Families Differ?

    ERIC Educational Resources Information Center

    Oerlemans, Anoek M.; Hartman, Catharina A.; Franke, Barbara; Buitelaar, Jan K.; Rommelse, Nanda N. J.

    2016-01-01

    Children with an autism spectrum disorder (ASD) and their unaffected siblings from 54 simplex (SPX, one individual in the family affected) and 59 multiplex (MPX, two or more individuals affected) families, and 124 controls were assessed on intelligence, social cognition and executive functions. SPX and MPX ASD probands displayed similar cognitive…

  7. Cognitive Impairments Are Different in Single-Incidence and Multi-Incidence ADHD Families

    ERIC Educational Resources Information Center

    Oerlemans, Anoek M.; Hartman, Catharina A.; Bruijn, Yvette G. E.; Franke, Barbara; Buitelaar, Jan K.; Rommelse, Nanda N. J.

    2015-01-01

    Background: We may improve our understanding of the role of common versus unique risk factors in attention-deficit/hyperactivity disorder (ADHD) by examining ADHD-related cognitive deficits in single- (SPX), and multi-incidence (MPX) families. Given that individuals from multiplex (MPX) families are likely to share genetic vulnerability for the…

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

    PubMed

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

    2017-04-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2002-12-01

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

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

    PubMed

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

    2016-03-01

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

  12. Sensitivity of individual-donation and minipool nucleic acid amplification test options in detecting window period and occult hepatitis B virus infections

    PubMed Central

    Vermeulen, Marion; Coleman, Charl; Mitchel, Josephine; Reddy, Ravi; van Drimmelen, Harry; Ficket, Tracy; Lelie, Nico

    2016-01-01

    BACKGROUND Several comparison studies showed that the Ultrio assay (Novartis Diagnostics) used in individual-donation nucleic acid amplification testing (ID-NAT) format was as sensitive as the TaqScreen assay (Roche) on minipools of six donations (MP6), but the sensitivity of HBV DNA detection has been improved in the new Ultrio Plus version of the assay. A head-to-head comparison study was designed to compare the clinical sensitivity of the Ultrio and Ultrio Plus assay in ID, MP4, and MP8 formats using TaqScreen MP6 as a reference assay. STUDY DESIGN AND METHODS Plasma samples of 107 hepatitis B surface antigen (HBsAg)-negative, HBV ID-NAT (Ultrio) positive-yield samples and 29 HBV DNA–negative, HBsAg-positive samples were used for comparison of NAT options in replicate testing of dilutions. Viral loads and relative sensitivities were determined by probit analysis against the Eurohep standard. RESULTS Ultrio Plus detected a significantly (p < 0.00001) higher proportion of replicate assays on HBV NAT yields (77%) than Ultrio ID (62%) and TaqScreen MP6 (47%), whereas Ultrio Plus MP4 and MP8 detected 53 and 41%, respectively. On HBsAg-yield samples missed by Ultrio screening, the reactivity rate increased significantly (p < 0.0001) from 23% in Ultrio to 65% in Ultrio Plus and further to 72% (p = 0.10) in the TaqScreen assay. The overall improvement factor of the analytical sensitivity offered by the target enhancer reagent in the Ultrio Plus assay was 2.5 (2.0–3.1)-fold on the Ultrio yield samples, but 43 (11–350)-fold on the HBsAg yields. In ID-NAT format the analytical sensitivity of TaqScreen relative to Ultrio Plus was 2.0 (1.0–4.2), 0.9 (0.7–1.3), and 1.6 (0.9–3.0) on the Eurohep standard, HBV NAT–, and HBsAg-yield samples respectively. CONCLUSION The clinical sensitivity of the currently available commercial NAT methods is mainly driven by the pool size. PMID:23621791

  13. Sensitivity of individual-donation and minipool nucleic acid amplification test options in detecting window period and occult hepatitis B virus infections.

    PubMed

    Vermeulen, Marion; Coleman, Charl; Mitchel, Josephine; Reddy, Ravi; van Drimmelen, Harry; Ficket, Tracy; Lelie, Nico

    2013-10-01

    Several comparison studies showed that the Ultrio assay (Novartis Diagnostics) used in individual-donation nucleic acid amplification testing (ID-NAT) format was as sensitive as the TaqScreen assay (Roche) on minipools of six donations (MP6), but the sensitivity of HBV DNA detection has been improved in the new Ultrio Plus version of the assay. A head-to-head comparison study was designed to compare the clinical sensitivity of the Ultrio and Ultrio Plus assay in ID, MP4, and MP8 formats using TaqScreen MP6 as a reference assay. Plasma samples of 107 hepatitis B surface antigen (HBsAg)-negative, HBV ID-NAT (Ultrio) positive-yield samples and 29 HBV DNA-negative, HBsAg-positive samples were used for comparison of NAT options in replicate testing of dilutions. Viral loads and relative sensitivities were determined by probit analysis against the Eurohep standard. Ultrio Plus detected a significantly (p < 0.00001) higher proportion of replicate assays on HBV NAT yields (77%) than Ultrio ID (62%) and TaqScreen MP6 (47%), whereas Ultrio Plus MP4 and MP8 detected 53 and 41%, respectively. On HBsAg-yield samples missed by Ultrio screening, the reactivity rate increased significantly (p < 0.0001) from 23% in Ultrio to 65% in Ultrio Plus and further to 72% (p = 0.10) in the TaqScreen assay. The overall improvement factor of the analytical sensitivity offered by the target enhancer reagent in the Ultrio Plus assay was 2.5 (2.0-3.1)-fold on the Ultrio yield samples, but 43 (11-350)-fold on the HBsAg yields. In ID-NAT format the analytical sensitivity of TaqScreen relative to Ultrio Plus was 2.0 (1.0-4.2), 0.9 (0.7-1.3), and 1.6 (0.9-3.0) on the Eurohep standard, HBV NAT-, and HBsAg-yield samples respectively. The clinical sensitivity of the currently available commercial NAT methods is mainly driven by the pool size. © 2013 American Association of Blood Banks.

  14. Varicella Coinfection in Patients with Active Monkeypox in the Democratic Republic of the Congo.

    PubMed

    Hoff, Nicole A; Morier, Douglas S; Kisalu, Neville K; Johnston, Sara C; Doshi, Reena H; Hensley, Lisa E; Okitolonda-Wemakoy, Emile; Muyembe-Tamfum, Jean Jacques; Lloyd-Smith, James O; Rimoin, Anne W

    2017-09-11

    From 2006 to 2007, an active surveillance program for human monkeypox (MPX) in the Democratic Republic of the Congo identified 151 cases of coinfection with monkeypox virus and varicella zoster virus from 1158 suspected cases of human MPX (13%). Using clinical and socio-demographic data collected with standardized instruments by trained, local nurse supervisors, we examined a variety of hypotheses to explain the unexpectedly high proportion of coinfections among the sample, including the hypothesis that the two viruses occur independently. The probabilities of disease incidence and selection necessary to yield the observed sample proportion of coinfections under an assumption of independence are plausible given what is known and assumed about human MPX incidence. Cases of human MPX are expected to be underreported, and more coinfections are expected with improved surveillance.

  15. Increased Sensory Processing Atypicalities in Parents of Multiplex ASD Families Versus Typically Developing and Simplex ASD Families.

    PubMed

    Donaldson, Chelsea K; Stauder, Johannes E A; Donkers, Franc C L

    2017-03-01

    Recent studies have suggested that sensory processing atypicalities may share genetic influences with autism spectrum disorder (ASD). To further investigate this, the adolescent/adult sensory profile (AASP) questionnaire was distributed to 85 parents of typically developing children (P-TD), 121 parents from simplex ASD families (SPX), and 54 parents from multiplex ASD families (MPX). After controlling for gender and presence of mental disorders, results showed that MPX parents significantly differed from P-TD parents in all four subscales of the AASP. Differences between SPX and MPX parents reached significance in the Sensory Sensitivity subscale and also in subsequent modality-specific analyses in the auditory and visual domains. Our finding that parents with high genetic liability for ASD (i.e., MPX) had more sensory processing atypicalities than parents with low (i.e., SPX) or no (i.e., P-TD) ASD genetic liability suggests that sensory processing atypicalities may contribute to the genetic susceptibility for ASD.

  16. Evaluation of monkeypox virus infection of prairie dogs (Cynomys ludovicianus) using in vivo bioluminescent imaging

    USGS Publications Warehouse

    Falendysz, Elizabeth A.; Londoño-Navas, Angela M.; Meteyer, Carol U.; Pussini, Nicola; Lopera, Juan G.; Osorio, Jorge E.; Rocke, Tonie E.

    2014-01-01

    Monkeypox (MPX) is a re-emerging zoonotic disease that is endemic in Central and West Africa, where it can cause a smallpox-like disease in humans. Despite many epidemiologic and field investigations of MPX, no definitive reservoir species has been identified. Using recombinant viruses expressing the firefly luciferase (luc) gene, we previously demonstrated the suitability of in vivo bioluminescent imaging (BLI) to study the pathogenesis of MPX in animal models. Here, we evaluated BLI as a novel approach for tracking MPX virus infection in black-tailed prairie dogs (Cynomys ludovicianus). Prairie dogs were affected during a multistate outbreak of MPX in the US in 2003 and have since been used as an animal model of this disease. Our BLI results were compared with PCR and virus isolation from tissues collected postmortem. Virus was easily detected and quantified in skin and superficial tissues by BLI before and during clinical phases, as well as in subclinical secondary cases, but was not reliably detected in deep tissues such as the lung. Although there are limitations to viral detection in larger wild rodent species, BLI can enhance the use of prairie dogs as an animal model of MPX and can be used for the study of infection, disease progression, and transmission in potential wild rodent reservoirs.

  17. Evaluation of monkeypox virus infection of black-tailed prairie dogs (Cynomys ludovicianus) using in vivo bioluminescent imaging.

    PubMed

    Falendysz, Elizabeth A; Londoño-Navas, Angela M; Meteyer, Carol U; Pussini, Nicola; Lopera, Juan G; Osorio, Jorge E; Rocke, Tonie E

    2014-07-01

    Monkeypox (MPX) is a re-emerging zoonotic disease that is endemic in Central and West Africa, where it can cause a smallpox-like disease in humans. Despite many epidemiologic and field investigations of MPX, no definitive reservoir species has been identified. Using recombinant viruses expressing the firefly luciferase (luc) gene, we previously demonstrated the suitability of in vivo bioluminescent imaging (BLI) to study the pathogenesis of MPX in animal models. Here, we evaluated BLI as a novel approach for tracking MPX virus infection in black-tailed prairie dogs (Cynomys ludovicianus). Prairie dogs were affected during a multistate outbreak of MPX in the US in 2003 and have since been used as an animal model of this disease. Our BLI results were compared with PCR and virus isolation from tissues collected postmortem. Virus was easily detected and quantified in skin and superficial tissues by BLI before and during clinical phases, as well as in subclinical secondary cases, but was not reliably detected in deep tissues such as the lung. Although there are limitations to viral detection in larger wild rodent species, BLI can enhance the use of prairie dogs as an animal model of MPX and can be used for the study of infection, disease progression, and transmission in potential wild rodent reservoirs.

  18. EVALUATION OF MONKEYPOX VIRUS INFECTION OF BLACK-TAILED PRAIRIE DOGS (CYNOMYS LUDOVICIANUS) USING IN VIVO BIOLUMINESCENT IMAGING

    PubMed Central

    Falendysz, Elizabeth A.; Londoño-Navas, Angela M.; Meteyer, Carol U.; Pussini, Nicola; Lopera, Juan G.; Osorio, Jorge E.; Rocke, Tonie E.

    2015-01-01

    Monkeypox (MPX) is a re-emerging zoonotic disease that is endemic in Central and West Africa, where it can cause a smallpox-like disease in humans. Despite many epidemiologic and field investigations of MPX, no definitive reservoir species has been identified. Using recombinant viruses expressing the firefly luciferase (luc) gene, we previously demonstrated the suitability of in vivo bioluminescent imaging (BLI) to study the pathogenesis of MPX in animal models. Here, we evaluated BLI as a novel approach for tracking MPX virus infection in black-tailed prairie dogs (Cynomys ludovicianus). Prairie dogs were affected during a multi-state outbreak of MPX in the USA in 2003 and have since been used as an animal model of this disease. Our BLI results were compared with PCR and virus isolation from tissues collected postmortem. Virus was easily detected and quantified in skin and superficial tissues by BLI before and during clinical phases, as well as in subclinical secondary cases, but was not reliably detected in deep tissues such as the lung. Although there are limitations to viral detection in larger wild rodent species, BLI can enhance the use of prairie dogs as an animal model of MPX and can be used for the study of infection, disease progression, and transmission in potential wild rodent reservoirs. PMID:24779460

  19. Handbook To Facilitate Faculty Awareness of Library Resources and Services: One Library's Initial Response to the College of Business Administration's Search for AACSB Accreditation.

    ERIC Educational Resources Information Center

    Earle, Katherine Weeks

    Created by the College of Business Administration (COBA) and the libraries of the University of Northern Colorado, this 1988-89 handbook was part of a strategic plan to achieve initial accreditation by the American Assembly of Collegiate Schools of Business (AACSB). Constructed by the reference librarian who works directly with COBA, the handbook…

  20. Efficacy of the antipoxvirus compound ST-246 for treatment of severe orthopoxvirus infection.

    PubMed

    Sbrana, Elena; Jordan, Robert; Hruby, Dennis E; Mateo, Rosa I; Xiao, Shu-Yuan; Siirin, Marina; Newman, Patrick C; DA Rosa, Amelia P A Travassos; Tesh, Robert B

    2007-04-01

    Efficacy of the new antipoxvirus compound ST-246 was evaluated as treatment of monkeypox (MPX) virus infection in a ground squirrel model of the disease. Ground squirrels were given a lethal dose of MPX virus and were then treated orally at various times post-inoculation (pi) with 100 mg/kg/day of ST-246. Morbidity and mortality, clinical laboratory results, viral load, and pathology of placebo and treatment groups were compared. All animals that started treatment with ST-246 on days 0, 1, 2, and 3 pi survived lethal challenge with MPX virus; 67% of animals treated on day 4 pi also survived. In contrast, 100% of the placebo group died. Most of the ST-246-treated animals showed no evidence of clinical disease or alteration of baseline clinical laboratory values and had minimal histopathologic changes. These results suggest that ST-246 is a promising candidate for early treatment of severe orthopoxvirus infection.

  1. Pathogen-Host Associations and Predicted Range Shifts of Human Monkeypox in Response to Climate Change in Central Africa

    PubMed Central

    Thomassen, Henri A.; Fuller, Trevon; Asefi-Najafabady, Salvi; Shiplacoff, Julia A. G.; Mulembakani, Prime M.; Blumberg, Seth; Johnston, Sara C.; Kisalu, Neville K.; Kinkela, Timothée L.; Fair, Joseph N.; Wolfe, Nathan D.; Shongo, Robert L.; LeBreton, Matthew; Meyer, Hermann; Wright, Linda L.; Muyembe, Jean-Jacques; Buermann, Wolfgang; Okitolonda, Emile; Hensley, Lisa E.; Lloyd-Smith, James O.; Smith, Thomas B.; Rimoin, Anne W.

    2013-01-01

    Climate change is predicted to result in changes in the geographic ranges and local prevalence of infectious diseases, either through direct effects on the pathogen, or indirectly through range shifts in vector and reservoir species. To better understand the occurrence of monkeypox virus (MPXV), an emerging Orthopoxvirus in humans, under contemporary and future climate conditions, we used ecological niche modeling techniques in conjunction with climate and remote-sensing variables. We first created spatially explicit probability distributions of its candidate reservoir species in Africa's Congo Basin. Reservoir species distributions were subsequently used to model current and projected future distributions of human monkeypox (MPX). Results indicate that forest clearing and climate are significant driving factors of the transmission of MPX from wildlife to humans under current climate conditions. Models under contemporary climate conditions performed well, as indicated by high values for the area under the receiver operator curve (AUC), and tests on spatially randomly and non-randomly omitted test data. Future projections were made on IPCC 4th Assessment climate change scenarios for 2050 and 2080, ranging from more conservative to more aggressive, and representing the potential variation within which range shifts can be expected to occur. Future projections showed range shifts into regions where MPX has not been recorded previously. Increased suitability for MPX was predicted in eastern Democratic Republic of Congo. Models developed here are useful for identifying areas where environmental conditions may become more suitable for human MPX; targeting candidate reservoir species for future screening efforts; and prioritizing regions for future MPX surveillance efforts. PMID:23935820

  2. Pathogen-host associations and predicted range shifts of human monkeypox in response to climate change in central Africa.

    PubMed

    Thomassen, Henri A; Fuller, Trevon; Asefi-Najafabady, Salvi; Shiplacoff, Julia A G; Mulembakani, Prime M; Blumberg, Seth; Johnston, Sara C; Kisalu, Neville K; Kinkela, Timothée L; Fair, Joseph N; Wolfe, Nathan D; Shongo, Robert L; LeBreton, Matthew; Meyer, Hermann; Wright, Linda L; Muyembe, Jean-Jacques; Buermann, Wolfgang; Okitolonda, Emile; Hensley, Lisa E; Lloyd-Smith, James O; Smith, Thomas B; Rimoin, Anne W

    2013-01-01

    Climate change is predicted to result in changes in the geographic ranges and local prevalence of infectious diseases, either through direct effects on the pathogen, or indirectly through range shifts in vector and reservoir species. To better understand the occurrence of monkeypox virus (MPXV), an emerging Orthopoxvirus in humans, under contemporary and future climate conditions, we used ecological niche modeling techniques in conjunction with climate and remote-sensing variables. We first created spatially explicit probability distributions of its candidate reservoir species in Africa's Congo Basin. Reservoir species distributions were subsequently used to model current and projected future distributions of human monkeypox (MPX). Results indicate that forest clearing and climate are significant driving factors of the transmission of MPX from wildlife to humans under current climate conditions. Models under contemporary climate conditions performed well, as indicated by high values for the area under the receiver operator curve (AUC), and tests on spatially randomly and non-randomly omitted test data. Future projections were made on IPCC 4(th) Assessment climate change scenarios for 2050 and 2080, ranging from more conservative to more aggressive, and representing the potential variation within which range shifts can be expected to occur. Future projections showed range shifts into regions where MPX has not been recorded previously. Increased suitability for MPX was predicted in eastern Democratic Republic of Congo. Models developed here are useful for identifying areas where environmental conditions may become more suitable for human MPX; targeting candidate reservoir species for future screening efforts; and prioritizing regions for future MPX surveillance efforts.

  3. KRAS Mutation Test in Korean Patients with Colorectal Carcinomas: A Methodological Comparison between Sanger Sequencing and a Real-Time PCR-Based Assay

    PubMed Central

    Lee, Sung Hak; Chung, Arthur Minwoo; Lee, Ahwon; Oh, Woo Jin; Choi, Yeong Jin; Lee, Youn-Soo; Jung, Eun Sun

    2017-01-01

    Background Mutations in the KRAS gene have been identified in approximately 50% of colorectal cancers (CRCs). KRAS mutations are well established biomarkers in anti–epidermal growth factor receptor therapy. Therefore, assessment of KRAS mutations is needed in CRC patients to ensure appropriate treatment. Methods We compared the analytical performance of the cobas test to Sanger sequencing in 264 CRC cases. In addition, discordant specimens were evaluated by 454 pyrosequencing. Results KRAS mutations for codons 12/13 were detected in 43.2% of cases (114/264) by Sanger sequencing. Of 257 evaluable specimens for comparison, KRAS mutations were detected in 112 cases (43.6%) by Sanger sequencing and 118 cases (45.9%) by the cobas test. Concordance between the cobas test and Sanger sequencing for each lot was 93.8% positive percent agreement (PPA) and 91.0% negative percent agreement (NPA) for codons 12/13. Results from the cobas test and Sanger sequencing were discordant for 20 cases (7.8%). Twenty discrepant cases were subsequently subjected to 454 pyrosequencing. After comprehensive analysis of the results from combined Sanger sequencing–454 pyrosequencing and the cobas test, PPA was 97.5% and NPA was 100%. Conclusions The cobas test is an accurate and sensitive test for detecting KRAS-activating mutations and has analytical power equivalent to Sanger sequencing. Prescreening using the cobas test with subsequent application of Sanger sequencing is the best strategy for routine detection of KRAS mutations in CRC. PMID:28013534

  4. Comparative Effectiveness of Dried-Plasma Hepatitis B Virus Viral Load (VL) Testing in Three Different VL Commercial Platforms Using ViveST for Sample Collection

    PubMed Central

    Zanoni, Michelle; Giron, Leila B.; Vilhena, Cintia; Sucupira, Maria Cecilia; Lloyd, Robert M.

    2012-01-01

    Ninety-six samples from hepatitis B virus (HBV)-infected individuals were used to compare ViveST samples to frozen samples in COBAS TaqMan, RealArt, and VERSANT. Correlation (r) between ViveST samples and frozen samples was 0.99 in all three platforms. Correlations among tests using frozen samples were 0.96 for COBAS and RealArt, 0.94 for COBAS and VERSANT, and 0.97 for VERSANT and RealArt. The results indicate that ViveST may be useful in clinical practice. Different HBV-VL platforms correlated well with one another. PMID:22012021

  5. Population- and Family-Based Studies Associate the "MTHFR" Gene with Idiopathic Autism in Simplex Families

    ERIC Educational Resources Information Center

    Liu, Xudong; Solehdin, Fatima; Cohen, Ira L.; Gonzalez, Maripaz G.; Jenkins, Edmund C.; Lewis, M. E. Suzanne; Holden, Jeanette J. A.

    2011-01-01

    Two methylenetetrahydrofolate reductase gene ("MTHFR") functional polymorphisms were studied in 205 North American simplex (SPX) and 307 multiplex (MPX) families having one or more children with an autism spectrum disorder. Case-control comparisons revealed a significantly higher frequency of the low-activity 677T allele, higher prevalence of the…

  6. Simplex and Multiplex Stratification in ASD and ADHD Families: A Promising Approach for Identifying Overlapping and Unique Underpinnings of ASD and ADHD?

    ERIC Educational Resources Information Center

    Oerlemans, Anoek M.; Hartman, Catharina A.; De Bruijn, Yvette G. E.; Van Steijn, Daphne J.; Franke, Barbara; Buitelaar, Jan K.; Rommelse, Nanda N. J.

    2015-01-01

    Autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD) are highly heterogeneous neuropsychiatric disorders, that frequently co-occur. This study examined whether stratification into single-incidence (SPX) and multi-incidence (MPX) is helpful in (a) parsing heterogeneity and (b) detecting overlapping and unique…

  7. Population- and Family-Based Studies Associate the "MTHFR" Gene with Idiopathic Autism in Simplex Families

    ERIC Educational Resources Information Center

    Liu, Xudong; Solehdin, Fatima; Cohen, Ira L.; Gonzalez, Maripaz G.; Jenkins, Edmund C.; Lewis, M. E. Suzanne; Holden, Jeanette J. A.

    2011-01-01

    Two methylenetetrahydrofolate reductase gene ("MTHFR") functional polymorphisms were studied in 205 North American simplex (SPX) and 307 multiplex (MPX) families having one or more children with an autism spectrum disorder. Case-control comparisons revealed a significantly higher frequency of the low-activity 677T allele, higher prevalence of the…

  8. DNA analysis of fingernail debris using different multiplex systems: a case report.

    PubMed

    Lederer, T; Betz, P; Seidl, S

    2001-01-01

    A 55-year-old male nurse was accused of having introduced his fingers by force into the anus of a 20-year-old female patient. Debris from the fingernails of the suspect recovered 2 days after the incident was analysed with the VNTR locus D1S80, the triplex PCR system AmpFlSTR Blue kit, the AmpFlSTR Profiler kit and the pentaplex system genRES MPX. The D1S80 singleplex reaction revealed indications of DNA from the victim in the fingernail debris of the left hand. Using the AmpFlSTR Blue kit and AmpFlSTR Profiler, DNA alleles of the victim were found at four additional loci, while allelic drop-out was observed at five other loci. Only the pentaplex kit genRES MPX revealed alleles at all loci which could be assigned to the victim. Calculation of likelihood ratios resulted in a value of 1.4 x 10(5) using the combination of the multiplex systems AmpF1STR Blue kit and AmpFlSTR Profiler and 2.8 x 10(8) for the genRES MPX kit. This case demonstrates the high sensitivity of the new genRES MPX kit and that DNA profiling of fingernail debris is possible despite a time lapse of 2 days between the incident and recovery of the evidential material.

  9. Simplex and Multiplex Stratification in ASD and ADHD Families: A Promising Approach for Identifying Overlapping and Unique Underpinnings of ASD and ADHD?

    ERIC Educational Resources Information Center

    Oerlemans, Anoek M.; Hartman, Catharina A.; De Bruijn, Yvette G. E.; Van Steijn, Daphne J.; Franke, Barbara; Buitelaar, Jan K.; Rommelse, Nanda N. J.

    2015-01-01

    Autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD) are highly heterogeneous neuropsychiatric disorders, that frequently co-occur. This study examined whether stratification into single-incidence (SPX) and multi-incidence (MPX) is helpful in (a) parsing heterogeneity and (b) detecting overlapping and unique…

  10. Identifying Unique Versus Shared Pre- and Perinatal Risk Factors for ASD and ADHD Using a Simplex-Multiplex Stratification.

    PubMed

    Oerlemans, Anoek M; Burmanje, Marlot J; Franke, Barbara; Buitelaar, Jan K; Hartman, Catharina A; Rommelse, Nanda N J

    2016-07-01

    Autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) frequently co-occur. Besides shared genetic factors, pre- and perinatal risk factors (PPFs) may determine if ASD, ADHD, or the combination of both disorders becomes manifest. This study aimed to test shared and unique involvement of PPFs for ASD and ADHD, using an approach that stratifies the sample into affected/unaffected offspring and single-incidence (SPX) versus multi-incidence (MPX) families. Pre- perinatal data based on retrospective parent-report were collected in 288 children (71 % males) from 31 SPX and 59 MPX ASD families, 476 children (65 % males) from 31 SPX and 171 MPX ADHD families, and 408 control children (42 % males). Except for large family size and more firstborns amongst affected offspring, no shared PFFs were identified for ASD and ADHD. PPFs predominantly related to ASD (maternal infections and suboptimal condition at birth) were more often reported in affected than unaffected siblings. PPFs associated with ADHD (low parental age, maternal diseases, smoking and stress) were shared between affected and unaffected siblings. Firstborn-ship was more frequent in SPX than MPX ASD probands. Our results suggest that the co-morbidity of ASD and ADHD is not likely explained by shared PPFs. Instead, PPFs might play a crucial role in the developmental pathways leading up to either disorder. PPFs in ADHD appear to index an increased shared risk, whereas in ASD PPFs possibly have a more determining role in the disorder. SPX-MPX stratification detected possible etiological differences in ASD families, but provided no deeper insight in the role of PPFs in ADHD.

  11. Multicenter Evaluation of a New High-Throughput HbA1c Testing Platform.

    PubMed

    Imdahl, R; Roddiger, R; Casis-Saenz, E

    2016-12-01

    This non-interventional, multicenter study with anonymized leftover patient samples was performed to evaluate the reliability and analytical performance of the novel high-throughput HbA1c cobas c 513 analyzer. A performance evaluation was carried out at three sites to validate the overall system functionality, user interaction and analytical performance of the new cobas c 513 analyzer using the Tina-quant® HbA1c Gen. 3 assay. HbA1c applications for both whole blood and hemolysate samples show a high precision using both quality control materials and pools of whole blood or hemolysates. The method comparison of HbA1c Gen. 3 on the cobas c 513 with HbA1c Gen. 2 on the Menarini HA-8180V using 249 whole blood samples shows high concordance. Moreover, analyte concentrations as measured by the cobas c 513 and Tosoh G8 and HbA1c Gen. 2 on COBAS INTEGRA® 800 CTS are comparable. The cobas c 513 has proven to be a reliable system with excellent analytical performance of the Tinaquant® HbA1c Gen. 3 assay in high throughput laboratories.

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

    PubMed Central

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

    2011-01-01

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

  13. A Phase I Study of Muscadine Grape Skin Extract in Men with Biochemically Recurrent Prostate Cancer: Safety, Tolerability, and Dose Determination

    PubMed Central

    Paller, CJ; Rudek, MA; Zhou, XC; Wagner, WD; Hudson, TS; Anders, N; Hammers, HJ; Dowling, D; King, S; Antonarakis, ES; Drake, CG; Eisenberger, MA; Denmeade, SR; Rosner, GL; Carducci, MA

    2015-01-01

    Background New therapies are being explored as therapeutic options for men with biochemically recurrent prostate cancer (BRPC) who wish to defer androgen deprivation therapy. MPX is pulverized muscadine grape (Vitis rotifundolia) skin that contains ellagic acid, quercetin, and resveratrol and demonstrates preclinical activity against prostate cancer cells in vitro. Methods In the phase I portion of this phase I/II study non-metastatic BRPC patients were assigned to increasing doses of MPX (Muscadine Naturals Inc., Clemmons, NC) in cohorts of 2 patients, with 6 patients at the highest dose, using a modified continual reassessment method. Initial dose selection was based on preclinical data showing the equivalent of 500 to 4,000 mg of MPX to be safe in mouse models. The primary end point was the recommended phase II dosing regimen. Results The cohort (n=14, 71% Caucasian, 29% black) had a median follow-up of 19.2 (6.2 – 29.7) months, median age 61 years, and median Gleason of 7. Four patients had possibly related gastrointestinal symptoms, including grade 1 flatulence, grade 1 soft stools, and grade 1 eructation. No other related adverse events were reported and one patient reported improvement of chronic constipation. Six of 14 patients came off study for disease progression (5 metastatic, 1 rising PSA) after exposure for a median of 15 months. One patient came off for myasthenia gravis that was unrelated to treatment. Seven patients remain on study. The lack of dose limiting toxicities led to the selection of 4000 mg/d as the highest dose for further study. Median within-patient PSADT increased by 5.3 months (non-significant, p = 0.17). No patients experienced a maintained decline in serum PSA from baseline. Conclusions These data suggest that 4000 mg of MPX is safe, and exploratory review of a lengthening in PSADT of a median of 5.3 months supports further exploration of MPX. Both low dose (500 mg) and high dose (4,000 mg) MPX are being further investigated in a

  14. A phase I study of muscadine grape skin extract in men with biochemically recurrent prostate cancer: Safety, tolerability, and dose determination.

    PubMed

    Paller, Channing J; Rudek, Michelle A; Zhou, Xian C; Wagner, William D; Hudson, Tamaro S; Anders, Nicole; Hammers, Hans J; Dowling, Donna; King, Serina; Antonarakis, Emmanuel S; Drake, Charles G; Eisenberger, Mario A; Denmeade, Samuel R; Rosner, Gary L; Carducci, Michael A

    2015-10-01

    New therapies are being explored as therapeutic options for men with biochemically recurrent prostate cancer (BRPC) who wish to defer androgen deprivation therapy. MPX is pulverized muscadine grape (Vitis rotundifolia) skin that contains ellagic acid, quercetin, and resveratrol and demonstrates preclinical activity against prostate cancer cells in vitro. In the phase I portion of this phase I/II study, non-metastatic BRPC patients were assigned to increasing doses of MPX (Muscadine Naturals. Inc., Clemmons, NC) in cohorts of two patients, with six patients at the highest dose, using a modified continual reassessment method. Initial dose selection was based on preclinical data showing the equivalent of 500 to 4,000 mg of MPX to be safe in mouse models. The primary endpoint was the recommended phase II dosing regimen. The cohort (n = 14, 71% Caucasian, 29% black) had a median follow-up of 19.2 (6.2-29.7) months, median age of 61 years, and median Gleason score of 7. Four patients had possibly related gastrointestinal symptoms, including grade 1 flatulence, grade 1 soft stools, and grade 1 eructation. No other related adverse events were reported and one patient reported improvement of chronic constipation. Six of 14 patients came off study for disease progression (five metastatic, one rising PSA) after exposure for a median of 15 months. One patient came off for myasthenia gravis that was unrelated to treatment. Seven patients remain on study. The lack of dose-limiting toxicities led to the selection of 4,000 mg/d as the highest dose for further study. Median within-patient PSADT increased by 5.3 months (non-significant, P = 0.17). No patients experienced a maintained decline in serum PSA from baseline. These data suggest that 4,000 mg of MPX is safe, and exploratory review of a lengthening in PSADT of a median of 5.3 months supports further exploration of MPX. Both low-dose (500 mg) and high-dose (4,000 mg) MPX are being further investigated in a randomized

  15. The Mars Plant Growth Experiment and Implications for Planetary Protection

    NASA Astrophysics Data System (ADS)

    Smith, Heather

    Plants are the ultimate and necessary solution for O2 production at a human base on Mars. Currently it is unknown if seeds can germinate on the Martian surface. The Mars Plant growth experiment (MPX) is a proposal for the first step in the development of a plant- based O2 production system by demonstrating plant germination and growth on the Martian surface. There is currently no planetary protection policy in place that covers plants on the Martian surface. We describe a planetary protection plan in compliance with NASA and COSPAR policy for a closed plant growth chamber on a Mars rover. We divide the plant growth chamber into two categories for planetary protection, the Outside: the outside of the chamber exposed to the Martian environment, and the Inside: the inside of the chamber which is sealed off from Mars atmosphere and contains the plant seeds and ancillary components for seed growth. We will treat outside surfaces of the chamber as other outside surfaces on the rover, wiped with a mixture of isopropyl alcohol and water as per Category IVb planetary protection requirements. All internal components of the MPX except the seeds and camera (including the water system, the plant growth stage and interior surface walls) will be sterilized by autoclave and subjected to sterilizing dry heat at a temperature of 125°C at an absolute humidity corresponding to a relative humidity of less than 25 percent referenced to the standard conditions of 0°C and 760 torr pressure. The seeds and internal compartments of the MPX in contact with the growth media will be assembled and tested to be free of viable microbes. MPX, once assembled, cannot survive Dry Heat Microbial Reduction. The camera with the radiation and CO2 sensors will be sealed in their own container and vented through HEPA filters. The seeds will be vernalized (microbe free) as per current Space Station methods described by Paul et al. 2001. Documentation of the lack of viable microbes on representative seeds

  16. High critical current density over 1 MA cm-2 at 13 T in BaZrO3 incorporated Ba(Fe,Co)2As2 thin film

    NASA Astrophysics Data System (ADS)

    Lee, Jongmin; Jiang, Jianyi; Kametani, Fumitake; Oh, Myeong Jun; Weiss, Jeremy D.; Collantes, Yesusa; Seo, Sehun; Yoon, Sejun; Tarantini, Chiara; Jo, Youn Jung; Hellstrom, Eric E.; Lee, Sanghan

    2017-08-01

    Achieving high critical current density (J c) under a high magnetic field in Fe based superconductors is indispensable for practical applications. Here we report that high critical current density over 1 MA cm-2 in high field (13 T) can be achieved in BaZrO3 (BZO) incorporated Ba(Fe,Co)2As2 (Co-Ba122) thin film grown on CaF2 substrate using pulsed laser deposition. The magnetization J c of Co-Ba122 thin film incorporated with 2 mol.% BZO reaches 1.3 MA cm-2 (Hǁc, 13 T and 4.2 K), 14 times higher than that of pure Co-Ba122 thin film. Transmission electron microscopy observation revealed that BZO forms nanorods of ˜4 nm in average diameter with mean separation of 10-11 nm which corresponds to a matching field of about 17-20 T. Incorporating BZO in Co-Ba122 thin films led to a strong vortex pinning effect and a significant enhancement of J c because a high density of BZO nanorods could form in the superconducting matrix without significant degradation of T c, and the diameter of BZO nanorods is approximately twice the coherence length of Co-Ba122 (ξ ab(0) ˜ 2.5 nm) which is the optimal size as pinning centers.

  17. Full STR profile of a 67-year-old bone found in a fresh water lake.

    PubMed

    Courts, Cornelius; Madea, Burkhard

    2011-01-01

    DNA extraction from and DNA typing of fresh water-exposed aged bone specimens poses a challenging task and is not very well examined. This study presents a new method to extract typable DNA from such problematic bone specimens. The procedure comprises low-heat drilling and cryogrinding, mild lysis conditions, and silica-column-based DNA cleaning. DNA quantity is assessed by quantitative PCR prior to short tandem repeat (STR) amplification. The procedure was employed with a 67-year-old tibia bone fragment recovered from a fresh water lake and succeeded to produce a full STR profile using the MPX-SP1 and MPX-SP2 mini-STR kits and a partial profile with 12 successfully amplified STRs using the Identifiler STR kit. The new method for the extraction of DNA from aged fresh water-exposed bone specimens presented herein was successfully applied to prepare DNA of sufficient quality and quantity to generate a full STR profile.

  18. Pox-like lesions and haemorrhagic fever in two concurrent cases in the Central African Republic: case investigation and management in difficult circumstances

    PubMed Central

    Froeschl, Guenter; Kayembe, Pitchou Kasongo

    2015-01-01

    Cases of monkeypox in humans are frequently reported from the Democratic Republic of Congo. The few reports from the Central African Republic have been limited to cases in the far South closely bordering the Congos. Team members of an international medical organisation have suspected clinically two human cases of MPX, associated with clinical signs of coagulopathy and haemorrhage in the North of the country. Key findings were history of a squirrel, fever and vesicular dermal eruptions. Subsequently patients developed profuse epistaxis and hematemesis, associated with clinical signs of shock. Both patients were isolated and treated symptomatically. Samples were sent to a regional reference laboratory, who initially issued a confirmation of the suspected diagnosis of MPX in both cases. The result was later revised, and additional analyses of samples could not confirm the diagnosis. PMID:26664524

  19. Nonhuman Primates are Protected from Smallpox Virus or Monkeypox Virus Challenges by the Antiviral Drug ST-246

    DTIC Science & Technology

    2009-06-01

    use of a licensed smallpox vaccine; however, potential serious side effects (e.g., eczema vaccinatum, progressive vaccinia, myocarditis, and death...patient suffering from acute eczema vaccinatum (12, 21). The NHP model is likely to be predictive of human disease outcome in that VAR- or MPX-induced...Karem, V. Olson, W. Davidson, G. Trindade, T. Bolken, R. Jordan, D. Tien, and J. Marcinak. 2008. Severe eczema vaccina- tum in a household contact of a

  20. Trypanosoma cruzi mitochondrial tryparedoxin peroxidase is located throughout the cell and its pull down provides one step towards the understanding of its mechanism of action.

    PubMed

    Peloso, E F; Dias, L; Queiroz, R M L; Leme, A F P Paes; Pereira, C N; Carnielli, C M; Werneck, C C; Sousa, M V; Ricart, C A O; Gadelha, F R

    2016-01-01

    Trypanosoma cruzi depends on the effectiveness of redox metabolism to survive and ensure infection in the host. Homeostasis of redox metabolism in T. cruzi is achieved by the actions of several proteins that differ in many aspects from host proteins. Although extensive research has been performed examining hydroperoxide cytosolic antioxidant defense centered on trypanothione, the mechanisms of mitochondrial antioxidant defense are not yet known. The aim of this study was to elucidate the partners of TcMPx antioxidant pathway and to determine the influence of the cellular context (physiological versus oxidative stress). Through co-precipitation coupled with a mass spectrometry approach, a variety of proteins were detected under physiological and oxidative stress conditions. Interestingly, functional category analysis of the proteins identified under physiological conditions showed that they were involved in the stress response, oxidoreduction, thiol transfer, and metabolic processes; this profile is distinct under oxidative stress conditions likely due to structural alterations. Our findings help to elucidate the reactions involving TcMPx and most importantly also reveal that this protein is present throughout the cell and that its interaction partners change following oxidative stress exposure. The involvement and significance of the proteins found to interact with TcMPx and other possible functions for this protein are discussed widening our knowledge regarding T. cruzi mitochondrial antioxidant defenses. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Variola and Monkeypox Viruses Utilize Conserved Mechanisms of Virion Motility and Release That Depend on Abl and Src Family Tyrosine Kinases▿ †

    PubMed Central

    Reeves, Patrick M.; Smith, Scott K.; Olson, Victoria A.; Thorne, Steve H.; Bornmann, William; Damon, Inger K.; Kalman, Daniel

    2011-01-01

    Vaccinia virus (VacV) enters mammalian cells, replicates extranuclearly, and produces virions that move to the cell surface along microtubules, fuse with the plasma membrane, and move from infected cells toward apposing cells on actin-filled membranous protrusions or actin tails. To form actin tails, cell-associated enveloped virions (CEV) require Abl and Src family tyrosine kinases. Furthermore, release of CEV from the cell requires Abl but not Src family tyrosine kinases and is blocked by imatinib mesylate (STI-571; Gleevec), an Abl family kinase inhibitor used to treat chronic myelogenous leukemia in humans. Here we demonstrate that the Poxviridae family members monkeypox virus (MPX) and variola virus (VarV) use conserved mechanisms for actin motility and extracellular enveloped virion (EEV) release. Furthermore, we show that imatinib mesylate is effective in a mouse model of infection with VacV, whether delivered prophylactically or postinfection, and restricts spread of virions from the site of inoculation. While inhibitors of both Src and Abl family kinases, such as dasatinib (BMS-354825; Sprycel), are effective in limiting dissemination of VacV, VarV, and MPX in vitro, members of this class of drugs appear to have immunosuppressive effects in vivo that preclude their use as anti-infectives. Together, these data suggest a possible utility for imatinib mesylate in treating smallpox or MPX infections or complications associated with vaccination. PMID:20962097

  2. Development of Fe-based superconducting wires for liquid-hydrogen level sensors

    NASA Astrophysics Data System (ADS)

    Ishida, S.; Tsuchiya, Y.; Mawatari, Y.; Eisaki, H.; Nakano, A.; Yoshida, Y.

    2017-07-01

    We developed liquid-hydrogen (LH2) level sensors with Ba(Fe1-x Co x )2As2 superconducting wires (Co-Ba122 wires) as their detection elements. We fabricated Co-Ba122 wires with different Co concentrations x by using the powder-in-tube method. The superconducting transition temperatures of the wires were successfully controlled in the range of 20-25 K by changing x from 0.06 to 0.10. The resistance-temperature curves of the wires exhibited sharp superconducting transitions with widths of 0.5-1.0 K. In addition, we performed an operation test of the Co-Ba122 level sensors with LH2. Close correspondence between the output resistance and the actual LH2 level was observed for a sensor equipped with x = 0.09 wire, demonstrating that this sensor can accurately measure LH2 levels.

  3. 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

  4. 75 FR 54154 - Medical Devices; Availability of Safety and Effectiveness Summaries for Premarket Approval...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-03

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

  5. Head-To-Head Assessment of Diagnostic Performance of Testosterone Immunoassays in Patients With Polycystic Ovary Syndrome.

    PubMed

    Schüring, Andreas N; Nolte, Stefan; Fobker, Manfred; Kannenberg, Frank; Nofer, Jerzy-Roch

    2016-09-01

    Determination of plasma testosterone is critical for the proper diagnosis of polycystic ovary syndrome (PCOS), but the interpretation of biochemical tests is hampered by inadequate specificity and precision of available immunoassays. We here compared the diagnostic performance of three testosterone immunoassays (Advia Centaur, Immulite 2000 XPi, Cobas e411) in PCOS patients using receiver operator characteristics curve analysis. Plasma levels of testosterone, androstendione, dehydroepiandrosterone sulfate, 17-hydroxyprogesterone, estradiol, progesterone, steroid hormone binding globulin, luteinizing hormone, and follicular stimulating hormone were determined in 188 patients with PCOS and 202 controls. Free testosterone (fT) levels and free androgen index (FAI) were calculated. Testosterone levels measured on Advia Centaur, Immulite 2000 XPi, and Cobas e411 showed clear linear relationship to each other. Testosterone measured with Advia Centaur showed discriminatory performance superior to Immulite 2000 XPi and Cobas e411. Calculation of fT or FAI improved the performance of Advia Centaur and Immulite 2000 XPi, which nevertheless performed better than Cobas e411. The performance of other parameters was inferior to that of testosterone, fT, and FAI. Present study documents striking differences between testosterone immunoassays with respect to their capacity to identify PCOS patients and favors the use of calculated parameters reflecting active testosterone in plasma. © 2015 Wiley Periodicals, Inc.

  6. The eutT gene of Salmonella enterica Encodes an oxygen-labile, metal-containing ATP:corrinoid adenosyltransferase enzyme.

    PubMed

    Buan, Nicole R; Suh, Sang-Jin; Escalante-Semerena, Jorge C

    2004-09-01

    The eutT gene of Salmonella enterica was cloned and overexpressed, and the function of its product was established in vivo and in vitro. The EutT protein has an oxygen-labile, metal-containing ATP:co(I)rrinoid adenosyltransferase activity associated with it. Functional redundancy between EutT and the housekeeping ATP:co(I)rrinoid adenosyltransferase CobA enzyme was demonstrated through phenotypic analyses of mutant strains. Lack of CobA and EutT blocked ethanolamine utilization. EutT was necessary and sufficient for growth of an S. enterica cobA eutT strain on ethanolamine as a carbon and energy or nitrogen source. A eutT+ gene provided in trans corrected the adenosylcobalamin-dependent transcription of a eut-lacZ operon fusion in a cobA strain. Cell extracts enriched for EutT protein contained strong, readily detectable ATP:co(I)rrinoid adenosyltransferase activity. The activity was only detected in extracts maintained under anoxic conditions, with complete loss of activity upon exposure to air or treatment with the Fe2+ ion chelator bathophenanthroline. While the involvement of another metal ion cannot be ruled out, the observed sensitivity to air and bathophenanthroline suggests involvement of Fe2+. We propose that the EutT protein is a unique metal-containing ATP:co(I)rrinoid adenosyltransferase. It is unclear whether the metal ion plays a structural or catalytic role.

  7. Cryoplasty Versus Conventional Balloon Angioplasty of the Femoropopliteal Artery in Diabetic Patients: Long-Term Results from a Prospective Randomized Single-Center Controlled Trial

    SciTech Connect

    Spiliopoulos, Stavros Katsanos, Konstantinos; Karnabatidis, Dimitris; Diamantopoulos, Athanasios; Kagadis, George C.; Christeas, Nikolaos; Siablis, Dimitris

    2010-10-15

    The purpose of this study was to investigate the immediate and long-term results of cryoplasty versus conventional balloon angioplasty in the femoropopliteal artery of diabetic patients. Fifty diabetic patients (41 men, mean age 68 years) were randomized to cryoplasty (group CRYO; 24 patients with 31 lesions) or conventional balloon angioplasty (group COBA; 26 patients with 34 lesions) of the femoropopliteal artery. Technical success was defined as <30% residual stenosis without any adjunctive stenting. Primary end points included technical success, primary patency, binary in-lesion restenosis (>50%), and freedom from target lesion recanalization. Cox proportional hazards regression analysis was performed to adjust for confounding factors of heterogeneity. In total, 61.3% (19 of 31) in group CRYO and 52.9% (18 of 34) in group COBA were de novo lesions. More than 70% of the lesions were Transatlantic Inter-Society Consensus (TASC) B and C in both groups, and 41.4% of the patients in group CRYO and 38.7% in group COBA suffered from critical limb ischemia. Immediate technical success rate was 58.0% in group CRYO versus 64.0% in group COBA (p = 0.29). According to 3-year Kaplan-Meier estimates, there were no significant differences with regard to patient survival (86.8% in group CRYO vs. 87.0% in group COBA, p = 0.54) and limb salvage (95.8 vs. 92.1% in groups CRYO and COBA, respectively, p = 0.60). There was a nonsignificant trend of increased binary restenosis in group CRYO (hazard ratio [HR] 1.3; 95% CI 0.6-2.6, p = 0.45). Primary patency was significantly lower in group CRYO compared with group COBA (HR 2.2; 95% CI 1.1-4.3, p = 0.02). Significantly more repeat intervention events because of recurrent symptoms were required in group CRYO (HR 2.5; 95% CI 1.2-5.3, p = 0.01). Cryoplasty was associated with lower primary patency and more clinically driven repeat procedures after long-term follow-up compared with conventional balloon angioplasty.

  8. Commutability and concordance of four hepatitis B virus DNA assays in an international multicenter study.

    PubMed

    Maasoumy, Benjamin; Bremer, Birgit; Lehmann, Patrick; Marins, Ed G; Michel-Treil, Véronique; Simon, Christian O; Njoya, Merlin; Cornberg, Markus; Paxinos, Ellen; Manns, Michael P; Vermehren, Johannes; Sarrazin, Christoph; Sohn, Ji Yeon; Cho, Yunjung; Wedemeyer, Heiner

    2017-08-01

    HBV DNA is the most important molecular marker in hepatitis B, used to determine treatment indication and monitoring. Most patients require lifelong hepatitis B virus (HBV) management, thus viral load (VL) monitoring may be performed at different laboratories, with different HBV assays, which may result in different VL results. This multicenter study compares the commutability and concordance of results from four different HBV DNA assays: CAP/CTM HBVv2, HPS/CTM HBVv2 and the new cobas 6800/8800 HBV and cobas 4800 HBV assays. Across all four assays, HBV limit of detection (LoD) and linearity at lower concentrations were assessed using panels traceable to the World Health Organization international standard, and concordance was investigated at the important medical decision cutoffs 2000 and 20,000 IU/ml, using specimens from HBV-positive patients. The calculated LoD via a probit curve was 2.7 IU/ml for cobas 6800/8800 HBV, 2.8 IU/ml for cobas 4800 HBV, 9.6 IU/ml for CAP/CTM HBVv2, and 6.2 IU/ml for HPS/CTM HBVv2. The average accuracy was comparable between cobas 6800/8800 HBV, cobas 4800 HBV and CAP/CTM HBVv2 (0.04-0.05 log10 IU/ml), while a slightly lower accuracy was documented for HPS/CTM HBVv2 (-0.16 log10 IU/ml). A total of 211-245 clinical samples were used for a pairwise comparison. Mean paired log differences ranged from -0.17 log10 IU/ml to -0.01 log10 IU/ml. Coefficient of determination was over 98% for all pairs with high overall percent agreement at the 2000 and 20,000 IU/ml cutoffs (from 91.7% to 96.3%). In a subset of samples with VL±0.5 log10 to the 2000 and 20,000 IU/ml thresholds, concordance was still 72% and 82%, respectively. The new cobas 6800/8800 HBV and 4800 HBV assays show high accuracy in samples with low-level viremia and a high concordance with the established HBV tests, CAP/CTM HBVv2 and HPS/CTM HBVv2, at 2000 and 20,000 IU/ml. Thus, all four HBV assays have high commutability and may be used interchangeably in routine clinical practice.

  9. Commutability and concordance of four hepatitis B virus DNA assays in an international multicenter study

    PubMed Central

    Maasoumy, Benjamin; Bremer, Birgit; Lehmann, Patrick; Marins, Ed G.; Michel-Treil, Véronique; Simon, Christian O.; Njoya, Merlin; Cornberg, Markus; Paxinos, Ellen; Manns, Michael P.; Vermehren, Johannes; Sarrazin, Christoph; Sohn, Ji Yeon; Cho, Yunjung; Wedemeyer, Heiner

    2017-01-01

    Background HBV DNA is the most important molecular marker in hepatitis B, used to determine treatment indication and monitoring. Most patients require lifelong hepatitis B virus (HBV) management, thus viral load (VL) monitoring may be performed at different laboratories, with different HBV assays, which may result in different VL results. This multicenter study compares the commutability and concordance of results from four different HBV DNA assays: CAP/CTM HBVv2, HPS/CTM HBVv2 and the new cobas 6800/8800 HBV and cobas 4800 HBV assays. Methods Across all four assays, HBV limit of detection (LoD) and linearity at lower concentrations were assessed using panels traceable to the World Health Organization international standard, and concordance was investigated at the important medical decision cutoffs 2000 and 20,000 IU/ml, using specimens from HBV-positive patients. Results The calculated LoD via a probit curve was 2.7 IU/ml for cobas 6800/8800 HBV, 2.8 IU/ml for cobas 4800 HBV, 9.6 IU/ml for CAP/CTM HBVv2, and 6.2 IU/ml for HPS/CTM HBVv2. The average accuracy was comparable between cobas 6800/8800 HBV, cobas 4800 HBV and CAP/CTM HBVv2 (0.04–0.05 log10 IU/ml), while a slightly lower accuracy was documented for HPS/CTM HBVv2 (−0.16 log10 IU/ml). A total of 211–245 clinical samples were used for a pairwise comparison. Mean paired log differences ranged from −0.17 log10 IU/ml to −0.01 log10 IU/ml. Coefficient of determination was over 98% for all pairs with high overall percent agreement at the 2000 and 20,000 IU/ml cutoffs (from 91.7% to 96.3%). In a subset of samples with VL±0.5 log10 to the 2000 and 20,000 IU/ml thresholds, concordance was still 72% and 82%, respectively. Conclusions The new cobas 6800/8800 HBV and 4800 HBV assays show high accuracy in samples with low-level viremia and a high concordance with the established HBV tests, CAP/CTM HBVv2 and HPS/CTM HBVv2, at 2000 and 20,000 IU/ml. Thus, all four HBV assays have high commutability and may be

  10. Prospective evaluation of a new automated nucleic acid extraction system using routine clinical respiratory specimens.

    PubMed

    Mengelle, C; Mansuy, J-M; Sandres-Sauné, K; Barthe, C; Boineau, J; Izopet, J

    2012-06-01

    The aim of the study was to evaluate the MagNA Pure 96™ nucleic acid extraction system using clinical respiratory specimens for identifying viruses by qualitative real-time PCR assays. Three extraction methods were tested, that is, the MagNA Pure LC™, the COBAS Ampliprep™, and the MagNA Pure 96™ with 10-fold dilutions of an influenza A(H1N1)pdm09 sample. Two hundred thirty-nine respiratory specimens, 35 throat swabs, 164 nasopharyngeal specimens, and 40 broncho-alveolar fluids, were extracted with the MagNA Pure 96™ and the COBAS Ampliprep™ instruments. Forty COBAS Ampliprep™ positive samples were also tested. Real-time PCRs were used to identify influenza A and influenza A(H1N1)pdm09, rhinovirus, enterovirus, adenovirus, varicella zoster virus, cytomegalovirus, and herpes simplex virus. Similar results were obtained on RNA extracted from dilutions of influenza A(H1N1)pdm09 with the three systems: the MagNA Pure LC™, the COBAS Ampliprep™, and the MagNA Pure 96™. Data from clinical respiratory specimens extracted with the MagNA Pure 96™ and COBAS Ampliprep™ instruments were in 98.5% in agreement (P < 0.0001) for influenza A and influenza A(H1N1)pdm09. Data for rhinovirus were in 97.3% agreement (P < 0.0001) and in 96.8% agreement for enterovirus. They were in 100% agreement for adenovirus. Data for cytomegalovirus and HSV1-2 were in 95.2% agreement (P < 0.0001). The MagNA Pure 96™ instrument is easy-to-use, reliable, and has a high throughput for extracting total nucleic acid from respiratory specimens. These extracts are suitable for molecular diagnosis with any type of real-time PCR assay.

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

    PubMed

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

    2017-08-08

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

  12. Application of a multiplex PCR to cervical cells collected by a paper smear for the simultaneous detection of all mucosal human papillomaviruses (HPVs) and typing of high-risk HPV types 16 and 18.

    PubMed

    Shukla, Shirish; Bharti, Alok C; Mahata, Sutapa; Hussain, Showket; Hedau, Suresh; Sharma, Rajyashri; Pillai, M Radhakrishna; Krishna, Sudhir; Chiplunkar, Shubhada; Tongaonkar, Hemant; Das, Bhudev C

    2010-11-01

    A simple paper smear (PS) method for dry collection and storage of cervical specimens was employed to develop an easy multiplex (MPX) PCR for simultaneous detection of generic human papillomaviruses (HPVs) as well as typing of the high-risk HPV-16 and -18, the two clinically most important HPV genotypes, which are responsible for more than 80 % of cervical cancers. Multiplexing was performed with a small amount of DNA eluted by boiling from a single PS punch in a single tube and using a mixture of four pairs of primers specific for the HPV L1 consensus sequence, HPV-16, HPV-18 and the β-globin gene. Sixty HPV-positive biopsies and corresponding PS specimens from cervical cancer patients as well as cervical smears from 100 healthy women with or without abnormal cytology were collected both as PSs and in PBS. Detection of HPV DNA from cervical biopsies collected in PBS and corresponding cervical scrapes on a PS or in PBS by conventional and MPX-PCR showed a concordance of 100 % and adequacy of 93 %. A similar comparative study in cervical scrapes from normal women also revealed 100 % concordance. The technique was validated in a multicentric study at four different national laboratories. PSs collected by different centres showed variable adequacy (73-82 %) but the use of multiple PS discs for DNA extraction significantly increased the adequacy. Integration of PSs with MPX-PCR for the detection and typing of HPVs is a highly convenient, efficient, simple and cost-effective method for large-scale clinico-epidemiological studies and is also suitable for HPV vaccine monitoring programmes in resource-poor settings.

  13. Evidence for broader autism phenotype characteristics in parents from multiple-incidence autism families.

    PubMed

    Bernier, Raphael; Gerdts, Jennifer; Munson, Jeff; Dawson, Geraldine; Estes, Annette

    2012-02-01

    The broader autism phenotype (BAP) was assessed in parents who have two or more children with autism spectrum disorder (ASD) (multiplex (MPX) autism), parents who have no more than one child with ASD (simplex autism), parents who have a child with developmental delay without ASD, and parents who have typically developing children. Clinicians, naive to parent group membership status, rated BAP characteristics from videotaped administration of the Broader Autism Phenotype Symptom Scale (BPASS). Differences among groups in BPASS scores in the four assessed domains (social motivation, conversational skills, expressiveness, and restricted interests) were examined using multivariate ANOVA and post hoc comparisons. Further, ratings of videotapes by observers naïve to family status were compared with live, non-naive ratings by observers who were aware of family status (non-naïve). Findings demonstrate that the BPASS is an instrument resistant to rater bias. Parents from MPX autism families showed significantly more autism phenotype characteristics than the parents in the other groups. Moreover, the parents from simplex autism families did not differ from the parents of children with developmental delay or typical development. Finally, no differences between live, non-naive ratings and videotaped, naive ratings were observed. These findings suggest that characteristics of the BAP, specifically in the social and communication domains, are present in MPX autism parents to a greater degree than simplex autism and control parents. Further, the results provide support for the notion that genetic transmission mechanisms may differ between families with more than one child with autism and families with only one child with autism.

  14. Phospholipase B activity and organophosphorus compound toxicity in cultured neural cells

    SciTech Connect

    Read, David J.; Langford, Lynda; Barbour, Helen R.; Forshaw, Philip J.; Glynn, Paul . E-mail: pg8@le.ac.uk

    2007-03-15

    Organophosphorus compounds (OP) such as phenyl saligenin phosphate (PSP) and mipafox (MPX) which cause delayed neuropathy, inhibit neuropathy target esterase (NTE), while OPs such as paraoxon (PXN) react more readily with acetylcholinesterase. In yeast and mammalian cell lines, NTE has been shown to have phospholipase B (PLB) activity which deacylates intracellular phosphatidylcholine to glycerophosphocholine (GroPCho) and can be detected by metabolic labeling with [{sup 14}C]choline. Here we investigated PLB activity in primary cultures of mouse neural cells. In cortical and cerebellar granule neurons and astrocytes, [{sup 14}C]GroPCho labeling was inhibited by PSP and MPX: phenyl dipentylphosphinate (PDPP), a non-neuropathic NTE inhibitor, was more potent, while PXN, was substantially less so. In all three cell types, conversion of [{sup 14}C]phosphatidylcholine to [{sup 14}C]GroPCho over 24 h was relatively small (2.3-14%). Consequently, even with > 80% inhibition of [{sup 14}C]GroPCho production, increased [{sup 14}C]phosphatidylcholine was not detected. At concentrations of 1-10 {mu}M, only PSP was cytotoxic to cortical and cerebellar granule neurons after 24-h exposure. Moreover, dramatic changes in glial cell morphology were induced by PSP, but not PDPP or MPX, with rapid (2-3 h) rounding up of astrocytes and of Schwann cells in cultures of dissociated mouse dorsal root ganglia. We conclude that PLB activity is present in a variety of cultured mouse neural cell types but that acute loss of this activity is not cytotoxic. Conversely, the rapid toxic effects of PSP in vitro suggest that a serine hydrolase distinct from NTE is required continuously by neurons and glia.

  15. Characterization of Monkeypox virus infection in African rope squirrels (Funisciurus sp.).

    PubMed

    Falendysz, Elizabeth A; Lopera, Juan G; Doty, Jeffrey B; Nakazawa, Yoshinori; Crill, Colleen; Lorenzsonn, Faye; Kalemba, Lem's N; Ronderos, Monica D; Mejia, Andres; Malekani, Jean M; Karem, Kevin; Carroll, Darin S; Osorio, Jorge E; Rocke, Tonie E

    2017-08-01

    Monkeypox (MPX) is a zoonotic disease endemic in Central and West Africa and is caused by Monkeypox virus (MPXV), the most virulent Orthopoxvirus affecting humans since the eradication of Variola virus (VARV). Many aspects of the MPXV transmission cycle, including the natural host of the virus, remain unknown. African rope squirrels (Funisciurus spp.) are considered potential reservoirs of MPXV, as serosurveillance data in Central Africa has confirmed the circulation of the virus in these rodent species [1,2]. In order to understand the tissue tropism and clinical signs associated with infection with MPXV in these species, wild-caught rope squirrels were experimentally infected via intranasal and intradermal exposure with a recombinant MPXV strain from Central Africa engineered to express the luciferase gene. After infection, we monitored viral replication and shedding via in vivo bioluminescent imaging, viral culture and real time PCR. MPXV infection in African rope squirrels caused mortality and moderate to severe morbidity, with clinical signs including pox lesions in the skin, eyes, mouth and nose, dyspnea, and profuse nasal discharge. Both intranasal and intradermal exposures induced high levels of viremia, fast systemic spread, and long periods of viral shedding. Shedding and luminescence peaked at day 6 post infection and was still detectable after 15 days. Interestingly, one sentinel animal, housed in the same room but in a separate cage, also developed severe MPX disease and was euthanized. This study indicates that MPXV causes significant pathology in African rope squirrels and infected rope squirrels shed large quantities of virus, supporting their role as a potential source of MPXV transmission to humans and other animals in endemic MPX regions.

  16. Preliminary Geological Map of the Ac-H-9 Occator Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Buczkowski, D.; Yingst, R. A.; Williams, D. A.; Mest, S. C.; Scully, J. E. C.; Crown, D. A.; Schenk, P.; Jaumann, R.; Roatsch, T.; Preusker, F.; Platz, T.; Nathues, A.; Hoffmann, M.; Schäfer, M.; Marchi, S.; De Sanctis, M. C.; Raymond, C. A.; Russell, C. T.

    2015-12-01

    We used geologic mapping applied to Dawn spacecraft data as a tool to understand the geologic history of the Ac-H-9 Occator quadrangle of dwarf planet Ceres. This region, located between 22˚S-22˚N and 216-288˚E, is one of two longitudinally distinct regions on Ceres where ESA Herschel space telescope data suggested a release of water vapor [1] and hosts: 1) the 92 km diameter impact crater Occator in the NW of the quadrangle, whose rim is scalloped and whose interior encompasses Hubble "Bright Spot 5"; 2) the 115 km diameter crater Kirnis, a degraded crater that contains a large dome-like feature on the western half of its floor; and 3) regional linear structures, that both cut crater rims (including Occator and Kirnis) and affect crater shapes. Key goals of the ongoing mapping are to 1) determine the source of the bright spots in Occator; 2) determine if the dome-like feature in Kirnis resulted from a mass-wasting or is a product of uplift; and 3) assess the relationships between linear structural features and impact craters, including the effects of surface stress regimes on crater formation and modification. At the time of this writing geologic mapping was performed on Framing Camera (FC) mosaics from late Approach (1.3 km/px) and Survey (415 m/px) orbits, including clear filter and color images and digital terrain models derived from stereo images. In Fall 2015 images from the High Altitude Mapping Orbit (140 m/px) will be used to refine the mapping, followed by Low Altitude Mapping Orbit (35 m/px) images starting in December 2015. Support of the Dawn Instrument, Operations, and Science Teams is acknowledged. This work is supported by grants from NASA through the Dawn project, and from the German and Italian Space Agencies. Reference: [1] Küppers, M., et al. (2014). Nature, v. 505, 525-527.

  17. Characterization of Monkeypox virus infection in African rope squirrels (Funisciurus sp.)

    USGS Publications Warehouse

    Falendysz, Elizabeth; Lopera, Juan G.; Doty, Jeffrey B.; Nakazawa, Yoshinori J.; Crill, Colleen; Lorenzsonn, Faye; Kalemba, Lem's N.; Ronderos, Monica; Meija, Andres; Malekani, Jean M.; Karem, Kevin L.; Caroll, Darrin; Osorio, Jorge E.; Rocke, Tonie E.

    2017-01-01

    Monkeypox (MPX) is a zoonotic disease endemic in Central and West Africa and is caused by Monkeypox virus (MPXV), the most virulent Orthopoxvirus affecting humans since the eradication of Variola virus (VARV). Many aspects of the MPXV transmission cycle, including the natural host of the virus, remain unknown. African rope squirrels (Funisciurus spp.) are considered potential reservoirs of MPXV, as serosurveillance data in Central Africa has confirmed the circulation of the virus in these rodent species [1,2]. In order to understand the tissue tropism and clinical signs associated with infection with MPXV in these species, wild-caught rope squirrels were experimentally infected via intranasal and intradermal exposure with a recombinant MPXV strain from Central Africa engineered to express the luciferase gene. After infection, we monitored viral replication and shedding via in vivo bioluminescent imaging, viral culture and real time PCR. MPXV infection in African rope squirrels caused mortality and moderate to severe morbidity, with clinical signs including pox lesions in the skin, eyes, mouth and nose, dyspnea, and profuse nasal discharge. Both intranasal and intradermal exposures induced high levels of viremia, fast systemic spread, and long periods of viral shedding. Shedding and luminescence peaked at day 6 post infection and was still detectable after 15 days. Interestingly, one sentinel animal, housed in the same room but in a separate cage, also developed severe MPX disease and was euthanized. This study indicates that MPXV causes significant pathology in African rope squirrels and infected rope squirrels shed large quantities of virus, supporting their role as a potential source of MPXV transmission to humans and other animals in endemic MPX regions.

  18. Preliminary Geological Map of the Ac-H-5 Fejokoo Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Hughson, K.; Russell, C.; Williams, D. A.; Buczkowski, D.; Mest, S. C.; Scully, J. E. C.; Hiesinger, H.; Platz, T.; Ruesch, O.; Schenk, P.; Frigeri, A.; Jaumann, R.; Roatsch, T.; Preusker, F.; Nathues, A.; Hoffmann, M.; Schäfer, M.; Park, R. S.; Marchi, S.; De Sanctis, M. C.; Raymond, C. A.

    2015-12-01

    In order to enable methodical geologic mapping of the surface of Ceres the Dawn Science Team divided its surface into fifteen quadrangles. A preliminary map of the Fejokoo quadrangle is presented here. This region, located between 21˚-66˚N and 270-0˚E, hosts four primary features: (1) the centrally located, 90 km diameter, distinctly hexagonal impact crater Fejokoo; (2) a small unnamed crater midway up the eastern boundary of the quadrangle which contains and is surrounded by bright material; (3) an unnamed degraded crater NW of Fejokoo that contains lobate material deposits on both sides of the crater's S rim; and (4) a heavily cratered unit in the NW portion of the quadrangle. Key objectives for the ongoing mapping of this quadrangle are to assess the types of processes that may be responsible for the creation of the hexagonal Fejokoo crater, identifying the source and nature of the bright material on the eastern boundary, establishing possible mechanisms for the emplacement of lobate material deposits in Fejokoo and the unnamed crater to its NW, and establishing a detailed geological history of the quadrangle. The Fejokoo region is not associated with any major albedo feature identified by the Hubble Space Telescope (Li et al., 2006). At the time of this writing geologic mapping was performed using Framing Camera (FC) mosaics from the Approach (1.3 km/px) and Survey (415 m/px) orbits, including grayscale and color images and digital terrain models derived from stereo images. Future images from the High Altitude Mapping Orbit (140 m/px) and Low Altitude Mapping Orbit (35 m/px) will be used to refine the maps. Support of the Dawn Instrument, Operations, and Science Teams is acknowledged. This work is supported by grants from NASA, and from the German and Italian Space Agencies.

  19. A Gamma Ray Spectrometer Based on Mobile Phone Technology

    NASA Astrophysics Data System (ADS)

    Moss, Kyle; Barzilov, Alexander; Womble, Phillip C.; Paschal, Jon

    2006-10-01

    We have developed a miniature spectrometer for gamma-ray detection and automatic isotope identification (RadPhone) which uses mobile phone technology to analyze the data and to distribute the results to security personnel. The RadPhone system consists of two modules, a detector module and wireless phone module. The detector module houses a detector, a small data acquisition system, Bluetooth transceiver, and power supply (battery). Using a Bluetooth channel, this module communicates to the Motorola^TM MPx220 wireless phone with data acquisition and analysis software which serves as a data acquisition computer. RadPhone offers a small, portable means of gamma-ray detection and identification.

  20. BoHV-4-Based Vector Single Heterologous Antigen Delivery Protects STAT1(-/-) Mice from Monkeypoxvirus Lethal Challenge

    PubMed Central

    Crump, Ryan W.; Doronin, Konstantin; Hembrador, Edguardo; Pompilio, Daniela; Tebaldi, Giulia; Estep, Ryan D.; Wong, Scott W.; Buller, Mark R.; Donofrio, Gaetano

    2015-01-01

    Monkeypox virus (MPXV) is the etiological agent of human (MPX). It is an emerging orthopoxvirus zoonosis in the tropical rain forest of Africa and is endemic in the Congo-basin and sporadic in West Africa; it remains a tropical neglected disease of persons in impoverished rural areas. Interaction of the human population with wildlife increases human infection with MPX virus (MPXV), and infection from human to human is possible. Smallpox vaccination provides good cross-protection against MPX; however, the vaccination campaign ended in Africa in 1980, meaning that a large proportion of the population is currently unprotected against MPXV infection. Disease control hinges on deterring zoonotic exposure to the virus and, barring that, interrupting person-to-person spread. However, there are no FDA-approved therapies against MPX, and current vaccines are limited due to safety concerns. For this reason, new studies on pathogenesis, prophylaxis and therapeutics are still of great interest, not only for the scientific community but also for the governments concerned that MPXV could be used as a bioterror agent. In the present study, a new vaccination strategy approach based on three recombinant bovine herpesvirus 4 (BoHV-4) vectors, each expressing different MPXV glycoproteins, A29L, M1R and B6R were investigated in terms of protection from a lethal MPXV challenge in STAT1 knockout mice. BoHV-4-A-CMV-A29LgD106ΔTK, BoHV-4-A-EF1α-M1RgD106ΔTK and BoHV-4-A-EF1α-B6RgD106ΔTK were successfully constructed by recombineering, and their capacity to express their transgene was demonstrated. A small challenge study was performed, and all three recombinant BoHV-4 appeared safe (no weight-loss or obvious adverse events) following intraperitoneal administration. Further, BoHV-4-A-EF1α-M1RgD106ΔTK alone or in combination with BoHV-4-A-CMV-A29LgD106ΔTK and BoHV-4-A-EF1α-B6RgD106ΔTK, was shown to be able to protect, 100% alone and 80% in combination, STAT1(-/-) mice against

  1. An Examination of Alternative Forms of Fit in Contingency Theory.

    DTIC Science & Technology

    1984-11-01

    adding up to knowledge of the total organization. As Bateson (1979) suggests, this constitutes an error of logical typing. By reducing or...Graham and Andrew H. Van de Ven 1983 "Central Perspectives and Debates in Organization Theory," 28: 245-273. Bateson , G. 1979 Mind and Nature, New York: E... Gregory USAFA/DFBL U.S. Air Force Academy, CO 80840 AFOSR/NL Building 410 Bolling AFB Was:iington, LC 23332 Department of the Air Force HOUSAF/MPX-L

  2. Photoelectrochemical cells including chalcogenophosphate photoelectrodes

    NASA Technical Reports Server (NTRS)

    Reichman, B.; Byvik, C. E. (Inventor)

    1984-01-01

    Photoelectrochemical cells employing chalcogenophosphate (MPX3) photoelectrodes are described where M is selected from the group of transition metal series of elements beginning with scandium (atomic number 21) through germanium (atomic number 32) yttrium (atomic number 39) through antimony (atomic number 51) and lanthanum (atomic number 57) through polonium (atomic number 84); P is phosphorus; and X is selected from the chalogenide series consisting of sulfur, selenium, and tellurium. These compounds have bandgaps in the desirable range from 2.0 eV to 2.2 eV for the photoelectrolysis of water and are stable when used as photoelectrodes for the same.

  3. Photoelectrochemical cells including chalcogenophosphate photoelectrodes

    NASA Astrophysics Data System (ADS)

    Reichman, B.; Byvik, C. E.

    1984-03-01

    Photoelectrochemical cells employing chalcogenophosphate (MPX3) photoelectrodes are described where M is selected from the group of transition metal series of elements beginning with scandium (atomic number 21) through germanium (atomic number 32) yttrium (atomic number 39) through antimony (atomic number 51) and lanthanum (atomic number 57) through polonium (atomic number 84); P is phosphorus; and X is selected from the chalogenide series consisting of sulfur, selenium, and tellurium. These compounds have bandgaps in the desirable range from 2.0 eV to 2.2 eV for the photoelectrolysis of water and are stable when used as photoelectrodes for the same.

  4. Comparative evaluation of three commercial systems for detection of high-risk human papillomavirus in cervical and vaginal ThinPrep PreservCyt samples and correlation with biopsy results.

    PubMed

    Binnicker, M J; Pritt, B S; Duresko, B J; Espy, M J; Grys, T E; Zarka, M A; Kerr, S E; Henry, M R

    2014-10-01

    Genital human papillomavirus (HPV) is the etiologic agent of more than 99% of all cervical cancers worldwide, with 14 genotypes being considered oncogenic or "high risk" because of their association with severe dysplasia and cervical carcinoma. Among these 14 high-risk types, HPV-16 and -18 account for approximately 70% of cervical cancers. The aim of this study was to evaluate three FDA-approved HPV nucleic acid-based tests for the ability to predict high-grade cervical intraepithelial neoplasias (CIN2 or worse) in corresponding tissue biopsy specimens. Residual specimens (total n = 793, cervical n = 743, vaginal n = 50) collected in ThinPrep PreservCyt medium with a cytologic result of ≥ atypical squamous cells of undetermined significance were tested by the Hybrid Capture 2 (HC2) assay (Qiagen, Gaithersburg, MD), the cobas HPV test (Roche Diagnostics, Indianapolis, IN), and the APTIMA HPV assay (Hologic, San Diego, CA). Genotyping for HPV-16 and HPV-18 was simultaneously performed by the cobas HPV test. Results were compared to cervical or vaginal biopsy findings, when they were available (n = 350). Among the 350 patients with corresponding biopsy results, 81 (23.1%) showed ≥ CIN2 by histopathology. The ≥ CIN2 detection sensitivity was 91.4% by the cobas and APTIMA assays and 97.5% by HC2 assay. The specificities of the cobas, APTIMA, and HC2 assays were 31.2, 42.0, and 27.1%, respectively. When considering only positive HPV-16 and/or HPV-18 genotype results, the cobas test showed a sensitivity and a specificity of 51.9 and 86.6%, respectively. While the HC2, cobas, and APTIMA assays showed similar sensitivities for the detection of ≥ CIN2 lesions, the specificities of the three tests varied, with the greatest specificity (86.6%) observed when the HPV-16 and/or HPV-18 genotypes were detected. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  5. Inhibitors of neutrophil recruitment identified using transgenic zebrafish to screen a natural product library.

    PubMed

    Wang, Xingang; Robertson, Anne L; Li, Jingyu; Chai, Ruth Jinfen; Haishan, Wang; Sadiku, Pranvera; Ogryzko, Nikolay V; Everett, Martin; Yoganathan, Kanagasundaram; Luo, Hongbo Robert; Renshaw, Stephen A; Ingham, Philip W

    2014-01-01

    Cell migration is fundamental to the inflammatory response, but uncontrolled cell migration and excess recruitment of neutrophils and other leukocytes can cause damage to the tissue. Here we describe the use of an in vivo model - the Tg(mpx:GFP)(i114) zebrafish line, in which neutrophils are labelled by green fluorescent protein (GFP) - to screen a natural product library for compounds that can affect neutrophil migratory behaviour. Among 1040 fungal extracts screened, two were found to inhibit neutrophil migration completely. Subfractionation of these extracts identified sterigmatocystin and antibiotic PF1052 as the active components. Using the EZ-TAXIScan chemotaxis assay, both compounds were also found to have a dosage-dependent inhibitory effect on murine neutrophil migration. Furthermore, neutrophils treated with PF1052 failed to form pseudopods and appeared round in shape, suggesting a defect in PI3-kinase (PI3K) signalling. We generated a transgenic neutrophil-specific PtdIns(3,4,5)P3 (PIP3) reporter zebrafish line, which revealed that PF1052 does not affect the activation of PI3K at the plasma membrane. In human neutrophils, PF1052 neither induced apoptosis nor blocked AKT phosphorylation. In conclusion, we have identified an antibiotic from a natural product library with potent anti-inflammatory properties, and have established the utility of the mpx:GFP transgenic zebrafish for high-throughput in vivo screens for novel inhibitors of neutrophil migration.

  6. Inhibitors of neutrophil recruitment identified using transgenic zebrafish to screen a natural product library

    PubMed Central

    Wang, Xingang; Robertson, Anne L.; Li, Jingyu; Chai, Ruth Jinfen; Haishan, Wang; Sadiku, Pranvera; Ogryzko, Nikolay V.; Everett, Martin; Yoganathan, Kanagasundaram; Luo, Hongbo Robert; Renshaw, Stephen A.; Ingham, Philip W.

    2014-01-01

    Cell migration is fundamental to the inflammatory response, but uncontrolled cell migration and excess recruitment of neutrophils and other leukocytes can cause damage to the tissue. Here we describe the use of an in vivo model – the Tg(mpx:GFP)i114 zebrafish line, in which neutrophils are labelled by green fluorescent protein (GFP) – to screen a natural product library for compounds that can affect neutrophil migratory behaviour. Among 1040 fungal extracts screened, two were found to inhibit neutrophil migration completely. Subfractionation of these extracts identified sterigmatocystin and antibiotic PF1052 as the active components. Using the EZ-TAXIScan chemotaxis assay, both compounds were also found to have a dosage-dependent inhibitory effect on murine neutrophil migration. Furthermore, neutrophils treated with PF1052 failed to form pseudopods and appeared round in shape, suggesting a defect in PI3-kinase (PI3K) signalling. We generated a transgenic neutrophil-specific PtdIns(3,4,5)P3 (PIP3) reporter zebrafish line, which revealed that PF1052 does not affect the activation of PI3K at the plasma membrane. In human neutrophils, PF1052 neither induced apoptosis nor blocked AKT phosphorylation. In conclusion, we have identified an antibiotic from a natural product library with potent anti-inflammatory properties, and have established the utility of the mpx:GFP transgenic zebrafish for high-throughput in vivo screens for novel inhibitors of neutrophil migration. PMID:24291762

  7. Side Chain Hydrophobicity Modulates Therapeutic Activity and Membrane Selectivity of Antimicrobial Peptide Mastoparan-X

    PubMed Central

    Gjetting, Torben; Andresen, Thomas L.

    2014-01-01

    The discovery of new anti-infective compounds is stagnating and multi-resistant bacteria continue to emerge, threatening to end the “antibiotic era”. Antimicrobial peptides (AMPs) and lipo-peptides such as daptomycin offer themselves as a new potential class of antibiotics; however, further optimization is needed if AMPs are to find broad use as antibiotics. In the present work, eight analogues of mastoparan-X (MPX) were investigated, having side chain modifications in position 1, 8 and 14 to modulate peptide hydrophobicity. The self-association properties of the peptides were characterized, and the peptide-membrane interactions in model membranes were compared with the bactericidal and haemolytic properties. Alanine substitution at position 1 and 14 resulted in higher target selectivity (red blood cells versus bacteria), but also decreased bactericidal potency. For these analogues, the gain in target selectivity correlated to biophysical parameters showing an increased effective charge and reduction in the partitioning coefficient for membrane insertion. Introduction of an unnatural amino acid, with an octyl side chain by amino acid substitution, at positions 1, 8 and 14 resulted in increased bactericidal potency at the expense of radically reduced membrane target selectivity. Overall, optimized membrane selectivity or bactericidal potency was achieved by changes in side chain hydrophobicity of MPX. However, enhanced potency was achieved at the expense of selectivity and vice versa in all cases. PMID:24621994

  8. Persistent Oxytetracycline Exposure Induces an Inflammatory Process That Improves Regenerative Capacity in Zebrafish Larvae

    PubMed Central

    Barros-Becker, Francisco; Romero, Jaime; Pulgar, Alvaro; Feijóo, Carmen G.

    2012-01-01

    Background The excessive use of antibiotics in aquaculture can adversely affect not only the environment, but also fish themselves. In this regard, there is evidence that some antibiotics can activate the immune system and reduce their effectiveness. None of those studies consider in detail the adverse inflammatory effect that the antibiotic remaining in the water may cause to the fish. In this work, we use the zebrafish to analyze quantitatively the effects of persistent exposure to oxytetracycline, the most common antibiotic used in fish farming. Methodology We developed a quantitative assay in which we exposed zebrafish larvae to oxytetracycline for a period of 24 to 96 hrs. In order to determinate if the exposure causes any inflammation reaction, we evaluated neutrophils infiltration and quantified their total number analyzing the Tg(mpx:GFP)i114 transgenic line by fluorescence stereoscope, microscope and flow cytometry respectively. On the other hand, we characterized the process at a molecular level by analyzing several immune markers (il-1β, il-10, lysC, mpx, cyp1a) at different time points by qPCR. Finally, we evaluated the influence of the inflammation triggered by oxytetracycline on the regeneration capacity in the lateral line. Conclusions Our results suggest that after 48 hours of exposure, the oxytetracycline triggered a widespread inflammation process that persisted until 96 hours of exposure. Interestingly, larvae that developed an inflammation process showed an improved regeneration capacity in the mechanosensory system lateral line. PMID:22590621

  9. New evidence for supernarrow dibaryons production in pd interactions

    NASA Astrophysics Data System (ADS)

    Fil'kov, L. V.; Kashevarov, V. L.; Konobeevski, E. S.; Mordovskoy, M. V.; Potashev, S. I.; Simonov, V. A.; Skorkin, V. M.; Zuev, S. V.

    The analysis of new experimental data, obtained at the Proton Linear Accelerator of INR, with the aim to search for supernarrow dibaryons in the pd|-->ppX1 and pd|-->pdX2 reactions is presented. Narrow peaks with an experimental width of 5 MeV at masses of 1904+/-2, 1926+/-2, and 1942+/-2 MeV have been observed in missing mass MpX1 spectra. In the missing mass MX1 spectra, the peaks at MX1 = 966+/-2, 986+/-2, and 1003+/-2 MeV have been found. The analysis of the data obtained leads to the conclusion that the observed peaks in MpX1 spectra are most likely supernarrow dibaryons, the decay of which into two nucleons is forbidden by the Pauli exclusion principle. An alternative interpretation of the spectra by assuming a decay of the supernarrow dibaryons in ``exotic baryon states'' with masses MX1 is discussed.

  10. Pitted Terrain on Dwarf Planet Ceres: Morphological Evidence for Shallow Volatiles at Low and Mid Latitudes

    NASA Astrophysics Data System (ADS)

    Sizemore, H. G.; Platz, T.; Prettyman, T. H.; Schorghofer, N.; Mest, S. C.; Crown, D. A.; Yingst, R. A.; Schenk, P.; Bland, M. T.; Schmidt, B. E.; De Sanctis, M. C.; Schmedemann, N.; Tosi, F.; Hughson, K.; Raymond, C. A.; Russell, C. T.

    2016-12-01

    The Dawn spacecraft entered orbit around Ceres, the largest body in the asteroid belt, on March 5, 2015. Over its first 16 months at Ceres, the spacecraft obtained morphological, topographical, mineralogical, elemental, and gravity data through a series of successively lower orbits. Framing Camera (FC) images from High Altitude Mapping Orbit (HAMO) and Low Altitude Mapping Orbit (LAMO) have provided global coverage of Ceres' morphology at pixel scales of 140 m/px and 35 m/px respectively. In the FC dataset we have identified distinct pitted terrains, characterized by clusters of round-to-irregular, rimless or low-rimmed pits in smooth crater materials. We describe the morphology, setting, and geographic distribution of these pitted materials, which exhibit striking similarities to pitted materials previously discovered by Dawn at Vesta1, and pitted materials identified in low-and mid-latitude martian craters2. We discuss likely production mechanisms for the cerean pitted materials, as well as implications for the geographic distribution and concentration of shallow volatiles on Ceres. 1Denevi, et al. 2012. Science, 338, 246-249. 2Tornabene, et al. 2012. Icarus, 220, 348-368.

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

    PubMed Central

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

    2006-01-01

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

  12. [Bacteriology and mycology of otitis externa in dogs].

    PubMed

    Bornand, V

    1992-01-01

    The bacterial and fungal flora of 1118 ears of dogs with otitis externa and 100 ears of healthy control dogs were studied in order to isolate the causative agents. The yeast Malassezia pachydermatis (56%) was by far the most common organism in otitic dogs followed by the bacteria Staphylococcus intermedius (23%), Pseudomonas aeruginosa (12%), Proteus spp. (6%) and Streptococcus canis (5%). A statistical analysis of observed results showed that the incidence of these organisms is significant in otitic dogs. Many strains of S.intermedius, P.aeruginosa and Proteus spp. are resistant to antimicrobial agents commonly used to treat otitis externa. Therefore an antimicrobial susceptibility testing was performed using "Cobas Bact" for these bacterias. Furthermore, 80 strains of M.pachydermatis were submitted to identification-kits (API 20 CAUX, API STAPH, Cobas Micro). The observed results showed that an identification with these tests was not possible.

  13. Nucleotide sequence of a Pseudomonas denitrificans 5.4-kilobase DNA fragment containing five cob genes and identification of structural genes encoding S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase and cobyrinic acid a,c-diamide synthase.

    PubMed Central

    Crouzet, J; Cauchois, L; Blanche, F; Debussche, L; Thibaut, D; Rouyez, M C; Rigault, S; Mayaux, J F; Cameron, B

    1990-01-01

    A 5.4-kilobase DNA fragment carrying Pseudomonas denitrificans cob genes has been sequenced. The nucleotide sequence and genetic analysis revealed that this fragment carries five different cob genes (cobA to cobE). Four of these genes present the characteristics of translationally coupled genes. cobA has been identified as the structural gene of S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase (SUMT) because the encoded protein has the same NH2 terminus and molecular weight as those determined for the purified SUMT. For the same reasons the cobB gene was shown to be the structural gene for cobyrinic acid a,c-diamide synthase. Genetic and biochemical data concerning cobC and cobD mutants suggest that the products of these genes are involved in the conversion of cobyric acid to cobinamide. PMID:2211520

  14. EDTA interference in electrochemiluminescence ACTH assay.

    PubMed

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

    2016-11-01

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

  15. Diagnostic challenges of tuberculous lymphadenitis using polymerase chain reaction analysis: a case study.

    PubMed

    Taniguchi, Hirokazu; Nakamura, Masahiko; Shimokawa, Kazuki; Kamiseki, Fumi; Ishizawa, Shin; Abo, Hitoshi; Furuse, Hideaki; Tsuda, Takeshi; Masaki, Yasuaki; Suzuki, Kensuke

    2015-01-01

    This report presents a case of tuberculous lymphadenitis that was difficult to diagnose using polymerase chain reaction analysis. An 80-year-old Japanese female was hospitalized due to swollen cervical lymph nodes. Her lymph node tests revealed paradoxical polymerase chain reaction results. Polymerase chain reaction analysis of two biopsy tissues using the Cobas TaqMan revealed a positive result for Mycobacterium avium and a negative result for Mycobacterium tuberculosis. However, polymerase chain reaction analysis of a cultured colony of acid-fast bacteria from biopsy tissue using the Cobas TaqMan and an alternative polymerase chain reaction analysis of biopsy tissue yielded discordant results. The patient was diagnosed as having tuberculous lymphadenitis. She was treated with antitubercular drugs and subsequently had a reduction in cervical lymph node swelling. Polymerase chain reaction analysis is not 100% accurate; hence, its use as a diagnostic tool for mycobacterial infection requires increased attention.

  16. Human Papillomavirus Genotyping Testing Practice in 2014: Results of a College of American Pathologists National Survey.

    PubMed

    Zhao, Chengquan; Crothers, Barbara A; Ghofrani, Mohiedean; Li, Zaibo; Souers, Rhona J; Hussain, Mujtaba; Fan, Fang; Ocal, Idris Tolgay; Goodrich, Kelly; Shen, Rulong; Davey, Diane D

    2016-12-01

    - College of American Pathologists (CAP) surveys are used to establish national benchmarks for laboratories. - To investigate human papillomavirus (HPV) genotyping testing practice patterns in laboratories in 2014. - Data were analyzed from the CAP HPV Genotyping Practices Supplemental Questionnaire distributed to 749 laboratories participating in the CAP Human Papillomavirus (High Risk) for Cytology Program. - Six hundred four of 749 laboratories (80.6%) responded to the survey. More laboratories offered HPV genotyping testing and performed in-house HPV genotyping testing as compared to previous surveys. The Roche cobas HPV test was the most commonly used genotyping method (37.0%; 160 of 433), followed by Hologic Aptima HPV16 18/45 (26.1%; 113 of 433) and Hologic Cervista HPV16/18 (14.3%; 62 of 433). Most laboratories (287 of 399; 71.9%) offered HPV genotyping for high-risk HPV cases regardless of Papanicolaou (Pap) test results and patient age; this pattern was more common in laboratories using cobas. The remaining laboratories specifically offered testing to women with a negative Pap test result at age 30 years and older (65.2%, 73 of 112) or all ages (37.5%, 42 of 112). The median reporting rates of HPV16 and/or HPV18 positivity were 20.6%, 25.7%, 21.1%, and 57.4% for women with positive high-risk HPV adjunctive negative Pap results, atypical squamous cells of undermined significance, low-grade squamous intraepithelial lesion, and high-grade squamous lesion, respectively. - Human papillomavirus genotyping testing has increased. Roche cobas and Hologic Aptima genotype methods were the most common, and laboratories using cobas usually offered genotyping regardless of Pap test result and age. The data provide a baseline and trend of HPV genotyping test practices in 2014.

  17. Development of candidate reference reagent for HIV-1 RNA and comparison analysis for different HIV-1 RNA quantitative assay.

    PubMed

    Park, Borae G; Park, Ae Ja; Choi, Jee-Hye; Park, Jina; Kim, Sung Soon; Wang, Jin-Sook; Kee, Mee Kyung; Choi, Ju-yeon

    2011-09-01

    Human immunodeficiency virus type-1 (HIV-1) RNA viral load is a surrogate marker that is routinely used to determine indications for, and monitor the effectiveness of HIV-1 treatment. We developed three reagents for potential use in routine quality control of HIV-1 RNA quantitative assays. In this report, we compare the stability of these re-agents in storage and compare their performance in three different HIV-1 RNA quantitative assays. The candidate reagents were derived from readily available pre-existing reagents and examined for stability at different storage temperatures. They were compared in three commercially available HIV-1 RNA quantitative assays: the Cobas TaqMan HIV-1 Test (Cobas TaqMan), the RealTime HIV-1 Assay (Abbott RealTime), and the NucliSens EasyQ HIV-1 Assay v1.1 (NucliSens EasyQ). The candidate reagent derived from an HIV culture supernatant (candidate CS) was the most stable of the three candidates and showed good reproducibility. Candidate CS yielded the highest HIV-1 titer of the three candidates in the Cobas TaqMan assay and the lowest HIV-1 titer and stability of the three candidates in the NucliSens EasyQ system. The candidate CS is the most appropriate of the three candidate reagents for quantitative testing of HIV-1 RNA. This working reagent should be useful for use in routine calibration for quality control in centers with limited financial resources. The Cobas TaqMan assay tended to yield higher viral load results than the other assays when used with our three candidate reagents.

  18. EGFR T790M mutation testing within the osimertinib AURA Phase I study.

    PubMed

    Dearden, Simon; Brown, Helen; Jenkins, Suzanne; Thress, Kenneth S; Cantarini, Mireille; Cole, Rebecca; Ranson, Malcolm; Jänne, Pasi A

    2017-07-01

    Reliable epidermal growth factor receptor (EGFR) mutation testing techniques are required to identify eligible patients with EGFR mutation/T790M positive advanced non-small cell lung cancer (NSCLC), for treatment with osimertinib (AZD9291), an oral, potent, irreversible EGFR tyrosine kinase inhibitor (TKI) selective for EGFR-TKI-sensitizing and T790M resistance mutations over wild-type EGFR. There is no current consensus regarding the best method to detect EGFR T790M mutations. The aim of this study was to describe the concordance between local testing, which used a variety of methods, and central testing, using the cobas(®) EGFR Mutation Test, for EGFR-sensitizing mutations and the T790M resistance mutation. Tumor samples were obtained from all patients screened for inclusion onto the osimertinib Phase I expansion component of the AURA Phase I/II study (NCT01802632). Samples underwent central laboratory testing for EGFR-sensitizing mutations and T790M resistance mutation using the cobas(®) EGFR Mutation Test. Results were compared with local laboratory test results, based on other testing methodologies including Sanger sequencing, therascreen(®), PNAClamp™, and Sequenom MassARRAY(®). Central laboratory testing was successful in 99% of samples passing histopathology review and testing success rates were comparable across the three central laboratories. Concordance between central and local testing for common sensitizing mutations was high (>98%) and concordance for the T790M mutation was also high (>90%). Tumor heterogeneity, along with other technical factors may have influenced this result. Within the osimertinib AURA Phase I study, EGFR mutation testing across three centralized laboratories using the cobas(®) EGFR Mutation Test was feasible and successful, with strong concordance between local and central laboratory results, including for T790M. The cobas(®) EGFR Mutation Test has subsequently been approved as the companion diagnostic test for

  19. An improved pyrogallol red-molybdate method for determining total urinary protein.

    PubMed

    Orsonneau, J L; Douet, P; Massoubre, C; Lustenberger, P; Bernard, S

    1989-11-01

    We adapted the pyrogallol red-molybdate method for total urinary protein to the Cobas Bio centrifugal analyzer. The method is simple, rapid, sensitive, and inexpensive. Addition of 25 mg of sodium dodecyl sulfate per liter to the reagent modifies protein reactivities so that the chromogenicity of human gamma globulins is the same as that of albumin. Results by this method and a comparison method that included gel filtration and a modified biuret reaction correlated well (r = 0.951).

  20. Systemic and Pulmonary Hypertension After Resuscitation with Cell-Free Hemoglobin

    DTIC Science & Technology

    1992-07-01

    according to published standards (24). Inorganic phosphate was measured on a blood chemistry analyzer (Cobas-Fara; Roche Diagnostic Systems, Nutley, NJ...alanine aminotransferase (ALT), and lactate dehydrogenase (LDH) on the blood chemistry analyzer . The final 4 ml of blood was heparinized, centrifuged...milliliter of blood was placed in 2 ml of ice-cold perchioric acid (70% wt/vol), which was used to determine whole blood lactate in the blood chemistry

  1. Development of a Multiplex PCR Test with Automated Genotyping Targeting E7 for Detection of Six High-Risk Human Papillomaviruses.

    PubMed

    Paes, Eliana Ferreira; de Assis, Angela Maria; Teixeira, Cirbia S Campos; Aoki, Francisco Hideo; Teixeira, Julio Cesar

    2015-01-01

    Cervical cancer is caused by high-risk human papillomaviruses (HPV) and viral detection tests aid in the diagnosis of precursor lesions. In the present study, a molecular test for detection of high-risk HPV DNA, called E7-HPV, was standardized and assessed in samples from women with pre-cancerous lesions. The development of the E7-HPV test for detection and genotyping of six high-risk HPV (types 16, 18, 31, 33, 45 and 52), consisted of evaluating primer quality and adjusting the multiplex PCR conditions. Primer design was based on the E7 region of each HPV, and the fluorochrome 6-FAM was added to PCR primers. Viral detection was performed by capillary electrophoresis in automated sequencer in samples obtained from 60 women (55 with ASC-H/HSIL cytology) from August to September 2013. A non-inferiority analysis was conducted with the cobas HPV test as a reference and following international guidelines for the development of new tests. The two tests had a high concordance rate in HPV16 detection (kappa=0.972), with only one discordant case (cervical intraepithelial neoplasia grade 3, negative with cobas and positive for HPV16 by E7-HPV) and complete agreement in HPV18 detection. When comparing detection of all high-risk HPV, three cases were positive with cobas but negative with E7-HPV, and another three cases were negative with cobas but positive with E7-HPV (HPV16, 31 and 52). When we evaluate the cases initially suspected by cytology, the two tests had the same sensitivity in detection CIN2 or worse. In conclusion, the E7-HPV test has satisfactory initial results, and its development can be continued.

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

    PubMed

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

    2008-03-01

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

  3. Workflow and Maintenance Characteristics of Five Automated Laboratory Instruments for the Diagnosis of Sexually Transmitted Infections

    PubMed Central

    Ratnam, Sam; Jang, Dan; Gilchrist, Jodi; Smieja, Marek; Poirier, Andre; Hatchette, Todd; Flandin, Jean-Frederic

    2014-01-01

    The choice of a suitable automated system for a diagnostic laboratory depends on various factors. Comparative workflow studies provide quantifiable and objective metrics to determine hands-on time during specimen handling and processing, reagent preparation, return visits and maintenance, and test turnaround time and throughput. Using objective time study techniques, workflow characteristics for processing 96 and 192 tests were determined on m2000 RealTime (Abbott Molecular), Viper XTR (Becton Dickinson), cobas 4800 (Roche Molecular Diagnostics), Tigris (Hologic Gen-Probe), and Panther (Hologic Gen-Probe) platforms using second-generation assays for Chlamydia trachomatis and Neisseria gonorrhoeae. A combination of operational and maintenance steps requiring manual labor showed that Panther had the shortest overall hands-on times and Viper XTR the longest. Both Panther and Tigris showed greater efficiency whether 96 or 192 tests were processed. Viper XTR and Panther had the shortest times to results and m2000 RealTime the longest. Sample preparation and loading time was the shortest for Panther and longest for cobas 4800. Mandatory return visits were required only for m2000 RealTime and cobas 4800 when 96 tests were processed, and both required substantially more hands-on time than the other systems due to increased numbers of return visits when 192 tests were processed. These results show that there are substantial differences in the amount of labor required to operate each system. Assay performance, instrumentation, testing capacity, workflow, maintenance, and reagent costs should be considered in choosing a system. PMID:24740081

  4. Evaluation of the immunoradiometric and electrochemiluminescence method for the measurement of serum insulin in children.

    PubMed

    Ochocińska, Agnieszka; Śnitko, Rafał; Czekuć-Kryśkiewicz, Edyta; Kępka, Alina; Szalecki, Mieczysław; Janas, Roman M

    2016-01-01

    Human insulin is a polypeptide hormone produced, stored, and secreted by the ß-cells in the pancreatic islets of Langerhans. Its secretion is stimulated by an increase of the glucose concentration in circulation. Non-radioactive assays are frequently used in many laboratories to measure hormone concentrations, as an alternative to the traditional "gold standard" radioimmuno- and immunoradiometric assays. The precise and reliable determination of the insulin concentration is an important concern in numerous diagnostic procedures. The aim of this study was to compare two commercially available assays (manual and automated) for measurement of serum insulin concentrations. Aliquots of the 86 randomly selected serum samples were measured by Elecsys Insulin Assay (cobas e411 immunoassay analyzer, Roche Diagnostics GmbH, Mannheim, Germany) and DIAsource INS-IRMA Kit (DIAsource ImmunoAssays S.A., Louvain-la-Neuve, Belgium). Compared assays exhibit good correlation (r = 0.996). Insulin concentrations were on average 4.2 μ IU/mL lower (p < 0.05) with the cobas e411 immunoassay analyzer when compared to those measured with DIAsouce Immunoassay. Our findings suggest that electrochemiluminescence method on the cobas e411 analyzer and manual IRMA method offered by the DIAsource for the serum insulin determination could be considered interchangeable.

  5. Reliability of the Xpert HPV assay to detect high-risk human papillomavirus DNA in a colposcopy referral population.

    PubMed

    Castle, Philip E; Smith, Katherine M; Davis, Thomas E; Schmeler, Kathleen M; Ferris, Daron G; Savage, Ashlyn H; Gray, Jermaine E; Stoler, Mark H; Wright, Thomas C; Ferenczy, Alex; Einstein, Mark H

    2015-01-01

    The Xpert HPV Assay (Xpert; Cepheid, Sunnyvale, CA) was developed for the multianalytic GeneXpert platform. In a colposcopy referral population of 708 women living in the United States, two cervical specimens, A and B, were collected, and both were tested by the Xpert assay for high-risk human papillomavirus (hrHPV) DNA, permitting an evaluation of its test reliability. Specimen B was also tested by Hybrid Capture 2 (hc2; Qiagen, Germantown, MD) and the cobas HPV Test (cobas; Roche Molecular Systems, Pleasanton, CA). The κ and percent agreement for any hrHPV for the two Xpert results were 0.88 and 94.5%, respectively. There was no statistical difference in testing positive on both specimens by Xpert (P = .62). The sensitivity for detection of cervical intraepithelial neoplasia grade 2 or more severe (CIN2+) was 89.0% using specimen A and 90.4% using specimen B for Xpert, 90.4% for cobas, and 81.6% for hc2. The Xpert assay was sensitive and reliable for the detection of hrHPV and the identification of women with CIN2+. Copyright© by the American Society for Clinical Pathology.

  6. Clinical evaluation of the cartridge-based GeneXpert human papillomavirus assay in women referred for colposcopy.

    PubMed

    Einstein, Mark H; Smith, Katherine M; Davis, Thomas E; Schmeler, Kathleen M; Ferris, Daron G; Savage, Ashlyn H; Gray, Jermaine E; Stoler, Mark H; Wright, Thomas C; Ferenczy, Alex; Castle, Philip E

    2014-06-01

    High-risk human papillomavirus (hrHPV) testing is now being introduced as a potential primary screening test for improved detection of cervical precancer and cancer. Current U.S. Food and Drug Administration-approved tests are batch tests that take several hours to complete. A rapid, non-batch test might permit point-of-care (POC) testing, which can facilitate same-day screen and management strategies. For a non-batch, random-access platform (GeneXpert; Cepheid, Sunnyvale, CA), a prototype hrHPV assay (Xpert) has been developed where testing for 14 hrHPV types can be completed in 1 h. In the first clinical evaluation, Xpert was compared to two validated hrHPV tests, the cobas HPV test (cobas, Roche Molecular Systems) and Hybrid Capture 2 (hc2, Qiagen), and to histologic outcomes using specimens from colposcopy referral populations at 7 clinical sites in the United States (n = 697). The sensitivity of Xpert for cervical intraepithelial neoplasia grade 2 or more severe diagnoses (CIN2+) (n = 141) was equal to that of cobas (90.8% versus 90.8%, P = 1) and greater than that of hc2 (90.8% versus 81.6%, P = 0.004). Xpert was more specific than cobas (42.6% versus 39.6%, P = 0.02) and less specific than hc2 (42.6% versus 47.7%, P < 0.001). Similar results were observed for cervical intraepithelial neoplasia grade 3 or higher (CIN3+) (n = 91). HPV16 detection by Xpert identified 41.8% of the CIN2+ specimens with a positive predictive value (PPV) of 54.6%. By comparison, HPV16 detection by cobas identified 42.6% of the CIN2+ specimens with a PPV of 55.0%. hrHPV detection by the Xpert demonstrated excellent clinical performance for identifying women with CIN2+ and CIN3+ that was comparable to that of currently available clinically validated tests. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  7. Preliminary Geological Map of the Ac-H-3 Dantu Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Kneissl, T.; Schmedemann, N.; Neesemann, A.; Williams, D. A.; Crown, D. A.; Mest, S. C.; Buczkowski, D.; Scully, J. E. C.; Frigeri, A.; Ruesch, O.; Hiesinger, H.; Walter, S. H. G.; Jaumann, R.; Roatsch, T.; Preusker, F.; Nathues, A.; Platz, T.; Hoffmann, M.; Schäfer, M.; De Sanctis, M. C.; Raymond, C. A.; Russell, C. T.; Kersten, E.; Naß, A.

    2015-12-01

    We are using Dawn spacecraft data to create a geologic map of the Ac-H-3 Dantu Quadrangle of dwarf planet Ceres. The quadrangle is located between 21-66˚N and 90-180˚E and includes the following dominant features: 1) the central and northern portion of the 124.6 km diameter impact crater Dantu; 2) crater chains and/or grooves oriented in an east-west direction; 3) a portion of the 84 km diameter impact crater Gaue, whose ejecta blanket covers the SW corner of the quadrangle. Dantu is a complex impact crater showing terraces, a central pit structure, concentric fractures, and smooth deposits on the crater floor. The materials interpreted to be ejecta deposits of Dantu show low crater frequencies and dominate the southern half of the quadrangle. These deposits appear to be relatively bright and correspond to parts of the #2 high albedo region observed by (1) with the HST indicating different composition and/or material properties than the surroundings. The east-west striking crater chains and grooves are mainly found in the southern half of the quadrangle. They seem to be connected to the crater chains found in Ac-H-4 Ezinu, the neighboring quadrangle to the east, and are potentially related to ballistic ejecta emplacement (see 2). Further work will be focused on Dantu crater and its complex interior and exterior. The current geologic map is based on Framing Camera (FC) image mosaics derived from Approach (~1.3 km/px) and Survey (~400 m/px) data as well as digital terrain models (DTMs) derived from stereo imagery. In the course of the mission, we will incorporate mosaics from the High Altitude Mapping Orbit (~140 m/px, Fall 2015) and Low Altitude Mapping Orbit (~35 m/px, Spring 2016) phases. We acknowledge the support of the Dawn Instrument, Operations, and Science Teams. This work is partly supported by the German Space Agency (DLR), grant 50 OW 1101. (1) Li, J-Y. et al. (2006), Icarus, 182, 143-160. (2) Scully, J.E.C. et al. (2015), this conference.

  8. Quantitative topographic analysis as a guide to rover-based research on Mars

    NASA Astrophysics Data System (ADS)

    Palucis, M. C.; Dietrich, W. E.; Parker, T. J.; Sumner, D. Y.; Williams, R. M. E.; Hayes, A.; Mangold, N.; Lewis, K. W.

    2014-12-01

    Satellite imagery of Mars now provides remarkable topographic data, often better than that on Earth in many countries. For decades, researchers have identified landforms on Mars that indicated the presence of gullies, rivers, deltas, fans, and lakes, pointing to the presence of surface waters, and the apparent necessity of an active hydrologic cycle involving rain or snow. Quantitative topographic analysis has provided a means to estimate volumes of runoff, sediment transport rates, and peak flow discharges, first using orbital imagery alone and then using laser altimetery coverage and higher resolution HiRISE (1 m/px), CTX (20 m/px) and HRSC (50 m/px) topography. Our detailed topographic analysis of the Peace Vallis fan near the Curiosity rover landing site in Gale Crater (Mars) suggested that the fan entered into a pre-existing enclosed basin that would likely contain lake sediments; sedimentary, mineralogical, and chemical analysis of this region, now named Yellowknife Bay, later found this to be the case, though debate remains on the exact origin and history of the deposit. The rover is currently heading to a 5 km high sedimentary mound (Aeolis Mons) with mineral signatures hypothesized to be the result of planet-wide changes in climate. Topographic features on the mound, which correspond in elevation with other large depositional features around the crater, suggest that a succession of lakes developed post-Noachian. Within Gale, we are in a unique position to determine the extent at which topography can tell us the evolutionary history of a place on another planet, since our hypotheses can actually be tested as the Curiosity rover makes its ascent up Aeolis Mons. Along the rover's traverse, we propose based on the geomorphic record that the sediments being examined were water soaked, perhaps several times under deep lakes, and that the rover will cross shorelines that may not be well-preserved, but are worth searching for. A quantitative topographic analysis

  9. Preliminary Geological Map of the Ac-H-14 Yalode Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Crown, D. A.; Yingst, R. A.; Mest, S. C.; Platz, T.; Williams, D. A.; Buczkowski, D.; Schenk, P.; Scully, J. E. C.; Jaumann, R.; Roatsch, T.; Preusker, F.; Nathues, A.; Hoffmann, M.; Schäfer, M.; Marchi, S.; De Sanctis, M. C.; Russell, C.; Raymond, C. A.

    2015-12-01

    We are conducting a geologic mapping investigation of the Ac-H-14 Yalode Quadrangle (21-66°S, 270-360°E) of Ceres to examine its surface geology and geologic history. At the time of this writing, geologic mapping has been performed on Dawn Framing Camera (FC) mosaics from the late Approach phase (up to 1.3 km/px) and Survey orbit (415 m/px), including clear filter and color images and digital terrain models derived from stereo images. In Fall 2015 images from the High Altitude Mapping Orbit (140 m/px) will be used to refine the mapping, followed by the Low Altitude Mapping Orbit (35 m/px) starting in December 2015. The Yalode Quadrangle is dominated by the ~300-km diameter impact basin Yalode and includes rugged and smooth terrains to the east. Yalode basin has a variably preserved rim, which is continuous and sharply defined to the north/northwest and is irregular or degraded elsewhere, and may have an interior ring structure. The basin floor includes hummocky and smooth areas (some bounded by scarps), crater chains, and a lineated zone. High-resolution images will be used to search for volcanic features on the basin floor and in association with basin structures. Yalode basin and its floor deposits appear to have been strongly affected by the Urvara impact to the west. Impact craters in Yalode Quadrangle display a range of preservation states. Degraded features, including Yalode basin and numerous smaller craters, exhibit subdued rims, lack discrete ejecta deposits, and have infilled interiors. More pristine features (including the large unnamed basin in the SE corner of the quadrangle and craters on Yalode basin floor) have well-defined, quasi-circular forms with prominent rims and in some cases discernible ejecta. Some of these craters have bowl-shaped interiors and others contain hills or mounds on their floors. Support of the Dawn Instrument, Operations, and Science Teams is acknowledged. This work is supported by grants from NASA, MPG, and DLR.

  10. Preliminary Geological Maps of the Ac-H-10 Rongo and Ac-H-15 Zadeni Quadrangles: An integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Platz, T.; Nathues, A.; Crown, D. A.; Mest, S. C.; Williams, D. A.; Hoffmann, M.; Schäfer, M.; Sizemore, H. G.; Yingst, R. A.; Ruesch, O.; Buczkowski, D.; Kneissl, T.; Schmedemann, N.; Hughson, K.; Preusker, F.; Russell, C. T.

    2015-12-01

    We used geologic mapping applied to Dawn spacecraft data as a tool to understand the geologic history of the Ac-H-10 Rongo and Ac-H-15 Zadeni quadrangles of dwarf planet Ceres. These regions, Rongo and Zadeni, are located between 22°S-22°N and 288°-360°E and 65-90°S and 0°-360°E, respectively. The Rongo Quadrangle hosts a number of features: 1) the southwest portion is dissected by curvilinear structures likely caused by Yalode basin formation; 2) the central part is marked by dome-like constructs up to 100 km across; 3) a peculiar bright, c.4 km tall, conical structure informally known as the 'pyramid'; 4) impact craters of various diameters appear moderately to highly degraded or are partially buried; and 5) bright material is primarily exposed in the central portion and often associated with craters. Rongo crater (68 km across) exhibits a central peak and scalloped walls indicative of its degraded appearance. The Zadeni Quadrangle is characterised by impact craters up to 130 km in diameter of which Zadeni crater is the largest. Impact craters across all sizes exhibit fresh to highly degraded morphologies or are partially buried. Many craters developed central peaks. Inter-crater plains are generally hummocky with isolated regions of smooth-textured surfaces. The south pole area (85-90°S) is poorly illuminated and may host a large impact structure. At the time of this writing geologic mapping was performed on Framing Camera (FC) mosaics from Approach (1.3 km/px) and Survey (415 m/px) orbits, including clear filter and colour images and digital terrain models derived from stereo images. In Fall 2015 images from the High Altitude Mapping Orbit (140 m/px) will be used to refine the mapping, followed by Low Altitude Mapping Orbit (35 m/px) starting in December 2015. Support of the Dawn Instrument, Operations, and Science Teams is acknowledged. This work is supported by grants from NASA through the Dawn project, and from the German and Italian Space Agencies.

  11. Preliminary Geological Map of the Ac-H-12 Toharu Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Mest, S. C.; Williams, D. A.; Crown, D. A.; Yingst, R. A.; Buczkowski, D.; Schenk, P.; Scully, J. E. C.; Jaumann, R.; Roatsch, T.; Preusker, F.; Platz, T.; Nathues, A.; Hoffmann, M.; Schäfer, M.; Marchi, S.; De Sanctis, M. C.; Russell, C. T.; Raymond, C. A.

    2015-12-01

    We are using recent data from the Dawn spacecraft to map the geology of the Ac-H-12 Toharu Quadrangle (21-66°S, 90-180°E) of the dwarf planet Ceres in order to examine its surface geology and understand its geologic history. At the time of this writing, mapping was performed on Framing Camera (FC) mosaics from late Approach (1.3 km/px) and Survey (415 m/px) orbits, including clear filter and color images and digital terrain models derived from stereo images. Images from the High Altitude Mapping Orbit (140 m/px) will be used to refine the map in Fall 2015, followed by the Low Altitude Mapping Orbit (35 m/px) starting in December 2015. The quad is named after crater Toharu (87 km diameter; 49°S, 155°E). The southern rim of Kerwan basin (284 km diameter) is visible along the northern edge of the quad, which is preserved as a low-relief scarp. The quad exhibits smooth terrain in the north, and more heavily cratered terrain in the south. The smooth terrain forms nearly flat-lying plains in some areas, such as on the floor and to the southeast of Kerwan, and overlies hummocky materials in other areas. These smooth materials extend over a much broader area outside of the quad, and appear to contain some of the lowest crater densities on Ceres. Impact craters exhibit a range of coinciding sizes and preservation styles. Smaller craters (<40 km) generally appear morphologically "fresh", and their rims are nearly circular and raised above the surrounding terrain. Larger craters, such as Toharu, appear more degraded, exhibiting irregularly shaped, sometimes scalloped, rim structures, and debris lobes on their floors. Numerous craters (> 20 km) contain central mounds; at current FC resolution, it is difficult to discern if these are primary structures (i.e., central peaks) or secondary features. Support of the Dawn Instrument, Operations, & Science Teams is acknowledged. This work is supported by grants from NASA, DLR and MPG.

  12. Preliminary Geological Map of the Ac-H-13 Urvara Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Williams, D. A.; Sizemore, H. G.; Platz, T.; O'Brien, D. P.; Mest, S. C.; Yingst, R. A.; Crown, D. A.; Buczkowski, D.; Schenk, P.; Scully, J. E. C.; Jaumann, R.; Roatsch, T.; Preusker, F.; Nathues, A.; De Sanctis, M. C.; Russell, C. T.; Raymond, C. A.

    2015-12-01

    We used geologic mapping applied to Dawn spacecraft data as a tool to understand the geologic history of the Ac-H-13 Urvara Quadrangle of dwarf planet Ceres. This region, located between 21˚S-66˚S and 180-270˚E, is dominated by the Urvara basin in the east and cratered plains in the west. The elevation of the cratered plains is intermediate between the identified "highland" and "lowland" units of Ceres. Plains in the SW corner of the quadrangle are hummocky and heavily cratered, while the NW corner is smoother and less densely cratered. Features of note include 1) the 200 km diameter Urvara basin, which includes a degraded northern rim and smooth interior and exterior material that hosts a significantly lower impact crater density than most of the rest of Ceres' surface; 2) semi-radial curvilinear structures extending to the east and west of Urvara; 3) two large-scale dome structures 10s of km in diameter exterior to Urvara; and 4) numerous small-scale domical structures (<12 km diameter) associated with the smooth material interior to the basin. Key goals of the ongoing mapping are to assess the types of resurfacing processes that might be responsible for producing the smooth units, and to assess the processes responsible for the development of large and small dome structures. At the time of this writing geologic mapping was performed on Framing Camera (FC) mosaics from the Approach (1.3 km/px) and Survey (415 m/px) orbits, including clear filter and color images and digital terrain models derived from stereo images. In Fall 2015 images from the High Altitude Mapping Orbit (140 m/px) will be used to refine the mapping, followed by Low Altitude Mapping Orbit (35 m/px) images starting in December 2015. Support of the Dawn Instrument, Operations, and Science Teams is acknowledged. This work is supported by grants from NASA, the Max Planck Society and from the German and Italian Space Agencies.

  13. Simple Technique for in Field Samples Collection in the Cases of Skin Rash Illness and Subsequent PCR Detection of Orthopoxviruses and Varicella Zoster Virus

    PubMed Central

    Magazani, Edmond K.; Garin, Daniel; Muyembe, Jean-Jacques T.; Bentahir, Mostafa; Gala, Jean-Luc

    2014-01-01

    Background In case of outbreak of rash illness in remote areas, clinically discriminating monkeypox (MPX) from severe form of chickenpox and from smallpox remains a concern for first responders. Objective The goal of the study was therefore to use MPX and chickenpox outbreaks in Democratic Republic of Congo (DRC) as a test case for establishing a rapid and specific diagnosis in affected remote areas. Methods In 2008 and 2009, successive outbreaks of presumed MPX skin rash were reported in Bena Tshiadi, Yangala and Ndesha healthcare districts of the West Kasai province (DRC). Specimens consisting of liquid vesicle dried on filter papers or crusted scabs from healing patients were sampled by first responders. A field analytical facility was deployed nearby in order to carry out a real-time PCR (qPCR) assay using genus consensus primers, consensus orthopoxvirus (OPV) and smallpox-specific probes spanning over the 14 kD fusion protein encoding gene. A PCR-restriction fragment length polymorphism was used on-site as backup method to confirm the presence of monkeypox virus (MPXV) in samples. To complete the differential diagnosis of skin rash, chickenpox was tested in parallel using a commercial qPCR assay. In a post-deployment step, a MPXV-specific pyrosequencing was carried out on all biotinylated amplicons generated on-site in order to confirm the on-site results. Results Whereas MPXV proved to be the agent causing the rash illness outbreak in the Bena Tshiadi, VZV was the causative agent of the disease in Yangala and Ndesha districts. In addition, each on-site result was later confirmed by MPXV-specific pyrosequencing analysis without any discrepancy. Conclusion This experience of rapid on-site dual use DNA-based differential diagnosis of rash illnesses demonstrates the potential of combining tests specifically identifying bioterrorism agents and agents causing natural outbreaks. This opens the way to rapid on-site DNA-based identification of a broad spectrum of

  14. Ceres' deformational surface features compared to other planetary bodies.

    NASA Astrophysics Data System (ADS)

    von der Gathen, Isabel; Jaumann, Ralf; Krohn, Katrin; Buczkowski, Debra L.; Elgner, Stephan; Kersten, Elke; Matz, Klaus-Dieter; Nass, Andrea; Otto, Katharina; Preusker, Frank; Roatsch, Thomas; Schröder, Stefanus E.; Schulzeck, Franziska; Stephan, Katrin; Wagner, Roland; De Sanctis, Maria C.; Schenk, Paul; Scully, Jennifer E. C.; Williams, Dave A.; Raymond, Carol A.

    2016-04-01

    On March 2015, NASA's Dawn spacecraft arrived at the dwarf planet Ceres and has been providing images of its surface. Based on High Altitude Mapping Orbiter (HAMO) clear filter images (140 m/px res.), a Survey mosaic (~400 m/px) and a series of Low Altitude Mapping Orbiter (LAMO) clear filter images (35 m/px) of the Dawn mission [1], deformational features are identified on the surface of Ceres. In order to further our knowledge about the nature and origin of these features, we start a comparative analysis of similar features on different planetary bodies, like Enceladus, Ganymede and the Moon, based on images provided by the Cassini, Galileo and Lunar Orbiter mission. This study focuses on the small scale fractures, mostly located on Ceres' crater floors, in comparison with crater fractures on the planetary bodies named above. The fractures were analyzed concerning the morphology and shape, the distribution, orientation and possible building mechanisms. On Ceres, two different groups of fractures are distinct. The first one includes fractures, normally arranged in subparallel pattern, which are usually located on crater floors, but also on crater rims. Their sense of direction is relatively uniform but in some cases they get deformed by shearing. The second group consists of joint systems, which spread out of one single location, sometimes arranged concentric to the crater rim. They were likely formed by cooling-melting processes linked to the impact process or up doming material. Fractures located on crater floors are also common on the icy satellite Enceladus [3]. While Enceladus' fractures don't seem to have a lot in common compared to those on Ceres, we assume that similar fracture patterns and therefore similar building mechanism can be found e.g. on Ganymede and especially on the Moon [2]. Further work will include the comparison of the fractures with additional planetary bodies and the trial to explain why fracturing e.g. on Enceladus differs from that on

  15. Preliminary Geological Map of the Ac-H-7 Kerwan Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Williams, D. A.; Crown, D. A.; Mest, S. C.; Buczkowski, D.; Schenk, P.; Scully, J. E. C.; Jaumann, R.; Roatsch, T.; Preusker, F.; Platz, T.; Nathues, A.; Hoffmann, M.; Schäfer, M.; Marchi, S.; De Sanctis, M. C.; Russell, C. T.; Raymond, C. A.

    2015-12-01

    We used geologic mapping applied to Dawn spacecraft data as a tool to understand the geologic history of the Ac-H-7 Kerwan Quadrangle of dwarf planet Ceres. This region, located between 22˚S-22˚N and 72-144˚E, hosts four primary features: 1) the northern part of the 284 km diameter impact basin Kerwan in the center and SE corner of the quadrangle, whose rim is degraded and whose interior has been filled with a 'smooth material' that hosts a significantly lower impact crater density than most of the rest of Ceres' surface; 2) a portion of the 125 km diameter crater Dantu, whose ejecta field covers the NE corner of the quadrangle and where color data show both bright and dark materials, suggesting excavation of terrains of different compositions; 3) an unnamed double crater in the NW corner of the quadrangle surrounded by an ejecta field; and 4) a heavily cratered plains unit in the SW corner of the quadrangle that appears to be part of the dominant unit across Ceres surface. Key goals of the ongoing mapping are to assess the types of processes that might be responsible for resurfacing by the smooth unit, and understanding the nature of the variably-colored Dantu ejecta. The Dantu region is one of two longitudinally distinct regions on Ceres where ESA Hershel space telescope data suggested a release of water vapor (1). At the time of this writing geologic mapping was performed on Framing Camera (FC) mosaics from the Approach (1.3 km/px) and Survey (415 m/px) orbits, including grayscale and color images and digital terrain models derived from stereo images. In Fall 2015 images from the High Altitude Mapping Orbit (140 m/px) will be used to refine the mapping, followed by Low Altitude Mapping Orbit (35 m/px) images in January 2016. Support of the Dawn Instrument, Operations, and Science Teams is acknowledged. This work is supported by grants from NASA, and from the German and Italian Space Agencies. Reference: (1) Küppers, M., et al. (2014). Nature, v. 505, 525-527.

  16. Preliminary Geological Map of the Ac-H-6 Haulani Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Roatsch, T.; Krohn, K.; Jaumann, R.; Naß, A.; Otto, K.; Schroeder, S.; Williams, D. A.; Buczkowski, D.; Mest, S. C.; Scully, J. E. C.; von der Gathen, I.; Kersten, E.; Matz, K. D.; Pieters, C. M.; Preusker, F.; De Sanctis, M. C.; Schulzeck, F.; Stephan, K.; Tosi, F.; Wagner, R. J.; Zambon, F.; Russell, C.; Raymond, C. A.

    2015-12-01

    We used geologic mapping applied to Dawn spacecraft data as a tool to understand the geologic history of the Ac-H-6 Haulani Quadrangle of dwarf planet Ceres. This region, located between 22˚S-22˚N and 0-72˚E, is dominated by the 31km diameter Haulani impact crater in the west. Haulani shows a bright interior and is surrounded by bright ejecta, which preferentially extends westward. Photometrically corrected data show that small rays radially extend over several hundred kilometers to the west. A heavily cratered elevated plain extends around the equator to the NE, interrupted by a trough in the east. This plain seems to be part of a dominant geological unit crossing Ceres. A crater in the southern part of the plain reveals possible flow features extending to the NW, maybe of volcanic origin. The quadrangle is also affected by many impact craters with modified floors: smooth infilling, melted material, central peaks, possible domes and mass wasting. Some candidate volcanic domes occur in the northwestern and southern parts of the quadrangle. Linear depressions cross the quadrangle in W-E direction, with a slight tendency to NW. A set of small linear depressions close to each other are found in the SE. They are orientated in NW direction crossed by one in WE direction. At the time of writing, geologic mapping was performed on Framing Camera (FC) mosaics from the Approach (1.3 km/px) and Survey (415 m/px) orbits, including grayscale and color images and digital terrain models derived from stereo images. In Fall 2015 images from the High Altitude Mapping Orbit (140 m/px) will be available to refine the mapping, followed by Low Altitude Mapping Orbit (35 m/px) images in January 2016. The key goal of the ongoing mapping is to analyze, whether the origin of the bright material of the Haulani crater is endogenic or exogenic. Additionally, domes and linear depressions could be of volcanic and volcanic-tectonic origin. This work is supported by the HGF Postdoc Program.

  17. Search for Supernarrow Dibaryons Production in pd [right arrow] p + pX1 and pd [right arrow] p + dX2 Reactions

    NASA Astrophysics Data System (ADS)

    Fil'kov, L. V.; Kashevarov, V. L.; Konobeevski, E. S.; Mordovskoy, M. V.; Potashev, S. I.; Simonov, V. A.; Skorkin, V. M.

    2002-06-01

    We study a production of supernarrow dibaryons, the decay of which into two nucleons is forbidden by the Pauli exclusion principle, in the reactions pd [right arrow] p+pX1 and pd [right arrow] p + dX2 at Linear Accelerator of INR (Moscow). Dibaryons with masses 1904plus-or-minus2, 1926plus-or-minus2 and 1942plus-or-minus2 MeV have been observed in missing mass MpX1 spectra. In missing mass MX1 spectra, the peaks at MX1 = 966plus-or-minus2, 986plus-or-minus2, and 1003plus-or-minus2 MeV have been found. The analysis of the data obtained leads to the conclusion that the observed dibaryons are supernarrow dibaryons. The possible interpretation of "exotic baryon states" with small masses is discussed.

  18. SIMBIO-SYS for BepiColombo: status and issues.

    NASA Astrophysics Data System (ADS)

    Flamini, E.; Capaccioni, F.; Cremonese, G.; Palumbo, P.; Formaro, R.; Mugnuolo, R.; Debei, S.; Ficai Veltroni, I.; Dami, M.; Tommasi, L.; SIMBIO-SYS Team

    The SIMBIO-SYS (Spectrometer and Imaging for MPO BepiColombo Integrated Observatory SYStem) is a complex instrument suite part of the scientific payload of the Mercury Planetary Orbiter for the BepiColombo mission, the last of the cornerstone missions of the European Space Agency (ESA) Horizon+ science program. The BepiColombo mission is compose by two scientific satellites on, Mercury Magnetic Orbiter-MMO, realized by the Japanese Space Agency JAXA, devoted to the study of the planet environment and the other, the Mercury Planetary Orbiter realized by ESA, devoted to the detailed study of the Hermean surface and interior. The SIMBIOSYS instrument will provide all the science imaging capability of the Bepicolombo MPO spacecraft. It consists of three channels: the STereo imaging Channel (STC), with broad spectral band in the 400-950 nm range and medium spatial resolution (up to 50 m/px), that will provide Digital Terrain Model of the entire surface of the planet with an accuracy better than 80 m; the High Resolution Imaging Channel HRIC), with broad spectral bands in the 400-900 nm range and high spatial resolution (up to 5 m/px), that will provide high resolution images of about 20% of the surface, and the Visible and near-Infrared Hyperspectral Imaging channel (VIHI), with high spectral resolution (up to 6 nm) in the 400-2000 nm range and spatial resolution up to 100 m/px, it will provide the global covergae at 400 m/px with the spectral information. SIMBIO-SYS will provide unprecedented high-resolution images, the Digital Terrain Model of the entire surface, and the surface composition in wide spectral range, at resolutions and coverage higher than the MESSENGER mission with a full co-alignememt of the three channels. The main scientific objectives can be summarized as follows: Definition of the impact flux in the inner Solar System: based on the impact crater population records Understanding of the accretional model of an end member of the Solar System: based on

  19. Analysis of the seasonal and interannual evolution of Jakobshavn Isbrae from 2010-2013 using high spatial/temporal resolution DEM and velocity data

    NASA Astrophysics Data System (ADS)

    Shean, D. E.; Joughin, I. R.; Smith, B. E.; Moratto, Z. M.; Alexandrov, O.; Floricioiu, D.; Morin, P. J.; Porter, C. C.; Beyer, R. A.; Fong, T.

    2013-12-01

    Greenland's large marine-terminating outlet glaciers have displayed marked retreat, speedup, and thinning in recent decades. Jakobshavn Isbrae, one of Greenland's largest outlet glaciers, has retreated ~15 km, accelerated ~150%, and thinned ~200 m since the early 1990s. Here, we present the first comprehensive analysis of high spatial (~2-5 m/px) and temporal (daily-monthly) resolution elevation and velocity data for Jakobshavn from 7/2010 to 7/2013. We have developed an automated processing pipeline using open-source software (Ames Stereo Pipeline, GDAL/OGR, NumPy/SciPy, etc.) to produce orthoimage, digital elevation model (DEM), and surface velocity products from DigitalGlobe WorldView-1/2 stereo imagery (~0.5 m/px, ~17 km swath width). Our timeseries consists of 35 WV DEMs (~2-4 m/px) covering the lower trunks of the main+north branches and fjord, but also extending >110 km inland. We supplement this record with 7 TanDEM-X DEMs (~5 m/px, ~35 km swath width) between 6/2011-9/2012. Elevation data from IceBridge ATM/LVIS, ICESat GLAS, and GPS campaigns provide absolute control data over fixed surfaces (i.e., exposed bedrock). Observed WV DEM offsets are consistent with DigitalGlobe's published value of 5.0 m CE90/LE90 horizontal/vertical accuracy. After DEM co-registration, we observe sub-meter horizontal and vertical absolute accuracy. Velocity data are derived from TerraSAR-X data with 11 day repeat interval. Supplemental velocity data are derived through correlation of high-resolution WV DEM/image data. The contemporaneous DEM and velocity data provide full 3D displacement vectors for each time interval, allowing for the analysis of both Eulerian and Lagrangian elevation change. The lower trunk of Jakobshavn displays significant seasonal velocity variations, with recent rates of ~8 km/yr during winter to >17 km/yr during summer. DEM data show corresponding elevation changes of -30 to -45 m in summer and +15 to +20 m in winter, corresponding to integrated volumes

  20. Attenuation of monkeypox virus by deletion of genomic regions

    USGS Publications Warehouse

    Lopera, Juan G.; Falendysz, Elizabeth A.; Rocke, Tonie E.; Osorio, Jorge E.

    2015-01-01

    Monkeypox virus (MPXV) is an emerging pathogen from Africa that causes disease similar to smallpox. Two clades with different geographic distributions and virulence have been described. Here, we utilized bioinformatic tools to identify genomic regions in MPXV containing multiple virulence genes and explored their roles in pathogenicity; two selected regions were then deleted singularly or in combination. In vitro and in vivostudies indicated that these regions play a significant role in MPXV replication, tissue spread, and mortality in mice. Interestingly, while deletion of either region led to decreased virulence in mice, one region had no effect on in vitro replication. Deletion of both regions simultaneously also reduced cell culture replication and significantly increased the attenuation in vivo over either single deletion. Attenuated MPXV with genomic deletions present a safe and efficacious tool in the study of MPX pathogenesis and in the identification of genetic factors associated with virulence.

  1. Distribution, origin and evolution of hypothesized mud volcanoes, thumbprint terrain, small mounds and giant polygons: Implications for sedimentary processes in the northern lowlands of Mars: Case study from the Acidalia Planitia.

    NASA Astrophysics Data System (ADS)

    Orgel, Csilla; Hauber, Ernst; van Gasselt, Stephan; Pozzobon, Riccardo; Skinner, James, Jr.

    2016-04-01

    This study is part of the activities of an ISSI International Team, which intends to produce new geomorphological maps of the northern lowlands of Mars along three long traverses across Acidalia, Utopia, and Arcadia Planitiae [1]. This specific study focuses on mounds of different sizes: Large Pitted Mounds (LPM), Thumbprint Terrain (TPT), Small Mounds (SM) as well as km-sized, giant polygons (GP) [2,3]. These landforms were formed on the Vastitas Borealis Formation (VBF) Marginal and Interior Units, which are interpreted as outflow channel deposits or sediments of a hypothesized ocean. The aim of our study is to map the above mentioned features in the northern lowlands and establish a formational history and stratigraphy of landforms using morphological observations and geostatistics in Acidalia Planitia. Our study is based on CTX mosaics (6 m/pixel) and we also used data from HiRISE (0.25 m/px), HRSC (images >10 m/px, HRSC- derived Digital Elevation Models [DEM], grid size 50-200 m), MOLA DEM (~460 m/px), and THEMIS Nighttime IR (~100 m/px). The TPT appears north of about 30°N in the termination zones of the Chryse outflow channels and shows a transition zone with the LPMs at around 36°N in Acidalia Planitia. North of 39°N, only LPM can be observed. LPM are typically surrounded by topographic moats. Sometimes more than 75% of a mound can be covered or embayed by „plain filling material" of varying thickness. The LPM are observed in the same area as large-scale polygon troughs (buried and fresh) associated with circular-shaped small mounds (SM). The SM are located from 34°N to 48°N, completely overlapping the area of LPM and partly the TPT. These features are randomly distributed, but commonly arranged in clusters. Their domical shape with the central pit shows morphological resemblance with the LPM. These features characterize the area from 35 N° to 61 N° and completely disappear in the Acidalia Colles region. The mapping results show a morphological

  2. Mars Express HRSC View of Western Olympus Mons: Evidence for Ice-bearing Deposit and High-Altitude Glaciation

    NASA Technical Reports Server (NTRS)

    Basilevsky, A. T.; Neukam, G.; Ivanov, B. A.; Werner, S. C.; vanGesselt, S.; Head, J. W.; Hauber, E.

    2005-01-01

    This study is based on the geological analysis of the HRSC images taken on the orbit 0143 (12 m/px in nadir channel). The study area includes the western segment of Olympus Mons and the adjacent lowland plains (Fig. 1). Part of the volcano above the scarp is rather flat and is called "summit plateau" below. What is often called the volcano scarp is a slope classified into three morphologic types: Type 1 (S1 in Fig.1) is the steepest and dominated by ravines in its upper part and by talus beneath; Type 2 (S2) is intermediate in steepness and dominated by downslope trending linear depressions, part of which have channel-like morphology; and Type 3 (S3), is the most gentle and covered by lava flows, continuing from the summit plateau down to the lowland plains.

  3. First analysis of the size-frequency distribution of boulders ge 7m on comet 67P

    NASA Astrophysics Data System (ADS)

    Pajola, M.; Vincent, J. B.; Güttler, C.; Lee, J.-C.; Massironi, M.; Bertini, I.; Simioni, E.; Marzari, F.; Giacomini, L.; Barbieri, C.; Cremonese, G.; Naletto, G.; Pommerol, A.; El Maarry, M. R.; Besse, S.; Küppers, M.; La Forgia, F.; Lazzarin, M.; Thomas, N.; Auger, A. T.; Ip, W.-H.; Lin, Z.-Y.; Sierks, H.; OSIRIS Team; A'Hearn, M. F.; Barucci, M. A.; Bertaux, J.-L.; Da Deppo, V.; Davidsson, B.; De Cecco, M.; Debei, S.; Ferri, F.; Fornasier, S.; Fulle, M.; Groussin, O.; Gutierrez, P. J.; Hviid, S. F.; Jorda, L.; Keller, H. U.; Knollenberg, J.; Koschny, D.; Kramm, J.-R.; Kürt, E.; Lamy, P.; Lara, L. M.; Lopez Moreno, J. J.; Magrin, S.; Michalik, H.; Moissl, R.; Mottola, S.; Oklay, N.; Preusker, F.; Rickman, H.; Rodrigo, R.; Scholten, F.; Tubiana, C.

    Images of the surface of comet 67P Churyumov-Gerasimenko taken by the OSIRIS camera on board the Rosetta spacecraft have been used to study the statistical distribution and morphological properties of both cluster and isolated roundish structures ('boulders') scattered all over the surface. We used NAC images taken on Aug 5-6, 2014, at a distance between 131.45 - 109.76 km, with a spatial resolution ranging from 2.44 - 2.03 m/px (Fig. 1). Such data cover a full rotation of 67P, providing the first ever full size frequency distribution coverage of boulders ≥ 7m visible on a cometary illuminated side. Boulders are ubiquitous on the head, neck, and body of 67P \\citep{thomas15}. The initial count of 4,976 boulders was reduced to 3,546 for statistical purposes taking into consideration only those with a diameter larger than 7 m \\citep{pajola15}.

  4. Skin tightening with fractional lasers, radiofrequency, Smartlipo.

    PubMed

    Collawn, Sherry S

    2010-05-01

    Skin tightening occurs with the use of fractional lasers, radiofrequency, and Smartlipo. The fractional lasers Fraxel (1550 nm; Solta Medical, Inc., Hayward, CA) and Affirm (1440 nm, 1320 nm) (Cynosure, Westford, MA) when used in combination tighten skin and lessen solar keratoses, and improve acne scars. With radiofrequency, further tightening occurs. Smartlipo (Cynosure, Westford, MA) (1064 nm or the newer MPX with combined 1064 nm and 1320 nm) results in skin tightening and has been very helpful in improving skin tightness and smoothness on the neck either singularly or in combination with the above procedures; and with the addition of the Affirm fractional CO2 laser (Cynosure, Westford, MA), further skin improvement and tightening occurs.

  5. Quantifying Ice-sheet/Ice-shelf Dynamics and Variability with Meter-scale DEM and Velocity Timeseries

    NASA Astrophysics Data System (ADS)

    Shean, D. E.; Joughin, I. R.; Smith, B. E.; Moratto, Z. M.; Porter, C.; Morin, P. J.

    2012-12-01

    Both the Antarctic and Greenland ice sheets are losing mass at an increasing rate, although loss due to accelerating flow and dynamic thinning remains poorly understood. We are using complementary data from repeat satellite and airborne observations to investigate the relationship between ice-sheet/ice-shelf dynamics and geometry on seasonal to interannual timescales. High-resolution along-track stereo imagery from commercial satellite vendors DigitalGlobe and GeoEye provides unprecedented spatial (~0.5 m/px with ~17 km swath width) and temporal (weekly/monthly) resolution for these efforts. We have developed an automated pipeline using open-source software to produce orthoimage, DEM, and surface velocity products from DigitalGlobe imagery. High-contrast surface texture (e.g. sastrugi, crevasses) visible at sub-meter resolution provides near-perfect image correlation (~99% success rate) during DEM and velocity map derivation. Elevation data from IceBridge ATM/LVIS, ICESat GLAS, and GPS campaigns are used to correct DEMs and perform accuracy assessment. Preliminary tests over exposed bedrock provide relative vertical accuracy estimates of <1-2 m for Worldview-1/2 DEMs. Velocity data from TerraSAR-X and GPS campaigns provide validation for surface velocity products, with horizontal error estimates of <10 m. Velocity and elevation change products with 2-4 m/px spatial resolution allow for unprecedented 3D dynamic characterization of sub-km flow transition zones (e.g. grounding lines, shear margins), capturing both local and regional variations due to melting and dynamic thinning. We present timeseries for West Greenland (Jakobshavn front - 20 observations, Jakobshavn south catchment - 10) and West Antarctica (Pine Island and Thwaites - 5 each) from 2009-2012. These observations complement ongoing efforts to measure and model outlet glacier dynamics, with implications for future ice-sheet mass balance estimates.

  6. Evaluation of H.264 and H.265 full motion video encoding for small UAS platforms

    NASA Astrophysics Data System (ADS)

    McGuinness, Christopher D.; Walker, David; Taylor, Clark; Hill, Kerry; Hoffman, Marc

    2016-05-01

    Of all the steps in the image acquisition and formation pipeline, compression is the only process that degrades image quality. A selected compression algorithm succeeds or fails to provide sufficient quality at the requested compression rate depending on how well the algorithm is suited to the input data. Applying an algorithm designed for one type of data to a different type often results in poor compression performance. This is mostly the case when comparing the performance of H.264, designed for standard definition data, to HEVC (High Efficiency Video Coding), which the Joint Collaborative Team on Video Coding (JCT-VC) designed for high-definition data. This study focuses on evaluating how HEVC compares to H.264 when compressing data from small UAS platforms. To compare the standards directly, we assess two open-source traditional software solutions: x264 and x265. These software-only comparisons allow us to establish a baseline of how much improvement can generally be expected of HEVC over H.264. Then, specific solutions leveraging different types of hardware are selected to understand the limitations of commercial-off-the-shelf (COTS) options. Algorithmically, regardless of the implementation, HEVC is found to provide similar quality video as H.264 at 40% lower data rates for video resolutions greater than 1280x720, roughly 1 Megapixel (MPx). For resolutions less than 1MPx, H.264 is an adequate solution though a small (roughly 20%) compression boost is earned by employing HEVC. New low cost, size, weight, and power (CSWAP) HEVC implementations are being developed and will be ideal for small UAS systems.

  7. 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.

  8. Polymerase chain reaction-free detection of hepatitis B virus DNA using a nanostructured impedance biosensor.

    PubMed

    Chen, Chun-Cheng; Lai, Zi-Lun; Wang, Gou-Jen; Wu, Chun-Ying

    2016-03-15

    A polymerase chain reaction (PCR)-free technique for the effective detection of genomic length hepatitis B virus (HBV) DNA is described in this study. The honeycomb-like barrier layer of an anodic aluminum oxide (AAO) film having a uniform nanohemisphere array was used as the substrate of the sensing electrode. A 30-nm gold film was sputtered onto the AAO barrier layer surface as the electrode, followed by electrochemical deposition of gold nanoparticles (GNPs) on the hemisphere surface. A specially designed single-strand 96-mer gene fragment of the target genomic DNA of HBV based on the genome sequences of HBV was immobilized on the nanostructured electrode as the capture probe. Target HBV DNA obtained from clinical samples was hybridized to the sensing probes. Detection results illustrate two dynamic linear ranges, 10(2)-10(3) and 10(3)-10(5.1) copies/mL, having R(2) values of 0.801 and 0.996 could be obtained, respectively. The detection limit of the proposed sending scheme was measured to be 111 copies/mL. The total of 45 target samples, including 20 samples with HBV concentration being lower than 10(2) copies/mL and 25 samples with HBV concentration being in the range of 10(3)-10(5.1) copies/mL, were used for real test. The concentration of these 45 HBV DNA samples was measured by the COBAS Ampliprep system. Comparing the measured results of the COBAS Ampliprep and our system, it was illustrated that the HBV DNA concentrations measured by the proposed method in this study had a high linear correlation with the COBAS Ampliprep, having R(2) values of 0.983. The proposed sensing scheme is highly feasible for future clinical applications.

  9. Analytic characteristics of three Bayer contour blood glucose monitoring systems in neonates.

    PubMed

    Dietzen, Dennis J; Nenninger, Denise A; Simmons, David A; Pardo, Scott; Pandya, Mauli; Fullam, Jeanellen

    2015-03-01

    Hypoglycemia in infants is common, is difficult to recognize, and may lead to permanent neurologic impairment. Low glucose concentrations and high hematocrits in newborns pose significant analytic challenges for whole blood glucose meters. Three Bayer glucose monitoring systems were evaluated using 211 blood samples from 162 neonates (age range 5 hours to 29 days, median age 3 days). Hematocrit and whole blood glucose were determined in heparinized whole blood, and plasma glucose was determined using the Roche Cobas 6000. Accuracy was evaluated against plasma concentrations using ISO 15197:2013 and CLSI POCT 12-A3 criteria. Glucose imprecision on the Cobas system was 1.8-2.6% (CV) from 26-610 mg/dL. Imprecision across all meter systems was 2.8% (CV) at 130 mg/dL. Glucose concentrations, hematocrit, and total bilirubin ranged from 20-150 mg/dL, 18 -75%, and 0.5-19.6 mg/dL, respectively. Linear regression analysis of whole blood versus plasma for the 3 combined systems yielded an average slope of 1.06 and correlation coefficient greater than 0.980. Bias between the Contour and Cobas was not significantly correlated with hematocrit. Greater than 99% of meter results were within 15 mg/dL and 20% of plasma results at glucose concentrations ≤ 75 and > 75 mg/dL, respectively. Of meter results, 97% were within 12.5 mg/dL of plasma results at concentrations ≤ 100 mg/dL, while 96% of meter results were within 12.5% of plasma at concentrations > 100 mg/dL. The Bayer CONTOUR Blood Glucose Monitoring Systems exceed ISO 15197:2013 and CLSI criteria in neonatal blood samples.

  10. Feasibility and accuracy evaluation of three human papillomavirus assays for FTA card-based sampling: a pilot study in cervical cancer screening.

    PubMed

    Wang, Shao-Ming; Hu, Shang-Ying; Chen, Wen; Chen, Feng; Zhao, Fang-Hui; He, Wei; Ma, Xin-Ming; Zhang, Yu-Qing; Wang, Jian; Sivasubramaniam, Priya; Qiao, You-Lin

    2015-11-04

    Liquid-state specimen carriers are inadequate for sample transportation in large-scale screening projects in low-resource settings, which necessitates the exploration of novel non-hazardous solid-state alternatives. Studies investigating the feasibility and accuracy of a solid-state human papillomavirus (HPV) sampling medium in combination with different down-stream HPV DNA assays for cervical cancer screening are needed. We collected two cervical specimens from 396 women, aged 25-65 years, who were enrolled in a cervical cancer screening trial. One sample was stored using DCM preservative solution and the other was applied to a Whatman Indicating FTA Elute® card (FTA card). All specimens were processed using three HPV testing methods, including Hybrid capture 2 (HC2), careHPV™, and Cobas®4800 tests. All the women underwent a rigorous colposcopic evaluation that included using a microbiopsy protocol. Compared to the liquid-based carrier, the FTA card demonstrated comparable sensitivity for detecting high grade Cervical Intraepithelial Neoplasia (CIN) using HC2 (91.7 %), careHPV™ (83.3 %), and Cobas®4800 (91.7 %) tests. Moreover, the FTA card showed a higher specificity compared to a liquid-based carrier for HC2 (79.5 % vs. 71.6 %, P = 0.015), comparable specificity for careHPV™ (78.1 % vs. 73.0 %, P > 0.05), but lower specificity for the Cobas®4800 test (62.4 % vs. 69.9 %, P = 0.032). Generally, the FTA card-based sampling medium's accuracy was comparable with that of liquid-based medium for the three HPV testing assays. FTA cards are a promising sample carrier for cervical cancer screening. With further optimization, it can be utilized for HPV testing in areas of varying economic development.

  11. Reference intervals for C-peptide and insulin derived from a general adult Danish population.

    PubMed

    Larsen, Pia Bükmann; Linneberg, Allan; Hansen, Torben; Friis-Hansen, Lennart

    2017-05-01

    Despite international efforts to standardize C-peptide and insulin calibrators and immunoassays, platform dependent differences still exist, and platform specific reference intervals are hence needed for correct interpretation. We therefore wanted to establish traceable reference intervals for C-peptide and insulin. In 623 consecutively recruited participants, insulin and C-peptide were measured using the Cobas e411 (Roche Diagnostics, Switzerland). Participants with diabetes were excluded (fasting Glucose ≥7.0mmol/L or HbA1c≥6.5%/≥48mmol/L) and reference intervals were calculated with and without the inclusion of persons who were prediabetic, according to two definitions (The World Health Organization (WHO) and American Diabetes Association (ADA)). To ensure the correctness of calibration, the control pools were analyzed by a reference laboratory. The reference intervals were calculated according to the IFCC guidelines, using the RefVal software (Solberg, Oslo, Norway). Comparison of our results with those from the reference laboratory revealed equivalence for C-peptide results whereas the insulin determined on the Cobas e411 assay were 15-20% higher. The difference is attributed to an incorrect conversion factor for converting from activity to metric units. The Cobas e411 assay uses the factor 6.945 for converting from U/mL to pmol/L. This is in disagreement with the biological activity of insulin which is 166.8×10(6)IU/mol or 6.00nmol/IU. We successfully established reference intervals for C-peptide and insulin for non-diabetic and prediabetic participants. The reference intervals for fasting C-peptide and fasting insulin are ready for implementation. A recertification of the insulin standards is needed. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Diol Dehydratase-Reactivase Is Essential for Recycling of Coenzyme B12 in Diol Dehydratase.

    PubMed

    Toraya, Tetsuo; Tanokuchi, Aya; Yamasaki, Ai; Nakamura, Takehiro; Ogura, Kenichi; Tobimatsu, Takamasa

    2016-01-12

    Holoenzymes of adenosylcobalamin-dependent diol and glycerol dehydratases undergo mechanism-based inactivation by glycerol and O2 inactivation in the absence of substrate, which accompanies irreversible cleavage of the coenzyme Co-C bond. The inactivated holodiol dehydratase and the inactive enzyme·cyanocobalamin complex were (re)activated by incubation with NADH, ATP, and Mg(2+) (or Mn(2+)) in crude extracts of Klebsiella oxytoca, suggesting the presence of a reactivating system in the extract. The reducing system with NADH could be replaced by FMNH2. When inactivated holoenzyme or the enzyme·cyanocobalamin complex, a model of inactivated holoenzyme, was incubated with purified recombinant diol dehydratase-reactivase (DD-R) and an ATP:cob(I)alamin adenosyltransferase in the presence of FMNH2, ATP, and Mg(2+), diol dehydratase activity was restored. Among the three adenosyltransferases (PduO, EutT, and CobA) of this bacterium, PduO and CobA were much more efficient for the reactivation than EutT, although PduO showed the lowest adenosyltransfease activity toward free cob(I)alamin. These results suggest that (1) diol dehydratase activity is maintained through coenzyme recycling by a reactivating system for diol dehydratase composed of DD-R, PduO adenosyltransferase, and a reducing system, (2) the releasing factor DD-R is essential for the recycling of adenosycobalamin, a tightly bound, prosthetic group-type coenzyme, and (3) PduO is a specific adenosylating enzyme for the DD reactivation, whereas CobA and EutT exert their effects through free synthesized coenzyme. Although FMNH2 was mainly used as a reductant in this study, a natural reducing system might consist of PduS cobalamin reductase and NADH.

  13. Head-to-head comparison of second-generation nucleic acid amplification tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae on urine samples from female subjects and self-collected vaginal swabs.

    PubMed

    Chernesky, Max; Jang, Dan; Gilchrist, Jodi; Hatchette, Todd; Poirier, André; Flandin, Jean-Frederic; Smieja, Marek; Ratnam, Sam

    2014-07-01

    In a comparison of 4 second-generation nucleic acid amplification tests performed with self-collected vaginal swab (SCVS) and first-void urine (FVU) specimens from 575 women, SCVS specimens indicated more infections than did FVU specimens in all assays. The prevalence rates were 9% (53/575 patients) for Chlamydia trachomatis and 2% (11/575 patients) for Neisseria gonorrhoeae. The clinical sensitivities for testing SCVS specimens for C. trachomatis were 98.1% on a Tigris system and 96.2% on a Panther system for the Aptima Combo 2 assay (Hologic Gen-Probe), 98.0% for the RealTime CT/NG assay on an m2000 instrument (Abbott), 90.6% for the ProbeTec CT/GC Q(x) assay on the Viper system (Becton Dickinson), and 84.6% for the cobas CT/NG assay on the cobas 4800 platform (Roche). Clinical sensitivities for C. trachomatis in FVU specimens were 88.7% (Tigris) and 88.0% (Panther) for the Aptima Combo 2 assay, 76.9% for the RealTime CT/NG assay, 75.5% for the ProbeTec CT/GC Q(x) assay, and 81.1% for the cobas CT/NG assay. Clinical sensitivities of the assays for N. gonorrhoeae, with limited positive results, ranged from 63.6% to 100%. Specificities for both infections ranged from 98.4 to 100%. Differences in analytical sensitivities and levels of molecular targets in clinical samples but not inhibitors of amplification may explain the differences in clinical sensitivities.

  14. Workflow and maintenance characteristics of five automated laboratory instruments for the diagnosis of sexually transmitted infections.

    PubMed

    Ratnam, Sam; Jang, Dan; Gilchrist, Jodi; Smieja, Marek; Poirier, Andre; Hatchette, Todd; Flandin, Jean-Frederic; Chernesky, Max

    2014-07-01

    The choice of a suitable automated system for a diagnostic laboratory depends on various factors. Comparative workflow studies provide quantifiable and objective metrics to determine hands-on time during specimen handling and processing, reagent preparation, return visits and maintenance, and test turnaround time and throughput. Using objective time study techniques, workflow characteristics for processing 96 and 192 tests were determined on m2000 RealTime (Abbott Molecular), Viper XTR (Becton Dickinson), cobas 4800 (Roche Molecular Diagnostics), Tigris (Hologic Gen-Probe), and Panther (Hologic Gen-Probe) platforms using second-generation assays for Chlamydia trachomatis and Neisseria gonorrhoeae. A combination of operational and maintenance steps requiring manual labor showed that Panther had the shortest overall hands-on times and Viper XTR the longest. Both Panther and Tigris showed greater efficiency whether 96 or 192 tests were processed. Viper XTR and Panther had the shortest times to results and m2000 RealTime the longest. Sample preparation and loading time was the shortest for Panther and longest for cobas 4800. Mandatory return visits were required only for m2000 RealTime and cobas 4800 when 96 tests were processed, and both required substantially more hands-on time than the other systems due to increased numbers of return visits when 192 tests were processed. These results show that there are substantial differences in the amount of labor required to operate each system. Assay performance, instrumentation, testing capacity, workflow, maintenance, and reagent costs should be considered in choosing a system. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  15. [Setting up of 15 POC blood gas analyzers at Montpellier Hosptital (France)].

    PubMed

    Marrocco, Alexandre; Cristol, Jean-Paul; Boularan, Anne-Marie

    2016-01-01

    The purpose of this article is to describe the setting up of 15 blood gas analyzers GEM(®) Premier™ 4000 (IL) at Montpellier hospital. This experience includes analytical characterization (within and between run coefficient of variation) using GSE and GHE IL controls, correlation of 35 samples with a routinely used laboratory blood gas analyzer (Cobas b221, Roche(®)). We shall also develop the training, the habilitation and its follow-up for the user staff (450 people) of the different hospital's units in the aim of the accreditation.

  16. EGFR mutation detection in ctDNA from NSCLC patient plasma: A cross-platform comparison of leading technologies to support the clinical development of AZD9291.

    PubMed

    Thress, Kenneth S; Brant, Roz; Carr, T Hedley; Dearden, Simon; Jenkins, Suzanne; Brown, Helen; Hammett, Tracey; Cantarini, Mireille; Barrett, J Carl

    2015-12-01

    To assess the ability of different technology platforms to detect epidermal growth factor receptor (EGFR) mutations, including T790M, from circulating tumor DNA (ctDNA) in advanced non-small cell lung cancer (NSCLC) patients. A comparison of multiple platforms for detecting EGFR mutations in plasma ctDNA was undertaken. Plasma samples were collected from patients entering the ongoing AURA trial (NCT01802632), investigating the safety, tolerability, and efficacy of AZD9291 in patients with EGFR-sensitizing mutation-positive NSCLC. Plasma was collected prior to AZD9291 dosing but following clinical progression on a previous EGFR-tyrosine kinase inhibitor (TKI). Extracted ctDNA was analyzed using two non-digital platforms (cobas(®) EGFR Mutation Test and therascreen™ EGFR amplification refractory mutation system assay) and two digital platforms (Droplet Digital™ PCR and BEAMing digital PCR [dPCR]). Preliminary assessment (38 samples) was conducted using all four platforms. For EGFR-TKI-sensitizing mutations, high sensitivity (78-100%) and specificity (93-100%) were observed using tissue as a non-reference standard. For the T790M mutation, the digital platforms outperformed the non-digital platforms. Subsequent assessment using 72 additional baseline plasma samples was conducted using the cobas(®) EGFR Mutation Test and BEAMing dPCR. The two platforms demonstrated high sensitivity (82-87%) and specificity (97%) for EGFR-sensitizing mutations. For the T790M mutation, the sensitivity and specificity were 73% and 67%, respectively, with the cobas(®) EGFR Mutation Test, and 81% and 58%, respectively, with BEAMing dPCR. Concordance between the platforms was >90%, showing that multiple platforms are capable of sensitive and specific detection of EGFR-TKI-sensitizing mutations from NSCLC patient plasma. The cobas(®) EGFR Mutation Test and BEAMing dPCR demonstrate a high sensitivity for T790M mutation detection. Genomic heterogeneity of T790M-mediated resistance may

  17. [Pediatric reference intervals : retrospective study on thyroid hormone levels].

    PubMed

    Ladang, A; Vranken, L; Luyckx, F; Lebrethon, M-C; Cavalier, E

    2017-01-01

    Defining reference range is an essential tool for diagnostic. Age and sexe influences on thyroid hormone levels have been already discussed. In this study, we are defining a new pediatric reference range for TSH, FT3 and FT4 for Cobas C6000 analyzer. To do so, we have taken in account 0 to 18 year old outclinic patients. During the first year of life, thyroid hormone levels change dramatically before getting stabilized around 3 years old. We also compared our results to those obtained in a Canadian large-scale prospective study (the CALIPER initiative).

  18. [Validation of plasma creatinine measurement on UniCel DxC 600 according to LAB GTA 04 recommendation].

    PubMed

    Chianea, Denis; Renard, Christophe; Garcia, Carine; Mbongo, Elvire; Monpeurt, Corine; Vest, Philippe

    2010-01-01

    The accreditation process, according to NF EN ISO 15189, implies a prior evaluation of the new reagent on-site for the implementation of each new assay technique. Thus, our new standardized method for determination of creatinine (non compensated method) in plasma or serum on UniCel DxC 600 (Beckman Coulter) has been tested according to LAB GTA 04 protocol. The reagent meets the quality criteria recommended by Valtec protocol, except fidelity with the low concentration standard (50 micromol/L). Besides there is no problem of results transferability with the two other techniques used in the laboratory (Jaffe compensated and enzymatic methods performed on Cobas Integra 800).

  19. Comparison of three real-time PCR assays for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in young pregnant women.

    PubMed

    Peuchant, Olivia; de Diego, Sabrina; Le Roy, Chloé; Frantz-Blancpain, Sandrine; Hocké, Claude; Bébéar, Cécile; de Barbeyrac, Bertille

    2015-12-01

    We compared 3 commercial real-time PCR assays, the Abbott RealTime CT/NG, the cobas® 4800 CT/NG, and the Cepheid Xpert® CT/NG, for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in vaginal swabs collected prospectively from pregnant women aged <25 years. The overall agreement among 2 assays ranged from 98.9% to 99.5% with a kappa score between 0.94 and 0.97 for C. trachomatis. For N. gonorrhoeae, the overall agreement was 100%. All kits allowed prompt and specific results for C. trachomatis and N. gonorrhoeae in young pregnant women.

  20. Interactions between Hepatitis C Virus and the Human Apolipoprotein H Acute Phase Protein: A Tool for a Sensitive Detection of the Virus

    PubMed Central

    Dubois, Grégor; Kaiser, Marco; Lucarz, Estelle; Gobby, Delphine; Bray, Dorothy; Ellerbrok, Heinz; Zarski, Jean Pierre; Veas, Francisco

    2015-01-01

    The Hepatitis C virus (HCV) infection exhibits a high global prevalence frequently associated with hepatocellular carcinoma, taking years to develop. Despite the standardization of highly sensitive HCV quantitative RT-PCR (qRT-PCR) detection methods, false-negative diagnoses may be generated with current methods, mainly due to the presence of PCR inhibitors and/or low viral loads in the patient’s sample. These false-negative diagnoses impact both public health systems, in developing countries, and an in lesser extent, in developed countries, including both the risk of virus transmission during organ transplantation and/or blood transfusion and the quality of the antiviral treatment monitoring. To adopt an appropriate therapeutic strategy to improve the patient’s prognosis, it is urgent to increase the HCV detection sensitivity. Based upon previous studies on HBV, we worked on the capacity of the scavenger acute phase protein, Apolipoprotein H (ApoH) to interact with HCV. Using different approaches, including immunoassays, antibody-inhibition, oxidation, ultracentrifugation, electron microscopy and RT-PCR analyses, we demonstrated specific interactions between HCV particles and ApoH. Moreover, when using a two-step HCV detection process, including capture of HCV by ApoH-coated nanomagnetic beads and a home-made real-time HCV-RT-PCR, we confirmed the presence of HCV for all samples from a clinical collection of HCV-seropositive patients exhibiting an RT-PCR COBAS® TaqMan® HCV Test, v2.0 (COBAS)-positive result. In contrast, for HCV-seropositive patients with either low HCV-load as determined with COBAS or exhibiting HCV-negative COBAS results, the addition of the two-step ApoH-HCV-capture and HCV-detection process was able to increase the sensitivity of HCV detection or more interestingly, detect in a genotype sequence-independent manner, a high-proportion (44%) of HCV/RNA-positive among the COBAS HCV-negative patients. Thus, the immune interaction between Apo

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

    PubMed

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

    2013-07-01

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

  2. Retrospective analysis of 88,429 serum and urine glucose EQA results obtained from professional laboratories and medical offices participating in surveys organized by three European EQA centers between 1996 and 2007.

    PubMed

    Morandi, Pierre-Alain; Deom, André; Kesseler, Dagmar; Cohen, Richard

    2010-09-01

    The aim of this study was to provide inter-laboratory imprecision comparisons of different groups of diagnostic systems as well as a comparison of professional laboratories with medical offices performance on the basis of 88,429 glucose results obtained in external quality assessment (EQA) schemes organized by three European EQA centers between 1996 and 2007. A simple, non-parametrical statistical model suited to all EQA results, including outliers, was used to calculate yearly and global performance. The best performance was obtained from professional laboratories with a group of three diagnostic systems--Hitachi, Integra, and Vitros, followed by Cobas Mira, and finally by Reflotron. For medical offices, the best performance was achieved with the Cobas Mira diagnostic systems, followed by the Reflotron, SpotChem, and Vitros DT60 diagnostic systems. A slight but overall improvement in performance over time was observed for most diagnostic devices. The analysis of glucose EQA results collected over a 12-year period showed that professional laboratories obtained better performances than medical offices, and that a general improvement in yearly performance was observed for both types of laboratories.

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

    PubMed

    McNicol, J; Debattista, J

    2013-06-01

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

  4. Comparison of two molecular assays for detection of cytomegalovirus DNA in whole blood and plasma samples from transplant recipients.

    PubMed

    Costa, Cristina; Sidoti, Francesca; Mantovani, Samantha; Gregori, Gabriella; Proietti, Alex; Ghisetti, Valeria; Cavallo, Rossana

    2016-07-01

    In immunosuppressed patients, pre-emptive therapy and a strict follow-up of CMV infection are the standard of care for the prevention of CMV disease. Several real-time PCR assays for CMV DNA quantification on whole blood (WB) and plasma (PL) are commercially available. This study compared and correlated CMV viral loads obtained by the Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) platform on plasma specimens with those obtained on corresponding whole blood specimens by the real-time PCR assay (ELITe MGB-CMV) in 185 sequential samples from 41 immunosuppressed patients. Correlation between the two assays was good. Kinetics of CMV DNA within the same patient was similar, but PL viral load was constantly 1 log lower than WB. In patients under antiviral therapy, low level of CMV DNA persisted in WB, while it was absent in PL. The good correlation between CMV DNA detected on both PL and WB supports the reliability of the two matrices for viral monitoring and the therapeutic management of CMV infection. Nevertheless, due to significant quantification differences between PL and WB CMV DNA, the same biological specimen should be used for a sequential and reliable follow-up of patients at high risk of CMV infection.

  5. Performance and Logistical Challenges of Alternative HIV-1 Virological Monitoring Options in a Clinical Setting of Harare, Zimbabwe

    PubMed Central

    Bronze, Michelle; Wellington, Maureen; Boender, Tamara Sonia; Manting, Corry; Steegen, Kim; Luethy, Rudi; Rinke de Wit, Tobias

    2014-01-01

    We evaluated a low-cost virological failure assay (VFA) on plasma and dried blood spot (DBS) specimens from HIV-1 infected patients attending an HIV clinic in Harare. The results were compared to the performance of the ultrasensitive heat-denatured p24 assay (p24). The COBAS AmpliPrep/COBAS TaqMan HIV-1 test, version 2.0, served as the gold standard. Using a cutoff of 5,000 copies/mL, the plasma VFA had a sensitivity of 94.5% and specificity of 92.7% and was largely superior to the VFA on DBS (sensitivity = 61.9%; specificity = 99.0%) or to the p24 (sensitivity = 54.3%; specificity = 82.3%) when tested on 302 HIV treated and untreated patients. However, among the 202 long-term ART-exposed patients, the sensitivity of the VFA decreased to 72.7% and to 35.7% using a threshold of 5,000 and 1,000 RNA copies/mL, respectively. We show that the VFA (either on plasma or on DBS) and the p24 are not reliable to monitor long-term treated, HIV-1 infected patients. Moreover, achieving acceptable assay sensitivity using DBS proved technically difficult in a less-experienced laboratory. Importantly, the high level of virological suppression (93%) indicated that quality care focused on treatment adherence limits virological failure even when PCR-based viral load monitoring is not available. PMID:25025031

  6. Semi-quantitative real-time PCR: A useful approach to identify persons with low replicative chronic hepatitis B.

    PubMed

    Castéra-Guy, Joany; Rubbo, Pierre-Alain; Kania, Dramane; Lemoine, Maud; Van de Perre, Philippe; Tuaillon, Edouard

    2017-06-01

    Antiviral therapy can be avoided during the low replicative phase of chronic Hepatitis B virus (HBV) infection which is characterized notably by HBV DNA concentration below 2000IU/ml. Simplified diagnostic tests can improve access to HBV DNA monitoring in resource-limited settings. The capacity of a new semi-quantitative real-time PCR approach based on sample-to-standard relative detection of the target to discriminate samples with HBV DNA levels above or below the clinical threshold of 2000IU/ml was compared to a quantitative assay (Roche CobasAmpliPrep/CobasTaqMan HBV Test v2.0). The semi-quantitative assay correctly identified 40/40 (100%) low replicative HBV DNA patients and 58/61 (95%) samples from HBV-infected subjects with moderate/high levels of viral DNA. Our results suggested that this alternative PCR test is efficient to guide therapeutic decision based on identification of low replicative HBV infection from all of the chronic hepatitis B carriers requiring treatment, and may be useful in resource-limited settings where the vast majority of cases live. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Automated determination of cross-linked fibrin derivatives in plasma.

    PubMed

    Elms, M J; Bundesen, P G; Rowbury, D; Goodall, S; Wakeham, N; Rowell, J A; Hillyard, C J; Rylatt, D B

    1993-02-01

    Automated assays for the measurement of cross-linked fibrin derivatives in plasma (XL-FbDP) have been developed utilizing latex beads coated with anti-D dimer monoclonal antibody (DD-3B6/22) for both the Cobas Fara Chemistry Centrifugal and the Cobas Mira analysers (Roche, Basle, Switzerland). The analysers were programmed to mix plasma and latex reagent simultaneously and analyse absorbance changes over a 10-15 min period. Results were interpolated by the analyser from a standard curve derived from a polymer of D-dimer. Both assays had high precision (< 5% CV) for values between 100 and 1000 ng/ml and provided clear discrimination between normal samples and samples from patients suffering from the thrombotic diseases, DVT/PE and DIC. The results obtained for XL-FbDP determination with both methods compared well with established methods: a high correlation was obtained with a semi-quantitative manual latex method for both the Fara (r = 0.92) and Mira (r = 0.83) and correlations (r) of 0.81 (Fara) and 0.84 (Mira) were obtained with an enzyme immunoassay (EIA). Correlation between the two automated procedures was high (r = 0.96). The automated method will enable laboratories to provide a rapid and accurate quantitation of XL-FbDP.

  8. Screening tests for hepatitis B virus, hepatitis C virus, and human immunodeficiency virus in blood donors: evaluation of two chemiluminescent immunoassay systems.

    PubMed

    Sommese, Linda; Sabia, Chiara; Paolillo, Rossella; Parente, Delia; Capuano, Maria; Iannone, Carmela; Cavalca, Francesco; Schiano, Concetta; Vasco, Maria; De Pascale, Maria Rosaria; Casamassimi, Amelia; Napoli, Claudio

    2014-09-01

    Automated chemiluminescent immunoassays (CLIAs) are useful for the detection of hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus 1/2 antigen/antibodies (HIV 1/2 Ag/Ab) in blood donor screening. Eight hundred and forty serum samples were tested for hepatitis B surface antigen (HBsAg), HCV antibodies (anti-HCV), and HIV1/2 Ag/Ab in parallel using 2 different CLIAs (Abbott Architect i2000SR and Roche Cobas e411). The concordance between the 2 systems was high (Cohen's kappa 0.97 for HBsAg, 0.77 for anti-HCV, 0.92 for HIV1/2 Ag/Ab) and the specificity and the positive predictive value were comparable. Among the 12 discrepant results, 11 were false-positive and 1 (reactive by Architect) was true-positive for anti-HCV. Positivity for HBV DNA, HCV RNA, and HIV RNA was recorded in 90.9%, 38.9%, and 100% of true-positive samples, respectively. This study represents the first stringent comparison between Architect i2000SR and Cobas e411 in blood donors. We observed a good correlation and high agreement among HBV, HCV, and HIV with the 2 automated systems.

  9. Relationship between serum levels of fetuin-A with apo-A1, apo-B100, body composition and insulin resistance in patients with type 2 diabetes

    PubMed Central

    Shidfar, Farzad; Zarrati, Mitra; Khamseh, Mohamad Ebrahim; Haghighat, Neda; Rostami, Ali; Zolfaghari, Hamid

    2014-01-01

    Background: Some results exist on fetuin-A as marker for vascular disease in type 2diabetes. We examined the relationship between serum fetuin-A with some factors, in patients with type 2 diabetes mellitus (T2DM). Methods: From October 2012 to June 2013, a total of 131 T2DM patients were recruited and evaluated for various parameters including HOMA-IR, Apo-A1, Apo-B100, body fat percentage and waist circumference. Serum fetuin-A levels were measured by enzyme-linkedimmunosorbent assay (ELISA), and Serum glucose with a Cobas MIRA analyzer by enzymatic method. Apo-B100 and apo-A1 were measured by immunoturbidimetry with a Cobas MIRA analyzer. HOMA-IR was calculated by the following formula: [fasting insulin (uIU/mL) × fasting blood glucose (mmol/L)]/22.5. Results: The mean levels of HOMA-IR were significantly increased progressively across fetuin-A tertiles (p for trend=0.04) in women but not men. Fetuin-A had just a significant positive correlation with Apo- A1(r=0.22, p=0.02). Conclusion: This present study showed that levels of serum fetuin-A are significantly associated with insulin resistance in women with T2DM. PMID:25664301

  10. Evaluation of the Corrosion of Five Different Bracket-Archwire Combination: An In-vitro Analysis Using Inductively Coupled Plasma Mass Spectrometry

    PubMed Central

    Behroozi, Zeinab; Momeni Danaei, Shahla; Sardarian, Ali Reza; Moshkelghosha, Vahid; Sardarian, Ahmad Reza

    2016-01-01

    Statement of the Problem: Stainless steel brackets release metallic ions following the process of corrosion in the oral environment. These released ions have potential adverse effects on health, friction between wire and bracket, staining, strength of brackets. Choosing a bracket with favorable corrosive properties; therefore, should be a goal of every practitioner. Purpose: The goal of this study is to compare the amount of corrosion among five different brands of brackets using inductively coupled plasma (ICP) mass spectrometry. Materials and Method: Five different brands of brackets (Dentaurum, 3M, Ortho Organizer, Cobas and O.R.G) were chosen and ten brackets were selected from each brand. A piece of stainless steel wire was ligated to each bracket. The bracket-archwire complex was then immersed in artificial saliva. Subsequently, the samples were analyzed using an ICP device and the levels of iron, chromium, nickel, and manganese ions were measured. Results: The findings of this study demonstrated that iron was released the most from the tested brackets, followed by nickel. We also found that the Cobas bracket had the most ion release among the tested brackets (p< 0.05), while Ortho Organizer and ORG performed favorably. There was no significant difference between Dentaurum and 3M (p> 0.05). Conclusion: Based on the results, Ortho Organizer and ORG brackets are suggested in terms of resistance to corrosion. PMID:27840839

  11. Evaluation of the Randox colorimetric serum copper and zinc assays against atomic absorption spectroscopy.

    PubMed

    Beckett, Jeffrey M; Hartley, Thomas F; Ball, Madeleine J

    2009-07-01

    Analysis of copper and zinc in serum is commonly performed using atomic absorption spectrometry (AAS); however, these methods are often not readily available in smaller laboratories. Randox colorimetric assays for copper and zinc in serum were evaluated on the Thermo Electron Data Pro analyser against flame AAS methods. Copper and zinc were measured in 48 serum samples using the Randox colorimetric copper (CU2340) and zinc (ZN2341) assays on the Data Pro analyser and the results compared with those from a Varian Spectra 880 atomic absorption spectrometer. A smaller set of samples (n = 15) were also analysed colorimetrically for zinc on the Roche Cobas Mira. Linear regression analyses of Bland and Altman plots from the Data Pro - AAS comparison gave the following results for copper: correlation r = 0.6669 (P < 0.01), slope = -0.2499 (P < 0.01), intercept = 3.219 (P < 0.01). For zinc, results were as follows: correlation r = 0.1976, slope = 0.1807, intercept = -1.922. For the smaller set of samples, the Cobas Mira - AAS comparison for zinc gave correlation r = 0.4379, slope = 0.5294, intercept = -4.074. The results indicated significant systematic and fixed bias between the colorimetric copper and the AAS method. Performances in comparison to AAS methods indicated the colorimetric methods, as used, are unsuitable for the accurate determination of copper and zinc in human serum.

  12. Multicountry Validation of SAMBA - A Novel Molecular Point-of-Care Test for HIV-1 Detection in Resource-Limited Setting.

    PubMed

    Ondiek, Johnson; Namukaya, Zikulah; Mtapuri-Zinyowera, Sekesai; Balkan, Suna; Elbireer, Ali; Ushiro Lumb, Ines; Kiyaga, Charles; Goel, Neha; Ritchie, Allyson; Ncube, Patience; Omuomu, Kenneth; Ndiege, Kenneth; Kekitiinwa, Adeodata; Mangwanya, Douglas; Fowler, Mary G; Nadala, Lou; Lee, Helen

    2017-10-01

    Early diagnosis of HIV-1 infection and the prompt initiation of antiretroviral therapy are critical to achieving a reduction in the morbidity and mortality of infected infants. The Simple AMplification-Based Assay (SAMBA) HIV-1 Qual Whole Blood Test was developed specifically for early infant diagnosis and prevention of mother-to-child transmission programs implemented at the point-of-care in resource-limited settings. We have evaluated the performance of this test run on the SAMBA I semiautomated platform with fresh whole blood specimens collected from 202 adults and 745 infants in Kenya, Uganda, and Zimbabwe. Results were compared with those obtained with the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 assay as performed with fresh whole blood or dried blood spots of the same subjects, and discrepancies were resolved with alternative assays. The performance of the SAMBA and CAP/CTM assays evaluated at 5 laboratories in the 3 countries was similar for both adult and infant samples. The clinical sensitivity, specificity, positive predictive value, and negative predictive value for the SAMBA test were 100%, 99.2%, 98.7%, and 100%, respectively, with adult samples, and 98.5%, 99.8%, 99.7%, and 98.8%, respectively, with infant samples. Our data suggest that the SAMBA HIV-1 Qual Whole Blood Test would be effective for early diagnosis of HIV-1 infection in infants at point-of-care settings in sub-Saharan Africa.

  13. Rapid Sputum Multiplex Detection of the M. tuberculosis Complex (MTBC) and Resistance Mutations for Eight Antibiotics by Nucleotide MALDI-TOF MS

    PubMed Central

    Su, Kang-Yi; Yan, Bo-Shiun; Chiu, Hao-Chieh; Yu, Chong-Jen; Chang, So-Yi; Jou, Ruwen; Liu, Jia-Long; Hsueh, Po-Ren; Yu, Sung-Liang

    2017-01-01

    The increasing incidence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) adds further urgency for rapid and multiplex molecular testing to identify the MTB complex and drug susceptibility directly from sputum for disease control. A nucleotide matrix-assisted-laser-desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based assay was developed to identify MTB (MTBID panel) and 45 chromosomal mutations for resistance to eight antibiotics (MTBDR panel). We conducted a 300 case trial from outpatients to evaluate this platform. An MTBID panel specifically identified MTB with as few as 10 chromosome DNA copies. The panel was 100% consistent with an acid-fast stain and culture for MTB, nontuberculous mycobacteria, and non-mycobacteria bacteria. The MTBDR panel was validated using 20 known MDR-MTB isolates. In a 64-case double-blind clinical isolates test, the sensitivity and specificity were 83% and 100%, respectively. In a 300-case raw sputum trial, the MTB identification sensitivity in smear-negative cases using MALDI-TOF MS was better than the COBAS assay (61.9% vs. 46.6%). Importantly, the failure rate of MALDI-TOF MS was better than COBAS (11.3% vs. 26.3%). To the best of our knowledge, the test described herein is the only multiplex test that predicts resistance for up to eight antibiotics with both sensitivity and flexibility. PMID:28134321

  14. Geological Mapping of the Ac-H-10 Rongo and Ac-H-15 Zadeni quadrangles of Ceres from NASA's Dawn Mission.

    NASA Astrophysics Data System (ADS)

    Platz, Thomas; Nathues, Andreas; Sizemore, Hanna; Ruesch, Ottaviano; Hoffmann, Martin; Schaefer, Michael; Crown, David; Mest, Scott; Aileen Yingst, R.; Williams, David; Buczkowski, Debra; Hughson, Kynan; Kneissl, Thomas; Schmedemann, Nico; Schorghofer, Norbert; Nass, Andrea; Preusker, Frank; Russell, Christopher

    2016-04-01

    On March 6, 2015 NASA's Dawn spacecraft arrived at (1) Ceres, the largest object in the main asteroid belt. Dawn is studying the dwarf planet more than one year through successively lower orbits at increasing resolution. Main orbital phases include Survey Orbit, High Altitude Mapping Orbit (HAMO), and Low Altitude Mapping Orbit (LAMO) where Framing Camera (FC) [1] resolution increased from c.400 m/px to c.140 m/px and c.35 m/px, respectively. The Dawn Science Team is conducting geological mapping campaigns for Ceres (as done before for Vesta [2,3]) and includes the production of a Survey/HAMO-based global geological map and a series of 15 LAMO-based geological quadrangle maps. This abstract presents HAMO-based geological maps of Ac-H-10 Rongo (22°N-22°S, 288-360°E) and Ac-H-15 Zadeni (65°-90°S, 0°-360°E) quadrangles. The Rongo Quadrangle is located at the equatorial region and comprises the unique isolated mountain Ahuna Mons (10.5°S/316.0°E; formerly known as the pyramid), abundant impact craters spanning a range in diameters and states of preservation - from fresh to highly degraded - , and a number of tholi, which may represent surface expressions of sub-surface diapir intrusions. The SW portion of the quandrangle is characterised by Yalode (D=260 km) sourced ejecta. The Zadeni Quadrangle is dominated by the 122-km-diameter crater Zadeni located at 70.2°S/37.4°E) and a suite of mid-sized craters whose morphologies range from fresh to highly degraded. Portions of the quadrangle are covered by Urvara [4] and Yalode [5] ejecta materials. The South Polar Region is poorly illuminated and the South Pole itself is likely located within a larger impact structure. Future work of this mapping campaign includes revision of HAMO-based line work (e.g., contacts) with higher resolution LAMO data. Final interpretations regarding the geological histories of these two quadrangles will also be based on FC colour and stereo-derived topography data, VIR spectra as well

  15. A close look at the Vestan Rheasilvia basin: The Tarpeia crater

    NASA Astrophysics Data System (ADS)

    Ammannito, E.; De Sanctis, M.; Capaccioni, F.; Capria, M.; Combe, J.; Frigeri, A.; Jaumann, R.; Longobardo, A.; Marchi, S.; McCord, T.; McFadden, L.; McSween, H.; Mittlefehldt, D.; Stephan, K.; Tosi, F.; Raymond, C.; Russell, C.

    2014-07-01

    From July 2011 to August 2012, the Dawn spacecraft orbited around Vesta [1] and the Visible InfraRed mapping Spectrometer (VIR) acquired spectra from 0.2 to 5 μ m of its surface [2]. The instrument has been operative during Survey, High Altitude Mapping (HAMO), and Low Altitude Mapping (LAMO) orbits as well as during Approach and Departure phases providing an almost global coverage of the surface. Data from LAMO are those with the highest resolution. 70 m/px is the nominal resolution in this orbit in comparison with 170 m/px and 700 m/px that are the typical resolutions during HAMO and Survey, respectively. While the VIR coverage in this mission phase is limited to less than 1 % of the surface, the LAMO dataset provides a detailed view of some localized areas. Vesta exhibits ubiquitous pyroxene absorption bands [3] with variations of band center position, band depth and other band parameters at both large and small scales [4]. In particular, there is a strong indication that the Rheasilvia basin has its own spectral characteristics: on average, the pyroxene absorption bands are deeper, wider, and their center positions are shifted towards shorter wavelengths, and the central mound has relatively low spectral diversity [5]. These spectral behaviors indicate the presence of Mg-pyroxene-rich terrains in Rheasilvia, occurrence confirmed by the Gamma-Ray and Neutron Detector [2] and the Framing Camera color data [6], the other two instruments on the Dawn spacecraft. The focus of the present study is the analysis of compositional variations of small-scale surface features within the Rheasilvia basin. We made use of LAMO data, which have the highest resolution and provide a detailed view of some localized areas of Vesta's surface. Most of LAMO data cover the South Polar region, where the giant impact basin RheaSilvia is located. An example is Tarpeia, a crater with a diameter of about 40 km located within the Rheasilvia basin at -70°lat and 29°E-lon (Claudia Coordinate

  16. Spectral modeling of water ice-rich areas on Ceres' surface from Dawn-VIR data analysis: abundance and grain size retrieval

    NASA Astrophysics Data System (ADS)

    Raponi, Andrea; De Sanctis, Maria Cristina; Ciarniello, Mauro; Tosi, Federico; Combe, Jean-Philippe; Frigeri, Alessandro; Zambon, Francesca; Ammannito, Eleonora; Giacomo Carrozzo, Filippo; Magni, Gianfranco; Capria, Maria Teresa; Formisano, Michelangelo; Longobardo, Andrea; Palomba, Ernesto; Pieters, Carle; Russell, Christopher T.; Raymond, Carol; Dawn/VIR Team

    2016-10-01

    Dawn spacecraft orbits around Ceres since early 2015 acquiring a huge amount of data at different spatial resolutions during the several phases of the mission. VIR, the visible and InfraRed spectrometer onboard Dawn [1] allowed to detect the principal mineralogical phases present on Ceres: a large abundance of dark component, NH4-phillosilicates and carbonates.Water has been detected in small areas on Ceres' surface by the Dawn-VIR instrument. The most obvious finding is located in Oxo crater [2]. Further detections of water have been made during the Survey observation phase (1.1 km/pixel) and High-Altitude Mapping Orbit (400 m/px) [3]. During the LAMO phase (Low Altitude Mapping Orbit), the data with increased spatial resolution (100 m/px) coming from both regions have improved the detection of water, highlighting clear diagnostic water ice absorption features. In this study, we focused on spectral modeling of VIR spectra of Oxo and another crater (lon = 227°, lat 57°), near Messor crater.The Hapke radiative transfer model [4] has been applied in order to retrieve the water ice properties. We consider two types of mixtures: areal and intimate mixing. In areal mixing, the surface is modelled as patches of pure water ice, with each photon scattered within one patch. In intimate mixing, the particles of water ice are in contact with particles of the dark terrain, and both are involved in the scattering of a single photon. The best fit with the measured spectra has been derived with the areal mixture. The water ice abundance obtained is up to 15-20% within the field of view, and the grain size retrieved is of the order of 100-200 μm. Phyllosilicates and carbonates, which are ubiquitous on Ceres surface [5], have been also detected and modeled in correspondence with the icy regions. The water ice is typically located near and within the shadows projected by the crater rims. Further analysis is required to study the thermal state of the ice and its origin

  17. Anomalous crater Marcia on asteroid 4 Vesta: Spectral signatures and their geological relationship

    NASA Astrophysics Data System (ADS)

    Giebner, T.; Jaumann, R.; Schroeder, S.; Krohn, K.

    2016-12-01

    DAWN Framing Camera (FC) images are used in this study to analyze the diverse spectral signatures of crater Marcia. As the FC offers high spatial resolution as well as several color filters it is well suited to resolve geological correlations on Vestas surface. Our approach comprises the analysis of images from four FC filters ( F3, F4, F5 and F6) that cover the pyroxene absorption band at 0.9 um and the comparison of Vesta data with HED meteorite spectra. We use the ratios R 750/915 (F3/F4) and R 965/830 (F5/F6) [nm] to separate HED lithologies spectrally and depict corresponding areas on HAMO mosaics ( 60 m/px). Additionally, higher resolution LAMO images ( 20 m/px) are analyzed to reveal the geologic setting. In this work, Marcia is broadly classified into three spectral regions. The first region is located in the northwestern part of the crater as well as in the central peak area and shows the most HED-like signature within the Marcia region. The other two regions, with one of them also describing Marcia ejecta, are spectrally further away from HED lithologies and likely display a mixing with more howarditic-rich material associated with carbonaceous chondrite clasts and relatively higher OH and H concentrations (e.g., [1], [2], [3]). In general, these other two regions are also associated with thick flow features within the crater, while the HED-like area does not show such prominent flows. Hence, these darker regions seem to display post-impact material inflow of the weathered howarditic surface regolith. We conclude that the Marcia impactor likely struck through the howarditic regolith and hit the eucritic crust underneath. Depicting this HED-like signature globally, it resides mostly in the Rheasilvia basin and ejecta blanket, as well as in very young crater ejecta in the equatorial region, consistent with it being a signature of fresh basaltic crust. [1] M. C. De Sanctis et al. (2012b) The Astrophysical Journal Letters, 758:L36 (5pp) [2] T. McCord et al

  18. Seasonal and interannual evolution of Jakobshavn Isbrae, Greenland from a 2008-2015 high-res DEM and velocity time series

    NASA Astrophysics Data System (ADS)

    Shean, D. E.; Joughin, I.; Smith, B.; Floricioiu, D.

    2015-12-01

    Greenland's large marine-terminating outlet glaciers have displayed marked retreat, speedup, and thinning in recent decades. Jakobshavn Isbrae, one of Greenland's largest outlet glaciers, has retreated ~15 km, accelerated ~150%, and thinned ~200 m since the early 1990s. Here, we present a comprehensive analysis of high-resolution elevation (~2-5 m/px) and velocity (~100 m/px) time series with dense temporal coverage (daily-monthly). The Jakobshavn DEM time series consists of >70 WorldView-1/2/3 stereo DEMs and >11 TanDEM-X DEMs spanning 2008-2015. Complementary point elevation data from Operation IceBridge (ATM, LVIS), pre-IceBridge ATM flights, and ICESat-1 GLAS extend the surface elevation record to 1999 and provide essential absolute control data, enabling sub-meter horizontal/vertical accuracy for gridded DEMs. Velocity data are primarily derived from TerraSAR-X/TanDEM-X image pairs with 11-day interval from 2009-2015. These elevation and velocity data capture outlet glacier evolution with unprecedented detail during the post-ICESat era. The lower trunk of Jakobshavn displays significant seasonal velocity variations, with recent rates of ~8 km/yr during winter and >17 km/yr during summer. DEM data show corresponding seasonal elevation changes of -30 to -45 m in summer and +15 to +20 m in winter, with decreasing magnitude upstream. Seasonal discharge varies from ~30-35 Gt/yr in winter to ~45-55 Gt/yr in summer, and we integrate these measurements for improved long-term mass-balance estimates. Recent interannual trends show increased discharge, velocity, and thinning (-15 to -20 m/yr), which is consistent with long-term altimetry records. The DEM time series also reveal new details about calving front and mélange evolution during the seasonal cycle. Similar time series are available for Kangerdlugssuaq and Helheim Glaciers. These observations are improving our understanding of outlet glacier dynamics, while complementing ongoing efforts to constrain estimates

  19. Self-similar clustering distribution of structural features on Ascraeus Mons (Mars): implications for magma chamber depth

    NASA Astrophysics Data System (ADS)

    Pozzobon, R.; Mazzarini, F.; Massironi, M.; Cremonese, G.

    2012-04-01

    The occurrence and spatial distribution of monogenic eruptive structures within volcanic areas are linked to fracture systems and associated stress fields. Moreover, they testify the presence of deep crustal or subcrustal magma reservoirs directly connected to the surface by a percolating fracture network. The correlation between vent distribution and fracture network properties (the so called backbone) can thus be studied in terms of self-similar (fractal) clustering. Self-similarity in vent distribution is described by a power law distribution with fractal exponent D and defined over a range of lengths (l) comprised between a lower limit (lower cutoff, Lco) and an upper limit (upper cutoff, Uco). The upper cutoff (Uco) for fractal clustering was compared with the respective crustal thickness obtained by existing independent geophysical data in the East African Rift System (Mazzarini and Isola, 2010). The computed Ucos for this sector well match the crustal thickness in these volcanic fields. More in detail this computational model verified the strong linear relationship existing between the upper cutoff of the power law distribution and the magma source depth. This method was thus applied to Ascraeus Mons on Mars, which displays basaltic magmatism and hundreds of collapse pits and vents around its flanks, giving a robust statistic to the calculations. Basing on a structural mapping performed on HRSC (High Resolution Stereo Camera onboard the ESA Mars Express mission) at 12 m/px and CTX (Context Camera, Mars Reconnaissance Orbiter mission) at 6 m/px mosaics, more than 2300 collapse pits and vents were analysed. Data analyses displayed a clustering in the structures distribution, showing two distinct populations. The obtained Uco values revealed the presence and the likely depth of both a deep big magma chamber and a small shallower chamber placed below the main caldera. Moreover, the resulting magma source depths are completely consistent and comparable with those

  20. An automatic modular procedure to generate high-resolution earthquake catalogues: application to the Alto Tiberina Near Fault Observatory (TABOO), Italy.

    NASA Astrophysics Data System (ADS)

    Di Stefano, R.; Chiaraluce, L.; Valoroso, L.; Waldhauser, F.; Latorre, D.; Piccinini, D.; Tinti, E.

    2014-12-01

    The Alto Tiberina Near Fault Observatory (TABOO) in the upper Tiber Valley (northern Appennines) is a INGV research infrastructure devoted to the study of preparatory processes and deformation characteristics of the Alto Tiberina Fault (ATF), a 60 km long, low-angle normal fault active since the Quaternary. The TABOO seismic network, covering an area of 120 × 120 km, consists of 60 permanent surface and 250 m deep borehole stations equipped with 3-components, 0.5s to 120s velocimeters, and strong motion sensors. Continuous seismic recordings are transmitted in real-time to the INGV, where we set up an automatic procedure that produces high-resolution earthquakes catalogues (location, magnitudes, 1st motion polarities) in near-real-time. A sensitive event detection engine running on the continuous data stream is followed by advanced phase identification, arrival-time picking, and quality assessment algorithms (MPX). Pick weights are determined from a statistical analysis of a set of predictors designed to correctly apply an a-priori chosen weighting scheme. The MPX results are used to routinely update earthquakes catalogues based on a variety of (1D and 3D) velocity models and location techniques. We are also applying the DD-RT procedure which uses cross-correlation and double-difference methods in real-time to relocate events with high precision relative to a high-resolution background catalog. P- and S-onset and location information are used to automatically compute focal mechanisms, VP/VS variations in space and time, and periodically update 3D VP and VP/VS tomographic models. We present results from four years of operation, during which this monitoring system analyzed over 1.2 million detections and recovered ~60,000 earthquakes at a detection threshold of ML 0.5. The high-resolution information is being used to study changes in seismicity patterns and fault and rock properties along the ATF in space and time, and to elaborate ground shaking scenarios adopting

  1. High-Throughput Serum 25-Hydroxy Vitamin D Testing with Automated Sample Preparation.

    PubMed

    Stone, Judy

    2016-01-01

    Serum from bar-coded tubes, and then internal standard, are pipetted to 96-well plates with an 8-channel automated liquid handler (ALH). The first precipitation reagent (methanol:ZnSO4) is added and mixed with the 8-channel ALH. A second protein precipitating agent, 1 % formic acid in acetonitrile, is added and mixed with a 96-channel ALH. After a 4-min delay for larger precipitates to settle to the bottom of the plate, the upper 36 % of the precipitate/supernatant mix is transferred with the 96-channel ALH to a Sigma Hybrid SPE(®) plate and vacuumed through for removal of phospholipids and precipitated proteins. The filtrate is collected in a second 96-well plate (collection plate) which is foil-sealed, placed in the autosampler (ALS), and injected into a multiplexed LC-MS/MS system running AB Sciex Cliquid(®) and MPX(®) software. Two Shimadzu LC stacks, with multiplex timing controlled by MPX(®) software, inject alternately to one AB Sciex API-5000 MS/MS using positive atmospheric pressure chemical ionization (APCI) and a 1.87 min water/acetonitrile LC gradient with a 2.1 × 20 mm, 2.7 μm, C18 fused core particle column (Sigma Ascentis Express). LC-MS/MS through put is ~44 samples/h/LC-MS/MS system with dual-LC channel multiplexing. Plate maps are transferred electronically from the ALH and reformatted into LC-MS/MS sample table format using the Data Innovations LLC (DI) Instrument Manager middleware application. Before collection plates are loaded into the ALS, the plate bar code is manually scanned to download the sample table from the DI middleware to the LC-MS/MS. After acquisition-LC-MS/MS data is analyzed with AB Sciex Multiquant(®) software using customized queries, and then results are transferred electronically via a DI interface to the LIS. 2500 samples/day can be extracted by two analysts using four ALHs in 4-6 h. LC-MS/MS analysis of those samples on three dual-channel LC multiplexed LC-MS/MS systems requires 19-21 h and data analysis can be

  2. Pine Island Glacier melt rates, grounding zone evolution, and dynamic response from 2008-2015

    NASA Astrophysics Data System (ADS)

    Shean, D. E.; Joughin, I.; Smith, B.; Berthier, E.

    2015-12-01

    Significant grounding line retreat, acceleration, and thinning have occurred along the Amundsen Sea sector of West Antarctica in recent decades. These changes are directly linked to ice-ocean interaction beneath ice shelves, but existing observations of the spatial distribution, timing, and magnitude of ice shelf basal melt are very limited. We generated ~2 m/px DEMs for all available 2010-2015 high-resolution stereo satellite imagery (WorldView-1/2/3 and GeoEye-1) of the West Antarctic coast (excluding the Ross and Ronne-Filchner ice shelves). Annual and sub-annual DEM mosaics were produced for the Amundsen Sea sector, with focus on the Pine Island Glacier (PIG). We integrated SPIRIT ~40 m/px DEMs to extend the PIG time series to 2007/2008, and incorporated surface velocity maps from TerraSAR-X/TanDEM-X from 2009-2015. We use these products to compute ice thickness, Eulerian dH/dt, and Lagrangian DH/Dt, which capture evolving grounding line position, shelf thickening/thinning, and upstream ice dynamics. Ice shelf basal melt rate estimates are derived from both lagrangian DH/Dt and dense flux gate mass budget analysis. We document the spatial and temporal evolution of melt rates for the 2008-2015 period, and compare with existing ICESat (2003-2008) melt estimates and oceanographic observations. Finally, we compare observed melt vs. depth relationships with existing ice flow model parameterizations. Estimated basal melt rates are >100-150 m/yr within the PIG inner cavity, with significantly lower rates of <50 m/yr beneath the outer shelf. Eulerian dh/dt observations show significant thinning (>5-10 m/yr) upstream of the PIG grounding line following the ~2008-2009 ungrounding of the PIG "ice plain," with additional thinning along lateral margins in subsequent years. A combination of reduced melt rates and increased flux resulted in ice shelf regrounding on a large transverse seabed ridge and significant ice shelf thickening. These new data provide critical

  3. Crater Mapping in the Pluto-Charon System: Considerations, Approach, and Progress

    NASA Astrophysics Data System (ADS)

    Robbins, S. J.; Singer, K. N.; Bray, V. J.; Schenk, P.; Zangari, A. M.; McKinnon, W. B.; Young, L. A.; Runyon, K. D.; Beyer, R. A.; Porter, S.; Lauer, T.; Weaver, H. A., Jr.; Olkin, C.; Ennico Smith, K.; Stern, A.

    2015-12-01

    NASA's New Horizons mission successfully made its closest approach to Pluto on July 14, 2015, at 11:49A.M. UTC. The flyby nature of the mission, distance to the system, and multiple planetary bodies to observe with a diverse instrument set required a complex imaging campaign marked by numerous trade-offs; these lead to a more complicated crater population mapping than a basic orbital mission. The Pluto and Charon imaging campaigns were full-disk or mosaics of the full disk until ≈3.5 hrs before closest approach when the pixel scale was 0.9 km/px. After this, several LORRI-specific imaging campaigns were conducted of the partial disk and later the full crescent, while additional strips were ride-alongs with other instruments. These should supply partial coverage at up to 70-80 m/px for Pluto and 160 m/px for Charon. The LORRI coverage at ≈0.4 km/px does not cover the entire encounter hemisphere, but the MVIC instrument provided comparable full-disk coverage (0.5 km/px) and partial disk at 0.3 km/px. The best images of the non-encounter hemispheres of Pluto and Charon are ≈21 km/px (taken midnight July 10-11). As with any single flyby mission, we are constrained by the best pixel scales and incidence angles at which images were taken during the flyby. While most high-resolution imaging by quantity has been done over areas of variable solar incidence as the spacecraft passed by Pluto and Charon, these cover a relatively small fraction of the bodies and most coverage has been at near-noon sun which makes crater identification difficult. Numerous team members are independently using a variety of crater mapping tools and image products, which will be reconciled and merged to make a more robust final database. We will present our consensus crater database to-date of both plutonian and charonian impact craters as well as correlations with preliminary geologic units. We will also discuss how the crater population compares with predictions and modeled Kuiper Belt

  4. Geological Mapping of the Ac-H-2 Coniraya Quadrangle of Ceres from NASA's Dawn Mission.

    NASA Astrophysics Data System (ADS)

    Hendrik Pasckert, Jan; Hiesinger, Harald; Williams, David; Crown, David; Mest, Scott; Buczkowski, Debra; Scully, Jennifer; Schmedemann, Nico; Jaumann, Ralf; Roatsch, Thomas; Preusker, Frank; Naß, Andrea; Nathues, Andreas; Hoffmann, Martin; Schäfer, Michael; De Sanctis, Maria Cristina; Raymond, Carol; Russell, Christopher

    2016-04-01

    Dwarf planet Ceres (˜950 km) is located at ˜2.8 AU in the main asteroid belt [1], and is currently orbited by NASA's Dawn spacecraft. Similar to Vesta [2], the 15 quadrangles of Ceres will be mapped on the basis of Framing Camera mosaics from Low Altitude Mapping Orbits (LAMO) with a spatial resolution of ˜35 m/px. Here we report on our preliminary geological map of the Ac-H-2 Coniraya Quadrangle (located between 21-66 ° N and 0-90 ° E) based on High Altitude Mapping Orbit (HAMO) data (˜120 m/px), as LAMO images are just becoming available. The Coniraya Quadrangle is dominated by craters of different sizes and degradation stages. Most of the craters are highly degraded and no ejecta blankets are visible (e.g., Coniraya: 136 km; 65.8° E/40.5° N). Only some craters like Gaue and Ikapati seem to be relatively fresh, and still have ejecta blankets. Such fresher impact craters could already be mapped in detail on HAMO data, and subdivided into crater ejecta, crater wall, crater floor, and crater central peak materials. At the crater floor and around Ikapati crater we also identified smooth materials that fill local depressions. The formation of the smooth material seems to be related to the formation of the impact crater, as crater densities of the smooth materials and the ejecta blanket are similar, as are their absolute model ages (AMAs), derived from crater size-frequency distribution (CSFD) measurements. Using the lunar derived chronology, CSFD measurements of Ikapati's ejecta blanket and the smooth materials located in and around the crater show AMAs of 300 to 390 Ma. CSFD measurements of Gaue crater show AMAs of 910-980 Ma. Both craters show background AMAs of 3.1 to 3.5 Ga, which might be related to old large craters (e.g., Coniraya or Kerwan). Apart from crater related units, we identified one dome-like structure (˜65 km wide; ˜3 km high) at the crater floor of a large degraded crater at the western edge of this quadrangle. This might be an indication

  5. New fluorescence polarization immunoassays for analysis of barbiturates and benzodiazepines in serum and urine: performance characteristics.

    PubMed

    Schwenzer, K S; Pearlman, R; Tsilimidos, M; Salamone, S J; Cannon, R C; Wong, S H; Gock, S B; Jentzen, J J

    2000-01-01

    The performance of the new fluorescence polarization immunoassay reagents Cassette COBAS INTEGRA Serum Benzodiazepines assay (SBENZ) and Cassette Serum Barbiturates assay (SBARB) was evaluated as compared to other immunoassays (Abbott TDx Serum Benzodiazepines, Abbott TDx Urine Benzodiazepines, Behring EMIT Serum Benzodiazepines, Abbott ADx Serum Barbiturates, Behring EMIT Serum Barbiturates, and the COBAS INTEGRA Barbiturates (BARB) urine assay) and gas chromatography-mass spectrometry (GC-MS). Recoveries of nordiazepam and secobarbital using the SBENZ and SBARB assays, respectively, were equivalent for serum, plasma, and urine. Cross-reactivities of structurally related benzodiazepines, barbiturates, and their metabolites were very similar in serum and urine for the SBENZ and SBARB assays. Precision was within 5.4% for SBENZ serum and within 11% from 10 to 100 ng/mL for urine. Precision was within 5% for SBARB serum and within 7% from 136 to 277 ng/mL for the urine application. The standard curves for SBENZ and SBARB were stable for at least 16 weeks with the reagents stored open on the COBAS INTEGRA analyzer. Clinical comparison of the SBENZ serum assay indicated an increased pickup rate, as confirmed by GC-MS, compared to TDx and EMIT. The diagnostic sensitivities of the SBENZ serum application, TDx, and EMIT versus GC-MS were 100%, 89%, and 36%, respectively. The diagnostic specificities were 71%, 79%, and 100%, respectively. The diagnostic sensitivities of the SBENZ urine application and TDx versus GC-MS were 100% and the diagnostic specificities were 88%. The increased positive pick-up of the SBENZ assay compared to the other immunoassays is most probably due to the difference in the limit of detection (LOD) and the increased cross-reactivity for the low-dose benzodiazepines. Clinical comparison of the SBARB serum assay indicated an increased positive pick-up rate, as confirmed by GC-MS. The diagnostic sensitivities of the SBARB serum application, ADx, and

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

    PubMed

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

    2007-08-01

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

  7. Real-time PCR assays for hepatitis B virus DNA quantification may require two different targets.

    PubMed

    Liu, Chao; Chang, Le; Jia, Tingting; Guo, Fei; Zhang, Lu; Ji, Huimin; Zhao, Junpeng; Wang, Lunan

    2017-05-12

    Quantification Hepatitis B virus (HBV) DNA plays a critical role in the management of chronic HBV infections. However, HBV is a DNA virus with high levels of genetic variation, and drug-resistant mutations have emerged with the use of antiviral drugs. If a mutation caused a sequence mismatched in the primer or probe of a commercial DNA quantification kit, this would lead to an underestimation of the viral load of the sample. The aim of this study was to determine whether commercial kits, which use only one pair of primers and a single probe, accurately quantify the HBV DNA levels and to develop an improved duplex real-time PCR assay. We developed a new duplex real-time PCR assay that used two pairs of primers and two probes based on the conserved S and C regions of the HBV genome. We performed HBV DNA quantitative detection of HBV samples and compared the results of our duplex real-time PCR assays with the COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. The target region of the discordant sample was amplified, sequenced, and validated using plasmid. The results of the duplex real-time PCR were in good accordance with the commercial COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. We showed that two samples from Chinese HBV infections underestimated viral loads when quantified by the Roche kit because of a mismatch between the viral sequence and the reverse primer of the Roche kit. The HBV DNA levels of six samples were undervalued by duplex real-time PCR assays of the C region because of mutations in the primer of C region. We developed a new duplex real-time PCR assay, and the results of this assay were similar to the results of commercial kits. The HBV DNA level could be undervalued when using the COBAS TaqMan HBV Test version 2 for Chinese HBV infections owing to a mismatch with the primer/probe. A duplex real-time PCR assay based on the S and C regions could solve this problem to some extent.

  8. HPV genotype distribution in Brazilian women with and without cervical lesions: correlation to cytological data.

    PubMed

    Martins, Toni Ricardo; Mendes de Oliveira, Cristina; Rosa, Luciana Reis; de Campos Centrone, Cristiane; Rodrigues, Célia Luiza Regina; Villa, Luisa Lina; Levi, José Eduardo

    2016-08-12

    Human Papillomavirus (HPV) genotype distribution varies according to the method of assessment and population groups. This study analyzed type-specific HPV infections among women ranging from 14-95 years old, displaying normal and abnormal cytology, from São Paulo and Barretos cities, Brazil. Women found positive for High Risk-HPVs DNA by either the Hybrid Capture 2 (HC2) or Cobas HPV Test (n = 431) plus a random sample of 223 negative by both assays and 11 samples with indeterminate results, totalizing 665 samples, were submitted to HPV detection by the PapilloCheck test. Cytological distribution included 499 women with a cytological result of Negative for Intraepithelial Lesion or Malignancy and 166 with some abnormality as follows: 54 Atypical Squamous Cells of Undetermined Significance; 66 Low-Grade Squamous Intraepithelial Lesion; 43 High-Grade Squamous Intraepithelial Lesion and 3 (0.5 %) Invasive Cervical Cancer. From the 323 samples (48.6 %) that had detectable HPV-DNA by the PapilloCheck assay, 31 were HPV negative by the cobas HPV and HC2 assays. Out of these 31 samples, 14 were associated with HR-HPVs types while the remaining 17 harbored exclusively low-risk HPVs. In contrast, 49 samples positive by cobas HPV and HC 2 methods tested negative by the PapilloCheck assay (19.8 %). Overall, the most frequent HR-HPV type was HPV 16 (23.2 %), followed by 56 (21.0 %), 52 (8.7 %) and 31 (7.7 %) and the most frequent LR-HPV type was HPV 42 (12.1 %) followed by 6 (6.2 %). Among the HR-HPV types, HPV 56 and 16 were the most frequent types in NILM, found in 19.1 and 17.7 % of the patients respectively while in HSIL and ICC cases, HPV 16 was the predominant type, detected in 37.2 and 66.7 % of these samples. In the population studied, HPV 16 and 56 were the most frequently detected HR-HPV types. HPV 56 was found mainly in LSIL and NILM suggesting a low oncogenic potential. HPV 16 continues to be the most prevalent type in high-grade lesions whereas HPV

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  11. GEMIN4 functions as a coregulator of the mineralocorticoid receptor.

    PubMed

    Yang, Jun; Fuller, Peter J; Morgan, James; Shibata, Hirotaka; Clyne, Colin D; Young, Morag J

    2015-04-01

    The mineralocorticoid receptor (MR) is a member of the nuclear receptor superfamily. Pathological activation of the MR causes cardiac fibrosis and heart failure, but clinical use of MR antagonists is limited by the renal side effect of hyperkalemia. Coregulator proteins are known to be critical for nuclear receptor-mediated gene expression. Identification of coregulators, which mediate MR activity in a tissue-specific manner, may allow for the development of novel tissue-selective MR modulators that confer cardiac protection without adverse renal effects. Our earlier studies identified a consensus motif among MR-interacting peptides, MPxLxxLL. Gem (nuclear organelle)-associated protein 4 (GEMIN4) is one of the proteins that contain this motif. Transient transfection experiments in HEK293 and H9c2 cells demonstrated that GEMIN4 repressed agonist-induced MR transactivation in a cell-specific manner. Furthermore, overexpression of GEMIN4 significantly decreased, while knockdown of GEMIN4 increased, the mRNA expression of specific endogenous MR target genes. A physical interaction between GEMIN4 and MR is suggested by their nuclear co-localization upon agonist treatment. These findings indicate that GEMIN4 functions as a novel coregulator of the MR. © 2015 Society for Endocrinology.

  12. Automated tracking of whiskers in videos of head fixed rodents.

    PubMed

    Clack, Nathan G; O'Connor, Daniel H; Huber, Daniel; Petreanu, Leopoldo; Hires, Andrew; Peron, Simon; Svoboda, Karel; Myers, Eugene W

    2012-01-01

    We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998% and identifies individual whiskers with 99.997% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px×352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.

  13. A novel optical design for planetary surface stereo-imaging: preliminary design of the stereoscopic imaging channel of SIMBIOSYS for the BepiColombo ESA mission

    NASA Astrophysics Data System (ADS)

    Da Deppo, Vania; Naletto, Giampiero; Cremonese, Gabriele; Debei, Stefano; Flamini, Enrico

    2006-06-01

    The optical design of the STereoscopic imaging Channel (STC) of the imaging/spectroscopic system SIMBIOSYS for the ESA BepiColombo mission is presented. The main aim of this system is the global stereo mapping of planet Mercury surface during the BepiColombo mission lifetime. The instrument consists of two identical cameras looking at +/-20° from nadir which are sharing some optical components and the detector. The instrument has a 23"/pixel scale factor, corresponding to 50 m/px at 400 km from the surface, on a 4°x 4° FoV; imaging in four different spectral bands, between 540 nm and 890 nm, is foreseen. The STC optical characteristics guarantee global stereo mapping of the whole Mercury surface with all the filters. The coupling of an achromatic air-spaced doublet with a relay lens system allows good aberration balancing over all the field of view: the diffraction Ensquared Energy inside one pixel of the detector is of the order of 80%. In addition, an intermediate field stop gives the possibility of designing an efficient baffling system for straylight rejection. To cope with the hazardous radiation environment in which the spacecraft will be immersed in during the mission, all the glasses selected for the design are rad-hard type. A preliminary tolerance analysis has also been undertaken showing a low criticality level for manufacturing, alignment and stability of the system.

  14. The effect of patellar taping on squat depth and the perception of pain in people with anterior knee pain.

    PubMed

    Clifford, Amanda M; Harrington, Elaine

    2013-01-01

    Patellar taping is a treatment adjunct commonly used in the management of anterior knee pain. The aim of this cross sectional study was to investigate the effects of medial glide patellar taping on sagittal plane lower-limb joint kinematics and knee pain during a unilateral squat in a symptomatic population complaining of anterior knee pain. Ten participants with a history of unilateral or bilateral anterior knee pain were included in the study. Subjects were required to squat on the symptomatic leg under three conditions: placebo tape, patellar tape and no tape. Kinematic data was recorded using the CODA mpx64 motion analysis system and subjects' pain was assessed using the Numerical Rating Scale. Patellar taping resulted in a significantly greater single-legged squat depth compared to placebo tape (p=0.008) and no tape (p=0.001) and a statistically significant reduction in pain during a squat compared to placebo tape (p=0.001) or no tape (p=0.001). Significant differences were not identified for maximum knee flexion in the patella taping compared to the no tape condition. This study may have significant clinical implications as participants reported less pain and alterations in sagittal plane movement following the application of patellar tape.

  15. Gamma radiation-induced synthesis and characterization of Polyvinylpyrrolidone nanogels

    NASA Astrophysics Data System (ADS)

    Ges, A. A.; Viltres, H.; Borja, R.; Rapado, M.; Aguilera, Y.

    2017-01-01

    Due to the importance of bioactive peptides, proteins and drug for pharmaceutical purpose, there is a growing interest for suitable delivery systems, able to increase their bioavailability and to target them to the desired location. Some of the most studied delivery systems involve encapsulation or entrapment of drugs into biocompatible polymeric devices. A multitude of techniques have been described for the synthesis of nanomaterials from polymers, however, the use of ionizing radiation (γ, e-), to obtain nano- and microgels polymer is characterized by the possibility of obtaining products with a high degree of purity. Although, in the world, electronic radiation is used for this purpose, gamma radiation has not been utilized for these purposes. In this paper is developed the formulation the formulation of Polyvinylpyrrolidone (PVP) nanogels synthesized by gamma radiation techniques, for their evaluation as potential system of drug delivery. Experiments were performed in absence of oxygen using aqueous solutions of PVP (0.05% -1%). Crosslinking reactions were carried out at 25° C in a gamma irradiation chamber with a 60Co source (MPX-γ 30). The Viscosimetry, Light Scattering, X-Ray Diffraction and Transmission Electron Microscopy (TEM), were used as characterization techniques.

  16. Molecular structure and vibrational properties of pyramidal MPc+ phthalocyanine cation in InPcI and LuPc(OAc) complexes

    NASA Astrophysics Data System (ADS)

    Hanuza, J.; Godlewska, P.; Kadłubański, P.; Ptak, M.; Mączka, M.; Gerasymchuk, Y. S.; Legendziewicz, J.

    2017-02-01

    Room temperature FT-IR spectra in the range 30-4000 cm-1 and FT-Raman spectra in the range 80-4000 cm-1 of indium and lutetium MPX-type phthalocyanines have been compared. The assignment of the observed bands has been accomplished on the basis of DFT chemical calculations using the B3LYP functional and its long range corrected version - CAM-B3LYP. The calculations were carried out for the indium derivative using the LANL2DZ, CC-PVDZ basis sets, i.e. the following approximations were used: B3LYP/CC-PVDZ, B3LYP/CC-PVTZ, B3LYP/LANL2DZ, CAM-B3LYP/CC-PVDZ and CAM-B3LYP/LANL2DZ. The molecular structures of these derivatives have been discussed in terms of group theory and geometry optimisation taking into account the shape and number of the bands corresponding to the stretching and bending vibrations of MN4 coordination polyhedron as well as the whole studied complex. The calculated structural parameters have been related to those from XRD studies. The usefulness of the proposed theoretical approaches in the prediction of the structural and vibrational data were analysed.

  17. Design of extensible meteorological data acquisition system based on FPGA

    NASA Astrophysics Data System (ADS)

    Zhang, Wen; Liu, Yin-hua; Zhang, Hui-jun; Li, Xiao-hui

    2015-02-01

    In order to compensate the tropospheric refraction error generated in the process of satellite navigation and positioning. Temperature, humidity and air pressure had to be used in concerned models to calculate the value of this error. While FPGA XC6SLX16 was used as the core processor, the integrated silicon pressure sensor MPX4115A and digital temperature-humidity sensor SHT75 are used as the basic meteorological parameter detection devices. The core processer was used to control the real-time sampling of ADC AD7608 and to acquire the serial output data of SHT75. The data was stored in the BRAM of XC6SLX16 and used to generate standard meteorological parameters in NEMA format. The whole design was based on Altium hardware platform and ISE software platform. The system was described in the VHDL language and schematic diagram to realize the correct detection of temperature, humidity, air pressure. The 8-channel synchronous sampling characteristics of AD7608 and programmable external resources of FPGA laid the foundation for the increasing of analog or digital meteorological element signal. The designed meteorological data acquisition system featured low cost, high performance, multiple expansions.

  18. Zebrafish Embryo Model of Bartonella henselae Infection

    PubMed Central

    Lima, Amorce; Cha, Byeong J.; Amin, Jahanshah; Smith, Lisa K.

    2014-01-01

    Abstract Bartonella henselae (Bh) is an emerging zoonotic pathogen that has been associated with a variety of human diseases, including bacillary angiomatosis that is characterized by vasoproliferative tumor-like lesions on the skin of some immunosuppressed individuals. The study of Bh pathogenesis has been limited to in vitro cell culture systems due to the lack of an animal model. Therefore, we wanted to investigate whether the zebrafish embryo could be used to model human infection with Bh. Our data showed that Tg(fli1:egfp)y1 zebrafish embryos supported a sustained Bh infection for 7 days with >10-fold bacterial replication when inoculated in the yolk sac. We showed that Bh recruited phagocytes to the site of infection in the Tg(mpx:GFP)uwm1 embryos. Infected embryos showed evidence of a Bh-induced angiogenic phenotype and an increase in the expression of genes encoding pro-inflammatory factors and pro-angiogenic markers. However, infection of zebrafish embryos with a deletion mutant in the major adhesin (BadA) resulted in little or no bacterial replication and a diminished host response, providing the first evidence that BadA is critical for in vivo infection. Thus, the zebrafish embryo provides the first practical model of Bh infection that will facilitate efforts to identify virulence factors and define molecular mechanisms of Bh pathogenesis. PMID:25026365

  19. Zebrafish embryo model of Bartonella henselae infection.

    PubMed

    Lima, Amorce; Cha, Byeong J; Amin, Jahanshah; Smith, Lisa K; Anderson, Burt

    2014-10-01

    Bartonella henselae (Bh) is an emerging zoonotic pathogen that has been associated with a variety of human diseases, including bacillary angiomatosis that is characterized by vasoproliferative tumor-like lesions on the skin of some immunosuppressed individuals. The study of Bh pathogenesis has been limited to in vitro cell culture systems due to the lack of an animal model. Therefore, we wanted to investigate whether the zebrafish embryo could be used to model human infection with Bh. Our data showed that Tg(fli1:egfp)(y1) zebrafish embryos supported a sustained Bh infection for 7 days with >10-fold bacterial replication when inoculated in the yolk sac. We showed that Bh recruited phagocytes to the site of infection in the Tg(mpx:GFP)uwm1 embryos. Infected embryos showed evidence of a Bh-induced angiogenic phenotype and an increase in the expression of genes encoding pro-inflammatory factors and pro-angiogenic markers. However, infection of zebrafish embryos with a deletion mutant in the major adhesin (BadA) resulted in little or no bacterial replication and a diminished host response, providing the first evidence that BadA is critical for in vivo infection. Thus, the zebrafish embryo provides the first practical model of Bh infection that will facilitate efforts to identify virulence factors and define molecular mechanisms of Bh pathogenesis.

  20. Theoretical Calculation of Jet Fuel Thermochemistry. 1; Tetrahydrodicylopentadiene (JP10) Thermochemistry Using the CBS-QB3 and G3(MP2)//B3LYP Methods

    NASA Technical Reports Server (NTRS)

    Zehe, Michael J.; Jaffe, Richard L.

    2010-01-01

    High-level ab initio calculations have been performed on the exo and endo isomers of gas-phase tetrahydrodicyclopentadiene (THDCPD), a principal component of the jet fuel JP10, using the Gaussian Gx and Gx(MPx) composite methods, as well as the CBS-QB3 method, and using a variety of isodesmic and homodesmotic reaction schemes. The impetus for this work is to help resolve large discrepancies existing between literature measurements of the formation enthalpy Delta (sub f)H deg (298) for exo-THDCPD. We find that use of the isodesmic bond separation reaction C10H16 + 14CH4 yields 12C2H6 yields results for the exo isomer (JP10) in between the two experimentally accepted values, for the composite methods G3(MP2), G3(MP2)//B3LYP, and CBS-QB3. Application of this same isodesmic bond separation scheme to gas-phase adamantane yields a value for Delta (sub f)H deg (298) within 5 kJ/mol of experiment. Isodesmic bond separation calculations for the endo isomer give a heat of formation in excellent agreement with the experimental measurement. Combining our calculated values for the gas-phase heat of formation with recent measurements of the heat of vaporization yields recommended values for Delta (sub f)H deg (298)liq of -126.4 and -114.7 kJ/mol for the exo and endo isomers, respectively.

  1. Overexpression of Mycothiol Disulfide Reductase Enhances Corynebacterium glutamicum Robustness by Modulating Cellular Redox Homeostasis and Antioxidant Proteins under Oxidative Stress

    PubMed Central

    Si, Meiru; Zhao, Chao; Zhang, Bing; Wei, Dawei; Chen, Keqi; Yang, Xu; Xiao, He; Shen, Xihui

    2016-01-01

    Mycothiol (MSH) is the dominant low-molecular-weight thiol (LMWT) unique to high-(G+C)-content Gram-positive Actinobacteria, such as Corynebacterium glutamicum, and is oxidised into its disulfide form mycothiol disulfide (MSSM) under oxidative conditions. Mycothiol disulfide reductase (Mtr), an NADPH-dependent enzyme, reduces MSSM to MSH, thus maintaining intracellular redox homeostasis. In this study, a recombinant plasmid was constructed to overexpress Mtr in C. glutamicum using the expression vector pXMJ19-His6. Mtr-overexpressing C. glutamicum cells showed increased tolerance to ROS induced by oxidants, bactericidal antibiotics, alkylating agents, and heavy metals. The physiological roles of Mtr in resistance to oxidative stresses were corroborated by decreased ROS levels, reduced carbonylation damage, decreased loss of reduced protein thiols, and a massive increase in the levels of reversible protein thiols in Mtr-overexpressing cells exposed to stressful conditions. Moreover, overexpression of Mtr caused a marked increase in the ratio of reduced to oxidised mycothiol (MSH:MSSM), and significantly enhanced the activities of a variety of antioxidant enzymes, including mycothiol peroxidase (MPx), mycoredoxin 1 (Mrx1), thioredoxin 1 (Trx1), and methionine sulfoxide reductase A (MsrA). Taken together, these results indicate that the Mtr protein functions in C. glutamicum by protecting cells against oxidative stress. PMID:27383057

  2. Use of the LIBS method in oil paintings examination based on examples of analyses conducted at the Wilanow Palace Museum

    NASA Astrophysics Data System (ADS)

    Modzelewska, ElŻbieta; Pawlak, Agnieszka; Selerowicz, Anna; Skrzeczanowski, Wojciech; Marczak, Jan

    2013-05-01

    This paper describes the preliminary results of a study of the paint layers in 17th-century paintings belonging to the collection of the Wilanow Palace Museum. The works chosen for examination are of great importance to the Museum, as they might have been painted by court artists of King John III Sobieski. The aim of the study was therefore to determine the technological structure of the paintings, to determine the scope of conservation interventions and, above all, to gather comparative material that would serve to conduct further multidisciplinary attributive research. The presentation relates to studies in which laser-induced breakdown spectroscopy (LIBS) and optical microscopy were used as diagnostic tools. LIBS is based on the evaporation of a small amount of the material under investigation, and the generation of plasma which emits continuum and line radiation. The analysis of line radiation allows us to identify the elements appearing in the sample being investigated. The microscope pictures were taken using a Bresser Digital Hand Micro 1.3Mpx and the Hirox 8700 microscopes. The results obtained have confirmed the utility of the LIBS method in the study of artworks. They have also proven that it can be used as a method to complement microchemical analysis, as well as an method to identify and examine artworks from which samples cannot be taken, as it is micro-destructive and the analysis can be conducted directly on the object, without the need to take samples.

  3. Astrometric studies of the results of a new reduction of old photographic observations of the Saturnian System based on the comparison with the modern theories of satellite motion

    NASA Astrophysics Data System (ADS)

    Kiseleva, T. P.; Vasil'eva, T. A.; Roshchina, E. A.; Izmailov, I. S.

    2016-11-01

    The paper shows the possibility of increasing the accuracy of the results of photographic observations of Saturn and its moons made in the 1970s and reduced using the old reference star catalogues and semiautomatic measurements. New celestial coordinates of the moons (from the third to the eighth), "satellite minus satellite" relative moon coordinates, and Saturn coordinates by positions of satellites are obtained without measuring its images. The results are stored in the Pulkovo Observatory database on the Solar System bodies and are available online at www.puldb.ru. The efficiency of the reduction method based on digitizing of astronegatives using 21 Mpx Canon digital camera and IZMCCD software is shown. The comparison of new results of old observations with the latest theories of moon motion has revealed a significant increase in satellite positioning accuracy. The investigation of the differences (O-C) of celestial coordinates from satellite positions in their apparent Saturn-centric orbits has revealed a noticeable motion of the differences (O-C) in right ascension depending on their distances from Saturn for all moons.

  4. Automated Tracking of Whiskers in Videos of Head Fixed Rodents

    PubMed Central

    Clack, Nathan G.; O'Connor, Daniel H.; Huber, Daniel; Petreanu, Leopoldo; Hires, Andrew; Peron, Simon; Svoboda, Karel; Myers, Eugene W.

    2012-01-01

    We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998% and identifies individual whiskers with 99.997% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px×352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception. PMID:22792058

  5. Spectrophotometric Properties of Gaspra’s Surface

    NASA Astrophysics Data System (ADS)

    Domingue, Deborah L.; Vilas, Faith; Stockstill-Cahill, Karen; Cahill, Joshua; Hendrix, Amanda

    2015-11-01

    Using the shape-model derived for Gaspra [1] we calculate the local incidence, emission, and phase angles on a pixel-by-pixel basis for the color image sets (164 m/px spatial resolution) acquired by the Galileo Solid State Imager (SSI) [2]. Using these geometric values, we derive a disk-resolved photometric correction for application to the to the spectral data set for more accurate regional examination of mineralogy and weathering across the surface. We use regional variations in color ratios of Gaspra’s surface to examine the degree of space weathering incurred upon the surface, and find subtle variations across its surface. Using mixing modeling methods that account for submicroscopic components, we examine evidence for space weathering variations correlated to composition and grain size. We note evidence of a young surface, with only moderate modification by space weathering processes. SSI radiometrically-calibrated data combined with shape-model derived incidence, emission, and phase angle backplanes have been archived in the Planetary Data System for broader use by the community [3, 4].[1] P. Thomas et al. 1994, Icarus 107, 23 - 36. [2] M. Belton et al. 1992, Science 257, 1647 - 1652. [3] D. Domingue 2015, Galileo SSI/Gaspra Radiometrically Calibrated Images V1.0. NASA PDS. [4] D. Domingue 2015, Galileo SSI/Gaspra Color and Geometry Image Cubes V1.0. NASA PDS, submitted.

  6. Composition of Rheasilvia Basin on Asteroid Vesta

    NASA Technical Reports Server (NTRS)

    Ammannito, Eleonora; DeSanctis, Maria Christina; Capaccioni, Fabrizio; Capria, Maria Teresa; Combe, Jean Philippe; Frigeri, Alessandro; Jaumann, Ralf; Longobardo, Andrea; Marchi, Somone; McCord, Thomas B.; McSween, Harry Y., Jr.; Mittlefehldt, David W.; Stephan, Katrin; Tosi, Federico; Raymond, Carol A.; Russell, Christopher T.

    2014-01-01

    The focus of the present study is the compositional analysis of small-scale surface features within the Rheasil-Aa basin on asteroid Vesta. We are using data acquired by the Visible and InfraRed mapping Spectrometer (VIR) on the Dawn mission. Nominal spatial resolution of the data set considered in this study is 70m/px. The portion of Rheasil-Aa basin below 65degS has a howarditic composition, with the higher concentration of diogenitic versus eucritic material in the region between 45deg and 225degE-lon. However, there are several locations, such as craters Tarpeia and Severina and Parentatio Rupes, with lithologic characteristics different from the surroundings regions. Tarpeia crater has a eucritic patch in the west side of the crater, the bottom part ofthe wall and part of the floor. Severina, located in a region of Mg-rich pyroxene, has some diogenitic units on the walls of the crater. Also the Parentatio Rupes has an ob-AOUS diogenitic unit. These units extend for 10-20km, and their location, especially in the case of the two craters, suggests they formed before the cratering events and also before the Rheasil-Aa impact event. The origin of these units is still unclear; however, their characteristics and locations suggests heterogeneity in the composition of the ancient Vestan crust in this particular location of the surface.

  7. Differential gene expression in whitefly Bemisia tabaci-infested tomato (Solanum lycopersicum) plants at progressing developmental stages of the insect's life cycle.

    PubMed

    Estrada-Hernández, María Gloria; Valenzuela-Soto, José Humberto; Ibarra-Laclette, Enrique; Délano-Frier, John Paul

    2009-09-01

    A suppression-subtractive-hybridization (SSH) strategy was used to identify genes whose expression was modified in response to virus-free whitefly Bemisia tabaci (Bt, biotype A) infestation in tomato (Solanum lycopersicum) plants. Thus, forward and reverse SSH gene libraries were generated at four points in the whitefly's life cycle, namely at (1) 2 days (adult feeding and oviposition: phase I); (2) 7 days (mobile crawler stage: phase II); (3) 12 days (second to third instar nymphal transition: phase III) and (4) 18 days (fourth instar nymphal stage: phase IV). The 169 genes with altered expression (up and downregulated) that were identified in the eight generated SSH libraries, together with 75 additional genes that were selected on the basis of their involvement in resistance responses against phytofagous insects and pathogens, were printed on a Nexterion(®) Slide MPX 16 to monitor their pattern of expression at the above phases. The results indicated that Bt infestation in tomato led to distinctive phase-specific expression/repression patterns of several genes associated predominantly with photosynthesis, senescence, secondary metabolism and (a)biotic stress. Most of the gene expression modifications were detected in phase III, coinciding with intense larval feeding, whereas fewer changes were detected in phases I and IV. These results complement previously reported gene expression profiles in Bt-infested tomato and Arabidopisis, and support and expand the opinion that Bt infestation leads to the downregulation of specific defense responses in addition to those controlled by jasmonic acid. Copyright © Physiologia Plantarum 2009.

  8. Review of ultraresolution (10-100 megapixel) visualization systems built by tiling commercial display components

    NASA Astrophysics Data System (ADS)

    Hopper, Darrel G.; Haralson, David G.; Simpson, Matthew A.; Longo, Sam J.

    2002-08-01

    Ultra-resolution visualization systems are achieved by the technique of tiling many direct or project-view displays. During the past fews years, several such systems have been built from commercial electronics components (displays, computers, image generators, networks, communication links, and software). Civil applications driving this development have independently determined that they require images at 10-100 megapixel (Mpx) resolution to enable state-of-the-art research, engineering, design, stock exchanges, flight simulators, business information and enterprise control centers, education, art and entertainment. Military applications also press the art of the possible to improve the productivity of warfighters and lower the cost of providing for the national defense. The environment in some 80% of defense applications can be addressed by ruggedization of commercial components. This paper reviews the status of ultra-resolution systems based on commercial components and describes a vision for their integration into advanced yet affordable military command centers, simulator/trainers, and, eventually, crew stations in air, land, sea and space systems.

  9. Smartphone based Tomographic PIV using colored shadows

    NASA Astrophysics Data System (ADS)

    Aguirre-Pablo, Andres A.; Alarfaj, Meshal K.; Li, Er Qiang; Thoroddsen, Sigurdur T.

    2016-11-01

    We use low-cost smartphones and Tomo-PIV, to reconstruct the 3D-3C velocity field of a vortex ring. The experiment is carried out in an octagonal tank of water with a vortex ring generator consisting of a flexible membrane enclosed by a cylindrical chamber. This chamber is pre-seeded with black polyethylene microparticles. The membrane is driven by an adjustable impulsive air-pressure to produce the vortex ring. Four synchronized smartphone cameras, of 40 Mpx each, are used to capture the location of particles from different viewing angles. We use red, green and blue LED's as backlighting sources, to capture particle locations at different times. The exposure time on the smartphone cameras are set to 2 seconds, while exposing each LED color for about 80 μs with different time steps that can go below 300 μs. The timing of these light pulses is controlled with a digital delay generator. The backlight is blocked by the instantaneous location of the particles in motion, leaving a shadow of the corresponding color for each time step. The image then is preprocessed to separate the 3 different color fields, before using the MART reconstruction and cross-correlation of the time steps to obtain the 3D-3C velocity field. This proof of concept experiment represents a possible low-cost Tomo-PIV setup.

  10. Phobos spectral clustering: comparison between the 0.5-0.9 micron slope on OMEGA and CRISM data sets

    NASA Astrophysics Data System (ADS)

    Pajola, Maurizio; Roush, Ted L.; Marzo, Giuseppe

    2016-10-01

    We analyzed the MEX-OMEGA (8) and MRO-CRISM (1) visible multispectral data sets of Phobos using I/F values at 0.5 and 0.9 micron and derived spectral slope from these. The purpose is to understand surface spectral variablity on Phobos. Combining the multispectral data sets provides nearly complete coverage for Phobos surface. Different observing scales ranging from 110 to 2000 m/px, with a range of phase angles from 37° to 101°.We applied an unsupervised K-means partitioning algorithm to evaluate the variability of the two I/F values. Each resulting cluster is characterized by an average, and its associated variability. This approach has been validated by application to different Solar System objects, e.g. asteroids, Mars, and Iapetus. The algorithm is agnostic of the physical meaning of the resulting clusters, and scientific interpretation is required for their subsequent evaluation.Using this techinque, 7 clusters were identified for each of the 9 Phobos data sets. For each cluster, we calculated the 0.5-0.9 micron slope within each Phobos data set. The calculated slopes change from a minimum of 0.1% to a maximum of 14.7%. These results indicate that Phobos surface may be more variable than previously suggested, however the exact cause of these variations remains to be determined. In this context, the OMEGA and CRISM data sets are fundamental for expanding our knowledge about Phobos.

  11. AIRSAR South American deployment: Operation plan, version 3.0

    NASA Technical Reports Server (NTRS)

    Kobrick, M.

    1993-01-01

    The United States National Aeronautics and Space Administration (NASA) and the Brazilian Commission for Space Activities (COBAE) are undertaking a joint experiment involving NASA's DC-8 research aircraft and the Airborne Synthetic Aperture Radar (AIRSAR) system during late May and June 1993. The research areas motivating these activities are: (1) fundamental research in the role of soils, vegetation, and hydrology in the global carbon cycle; and (2) in cooperation with South American scientists, airborne remote sensing research for the upcoming NASA Spaceborne Imaging Radar (SIR)-C/X-SAR flights on the Space Shuttle. A flight schedule and plans for the deployment that were developed are included. Maps of the site locations and schematic indications of flight routes and dates, plots showing swath locations derived from the flight requests and generated by flight planning software, and, most importantly, a calendar showing which sites will be imaged each day are included.

  12. Urinary Albumin Detection: Comparison of Two Different Methods.

    PubMed

    Molinario, Rossana; Pocino, Krizia; Daloiso, Pio Dante; Giannace, Angela; Spirito, Giulia; Zuppi, Cecilia; Antenucci, Mirca

    2016-11-01

    Monitoring urinary albumin is a useful method in clinical practice for the management of diabetic nephropathy, chronic kidney disease, and hypertension. Currently there are neither standardized methods nor reference material for the determination of urinary albumin; for this reason it is useful to compare different assays used in clinical laboratory. The aim of this study is to verify analytical performance of an immunoturbidimetric assay on Roche Cobas 8000 platform and to compare urinary albumin results with those obtained by immunonephelometry on Siemens Dade Behring BN II Nephelometer. The method comparison showed a good linear relationship, confirmed by Passing-Bablok and Bland-Altman plots. The turbidimetric assay meets the requirements of accuracy and precision for the practice of medical diagnostics and clinical use. The present study can contribute to the methods standardization and harmonization of urinary albumin assay. © 2016 Wiley Periodicals, Inc.

  13. Efficacy of combined hepatitis B immunoglobulin and hepatitis B vaccine in blocking father-infant transmission of hepatitis B viral infection.

    PubMed

    Cao, L-H; Liu, Z-M; Zhao, P-L; Sun, S-C; Xu, D-B; Shao, M-H; Zhang, J-D

    2015-05-04

    The aim of this study was to examine the efficacy of combined immunization of hepatitis B immunoglobulin (HBIG) and hepatitis B vaccine (HBVac) in blocking father-infant transmission of hepatitis B virus (HBV). Newborns positive at birth for blood HBV sur-face antigen (HBsAg) and/or HBV DNA were selected and immunized with HBIG combination HBVac. At 7 months, HBV markers and HBV DNA of each neonate were measured using electrochemiluminescence with the Cobas-e-411 Automatic Electrochemiluminescence Immuno-assay Analyzer and fluorescence quantitative polymerase chain reaction. Among all 7-month-old subjects, the negative conversion rates of HBV DNA and HBsAg were 48/61 (78.7%) and 19/41 (46.3%), respectively. Therefore, this study demonstrated that prompt combination injection of HBIG and HBVac can protect some of the HBV DNA- and/ or HBsAg-positive newborns from HBV.

  14. Hemoglobin variants detected by hemoglobin A1c (HbA1c) analysis and the effects on HbA1c measurements.

    PubMed

    Nasir, Nadzimah Mohd; Thevarajah, M; Yean, Chew Yee

    2010-04-01

    Hemoglobin (Hb) A1c is a tool widely used to monitor long-term glycemic control in diabetic patients. The objective of our study is to compare the HbA1c values measured on high performance liquid chromatography (HPLC) and immunoassay in patients who were detected to have hemoglobin variant after HbA1c analysis. We compared the HbA1c values measured using the Arkray Adams A1c HA-8160 (HPLC method) and Roche Cobas Integra (immunoturbidimetric method) from diabetic patients who were diagnosed with hemoglobin variants. Forty-three diabetic patients were diagnosed with hemoglobin variants: 13 elevated Hb F, 12 Hb E trait, seven Hb S trait, seven Hb D trait, two Hb E / beta-Thalassemia, one Hb C trait, and one homozygous Hb S. Knowledge of hemoglobin variants affecting HbA1c measurements is essential, in order to avoid mismanagement of diabetic patients.

  15. Evaluation of a novel ELISA for the tumor-associated antigen CA 72–4 in patients with ovarian cancer

    PubMed Central

    Buderath, Paul; Kasimir-Bauer, Sabine; Aktas, Bahriye; Rasch, Jens; Kimmig, Rainer; Zeller, Thomas; Heubner, Martin

    2016-01-01

    Aim: Cancer antigen 72–4 (CA 72–4) is an established tumor marker in ovarian cancer. We evaluated a new solid-phase ELISA (DRG TM-CA 72–4 ELISA). Materials & methods: Repeated measures of test samples and controls were performed to evaluate reliability and reproducibility. Afterward, we performed analyses on the sera of 150 patients with primarily diagnosed ovarian cancer. Results were compared with those of the Cobas CA 72–4 kit. Results were correlated with clinical patient data. Results: Results of the DRG TM-CA 72–4 ELISA were reproducible with acceptable deviations within measures, and the measured CA 72–4 serum concentrations were well in accordance with the references. High concentrations were significantly associated with grading, tumor stage and tumor residuals after surgery. PMID:28116127

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

    PubMed

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

    2016-11-01

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

  17. 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.

  18. Evaluation of the Stratus CS fluorometer for the determination of plasma myoglobin.

    PubMed

    Couck, P; Claeys, R; Vanderstraeten, E; Gorus, F K

    2005-01-01

    Circulating myoglobin is recognized as an early and sensitive marker of acute coronary diseases. Long turnaround time of myoglobin assays jeopardize their clinical utility. We evaluated the analytical performance of the Stratus CS fluorometric enzyme immunoassay based on dendrimer technology, and claimed to achieve a fast and reliable determination of plasma myoglobin concentrations. Precision complied with the recommended analytical performance criteria. Method comparison and recovery experiments indicated, that despite good between-method correlations, the Stratus CS method overestimated myoglobin concentrations in comparison with values obtained on Cobas Integra 400 and BN A. However, since the manufacturers' cut-off for elevated plasma myoglobin levels was higher for Stratus CS than for other techniques, few discrepant results were observed between methods. Elevated levels of hemoglobin, triglycerides and rheumatoid factors did not interfere in the Stratus CS method but hyperbilirubinemia caused a positive difference.

  19. Examination of the peak in dICO/dlnt in weak-linked high Tc superconductors caused by trapped flux

    NASA Astrophysics Data System (ADS)

    Rezeq, Moh'd.; LeBlanc, M. A. R.

    2007-04-01

    Altshuler et al discovered that dICO/dlnt, the rate of increase of the critical current IC with time in polycrystalline high TC samples, traced a peak when measured versus HM, the amplitude of the sweep of the flux trapping magnetic field. We show that the sharp peak in dICO/dlnt which their model generates arises from a special feature of the formulae they use to describe IC versus HM. Pursuing an extension of these formulae, and exploiting a Brandt-Indenbom formula for the return field of the magnetized grains, we (i) reproduce observations of Altshuler et al, Batista-Leyva et al and a family of curves of dICO/dlnt reported by Cobas et al, and (ii) estimate the return fields. We also explore the peak structure of dICO/dlnt versus HM generated by using two well known empirical expressions for IC(H), and the Brandt-Indenbom formula.

  20. Analytical and clinical performance of the Hologic Aptima HCV Quant Dx Assay for the quantification of HCV RNA in plasma samples.

    PubMed

    Schønning, Kristian; Pedersen, Martin Schou; Johansen, Kim; Landt, Bodil; Nielsen, Lone Gilmor; Weis, Nina; Westh, Henrik

    2017-10-01

    Chronic hepatitis C virus (HCV) infection can be effectively treated with directly acting antiviral (DAA) therapy. Measurement of HCV RNA is used to evaluate patient compliance and virological response during and after treatment. To compare the analytical performance of the Aptima HCV Quant Dx Assay (Aptima) and the COBAS Ampliprep/COBAS TaqMan HCV Test v2.0 (CAPCTMv2) for the quantification of HCV RNA in plasma samples, and compare the clinical utility of the two tests in patients undergoing treatment with DAA therapy. Analytical performance was evaluated on two sets of plasma samples: 125 genotyped samples and 172 samples referred for quantification of HCV RNA. Furthermore, performance was evaluated using dilutions series of four samples containing HCV genotype 1a, 2b, 3a, and 4a, respectively. Clinical utility was evaluated on 118 plasma samples obtained from 13 patients undergoing treatment with DAAs. Deming regression of results from 187 plasma samples with HCV RNA >2 Log IU/mL indicated that the Aptima assay quantified higher than the CAPCTMv2 test for HCV RNA >4.9 Log IU/mL. The linearity of the Aptima assay was excellent across dilution series of four HCV genotypes (slope of the regression line: 1.00-1.02). The Aptima assay detected significantly more replicates below targeted 2 Log IU/mL than the CAPCTMv2 test, and yielded clearly interpretable results when used to analyze samples from patients treated with DAAs. The analytical performance of the Aptima assay makes it well suited for monitoring patients with chronic HCV infection undergoing antiviral treatment. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Early diagnosis of in utero and intrapartum HIV infection in infants prior to 6 weeks of age.

    PubMed

    Lilian, Rivka R; Kalk, Emma; Bhowan, Kapila; Berrie, Leigh; Carmona, Sergio; Technau, Karl; Sherman, Gayle G

    2012-07-01

    Early initiation of antiretroviral therapy reduces HIV-related infant mortality. The early peak of pediatric HIV-related deaths in South Africa occurs at 3 months of age, coinciding with the earliest age at which treatment is initiated following PCR testing at 6 weeks of age. Earlier diagnosis is necessary to reduce infant mortality. The performances of the Amplicor DNA PCR, COBAS AmpliPrep/COBAS TaqMan (CAP/CTM), and Aptima assays for detecting early HIV infection (acquired in utero and intrapartum) up to 6 weeks of age were compared. Dried blood spots (DBS) were collected at birth and at 2, 4, and 6 weeks from HIV-exposed infants enrolled in an observational cohort study in Johannesburg, South Africa. HIV status was determined at 6 weeks by DNA PCR on whole blood. Serial DBS samples from all HIV-infected infants and two HIV-uninfected, age-matched controls were tested with the 3 assays. Of 710 infants of known HIV status, 38 (5.4%) had in utero (n = 29) or intrapartum (n = 9) infections. By 14 weeks, when treatment should have been initiated, 13 (45%) in utero-infected and 2 (22%) intrapartum-infected infants had died or were lost to follow-up. The CAP/CTM and Aptima assays identified 76.3% of all infants with early HIV infections at birth and by 4 weeks were 96% sensitive. DNA PCR demonstrated lower sensitivities at birth and 4 weeks of 68.4% and 87.5%, respectively. All assays had the lowest sensitivity at 2 weeks of age. CAP/CTM was the only assay with 100% specificity at all ages. Testing at birth versus 6 weeks of age identifies a higher total number of HIV-infected infants, irrespective of the assay.

  2. Clinical Significance of Two Real-Time PCR Assays for Chronic Hepatitis C Patients Receiving Protease Inhibitor-Based Therapy

    PubMed Central

    Inoue, Takako; Hmwe, Su Su; Shimada, Noritomo; Kato, Keizo; Ide, Tatsuya; Torimura, Takuji; Kumada, Takashi; Toyoda, Hidenori; Tsubota, Akihito; Takaguchi, Koichi; Wakita, Takaji; Tanaka, Yasuhito

    2017-01-01

    The aim of this study was to determine the efficacy of two hepatitis C virus (HCV) real-time PCR assays, the COBAS AmpliPrep/COBAS TaqMan HCV test (CAP/CTM) and the Abbott RealTime HCV test (ART), for predicting the clinical outcomes of patients infected with HCV who received telaprevir (TVR)-based triple therapy or daclatasvir/asunaprevir (DCV/ASV) dual therapy. The rapid virological response rates in patients receiving TVR-based triple therapy were 92% (23/25) and 40% (10/25) for CAP/CTM and ART, respectively. The false omission rate (FOR) of ART was 93.3% (14/15), indicating that CAP/CTM could accurately predict clinical outcome in the early phase. In an independent examination of 20 patients receiving TVR-based triple therapy who developed viral breakthrough or relapse, the times to HCV disappearance by ART were longer than by CAP/CTM, whereas the times to HCV reappearance were similar. In an independent experiment of WHO standard HCV RNA serially diluted in serum containing TVR, the analytical sensitivities of CAP/CTM and ART were similar. However, cell cultures transfected with HCV and grown in medium containing TVR demonstrated that ART detected HCV RNA for a longer time than CAP/CTM. Similar results were found for 42 patients receiving DCV/ASV dual therapy. The FOR of ART was 73.3% (11/15) at week 8 after initiation of therapy, indicating that ART at week 8 could not accurately predict the clinical outcome. In conclusion, although CAP/CTM and ART detected HCV RNA with comparable analytical sensitivity, CAP/CTM might be preferable for predicting the clinical outcomes of patients receiving protease inhibitor-based therapy. PMID:28118381

  3. Low hepatitis E virus RNA prevalence in a large-scale survey of United States source plasma donors.

    PubMed

    Roth, Nathan J; Schäfer, Wolfram; Alexander, Rick; Elliott, Kevin; Elliott-Browne, Wlenyeno; Knowles, Jonathan; Wenzel, Jürgen J; Simon, Toby L

    2017-08-21

    Hepatitis E virus (HEV) is a small, nonenveloped, single-stranded, RNA virus of emerging concern in industrialized countries. HEV transmission through transfusion of blood components has been reported, but not via plasma-derived medicinal products (PDMPs) manufactured with virus inactivation and/or removal steps. This study aimed to determine the prevalence of HEV among US source plasma donors. Samples were collected from US source plasma donors at centers across the United States and were initially screened for HEV RNA in 96-sample minipools using the Roche cobas HEV test on the cobas 8800 system. Assuming a sensitivity of 18.6 IU/mL, the minipool screening strategy allowed for reliable detection of individual donations with HEV RNA titers of more than 2 × 10(3) IU/mL. Reactive minipools were resolved to individual donations, which were further analyzed to quantify viral RNA concentration, determine HEV genotype, and immunoglobulin (Ig)G and IgM HEV antibody status. A total of 128,020 samples were collected from 96 CSL Plasma centers in the United States, representing 27 states. The prevalence of HEV RNA-positive samples was 0.002% with three unique HEV-positive donors identified, all HEV Subgenotype 3a. Virus titers of HEV-positive samples were relatively low (10(3) -10(4) IU HEV RNA/mL). One positive donation was HEV IgG seropositive. Routine screening of US source plasma donations for HEV would not substantially improve the safety of most PDMPs. The low prevalence and potential viral load of HEV, together with effective virus reduction steps in manufacturing processes, results in a low residual risk and acceptable safety margins for PDMPs derived from US plasma donors. © 2017 The Authors Transfusion published by Wiley Periodicals, Inc. on behalf of AABB.

  4. Hepatitis B viral load in dried blood spots: a validation study in Zambia

    PubMed Central

    Vinikoor, Michael J.; Zürcher, Samuel; Musukuma, Kalo; Kachuwaire, Obert; Rauch, Andri; Chi, Benjamin H.; Gorgievski, Meri; Zwahlen, Marcel; Wandeler, Gilles

    2016-01-01

    Background Access to hepatitis B viral load (VL) testing is poor in sub-Saharan Africa (SSA) due to economic and logistical reasons. Objectives To demonstrate the feasibility of testing dried blood spots (DBS) for hepatitis B virus (HBV) VL in a laboratory in Lusaka, Zambia, and to compare HBV VLs between DBS and plasma samples. Study design Paired plasma and DBS samples from HIV-HBV co-infected Zambian adults were analyzed for HBV VL using the COBAS AmpliPrep/COBAS TaqMan HBV test (Version 2.0) and for genotype by direct sequencing. We used Bland-Altman analysis to compare VLs between sample types and by HBV genotype. Logistic regression analysis was conducted to assess the probability of an undetectable DBS result by plasma VL. Results Among 68 participants, median age was 34 years, 61.8% were men, and median plasma HBV VL was 3.98 log IU/ml (interquartile range, 2.04–5.95). Among sequenced viruses, 28 were genotype A1 and 27 were genotype E. Bland-Altman plots suggested strong agreement between DBS and plasma VLs. DBS VLs were on average 1.59 log IU/ml lower compared to plasma with 95% limits of agreement of −2.40 to −0.83 log IU/ml. At a plasma VL ≥2,000 IU/ml, the probability of an undetectable DBS result was 1.8% (95% CI: 0.5–6.6). At plasma VL ≥20,000 IU/ml this probability reduced to 0.2% (95% CI: 0.03–1.7). Conclusions In a Zambian laboratory, we observed strong agreement between DBS and plasma VLs and high sensitivity in DBS at plasma VL ≥2,000 IU/ml. As HBV treatment expands, DBS could increase access to HBV VL testing in SSA settings. PMID:26356987

  5. Abbott RealTime HBV assay is more sensitive in detection of low viral load and little impacted by drug resistant mutation in chronic hepatitis B patients under nucleot(s)ide analogues therapy.

    PubMed

    Yeh, Ming-Lun; Huang, Chung-Feng; Huang, Ching-I; Liu, Shu-Fen; Yang, Hua-Ling; Hsieh, Ming-Yen; Huang, Jee-Fu; Dai, Chia-Yen; Chuang, Wan-Long; Yu, Ming-Lung

    2014-01-01

    Selection of drug-resistant strains may lead to failure of HBV antiviral therapy. There is little information whether there is detection difference in drug resistant mutations between different viral load assays of HBV. This study is aimed to investigate whether there is drug-resistant strains related detection difference between Abbott RealTime HBV (RealTime) and CobasAmpliPrep/CobasTaqMan HBV assays 2.0 (TaqMan). One hundred and thirty-four CHB patients who received HBV anti-viral therapy were enrolled. HBV virological markers were tested 3 months apart regularly. Serum HBV DNA levels were determined using the TaqMan and RealTime. YMDD (rt180M and rt204V) mutation was checked in patients who experienced virologic breakthrough (VBT). The correlation of HBV DNA observed between the RealTime and TaqMan was good for all 571 samples (R2 = 0.797; P<0.001). However, the correlation in the 434 samples with HBV DNA level <3 log10 IU/ml was not as good as in all samples (R2 = 0.457). Overall, 21.5% of samples had a detection difference of ≥ 1 log10 IU/ml with 91.9% of these having HBV DNA level <3 log10 IU/ml. Twenty-four patients experienced VBT. Three of these patients had acquired the YMDD mutation and exhibited discordant viral load results between the two methods tested. In each case, persistent HBV DNA was detected by RealTime and undetectable with TaqMan. Of the patients who experienced a VBT and had acquired YMDD mutation, 4.7% had undetectable HBV DNA by TaqMan while all were detectable with RealTime. RealTime assay is more sensitive and is little impacted by the development of drug resistant mutation.

  6. Evaluation of the Whole-Blood Alere Q NAT Point-of-Care RNA Assay for HIV-1 Viral Load Monitoring in a Primary Health Care Setting in Mozambique

    PubMed Central

    Meggi, Bindiya; Vubil, Adolfo; Sitoe, Nádia E.; Bhatt, Nilesh; Tobaiwa, Ocean; Quevedo, Jorge I.; Loquiha, Osvaldo; Lehe, Jonathan D.; Vojnov, Lara; Peter, Trevor F.

    2016-01-01

    Viral load testing is the WHO-recommended monitoring assay for patients on HIV antiretroviral therapy (ART). Point-of-care (POC) assays may help improve access to viral load testing in resource-limited settings. We compared the performance of the Alere Q NAT POC viral load technology (Alere Technologies, Jena, Germany), measuring total HIV RNA using finger prick capillary whole-blood samples collected in a periurban health center, with that of a laboratory-based plasma RNA test (Roche Cobas Ampliprep/Cobas TaqMan v2) conducted on matched venous blood samples. The whole-blood Alere Q NAT POC assay produced results with a bias of 0.8593 log copy/ml compared to the laboratory-based plasma assay. However, at above 10,000 copies/ml, the bias was 0.07 log copy/ml. Using the WHO-recommended threshold to determine ART failure of 1,000 copies/ml, the sensitivity and specificity of the whole-blood Alere Q NAT POC assay were 96.83% and 47.80%, respectively. A cutoff of 10,000 copies/ml of whole blood with the Alere Q NAT POC assay appears to be a better predictor of ART failure threshold (1,000 copies/ml of plasma), with a sensitivity of 84.0% and specificity of 90.3%. The precision of the whole-blood Alere Q NAT POC assay was comparable to that observed with the laboratory technology (5.4% versus 7.5%) between detectable paired samples. HIV POC viral load testing is feasible at the primary health care level. Further research on the value of whole-blood viral load to monitor antiretroviral therapy is warranted. PMID:27252459

  7. HPV infection-associated anogenital cyto-colpo-histological findings and molecular typing in HIV-positive women.

    PubMed

    Tso, F K; Rodrigues, C L L; Levi, J E; Mattosinho de Castro Ferraz, M G; Speck, N M G; Ribalta, J C L

    2015-12-21

    HIV and human papillomavirus (HPV) coinfection is increasing, especially in the anal canal (AC) and cervico-vaginal regions. We identified anal epithelium abnormalities related to high-risk HPV (HR-HPV) lesions in the lower genital tracts (LGTs) of HIV-positive women, described the HPV genotypes identified, and assessed the expression of E6/E7 oncogenes in coinfected patients. Ninety-eight women were enrolled in groups combining HIV status and presence or absence of HPV in the LGT. Anal and cervical smears were collected for cytology and HR-HPV assays using Cobas(®) and/or PapilloCheck(®). Samples with highly oncogenic HPV genotypes were confirmed by NucliSENS EasyQ(®). Forty-two HIV-positive (25-52; mean age 39.5) and 56 HIV-negative (18-58; mean age 35.7) patients were included. E2 and C1 groups presented AC alterations (P = 0.002); altered images for high-resolution anoscopy were higher in E1 and C2 (P < 0.001). Of the 29 women with alterations, 41.38% were HIV-negative and 58.62% were HIV-positive (P < 0.001). HIV-positive patients accounted for 29% of the anal high-grade squamous intraepithelial lesions (P = 0.015). The Cobas(®) positive result frequency was higher in three AC groups than in the other groups. There was variation in the number of HPV types in the cervico-vaginal samples among the study groups (P < 0.001). Anal cytology and anoscopy showed more altered findings in HIV-positive patients with HPV in the LGT. HR-HPV anal infections by various genotypes are common and are associated with cervical infections in HIV-positive patients. E6/E7 expression is apparently more common in the AC of HIV-positive women.

  8. Agreement between whole blood and plasma sodium measurements in profound hyponatremia.

    PubMed

    Geoghegan, Pierce; Koch, Christopher D; Wockenfus, Amy M; Harrison, Andrew M; Dong, Yue; Kashani, Kianoush B; Karon, Brad S

    2015-05-01

    We compared two different methods of whole blood sodium measurement to plasma sodium measurement using samples in the profoundly hyponatremic range (Na < 120 mmol/L). Whole blood pools with a range of low sodium values were generated using combinations and dilutions of pooled electrolyte-balanced lithium heparin samples submitted for arterial blood gas analysis. Each pool was analyzed five times on a Radiometer 827 blood gas analyzer and iSTAT analyzer. Pools were centrifuged to produce plasma, which was analyzed five times on a Roche Cobas c501 chemistry analyzer. An additional 40 fresh (analyzed on day of collection) excess lithium heparin arterial blood gas samples from 36 patients were analyzed on the Radiometer 827, iSTAT, and Cobas c501 as described above. The setting was a tertiary referral center. Blood samples were collected from a combination of patients in the intensive care unit, operating theaters and emergency room. All methods demonstrated excellent precision, even in the profoundly hyponatremic measurement range (Na < 120 mmol/L using a plasma reference method). However, agreement between the methods varied with the degree of hyponatremia. In the profoundly hyponatremic range, Radiometer whole blood sodium values were nearly identical to plasma reference sodium, while iSTAT whole blood sodium showed a consistent positive bias relative to plasma sodium in this range. If whole blood direct sodium measurements are compared with plasma sodium in profoundly hyponatremic patients consideration should be given to the use of Radiometer blood gas analyzers over iSTAT since the latter shows a positive bias relative to a plasma comparative method. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  9. Hepatitis C Virus RNA Real-Time Quantitative RT-PCR Method Based on a New Primer Design Strategy.

    PubMed

    Chen, Lida; Li, Wenli; Zhang, Kuo; Zhang, Rui; Lu, Tian; Hao, Mingju; Jia, Tingting; Sun, Yu; Lin, Guigao; Wang, Lunan; Li, Jinming

    2016-01-01

    Viral nucleic acids are unstable when improperly collected, handled, and stored, resulting in decreased sensitivity of currently available commercial quantitative nucleic acid testing kits. Using known unstable hepatitis C virus RNA, we developed a quantitative RT-PCR method based on a new primer design strategy to reduce the impact of nucleic acid instability on nucleic acid testing. The performance of the method was evaluated for linearity, limit of detection, precision, specificity, and agreement with commercial hepatitis C virus assays. Its clinical application was compared to that of two commercial kits--Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) and Kehua. The quantitative RT-PCR method delivered a good performance, with a linearity of R(2) = 0.99, a total limit of detection (genotypes 1 to 6) of 42.6 IU/mL (95% CI, 32.84 to 67.76 IU/mL), a CV of 1.06% to 3.34%, a specificity of 100%, and a high concordance with the CAP/CTM assay (R(2) = 0.97), with a means ± SD value of -0.06 ± 1.96 log IU/mL (range, -0.38 to 0.25 log IU/mL). The method was superior to commercial assays in detecting unstable hepatitis C virus RNA (P < 0.05). This quantitative RT-PCR method can effectively eliminate the influence of RNA instability on nucleic acid testing. The principle of primer design strategy may be applied to the detection of other RNA or DNA viruses. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  10. A novel multiplex real-time PCR assay for the concurrent detection of hepatitis A, B and C viruses in patients with acute hepatitis.

    PubMed

    Park, Yongjung; Kim, Beom Seok; Choi, Kyu Hun; Shin, Dong Ho; Lee, Mi Jung; Cho, Yonggeun; Kim, Hyon-Suk

    2012-01-01

    A novel multiplex real-time PCR assay for concurrent detection of hepatitis viruses was evaluated for its clinical performance in screening patients with acute hepatitis. A total of 648 serum samples were collected from patients with acute symptoms of hepatitis. Concurrent detection of nucleic acids of HAV, HBV and HCV was performed using the Magicplex™ HepaTrio Real-time Detection test. Serum nucleic acid levels of HBV and HCV were also quantified by the Cobas® AmpliPrep/Cobas® TaqMan® (CAP/CTM) HBV and HCV tests. Patients' medical records were also reviewed. Concordance rates between the results from the HepaTrio and the CAP/CTM tests for the detection of HBV and HCV were 94.9% (k = 0.88) and 99.2% (k = 0.98), respectively. The cycle threshold values with the HepaTrio test were also correlated well with the levels of HBV DNA (r = -0.9230) and HCV RNA (r = -0.8458). The sensitivity and specificity of the HepaTrio test were 93.8% and 98.2%, respectively, for detecting HBV infection, and 99.1% and 100.0%, respectively, for HCV infection. For the HepaTrio test, 21 (3.2%) cases were positive for both HBV and HCV. Among the positive cases, 6 (0.9%) were true coinfections. This test also detected 18 (2.8%) HAV positives. The HepaTrio test demonstrated good clinical performance and produced results that agreed well with those of the CAP/CTM assays, especially for the detection of HCV. This assay was also able to detect HAV RNA from anti-HAV IgM-positive individuals. Therefore, this new multiplex PCR assay could be useful for the concurrent detection of the three hepatitis viruses.

  11. Discordant rapid HIV tests: lessons from a low-resource community.

    PubMed

    Adetunji, A A; Kuti, M A; Audu, R A; Muyibi, S A; Imhansoloeva, M; Mosuro, O A; Solanke, E A; Akpa, O M; Irabor, A E; Ladipo, Mma; Berzins, B; Robertson, K; Ogunniyi, A; Adewole, I F; Taiwo, B O

    2017-07-31

    HIV rapid antibody tests are widely used in Africa, but dual testing sometimes produces discordant results. It is not clear if discordant rapid HIV tests should always heighten suspicion by frontline health workers that early HIV infection is present. Some studies have reported that discordant rapid tests have value for identifying early HIV infection in high HIV prevalence populations. It is not known if rapid test performance influenced this conclusion, or if this observation will hold true for low HIV prevalence populations. We therefore explored the occurrence of discordant rapid HIV tests in a low-resource community. A cross-sectional sample of HIV status-unaware adults with recent exposure to unsafe sex was assessed using a validated risk-based tool (University of North Carolina (UNC)-Malawi Risk Screening Score) for acute HIV infection. Participants received rapid testing with Determine™ HIV 1/2 and Uni-Gold™ HIV assays, plus plasma HIV-1 antigen testing with the COBAS(®) Ampliprep/COBAS(®) Taqman(®) HIV-1 assay, followed by western blot in those with detected HIV-1 antigen. Of 408 participants, 1.0% were confirmed to have established HIV infection. The discordance between rapid tests at initial screening was 2.45 and 2.94% when the two assays were used sequentially and simultaneously, respectively. Discordant rapid tests were strongly associated with risk scores > 2 [odds ratio (OR) 10.88; 95% confidence interval (CI) 2.35-50.43], and with detected HIV-1 RNA (OR 26.06; 95% CI 3.91-173.60). When the sample occurrence of discordance between the first and second tests is below 5%, discordant rapid tests in an adult with sexual risk behaviour should trigger strong suspicion of early HIV infection in low HIV prevalence populations. © 2017 British HIV Association.

  12. [Comparison of commercial HIV-1 viral load tests by using proficiency test results in China, 2013- 2015].

    PubMed

    Zhang, L; Jin, C; Jiang, Z; Tang, T; Jiang, Y; Pan, P L

    2017-09-10

    Objective: To compare the bio-equivalence among commercial HIV-1 viral load tests, including EasyQ HIV-1 v2.0 (EasyQ) from bioMerieux NucliSens of France; VERSANT HIV-1 RNA 3.0 assay (bDNA) from Siemens Healthcare Diagnostics of USA; COBAS AmpliPrep/COBAS TaqMan HIV-1 test (Taqman) from Roche Molecular Diagnosis of USA; Abbott Real Time HIV-1 Kit (M2000) from Abbott Molecular of USA and two domestic HIV-1 viral load test kits (domestic kit) from DaAn Gene Company of Sun Yat-Sen University and Liaoning Bio-Pharmaceutical company of Northeast pharmaceutical group, by using proficiency test results in China from 2013 to 2015. Methods: A total of 2 954 proficiency test results, obtained from 22 positive samples of 6 proficiency tests in 155 laboratories conducted by China CDC were analyzed during 2013-2015. The results from each sample were first logarithmic transformed and then grouped according to the method used, the mean value of logarithmic results was calculated. Subsequently, 22 clusters of mean values were analyzed by Bland-Altman analysis for the consistency, and linear regression analysis for the interdependency. Results: The results indicated that, by taking Taqman as the reference, EasyQ, M2000, bDNA and domestic kit had good consistency (90%-100%) and interdependency. Conclusion: All the viral load tests were bio-equivalent. Moreover, according to the conversion formula derived from domestic proficiency test results, all the viral load results could be converted, which is critical for epidemiological analysis.

  13. Evaluation of the Whole-Blood Alere Q NAT Point-of-Care RNA Assay for HIV-1 Viral Load Monitoring in a Primary Health Care Setting in Mozambique.

    PubMed

    Jani, Ilesh V; Meggi, Bindiya; Vubil, Adolfo; Sitoe, Nádia E; Bhatt, Nilesh; Tobaiwa, Ocean; Quevedo, Jorge I; Loquiha, Osvaldo; Lehe, Jonathan D; Vojnov, Lara; Peter, Trevor F

    2016-08-01

    Viral load testing is the WHO-recommended monitoring assay for patients on HIV antiretroviral therapy (ART). Point-of-care (POC) assays may help improve access to viral load testing in resource-limited settings. We compared the performance of the Alere Q NAT POC viral load technology (Alere Technologies, Jena, Germany), measuring total HIV RNA using finger prick capillary whole-blood samples collected in a periurban health center, with that of a laboratory-based plasma RNA test (Roche Cobas Ampliprep/Cobas TaqMan v2) conducted on matched venous blood samples. The whole-blood Alere Q NAT POC assay produced results with a bias of 0.8593 log copy/ml compared to the laboratory-based plasma assay. However, at above 10,000 copies/ml, the bias was 0.07 log copy/ml. Using the WHO-recommended threshold to determine ART failure of 1,000 copies/ml, the sensitivity and specificity of the whole-blood Alere Q NAT POC assay were 96.83% and 47.80%, respectively. A cutoff of 10,000 copies/ml of whole blood with the Alere Q NAT POC assay appears to be a better predictor of ART failure threshold (1,000 copies/ml of plasma), with a sensitivity of 84.0% and specificity of 90.3%. The precision of the whole-blood Alere Q NAT POC assay was comparable to that observed with the laboratory technology (5.4% versus 7.5%) between detectable paired samples. HIV POC viral load testing is feasible at the primary health care level. Further research on the value of whole-blood viral load to monitor antiretroviral therapy is warranted. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  14. Evaluation of Hologic Aptima HIV-1 Quant Dx Assay on the Panther System on HIV Subtypes.

    PubMed

    Manak, Mark M; Hack, Holly R; Nair, Sangeetha V; Worlock, Andrew; Malia, Jennifer A; Peel, Sheila A; Jagodzinski, Linda L

    2016-10-01

    Quantitation of the HIV-1 viral load in plasma is the current standard of care for clinical monitoring of HIV-infected individuals undergoing antiretroviral therapy. This study evaluated the analytical and clinical performances of the Aptima HIV-1 Quant Dx assay (Hologic, San Diego, CA) for monitoring viral load by using 277 well-characterized subtype samples, including 171 cultured virus isolates and 106 plasma samples from 35 countries, representing all major HIV subtypes, recombinants, and circulating recombinant forms (CRFs) currently in circulation worldwide. Linearity of the Aptima assay was tested on each of 6 major HIV-1 subtypes (A, B, C, D, CRF01_AE, and CRF02_AG) and demonstrated an R(2) value of ≥0.996. The performance of the Aptima assay was also compared to those of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 v.2 (CAP/CTM) and Abbott m2000 RealTime HIV-1 (RealTime) assays on all subtype samples. The Aptima assay values averaged 0.21 log higher than the CAP/CTM values and 0.30 log higher than the RealTime values, and the values were >0.4 log higher than CAP/CTM values for subtypes F and G and than RealTime values for subtypes C, F, and G and CRF02_AG. Two samples demonstrated results with >1-log differences from RealTime results. When the data were adjusted by the average difference, 94.9% and 87.0% of Aptima results fell within 0.5 log of the CAP/CTM and RealTime results, respectively. The linearity and accuracy of the Aptima assay in correctly quantitating all major HIV-1 subtypes, coupled with the completely automated format and high throughput of the Panther system, make this system well suited for reliable measurement of viral load in the clinical laboratory. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  15. The ATHENA HPV study underrepresents "other" high-risk HPV genotypes when compared with a diverse New York City population.

    PubMed

    Ramos Rivera, G; Khader, S N; Lajara, S; Schlesinger, K; Goldstein, D Y; Naeem, R C; Suhrland, M J; Fox, A S

    2017-10-01

    Persistent infection with oncogenic high risk HPV (hrHPV) types causes virtually all cases of cervical cancer. HPV 16 and 18 have been targeted for individual genotyping and vaccination because of their presence in 71% of invasive cervical cancers worldwide. Montefiore Medical Center, Bronx, New York serves a population known for ethnic and racial diversity. Given this diversity it is possible that HPV genotypes not individually detected by current testing are causing significant disease. We conducted a retrospective analysis of liquid based cervicovaginal cytology and Cobas HPV results reported between October 5, 2015 and March 30, 2016. This included 20 483 samples from patients aged 16-95 (average age 42), with racial distribution including: African-American 32.4%, Other (includes denied, unknown, mixed, Hispanic) 52.1%, Caucasian 14.5%, Asian 0.7%, American Indian/Alaskan Native 0.3%. In all, 14 938 samples (72.9%) were submitted for clinically requested COBAS 4800 HPV testing, which separately reports HPV 16, 18 and a pool of 12 other hrHPV. A total of 3180 (21.5%) tested hrHPV positive. The percentage of patients with cytologic diagnosis of HSIL (high-grade squamous intraepithelial lesion) that were positive only for HPV 16 was 19.4% vs 1.8% for all cytologic diagnoses. However, only one of the HSIL cases was HPV 18 positive along with other hrHPV (OHR). Surprisingly, a majority (64.5%) was positive for only OHR. Further evaluation is needed to determine if this pool of other hrHPV includes individual genotypes that in our population carry a higher risk of persistence and progression to cancer. © 2017 John Wiley & Sons Ltd.

  16. Evaluation of a new random-access HBV DNA molecular assay: The VERIS HBV assay.

    PubMed

    Fourati, Slim; Challine, Dominique; Poveda, Jean-Dominique; Laperche, Syria; Rallier, Sandrine; Pawlotsky, Jean-Michel; Chevaliez, Stéphane

    2017-07-01

    Detection and quantification of HBV DNA are essential to diagnose chronic HBV infection, monitor the virological response to treatment and the possible selection of resistant viruses in order to tailor therapy. The VERIS/MDx System HBV Assay is a random-access system that quantifies HBV DNA in clinical samples using unique single sample and reagent access during the workflow process without the need to reload other tests and delivers results within 1.2h following sampling. The goal of this study was to evaluate the analytical performance of the VERIS HBV assay for HBV DNA detection and quantification in clinical samples from a series of patients chronically infected with different HBV genotypes. The specificity of the VERIS HBV assay was estimated to be over 99.5%. The limit of detection (LOD) was estimated to be 4.1IU/mL (95%CI: 3.20-5.90IU/mL). Using an HBV linearity panel and controls (Seracare LifeScience), intra-assay and inter-assay coefficients of variation ranged from 0.12% to 3.64% and from 1.05% to 7.35%, respectively. The influence of the HBV genotype was evaluated from 120 clinical specimens containing HBV genotypes A to G tested in parallel with the VERIS HBV assay and the COBAS AmpliPrep/COBAS TaqMan HBV v2.0 assay. A linear relationship between the HBV DNA levels measured with both assays was found. A modest bias of HBV DNA levels was observed in the VERIS assay as compared to CAP/CTM HBV v2.0 in most of the samples tested (mean VERIS minus CAP/CTM difference: -0.395 log IU/mL). Overall, the VERIS HBV assay is well suited to monitoring clinical HBV DNA levels in infected patients according to current clinical practice guidelines. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Evaluation of fully automated assays for the detection of Rubella IgM and IgG antibodies by the Elecsys(®) immunoassay system.

    PubMed

    van Helden, Josef; Grangeot-Keros, Liliane; Vauloup-Fellous, Christelle; Vleminckx, Renaud; Masset, Frédéric; Revello, Maria-Grazia

    2014-04-01

    Screening for acute rubella infection in pregnancy is an important element of antenatal care. This study compared the sensitivity, specificity and reproducibility of two new, fully automated Elecsys(®) Rubella IgM and IgG immunoassays designed for the Elecsys 2010, Modular Analytics E170, COBAS e-411 and COBAS e-601 and e602 analytical platforms, with current assays using serum from patients with primary rubella infections, vaccinated patients, patients with potentially cross-reacting infections and on routine samples in clinical laboratories in France, Germany and Italy. Both assays showed good within-run and within-laboratory precision. A sensitivity of 79.8-96.0% was demonstrated for Elecsys IgM in primary, early acute infection, consistent with existing assays. In samples obtained from routine antenatal screening, the Elecsys Rubella IgM assay revealed high specificity (98.7-99.0%). A significantly (p<0.0001) lower reactivity was demonstrated in samples from previously infected patients where acute rubella infection was excluded, and the incidence of false positives in patients with potentially cross-reacting infections was lower with Elecsys Rubella IgM compared with other. The Elecsys Rubella IgG assay exhibited a relative sensitivity of 99.9-100.0% and specificity of 97.4-100.0% in samples from routine antenatal screening. The Elecsys Rubella IgM and IgG assays allow convenient, rapid and reliable determination of anti-rubella antibodies. Sensitivity, specificity and reproducibility were comparable with existing assay systems. Assay results were available in approximately half the time required for currently employed methods and the assays are compatible with widely used analytical platforms.

  18. Evaluation of a Novel PCR-Based Assay for Detection and Identification of Chlamydia trachomatis Serovars in Cervical Specimens▿

    PubMed Central

    Quint, Koen; Porras, Carolina; Safaeian, Mahboobeh; González, Paula; Hildesheim, Allan; Quint, Wim; van Doorn, Leen-Jan; Silva, Sandra; Melchers, Willem; Schiffman, Mark; Rodríguez, Ana Cecilia; Wacholder, Sholom; Freer, Enrique; Cortes, Bernal; Herrero, Rolando

    2007-01-01

    The aims of this study were to compare a novel PCR-based Chlamydia trachomatis detection and genotyping (Ct-DT) assay with the FDA-approved, commercially available C. trachomatis detection Hybrid Capture 2 (HC2) assay and to investigate the C. trachomatis serovar distribution among young women in a rural Costa Rican study population. A total of 5,828 sexually active women participating in a community-based trial in Costa Rica were tested for C. trachomatis by HC2. A sample of 1,229 specimens consisting of 100% HC2 C. trachomatis-positive specimens (n = 827) and a random sample of 8% HC2 C. trachomatis-negative specimens (n = 402) were tested with the Ct-DT assay. Agreement between the two assays was determined by the unweighted kappa statistic. Discrepant specimens were tested with a second commercially available test (COBAS TaqMan). The Ct-DT-positive specimens were further analyzed with the Ct-DT genotyping step to investigate the distribution of 14 different C. trachomatis serovars (A, B/Ba, C, D/Da, E, F, G/Ga, H, I/Ia, J, K, L1, L2/L2a, and L3). After accounting for the sampling fraction selected for Ct-DT testing, crude agreement with the HC2 assay was 98% and the kappa was 0.92 (95% confidence interval [CI], 0.89 to 0.97). The 33 discordant samples that were further analyzed with the COBAS TaqMan test showed better agreement with the Ct-DT assay (31/33, P < 0.001). Among the 806 Ct-DT-positive samples, serovar E was the most common serovar (31%), followed by serovars F and D (both 21%) and serovar I (15%). In conclusion, the novel Ct-DT assay permits reliable detection and identification of C. trachomatis serovars. PMID:17959760

  19. p16/Ki-67 co-expression associates high risk human papillomavirus persistence and cervical histopathology: a 3-year cohort study in China.

    PubMed

    Yu, Lu-Lu; Guo, Hui-Qin; Lei, Xiao-Qin; Qin, Yu; Wu, Ze-Ni; Kang, Le-Ni; Zhang, Xun; Qiao, You-Lin; Chen, Wen

    2016-10-04

    To evaluate the association of p16/Ki-67 co-expression and persistence of high-risk human papillomavirus (HR-HPV) infection as well as cervical abnormalities. We performed a 3-year cohort study among which 2498 Chinese women aged 25 to 65 years were screened by different HPV tests in 2011. 690 women who were positive at any of the tests and a random sample of 164 women with all negative results received colposcopy, cervical specimens for cobas HPV test (Roche diagnostics) were collected before colposcopy; of this group, 737 cervical specimens were collected to perform cobas, Liquid-based cytology, HPV E6 test (Arbor Vita Corporation) and p16/Ki-67 dual staining (Roche diagnostics) in 2014. Colposcopy and biopsies was performed on women with any abnormal result. Compared to women without HR-HPV persistent infection, women in the HR-HPV persistence group had a higher risk of p16/Ki-67 positive, with an adjusted Odds Ratio(OR) and 95% confidence interval (CI) of 6.29 (4.07-9.72); moreover, adjusted odds ratio for women who had HPV16/18 persistent infection was nearly 4-folder higher than women with other 12 HR-HPV persistent infection (adjusted OR = 17.15, 95% CI: 7.11-41.33 vs adjusted OR = 4.68, 95% CI: 2.89-7.58). Additionally, p16/Ki-67 positivity rate significantly increased with the severity of the cytological and histological abnormalities, and resulted strongly associated with a CIN2+ diagnosis (OR = 16.03, 95% CI: 4.46-57.59). p16/Ki-67 co-expressions associated strongly with HR-HPV persistence, especially with HPV16/18, and the presence of a CIN2+ lesion. Therefore, p16/Ki-67 could be considered as a suitable biomarker for cervical cancer screening, particularly in HPV-based screening programs.

  20. A preliminary retrospective study about the relationship between ductus venosus Doppler indices, nuchal translucency (NT) and biochemical markers in the first and second trimester screening tests.

    PubMed

    Demirturk, Fazli; Caliskan, Ahmet Cantug; Aytan, Hakan; Sahin, Semsettin

    2012-05-01

    In our study, we tried to assess the relation between ductus venosus Doppler indices [pulsatility index (PI), resistance index (RI) and S/D] and first-trimester screening markers (MoM of serum pregnancy-associated plasma protein A, pappalysin 1 (PAPP-A), MoM of serum free β-human chorionic gonadotrophin (β-hCG), and nuchal translucency (NT) and second trimester screening markers (MoM of serum α-fetoprotein, MoM of serum total β-hCG and MoM of serum estriol). We analyzed the data of 121 singleton pregnancies. Roche cobas e 601ECLIA (electrochemiluminescence immunoassay) was used to measure MoM of serum PAPP-A and Roche cobas e 602 ECLIA (electrochemiluminescence immunoassay) was used to measure MoM of serum free β-hCG in the first trimester. Beckman Coulter Access 2 Immunoassay was used to measure MoM of serum α-fetoprotein, MoM of serum total β-hCG and MoM of serum estriol in the second trimester. The first author performed all ultrasound screenings and ductus venosus Doppler studies. What we found new in our study is presented as following; MoM of serum α-fetoprotein had a negative correlation with RI of ductus venosus Doppler, MoM of serum estriol had a negative correlation with RI of ductus venosus Doppler and MoM of serum estriol had a negative correlation with S/D of ductus venosus doppler. The results of our study suggest that ductus venosus Doppler can be used to increase the effectiveness of the second trimester screening test.

  1. BRAF mutation testing with a rapid, fully integrated molecular diagnostics system

    PubMed Central

    Huang, Helen J.; Falchook, Gerald S.; Devogelaere, Benoit; Kockx, Mark; Bempt, Isabelle Vanden; Reijans, Martin; Naing, Aung; Fu, Siqing; Piha-Paul, Sarina A.; Hong, David S.; Holley, Veronica R.; Tsimberidou, Apostolia M.; Stepanek, Vanda M.; Patel, Sapna P.; Kopetz, E. Scott; Subbiah, Vivek; Wheler, Jennifer J.; Zinner, Ralph G.; Karp, Daniel D.; Luthra, Rajyalakshmi; Roy-Chowdhuri, Sinchita; Sablon, Erwin; Meric-Bernstam, Funda; Maertens, Geert; Kurzrock, Razelle

    2015-01-01

    Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTM BRAF Mutation Test has high sensitivity and shorter turnaround times compared to other methods. We used Idylla to detect BRAF V600 mutations in archived formalin-fixed paraffin-embedded (FFPE) tumor samples and compared these results with those obtained using the cobas 4800 BRAF V600 Mutation Test or MiSeq deep sequencing system and with those obtained by a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory employing polymerase chain reaction–based sequencing, mass spectrometric detection, or next-generation sequencing. In one set of 60 FFPE tumor samples (15 with BRAF mutations per Idylla), the Idylla and cobas results had an agreement of 97%. Idylla detected BRAF V600 mutations in two additional samples. The Idylla and MiSeq results had 100% concordance. In a separate set of 100 FFPE tumor samples (64 with BRAF mutation per Idylla), the Idylla and CLIA-certified laboratory results demonstrated an agreement of 96% even though the tests were not performed simultaneously and different FFPE blocks had to be used for 9 cases. The IdyllaTM BRAF Mutation Test produced results quickly (sample to results time was about 90 minutes with about 2 minutes of hands on time) and the closed nature of the cartridge eliminates the risk of PCR contamination. In conclusion, our observations demonstrate that the Idylla test is rapid and has high concordance with other routinely used but more complex BRAF mutation–detecting tests. PMID:26330075

  2. Evaluation of Hologic Aptima HIV-1 Quant Dx Assay on the Panther System on HIV Subtypes

    PubMed Central

    Hack, Holly R.; Nair, Sangeetha V.; Worlock, Andrew; Malia, Jennifer A.; Peel, Sheila A.; Jagodzinski, Linda L.

    2016-01-01

    Quantitation of the HIV-1 viral load in plasma is the current standard of care for clinical monitoring of HIV-infected individuals undergoing antiretroviral therapy. This study evaluated the analytical and clinical performances of the Aptima HIV-1 Quant Dx assay (Hologic, San Diego, CA) for monitoring viral load by using 277 well-characterized subtype samples, including 171 cultured virus isolates and 106 plasma samples from 35 countries, representing all major HIV subtypes, recombinants, and circulating recombinant forms (CRFs) currently in circulation worldwide. Linearity of the Aptima assay was tested on each of 6 major HIV-1 subtypes (A, B, C, D, CRF01_AE, and CRF02_AG) and demonstrated an R2 value of ≥0.996. The performance of the Aptima assay was also compared to those of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 v.2 (CAP/CTM) and Abbott m2000 RealTime HIV-1 (RealTime) assays on all subtype samples. The Aptima assay values averaged 0.21 log higher than the CAP/CTM values and 0.30 log higher than the RealTime values, and the values were >0.4 log higher than CAP/CTM values for subtypes F and G and than RealTime values for subtypes C, F, and G and CRF02_AG. Two samples demonstrated results with >1-log differences from RealTime results. When the data were adjusted by the average difference, 94.9% and 87.0% of Aptima results fell within 0.5 log of the CAP/CTM and RealTime results, respectively. The linearity and accuracy of the Aptima assay in correctly quantitating all major HIV-1 subtypes, coupled with the completely automated format and high throughput of the Panther system, make this system well suited for reliable measurement of viral load in the clinical laboratory. PMID:27510829

  3. Comparison of Standardized Cytomegalovirus (CMV) Viral Load Thresholds in Whole Blood and Plasma of Solid Organ and Hematopoietic Stem Cell Transplant Recipients with CMV Infection and Disease.

    PubMed

    Dioverti, M Veronica; Lahr, Brian D; Germer, Jeffrey J; Yao, Joseph D; Gartner, Michelle L; Razonable, Raymund R

    2017-01-01

    Quantification of cytomegalovirus (CMV) deoxyribonucleic acid (DNA) has important diagnostic, prognostic, and therapeutic implications in the management of transplant recipients. We aimed to assess a viral load in plasma and whole blood that distinguishes CMV disease from asymptomatic infection in a cohort of solid organ and hematopoietic stem cell transplantation. We prospectively measured and compared CMV viral load in paired plasma and whole blood samples collected from transplant recipients with CMV infection and disease. Cytomegalovirus viral loads were determined by a commercially available US Food and Drug Administration-approved quantitative assay (COBAS AmpliPrep/COBAS TaqMan CMV Test [CAP/CTM CMV]) calibrated to the first World Health Organization International Standard for CMV DNA quantification. Moderate agreement of CMV viral load was observed between plasma and whole blood, with 31% of samples having discordant findings, particularly among samples with low DNA levels. Among the subset of samples where both paired samples had quantifiable levels, we observed a systematic bias that reflected higher viral load in whole blood compared with plasma. Based on receiver operating curve analysis, an initial plasma CMV viral load threshold of 1700 IU/mL in solid organ transplant recipients (sensitivity 80%, specificity 74%) and 1350 IU/mL in allogeneic hematopoietic stem cell transplant recipients (sensitivity 87%, specificity 87%) distinguished CMV disease and asymptomatic infection. This study identifies standardized viral load thresholds that distinguish CMV disease from asymptomatic infection using CAP/CTM CMV assay. We propose these thresholds as potential triggers to be evaluated in prospective studies of preemptive therapy. Plasma was better than whole blood for measuring viral load using the CAP/CTM CMV assay.

  4. Comparison of Standardized Cytomegalovirus (CMV) Viral Load Thresholds in Whole Blood and Plasma of Solid Organ and Hematopoietic Stem Cell Transplant Recipients with CMV Infection and Disease

    PubMed Central

    Dioverti, M Veronica; Lahr, Brian D; Germer, Jeffrey J; Yao, Joseph D; Gartner, Michelle L

    2017-01-01

    Abstract Background Quantification of cytomegalovirus (CMV) deoxyribonucleic acid (DNA) has important diagnostic, prognostic, and therapeutic implications in the management of transplant recipients. We aimed to assess a viral load in plasma and whole blood that distinguishes CMV disease from asymptomatic infection in a cohort of solid organ and hematopoietic stem cell transplantation. Methods We prospectively measured and compared CMV viral load in paired plasma and whole blood samples collected from transplant recipients with CMV infection and disease. Cytomegalovirus viral loads were determined by a commercially available US Food and Drug Administration-approved quantitative assay (COBAS AmpliPrep/COBAS TaqMan CMV Test [CAP/CTM CMV]) calibrated to the first World Health Organization International Standard for CMV DNA quantification. Results Moderate agreement of CMV viral load was observed between plasma and whole blood, with 31% of samples having discordant findings, particularly among samples with low DNA levels. Among the subset of samples where both paired samples had quantifiable levels, we observed a systematic bias that reflected higher viral load in whole blood compared with plasma. Based on receiver operating curve analysis, an initial plasma CMV viral load threshold of 1700 IU/mL in solid organ transplant recipients (sensitivity 80%, specificity 74%) and 1350 IU/mL in allogeneic hematopoietic stem cell transplant recipients (sensitivity 87%, specificity 87%) distinguished CMV disease and asymptomatic infection. Conclusions This study identifies standardized viral load thresholds that distinguish CMV disease from asymptomatic infection using CAP/CTM CMV assay. We propose these thresholds as potential triggers to be evaluated in prospective studies of preemptive therapy. Plasma was better than whole blood for measuring viral load using the CAP/CTM CMV assay. PMID:28852681

  5. Detection of Hepatitis B Virus Covalently Closed Circular DNA in the Plasma of Iranian HBeAg-Negative Patients With Chronic Hepatitis B

    PubMed Central

    Tajik, Zahra; Keyvani, Hossein; Bokharaei-Salim, Farah; Zolfaghari, Mohammad Reza; Fakhim, Shahin; Keshvari, Maryam; Alavian, Seyed Moayed

    2015-01-01

    Background: Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is a marker of HBV replication in the liver of patients infected with HBV. Objectives: This study aimed to investigate the association between the presence of cccDNA in the plasma samples of Iranian treatment-naive patients with chronic hepatitis B infection and HBV viral load and HBsAg levels. Patients and Methods: From April 2012 to May 2015, 106 treatment-naive patients with chronic hepatitis B infection were enrolled in this cross-sectional study. The HBsAg titer was measured by the Roche HBsAg II assay on the Cobas e411 system, and HBV DNA quantitation was performed using the COBAS TaqMan 48 kit. Real-time polymerase chain reaction was performed for the detection of HBV cccDNA. Results: The mean (SD) age of the patients was 41.1 ± 12.4 years (range, 20 - 62 years). From a total of 106 study participants, 67 (63.2%) were males. The HBV cccDNA was detected in plasma specimens in 19 (17.9%) out of the total 106 patients, and a significant relationship was found between the presence of cccDNA in plasma sample of males (23.9%) and females (7.7%) (P = 0.039). Also, a significant correlation was found between the presence of cccDNA in plasma sample of the patients and HBV viral load level (P < 0.0001) and HBsAg titer (P = 0.0043). Conclusions: This study showed that cccDNA can be detected in the plasma specimen of 17.9% of Iranian treatment-naive patients with chronic hepatitis B infection. Therefore, designing prospective studies focusing on the detection of cccDNA in these patients would provide more information. PMID:26504471

  6. Applicability of Hepatitis C Virus RNA Viral Load Thresholds for 8-Week Treatments in Patients With Chronic Hepatitis C Virus Genotype 1 Infection.

    PubMed

    Vermehren, Johannes; Maasoumy, Benjamin; Maan, Raoel; Cloherty, Gavin; Berkowski, Caterina; Feld, Jordan J; Cornberg, Markus; Pawlotsky, Jean-Michel; Zeuzem, Stefan; Manns, Michael P; Sarrazin, Christoph; Wedemeyer, Heiner

    2016-05-15

    Interferon-free treatment of chronic hepatitis C virus (HCV) genotype 1 infection may be shortened to 8 weeks in treatment-naive, noncirrhotic patients with baseline HCV RNA levels of <4 or <6 million (M) IU/mL based on post-hoc analyses of phase 3 trial data. The applicability of these viral load thresholds in clinical practice is unknown. Pretreatment and on-treatment serum samples (n = 740) from patients with HCV genotype 1 infection were included for HCV RNA analysis with 2 widely used assays, Cobas AmpliPrep/CobasTaqMan (CAP/CTM) and Abbott RealTime HCV (ART) assays. HCV RNA levels were significantly higher with CAP/CTM than with ART (overall difference, +0.11 log10 IU/mL; P < .001). In treatment-naive, noncirrhotic patients, discordance rates around the clinical cutoffs at 4M and 6M IU/mL were 23% and 18%, respectively. The mean differences between assays in discordant samples were 0.38 (4M) and 0.41 (6M) log10 IU/mL, respectively. Overall, 87% and 95% of treatment-naive, noncirrhotic patients, respectively, had baseline HCV RNA levels below 4M and 6M IU/mL with ART. These rates were significantly higher than those measured with CAP/CTM (64% and 78%, respectively; P < .001). Finally, discordance rates around the proposed thresholds in 2 consecutive samples of the same patient were in the range of 1%-2% for ART and 13%-17% for CAP/CTM. Selection of patients for 8-week regimens on the basis of a single HCV RNA determination may not be reliable because viral load levels around the proposed clinical thresholds show significant interassay and intrapatient variability. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  7. Clinical significance of residual viremia detected by two real-time PCR assays for response-guided therapy of HCV genotype 1 infection.

    PubMed

    Vermehren, Johannes; Aghemo, Alessio; Falconer, Karolin; Susser, Simone; Lunghi, Giovanna; Zeuzem, Stefan; Colombo, Massimo; Weiland, Ola; Sarrazin, Christoph

    2014-05-01

    The duration of current standard dual and protease inhibitor-based triple therapies for chronic hepatitis C is determined by assessment of early viral kinetics. Little is known about differences between HCV RNA assays for the use in response guided therapy. HCV RNA was assessed by two widely used real-time PCR-based assays, Cobas Ampliprep/Cobas TaqMan (CAP), and Real-Time HCV (ART) in 903 samples of hepatitis C genotype 1 patients treated with dual (n=169) or telaprevir-based triple therapy (n=164) in three European countries. Overall, CAP and ART were in excellent agreement for the determination of HCV-RNA concentrations (mean difference 0.21 log10 IU/ml). For treatment-naïve patients treated with peginterferon-alfa and ribavirin a lower rate of undetectable HCV-RNA at week 4 (RVR) was observed for ART (9%) vs. CAP (16%). Although 11/27 (41%) of patients with shortened treatment (24weeks) had detectable HCV-RNA <12IU/ml by ART at week 4 none of these patients experienced virologic relapse after treatment cessation. In patients who received triple therapy, 67% and 37% had undetectable HCV-RNA at week 4 by CAP and ART, respectively. However, 18/31 (58%) eligible patients for shortened treatment based on CAP had detectable HCV-RNA by ART at week 4. Again, relapse was not observed in these patients. Lower rates of undetectable HCV-RNA at week 4 were observed with ART compared to CAP in patients treated with dual and triple therapies. For ART, detectable <12IU/ml HCV-RNA levels at week 4 may be sufficient as part of the criteria used for selecting patients who receive a shortened treatment regimen. Copyright © 2014 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

  8. Performance of Two HCV RNA Assays during Protease Inhibitor-Based Triple Therapy in Patients with Advanced Liver Fibrosis and Cirrhosis

    PubMed Central

    Calvaruso, Vincenza; Makara, Mihály; Vermehren, Johannes; Haragh, Attila; Susser, Simone; Bremer, Birgit; Cloherty, Gavin; Manns, Michael P.; Craxì, Antonio; Wedemeyer, Heiner; Sarrazin, Christoph

    2014-01-01

    Introduction On-treatment HCV RNA measurements are crucial for the prediction of a sustained virological response (SVR) and to determine treatment futility during protease inhibitor-based triple therapies. In patients with advanced liver disease an accurate risk/benefit calculation based on reliable HCV RNA results can reduce the number of adverse events. However, the different available HCV RNA assays vary in their diagnostic performance. Aim To investigate the clinical relevance of concordant and discordant results of two HCV RNA assays during triple therapy with boceprevir and telaprevir in patients with advanced liver fibrosis/cirrhosis. Methods We collected on-treatment samples of 191 patients with advanced liver fibrosis/cirrhosis treated at four European centers for testing with the Abbott RealTime (ART) and COBAS AmpliPrep/COBAS TaqMan HCV v2.0 (CTM) assays. Results Discordant test results for HCV RNA detectability were observed in 23% at week 4, 17% at week 8/12 and 9% at week 24 on-treatment. The ART detected HCV RNA in 41% of week 4 samples tested negative by the CTM. However, the positive predictive value of an undetectable week 4 result for SVR was similar for both assays (80% and 82%). Discordance was also found for application of stopping rules. In 27% of patients who met stopping rules by CTM the ART measured levels below the respective cut-offs of 100 and 1000 IU/ml, respectively, which would have resulted in treatment continuation. In contrast, in nine patients with negative HCV RNA by CTM at week 24 treatment would have been discontinued due to detectable residual HCV RNA by the ART assay. Importantly, only 4 of these patients failed to achieve SVR. Conclusion Application of stopping rules determined in approval studies by one assay to other HCV RNA assays in clinical practice may lead to over and undertreatment in a significant number of patients undergoing protease inhibitor-based triple therapy. PMID:25389779

  9. Performance of two HCV RNA assays during protease inhibitor-based triple therapy in patients with advanced liver fibrosis and cirrhosis.

    PubMed

    Maasoumy, Benjamin; Hunyady, Bela; Calvaruso, Vincenza; Makara, Mihály; Vermehren, Johannes; Haragh, Attila; Susser, Simone; Bremer, Birgit; Cloherty, Gavin; Manns, Michael P; Craxì, Antonio; Wedemeyer, Heiner; Sarrazin, Christoph

    2014-01-01

    On-treatment HCV RNA measurements are crucial for the prediction of a sustained virological response (SVR) and to determine treatment futility during protease inhibitor-based triple therapies. In patients with advanced liver disease an accurate risk/benefit calculation based on reliable HCV RNA results can reduce the number of adverse events. However, the different available HCV RNA assays vary in their diagnostic performance. To investigate the clinical relevance of concordant and discordant results of two HCV RNA assays during triple therapy with boceprevir and telaprevir in patients with advanced liver fibrosis/cirrhosis. We collected on-treatment samples of 191 patients with advanced liver fibrosis/cirrhosis treated at four European centers for testing with the Abbott RealTime (ART) and COBAS AmpliPrep/COBAS TaqMan HCV v2.0 (CTM) assays. Discordant test results for HCV RNA detectability were observed in 23% at week 4, 17% at week 8/12 and 9% at week 24 on-treatment. The ART detected HCV RNA in 41% of week 4 samples tested negative by the CTM. However, the positive predictive value of an undetectable week 4 result for SVR was similar for both assays (80% and 82%). Discordance was also found for application of stopping rules. In 27% of patients who met stopping rules by CTM the ART measured levels below the respective cut-offs of 100 and 1000 IU/ml, respectively, which would have resulted in treatment continuation. In contrast, in nine patients with negative HCV RNA by CTM at week 24 treatment would have been discontinued due to detectable residual HCV RNA by the ART assay. Importantly, only 4 of these patients failed to achieve SVR. Application of stopping rules determined in approval studies by one assay to other HCV RNA assays in clinical practice may lead to over and undertreatment in a significant number of patients undergoing protease inhibitor-based triple therapy.

  10. The New Aptima HBV Quant Real-Time TMA Assay Accurately Quantifies Hepatitis B Virus DNA from Genotypes A to F.

    PubMed

    Chevaliez, Stéphane; Dauvillier, Claude; Dubernet, Fabienne; Poveda, Jean-Dominique; Laperche, Syria; Hézode, Christophe; Pawlotsky, Jean-Michel

    2017-04-01

    Sensitive and accurate hepatitis B virus (HBV) DNA detection and quantification are essential to diagnose HBV infection, establish the prognosis of HBV-related liver disease, and guide the decision to treat and monitor the virological response to antiviral treatment and the emergence of resistance. Currently available HBV DNA platforms and assays are generally designed for batching multiple specimens within an individual run and require at least one full day of work to complete the analyses. The aim of this study was to evaluate the ability of the newly developed, fully automated, one-step Aptima HBV Quant assay to accurately detect and quantify HBV DNA in a large series of patients infected with different HBV genotypes. The limit of detection of the assay was estimated to be 4.5 IU/ml. The specificity of the assay was 100%. Intra-assay and interassay coefficients of variation ranged from 0.29% to 5.07% and 4.90% to 6.85%, respectively. HBV DNA levels from patients infected with HBV genotypes A to F measured with the Aptima HBV Quant assay strongly correlated with those measured by two commercial real-time PCR comparators (Cobas AmpliPrep/Cobas TaqMan HBV test, version 2.0, and Abbott RealTime HBV test). In conclusion, the Aptima HBV Quant assay is sensitive, specific, and reproducible and accurately quantifies HBV DNA in plasma samples from patients with chronic HBV infections of all genotypes, including patients on antiviral treatment with nucleoside or nucleotide analogues. The Aptima HBV Quant assay can thus confidently be used to detect and quantify HBV DNA in both clinical trials with new anti-HBV drugs and clinical practice. Copyright © 2017 American Society for Microbiology.

  11. Impact of HCV kinetics on treatment outcome differs by the type of real-time HCV assay in NS3/4A protease inhibitor-based triple therapy.

    PubMed

    Ogawa, Eiichi; Furusyo, Norihiro; Murata, Masayuki; Hayashi, Takeo; Shimizu, Motohiro; Mukae, Haru; Toyoda, Kazuhiro; Hotta, Taeko; Uchiumi, Takeshi; Hayashi, Jun

    2016-02-01

    Repeated measurement of the HCV RNA level is essential for properly monitoring treatment efficacy. The aim of this study was to determine the utility of two HCV real-time assays in the evaluation of the impact of hepatitis C virus (HCV) kinetics on the outcome of triple therapy with NS3/4A protease inhibitors (PIs), telaprevir or simeprevir. This study consisted of 171 Japanese patients infected with HCV genotype 1. All 3266 serum samples taken during and post treatment were tested with both the COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HCV Test v2.0 and the Abbott RealTime (ART) HCV Test. Of the 2597 samples undetectable (lower limit of detection [

  12. Higher specificity of nucleic acid sequence-based amplification isothermal technology than of real-time PCR for quantification of HIV-1 RNA on dried blood spots.

    PubMed

    Mercier-Delarue, Severine; Vray, Muriel; Plantier, Jean Christophe; Maillard, Theodora; Adjout, Zidan; de Olivera, Fabienne; Schnepf, Nathalie; Maylin, Sarah; Simon, Francois; Delaugerre, Constance

    2014-01-01

    Dried blood spots (DBS) are widely proposed as a plasma surrogate for monitoring antiretroviral treatment efficacy based on the HIV-1 RNA level (viral load [VL]) in resource-limited settings. Interfering coamplification of cell-associated HIV-1 DNA during reverse transcription (RT)-PCR can be avoided by using nucleic acid sequence-based amplification (NASBA) technology, which is based on an RNA template and isothermic conditions. We analyzed VL values obtained with DBS and plasma samples by comparing isothermic NASBA (NucliSENS EasyQ HIV-1 V2.0; bioMérieux) with real-time RT-PCR (Cobas TaqMan HIV-1 V2.0; Roche). Samples from 197 HIV-1-infected patients were tested (non-B subtypes in 51% of the cases). Nucleic acid extractions were performed by use of NucliSENS EasyMAG (bioMérieux) and Cobas AmpliPrep (Roche) before the NASBA and RT-PCR quantifications, respectively. Both quantification assays have lower limits of detection of 20 (1.3) and 800 (2.9) log10 copies/ml (log) in plasma and DBS, respectively. The mean (DBS minus plasma) differences were -0.39 and -0.46 log, respectively, for RT-PCR and NASBA. RT-PCR on DBS identified virological failure in 122 of 126 patients (sensitivity, 97%) and viral suppression in 58 of 70 patients (specificity, 83%), yielding 12 false-positive results (median, 3.2 log). NASBA on DBS identified virological failure in 85 of 96 patients (sensitivity, 89%) and viral suppression in 95 of 97 patients (specificity, 98%) and yielded 2 false-positive results (3.0 log for both). Both technologies detected HIV-1 RNA in DBS at a threshold of 800 copies/ml. This higher specificity of NASBA technology could avoid overestimation of poor compliance or the emergence of resistance when monitoring antiretroviral efficacy with the DBS method.

  13. Estimation of two real-time RT-PCR assays for quantitation of hepatitis C virus RNA during PEG-IFN plus ribavirin therapy by HCV genotypes and IL28B genotype.

    PubMed

    Miyagi, Yugo; Nomura, Hideyuki; Yamashita, Nobuyuki; Tanimoto, Hironori; Ito, Kiyoaki; Masaki, Naohiko; Mizokami, Masashi; Shibuya, Tsunefumi

    2013-02-01

    Hepatitis C virus (HCV) RNA values measured with two real-time PCR methods (Cobas Ampliprep/Cobas TaqMan, CAP/CTM, and the Abbott real-time PCR test, ART) vary among patients with genotype 1. We investigated HCV RNA values measured by two real-time PCR assays during pegylated interferon plus ribavirin (PEG-IFN/RBV) therapy. We evaluated 185 cases of chronic hepatitis C patients, among which 97 patients received the PEG-IFN/RBV therapy. HCV RNA values of CAP/CTM for genotype 1 were significantly higher than those of ART (p < 0.05) The difference in HCV RNA values (CAP/CTM minus ART) of genotype 1 was significantly higher than those in genotype 2 (p < 0.0001). The positive rate (>0) of the difference of HCV RNA values in genotype 1 was 100 % (55/55), which was significantly higher than the 78.6 % (33/42) of genotype 2 (p < 0.001). There was no difference between TT and TG/GG genotype groups in terms of difference of HCV RNA values (CAP/CTM minus ART). After PEG-IFN/RBV therapy was administered, reduction of HCV measurements was observed from day 1 for both assays regardless of genotype. The HCV value of CAP/CTM during PEG-IFN/RBV therapy was consistently higher than the value of ART, although the difference in these two values gradually became smaller during the course of therapy, and eventually no significant difference was observed near the detection level. No correlation was observed between the sustained virological response (SVR) rate and the difference between the CAP/CTM HCV values and the ART HCV value before treatment.

  14. p16/Ki-67 co-expression associates high risk human papillomavirus persistence and cervical histopathology: a 3-year cohort study in China

    PubMed Central

    Yu, Lu-Lu; Guo, Hui-Qin; Lei, Xiao-Qin; Qin, Yu; Wu, Ze-Ni; Kang, Le-Ni; Zhang, Xun; Qiao, You-Lin; Chen, Wen

    2016-01-01

    Purpose To evaluate the association of p16/Ki-67 co-expression and persistence of high-risk human papillomavirus (HR-HPV) infection as well as cervical abnormalities. Methods We performed a 3-year cohort study among which 2498 Chinese women aged 25 to 65 years were screened by different HPV tests in 2011. 690 women who were positive at any of the tests and a random sample of 164 women with all negative results received colposcopy, cervical specimens for cobas HPV test (Roche diagnostics) were collected before colposcopy; of this group, 737 cervical specimens were collected to perform cobas, Liquid-based cytology, HPV E6 test (Arbor Vita Corporation) and p16/Ki-67 dual staining (Roche diagnostics) in 2014. Colposcopy and biopsies was performed on women with any abnormal result. Results Compared to women without HR-HPV persistent infection, women in the HR-HPV persistence group had a higher risk of p16/Ki-67 positive, with an adjusted Odds Ratio(OR) and 95% confidence interval (CI) of 6.29 (4.07-9.72); moreover, adjusted odds ratio for women who had HPV16/18 persistent infection was nearly 4-folder higher than women with other 12 HR-HPV persistent infection (adjusted OR = 17.15, 95% CI: 7.11-41.33 vs adjusted OR = 4.68, 95% CI: 2.89-7.58). Additionally, p16/Ki-67 positivity rate significantly increased with the severity of the cytological and histological abnormalities, and resulted strongly associated with a CIN2+ diagnosis (OR = 16.03, 95% CI: 4.46-57.59). Conclusions p16/Ki-67 co-expressions associated strongly with HR-HPV persistence, especially with HPV16/18, and the presence of a CIN2+ lesion. Therefore, p16/Ki-67 could be considered as a suitable biomarker for cervical cancer screening, particularly in HPV-based screening programs. PMID:27588487

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

    PubMed Central

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

    2015-01-01

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

  16. Detection of hepatitis B virus infection: A systematic review

    PubMed Central

    Ghosh, Mallika; Nandi, Srijita; Dutta, Shrinwanti; Saha, Malay Kumar

    2015-01-01

    AIM: To review published methods for detection of hepatitis B virus (HBV) infection. METHODS: A thorough search on Medline database was conducted to find original articles describing different methods or techniques of detection of HBV, which are published in English in last 10 years. Articles outlining methods of detection of mutants or drug resistance were excluded. Full texts and abstracts (if full text not available) were reviewed thoroughly. Manual search of references of retrieved articles were also done. We extracted data on different samples and techniques of detection of HBV, their sensitivity (Sn), specificity (Sp) and applicability. RESULTS: A total of 72 studies were reviewed. HBV was detected from dried blood/plasma spots, hepatocytes, ovarian tissue, cerumen, saliva, parotid tissue, renal tissue, oocytes and embryos, cholangiocarcinoma tissue, etc. Sensitivity of dried blood spot for detecting HBV was > 90% in all the studies. In case of seronegative patients, HBV DNA or serological markers have been detected from hepatocytes or renal tissue in many instances. Enzyme linked immunosorbent assay and Chemiluminescent immunoassay (CLIA) are most commonly used serological tests for detection. CLIA systems are also used for quantitation. Molecular techniques are used qualitatively as well as for quantitative detection. Among the molecular techniques version 2.0 of the CobasAmpliprep/CobasTaqMan assay and Abbott’s real time polymerase chain reaction kit were found to be most sensitive with a lower detection limit of only 6.25 IU/mL and 1.48 IU/mL respectively. CONCLUSION: Serological and molecular assays are predominant and reliable methods for HBV detection. Automated systems are highly sensitive and quantify HBV DNA and serological markers for monitoring. PMID:26483870

  17. Clinical performances of two real-time PCR assays and bDNA/TMA to early monitor treatment outcome in patients with chronic hepatitis C.

    PubMed

    Martinot-Peignoux, Michelle; Khiri, Hacène; Leclere, Laurence; Maylin, Sarah; Marcellin, Patrick; Halfon, Philippe

    2009-11-01

    Early viral monitoring is essential for the management of treatment outcome in patients with chronic hepatitis C. A variety of commercially available assays are now available to quantify HCV-RNA in routine clinical practice. Compare the clinical results of 3 commercially available assays to evaluate the positive predictive value (PPV) and the negative predictive value (NPV) of rapid virological response (RVR) at week 4 and early virological response (EVR) at week 12. 287 patients treated with standard care regimen combination therapy were studied. HCV-RNA values measured at baseline, week 4, week 12 with VERSANT HCV 3.0 Assay (bDNA), and VERSANT HCV-RNA Qualitative Assay (TMA) (bDNA/TMA); COBAS Ampliprep/COBAS/TaqMan (CAP/CTM) and Abbott m2000sp extraction/m2000rt amplification system (ART). RVR was defined as undetectable serum HCV-RNA and EVR as a > OR =2 log decline in baseline viral load (BLV). Median (range) BVLs were: 5.585(2.585-6.816), 5.189(2.792-7.747) and 4.804(2.380-6.580) log(10)IU/ml, with bDNA/TMA, CAP/CTM and ART, respectively (p<0.01); RVR was observed in 22%, 30% and 27% of the patients and PPVs were 97%, 91% and 94% with bDNA/TMA, CAP/CTM and ART, respectively (p=0.317). EVR was observed in 76%, 73% and 67% of the patients and NPVs were 93%, 83% and 79% with bDNA/TMA, CAP/CTM and ART, respectively (p=0.09). Treatment monitoring should include both detection of serum HCV-RNA at week 4 to predict SVR and at week 12 to predict non-SVR. The value of all 3 assays was similar for evaluating RVR or EVR. Because of viral load discrepancies the same assay should be used throughout patient treatment follow-up.

  18. The New Aptima HCV Quant Dx Real-time TMA Assay Accurately Quantifies Hepatitis C Virus Genotype 1-6 RNA.

    PubMed

    Chevaliez, Stéphane; Dubernet, Fabienne; Dauvillier, Claude; Hézode, Christophe; Pawlotsky, Jean-Michel

    2017-06-01

    Sensitive and accurate hepatitis C virus (HCV) RNA detection and quantification is essential for the management of chronic hepatitis C therapy. Currently available platforms and assays are usually batched and require at least 5hours of work to complete the analyses. The aim of this study was to evaluate the ability of the newly developed Aptima HCV Quant Dx assay that eliminates the need for batch processing and automates all aspects of nucleic acid testing in a single step, to accurately detect and quantify HCV RNA in a large series of patients infected with different HCV genotypes. The limit of detection was estimated to be 2.3 IU/mL. The specificity of the assay was 98.6% (95% confidence interval: 96.1%-99.5%). Intra-assay and inter-assay coefficients of variation ranged from 0.09% to 5.61%, and 1.05% to 3.65%, respectively. The study of serum specimens from patients infected with HCV genotypes 1 to 6 showed a satisfactory relationship between HCV RNA levels measured by the Aptima HCV Quant Dx assay, and both real-time PCR comparators (Abbott RealTime HCV and Cobas AmpliPrep/Cobas TaqMan HCV Test, version 2.0, assays). the new Aptima HCV Quant Dx assay is rapid, sensitive, reasonably specific and reproducible and accurately quantifies HCV RNA in serum samples from patients with chronic HCV infection, including patients on antiviral treatment. The Aptima HCV Quant Dx assay can thus be confidently used to detect and quantify HCV RNA in both clinical trials with new anti-HCV drugs and clinical practice in Europe and the US. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Spectrophotometry, colors, and photometric properties of the 67P/Churyumov-Gerasimenko nucleus from the OSIRIS instrument onboard the ROSETTA mission

    NASA Astrophysics Data System (ADS)

    Fornasier, Sonia; Hasselmann, Pedro; Feller, Clement; Barucci, Maria Antonietta; Lara, Luisa; Oklay, Nilda; Tubiana, Cecilia; Besse, Sebastien; Scholten, Frank; Sierks, Holger; Leyrat, Cedric; La Forgia, Fiorangela; Lazzarin, Monica; Pajola, Maurizio; Thomas, Nick; Pommerol, Antoine; Massironi, Matteo

    2015-04-01

    Rosetta is the cornerstone mission of the European Space Agency devoted to the study of Solar System minor bodies. Launched on 2 March 2004, Rosetta arrived on August 6, 2014, at the comet 67P/Churyumov-Gerasimenko after 10 years of interplanetary journey. Rosetta is now in the main science escort phase of the comet after the successful delivery of the lander Philae on its surface on November 12, 2014. In this work we present the results on the 67P nucleus physical properties derived from the OSIRIS imaging system observations obtained in July- mid August 2014, during the comet approach phase and the first bound orbits. In this timeframe, OSIRIS has mapped the comet surface with a resolution up to 2 m/px with several filters covering the 250-1000 nm range, and at different phase angles (1.3-54 degrees). The images have been reduced using the OSIRIS standard pipeline, and then transformed into I/F reflectance. A 3D shape model of the nucleus, determined from the images obtained during the mapping phase, has been used to retrieve the illumination and geometric conditions of each image. Color cubes of the surface have been hence produced by stacking registered and photometrically corrected images. Globally, the nucleus has spectrophotometric properties in the NUV-VIS-NIR range similar to those of bare cometary nuclei, of primitive D-type asteroids such us Jupiter Trojans, and of the moderately red Transneptunians and Centaurs. No clear absorption bands have been detected so far at the resolution of the used filters. The global spectral slope, evaluated in the 535-880 nm range, varies between 11 %/(100 nm) at a phase angle of 1.3 degrees and 16 %/(100 nm) at a phase angle of 52 degrees, implying a significant phase reddening. Despite the different types of terrains and morphological features seen on the comet (Thomas et al. 2015), the nucleus shows small color variations, with the notable exception of the Hapi region (Sierks et al., 2015). This region is located

  20. Morphometric Characterization and Classification of Alluvial Fans in Eastern Oman

    NASA Astrophysics Data System (ADS)

    Leuschner, Annette; Mattern, Frank; van Gasselt, Stephan

    2015-04-01

    Morphologic characteristics of alluvial fans are a product of fluvial erosion, transportation and deposition. Consequently, fans have been described and defined on the basis of their shape, their composition, conditions and processes under which they from, their so-called "controlling factors", and their geomorphic and tectonic settings. The aim of our study is to reconstruct the morphologic evolution and to relate it to past and present climate conditions. In order to achieve this, we first characterize alluvial fans based on their climatic settings and conditions and classify them accordingly using satellite image data and digital elevation models. For mapping of different alluvial fan bodies multispectral images of the Landsat Enhanced Thematic Mapper (ETM+) with a scale of 15-30 m/px were utilized. For the detection of morphometric parameters as input data for subsequent hydrological studies digital terrain model data of the Shuttle Radar Topography Mission (SRTM) and the ASTER GDEM with a scale of 90 m/px and 30m, respectively, were used. Using these datasets morphological characteristics, such as sizes of drainage basins, transport areas and areas of deposition derived from spatial semi-automatic analysis, have been computed. The area of Muscat at the Oman Mountains has been selected as a study area because of its size, accessibility and climate conditions and it is considered well-suited for studying the development of alluvial fans and their controlling factors. The Oman Mountains are well-known for the world's largest intact and best exposed obducted ophiolite complex, the Semail Ophiolite. They are today subjected to a mild desert climate (Bwh), influenced by the Indian Ocean but they have experienced extensive pluvial periods in the geologic past. Formation of alluvial fans was, therefore, likely triggered by the interplay of increased sediment production caused by high rainfalls with enhanced erosion of hillslopes and transport rates during pluvial

  1. Seasonal effects on the nucleus of comet 67P revealed by Rosetta/VIRTIS

    NASA Astrophysics Data System (ADS)

    Tosi, Federico; Capaccioni, Fabrizio; Filacchione, Gianrico; Erard, Stéphane; Rouseeau, Batiste; Combe, Jean-Philippe; Capria, Maria Teresa; Leyrat, Cédric; Longobardo, Andrea; Bockelée-Morvan, Dominique; Kappel, David; Arnold, Gabriele; Fonti, Sergio; Mancarella, Francesca; Kuehrt, Ekkehard; Mottola, Stefano

    2016-04-01

    hemisphere. These three regions are chosen so as to be relatively smooth at the spatial resolution that is achieved from a distance of about 100 km (25 m/px for VIRTIS-M, 50×150 m/px for VIRTIS-H), in order to limit the effects of large-scale surface roughness. Acknowledgements: The authors would like to thank the following institutions and agencies, which supported this work: Italian Space Agency (ASI - Italy), Centre National d'Etudes Spatiales (CNES- France), Deutsches Zentrum für Luft- und Raumfahrt (DLR-Germany), National Aeronautic and Space Administration (NASA-USA) Rosetta Program, Science and Technology Facilities Council (UK). VIRTIS has been built by a consortium, which includes Italy, France and Germany, under the scientific responsibility of the Istituto di Astrofisica e Planetologia Spaziali of INAF, Italy, which guides also the scientific operations. The VIRTIS instrument development has been funded and managed by ASI, with contributions from Observatoire de Meudon financed by CNES, and from DLR. The computational resources used in this research have been supplied by INAF-IAPS through the DataWell project.

  2. Effets de rayonnement sur les detecteurs au silicium a pixels du detecteur ATLAS

    NASA Astrophysics Data System (ADS)

    Lebel, Celine

    Two detection systems are using pixel silicon detectors in the ATLAS detector: the Pixel, which is the subdetector closest to the interaction point, and the MPX network. The activation of the materials present in the Pixel produced by radiation has been measured in two experiments which we performed at CERF (CERN) and NPI-ASCR (Czech Republic). These experimental studies of activation are compared with GEANT4 simulations. The results of these comparisons show that the simulation can predict the activities with a precision of an order of magnitude. They also show that GEANT4 fails to produce certain radioisotopes seen in the experimental activation studies. The contribution to background and the residual doses due to the desintegration of the radioisotopes produced by fast neutrons (category in which falls the expected average neutron energy of 1 MeV in ATLAS) are extrapolated to ATLAS conditions. It is found that this background in the ATLAS Pixel subdetector will be negligible and that the doses are well below safety concerns for detector manipulation during maintenance and repair periods. The radiation field also inflicts damages to the silicon detectors thus reducing their detection efficiency. A modified Hecht model is presented using an electric field description which includes the double junction effect and a small exponential component in areas usually considered without electric field. This model allows the description of the detection efficiency as a function of applied bias voltage and irradiation fluence for several types of silicon detectors irradiated by particles of different types and energies. On top of validating the Hecht model proposed in this thesis, the studies of the radiation damage on silicon detectors has allowed to conclude that the N1EL hypothesis has to be revised (study with different energies). Using the variation with irradiation fluence of the effective doping concentration and of the leakage current, it is shown that silicon

  3. The application of ICP-MS and ICP-OES in determination of micronutrients in wood ashes used as soil conditioners.

    PubMed

    Górecka, H; Chojnacka, K; Górecki, H

    2006-12-15

    In the present paper, the elemental composition of wood ashes obtained by the combustion of wood in a fireplace was determined with the use of ICP-MS and ICP-OES techniques. Wood ashes may find a potential application as deacidifying agents and soil conditioners, since they contain calcium (in the form of CaCO(3) and CaO), potassium (in the form of K(2)SO(4) and K(2)CO(3)) and significant levels of micronutrients. However, if applied to soil, it is important to assess the bioavailability of particular elements to plants. This process can be simulated by proper extraction procedures. Various species of wood were combusted in a firestove in a single-family house. The ashes underwent multielemental analyses with ICP-MS Varian Ultra Mass 700 (Australia) and ICP-OES Vista-MPX from Varian (Australia) in order to determine the content of macro- and micronutrients as well as toxic elements. Ashes were also extracted with solutions of 0.1M NaNO(3) and water in order to simulate the process of elemental transfer from ash (used as soil conditioner) to soil solution and consequently to plants. Also, the environmental impact of ash supplementation to soil was assessed in these experiments. Soil was supplemented with 0-20% of ash. After elution, the eluent underwent multielemental analysis by ICP-MS and ICP-OES techniques to determine the content of macronutrients (P, K, Mg), micronutrients (Fe, Mn, Co, Mo, Zn, Cu and Ti) and toxic elements (Hg, Pb, As and Cd). It was shown that fireplace ashes can be applied for deacidification of homestead gardens. Ash may be described as a valuable soil conditioner with N:P:K formula 0:1:3. It is concluded therefore that in order to achieve full fertilization, additional supplementation with nitrogen fertilizer would be necessary.

  4. Colour Images Of The Moon From Amie On Smart-1: A Preliminary Analysys Of The Region Of Oppenheimer.

    NASA Astrophysics Data System (ADS)

    Cerroni, Priscilla; Besse, S.; De Sanctis, M. C.; Josset, J.; Beauvivre, S.; Pinet, P.; Chevrel, S.; Barucci, M. A.; Langevin, Y.; Koshny, D.; Almeida, M.; Foing, B.; AMIE Team

    2006-09-01

    The Advanced Moon micro-Imager Experiment (AMIE) is the imaging system on board the ESA mission to the Moon SMART-1 which is closing towards its end on September 3rd, 2006. During the time spent in lunar orbit the AMIE camera provided high resolution CCD images of selected lunar areas where it performed colour imaging through three filters at 750, 915 and 960 nm with a maximum resolution of 27 m /pixel at the perilune of 300 km. The spectral bands have been selected in order to allow discrimination between mafic minerals which dominate the mare (revealed by the Fe2+ absorption feature at 950 nm) and the anorthosite rich highland materials. Data acquired by AMIE in push-broom modality on November 25th, 2005 for the lunar region of Oppenheimer centered at 36 S, 194 E have been preliminarily analysed . The ground resolution for these observations is of 73 m/px. A new calibration has been applied to the images based on flat-fielding from in-flight data; for the region considered three filters images have been co-registered, colour images and band-ratio images have been produced. An assessment of the results and a comparison with Clementine data from the same region is presented . Spectra have been extracted from a region in the floor of Oppenheimer and on the rim of a crater : a comparison with spectra from Clementine yields consistent results. Acknowledgements: P. Cerroni and M.C. De Sanctis acknowledge the support of ASI grant I/030/05

  5. Comparison of monkeypox viruses pathogenesis in mice by in vivo imaging

    USGS Publications Warehouse

    Osorio, Jorge E.; Iams, Keith P.; Meteyer, Carol U.; Rocke, Tonie E.

    2009-01-01

    Monkeypox viruses (MPXV) cause human monkeypox, a zoonotic smallpox-like disease endemic to Africa, and are of worldwide public health and biodefense concern. Using viruses from the Congo (MPXV-2003-Congo-358) and West African (MPXV-2003-USA-044) clades, we constructed recombinant viruses that express the luciferase gene (MPXV-Congo/Luc+and MPXV-USA-Luc+) and compared their viral infection in mice by biophotonic imaging. BALB/c mice became infected by both MPXV clades, but they recovered and cleared the infection within 10 days post-infection (PI). However, infection in severe combined immune deficient (SCID) BALB/c mice resulted in 100% lethality. Intraperitoneal (IP) injection of both MPXV-Congo and MPXV-Congo/Luc+resulted in a systemic clinical disease and the same mean time-to-death at 9 (??0) days post-infection. Likewise, IP injection of SCID-BALB/c mice with MPXV-USA or the MPXV-USA-Luc+, resulted in similar disease but longer (P<0.05) mean time-to-death (11??0 days) for both viruses compared to the Congo strains. Imaging studies in SCID mice showed luminescence in the abdomen within 24 hours PI with subsequent spread elsewhere. Animals infected with the MPXV-USA/Luc+had less intense luminescence in tissues than those inoculated with MPXV-Congo/Luc+, and systemic spread of the MPXV-USA/Luc+virus occurred approximately two days later than the MPXV-Congo/Luc+. The ovary was an important target for viral replication as evidenced by the high viral titers and immunohistochemistry. These studies demonstrate the suitability of a mouse model and biophotonic imaging to compare the disease progression and tissue tropism of MPX viruses.

  6. The CaSSIS imaging system: optical performance overview

    NASA Astrophysics Data System (ADS)

    Gambicorti, L.; Piazza, D.; Pommerol, A.; Roloff, V.; Gerber, M.; Ziethe, R.; El-Maarry, M. R.; Weigel, T.; Johnson, M.; Vernani, D.; Pelo, E.; Da Deppo, V.; Cremonese, G.; Ficai Veltroni, I.; Thomas, N.

    2016-07-01

    The Colour and Stereo Surface Imaging System (CaSSIS) is the high-resolution scientific imager on board the European Space Agency's (ESA) ExoMars Trace Gas Orbiter (TGO) which was launched on 14th March 2016 to Mars. CaSSIS will observe the Martian surface from an altitude of 400 km with an optical system based on a modified TMA telescope (Three Mirrors Anastigmatic configuration) with a 4th powered folding mirror. The camera EPD (Entrance Pupil Diameter) is 135 mm, and the expected focal length is 880 mm, giving an F# 6.5 in the wavelength range of 400- 1100 nm with a distortion designed to be less than 2%. CaSSIS will operate in a "push-frame" mode with a monolithic Filter Strip Assembly (FSA) produced by Optics Balzers Jena GmbH selecting 4 colour bands and integrated on the focal plane by Leonardo-Finmeccanica SpA (under TAS-I responsibility). The detector is a spare of the Simbio-Sys detector of the Italian Space Agency (ASI), developed by Raytheon Vision Systems. It is a 2kx2k hybrid Si-PIN array with a 10 μm pixel pitch. A scale of 4.6 m/px from the nominal orbit is foreseen to produce frames of 9.4 km × 47 km on the Martian surface. The University of Bern was in charge of the full instrument integration as well as the characterization of the focal plane and calibration of the entire instrument. The paper will present an overview of the CaSSIS telescope and FPA optical performance. The preliminary results of on-ground calibration and the first commissioning campaign (April 2016) will be described.

  7. Analysis of accuracy in photogrammetric roughness measurements

    NASA Astrophysics Data System (ADS)

    Olkowicz, Marcin; Dąbrowski, Marcin; Pluymakers, Anne

    2017-04-01

    Regarding permeability, one of the most important features of shale gas reservoirs is the effective aperture of cracks opened during hydraulic fracturing, both propped and unpropped. In a propped fracture, the aperture is controlled mostly by proppant size and its embedment, and fracture surface roughness only has a minor influence. In contrast, in an unpropped fracture aperture is controlled by the fracture roughness and the wall displacement. To measure fracture surface roughness, we have used the photogrammetric method since it is time- and cost-efficient. To estimate the accuracy of this method we compare the photogrammetric measurements with reference measurements taken with a White Light Interferometer (WLI). Our photogrammetric setup is based on high resolution 50 Mpx camera combined with a focus stacking technique. The first step for photogrammetric measurements is to determine the optimal camera positions and lighting. We compare multiple scans of one sample, taken with different settings of lighting and camera positions, with the reference WLI measurement. The second step is to perform measurements of all studied fractures with the parameters that produced the best results in the first step. To compare photogrammetric and WLI measurements we regrid both data sets onto a regular 10 μm grid and determined the best fit, followed by a calculation of the difference between the measurements. The first results of the comparison show that for 90 % of measured points the absolute vertical distance between WLI and photogrammetry is less than 10 μm, while the mean absolute vertical distance is 5 μm. This proves that our setup can be used for fracture roughness measurements in shales.

  8. Using Zebrafish Models of Human Influenza A Virus Infections to Screen Antiviral Drugs and Characterize Host Immune Cell Responses.

    PubMed

    Sullivan, Con; Jurcyzszak, Denise; Goody, Michelle F; Gabor, Kristin A; Longfellow, Jacob R; Millard, Paul J; Kim, Carol H

    2017-01-20

    Each year, seasonal influenza outbreaks profoundly affect societies worldwide. In spite of global efforts, influenza remains an intractable healthcare burden. The principle strategy to curtail infections is yearly vaccination. In individuals who have contracted influenza, antiviral drugs can mitigate symptoms. There is a clear and unmet need to develop alternative strategies to combat influenza. Several animal models have been created to model host-influenza interactions. Here, protocols for generating zebrafish models for systemic and localized human influenza A virus (IAV) infection are described. Using a systemic IAV infection model, small molecules with potential antiviral activity can be screened. As a proof-of-principle, a protocol that demonstrates the efficacy of the antiviral drug Zanamivir in IAV-infected zebrafish is described. It shows how disease phenotypes can be quantified to score the relative efficacy of potential antivirals in IAV-infected zebrafish. In recent years, there has been increased appreciation for the critical role neutrophils play in the human host response to influenza infection. The zebrafish has proven to be an indispensable model for the study of neutrophil biology, with direct impacts on human medicine. A protocol to generate a localized IAV infection in the Tg(mpx:mCherry) zebrafish line to study neutrophil biology in the context of a localized viral infection is described. Neutrophil recruitment to localized infection sites provides an additional quantifiable phenotype for assessing experimental manipulations that may have therapeutic applications. Both zebrafish protocols described faithfully recapitulate aspects of human IAV infection. The zebrafish model possesses numerous inherent advantages, including high fecundity, optical clarity, amenability to drug screening, and availability of transgenic lines, including those in which immune cells such as neutrophils are labeled with fluorescent proteins. The protocols detailed here

  9. Comparison of monkeypox viruses pathogenesis in mice by in vivo imaging.

    PubMed

    Osorio, Jorge E; Iams, Keith P; Meteyer, Carol U; Rocke, Tonie E

    2009-08-11

    Monkeypox viruses (MPXV) cause human monkeypox, a zoonotic smallpox-like disease endemic to Africa, and are of worldwide public health and biodefense concern. Using viruses from the Congo (MPXV-2003-Congo-358) and West African (MPXV-2003-USA-044) clades, we constructed recombinant viruses that express the luciferase gene (MPXV-Congo/Luc+and MPXV-USA-Luc+) and compared their viral infection in mice by biophotonic imaging. BALB/c mice became infected by both MPXV clades, but they recovered and cleared the infection within 10 days post-infection (PI). However, infection in severe combined immune deficient (SCID) BALB/c mice resulted in 100% lethality. Intraperitoneal (IP) injection of both MPXV-Congo and MPXV-Congo/Luc+resulted in a systemic clinical disease and the same mean time-to-death at 9 (+/-0) days post-infection. Likewise, IP injection of SCID-BALB/c mice with MPXV-USA or the MPXV-USA-Luc+, resulted in similar disease but longer (P<0.05) mean time-to-death (11+/-0 days) for both viruses compared to the Congo strains. Imaging studies in SCID mice showed luminescence in the abdomen within 24 hours PI with subsequent spread elsewhere. Animals infected with the MPXV-USA/Luc+had less intense luminescence in tissues than those inoculated with MPXV-Congo/Luc+, and systemic spread of the MPXV-USA/Luc+virus occurred approximately two days later than the MPXV-Congo/Luc+. The ovary was an important target for viral replication as evidenced by the high viral titers and immunohistochemistry. These studies demonstrate the suitability of a mouse model and biophotonic imaging to compare the disease progression and tissue tropism of MPX viruses.

  10. Diffraction-limited 8- to 20-m telescope with an active and adaptive tertiary

    NASA Astrophysics Data System (ADS)

    Lemaitre, Gerard R.

    1998-08-01

    Active Optics Methods are extremely performing to obtain highly aspherical mirrors. The development of these methods is underlined with the presently proposed 4 to 5 mirror large telescope in the 8 - 20 m class. In this design, a particular emphasis has been placed to achieve the following main features: diffraction limited images over a restricted 1 or 2 arcmin field of view at f/30 for separate use with 16 Mpx detectors, diffraction limited images over a 2 to 5 arcsec field of view at the interferometric Mersenne focus, fast primary mirror of spherical shape, next mirrors the smallest as possible, low asphericity secondary and a tertiary spherically polished. It was found from optimization process with, for instance a 8 m primary at f/1.75, that, of the four mirrors required to achieve a diffraction limited afocal beam to a Mersenne focus, the spherical tertiary is the only mirror to be actively aspherized. Thus, due to a small aperture of this mirror (0.7 m), the vase form already developed from elasticity analysis would allow accurate aspherization by active optics. Similarly to our previous proposal TEMOS, the tertiary figure at f/6 can be achieved in situ, from a spherical polishing, by air depressure inside the mirror. The Sphe3 deformation sag of this mirror is quite large since is congruent to 1.3 mm ptv. Further, slight variations of the loading intensity allow a full optimization of the system as a function of the selected spectral range. The telescope design includes a pupil transfer on the tertiary realized by a doublet-lens. Thus, an adaptive optics system can be co- added to the same mirror. Finally, a concept for an active- adaptive tertiary is proposed.

  11. Spectral heterogeneity on Phobos and Deimos: HiRISE observations and comparisons to Mars Pathfinder results

    USGS Publications Warehouse

    Thomas, N.; Stelter, R.; Ivanov, A.; Bridges, N.T.; Herkenhoff, K. E.; McEwen, A.S.

    2011-01-01

    The High-Resolution Imaging Science Experiment (HiRISE) onboard Mars Reconnaissance Orbiter (MRO) has been used to observe Phobos and Deimos at spatial scales of around 6 and 20 m/px, respectively. HiRISE (McEwen et al.; JGR, 112, CiteID E05S02, DOI: 10.1029/2005JE002605, 2007) has provided, for the first time, high-resolution colour images of the surfaces of the Martian moons. When processed, by the production of colour ratio images for example, the data show considerable small-scale heterogeneity, which might be attributable to fresh impacts exposing different materials otherwise largely hidden by a homogenous regolith. The bluer material that is draped over the south-eastern rim of the largest crater on Phobos, Stickney, has been perforated by an impact to reveal redder material and must therefore be relatively thin. A fresh impact with dark crater rays has been identified. Previously identified mass-wasting features in Stickney and Limtoc craters stand out strongly in colour. The interior deposits in Stickney appear more inhomogeneous than previously suspected. Several other local colour variations are also evident. Deimos is more uniform in colour but does show some small-scale inhomogeneity. The bright streamers (Thomas et al.; Icarus, 123, 536556,1996) are relatively blue. One crater to the south-west of Voltaire and its surroundings appear quite strongly reddened with respect to the rest of the surface. The reddening of the surroundings may be the result of ejecta from this impact. The spectral gradients at optical wavelengths observed for both Phobos and Deimos are quantitatively in good agreement with those found by unresolved photometric observations made by the Imager for Mars Pathfinder (IMP; Thomas et al.; JGR, 104, 90559068, 1999). The spectral gradients of the blue and red units on Phobos bracket the results from IMP. ?? 2010 Elsevier Ltd. All rights reserved.

  12. Small-Scale Spectral and Color Analysis of Ritchey Crater Impact Materials

    NASA Astrophysics Data System (ADS)

    Bray, Veronica; Chojnacki, Matthew; McEwen, Alfred; Heyd, Rodney

    2014-11-01

    Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) analysis of Ritchey crater on Mars has allowed identification of the minerals uplifted from depth within its central peak as well as the dominant spectral signature of the crater fill materials which surround it. However, the 18m/px resolution of CRISM prevents full analysis of the nature of small-scale dykes, mega breccia blocks and finer scale crater-fill units. We extend our existing CRISM-based compositional mapping of the Ritchey crater interior to sub-CRISM pixel scales with the use of High Resolution Imaging Science Experiment (HiRISE) Color Ratio Products (CRPs). These CRPs are then compared to CRISM images; correlation between color ratio and CRISM spectral signature for a large bedrock unit is defined and used to suggest similar composition for a smaller unit with the same color ratio. Megabreccia deposits, angular fragments of rock in excess of 1 meter in diameter within a finer grained matrix, are common at Ritchey. The dominant spectral signature from each megabreccia unit varies with location around Ritchey and appears to reflect the matrix composition (based on texture and albedo similarities to surrounding rocks) rather than clast composition. In cases where the breccia block size is large enough for CRISM analysis, many different mineral compositions are noted (low calcium pyroxene (LCP) olivine (OL), alteration products) depending on the location. All block compositions (as inferred from CRPs) are observed down to the limit of HiRISE resolution. We have found a variety of dyke compositions within our mapping area. Correlation between CRP color and CRISM spectra in this area suggest that large 10 m wide) dykes within LCP-bearing bedrock close to the crater center tend to have similar composition to the host rock. Smaller dykes running non-parallel to the larger dykes are inferred to be OL-rich suggesting multiple phases of dyke formation within the Ritchey crater and its bedrock.

  13. Infection of zebrafish embryos with live fluorescent Streptococcus pneumoniae as a real-time pneumococcal meningitis model.

    PubMed

    Jim, Kin Ki; Engelen-Lee, JooYeon; van der Sar, Astrid M; Bitter, Wilbert; Brouwer, Matthijs C; van der Ende, Arie; Veening, Jan-Willem; van de Beek, Diederik; Vandenbroucke-Grauls, Christina M J E

    2016-08-19

    Streptococcus pneumoniae is one of the most important causes of bacterial meningitis, an infection where unfavourable outcome is driven by bacterial and host-derived toxins. In this study, we developed and characterized a pneumococcal meningitis model in zebrafish embryos that allows for real-time investigation of early host-microbe interaction. Zebrafish embryos were infected in the caudal vein or hindbrain ventricle with green fluorescent wild-type S. pneumoniae D39 or a pneumolysin-deficient mutant. The kdrl:mCherry transgenic zebrafish line was used to visualize the blood vessels, whereas phagocytic cells were visualized by staining with far red anti-L-plastin or in mpx:GFP/mpeg1:mCherry zebrafish, that have green fluorescent neutrophils and red fluorescent macrophages. Imaging was performed by fluorescence confocal and time-lapse microscopy. After infection by caudal vein, we saw focal clogging of the pneumococci in the blood vessels and migration of bacteria through the blood-brain barrier into the subarachnoid space and brain tissue. Infection with pneumolysin-deficient S. pneumoniae in the hindbrain ventricle showed attenuated growth and migration through the brain as compared to the wild-type strain. Time-lapse and confocal imaging revealed that the initial innate immune response to S. pneumoniae in the subarachnoid space mainly consisted of neutrophils and that pneumolysin-mediated cytolytic activity caused a marked reduction of phagocytes. This new meningitis model permits detailed analysis and visualization of host-microbe interaction in pneumococcal meningitis in real time and is a very promising tool to further our insights in the pathogenesis of pneumococcal meningitis.

  14. Composition of Rheasilvia Basin on Asteroid Vesta.

    NASA Astrophysics Data System (ADS)

    Ammannito, E.; De Sanctis, M. C.; Capaccioni, F.; Capria, M. T.; Combe, J. P.; Frigeri, A.; Jaumann, R.; Longobardo, A.; Marchi, S.; McCord, T. B.; McSween, H. Y., Jr.; Mittlefehldt, D. W.; Stephan, K.; Tosi, F.; Raymond, C. A.; Russell, C. T.

    2014-12-01

    The focus of the present study is the compositional analysis of small-scale surface features within the Rheasilvia basin on asteroid Vesta. We are using data acquired by the Visible and InfraRed mapping Spectrometer (VIR) on the Dawn mission. Nominal spatial resolution of the data set considered in this study is 70m/px. The portion of Rheasilvia basin below 65°S has a howarditic composition, with the higher concentration of diogenitic versus eucritic material in the region between 45° and 225°E-lon. However, there are several locations, such as craters Tarpeia and Severina and Parentatio Rupes, with lithologic characteristics different from the surroundings regions. Tarpeia crater has a eucritic patch in the west side of the crater, the bottom part of the wall and part of the floor. Severina, located in a region of Mg-rich pyroxene, has some diogenitic units on the walls of the crater. Also the Parentatio Rupes has an obvious diogenitic unit. These units extend for 10-20km, and their location, especially in the case of the two craters, suggests they formed before the cratering events and also before the Rheasilvia impact event. The origin of these units is still unclear; however, their characteristics and locations suggests heterogeneity in the composition of the ancient Vestan crust in this particular location of the surface. Acknowledgements: The authors gratefully acknowledge the contribution of the Dawn Instruments and Operations Teams. This work is supported by NASA through the Dawn project and by an Italian Space Agency grant. The VIR spectrometer is funded by ASI. It was built by Selex-Galileo, Florence, Italy and is now managed by INAF - Istituto di Astrofisica e Planetologia Spaziali, Rome, Italy.

  15. Small Impact Craters on Triton: Evidence for a Turn-up in the Size-frequency Distribution of Small (sub-km) KBOs, and Arguments Against a Planetocentric Origin

    NASA Astrophysics Data System (ADS)

    McKinnon, William B.; Singer, K. N.

    2010-10-01

    We report crater counts on the 10-frame, highest-resolution (350-420 m/px) Voyager 2 Triton mosaic (kindly MTF-sharpened and photometrically corrected by P.M. Schenk). Despite variable degrees of smear, crater counting on portions of these images is straightforward, and on the smoothest, presumably cryovolcanic plains, abundant craters are seen down to the resolution limit (craters 1 km in diameter). These counts complement those by Schenk & Zahnle (2007) on their 1.65 km/px global basemap. We find a fairly steep cumulative crater distribution (-3.2 slope), which implies a differential impactor index q ≈ 3.5. This is consistent with the classic Dohnanyi slope for a collisionally evolved population; more importantly, the transition from q = 2.8 (Schenk & Zahnle 2007) to 3.5 (or higher on Cipango Planum, which while less cratered, offers the "cleanest” counting surface and the sharpest MTF), as crater diameters drop below 10 km (and thus impactor diameters drop below 1 km), may be a signature of the strength-gravity transition in terms of disruption energy for KBOs (O'Brien & Greenberg 2003). These craters cannot be secondaries, as they are larger than any plausible "crossover diameter” for Triton's young surface. But do Triton's craters represent the impacts of small KBOs? Schenk & Zahnle (and others) have argued for a prograde planetocentric origin, based mostly on the geographic concentration of Triton's craters on its leading hemisphere. We argue that the trailing hemisphere cantaloupe terrain, a unique and topographically complex terrain of unknown compositional and crater retention properties, should be sparsely cratered. Conversely, their proposal for inner satellite sesquinaries would require, e.g., a fortuitous, >60-km-diameter impact crater on Proteus, which would launch ice blocks to speeds ≥1.6 km/s in order to reach Triton. Scaling from Pwyll secondaries on Europa (a best case analogy) indicates the ice blocks will not be big enough.

  16. Spore Density and Viability of Entomopathogenic Fungal Isolates from Indonesia, and Their Virulence against Aphis gossypii Glover (Homoptera: Aphididae).

    PubMed

    Herlinda, Siti

    2010-08-01

    The focus of this study was on quantifying fitness attributes, such as spore density and viability, and determining the virulence level against aphid (Aphis gossypii) nymphs of isolates from the fungal species Beauveria bassiana and Metarhizium anisopliae. The fungal isolates were obtained from several insects, including Plutella xylostella, Hypothenemus hampei, Bronstispa longissima, A. gossypii, Tenebrio molitor, and Leptocorisa acuta, that were collected from Indonesian islands, such as Sumatera, Java, and Sulawesi. Third instar aphid nymphs were inoculated via topical application of 10(6) conidia ml(-1) of the entomopathogenic fungal isolates. All of the B. bassiana and M. anisopliae isolates could produce very dense spores. The M. anisopliae isolate MaAg, which was obtained from the aphid, had the highest spore density at 6.70 × 10(8) conidia ml(-1). Among the B. bassiana isolates, the highest conidial viability belonged to isolate CPJW8, which was obtained from Chrysodeixis chalcites, with a 39% average viability. Among the M. anisopliae isolates, the highest viabilities belonged to the isolates MaAg and MaLa, which were obtained from L. acuta, with a 33% and 32% average viabilities, respectively. All of the B. bassiana and M. anisopliae isolates were virulent against aphid nymphs, with mortality rates ranging from 64% to 94%. The three most virulent isolates were BBY715 (94%), MPx (92%), and MaTm (92%), and the least virulent isolate was MaLa (64%). BBY715, the most virulent isolate, had the shortest lethal time median (LT50) against aphid nymphs at 2.97 hours, and MaLa had the longest LT50 at 61.81 hours.

  17. The southern hemisphere of 67P/Churyumov-Gerasimenko: Analysis of the preperihelion size-frequency distribution of boulders ≥7 m

    NASA Astrophysics Data System (ADS)

    Pajola, Maurizio; Lucchetti, Alice; Vincent, Jean-Baptiste; Oklay, Nilda; El-Maarry, Mohamed R.; Bertini, Ivano; Naletto, Giampiero; Lazzarin, Monica; Massironi, Matteo; Sierks, Holger; Barbieri, Cesare; Lamy, Philippe; Rodrigo, Rafael; Koschny, Detlef; Rickman, Hans; Keller, Horst U.; Agarwal, Jessica; A'Hearn, Michael F.; Barucci, Maria A.; Bertaux, Jean-Loup; Boudreault, Steve; Cremonese, Gabriele; Da Deppo, Vania; Davidsson, Björn; Debei, Stefano; De Cecco, Mariolino; Deller, Jakob; Fornasier, Sonia; Fulle, Marco; Gicquel, Adeline; Groussin, Olivier; Gutierrez, Pedro J.; Güttler, Carsten; Hofmann, Marc; Höfner, Sebastian; Hviid, Stubbe F.; Ip, Wing-Huen; Jorda, Laurent; Knollenberg, Jörg; Kramm, J.-Rainer; Kührt, Ekkehard; Küppers, Michael; La Forgia, Fiorangela; Lara, Luisa M.; Lee, Jui-Chi; Lin, Zhong-Yi; Lopez Moreno, Jose J.; Marzari, Francesco; Michalik, Harald; Mottola, Stefano; Preusker, Frank; Scholten, Frank; Thomas, Nicholas; Toth, Imre; Tubiana, Cecilia

    2016-07-01

    Aims: We calculate the size-frequency distribution of the boulders on the southern hemisphere of comet 67P Churyumov-Gerasimenko (67P), which was in shadow before the end of April 2015. We compare the new results with those derived from the northern hemisphere and equatorial regions of 67P, highlighting the possible physical processes that lead to these boulder size distributions. Methods: We used images acquired by the OSIRIS Narrow Angle Camera (NAC) on 2 May 2015 at a distance of 125 km from the nucleus. The scale of this dataset is 2.3 m/px; the high resolution of the images, coupled with the favorable observation phase angle of 62°, provided the possibility to unambiguously identify boulders ≥7 m on the surface of 67P and to manually extract them with the software ArcGIS. We derived the size-frequency distribution of the illuminated southern hemisphere. Results: We found a power-law index of -3.6 ± 0.2 for the boulders on the southern hemisphere with a diameter range of 7-35 m. The power-law index is equal to the one previously found on northern and equatorial regions of 67P, suggesting that similar boulder formation processes occur in both hemispheres. The power-law index is related to gravitational events triggered by sublimation and/or thermal fracturing causing regressive erosion. In addition, the presence of a larger number of boulders per km2 in the southern hemisphere, which is a factor of 3 higher with respect to the northern hemisphere, suggests that the southernmost terrains of 67P are affected by a stronger thermal fracturing and sublimating activity, hence possibly causing larger regressive erosion and gravitational events.

  18. Multilocus Sequence Typing (MLST) for Lineage Assignment and High Resolution Diversity Studies in Trypanosoma cruzi

    PubMed Central

    Yeo, Matthew; Mauricio, Isabel L.; Messenger, Louisa A.; Lewis, Michael D.; Llewellyn, Martin S.; Acosta, Nidia; Bhattacharyya, Tapan; Diosque, Patricio; Carrasco, Hernan J.; Miles, Michael A.

    2011-01-01

    Background Multilocus sequence typing (MLST) is a powerful and highly discriminatory method for analysing pathogen population structure and epidemiology. Trypanosoma cruzi, the protozoan agent of American trypanosomiasis (Chagas disease), has remarkable genetic and ecological diversity. A standardised MLST protocol that is suitable for assignment of T. cruzi isolates to genetic lineage and for higher resolution diversity studies has not been developed. Methodology/Principal Findings We have sequenced and diplotyped nine single copy housekeeping genes and assessed their value as part of a systematic MLST scheme for T. cruzi. A minimum panel of four MLST targets (Met-III, RB19, TcGPXII, and DHFR-TS) was shown to provide unambiguous assignment of isolates to the six known T. cruzi lineages (Discrete Typing Units, DTUs TcI-TcVI). In addition, we recommend six MLST targets (Met-II, Met-III, RB19, TcMPX, DHFR-TS, and TR) for more in depth diversity studies on the basis that diploid sequence typing (DST) with this expanded panel distinguished 38 out of 39 reference isolates. Phylogenetic analysis implies a subdivision between North and South American TcIV isolates. Single Nucleotide Polymorphism (SNP) data revealed high levels of heterozygosity among DTUs TcI, TcIII, TcIV and, for three targets, putative corresponding homozygous and heterozygous loci within DTUs TcI and TcIII. Furthermore, individual gene trees gave incongruent topologies at inter- and intra-DTU levels, inconsistent with a model of strict clonality. Conclusions/Significance We demonstrate the value of systematic MLST diplotyping for describing inter-DTU relationships and for higher resolution diversity studies of T. cruzi, including presence of recombination events. The high levels of heterozygosity will facilitate future population genetics analysis based on MLST haplotypes. PMID:21713026

  19. Multicentric performance analysis of HCV quantification assays and its potential relevance for HCV treatment.

    PubMed

    Wiesmann, F; Naeth, G; Berger, A; Hirsch, H H; Regenass, S; Ross, R S; Sarrazin, C; Wedemeyer, H; Knechten, H; Braun, P

    2016-06-01

    An accurate quantification of low viremic HCV RNA plasma samples has gained importance since the approval of direct acting antivirals and since only one single measurement predicts the necessity of a prolonged or shortened therapy. As reported previously, HCV quantification assays such as Abbott RealTime HCV and Roche COBAS AmpliPrep/COBAS TaqMan HCV version 2 (CTM v2) may vary in sensitivity and precision particularly in low-level viremia. Importantly, substantial variations were previously demonstrated between some of these assays compared to the Roche High Pure System/COBAS TaqMan assay (HPS) reference assay, which was used to establish the clinical decision points in clinical studies. In this study, the reproducibility of assay performances across several laboratories was assessed by analysing quantification results generated by six independent laboratories (3× RealTime, 3× CTM v2) in comparison with one HPS reference laboratory. The 4th WHO Standard was diluted to 100, 25 and 10 IU/ml, and aliquots were tested in triplicates in 5 independent runs by each assay in the different laboratories to assess assay precision and detection rates. In a second approach, 2 clinical samples (GT 1a & GT 1b) were diluted to 100 and 25 IU/ml and tested as described above. While the result range for WHO 100 IU/ml replicates across all laboratories was similar in this analysis, the CVs of each laboratory ranged from 19.3 to 25.6 % for RealTime laboratories and were lower than CVs of CTM v2 laboratories with a range of 26.1-47.3 %, respectively, and also in comparison with the CV of the HPS reference laboratory (34.9 %). At WHO standard dilution of 25 IU/ml, 24 replicates were quantified by RealTime compared to 8 replicates with CTM v2. Results of clinical samples again revealed a higher variation of CTM v2 results as compared to RealTime values. (CVs at 100 IU/ml: RealTime: 13.1-21.0 % and CTM v2: 15.0-32.3 %; CVs at 25 IU/ml: RealTime 17.6-34.9 % and CTM v2 28

  20. Doping-dependent critical current properties in K, Co, and P-doped BaF e2A s2 single crystals

    NASA Astrophysics Data System (ADS)

    Ishida, Shigeyuki; Song, Dongjoon; Ogino, Hiraku; Iyo, Akira; Eisaki, Hiroshi; Nakajima, Masamichi; Shimoyama, Jun-ichi; Eisterer, Michael

    2017-01-01

    In order to establish the doping dependence of the critical current properties in the iron-based superconductors, the in-plane critical current density Jc of BaF e2A s2 -based superconductors B a1 -xKxF e2A s2 (K-Ba122), Ba (F e1 -xC ox)2A s2 (Co-Ba122), and BaF e2(As1-xPx) 2 (P-Ba122) in a wide range of doping concentration x was investigated by means of magnetization hysteresis loop (MHL) measurements on single-crystal samples. Depending on the dopant elements and their concentration, Jc exhibits a variety of magnetic-field H and temperature T dependences. (1) In the case of K-Ba122, the MHL of the underdoped samples (x ≤0.33 ) exhibits a second magnetization peak (SMP), which sustains high Jc at high H and high T , exceeding 105A /c m2 at T = 25 K and μ0H = 6 T for x = 0.30 . On the other hand, the SMP is missing in the optimally (x ˜ 0.36 -0.40 ) and overdoped (x ˜ 0.50 ) samples and consequently Jc rapidly decreases by more than one order of magnitude, although the change in Tc is within a few K. (2) For Co-Ba122, the SMP is always present over the entire superconducting (SC) dome from the underdoped (x ˜ 0.05 ) to the overdoped (x ˜ 0.12 ) region. However, the magnitude of Jc significantly changes with x , exhibiting a sharp maximum at x ˜ 0.057 , which is a slightly underdoped composition for Co-Ba122. (3) For P-Ba122, the highest Jc is attained at x = 0.30 , corresponding to the highest Tc composition. For the overdoped samples, the MHL is characterized by a SMP located close to the irreversibility field Hirr. Common to the three doping variations, Jc becomes highest at the underdoping side of the SC dome near the phase boundary between the SC phase and the antiferromagnetic-orthorhombic (AFO) phase. Also, the peak appears in a narrow range of doping, distinct from the Tc dome with a broad maximum. These similarities in the three cases indicate that the observed doping dependence of Jc is intrinsic to the BaF e2A s2 -based superconductors. The

  1. 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.

  2. Comparative Analysis of Real-Time Polymerase Chain Reaction Methods to Typing HLA-B*57:01 in HIV-1-Positive Patients

    PubMed Central

    Falasca, Francesca; Russo, Cinzia Dello; Mora, Barbara; Pirazzoli, Antonella; Fantauzzi, Alessandra; Navarra, Pierluigi; Pizzuti, Antonio; De Vito, Corrado; Antonelli, Guido

    2016-01-01

    Abstract The HLA-B*57:01 allele is strongly associated with the hypersensitivity reaction to Abacavir (ABC). Therefore, treatment guidelines recommend that patients initiating ABC are preventively tested for the presence of this allele. To date, four different commercial assays based on the real-time quantitative polymerase chain reaction (Q-PCR) technique are available for the detection of HLA-B*57:01: Duplicα-RealTime Reagent Set HLA-B*57:01 by Euroclone, HLA-B*57:01 Real-TM by Sacace Biotechnologies, COBAS AmpliPrep/COBAS TaqMan HLA-B*57:01 Screening Test by Roche Diagnostic, and HLA-B*57:01 by Nuclear Laser Medicine. The study was carried out to compare the performance of the first three commercially available Q-PCR kits in a routine clinical setting. A total of 98 samples from Policlinico Umberto I Hospital were tested. Results obtained by the Duplicα-RealTime Genotyping kit and AmpliPrep/TaqMan system were 100% concordant. In contrast, genotyping by the HLA-B*57:01 Real-TM kit showed poor agreement with the other systems, that is, 12 out of 33 positive samples were detected as HLA-B*57:01 negative. To confirm the correct genotype of these discordant samples, two additional methods with rapid turnaround times and already implemented into routine clinical practice were used, that is, a PCR-based microsequence-specific primer DNA typing test and a laboratory-developed screening test in Q-PCR. All 12 discordant samples were genotyped as HLA-B*57:01-positive samples using these two additional methods in a single-blinded manner, thus confirming the low sensitivity of HLA-B*57:01 Real-TM test. These findings underline the need to compare results obtained with commercial assays before choosing a test suitable for use in a routine clinical laboratory. PMID:26750774

  3. [Utilization of self-sampling kits for HPV testing in cervical cancer screening - pilot study].

    PubMed

    Ondryášová, H; Koudeláková, V; Drábek, J; Vaněk, P; Slavkovský, R; Hajdúch, M

    2015-12-01

    To get initial experience with alternative sampling (self-sampling) for HPV testing as the means of cervical cancer screening program. Original work. Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc. Based on expression of interest, 215 self-sampling kits were posted to women. Evalyn(®) Brush Vaginal swabs obtained by self-sampling were analyzed for the presence of HPV infection by Cobas 4800 HPV (Roche) followed by genotyping using PapilloCheck(®) HPV-Screening (Greiner Bio-One). Sixty women randomly chosen from our sample were sent a questionnaire focused on their experience with self-sampling. One hundred seventy-four of 215 (81%) distributed self-sampling devices have been delivered to analysis. All cervicovaginal swabs were sampled correctly and it was possible to analyze them by Cobas 4800 HPV test. Similarly, 98% (171/174) samples were analyzable by PapilloCheck(®) HPV-Screening.One hundred twenty-five (72%) of 174 tested samples were HPV negative. Low risk HPV infection was detected only in 7 samples (4%), and high risk HPV (hrHPV) infection was present in 42 samples (24%). The most frequently detected hrHPV genotypes were HPV16 (11/42; 26%) and HPV53 (6/42; 14%). HrHPV co-infection was detected in 10 cases, in 5 of them lrHPV infection was find also.Of the 60 questionnaires, 48 (80%) were returned. From this group, 47 (98%) women rated their experience with self-sampling device as good to excellent. User manual of self-sampling device was considered good to excellent by all women (100%). All women also rated the convenience of self-sampling device using as good to excellent. As expected, most of the women (n = 42 [88%]) preferred self-sampling to physician sampling. Cervicovaginal self-sampling leads to valid results of HPV screening using two molecular genetics methods and was accepted by Czech women very well. The self-sampling as an opportunity to participate in cervical cancer

  4. Highly variable sensitivity of five binding and two bio-assays for TSH-receptor antibodies.

    PubMed

    Diana, T; Wüster, C; Kanitz, M; Kahaly, G J

    2016-10-01

    TSH-receptor (TSHR) antibodies (Ab) can be measured with binding or bio-assays. Sensitivity and specificity of five binding and two bio-assays were compared. TSHR-blocking (TBAb) and TSHR-stimulating (TSAb) Ab were measured with reporter bio-assays. Blocking activity was defined as percent inhibition of luciferase expression relative to induction with bTSH alone. TSAb was reported as percentage of specimen-to-reference ratio (SRR%). TSHR-binding inhibitory immunoglobulins (TBII) were measured with Kronus, Dynex, Kryptor, Cobas, and Immulite. Sixty patients with Graves' disease (GD), 20 with Hashimoto's thyroiditis (HT), and 20 healthy controls (C) were included. C tested negative in all assays (specificity 100 %) while all 60 hyperthyroid GD patients tested positive in the TSAb bio-assay (sensitivity 100 %). Among these 60 GD patients, 20 had low TSAb positivity (SRR% 140-279), but were TBII positive in only 20 (100 %), 7 (35 %), 9 (45 %), 11 (55 %), and 18 (90 %) using the Kronus, Dynex, Kryptor, Cobas, and Immulite, respectively. In 20 moderate TSAb-positive (SRR% 280-420) patients, TBII tested positive in 20 (100 %), 14 (70 %), 13 (65 %), 16 (80 %), and 19 (95 %), respectively. The high (SRR% > 420) TSAb-positive patients were all TBII positive. All 20 hypothyroid HT patients tested TBAb positive (sensitivity 100 %) in the bio-assay while they tested TBII positive in 20 (100 %), 18 (90 %), 20, 20, and 18, respectively. Results obtained with two luminometers correlated for TSAb positive (r = 0.99, p < 0.001), TBAb positive (r = 0.88, p < 0.001), and C (r = 0.86, p < 0.001). None of the binding assays differentiated between TSAb and TBAb. Sensitivity is highly variable between binding and bio-assays for TSHR-Abs.

  5. Multi-center analytical evaluation of a novel automated tacrolimus immunoassay.

    PubMed

    Shipkova, Maria; Vogeser, Michael; Ramos, Pedro Alía; Verstraete, Alain G; Orth, Matthias; Schneider, Christian; Wallemacq, Pierre

    2014-08-01

    Tacrolimus (TAC) is a post-transplantation immunosuppressant drug used in patients for whom careful monitoring of TAC concentration is essential. A new semi-automated immunoassay for TAC measurement, the Elecsys Tacrolimus assay, is available and has been assessed in a multi-center evaluation. Residual whole blood samples from patients undergoing TAC therapy after organ transplant were used in assay evaluation at five clinical laboratories in Europe. Experiments included imprecision according to CLSI EP5-A2 (within-run and intermediate), functional sensitivity, linearity according to CLSI EP6-A, and recovery from external quality assessment scheme (EQAS) samples. The assay was compared to LC-MS/MS used routinely at each investigational site, and to the Abbott Architect immunoassay. Linearity from 0.5 to 40 μg/L was observed and functional sensitivity of 0.3 μg/L (CV ≤ 20%) was determined. Within-run imprecision was ≤ 5.1% on cobas e 602 (5.1% at 1.5 μg/L) and ≤ 8.9% (8.9% at 0.8μg/L) on cobas e 411. The intermediate imprecision for TAC concentrations ≥ 6.8 μg/L was ≤ 6.5%. At lower therapeutic concentrations (to 1.5 μg/L) it was consistently ≤ 10%. Deming regression analysis of method comparison to LC-MS/MS yielded slopes of 1.07 (95%CI: 1.05/1.10) for heart transplant samples, 1.13 (95%CI: 1.09/1.16) for kidney, and 1.05 (95%CI: 1.02/1.08) for lung transplant samples. The Elecsys Tacrolimus assay has good linearity, functional sensitivity and intermediate imprecision and is comparable to LC-MS/MS methods. The over-all performance of ECLIA demonstrates a modern generation TAC assay that meets the demands of monitoring drug concentrations in current immunosuppressive regimens. Copyright © 2014. Published by Elsevier Inc.

  6. Estimation of measurement error in plasma HIV-1 RNA assays near their limit of quantification

    PubMed Central

    Wang, Lu; Brumme, Chanson; Wu, Lang; Montaner, Julio S. G.; Harrigan, P. Richard

    2017-01-01

    Background Plasma HIV-1 RNA levels (pVLs), routinely used for clinical management, are influenced by measurement error (ME) due to physiologic and assay variation. Objective To assess the ME of the COBAS HIV-1 Ampliprep AMPLICOR MONITOR ultrasensitive assay version 1.5 and the COBAS Ampliprep Taqman HIV-1 assay versions 1.0 and 2.0 close to their lower limit of detection. Secondly to examine whether there was any evidence that pVL measurements closest to the lower limit of quantification, where clinical decisions are made, were susceptible to a higher degree of random noise than the remaining range. Methods We analysed longitudinal pVL of treatment-naïve patients from British Columbia, Canada, during their first six months on treatment, for time periods when each assay was uniquely available: Period 1 (Amplicor): 08/03/2000–01/02/2008; Period 2 (Taqman v1.0): 07/01/2010–07/03/2012; Period 3 (Taqman v2.0): 08/03/2012–30/06/2014. ME was estimated via generalized additive mixed effects models, adjusting for several clinical and demographic variables and follow-up time. Results The ME associated with each assay was approximately 0.5 log10 copies/mL. The number of pVL measurements, at a given pVL value, was not randomly distributed; values ≤250 copies/mL were strongly systematically overrepresented in all assays, with the prevalence decreasing monotonically as the pVL increased. Model residuals for pVL ≤250 copies/mL were approximately three times higher than that for the higher range, and pVL measurements in this range could not be modelled effectively due to considerable random noise of the data. Conclusions Although the ME was stable across assays, there is substantial increase in random noise in measuring pVL close to the lower level of detection. These findings have important clinical significance, especially in the range where key clinical decisions are made. Thus, pVL values ≤250 copies/mL should not be taken as the “truth” and repeat p

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

    PubMed

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

    2003-07-01

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

  8. Gap structure of iron-based superconductors via directional thermal conductivity

    NASA Astrophysics Data System (ADS)

    Reid, Jean-Philippe

    2012-02-01

    Because the structure of the superconducting gap as a function of direction reflects the pairing interaction, it can shed light on the nature of the pairing mechanism. In the iron pnictides, the experimental situation in this respect remains unclear and so far suggests the lack of a universal picture. Here I present a systematic study of the superconducting gap structure through directional thermal conductivity measurements [1] on hole-doped K-Ba122 [2,3], electron-doped Co-Ba122 [4,5], self-doped LiFeAs [6] and the chalcogenide FeTeSe. We observe a general trend for the evolution of the superconducting gap with doping. At optimal doping, the gap structure is nodeless and isotropic (3D). Away from optimal doping, nodes appear on the Fermi surface at the edges of the superconducting dome, as seen for K-Ba122 and Co-Ba122. This strongly suggests that the presence of these nodes is accidental and therefore not imposed by symmetry. It would instead depend on the competition between intra- and inter-band interactions controlled by the evolving band structure and Fermi surface, and by the onset of antiferromagnetic order.[4pt] Work done in collaboration with M. A. Tanatar, X. G. Luo, H. Shakeripour, R. Gordon, A. Juneau-Fecteau, N. Doiron-Leyraud, S. Ren'e de Cotret, F. Lalibert'e, E. Hassinger, J. Chang, N. Ni, S. L. Bud'ko, P. C. Canfield, H. Kim, R. Prozorov, B. Shen, H. Luo, Z. Wang, H.-H. Wen, K. Cho, Y. J. Song, Y. S. Kwon, and Louis Taillefer.[4pt] [1] H. Shakeripour et al., New Journal of Physics 11, 055065 (2009).[0pt] [2] X. G. Luo et al., Physical Review B 80, 140503 (2009).[0pt] [3] J.-Ph. Reid et al., arXiv:1105:2232.[0pt] [4] M. A. Tanatar et al., Physical Review Letters 104, 067002 (2010).[0pt] [5] J.-Ph. Reid et al., Physical Review B 82, 064501 (2010).[0pt] [6] M. A. Tanatar et al., Physical Review B 84, 054507 (2011).

  9. Difference in factors associated with low-level viraemia and virological failure: results from the Austrian HIV Cohort Study.

    PubMed

    Leierer, Gisela; Rieger, Armin; Steuer, Andrea; Sarcletti, Mario; Geit, Maria; Haas, Bernhard; Taylor, Ninon; Kanatschnig, Manfred; Rappold, Michaela; Ledergerber, Bruno; Zangerle, Robert

    2014-01-01

    For some patients, it remains a challenge to achieve complete virological suppression which is the goal of antiretroviral therapy (ART). Identifying factors associated with low-level viraemia (LLV) and virological failure (VF) under ART might help to optimize management of these patients. We investigated patients from the Austrian HIV Cohort Study receiving unmodified ART for >6 months with two nucleoside reverse-transcriptase inhibitors (NRTIs) with either a non-nucleoside reverse-transcriptase inhibitor (NNRTI) or a boosted protease inhibitor (PI) or an integrase inhibitor (INSTI) between 1 July 2012 and 1 July 2013 with at least one viral load (VL) measurement below the limit of detection (BLD) or below level of quantification (BLQ) in their treatment history. VF was defined as HIV-RNA levels ≥200 copies/mL and all other quantifiable measurements were classified as LLV. Factors associated with LLV and VF compared to BLD and BLQ were identified by using logistic regression models. Of the 2,276 patients analyzed, 1,972 (86.6%) were BLD or BLQ, 222 (9.8%) showed LLV and 82 (3.6%) had VF. A higher risk for LLV and VF was found in patients with ART interruptions and in patients with boosted PI therapy. The risk for LLV and VF was lower in patients from a centre which uses Abbott RealTime HIV-1 assay compared to the other centres measuring VL by the Roche Cobas AmpliPrep/Cobas TaqMan 2.0. A higher risk for LLV but not for VF was found in patients with a higher VL before ART and shorter ART duration. A higher risk for VF but not for LLV was found in patients of younger age, originating from a high prevalence country, with a lower CD4 count and in male injecting drug users. This study of well-defined patients on stable ART over a period of more than six months gives insights into the different factors associated with LLV and VF. In patients with VF, factors associated with adherence play a prominent role, whereas in patients with LLV, the biology of viral replication

  10. Difference in factors associated with low-level viraemia and virological failure: results from the Austrian HIV Cohort Study

    PubMed Central

    Leierer, Gisela; Rieger, Armin; Steuer, Andrea; Sarcletti, Mario; Geit, Maria; Haas, Bernhard; Taylor, Ninon; Kanatschnig, Manfred; Rappold, Michaela; Ledergerber, Bruno; Zangerle, Robert

    2014-01-01

    Introduction For some patients, it remains a challenge to achieve complete virological suppression which is the goal of antiretroviral therapy (ART). Identifying factors associated with low-level viraemia (LLV) and virological failure (VF) under ART might help to optimize management of these patients. Materials and Methods We investigated patients from the Austrian HIV Cohort Study receiving unmodified ART for >6 months with two nucleoside reverse-transcriptase inhibitors (NRTIs) with either a non-nucleoside reverse-transcriptase inhibitor (NNRTI) or a boosted protease inhibitor (PI) or an integrase inhibitor (INSTI) between 1 July 2012 and 1 July 2013 with at least one viral load (VL) measurement below the limit of detection (BLD) or below level of quantification (BLQ) in their treatment history. VF was defined as HIV-RNA levels ≥200 copies/mL and all other quantifiable measurements were classified as LLV. Factors associated with LLV and VF compared to BLD and BLQ were identified by using logistic regression models. Results Of the 2,276 patients analyzed, 1,972 (86.6%) were BLD or BLQ, 222 (9.8%) showed LLV and 82 (3.6%) had VF. A higher risk for LLV and VF was found in patients with ART interruptions and in patients with boosted PI therapy. The risk for LLV and VF was lower in patients from a centre which uses Abbott RealTime HIV-1 assay compared to the other centres measuring VL by the Roche Cobas AmpliPrep/Cobas TaqMan 2.0. A higher risk for LLV but not for VF was found in patients with a higher VL before ART and shorter ART duration. A higher risk for VF but not for LLV was found in patients of younger age, originating from a high prevalence country, with a lower CD4 count and in male injecting drug users. Conclusions This study of well-defined patients on stable ART over a period of more than six months gives insights into the different factors associated with LLV and VF. In patients with VF, factors associated with adherence play a prominent role, whereas

  11. 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

  12. Time-Motion Analysis of Four Automated Systems for the Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Nucleic Acid Amplification Testing.

    PubMed

    Williams, James A; Eddleman, Laura; Pantone, Amy; Martinez, Regina; Young, Stephen; Van Der Pol, Barbara

    2014-08-01

    Next-generation diagnostics for Chlamydia trachomatis and Neisseria gonorrhoeae are available on semi- or fully-automated platforms. These systems require less hands-on time than older platforms and are user friendly. Four automated systems, the ABBOTT m2000 system, Becton Dickinson Viper System with XTR Technology, Gen-Probe Tigris DTS system, and Roche cobas 4800 system, were evaluated for total run time, hands-on time, and walk-away time. All of the systems evaluated in this time-motion study were able to complete a diagnostic test run within an 8-h work shift, instrument setup and operation were straightforward and uncomplicated, and walk-away time ranged from approximately 90 to 270 min in a head-to-head comparison of each system. All of the automated systems provide technical staff with increased time to perform other tasks during the run, offer easy expansion of the diagnostic test menu, and have the ability to increase specimen throughput. © 2013 Society for Laboratory Automation and Screening.

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

    PubMed

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

    2011-11-01

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

  14. Synthesis and characterization of poly ( n-butyl acrylate)-poly (methyl methacrylate) latex interpenetrating polymer networks by radiation-induced seeded emulsion polymerization

    NASA Astrophysics Data System (ADS)

    Yu, Haibo; Peng, Jing; Zhai, Maolin; Li, Jiuqiang; Wei, Genshuan; Qiao, Jinliang

    2007-11-01

    A series of latex interpenetrating polymer networks (LIPNs) were prepared via a two-stage emulsion polymerization of methyl methacrylate (MMA) or mixture of MMA and n-butyl acrylate ( n-BA) on crosslinked poly( n-butyl acrylate)(PBA) seed latex using 60Co γ-ray radiation. The particles of resultant latex were produced with diameters between 150 and 250 nm. FTIR spectra identified the formation of crosslinked copolymers of PMMA or P(MMA- co-BA). Dynamic light scattering (DLS) showed that with increasing n-BA concentration in second-stage monomers, the particle size of LIPN increased. Transmission electron microscope(TEM) photographs showed that the morphology of resultant acrylate interpenetrating polymer network (IPN) latex varied from the distinct core-shell structure to homogenous particle structure with the increase of n-BA concentration, and the morphology was mainly controlled by the miscibility between crosslinked PBA seed and second-stage copolymers and polarity of P(MMA- co-BA)copolymers. In addition, differential scanning calorimeter (DSC) measurements indicated the existence of reinforced miscibility between PBA seed and P(MMA- co-BA)copolymer in prepared LIPNs.

  15. Ethamsylate (Dicynone) interference in determination of serum creatinine, uric acid, triglycerides, and cholesterol in assays involving the Trinder reaction; in vivo and in vitro.

    PubMed

    Dastych, Milan; Wiewiorka, Ondrej; Benovská, Miroslava

    2014-01-01

    The aim of our research was the quantification of interfering properties of the haemostatic drug Dicynone (ethamsylate) in serum creatinine, uric acid, cholesterol, and triglyceride assays using the Trinder reaction. Blood from patients was collected before and 15 minutes after administration of 500 mg Dicynone dose i.v. and the above mentioned analytes were quantified using Roche assays (Cobas 8000). In our in vitro experiment, we measured concentrations of the analytes in pooled serum aliquots with final concentrations of Dicynone additions 0, 30, 60, 150, and 300 mg/L. Aliquots with 60 mg/L Dicynone were also measured at 2, 6, and 8 hours after initial measurement when stored in 22 degrees C and 4 degrees C for comparison. Concentrations of the measured analytes in samples from patients administered with a 500 mg dose of Dicynone were lower in all cases (n = 10) when compared to values in samples taken immediately before treatment. The in vitro samples showed that considerable negative interference occurred even with the low concentrations of Dicynone additions (30 and 60 mg/L), showing the strongest negative interference in creatinine values, followed by uric acid, triglycerides, and cholesterol. Using in vitro samples, we showed strong time and temperature dependence on Dicynone interference. We found and proved significant negative interference of the drug Dicynone (ethamsylate) in the clinical analysis of blood using in vivo and in vitro experiments. Furthermore, we observed a change of this effect in serum matrix over time and at different storage temperatures.

  16. Transcriptional changes are involved in phenotype switching in Streptococcus equi subspecies equi.

    PubMed

    Steward, Karen F; Robinson, Carl; Waller, Andrew S

    2016-04-01

    Phenotypic heterogeneity within a population of bacteria, through genetic or transcriptional variation, enables survival and persistence in challenging and changing environments. We report here that a recent clinical isolate of S. equi, strain 1691 (Se1691), yielded a mixture of reduced capsule and mucoid colonies on primary isolation when grown on colistin-oxolinic acid blood agar (COBA) streptococcal selective plates. Passaging colonies of Se1691, with a reduced capsule phenotype maintained this mixed phenotype. In contrast, passaging mucoid colonies fixed the mucoid phenotype, suggesting adaptive genetic or transcriptional changes in response to growth on artificial media. However, despite obvious phenotypic and transcriptional differences, there were no apparent differences in the genome sequences of Se1691 recovered from colonies with a mucoid or reduced capsule phenotype. We identified 105 differentially transcribed genes in the transcriptomes of reduced capsule and mucoid colonies. The reduced capsule phenotype was associated with a significant reduction in transcription of the has locus (SEQ_0269 Q = 0.0015, SEQ_0270 Q = 0.0015, SEQ_0271 Q = 0.0285) and the amount of hyaluronic acid on the surface of S. equi recovered from non-mucoid colonies (P = 0.017). Significant differences in the transcription of 21 surface and secreted proteins were also observed. Our data show that changes in the bacterial transcriptome are linked to the mixed colony phenotype of Se1691.

  17. Detection of high-risk human papillomavirus infection in tonsillar specimens using 2 commercially available assays.

    PubMed

    Cockerill, Cara C; Orvidas, Laura J; Moore, Eric J; Binnicker, Matthew J; Duresko, Brian J; Espy, Mark J; Cockerill, Franklin R; Tombers, Nicole M; Pritt, Bobbi S

    2016-12-01

    THE OBJECTIVE OF THE STUDY IS TO DETERMINE THE PREVALENCE OF HIGH-RISK HUMAN PAPILLOMAVIRUS (HRHPV) INFECTION IN TONSILLAR SWABS AND TISSUE: Patients undergoing tonsillectomy for nonmalignant causes were enrolled. A flocked swab and fresh tissue were collected from the left and right tonsil of each patient. Specimens were tested for hrHPV DNA using the Roche cobas test and for the presence of E6/E7 messenger RNA using the Hologic Aptima hrHPV test. Of the 193 patients enrolled, 129 were in the pediatric group (ages 1-12years; median, 5years), and 64 were in the adult group (ages 13-55; median, 22years). All swab and tissue specimens were negative for hrHPV by both methods. Positive, negative, and internal controls performed as expected. We found a 0% rate of infection indicating that detectable hrHPV infection in tonsillar tissue appears to be uncommon in the children and adults in the population sampled. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Human Papillomavirus Test for Triage of Japanese Women With Low-Grade Squamous Intraepithelial Lesions.

    PubMed

    Iwata, Takashi; Hasegawa, Toshihiko; Ochiai, Kazunori; Takizawa, Ken; Umezawa, Satoshi; Kuramoto, Hiroyuki; Ohmura, Mineo; Kubushiro, Kaneyuki; Arai, Hiroharu; Sakamoto, Masaru; Motoyama, Teiichi; Watanabe, Kayoko; Aoki, Daisuke

    2015-12-01

    We evaluated high-risk human papillomavirus (HR-HPV) DNA testing for high-grade cervical intraepithelial neoplasia (CIN) lesions by cobas HPV test and diagnostic HPV16/18 genotyping in Japanese women with low-grade squamous intraepithelial lesions. Of 357 patients, HR-HPV positivity prevalence was 75.6%, and 21.3% had grade 2 or higher CIN lesions (CIN2+), with the highest prevalence at 30 to 34 years. Negative predictive values of HR-HPV for CIN2+ in our patients were 93.1% (any age) and 94.9% (40-50 years). Absolute risk for CIN2+ in HR-HPV positive and HPV16/18 positive individuals was 25.9 and 35.1, respectively. Relative risk for CIN2+ lesions was 5.1 for HPV16/18 positive versus HR-HPV negative, and 3.8 for HR-HPV positive versus HR-HPV negative women. Predictive values of CIN2+ positive were higher for HPV16/18 positive women (any age) than 12 other HPV positive-genotypes, and highest (50%) at 40-50 years. The HPV16/18 genotyping might prevent women (>40 years) at risk of high-grade CIN lesions from undergoing unnecessary colposcopy/overtreatment of nonprogressive lesions. © The Author(s) 2015.

  19. System Accuracy Evaluation of 43 Blood Glucose Monitoring Systems for Self-Monitoring of Blood Glucose according to DIN EN ISO 15197

    PubMed Central

    Freckmann, Guido; Schmid, Christina; Baumstark, Annette; Pleus, Stefan; Link, Manuela; Haug, Cornelia

    2012-01-01

    Background The accuracy of systems for self-monitoring of blood glucose is important, as reliable measurement results are a prerequisite for therapeutic decisions. Methods This system accuracy evaluation study was performed according to DIN EN ISO 15197:2003 for 43 Conformité Européenne (CE)-labeled blood glucose (BG) monitoring systems. Measurement results of each system were compared with results of the designated comparison method (manufacturer’s measurement procedure): glucose oxidase method (YSI 2300 glucose analyzer) or hexokinase method (Hitachi 917/ cobas 501). Results Complete assessment according to the International Organization for Standardization (ISO) standard was performed for 34 out of 43 systems, and 27 (79.4%) meet the requirements of the standard, i.e., ≥95% of their results showed at least the minimum acceptable accuracy. For 9 of the 43 systems, complete accuracy assessment was not performed due to an oxygen sensitivity (manufacturer’s labeling). The bias (according to Bland and Altman) of all 43 evaluated systems ranged from -14.1% to +12.4%. Conclusions From the 34 systems completely assessed, 7 systems did not fulfill the minimal accuracy requirements of the ISO standard. The CE mark apparently does not guarantee that all BG systems provide accuracy according to the standard. Because inaccurate systems bear the risk of false therapeutic decisions, regular and standardized evaluation of BG meters and test strips should be requested in order to ensure adherence to quality standards. PMID:23063032

  20. Hepatitis C virus core antigen in the management of patients treated with new direct-acting antivirals.

    PubMed

    Arboledas, Juan Carlos Alados; Guerrero, Inmaculada Pavón; Rodríguez, María José Blanco; Martos, Eva Torres; Pérez, Ana Belén; León, Cristina Cepero; Sierra Sánchez, Jesus F; Prieto, María Dolores López; Porcuna, Natalia Chueca; Mochón, María Dolores Ocete; Macías, Juan; de la Iglesia Salgado, Alberto; Granger, Javier Rodríguez; Fernández, Marcial Delgado; Lozano, Inmaculada Guerrero; Ramírez, Elena Reigadas; Rivero, Antonio; Del Carmen Lozano Domínguez, María; Viciana, Isabel; Montemayor, Juan Carlos Galán; García, Federico García

    2017-09-01

    We evaluated the utility of Architect core antigen assay® Abbott Diagnostics (HCVAg) for monitoring patients with HCV infection and compared to HCV-RNA quantification (Cobas Ampliprep TaqMan-Roche Diagnostics). Samples from 262 patients were studied. Mean baseline HCV RNA and HCVAg levels were similar for responders (6.2 log IU/mL and 3.4 log fmol/L) and non-responders (6.1 log IU/mL and 3.2 log fmol/L), respectively. Only 10 patients failed to achieve SVR12 and all were detected by both assays. To evaluate HCVAg quantification as a tool for the detection of failure to DAAs, we performed a retrospective study of 132 non-responder patients. Mean HCV RNA and HCVAg levels at the time of detection of therapeutic failure were 5.88±0.97 log IU/mL and 3.19±0.79 log fmol/L, respectively. HCVAg (>3 fmol/L) was detected in 130/132 patients (98.5%). HCVAg assay was useful for patient selection and for evaluating virological response to DAAs in the real world. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. COBAS® TaqMan® MTB, smear positivity grade and MGIT culture; correlation analyses of three methods for bacillary quantification.

    PubMed

    Chikamatsu, Kinuyo; Aono, Akio; Kato, Tomoko; Takaki, Akiko; Yamada, Hiroyuki; Sasaki, Yuka; Izumi, Kiyohiko; Yi, Lina; Mitarai, Satoshi

    2016-01-01

    We investigated the correlation between the cycle threshold (Ct) value of the COBAS(®) TaqMan(®) MTB (TaqMan MTB), the mycobacterial smear positivity grade, and the time to detection (TTD) in the Mycobacteria Growth Indicator Tube (MGIT) for quantification of Mycobacterium tuberculosis (MTB). For 57 sputum samples, significant correlations were observed between the Ct value, the smear positivity grade, and the MGIT TTD (Spearman's rank correlation coefficient: r(s) = -0.940, P < 0.001 and Pearson's correlation coefficient: r(p) = 0.737, P < 0.001). In addition, a correlation was observed between the number of bacteria estimated based on the smear positivity grade and the number of MTB bacilli calculated by the Ct value (r(s) = 0.930, P < 0.001). This study has demonstrated the possible estimation of the smear positivity grade and MGIT TTD using the Ct value of TaqMan MTB, which is based on a real-time PCR system, for diagnostic samples.

  2. Use of chimeric influenza viruses as a novel internal control for diagnostic rRT-PCR assays.

    PubMed

    Wang, Xueliang; Liu, Fen; Jiang, Lingli; Bao, Yun; Xiao, Yanqun; Wang, Hualiang

    2016-02-01

    Real-time quantitative reverse transcriptase polymerase chain reaction (rRT-PCR) is now widely used to detect viral pathogens in various human specimens. The application of internal controls to validate the entire process of these assays is necessary to prevent false-negative results caused by unexpected inhibition or inefficient extraction. In the present study, we describe a strategy to produce a stable internal control for rRT-PCR by packaging foreign RNA into influenza virions using plasmid-based reverse genetics technology. The envelope structure of influenza virus can effectively protect RNA segments from RNase digestion, which provides an advantage for its routine use as an internal control. Utilizing this approach, we successfully generated a recombinant influenza virus (rPR8-HCV) containing the 5′ untranslated region (5′UTR) of the hepatitis C virus (HCV) RNA genome. After inactivation and purification, the rPR8-HCV particles were demonstrated to be RNase resistant and stable at 4 °C for at least 252 days in human plasma, with no degradation even after being frozen and thawed multiple times. These results were reproducible in the COBAS TaqMan HCV test for 164 days. Moreover, the chimeric influenza virus particles could be easily produced in embryonated eggs and were noninfectious after inactivation treatment. Additionally, this strategy could also be adapted for real-time clinical applications of other RNA targets, providing a universal approach with broad clinical applications in rRT-PCR assays.

  3. Identification of haemoglobin New York by haemoglobin A1c measurement using the Sebia Capillarys 2 Flex Piercing system.

    PubMed

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

    2017-01-01

    Haemoglobinopathies may interfere with the haemoglobin A1c (HbA1c) measurement, leading to incorrect diagnosis and inappropriate treatment. It is essential that HbA1c assays are capable of identifying haemoglobinopathies. We report two cases of haemoglobin New York (HbNY) discovered through HbA1c analysis using capillary electrophoresis (Capillarys 2 Flex Piercing [C2FP], Sebia). We used these samples to evaluate the ability of three other HbA1c assays to identify this variant: ion-exchange high-performance liquid chromatography (Variant II Turbo [VII-T], Bio-Rad); boronate affinity high-performance liquid chromatography (Ultra(2), Trinity Biotech) and immunoassay (Cobas c501 Tina-quant Generation 3, Roche Diagnostics). Each method was used for HbA1c assay of in samples from two cases of heterozygous haemoglobinopathy: β(0)-thalassemia/HbNY (Case 1) and HbA/NY (Case 2). Only the C2FP system detected HbNY (an additional peak appeared between HbA1c and HbA0). Clinical laboratories should be aware of the limitations of their HbA1c assay methods especially in geographic areas, where haemoglobinopathy prevalence is high.

  4. Retrospective analysis of 55,769 HbA1c EQA results obtained from professional laboratories and medical offices participating in surveys organized by two European EQA centers over a nine-year period.

    PubMed

    Morandi, Pierre-Alain; Deom, André; Kesseler, Dagmar; Cohen, Richard

    2011-01-01

    External Quality Assessment (EQA) is an essential tool for laboratories to monitor the performances of their analyses. It also allows a comparison of methods and types of laboratories (professional laboratories vs. medical offices). We, therefore, compared 55,769 HbA1c EQA results obtained between 1999 and 2008 by laboratories participating in EQA schemes organized by two European centers, Switzerland (center 1) and France (center 2). We used simple, nonparametrical statistics suited to EQA results to calculate the yearly and global precision performances. All the results, including the outliers, were included in the calculations. The best global precision performances were obtained by professional laboratories and medical offices using DCA POCT devices, followed by professional laboratories with the Integra, Hitachi, Cobas Mira, and HPLC groups of devices, and finally by both types of laboratories with the NycoCard POCT devices. When considering yearly precision performances, an overall improvement over time was observed for almost all diagnostic devices of center 1, whereas the trend was less clear for center 2. The HbA1c EQA results collected and analyzed over a 9-year period showed that the DCA POCT devices used either by professional laboratories or medical offices had better reproducibility than laboratory devices (other than POCT) and that a general improvement of yearly precision performances was observed, especially when frequent EQA schemes were organized. © 2011 Wiley-Liss, Inc.

  5. [The Evaluation of Toxoplasma gondii (T.gondii) Serology Results Among Cases Who Admitted to the Serology Laboratory of a Hospital in Afyon City].

    PubMed

    Aşcı, Zerrin; Akgün, Sema

    2015-03-01

    The aim of this study is to evaluate Toxoplasma gondii (T. gondii) serology results in different age groups among cases who admitted to the Medical Serology Laboratory of a secondary level hospital in Afyon. The patients who has positive result for Toxoplasma gondii IgG and IgM by electrochemiluminescence method (Cobas e-170 Analyzer, Roche Diagnostics) between January and December 2013 were included the study. Patients included the study were aged 1-68 years (mean age: 24 ± 9). Of the total 1887 sera tested for T. gondii IgG and IgM, 452 were found to be positive (24%) in a period of 12 months. Seropositivity was found to be 4%, 11,1%, 20,2%, 25,3%, 33,3% and 46,6% in 1-8, 9-18, 19-23, 24-28, 29-35 and 36-68 age groups, respectively. Because of the high seroprevalence in our country, the knowledge about the values of anti-Toxoplasma gondii antibodies in pre-pregnancy period has an importance for evaluation and follow-up during the pregnancy. In this study, it was determined that there is a relationship between seroprevalence and age. All people should be educated about ways to minimize exposure to T. gondii.

  6. Focused molecular analysis of small cell lung cancer: feasibility in routine clinical practice.

    PubMed

    Abdelraouf, Fatma; Sharp, Adam; Maurya, Manisha; Mair, Debbie; Wotherspoon, Andrew; Leary, Alex; Gonzalez de Castro, David; Bhosle, Jaishree; Nassef, Ayatallah; Gaafar, Taghrid; Popat, Sanjay; Yap, Timothy A; O'Brien, Mary

    2015-11-18

    There is an urgent need to identify molecular signatures in small cell lung cancer (SCLC) that may select patients who are likely to respond to molecularly targeted therapies. In this study, we investigate the feasibility of undertaking focused molecular analyses on routine diagnostic biopsies in patients with SCLC. A series of histopathologically confirmed formalin-fixed, paraffin-embedded SCLC specimens were analysed for epidermal growth factor receptors (EGFR), KRAS, NRAS and BRAF mutations, ALK gene rearrangements and MET amplification. EGFR and KRAS mutation testing was evaluated using real time polymerase chain reaction (RT-PCR cobas(®)), BRAF and NRAS mutations using multiplex PCR and capillary electrophoresis-single strand conformation analysis, and ALK and MET aberrations with fluorescent in situ hybridization. All genetic aberrations detected were validated independently. A total of 105 patients diagnosed with SCLC between July 1990 and September 2006 were included. 60 (57 %) patients had suitable tumour tissue for molecular testing. 25 patients were successfully evaluated for all six pre-defined molecular aberrations. Eleven patients failed all molecular analysis. No mutations in EGFR, KRAS and NRAS were detected, and no ALK gene rearrangements or MET gene amplifications were identified. A V600E substitution in BRAF was detected in a Caucasian male smoker diagnosed with SCLC with squamoid and glandular features. The paucity of patients with sufficient tumour tissue, quality of DNA extracted and low frequency of aberrations detected indicate that alternative molecular characterisation approaches are necessary, such as the use of circulating plasma DNA in patients with SCLC.

  7. Performance characteristics of selected immunoassays for preliminary test of 3,4-methylenedioxymethamphetamine, methamphetamine, and related drugs in urine specimens.

    PubMed

    Hsu, Jui; Liu, Chiareiy; Liu, C P; Tsay, Wen-Ing; Li, Jih-Heng; Lin, Dong-Liang; Liu, Ray H

    2003-10-01

    Eight commercially available immunoassays for amphetamines (DRI Amphetamines, CEDIA DAU Amphetamines-Semiquantitative, EMIT d.a.u. Monoclonal Amphetamine/Methamphetamine, Synchron CX Systems AMPH, TDx/TDxFLx Amphetamine/Methamphetamine II, CEDIA Amphetamines/Ecstasy, COBAS INTEGRA Amphetamines, and Abuscreen((R)) OnLine HS Amphetamine/MDMA) are evaluated for their effectiveness in serving as the preliminary test methodology for the analysis of 3,4-methylenedioxymethamphetamine/3,4-methylenedioxyamphetamine (MDMA/MDA) and methamphetamine/amphetamine (MA/AM). Standard solutions (in urine matrix) of MDMA, MDA, MA, and AM are used to determine these immunoassays' reactivities (or cross-reactivities) toward these compounds of interest. Case specimens containing MDMA/MDA and MA/AM are also used to study the correlations of the apparent immunoassay MDMA (or MA) concentrations and the gas chromatographic-mass spectrometric concentrations of these compounds. Data resulting from this study suggest that CEDIA Amphetamines/Ecstasy can best predict the concentrations of MDMA and MA in case specimens and can also detect the presence of MDMA at low levels, whereas Abuscreen OnLine HS Amphetamine/MDMA can detect both MDMA and MA at low concentrations.

  8. False-positive methadone urine drug screen in a patient treated with quetiapine.

    PubMed

    Lasić, Davor; Uglesić, Boran; Zuljan-Cvitanović, Marija; Supe-Domić, Daniela; Uglesić, Lovro

    2012-06-01

    We present a case of T.M. admitted to University Department of Psychiatry, Split University Hospital Center, in Croatia, because of the acute psychotic reaction (F23.9). The patient's urine tested positive for methadone without a history of methadone ingestion. Urine drug screen was performed with the COBAS Integra Methadone II test kit (kinetic interaction of microparticles in solution /KIMS/ methodology) by Roche. Drugs that have been shown to cross-react with methadone feature a tricyclic structure with a sulfur and nitrogen atom in the middle ring, which is common for both quetiapine and methadone. Therefore, it is plausible that this structural similarity between quetiapine and methadone could underlie the cross-reactivity on methadone drug screen. Besides quetiapine, a number of routinely prescribed medications have been associated with triggering false-positive urine drug screen results. Verification of the test results with a different screening test or additional analytical tests should be performed to avoid adverse consequences for the patients.

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

    PubMed

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

    2014-01-01

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

  10. Comparison of PCR and other diagnostic techniques for detection of Helicobacter pylori infection in dyspeptic patients.

    PubMed Central

    Weiss, J; Mecca, J; da Silva, E; Gassner, D

    1994-01-01

    A sensitive and specific PCR-based assay to detect the Helicobacter pylori 16S rRNA gene present in formalin-fixed paraffin-embedded gastric biopsy specimens has been developed. A total of 95 patients with dyspepsia were evaluated for the presence of chronic active gastritis and an infection with H. pylori through the use of diagnostic assays based on biopsy specimens and serology. The "gold standard" for the presence of the bacteria was direct detection in histological sections of biopsy specimens by Giemsa stain. The results obtained with the PCR assay performed on the biopsy specimens (94% sensitivity and 100% specificity) were equivalent to the detection of H. pylori immunoglobulin G antibodies by the commercially available second-generation Cobas Core anti-H. pylori immunoglobulin G enzyme immunoassay (94% sensitivity and 98% specificity) for the diagnosis of H. pylori infection. Urease testing and bacterial culture of the biopsy specimens were inferior (88 and 70% sensitivity and 96% and 98% specificity, respectively). A Western blot (immunoblot) analysis had slightly greater sensitivity (96%), although specificity was reduced to 93%. This research prototype PCR assay was shown to be highly reliable for the detection of infection with H. pylori and the presence of chronic active gastritis in the population studied. PMID:7929755

  11. Coproporphyrin Excretion and Low Thiol Levels Caused by Point Mutation in the Rhodobacter sphaeroides S-Adenosylmethionine Synthetase Gene ▿ †

    PubMed Central

    Sabaty, Monique; Adryanczyk, Géraldine; Roustan, Chloë; Cuiné, Stephan; Lamouroux, Christine; Pignol, David

    2010-01-01

    A spontaneous mutant of Rhodobacter sphaeroides f. sp. denitrificans IL-106 was found to excrete a large amount of a red compound identified as coproporphyrin III, an intermediate in bacteriochlorophyll and heme synthesis. The mutant, named PORF, is able to grow under phototrophic conditions but has low levels of intracellular cysteine and glutathione and overexpresses the cysteine synthase CysK. The expression of molybdoenzymes such as dimethyl sulfoxide (DMSO) and nitrate reductases is also affected under certain growth conditions. Excretion of coproporphyrin and overexpression of CysK are not directly related but were both found to be consequences of a diminished synthesis of the key metabolite S-adenosylmethionine (SAM). The wild-type phenotype is restored when the gene metK encoding SAM synthetase is supplied in trans. The metK gene in the mutant strain has a mutation leading to a single amino acid change (H145Y) in the encoded protein. This point mutation is responsible for a 70% decrease in intracellular SAM content which probably affects the activities of numerous SAM-dependent enzymes such as coproporphyrinogen oxidase (HemN); uroporphyrinogen III methyltransferase (CobA), which is involved in siroheme synthesis; and molybdenum cofactor biosynthesis protein A (MoaA). We propose a model showing that the attenuation of the activities of SAM-dependent enzymes in the mutant could be responsible for the coproporphyrin excretion, the low cysteine and glutathione contents, and the decrease in DMSO and nitrate reductase activities. PMID:20038586

  12. Prognostic role of serum concentrations of high-sensitivity C-reactive protein in patients with metastatic colorectal cancer: results from the ITACa trial

    PubMed Central

    Scarpi, Emanuela; Maltoni, Paolo; Dorizzi, Romolo M.; Passardi, Alessandro; Frassineti, Giovanni Luca; Cortesi, Pietro; Giannini, Maria Benedetta; Marisi, Giorgia; Amadori, Dino; Lucchesi, Alessandro

    2016-01-01

    Serum levels of C-reactive protein are (CRP) higher in patients with neoplastic conditions and numerous studies have been performed to clarify the etiologic and prognostic role of the high-sensitivity CRP (hs-CRP) in cancer. Our study was conducted on patients enrolled in the prospective randomized “Italian Trial in Advanced Colorectal Cancer (ITACa)” to assess hs-CRP levels and their impact on overall survival (OS) and progression-free survival (PFS). Serum samples from 132 ITACa patients were collected at baseline and 2 months after starting first-line chemotherapy. The supernatant was immediately transferred to cryovials and stored at −80°C. After thawing, hs-CRP was measured with the Cobas c501 analyzer. High levels of hs-CRP (≥ 13.1 mg/L) were associated with poorer median PFS (p < 0.0001) and OS (p < 0.0001) than low hs-CRP levels (< 13.1 mg/L). hs-CRP values in 107 patients were evaluated again after 2 months of therapy, revealing that patients with low hs-CRP levels in both baseline and second serum samples had the best median PFS and OS. Our study confirms the prognostic value of hs-CRP in patients with metastatic colorectal carcinoma. PMID:26848624

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

    PubMed

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

    2014-10-01

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

  14. [Evaluation of an automated system in bacteriology. Application to bacteriological susceptibility tests].

    PubMed

    Philippin, J L; Pitton, J S; Fournier, P

    1991-05-01

    Susceptibility tests have been compared between a new automated system and the reference method by agar diffusion. The COBAS-Micro apparatus for bacterial susceptibility tests is intended for rapid determinations with, normally, an incubation time of 5 h at 37 degrees C. Its is compatible with strains requiring greater than 18 h incubation. With this technique a large range of antibacterial substances (greater than 60) can be studied, in groups of fifteen. With the help of a computerized soft-ware, one growth-index:EPR (End Point Ratio) is calculated, in comparison with a standard, for each antibacterial agent tested and expressed in three categories: SIR. The findings are optimized according to the limits prescribed by the NCCLS. The reference method, by agar-diffusion, is as described by the Comité de l'Antibiogramme de la Société Française de Microbiologie (CA-SFM). A total of 1,048 strains were tested by the two techniques: 518 Gram negative rods, 530 Gram positive cocci, with four common antibiotics. The percentages of agreement between the two groups were: 96% full agreement and minor discrepancy, 4% major and very major discrepancy. This automated system seems to be perfectly suitable for susceptibility testing in a routine laboratory, especially with strains isolated from ambulatory patients.

  15. Comparison of Human Papillomavirus Detection in Urine and Cervical Samples Using High-Risk HPV DNA Testing in Northern Thailand

    PubMed Central

    Settakorn, Jongkolnee; Sukpan, Kornkanok; Lekawanvijit, Suree; Katruang, Narisara; Siriaunkgul, Sumalee

    2016-01-01

    Objective. To evaluate the performance of high-risk human papillomavirus (HPV) DNA testing in urine samples compared to that of cervical sample testing in Northern Thailand. Methods. Paired urine and cervical samples were collected during the follow-up of women with a previous positive HPV test. HPV testing was performed using the Cobas 4800 HPV Test. Linear Array assay was used for genotyping in selected cases. Results. Paired urine and cervical samples were obtained from 168 women. Of 123 paired samples with valid results, agreement in the detection of high-risk HPV DNA was present in 106 cases (86.2%), with a kappa statistic of 0.65 (substantial agreement). Using the cervical HPV results as a reference, the sensitivity of urine HPV testing was 68.6% (24/35) and the specificity 93.2% (82/88). For the detection of histologic high-grade squamous intraepithelial lesion or worse (HSIL+), the sensitivity of urine HPV testing was 80.0% (4/5) and the specificity 78.0% (92/118). Conclusion. Although urine HPV testing had a rather low sensitivity for HPV detection, its sensitivity for histologic HSIL+ detection was high. For clinical use of urine HPV testing, standardization of specimen collection and processing techniques or application of a more sensitive test, especially in the detection of HPV52 and HPV58, is necessary. PMID:28101107

  16. Interference of hemoglobinA1c (HbA1c) detection using ion-exchange high