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Sample records for cobas taqscreen mpx

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    PubMed Central

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

    1998-01-01

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

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

    PubMed

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

    1998-10-01

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

  14. 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

  15. 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

  16. 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+.

  17. 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.

  18. 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.

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

    PubMed Central

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

    2005-01-01

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

  20. Homogeneous enzyme immunoassay (EMIT) protocol for monitoring tricyclic antidepressants on the COBAS-BIO centrifugal analyzer.

    PubMed

    Ernst, R; Williams, L; Dalbey, M; Collins, C; Pankey, S

    1987-01-01

    EMIT tests are available for quantitative determination of the tricyclic antidepressants amitriptyline (AMI), nortriptyline (NORT), imipramine (IMI), and desipramine (DMI). An extraction step before analysis eliminates cross-reacting polar metabolites. Excellent correlation between EMIT and high-performance liquid chromatography (HPLC) has been previously established. Most published protocols for using EMIT reagents on COBAS-BIO centrifugal analyzers were designed for analytes present at 1-50 mg/L in serum. AMI, NORT, IMI, and DMI are usually present at far less than 1 mg/L. We describe a COBAS-BIO EMIT protocol for assaying these analytes. Patient sample correlation between COBAS-BIO EMIT and EMIT-AutoLab were greater than 0.99. Between-run precision for single-point determinations was comparable to SYVA AutoLab performance [less than or equal to 11% at 40 micrograms/L AMI, NORT, IMI (80 micrograms/L DMI), and less than or equal to 4% at 200 micrograms/L AMI, NORT, IMI (400 micrograms/L DMI)]. With stored-curve updating, working reagents were usable for at least 14 days (AMI) or 23 days (DMI).

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

    PubMed Central

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

    1999-01-01

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

  2. 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.

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

    PubMed Central

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

    1998-01-01

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

  4. 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

  5. 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

  6. 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.

  7. 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.

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

    PubMed Central

    Rimek, Dagmar; Tyagi, Sachin; Kappe, Reinhard

    2002-01-01

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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    PubMed

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

    2014-01-01

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

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

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

    PubMed

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

    2015-01-01

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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. [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.

  9. 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.

  10. 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

  11. 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.

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

    PubMed Central

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

    2000-01-01

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

  13. 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.

  14. 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.

  15. [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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

    2016-12-26

    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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  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. 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

  11. 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

  12. 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

  13. 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.

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

    PubMed

    Koch, Carmo; Araújo, Fernando

    2013-01-01

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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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

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

    NASA Astrophysics Data System (ADS)

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

    1982-10-01

    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.

  2. 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

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

    DTIC Science & Technology

    1979-08-09

    via reflection and diffration around buildings (guided street propagation) . on the other hand, in the case of the 27 MHz and 446 MHz measurements...Buildings and Other Structures 3-14 we assume that the urban propagation problem can be represented qualitatively by a single knife-edge diffration

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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…

  12. 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…

  13. 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.

  14. 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.

  15. 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…

  16. Insulin and Breast Cancer Risk

    DTIC Science & Technology

    2002-06-01

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

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

    DTIC Science & Technology

    1986-11-14

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

  18. 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

  19. 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

  20. 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

  1. 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…

  2. 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.

  3. 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…

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Application of Copper Indium Gallium Diselenide Photovoltaic Cells to Extend the Endurance and Capabilities of the Raven RQ-11B Unmanned Aerial Vehicle

    DTIC Science & Technology

    2010-09-01

    Unmanned Aerial Vehicle 6. AUTHOR( S ) Javier V. Coba 5. FUNDING NUMBERS 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) Naval Postgraduate...School Monterey, CA 93943-5000 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING /MONITORING AGENCY NAME( S ) AND ADDRESS(ES) Unmanned Aerial...73 D. ENERGY CALCULATIONS ...............................75 1. Fully Charged Battery ........................75 2. Raven’s Energy

  15. 76 FR 47210 - Medical Devices; Availability of Safety and Effectiveness Summaries for Premarket Approval...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-04

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

  16. 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...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. An Analysis of Bayesian Inference for Non-Parametric Regression.

    DTIC Science & Technology

    1986-10-01

    that in principle one can solve virtually any statistical decision or inference problem. In particular, one can provide an accuracy assessment for fn...E [P Yn ] using posterior probability regions. For instance, letting 1lll denote L2 [0,1] norm, one can in principle determine a number An such...Using (3.2), one can show that if -,Vm? < p < 1 -,m, then asX A0 Ck,\\Qp) -,x-(P+elm) fz2mp[X +X -dz 0 = ,\\-(P+’/Ŗ)B (p + 1/2rn, c-p- 1/2 m) (3.3) where

  6. 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

  7. 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

  8. 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.

  9. 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

  10. [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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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.

  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. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  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. 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}.

  1. [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).

  2. 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.

  3. 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.

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

    PubMed

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

    2013-07-01

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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  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. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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 [

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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).

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  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

    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.

  10. 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.

  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. 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

  14. 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.

  15. 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.

  16. An automated enzymatic method for measurement of D-arabinitol, a metabolite of pathogenic Candida species.

    PubMed

    Switchenko, A C; Miyada, C G; Goodman, T C; Walsh, T J; Wong, B; Becker, M J; Ullman, E F

    1994-01-01

    An automated enzymatic method was developed for the measurement of D-arabinitol in human serum. The assay is based on a novel, highly specific D-arabinitol dehydrogenase from Candida tropicalis. This enzyme catalyzes the oxidation of D-arabinitol to D-ribulose and the concomitant reduction of NAD+ to NADH. The NADH produced is used in a second reaction to reduce p-iodonitrotetrazolium violet (INT) to INT-formazan, which is measured spectrophotometrically. The entire reaction sequence can be performed automatically on a COBAS MIRA-S clinical chemistry analyzer (Roche Diagnostic Systems, Inc., Montclair, N.J.). Replicate analyses of human sera supplemented with D-arabinitol over a concentration range of 0 to 40 microM demonstrated that the pentitol could be measured with an accuracy of +/- 7% and a precision (standard deviation) of +/- 0.4 microM. Serum D-arabinitol measurements correlated with those determined by gas chromatography (r = 0.94). The enzymatic method is unaffected by L-arabinitol, D-mannitol, or other polyols commonly found in human serum. Any of 17 therapeutic drugs potentially present in serum did not significantly influence assay performance. Data illustrating the application of the assay in patients for possible diagnosis of invasive candidiasis and the monitoring of therapeutic intervention are presented. The automated assay described here was developed to facilitate the investigation of D-arabinitol as a serum marker for invasive Candida infections.

  17. Development of a new microparticle-enhanced turbidimetric assay for C-reactive protein with superior features in analytical sensitivity and dynamic range.

    PubMed

    Eda, S; Kaufmann, J; Roos, W; Pohl, S

    1998-01-01

    Novel assay techniques were applied to a newly developed microparticle-based assay for C-reactive protein (CRP). By using two different sized microparticles covalently coated with two monoclonal antibodies of different reactivity, high analytical sensitivity and a high upper measuring limit could be simultaneously attained, resulting in a remarkably wide dynamic range. This range was further increased by calculating the signal (reaction rate) optimally with a new software capability of COBAS INTEGRA, a clinical chemistry analyzer. The assay showed high precision between 2 mg/l and 160 mg/l with use of only 2.5 microl specimen. The detection limit was estimated as 0.3 mg/l CRP. The assay was four to eight times more sensitive and precise than existing turbidimetric or nephelometric assays with comparable upper measuring limits. The assay also showed good linearity and correlated well with commercial assays. This new microparticle-based CRP assay provides the accuracy and precision that are required to determine CRP at low concentrations where new clinical implications such as prognosis of cardiovascular diseases are envisaged. The assay's wide dynamic range will additionally lead to a reduction in the number of repeated analyses, thus improving the efficiency of CRP determinations in clinical laboratories.

  18. Global cost modeling analysis of HIV-1 and HCV viral load assays.

    PubMed

    Elbeik, Tarek; Chen, Yi-Ming Arthur; Soutchkov, Serguei V; Loftus, Richard A; Beringer, Scott

    2003-08-01

    This review addresses hidden costs associated with the Bayer VERSANT assay, Roche AMPLICOR MONITOR test and COBAS AMPLICOR MONITOR test and how these influence the final per reportable cost to a testing laboratory in resource-rich and -poor countries. An in-depth evaluation and recommendation of the most cost-effective approach for these tests is presented. The analyses demonstrate the need for manufacturers to consider labor and supply costs when marketing a kit in resource-poor countries, noting that marketing strategies need to change. In the absence of any proven monitoring alternative, emphasis is placed on increasing market share to promote significant reduction in kit prices to suit the demands of markets in resource-poor countries. Finally, recommendations are made to improve the overall cost structure of viral load testing. This review is intended as a tool to optimize assay usage in attaining the lowest performance costs by assay and is not to endorse any test, as will become apparent.

  19. Organ donor screening using parallel nucleic acid testing allows assessment of transmission risk and assay results in real time.

    PubMed

    Baleriola, C; Tu, E; Johal, H; Gillis, J; Ison, M G; Law, M; Coghlan, P; Rawlinson, W D

    2012-06-01

    Expansion of the donor pool may lead to utilization of donors with risk factors for viral infections. Donor laboratory screening relies on serological and nucleic acid testing (NAT). The increased sensitivity of NAT in low prevalence populations may result in false-positive results (FPR) and may cause unnecessary discard of organs.We developed a screening algorithm to deal, in real time, with potential FPR. Three NAT assays: COBAS AmpliScreen assay (CAS), AmpliPrep Total Nucleic Acid Isolation/CAS, and AmpliPrep/TaqMan assays, were validated and used in parallel for prospective screening of increased-risk donors (IRD), and the probability of FPR was calculated. The lower limit of detection of this algorithm was 9.79, 21.02, and 4.31 IU/mL for human immunodeficiency virus-1, hepatitis C virus, and hepatitis B virus, respectively, with an average turn-around-time of 7.67 h from sample receipt to result reporting. The probability that a donor is potentially infectious with two NAT concordant results was >90%. NAT screening of 35 IRD within 18 months resulted in transplantation of 102 additional organs that without screening would either not be used or used with restrictions in Australia. Using a parallel testing algorithm, real-time confirmation of seropositive donors allows use of organs from IRD and safer expansion of the donor pool.

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

    PubMed

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

    2014-10-01

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

  1. Simulated Respiratory Secretion for Use in the Development of Influenza Diagnostic Assays

    PubMed Central

    McCaul, Kate C.; Mei, Hong; Sasman, Amy; He, Jie; Kramp, William; Shively, Roxanne; Yan, Ke; Henrickson, Kelly J.

    2016-01-01

    Many assays have been developed for the detection of influenza virus which is an important respiratory pathogen. Development of these assays commonly involves the use of human clinical samples for validation of their performance. However, clinical samples can be difficult to obtain, deteriorate over time, and be inconsistent in composition. The goal of this study was to develop a simulated respiratory secretion (SRS) that could act as a surrogate for clinical samples. To this end, we determined the effects major respiratory secretion components (Na+, K+, Ca2+, cells, albumin IgG, IgM, and mucin) have on the performance of influenza assays including both nucleic acid amplification and rapid antigen assays. Minimal effects on the molecular assays were observed for all of the components tested, except for serum derived human IgG, which suppressed the signal of the rapid antigen assays. Using dot blots we were able to show anti-influenza nucleoprotein IgG antibodies are common in human respiratory samples. We composed a SRS that contained mid-point levels of human respiratory sample components and studied its effect compared to phosphate buffered saline and virus negative clinical sample matrix on the Veritor, Sofia, CDC RT-PCR, Simplexa, cobas Liat, and Alere i influenza assays. Our results demonstrated that a SRS can interact with a variety of test methods in a similar manner to clinical samples with a similar impact on test performance. PMID:27870895

  2. Magnetic nanowires for rapid and ultrasensitive isolation of DNA from cervical specimens for the detection of multiple human papillomaviruses genotypes.

    PubMed

    Lee, HyungJae; Hwang, Na Rae; Hwang, Sang-Hyun; Cho, Youngnam

    2016-12-15

    Detecting human papillomavirus (HPV) is central in diagnosing and monitoring HPV-related disease. However, limited sensitivity and the wide variability of the HPV genome pose challenges in the identification of HPV genes, particularly high-risk types. This study reports the development of polyethyleneimine-conjugated magnetic nanowires (PEI-MNWs) and their use in the isolation, identification, and analysis of multiple genotypes of HPV DNA from cervical cancer specimens. The nanowires are electrochemically doped with a high density of magnetic nanoparticles and biotin moieties during potentiostatic deposition, thereby allowing conjugating cationic branched polymers to direct the attachment of negatively charged DNA molecules with strong magnetic response. For proof of concept, the rapid and ultrasensitive isolation of HPV DNA is performed at concentrations as low as 10pg/mL with an efficiency of >95%. For clinical optimization, the analytical and clinical sensitivity of PEI-MNWs is compared with that of the Roche Cobas 4800 HPV Test and demonstrates excellent correlation for multiple HPV DNA genotypes with superior threshold cycle values. The high sensitivity, specificity, and good reproducibility of PEI-MNWs are particularly well suited for the recovery of DNA and provide significant and clinically meaningful evidence for the early detection and treatment of HPV-associated cancers.

  3. 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.

  4. 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

  5. Advanced oxidation protein products (AOPP) for monitoring oxidative stress in critically ill patients: a simple, fast and inexpensive automated technique.

    PubMed

    Selmeci, László; Seres, Leila; Antal, Magda; Lukács, Júlia; Regöly-Mérei, Andrea; Acsády, György

    2005-01-01

    Oxidative stress is known to be involved in many human pathological processes. Although there are numerous methods available for the assessment of oxidative stress, most of them are still not easily applicable in a routine clinical laboratory due to the complex methodology and/or lack of automation. In research into human oxidative stress, the simplification and automation of techniques represent a key issue from a laboratory point of view at present. In 1996 a novel oxidative stress biomarker, referred to as advanced oxidation protein products (AOPP), was detected in the plasma of chronic uremic patients. Here we describe in detail an automated version of the originally published microplate-based technique that we adapted for a Cobas Mira Plus clinical chemistry analyzer. AOPP reference values were measured in plasma samples from 266 apparently healthy volunteers (university students; 81 male and 185 female subjects) with a mean age of 21.3 years (range 18-33). Over a period of 18 months we determined AOPP concentrations in more than 300 patients in our department. Our experiences appear to demonstrate that this technique is especially suitable for monitoring oxidative stress in critically ill patients (sepsis, reperfusion injury, heart failure) even at daily intervals, since AOPP exhibited rapid responses in both directions. We believe that the well-established relationship between AOPP response and induced damage makes this simple, fast and inexpensive automated technique applicable in daily routine laboratory practice for assessing and monitoring oxidative stress in critically ill or other patients.

  6. 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

  7. Occult hepatitis B in HIV-HCV coinfected patients.

    PubMed

    Piroth, Lionel; Lafon, Marie-Edith; Binquet, Christine; Bertillon, Pascale; Gervais, Anne; Lootvoet, Enguerrand; Lang, Jean-Marie; De Jaureguiberry, Jean Pierre; Chene, Geneviève; Leport, Catherine

    2008-01-01

    The prevalence of occult hepatitis B infection in HIV infected patients is controversial, varying from less than 1% to 62% in different studies. Blood samples of 111 HIV-infected patients, HCV-positive, HBs antigen negative, followed in the APROCO-ANRS EP11 cohort, were used to detect HBV DNA by using 2 different validated assays (Cobas Amplicor HBV Monitor Test and INSERM U271 qualitative ultra-sensitive PCR), completed when positive by HBV real-time PCR. HBV DNA was found in 6 (5.4%, 95% CI 1.2%-9.6%) patients by at least 1 of these assays, but none tested positive in all 3 assays. All 6 patients had anti-HBc without anti-HBs antibodies; 5 were not on lamivudine. Their median CD4 and CD8 counts were significantly lower and their HIV viral load higher than in the other 105 patients. In conclusion, the prevalence of occult hepatitis B may vary significantly according to the molecular assay used, even though these assays are validated with high specificity and quite high sensitivity. Occult hepatitis B may be encountered in HIV-HCV coinfected patients without anti-HBV treatment, with anti-HBc but without anti-HBs antibodies, and relatively low immunity, suggesting a potential risk of further reactivation, as already sporadically reported.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Addressing Inpatient Glycaemic Control with an Inpatient Glucometry Alert System

    PubMed Central

    Seheult, J. N.; Pazderska, A.; Gaffney, P.; Fogarty, J.; Sherlock, M.; Gibney, J.; Boran, G.

    2015-01-01

    Background. Poor inpatient glycaemic control has a prevalence exceeding 30% and results in increased length of stay and higher rates of hospital complications and inpatient mortality. The aim of this study was to improve inpatient glycaemic control by developing an alert system to process point-of-care blood glucose (POC-BG) results. Methods. Microsoft Excel Macros were developed for the processing of daily glucometry data downloaded from the Cobas IT database. Alerts were generated according to ward location for any value less than 4 mmol/L (hypoglycaemia) or greater than 15 mmol/L (moderate-severe hyperglycaemia). The Diabetes Team provided a weekday consult service for patients flagged on the daily reports. This system was implemented for a 60-day period. Results. There was a statistically significant 20% reduction in the percentage of hyperglycaemic patient-day weighted values >15 mmol/L compared to the preimplementation period without a significant change in the percentage of hypoglycaemic values. The time-to-next-reading after a dysglycaemic POC-BG result was reduced by 14% and the time-to-normalization of a dysglycaemic result was reduced from 10.2 hours to 8.4 hours. Conclusion. The alert system reduced the percentage of hyperglycaemic patient-day weighted glucose values and the time-to-normalization of blood glucose. PMID:26290664

  15. 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.

  16. 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.

  17. What is the acceptable hemolysis index for the measurements of plasma potassium, LDH and AST?

    PubMed

    Rousseau, Nathalie; Pige, Raphaëlle; Cohen, Richard; Pecquet, Matthieu

    2016-06-01

    Hemolysis is a cause of variability in test results for plasma potassium, LDH and AST and is a non-negligible part of measurement uncertainty. However, allowable levels of hemolysis provided by reagent suppliers take neither analytical variability (trueness and precision) nor the measurand into account. Using a calibration range of hemolysis, we measured the plasma concentrations of potassium, LDH and AST, and hemolysis indices with a Cobas C501 analyzer (Roche Diagnostics(®), Meylan, France). Based on the allowable total error (according to Ricós et al.) and the expanded measurement uncertainty equation we calculated the maximum allowable bias for two concentrations of each measurand. Finally, we determined the allowable hemolysis indices for all three measurands. We observed a linear relationship between the observed increases of concentration and hemolysis indices. The LDH measurement was the most sensitive to hemolysis, followed by AST and potassium measurements. The determination of the allowable hemolysis index depends on the targeted measurand, its concentration and the chosen level of requirement of allowable total error.

  18. Feruloyl-L-arabinose attenuates migration, invasion and production of reactive oxygen species in H1299 lung cancer cells.

    PubMed

    Fang, Hsin-Yu; Wang, Hui-Min; Chang, Kuo-Feng; Hu, Huei-Ting; Hwang, Lian-Je; Fu, Tzu-Fun; Lin, Yin-Chieh; Chang, Wei-Chiao; Chiu, Tsu-Pei; Wen, Zhi-Hong; Fong, Yao; Chiu, Chien-Chih; Chen, Bing-Hung

    2013-08-01

    Ferulic acid (FA), a phenolic compound, is an abundant dietary antioxidant and exerts the mitogenic effect on cells. Recently, we isolated an active FA derivative, namely feruloyl-L-arabinose (FAA), from coba husk. The aim of this study was to investigate the effects of FAA on the proliferation, migration and invasion of H1299 human lung cancer cells. Our results showed a strong antioxidant potential of FAA. Additionally, FAA inhibited the migration and invasion ability, while causing a significant accumulation of G2/M-population, of H1299 tumor cells in a dose-dependent manner, whereas no significant change on cell proliferation was observed. Results from the wound healing assay revealed that cell migration ability was markedly inhibited by FAA treatments. Similarly, results of gelatin zymography study showed that FAA treatments significantly decreased the activities of matrix metalloproteinase (MMP)-2 and MMP-9, suggesting that FAA-mediated inhibition on migration and invasion of lung cancer cells may be achieved by the down-regulation of the MMPs activities. Taken together, our present work provides a new insight into the novel inhibitory function of FAA on cell migration in H1299 cells, suggesting its promising role in the chemoprevention of lung cancer.

  19. Purification, characterization, and molecular cloning of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Methanobacterium ivanovii.

    PubMed Central

    Blanche, F; Robin, C; Couder, M; Faucher, D; Cauchois, L; Cameron, B; Crouzet, J

    1991-01-01

    An S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase (SUMT) activity has been identified in Methanobacterium ivanovii and was purified 4,500-fold to homogeneity with a 38% yield. The enzyme had an apparent molecular weight of 58,200 by gel filtration and consisted of two identical subunits of Mr 29,000, as estimated by gel electrophoresis under denaturing conditions. The Km value for uroporphyrinogen III was 52 nM. The enzyme catalyzed the two C-2 and C-7 methylation reactions converting uroporphyrinogen III into precorrin-2. Unlike Pseudomonas denitrificans SUMT, the only SUMT characterized to date (F. Blanche, L. Debussche, D. Thibaut, J. Crouzet and B. Cameron, J. Bacteriol. 171:4222-4231, 1989), M. ivanovii SUMT did not show substrate inhibition at uroporphyrinogen III concentrations of up to 20 microM. Oligonucleotide probes from limited peptide sequence information were used to clone the corresponding gene. The encoded polypeptide showed more than 40% strict homology with P. denitrificans SUMT. The M. ivanovii SUMT structural gene is likely to be, as is P. denitrificans cobA, involved in corrinoid synthesis. Images PMID:1856165

  20. Value of repeat testing using Cepheid GeneXpert CT/NG for indeterminate PCR results when diagnosing Chlamydia trachomatis and Neisseria gonorrhoeae.

    PubMed

    Parcell, Benjamin J; Ratnayake, Lasantha; Kaminski, Geraldine; Olver, William J; Yirrell, David L

    2015-01-01

    Nucleic acid amplification tests (NAATs) are the most sensitive method for diagnosing chlamydia and gonorrhoea. We use the COBAS 4800 CT/NG combined assay (Roche Molecular Diagnostics, CA, USA), and whilst the majority of samples yield definitive results, a small proportion are reported as indeterminate. In these instances, it is usual practice to request repeat samples which delays diagnosis. This audit was twofold: first to establish the proportion of indeterminate results with current NAAT testing requiring re-sampling. Second, to determine whether a second NAAT such as Cepheid GeneXpert CT/NG assay (Cepheid, CA, USA) could be used on initial indeterminate samples to resolve indeterminate results, therefore reducing need for repeat sampling. During 2012, 144/21,931 (0.66%) samples were indeterminate for Neisseria gonorrhoeae, Chlamydia trachomatis or both, and a repeat sample was received in only 51.77% of patients with final results being delayed for more than 24 h. Over the next six months, there were 77/9472 (0.81%) indeterminate results. After an evaluation and introduction of the Cepheid assay, the number of indeterminate results fell to 9 (0.10%). Thus, use of the Cepheid assay significantly reduced indeterminate results, reduced reliance on a repeat sampling and significantly improved turnaround time, laboratory workflow and patient experience.

  1. Estimation of postmortem interval using the data of insulin level in the cadaver׳s blood.

    PubMed

    Kumar, Sachil; Verma, Anoop K

    2016-06-01

    An assessment of levels of Insulin in cadaveric fluids, to estimate the postmortem interval (PMI) was carried out. To profile postmortem changes of Insulin, it was extracted at different intervals i.e. (0, 3, 6, 12, 24 h), from the heart of 22 human cadavers. The cases included were the subjects of accidental deaths without any prior history of disease and their exact time of death was known. Immunoanalyzer Cobas e-411 instrument was used to detect the relationship between the amount of Insulin and PMI. Level of Insulin was measured in cardiac blood. Statically, significant correlations between levels of Insulin and PMI were studied and correlation coefficients were calculated. SPSS (version 12.0) was used for statistical analysis. Insulin levels in cadaver blood are correlated significantly with PMI with a p value of <0.001. When insulin level increases by 1 unit the duration decreases by 0.93 units. The least square regression line is: [Duration(Y)=22.71-0.93 Insulin level (X)].

  2. Contrast-Enhanced Ultrasound (CEUS) for Echographic Detection of Hepato Cellular Carcinoma in Cirrhotic Patients Previously Treated with Multiple Techniques: Comparison of Conventional US, Spiral CT and 3-Dimensional CEUS with Navigator Technique (3DNav CEUS)

    PubMed Central

    Giangregorio, Francesco

    2011-01-01

    A commercially available technique named “NAVIGATOR” (Esaote, Italy) easily enables a 3-D reconstruction of a single 2-D acquisition of Contrast Enhanced Ultrasound (CEUS) imaging of the whole liver (with a volumetric correction thanks to the electromagnetic device of NAVIGATOR). Aim of the study was to evaluate this “panoramic” technique in comparison with conventional US and spiral CT in the detection of new hepatic lesions. 144 cirrhotic patients (previously treated for hepato cellular carcinoma (HCC)) in follow-up with detection of 98 new nodules (N), 28 multinodular (Nmulti), 14 loco-regional regrowth (LR) 94 efficaciously treated without new nodules (neg) and four multinodular without new nodules, were submitted to 200 examinations with this new technique from November 2008 to November 2009. 3DNavCEUS was performed using SonoVue (Bracco), as contrast agent, and a machine (Technos MPX, Esaote). Spiral CT and 3DNav CEUS were performed in the same month during follow up. Sens.,Spec.,diagn.-Acc.,PPV and NPV were evaluated; comparison and differences between the techniques were obtained with chi-square (SPSS release-15). Final diagnosis was: 98 new lesions (N) (one to three), 28 multinodular HCC (Nmulti) and 14 loco-regional regrowth (LR); in 94 no more lesions were observed during follow-up; conventional US obtained: 58 N (+18 multinodularN and 8 LR), 40 false negative (+10 Nmulti and 6 LR) (sens:59.2, spec:100%, Diagn Accur:73.6, PPV:100; NPV:70.1); spiral CT obtained: 84N (+26-multinodularN and 14-LR), 14 false-negative (+2-Nmulti), and one false-positive (sens:85.7, spec:97.9%, Diagn Accur:90.9, PPV:97.7; NPV:86.8); 3DNAV obtained: 92N (+28 multinodularN and 14LR), 6 false-negative, and two false-positives (sens:93.9, spec:97.9%, Diagn Accur:95.6, PPV:97.9; NPV:93.9). 3-DNav CEUS is significantly better than US and almost similar to spiral CT for detection of new HCC. This technique, in particular, showed the presence of lesions even in the cases not

  3. Size-frequency distribution of boulders ≥7 m on comet 67P/Churyumov-Gerasimenko

    NASA Astrophysics Data System (ADS)

    Pajola, Maurizio; Vincent, Jean-Baptiste; Güttler, Carsten; Lee, Jui-Chi; Bertini, Ivano; Massironi, Matteo; Simioni, Emanuele; Marzari, Francesco; Giacomini, Lorenza; Lucchetti, Alice; Barbieri, Cesare; Cremonese, Gabriele; Naletto, Giampiero; Pommerol, Antoine; El-Maarry, Mohamed R.; Besse, Sébastien; Küppers, Michael; La Forgia, Fiorangela; Lazzarin, Monica; Thomas, Nicholas; Auger, Anne-Thérèse; Sierks, Holger; Lamy, Philippe; Rodrigo, Rafael; Koschny, Detlef; Rickman, Hans; Keller, Horst U.; Agarwal, Jessica; A'Hearn, Michael F.; Barucci, Maria A.; Bertaux, Jean-Loup; Da Deppo, Vania; Davidsson, Björn; De Cecco, Mariolino; Debei, Stefano; Ferri, Francesca; Fornasier, Sonia; Fulle, Marco; Groussin, Olivier; Gutierrez, Pedro J.; Hviid, Stubbe F.; Ip, Wing-Huen; Jorda, Laurent; Knollenberg, Jörg; Kramm, J.-Rainer; Kürt, Ekkehard; Lara, Luisa M.; Lin, Zhong-Yi; Lopez Moreno, Jose J.; Magrin, Sara; Marchi, Simone; Michalik, Harald; Moissl, Richard; Mottola, Stefano; Oklay, Nilda; Preusker, Frank; Scholten, Frank; Tubiana, Cecilia

    2015-11-01

    Aims: We derive for the first time the size-frequency distribution of boulders on a comet, 67P/Churyumov-Gerasimenko (67P), computed from the images taken by the Rosetta/OSIRIS imaging system. We highlight the possible physical processes that lead to these boulder size distributions. Methods: We used images acquired by the OSIRIS Narrow Angle Camera, NAC, on 5 and 6 August 2014. The scale of these images (2.44-2.03 m/px) is such that boulders ≥7 m can be identified and manually extracted from the datasets with the software ArcGIS. We derived both global and localized size-frequency distributions. The three-pixel sampling detection, coupled with the favorable shadowing of the surface (observation phase angle ranging from 48° to 53°), enables unequivocally detecting boulders scattered all over the illuminated side of 67P. Results: We identify 3546 boulders larger than 7 m on the imaged surface (36.4 km2), with a global number density of nearly 100/km2 and a cumulative size-frequency distribution represented by a power-law with index of -3.6 +0.2/-0.3. The two lobes of 67P appear to have slightly different distributions, with an index of -3.5 +0.2/-0.3 for the main lobe (body) and -4.0 +0.3/-0.2 for the small lobe (head). The steeper distribution of the small lobe might be due to a more pervasive fracturing. The difference of the distribution for the connecting region (neck) is much more significant, with an index value of -2.2 +0.2/-0.2. We propose that the boulder field located in the neck area is the result of blocks falling from the contiguous Hathor cliff. The lower slope of the size-frequency distribution we see today in the neck area might be due to the concurrent processes acting on the smallest boulders, such as i) disintegration or fragmentation and vanishing through sublimation; ii) uplifting by gas drag and consequent redistribution; and iii) burial beneath a debris blanket. We also derived the cumulative size-frequency distribution per km2 of

  4. Imaging Asteroid 4 Vesta Using the Framing Camera

    NASA Technical Reports Server (NTRS)

    Keller, H. Uwe; Nathues, Andreas; Coradini, Angioletta; Jaumann, Ralf; Jorda, Laurent; Li, Jian-Yang; Mittlefehldt, David W.; Mottola, Stefano; Raymond, C. A.; Schroeder, Stefan E.

    2011-01-01

    The Framing Camera (FC) onboard the Dawn spacecraft serves a dual purpose. Next to its central role as a prime science instrument it is also used for the complex navigation of the ion drive spacecraft. The CCD detector with 1024 by 1024 pixels provides the stability for a multiyear mission and its high requirements of photometric accuracy over the wavelength band from 400 to 1000 nm covered by 7 band-pass filters. Vesta will be observed from 3 orbit stages with image scales of 227, 63, and 17 m/px, respectively. The mapping of Vesta s surface with medium resolution will be only completed during the exit phase when the north pole will be illuminated. A detailed pointing strategy will cover the surface at least twice at similar phase angles to provide stereo views for reconstruction of the topography. During approach the phase function of Vesta was determined over a range of angles not accessible from earth. This is the first step in deriving the photometric function of the surface. Combining the topography based on stereo tie points with the photometry in an iterative procedure will disclose details of the surface morphology at considerably smaller scales than the pixel scale. The 7 color filters are well positioned to provide information on the spectral slope in the visible, the depth of the strong pyroxene absorption band, and their variability over the surface. Cross calibration with the VIR spectrometer that extends into the near IR will provide detailed maps of Vesta s surface mineralogy and physical properties. Georeferencing all these observation will result in a coherent and unique data set. During Dawn s approach and capture FC has already demonstrated its performance. The strong variation observed by the Hubble Space Telescope can now be correlated with surface units and features. We will report on results obtained from images taken during survey mode covering the whole illuminated surface. Vesta is a planet-like differentiated body, but its surface

  5. Protective Yeasts Control V. anguillarum Pathogenicity and Modulate the Innate Immune Response of Challenged Zebrafish (Danio rerio) Larvae.

    PubMed

    Caruffo, Mario; Navarrete, Natalie C; Salgado, Oscar A; Faúndez, Nelly B; Gajardo, Miguel C; Feijóo, Carmen G; Reyes-Jara, Angélica; García, Katherine; Navarrete, Paola

    2016-01-01

    We investigated mechanisms involved in the protection of zebrafish (Danio rerio) larvae by two probiotic candidate yeasts, Debaryomyces hansenii 97 (Dh97) and Yarrowia lypolitica 242 (Yl242), against a Vibrio anguillarum challenge. We determined the effect of different yeast concentrations (10(4)-10(7) CFU/mL) to: (i) protect larvae from the challenge, (ii) reduce the in vivo pathogen concentration and (iii) modulate the innate immune response of the host. To evaluate the role of zebrafish microbiota in protection, the experiments were performed in conventionally raised and germ-free larvae. In vitro co-aggregation assays were performed to determine a direct yeast-pathogen interaction. Results showed that both yeasts significantly increased the survival rate of conventionally raised larvae challenged with V. anguillarum. The concentration of yeasts in larvae tended to increase with yeast inoculum, which was more pronounced for Dh97. Better protection was observed with Dh97 at a concentration of 10(6) CFU/mL compared to 10(4) CFU/mL. In germ-free conditions V. anguillarum reached higher concentrations in larvae and provoked significantly more mortality than in conventional conditions, revealing the protective role of the host microbiota. Interestingly, yeasts were equally (Dh97) or more effective (Yl242) in protecting germ-free than conventionally-raised larvae, showing that protection can be exerted only by yeasts and is not necessarily related to modulation of the host microbiota. Although none of the yeasts co-aggregated with V. anguillarum, they were able to reduce its proliferation in conventionally raised larvae, reduce initial pathogen concentration in germ-free larvae and prevent the upregulation of key components of the inflammatory/anti-inflammatory response (il1b, tnfa, c3, mpx, and il10, respectively). These results show that protection by yeasts of zebrafish larvae challenged with V. anguillarum relates to an in vivo anti-pathogen effect, the modulation

  6. Preliminary Geological Map of the Ac-H-2 Coniraya Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Hiesinger, H.; Pasckert, J. H.; 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.; Marchi, S.; De Sanctis, M. C.; Russell, C. T.; Raymond, C. A.

    2015-12-01

    To better understand the geologic history of dwarf planet Ceres, the surface has been divided into 15 quadrangles that are systematically mapped on the basis of images obtained by NASA's Dawn spacecraft, which began orbiting Ceres in April 2015. We will report on preliminary mapping results for the Ac-H-2 Coniraya Quadrangle based on Framing Camera (FC) mosaics from the Dawn Approach (1.3 km/px) and Survey (415 m/px) orbits. This quadrangle is located between 21-66°N and 0-90°E and is dominated by mostly highly degraded impact craters of diameters between 50 and 200 km and clusters of small- to midsize impact craters. Color data show that this quadrangle is generally darker than most regions of the southern hemisphere. Two prominent impact craters in this quadrangle have been named Coniraya and Gaue crater, respectively. Coniraya is the largest more or less intact impact crater with a diameter of 136 km, centered at 65.8°N/40.5°E. It appears shallow and its crater rim is heavily degraded but still continuous. At the current image resolution, textural differences between the interior and exterior of the crater are not visible. With a diameter of 84 km, Gaue crater appears to be the freshest large impact crater in this quadrangle. It is located at the eastern border of the Coniraya Quadrangle with a small central peak at 30°N/85.7°E. The crater rim is quite sharp and the ejecta blanket can be traced around the crater to a distance of ~200km from the crater center. Most of the crater floor around the central peak is covered by a smooth uniform unit with a lower impact crater population than the surrounding surfaces. Color data show that this smooth unit is darker than the surrounding surfaces. A similar unit can be found on the floor of a complex cluster of 10-56 km diameter craters at 32°N/40°E. With upcoming higher resolution data we will refine our geologic map and will specifically investigate possible formation processes of these smooth units.

  7. Water and carbon dioxide distribution in the 67P/Churyumov-Gerasimenko coma from VIRTIS-M infrared observations

    NASA Astrophysics Data System (ADS)

    Migliorini, A.; Piccioni, G.; Capaccioni, F.; Filacchione, G.; Bockelée-Morvan, D.; Erard, S.; Leyrat, C.; Combi, M. R.; Fougere, N.; Crovisier, J.; Taylor, F. W.; De Sanctis, M. C.; Capria, M. T.; Grassi, D.; Rinaldi, G.; Tozzi, G. P.; Fink, U.

    2016-05-01

    Context. Studying the coma environment of comet 67P/Churyumov-Gerasimenko (67P) is one of the primary scientific goals of the VIRTIS experiment on the ESA Rosetta mission. Aims: The distribution and variability of water vapour and carbon dioxide in the comet's coma are needed to estimate their production rate, abundances in the nucleus, and the spatial distribution of the active regions. Methods: Infrared emission lines from vibrational bands of water and carbon dioxide at 2.67 and 4.27 μm, respectively, were observed by the VIRTIS-M imaging channel and mapped from close to the nucleus up to ~10 km altitude with a resolution of ~40 m/px. A dataset consisting of 74 observations in the 1-5 μm spectral range acquired from 8 to 14 April 2015 when 67P was at a heliocentric distance of 1.9 AU is analysed in this work. A statistical correlation between the gas distribution and the surface's active regions was performed. Results: The maximum H2O emission is observed within 3 km from the nucleus and is mainly concentrated above two active regions, Aten-Babi and Seth-Hapi, while the CO2 distribution appears more uniform with significant emissions coming from both the "head" and southern latitude regions. In the equatorial region, the column densities of both species decrease with altitude, although CO2 decreases more rapidly than H2O. The calculated CO2/H2O column density ratios above Aten-Babi and Seth-Hapi are 2.4 ± 0.6% and 3.0 ± 0.7%, respectively. A value equal to 3.9 ± 1.0% is observed at equatorial latitudes in the region encompassing Imothep. Conclusions: VIRTIS-M has mapped the distribution of water vapour and carbon dioxide around the nucleus of 67P with unprecedented spatial resolution. The different water and carbon dioxide outgassing above the surface, seen in the VIRTIS-M data, might be indicative of a different thermal history of the northern and southern hemispheres of 67P.

  8. Aftershock Seismicity of the 27 February 2010 Mw 8.8 Maule Earthquake Rupture Zone

    NASA Astrophysics Data System (ADS)

    Lange, D.; Tilmann, F. J.; Barrientos, S. E.; Bataille, K.; Beck, S. L.; Bernard, P.; Campos, J. A.; Comte, D.; Haberland, C. A.; Heit, B.; Methe, P.; Peyrat, S.; Rietbrock, A.; Roecker, S.; Schurr, B.; Vilotte, J.

    2010-12-01

    On 27 February 2010 the Mw 8.8 Maule earthquake in Central Chile ruptured a well known seismic gap, which last broke in 1835. Shortly after the mainshock Chilean agencies (UC Santiago, UC Concepción) and the international seismological community (USA (IRIS), France (IPGP), UK (University of Liverpool), Germany (GFZ)) installed a total of 142 portable seismic stations along the whole rupture zone in order to capture the aftershock activity. Here, we present the aftershock distribution based on automatic detection algorithms and picking engines (MPX; STA/LTA) which will be calibrated with a subset of manually picked events. Initial processing of 70 days of continuous data (20 March until 29 May 2010) from IRIS and GFZ stations resulted in the detection of well over 30,000 events. Of these, we consider a higher quality subset of 12,824 hypocentres based on more than 12 automatically picked P arrivals. Because picking errors can be large for the smaller arrivals, the depths of located events are not always reliable, particularly far from the coast. Nevertheless, a few first order features can be identified: 1.) A pronounced cluster of seismicity is apparent at 25-35 km depth and 50-120 km perpendicular distance from the trench (with some NS variation). 2.) A secondary band of seismicity can be identified at 40-50 km depth and ~150-160 km perpendicular trench distance and between 34° and 37°S. Although the secondary band lies along the continuation of the primary one, it is clearly separated from it by a gap with sparse seismicity. It is not yet possible to state whether these events occurred on the plate interface or in the downgoing plate. 3.) Intense crustal seismicity is found in the region of Pichilemu. This region hosted the strongest aftershock (Mw=6.9), a normal faulting event with NW strike. The aftershocks extend from the plate interface to the surface and are aligned on a NNW-SSE oriented band in map view. 4.) An isolated shallow cluster of crustal

  9. MRO CTX-based Digital Terrain Models

    NASA Astrophysics Data System (ADS)

    Dumke, Alexander

    2016-04-01

    In planetary surface sciences, digital terrain models (DTM) are paramount when it comes to understanding and quantifying processes. In this contribution an approach for the derivation of digital terrain models from stereo images of the NASA Mars Reconnaissance Orbiter (MRO) Context Camera (CTX) are described. CTX consists of a 350 mm focal length telescope and 5000 CCD sensor elements and is operated as pushbroom camera. It acquires images with ~6 m/px over a swath width of ~30 km of the Mars surface [1]. Today, several approaches for the derivation of CTX DTMs exist [e. g. 2, 3, 4]. The discussed approach here is based on established software and combines them with proprietary software as described below. The main processing task for the derivation of CTX stereo DTMs is based on six steps: (1) First, CTX images are radiometrically corrected using the ISIS software package [5]. (2) For selected CTX stereo images, exterior orientation data from reconstructed NAIF SPICE data are extracted [6]. (3) In the next step High Resolution Stereo Camera (HRSC) DTMs [7, 8, 9] are used for the rectification of CTX stereo images to reduce the search area during the image matching. Here, HRSC DTMs are used due to their higher spatial resolution when compared to MOLA DTMs. (4) The determination of coordinates of homologous points between stereo images, i.e. the stereo image matching process, consists of two steps: first, a cross-correlation to obtain approximate values and secondly, their use in a least-square matching (LSM) process in order to obtain subpixel positions. (5) The stereo matching results are then used to generate object points from forward ray intersections. (6) As a last step, the DTM-raster generation is performed using software developed at the German Aerospace Center, Berlin. Whereby only object points are used that have a smaller error than a threshold value. References: [1] Malin, M. C. et al., 2007, JGR 112, doi:10.1029/2006JE002808 [2] Broxton, M. J. et al

  10. Protective Yeasts Control V. anguillarum Pathogenicity and Modulate the Innate Immune Response of Challenged Zebrafish (Danio rerio) Larvae

    PubMed Central

    Caruffo, Mario; Navarrete, Natalie C.; Salgado, Oscar A.; Faúndez, Nelly B.; Gajardo, Miguel C.; Feijóo, Carmen G.; Reyes-Jara, Angélica; García, Katherine; Navarrete, Paola

    2016-01-01

    We investigated mechanisms involved in the protection of zebrafish (Danio rerio) larvae by two probiotic candidate yeasts, Debaryomyces hansenii 97 (Dh97) and Yarrowia lypolitica 242 (Yl242), against a Vibrio anguillarum challenge. We determined the effect of different yeast concentrations (104–107 CFU/mL) to: (i) protect larvae from the challenge, (ii) reduce the in vivo pathogen concentration and (iii) modulate the innate immune response of the host. To evaluate the role of zebrafish microbiota in protection, the experiments were performed in conventionally raised and germ-free larvae. In vitro co-aggregation assays were performed to determine a direct yeast-pathogen interaction. Results showed that both yeasts significantly increased the survival rate of conventionally raised larvae challenged with V. anguillarum. The concentration of yeasts in larvae tended to increase with yeast inoculum, which was more pronounced for Dh97. Better protection was observed with Dh97 at a concentration of 106 CFU/mL compared to 104 CFU/mL. In germ-free conditions V. anguillarum reached higher concentrations in larvae and provoked significantly more mortality than in conventional conditions, revealing the protective role of the host microbiota. Interestingly, yeasts were equally (Dh97) or more effective (Yl242) in protecting germ-free than conventionally-raised larvae, showing that protection can be exerted only by yeasts and is not necessarily related to modulation of the host microbiota. Although none of the yeasts co-aggregated with V. anguillarum, they were able to reduce its proliferation in conventionally raised larvae, reduce initial pathogen concentration in germ-free larvae and prevent the upregulation of key components of the inflammatory/anti-inflammatory response (il1b, tnfa, c3, mpx, and il10, respectively). These results show that protection by yeasts of zebrafish larvae challenged with V. anguillarum relates to an in vivo anti-pathogen effect, the modulation of

  11. Aswan site on comet 67P/Churyumov-Gerasimenko: Morphology, boulder evolution, and spectrophotometry

    NASA Astrophysics Data System (ADS)

    Pajola, Maurizio; Oklay, Nilda; La Forgia, Fiorangela; Giacomini, Lorenza; Massironi, Matteo; Bertini, Ivano; El-Maarry, M. R.; Marzari, Francesco; Preusker, Frank; Scholten, Frank; Höfner, Sebastian; Lee, Jui-Chi; Vincent, Jean-Baptiste; Groussin, Olivier; Naletto, Giampiero; Lazzarin, Monica; Barbieri, Cesare; Sierks, Holger; Lamy, Philippe; Rodrigo, Rafael; Koschny, Detlef; Rickman, Hans; Keller, Horst U.; Agarwal, Jessica; A'Hearn, Michael F.; Barucci, Maria A.; Bertaux, Jean-Loup; Cremonese, Gabriele; Da Deppo, Vania; Davidsson, Björn; De Cecco, Mariolino; Debei, Stefano; Ferri, Francesca; Fornasier, Sonia; Fulle, Marco; Güttler, Carsten; Gutierrez, Pedro J.; Hviid, Stubbe F.; Ip, Wing-Huen; Jorda, Laurent; Knollenberg, Jörg; Kramm, J.-Rainer; Küppers, Michael; Kürt, Ekkehard; Lara, Luisa M.; Lin, Zhong-Yi; Lopez Moreno, Jose J.; Magrin, Sara; Michalik, Harald; Mottola, Stefano; Thomas, Nicholas; Tubiana, Cecilia

    2016-07-01

    Aims: We provide a detailed morphological analysis of the Aswan site on comet 67P/Churyumov-Gerasimenko (67P). We derive the size-frequency distribution of boulders ≥2 m and correlate this distribution with the gravitational slopes for the first time on a comet. We perform the spectral analysis of this region to understand if possible surface variegation is related to thedifferent surface textures observable on the different units. Methods: We used two OSIRIS Narrow Angle Camera (NAC) image data sets acquired on September 19 and 22, 2014, with a scale of 0.5 m/px. Gravitational slopes derived from the 3D shape model of 67P were used to identify and interpret the different units of the site. By means of the high-resolution NAC data sets, boulders ≥2.0 m can be unambiguously identified and extracted using the software ArcGIS. Coregistered and photometrically corrected color cubes were used to perform the spectral analyses, and we retrieved the spectral properties of the Aswan units. Results: The high-resolution morphological map of the Aswan site (0.68 km2) shows that this site is characterized by four different units: fine-particle deposits located on layered terrains, gravitational accumulation deposits, taluses, and the outcropping layered terrain. Multiple lineaments are identified on the Aswan cliff, such as fractures, exposed layered outcrops, niches, and terraces. Close to the terrace margin, several arched features observed in plan view suggest that the margin progressively retreats as a result of erosion. The size-frequency of boulders ≥2 m in the entire study area has a power-law index of -3.9 +0.2/-0.3 (1499 boulders ≥2 m/km2), suggesting that the Aswan site is mainly dominated by gravitational events triggered by sublimation and/or thermal insolation weathering causing regressive erosion. The boulder size-frequency distribution versus gravitational slopes indicates that when higher gravitational slope terrains are considered, only boulders ≤10 m

  12. The global size-frequency distribution of boulders > 7 m on Comet 67P Churyumov-Gerasimenko

    NASA Astrophysics Data System (ADS)

    Pajola, Maurizio; Baptiste Vincent, Jean; Lee, Jui-Chi; Ip, Wing-Huen; Lin, Zhong-Yi; Bertini, Ivano; Massironi, Matteo; Simioni, Emanuele; Barbieri, Cesare; Cremonese, Gabriele; Marzari, Francesco; Naletto, Giampiero; Giacomini, Lorenza; Jorda, Laurent; Thomas, Nicholas; Pommerol, Antoine; Kueppers, Michael; Moissl, Richard; Besse, Sebastien; Sierks, Holger

    2015-04-01

    After a ten years journey through the Solar System, the ESA Rosetta spacecraft reached on 6 August 2014 its primary target, the Jupiter family comet 67P/Churyumov-Gerasimenko, hereafter 67P. During the approaching phase, several images of the nucleus of comet 67P, captured by the OSIRIS scientific imaging camera, have been taken to study its structure, activity and the surface morphology. The close distance between spacecraft and comet, and the high resolution of our images, provided a unique opportunity to study features which could not have been detected before on other comets, but yet hold key parameters to derive the physical properties of the surface. We made use of the images acquired by the OSIRIS Narrow Angle Camera, NAC, on 5 and 6 August 2014 in order to study the statistical size-frequency distribution and the morphological properties of both clustered and isolated roundish structures ("boulders") scattered all over the currently illuminated side of the comet (70% of the total surface). Such dataset has been taken at a distance ranging between 131.45 and 109.76 km far from the comet center and the scale of these images (2.44 - 2.03 m/px) is such that boulders ≥ 7 m can be unequivocally identified and extracted. These images are the last ones where the entire comet is 2048 x 2048 pixels full frame and they cover a complete comet rotation (12.4 h), hence providing the possibility to derive a global size-frequency distribution statistics of the presently illuminated surface of 67P. A total amount of 3526 boulders has been identified on the surface of the comet: i) 2218 belonging to the big lobe, body, ii) 1115 boulders are located on the small lobe, head, while iii) 213 boulders belong to the transition region between the two lobes, called the neck. Here, global cumulative size-frequency distributions of boulders per square km are presented, together with specific and localized areas distributions. Moreover we indicate the different formation processes

  13. Determinants of viral oncogenes E6-E7 mRNA over-expression in a population-based large sample of women infected by high risk HPV types.

    PubMed

    Giorgi Rossi, Paolo; Bisanzi, Simonetta; Allia, Elena; Mongia, Alessandra; Carozzi, Francesca; Gillio-Tos, Anna; De Marco, Laura; Ronco, Guglielmo; Gustinucci, Daniela; Del Mistro, Annarosa; Frayle, Helena; Iossa, Anna; Fantacci, Giulia; Pompei, Giampaolo; Cesarini, Elena; Bulletti, Simonetta; Passamonti, Basilio; Rizzi, Martina; Penon, Maria Gabriella; Barca, Alessandra; Benevolo, Maria

    2017-01-18

    Cervical cancer screening by HPV-DNA testing with cytology triage is more effective than cytology testing. Compared to cytology, the HPV-DNA test higher sensitivity, that allows better protection with longer intervals, makes it necessary to triage the women with a positive result to compensate its lower specificity.We are conducting a large randomized clinical trial (New Technologies for Cervical Cancer 2, NTCC2) within organized population-based screening programs in Italy using HPV-DNA as primary screening test, to evaluate, by Aptima HPV Assay (Hologic), HPV E6-E7 mRNA as triage test in comparison to cytology.By the end of June 2016, data are available for 35877 out of 38535enrolled women, 2651 (7.4%) of whom are HPV-DNA positive. Among them, 2453 samples were tested also by Aptima, and 1649 (67.2%) gave a positive result. The proportion of mRNA positivity was slightly higher among samples tested for HPV-DNA by Cobas 4800 HPV (Roche) than by HC2 assay (Qiagen) .In our setting, the observed E6-E7 mRNA positivity rate, if used as a triage test, would bring to an immediate referral to colposcopy of about 4-5%. This value is higher than that observed with cytology triage for both immediate and delayed referral to colposcopy. Only showing a very high sensitivity, thus allowing longer interval for HPV-DNA positive/HPV-mRNA negative women, a triage by this test might be efficient in comparison to cytology.

  14. Arterial ammonia levels: Prognostic marker in traumatic hemorrhage

    PubMed Central

    Singla, Anurag; Kaur, Satinder; Kaur, Navjot; Gill, CS

    2016-01-01

    Background: In blunt trauma, extent of hemorrhage cannot be determined by physical examination, and vital signs may also not give clear picture in all the patients, especially young healthy ones. Hemorrhagic shock has been reported to increase blood ammonia levels. Arterial ammonia was analyzed in blunt trauma abdomen patients and correlated with shock index (SI). Its predictive value was determined for timely decision of intervention. Materials and Methods: Hundred blunt trauma abdomen patients presented in the emergency ward of tertiary care hospital were included in the study. Group I comprised 62 patients requiring either blood transfusion ≥2 units and/or intervention to control bleeding within 24 h following admission. Group II had 38 patients: Not requiring transfusion/intervention during hospital stay. Arterial blood sample was taken immediately after admission; ammonia was analyzed within 20 min of sampling on Cobas 6000 (Roche). SI was calculated. Predictive value of ammonia was determined using receiver operating characteristic curve. Results: Ammonia levels and SI were significantly (P < 0.001) higher in Group I compared to Group II patients (68.55 ± 14.36 umol/L vs. 37.55 ± 7.41 umol/L and 1.28 ± 0.5 vs. 0.74 ± 0.12, respectively). Significantly higher number of patients in Group I (88.7% vs. 13%) had SI > 0.9. Ammonia levels were significantly higher in patients with complications and in those expired. Conclusions: Ammonia levels were significantly higher in patients requiring blood transfusion/intervention in 24 h of admission. The best cutoff value to maximize sensitivity and specificity was ammonia >58.85 μmol/L. Ammonia estimation at admission can be clinically significant indicator of traumatic hemorrhage needing intervention. PMID:27857892

  15. A new method for the determination of carboxyhemoglobin in blood of newborns. Possible clinical implications of elevated levels.

    PubMed

    Zwart, A; Siepel, H; Heerspink, W

    1990-01-01

    Spectral differences between hemoglobin derivatives from adult-(HbA) and fetal-hemoglobin (HbF) make the accurate determination of carboxyhemoglobin (COHb) troublesome in blood of newborns. Only the newest dedicated instruments for the determination of COHb take these differences into account. However, since there are virtually no spectral differences between both hemoglobins in the deoxygenated state, reduction of neonatal blood with sodium dithionite eliminates that spectrophotometric error. Based on this principle, an easy, fast and accurate method for the determination of COHb in minimal amounts of blood was developed; equally well suited for blood of newborns and adults. The instrument used with this new method is a general purpose centrifugal clinical chemistry analyzer (COBAS-FARA, Roche, Basle, Switzerland). After the reduction of blood with sodium dithionite, a simple two component system (Hb and COHb) is formed, which can be spectrophotometrically quantitated by measuring at two suitable wavelengths, i.e., 579 nm and 534 nm. The COHb fraction is calculated with the help of: COHb % = 177.73.(A534/A579)-176.66. Comparison with the OSM3 Hemoximeter (Radiometer A/S, Denmark) for 145 adult blood samples with varying COHb levels (0-30%) yielded a mean difference in COHb % of about 0.06% (SD = 0.38). For fetal blood (N = 63) about the same difference was found when the OSM3 was used in the so-called fetal mode, while comparison with the regular adult mode yielded a difference of about 3.1%. This indicates that the new method is indeed not disturbed by the spectral differences between HbA and HbF.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. Reference intervals for serum cystatin C and serum creatinine in adults.

    PubMed

    Erlandsen, E J; Randers, E; Kristensen, J H

    1998-06-01

    The aim of this study was to establish reference intervals for cerum cystatin C and serum creatinine in adults. Blood samples were collected from 270 healthy blood donors (135 men and 135 women between 20 and 65 years old with 15 men and 15 women in each five-year-interval). Serum cystatin C was analyzed using an automated particle-enhanced immunoassay (DAKO Cystatin C PET kit) on the Cobas Mira S analyzer. Serum creatinine was analyzed using the Vitros Creatinine Slide, an enzymatic method on the Vitros 950 chemistry analyzer. The calculated reference intervals for serum cystatin C were 0.62-1.15 mg/l in women (median 0.84 mg/l, range 0.56-1.29 mg/l) and 0.51-1.25 mg/l in men (median 0.87 mg/l, range 0.42-1.39 mg/l). The Mann-Whithey U-test revealed no gender-related difference for cystatin C (p = 0.48). A common reference interval in women and men was calculated to be 0.54-1.21 mg/l (median 0.85 mg/l, range 0.42-1.39 mg/l). The non-parametric reference interval for serum creatinine was 57-95 mumol/l in women (median 72 mumol/l, range 44-105 mumol/l) and 69-111 mumol/l in men (median 89 mumol/l, range 58-123 mumol/l).

  17. Prediction of the hematocrit of dried blood spots via potassium measurement on a routine clinical chemistry analyzer.

    PubMed

    Capiau, Sara; Stove, Veronique V; Lambert, Willy E; Stove, Christophe P

    2013-01-02

    The potential of dried blood spot (DBS) sampling as an alternative for classical venous sampling is increasingly recognized, with multiple applications in, e.g., therapeutic drug monitoring and toxicology. Although DBS sampling has many advantages, it is associated with several issues, the hematocrit (Hct) issue being the most widely discussed challenge, given its possible strong impact on DBS-based quantitation. Hitherto, no approaches allow Hct prediction from nonvolumetrically applied DBS. Following a simple and rapid extraction protocol, K(+) levels from 3 mm DBS punches were measured via indirect potentiometry, using the Roche Cobas 8000 routine chemistry analyzer. The extracts' K(+) concentrations were used to calculate the approximate Hct of the blood used to generate DBS. A linear calibration line was established, with a Hct range of 0.19 to 0.63 (lower limit of quantification, LLOQ, to upper limit of quantification, ULOQ). The procedure was fully validated; the bias and imprecision of quality controls (QCs) at three Hct levels and at the LLOQ and ULOQ was less than 5 and 12%, respectively. In addition, the influence of storage (pre- and postextraction), volume spotted, and punch homogeneity was evaluated. Application on DBS from patient samples (n = 111), followed by Bland and Altman, Passing and Bablok, and Deming regression analysis, demonstrated a good correlation between the "predicted Hct" and the "actual Hct". After correcting for the observed bias, limits of agreement of ±0.049 were established. Incurred sample reanalysis demonstrated assay reproducibility. In conclusion, potassium levels in extracts from 3 mm DBS punches can be used to get a good prediction of the Hct, one of the most important "unknowns" in DBS analysis.

  18. Variables that influence HIV-1 cerebrospinal fluid viral load in cryptococcal meningitis: a linear regression analysis

    PubMed Central

    2009-01-01

    Background The central nervous system is considered a sanctuary site for HIV-1 replication. Variables associated with HIV cerebrospinal fluid (CSF) viral load in the context of opportunistic CNS infections are poorly understood. Our objective was to evaluate the relation between: (1) CSF HIV-1 viral load and CSF cytological and biochemical characteristics (leukocyte count, protein concentration, cryptococcal antigen titer); (2) CSF HIV-1 viral load and HIV-1 plasma viral load; and (3) CSF leukocyte count and the peripheral blood CD4+ T lymphocyte count. Methods Our approach was to use a prospective collection and analysis of pre-treatment, paired CSF and plasma samples from antiretroviral-naive HIV-positive patients with cryptococcal meningitis and assisted at the Francisco J Muñiz Hospital, Buenos Aires, Argentina (period: 2004 to 2006). We measured HIV CSF and plasma levels by polymerase chain reaction using the Cobas Amplicor HIV-1 Monitor Test version 1.5 (Roche). Data were processed with Statistix 7.0 software (linear regression analysis). Results Samples from 34 patients were analyzed. CSF leukocyte count showed statistically significant correlation with CSF HIV-1 viral load (r = 0.4, 95% CI = 0.13-0.63, p = 0.01). No correlation was found with the plasma viral load, CSF protein concentration and cryptococcal antigen titer. A positive correlation was found between peripheral blood CD4+ T lymphocyte count and the CSF leukocyte count (r = 0.44, 95% CI = 0.125-0.674, p = 0.0123). Conclusion Our study suggests that CSF leukocyte count influences CSF HIV-1 viral load in patients with meningitis caused by Cryptococcus neoformans.

  19. Paraprotein interference with turbidimetric gentamicin assay

    PubMed Central

    Bassett, Kendra; Brown, Nigel

    2015-01-01

    Introduction Gentamicin due to its low level of resistance and rapid bactericidal activity is commonly used to treat gram-negative bacteria. However, due to its toxic effects it needs to be monitored. To date, no interference has been reported with gentamicin assays. Materials and methods A patient with leg cellulitis and sepsis received a single dose of gentamicin and a sample was sent for gentamicin analysis. The sample showed high blank absorbance readings on Beckman DxC800 and DC800 analysers with various dilutions. A second sample was received and analysed on a Roche Cobas system to obtain a result. A third sample was received 107 hours later with the same results and this sample was then analysed neat and post ethanol precipitation on all the turbidimetric assays available on the DxC800 analyser. Results The high blank absorbance was observed upon addition of the reactive reagents due to protein precipitation. Although not obvious from the patient protein results, it was shown the presence of high IgM paraprotein, 18.9 g/L (reference range 0.4-2.3 g/L) was the cause of precipitation, giving high blank readings. Of all the other turbidimetric assays, only vancomicin and valproate showed similar high blank absorbance readings. To be able to provide more rapid results it was shown ethanol could be used as a precipitant of proteins in both calibrators and patient samples with acceptable recovery. Conclusion IgM paraprotein was identified as the cause of interference with the gentamicin, vancomicin and valproate assays. Protein interference in these assays can be overcome by precipitation with ethanol. PMID:25672475

  20. Serum and urine concentrations of flunitrazepam and metabolites, after a single oral dose, by immunoassay and GC-MS.

    PubMed

    Snyder, H; Schwenzer, K S; Pearlman, R; McNally, A J; Tsilimidos, M; Salamone, S J; Brenneisen, R; ElSohly, M A; Feng, S

    2001-01-01

    A clinical study was conducted to assess the ability of commercially available immunoassays to detect flunitrazepam (FNP) in plasma and urine samples and to compare the results with those obtained by gas chromatography-mass spectrometry (GC-MS). The clinical study consisted of four individuals (two male and two female) who had taken a single 2-mg dose of FNP. Serum was collected over a 48-h period and urine was collected over a 72-h period. The serum and urine samples were analyzed by the COBAS INTEGRA Serum Benzodiazepines assay (SBENZ), the TDx serum and urine Benzodiazepines assay, and GC-MS. The GC-MS procedure was developed for analysis of FNP and metabolites in plasma and urine using an acid hydrolysis step resulting in the formation of specific benzophenones corresponding to FNP and its metabolites. The relative sensitivities of the assays for the detection of FNP and metabolites in serum and urine were GC-MS > SBENZ > TDx. The immunoassay results for serum samples showed peak concentrations of FNP metabolites at 8 h after FNP ingestion for three individuals and at about 1 h for the fourth individual. The GC-MS, SBENZ, and TDx urine immunoassays detected drug above the stated limit of detection (LOD) in 44, 41, and 35 serial FNP urine samples, respectively. FNP metabolites were detected in urine samples with all three assays for up to 72 h after a 2-mg dose. The improved detection rate with the SBENZ assay as compared to the TDx assay is likely explained by its higher cross-reactivity with the major metabolite, 7-amino-flunitrazepam (7-amino-FNP), and its lower LOD.

  1. Multicenter Comparison of Seven 25OH Vitamin D Automated Immunoassays

    PubMed Central

    Lippi, Giuseppe; Salvagno, Gian Luca; Fortunato, Antonio; Dipalo, Mariella; Aloe, Rosalia; Da Rin, Giorgio; Giavarina, Davide

    2015-01-01

    Summary Background The measurement of 25OH vitamin D continues to grow in clinical laboratories. The aim of this multi-center study was to compare the results of seven automated commercial immunoassays with a reference HPLC technique. Methods One hundred and twenty consecutive outpatient serum samples were centrifuged, divided in aliquots, frozen and shipped to the participating laboratories. 25OH Vitamin D was measured with a reference HPLC system and with seven automated commercial immunoassays (Roche Cobas E601, Beckman Coulter Unicel DXI 800, Ortho Vitros ES, DiaSorin Liaison, Siemens Advia Centaur, Abbott Architect i System and IDS iSYS). Results Compared to the reference method, the regression coefficients ranged from 0.923 to 0.961 (all p<0.001). The slope of Deming fit ranged from 0.95 to 1.06, whereas the intercept was comprised between −15.2 and 9.2 nmol/L. The bias from the reference HPLC technique varied from −14.5 to 8.7 nmol/L. The minimum performance goal for bias was slightly exceeded by only one immunoassay. The agreement between HPLC and the different immunoassays at 50 nmol/L 25OH Vitamin D varied between 0.61 and 0.85 (all p<0.001). The percentage of samples below this cut-off was significantly different with only one immunoassay. Conclusions The excellent correlation with the reference HPLC technique attests that all seven automated immunoassays may be reliably used for routine assessment of 25OH-D in clinical laboratories. The significant bias among the different methods seems mostly attributable to the lack of standardization and calls for additional efforts for improving harmonization of 25OH-D immunoassays. PMID:28356846

  2. Importance of very early HCV RNA kinetics for prediction of treatment outcome of highly effective all oral direct acting antiviral combination therapy.

    PubMed

    Sarrazin, Christoph; Wedemeyer, Heiner; Cloherty, Gavin; Cohen, Daniel E; Chevaliez, Stephane; Herman, Christine; Bernstein, Barry; Pawlotsky, Jean Michel

    2015-03-01

    Interferon-free combination therapies lead to rapid suppression of HCV RNA early during treatment. The potential to predict virologic response and failure as well as to guide treatment duration with measurement of HCV RNA very early during treatment by highly sensitive assays is not well known. In 11 IL28B CC (rs12979860) patients infected with HCV genotype 1, who received DAA combination therapy with the NS3 protease inhibitor ABT-450/r together with the non-nucleoside NS5B polymerase inhibitor ABT-072 and ribavirin for 12 weeks, HCV RNA was assessed frequently by the RealTime HCV (ART) and the High-Pure-System/Cobas TaqMan (HPS) assays during and after treatment. Overall, at 33 of 131 time points during treatment residual HCV RNA was detectable by ART but undetectable by HPS while the converse was observed in only two samples. Of the two patients who experienced virologic relapse, one patient had residual viremia at week 6 of treatment by ART only while the other patient never had undetectable HCV RNA by the ART assay. However, residual viremia was also observed by ART as late as therapy weeks 9, 10 and 12 in patients with subsequent sustained virologic response. In patients with sustained response no viremia was observed at multiple time points during post-treatment follow up by either assay. The higher sensitivity of the ART in comparison to the HPS assay may be associated with more frequent detection of residual viremia during highly effective, interferon-free combination therapies. However, the significance of this finding in predicting virologic failure appears to be limited.

  3. Correlation of Serum Cystatin C with Glomerular Filtration Rate in Patients Receiving Platinum-Based Chemotherapy.

    PubMed

    Cavalcanti, Ernesta; Barchiesi, Vittoria; Cerasuolo, Dionigio; Di Paola, Flaviano; Cantile, Monica; Cecere, Sabrina Chiara; Pignata, Sandro; Morabito, Alessandro; Costanzo, Raffaele; Di Maio, Massimo; Perrone, Francesco

    2016-01-01

    Objectives. Serum cystatin C seems to be an accurate marker of glomerular filtration rate (GFR) compared to serum creatinine. The aim of this work was to explore the possibility of using serum cystatin C instead of serum creatinine to early predict renal failure in cancer patients who received platinum based chemotherapy. Design and Methods. Serum creatinine, serum cystatin C concentrations, and GFR were determined simultaneously in 52 cancer patients received carboplatin-based or cisplatin-based chemotherapy. Serum creatinine was assayed on Cobas C6000-Roche, serum cystatin C assay was performed on AIA 360-Tosoh, and GFR was determined in all patients, before the first cycle of chemotherapy and before the subsequent administrations. Results. In the overall series, for the prediction of a fall of GFR < 80 mL/min/1.73 m(2), the AUC of the ROC curve for cystatin C was 0,667 and the best threshold was 1.135 mg/L (sensitivity 90.5%, specificity 61.1%). For a GFR fall < 60 mL/min/1.73 m(2), the AUC of ROC curve for cystatin C was 74.3% and the best threshold was 1.415 mg/L (sensitivity 66.7%, specificity 73.2%). Conclusions. Baseline cystatin C values were not able to predict renal failure during subsequent treatment. In conclusion, serum cystatin C is not a reliable early marker to efficiently predict renal failure in patients receiving chemotherapy.

  4. Urinary orosomucoid: validation of an automated immune turbidimetric test and its possible clinical use

    PubMed Central

    Kustán, Péter; Szirmay, Balázs; Horváth-Szalai, Zoltán; Ludány, Andrea; Lakatos, Ágnes; Mühl, Diána; Christensen, Per Hjort; Miseta, Attila; Kovács, Gábor L.; Kőszegi, Tamás

    2016-01-01

    Introduction Besides routine serum markers of inflammatory diseases, the diagnostic potential of selected urinary proteins has not been fully exploited yet. Former studies revealed that urinary orosomucoid (u-ORM) might have complementary information in inflammatory disorders. Our aim was to develop and validate a fully automated method for u-ORM measurements and to evaluate its potential clinical impact on systemic inflammatory diseases. Materials and methods A particle-enhanced immune turbidimetric assay was validated for a Cobas 8000/c502 analyzer to determine u-ORM levels. Spot urine samples from 72 healthy individuals, 28 patients with Crohn’s disease and 30 septic patients were studied. Results Our assay time was 10 minutes and the detection limit of u-ORM was 0.02 mg/L. The intra- and inter-assay imprecision expressed as CV was less than 5%, and the recovery ranged between 95–103%. Within 10 to 60 years of age, a preliminary reference range for urinary orosomucoid/creatinine ratio (u-ORM/u-CREAT) was found to be 0.08 (0.01–0.24) mg/mmol [median (2.5–97.5 percentiles)]. Compared to controls, a five-fold increase of u-ORM/u-CREAT values in Crohn’s disease and approximately a 240-fold increase in sepsis were observed. Conclusions We set up a fast, sensitive and precise turbidimetric approach for automated u-ORM determination. Our highly sensitive assay is ideal for routine u-ORM measurements and might be a potential novel laboratory test in the management of systemic inflammatory processes. PMID:27812309

  5. Correlation of Serum Cystatin C with Glomerular Filtration Rate in Patients Receiving Platinum-Based Chemotherapy

    PubMed Central

    Barchiesi, Vittoria; Cerasuolo, Dionigio; Di Paola, Flaviano; Cantile, Monica; Cecere, Sabrina Chiara; Pignata, Sandro; Morabito, Alessandro; Costanzo, Raffaele; Di Maio, Massimo; Perrone, Francesco

    2016-01-01

    Objectives. Serum cystatin C seems to be an accurate marker of glomerular filtration rate (GFR) compared to serum creatinine. The aim of this work was to explore the possibility of using serum cystatin C instead of serum creatinine to early predict renal failure in cancer patients who received platinum based chemotherapy. Design and Methods. Serum creatinine, serum cystatin C concentrations, and GFR were determined simultaneously in 52 cancer patients received carboplatin-based or cisplatin-based chemotherapy. Serum creatinine was assayed on Cobas C6000-Roche, serum cystatin C assay was performed on AIA 360-Tosoh, and GFR was determined in all patients, before the first cycle of chemotherapy and before the subsequent administrations. Results. In the overall series, for the prediction of a fall of GFR < 80 mL/min/1.73 m2, the AUC of the ROC curve for cystatin C was 0,667 and the best threshold was 1.135 mg/L (sensitivity 90.5%, specificity 61.1%). For a GFR fall < 60 mL/min/1.73 m2, the AUC of ROC curve for cystatin C was 74.3% and the best threshold was 1.415 mg/L (sensitivity 66.7%, specificity 73.2%). Conclusions. Baseline cystatin C values were not able to predict renal failure during subsequent treatment. In conclusion, serum cystatin C is not a reliable early marker to efficiently predict renal failure in patients receiving chemotherapy. PMID:28078200

  6. p,p'-Dichlorodiphenyltrichloroethane (p,p'-DDT) and p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE) repress prostate specific antigen levels in human prostate cancer cell lines.

    PubMed

    Wong, Lilian I L; Labrecque, Mark P; Ibuki, Naokazu; Cox, Michael E; Elliott, John E; Beischlag, Timothy V

    2015-03-25

    Despite stringent restrictions on their use by many countries since the 1970s, the endocrine disrupting chemicals, DDT and DDE are still ubiquitous in the environment. However, little attention has been directed to p,p'-DDT and the anti-androgen, p,p'-DDE on androgen receptor (AR) target gene transcription in human cells. Inhibitors of androgenic activity may have a deleterious clinical outcome in prostate cancer screens and progression, therefore we determined whether environmentally relevant concentrations of p,p'-DDT and p,p'-DDE negatively impact AR-regulated expression of prostate-specific antigen (PSA), and other AR target genes in human LNCaP and VCaP prostate cancer cells. Quantitative real-time PCR and immuno-blotting techniques were used to measure intracellular PSA, PSMA and AR mRNA and protein levels. We have shown for the first time that p,p'-DDT and p,p'-DDE repressed R1881-inducible PSA mRNA and protein levels in a dose-dependent manner. Additionally, we used the fully automated COBAS PSA detection system to determine that extracellular PSA levels were also significantly repressed. These chemicals achieve this by blocking the recruitment of AR to the PSA promoter region at 10 μM, as demonstrated by the chromatin immunoprecipitation (ChIP) in LNCaP cells. Both p,p'-DDT and p,p'-DDE repressed R1881-inducible AR protein accumulation at 10 μM. Thus, we conclude that men who have been exposed to either DDT or DDE may produce a false-negative PSA test when screening for prostate cancer, resulting in an inaccurate clinical diagnosis. More importantly, prolonged exposure to these anti-androgens may mimic androgen ablation therapy in individuals with prostate cancer, thus exacerbating the condition by inadvertently forcing adaptation to this stress early in the disease.

  7. Comparative Study of Serum Copper, Iron, Magnesium, and Zinc in Type 2 Diabetes-Associated Proteinuria.

    PubMed

    Khan, Farah Aziz; Al Jameil, Noura; Arjumand, Sadia; Khan, Mohammad Fareed; Tabassum, Hajera; Alenzi, Naif; Hijazy, Sereen; Alenzi, Samyah; Subaie, Sahar; Fatima, Sabiha

    2015-12-01

    Trace element (TE) disturbances are well noted in type 2 diabetes mellitus (T2DM) and its associated complications. In present study, the effect of proteinuria on serum copper (Cu), iron (Fe), magnesium (Mg), and zinc (Zn) in T2DM patients with and without proteinuria was seen. Total subjects were aged between 30 and 90 years; 73 had proteinuria, 76 had T2DM with proteinuria, 76 had T2DM, and 75 were controls. Serum Cu(II), Fe(III), Mg(II), and Zn(II) were assayed by inductively coupled plasma optical emission spectrometer (ICP-OES). Urinary albumin estimation was performed by turbidimetric method. Other biochemical parameters were analyzed by ROCHE Module COBAS 6000 analyzer. Statistical analysis was performed using analysis of variance (ANOVA) at P<0.0001 followed by t test. Pearson correlation was applied to estimate the effect of proteinuria on TE. Serum Cu(II) level was increased in T2DM patients with proteinuria while Fe(III) was found elevated in T2DM (P<0.0001) compared to control groups. Zn(II) and Mg(II) were significantly low in proteinuria, T2DM with proteinuria, and T2DM (P<0.0001) compare to controls. Serum Cu(II) showed strong positive association with albumin creatinine ratio (ACR) in T2DM with proteinuria group and T2DM group (P<0.01). Fe(III) was positively and Zn(II) was negatively associated with ACR at P<0.10, in T2DM with proteinuria group. Mg(II) was negatively linked with ACR P<0.01 in proteinuria, T2DM with proteinuria, and T2DM group. TE were observed more disturbed in T2DM with proteinuria group, thus considered to be the part of T2DM routine checkup and restricts the disease towards its progression.

  8. Differential Detection of Human Papillomavirus Genotypes and Cervical Intraepithelial Neoplasia by Four Commercial Assays

    PubMed Central

    Bonde, Jesper; Preisler, Sarah; Ejegod, Ditte; Rygaard, Carsten; Lynge, Elsebeth

    2016-01-01

    Laboratories now can choose from >100 human papillomavirus (HPV) assays for cervical screening. Our previous analysis based on the data from the Danish Horizon study, however, showed that four widely used assays, Hybrid Capture 2 (HC2), cobas, CLART, and Aptima, frequently do not detect the same HPV infections. Here, we determined the characteristics of the concordant samples (all four assays returning a positive HPV test result) and discordant samples (all other HPV-positive samples) in primary cervical screening at 30 to 65 years of age (n = 2,859) and in a concurrent referral population from the same catchment area (n = 885). HPV testing followed the manufacturers' protocols. Women with abnormal cytology were managed according to the routine recommendations. Cytology-normal/HPV-positive women were invited for repeated testing in 18 months. Screening history and histologically confirmed cervical intraepithelial neoplasia (CIN) in 2.5 years after the baseline testing were determined from the national pathology register. HPV-positive women undergoing primary screening having concordant samples were more likely to harbor high-risk infections and less likely to harbor only low-risk infections than women with discordant samples. Additionally, assay signal strengths were substantially higher in concordant samples. More than 80% of ≥CIN2 results were found for women with concordant samples, and no ≥CIN2 results were found when the infection was detected by only one assay. These patterns were similar in the referral population despite the younger age and higher number of HPV infections. HPV test result discordance identified a cluster of low-risk HPV infections that were hardly ever associated with high-grade CIN and, almost exclusively, represented false-positive screening findings. PMID:27535689

  9. Usage Pattern and Serum Level Measurement of Amikacin in the Internal Medicine Ward of the Largest Referral Hospital in the South of Iran: A Pharmacoepidemiological Study

    PubMed Central

    Namazi, Soha; Sagheb, Mohammad Mahdi; Hashempour, Mohammad Mahdi; Sadatsharifi, Arman

    2016-01-01

    Background: The inappropriate use of aminoglycosides has harmful effects such as the development of resistant pathogens and the incidence of nephrotoxicity and ototoxicity. Therefore, drug utilization evaluation of these drugs may improve their usage remarkably. The aim of this study was to assess the usage pattern of amikacin in an internal medicine ward. Methods: This cross-sectional study was conducted in the Internal Medicine Ward of Nemazee Teaching Hospital, Shiraz, Iran, in 2011. The guideline for amikacin use was approved by the institutional Pharmacy and Therapeutics Committee, and the study criteria were developed to assess several parameters involved in amikacin therapy such as appropriateness of drug use, dosage, duration of therapy, toxicity monitoring, and serum concentration assay. Serum concentration was assayed using a Cobas Mira AutoAnalyzer. Clinical and paraclinical parameters such as glomerular filtration rate, culture, microbial sensitivity, white blood cell count, and fever were collected. Results: Sixty-three patients were evaluated. Fifty-seven percent of the patients needed dose readjustment; however, it was not performed for 89% of them. Culture between 48 and 72 hours after amikacin administration was not controlled for 79% of the patients. In 19% of the patients, optimum therapeutic effect was not achieved. The mean±SD of the trough and peak concentrations was 7.63±5.4 μg/mL and 15.67±7.79 μg/mL, respectively. Forty-five percent of the trough and 38% of the peak levels were within the therapeutic range. The overall adherence of amikacin usage to the guideline was only 48%. Conclusion: To achieve appropriate treatment and prevent toxic effects, we recommend that pharmacokinetic dosing methods, amikacin guideline, and serum monitoring be considered. PMID:27217603

  10. Performance of two updated blood glucose monitoring systems: an evaluation following ISO 15197:2013.

    PubMed

    Pleus, Stefan; Baumstark, Annette; Rittmeyer, Delia; Jendrike, Nina; Haug, Cornelia; Freckmann, Guido

    2016-05-01

    Objective For patients with diabetes, regular self-monitoring of blood glucose (SMBG) is essential to ensure adequate glycemic control. Therefore, accurate and reliable blood glucose measurements with SMBG systems are necessary. The international standard ISO 15197 describes requirements for SMBG systems, such as limits within which 95% of glucose results have to fall to reach acceptable system accuracy. The 2013 version of this standard sets higher demands, especially regarding system accuracy, than the currently still valid edition. ISO 15197 can be applied by manufacturers to receive a CE mark for their system. Research design and methods This study was an accuracy evaluation following ISO 15197:2013 section 6.3 of two recently updated SMBG systems (Contour * and Contour TS; Bayer Consumer Care AG, Basel, Switzerland) with an improved algorithm to investigate whether the systems fulfill the requirements of the new standard. For this purpose, capillary blood samples of approximately 100 participants were measured with three test strip lots of both systems and deviations from glucose values obtained with a hexokinase-based comparison method (Cobas Integra † 400 plus; Roche Instrument Center, Rotkreuz, Switzerland) were determined. Percentages of values within the acceptance criteria of ISO 15197:2013 were calculated. This study was registered at clinicaltrials.gov (NCT02358408). Main outcome Both updated systems fulfilled the system accuracy requirements of ISO 15197:2013 as 98.5% to 100% of the results were within the stipulated limits. Furthermore, all results were within the clinically non-critical zones A and B of the consensus error grid for type 1 diabetes. Conclusions The technical improvement of the systems ensured compliance with ISO 15197 in the hands of healthcare professionals even in its more stringent 2013 version. Alternative presentation of system accuracy results in radar plots provides additional information with certain advantages. In addition

  11. Prevalence and clinical relevance of occult hepatitis B in the fibrosis progression and antiviral response to INF therapy in HIV-HCV-coinfected patients.

    PubMed

    Laguno, Montserrat; Larrousse, Maria; Blanco, José Luis; Leon, Agathe; Milinkovic, Ana; Martínez-Rebozler, Maria; Loncá, Montserrat; Martinez, Esteban; Sanchez-Tapias, Jose Maria; de Lazzari, Elisa; Gatell, José Maria; Costa, Josep; Mallolas, Josep

    2008-04-01

    Occult hepatitis B virus (HBV) infection is diagnosed when HBc antibodies (HBcAb) and HBV DNA are detectable in serum while hepatitis B surface antigen (HBsAg) is not. This situation has been frequently described in patients with chronic hepatitis C virus (HCV) infection. The objective of this study was to evaluate the prevalence of occult hepatitis B in HIV-HCV-coinfected patients and its clinical relevance in liver histology and viral response after interferon therapy for HCV. A total of 238 HIV-HCV-infected patients,negative for HBsAg, were included. Serum samples were analyzed for the presence of HBV DNA and HBcAb.HBV DNA quantification was determined with the Cobas TaqMan HBV Test (detection limit 6 IU/ml). Data from liver biopsy and laboratory tests were also analyzed. HBcAb resulted in 142 (60%) patients, being the independent associated factors: male gender, previous history of intravenous drug use, age, CD4 count,and HAV antibody presence. Among 90 HBcAb patients that we could analyze, HBV DNA was positive in 15 (16.7% of occult hepatitis B infection in this group, and 6.3% in the whole HIV-HCV cohort studied). No baseline factors, liver histology, or HCV therapy response were related to the presence of HBV DNA. We found that occult hepatitis B is a frequent condition present in at least 6.3% of our HCV-HIV patients and in more than 16% of those with HBcAb. Despite the high prevalence, this phenomenon does not seem to affect the clinical evolution of chronic hepatitis C or modify the viral response to interferon-based HCV therapies

  12. Investigation de l'anisotropie du gap supraconducteur dans les composes Ba(Fe(1-x)Co(x))2As2, Ba(1-x)K(x)Fe2As2, LiFeAs et Fe1-deltaTe(1-x)Se(x)

    NASA Astrophysics Data System (ADS)

    Reid, Jean-Philippe

    ommaire La structure du gap supraconducteur et sa modulation sont intimement liees au potentiel d'interaction responsable de l'appariement des electrons d'un supraconducteur. Ainsi, l'etude de la structure du gap-SC et de sa modulation permettent de faire la lumiere sur la nature du mecanisme d'appariement des electrons. A cet egard, les resultats experimentaux des supraconducteurs a base de fer ne cadrent pas dans un seul ensemble, ce qui est en opposition au gap-SC universel des cuprates. Dans ce qui suit, nous presenterons une etude systematique du gap-SC pour plusieurs pnictides. En effet, en utilisant la conductivite thermique, une sonde directionnelle du gap-SC, nous avons ete en mesure de reveler la structure du gap-SC pour les composes suivants : Ba1-xKxFe 2As2, Ba(Fe1-xCo x)2As2, LiFeAs et Fe1-deltaTe 1-xSex. L'etude de ces quatre composes, de trois differentes familles structurales, a pu etablir un tableau partiel mais tres exhaustif de la structure du gap-SC de pnictides. En effet, tel qu'illustre dans cette these, ces quatre composes ne possedent aucun noeud dans leur structure du gap-SC a dopage optimal. Toutefois, a une concentration differente de celle optimale pour les composes K-Ba122 et Co-Ba122, des noeuds apparaissent sur la surface de Fermi, aux extremites 'du dome supraconducteur. Ceci suggere fortement que, pour ces composes, la presence de noeuds sur la surface de Fermi est nuisible a la phase supraconductrice. Mots-cles: Supraconducteurs a base de fer, Pnictides, Structure du gap supraconducteur, Conductivite thermique

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

    PubMed

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

    2006-01-01

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

  14. Short-term effects of replacing milk with cola beverages on insulin-like growth factor-I and insulin-glucose metabolism: a 10 d interventional study in young men.

    PubMed

    Hoppe, Camilla; Kristensen, Mette; Boiesen, Marlene; Kudsk, Jane; Fleischer Michaelsen, Kim; Mølgaard, Christian

    2009-10-01

    In the Western world, a trend towards increased consumption of carbonated soft drinks combined with a decreasing intake of milk is observed. This may affect circulating insulin-like growth factor I (IGF-I) and fasting insulin, as seen in pre-pubertal children. The present study was designed to reflect the trend of replacing milk with carbonated beverages in young men and to study the effects of this replacement on IGF-I, IGF-binding protein 3 (IGFBP-3), IGF-I:IGFBP-3 and glucose-insulin metabolism. A randomised, controlled crossover intervention study, in which eleven men aged 22-29 years were given a low-Ca diet in two 10 d periods with 10 d washout in between. In one period, they drank 2.5 litres of Coca Cola(R) per day and the other period 2.5 litres of semi-skimmed milk. Serum IGF-I, IGFBP-3 (RIA), insulin (fluoro immunoassay) and glucose (Cobas) were determined at baseline and end point of each intervention period. Insulin resistance and beta-cell function were calculated with the homeostasis model assessment. A decrease in serum IGF-I was observed in the cola period compared with the milk period (P < 0.05). No effects of treatment were observed on IGFBP-3, IGF-I:IGFBP-3, insulin, glucose, insulin resistance or beta-cell function. The present study demonstrates that high intake of cola over a 10 d period decreases total IGF-I compared with a high intake of milk, with no effect on glucose-insulin metabolism in adult men. It is unknown whether this is a transient phenomenon or whether it has long-term consequences.

  15. [The link between trace elements and metabolic syndrome/oxidative stress in essential hypertension with or without type 2 diabetes].

    PubMed

    Gouaref, Ines; Bellahsene, Zina; Zekri, Samia; Alamir, Barkahoum; Koceir, Elhadj-Ahmed

    2016-01-01

    The relationship between trace elements (TE) and essential hypertension (EH) is subtle and complex. This relationship is mediated by endothelial dysfunction, insulin resistance, oxidative stress (OS) and athero-inflammatory state. The aim of this study was to examine the TE impact; particularly selenium (Se), zinc (Zn), copper (Cu) and manganese (Mn) as predictive type 2 diabetes biomarkers in a hypertensive subject. The study was undertaken on 400 adult patients (40-60 years), who were divided in 4 groups: hypertensive (H), type 2 diabetes (T2D), hypertensive-diabetic (HD) and healthy group. Patients were phenotyped regarding their metabolic syndrome profile using the NCEP/ATPIII criteria. Hypertension was defined as systolic (SBP) and diastolic (DBP) blood pressure ≥ 140/90 mmHg, respectively. The SBP and DBP measurements by electronic blood pressure using Omron 705 CP(®) type. Insulin resistance was assessed by Homa-IR model. Metabolic and inflammatory parameters were determined by Cobas Integra(®); the TE investigated by mass spectrometric atomic absorption; the OS markers evaluated by Randox kits. Serum Se concentrations are reduced in all groups, concomitantly with a marked depletion GPx activity in the HD group. However, Zn levels were decreased than in H and HD groups, but unchanged in T2D group. In contrast, Mn levels are increased in all groups; whereas the Cu levels increased only in H and HD groups, concomitantly with cytosolic SOD-Cu/Zn and mitochondrial SOD-Mn depletion. The Zn/Cu ratio decreases significantly in hypertensive group but not in diabetics groups. It appears that Zn/Cu ratio reflects the transition from hypertension phase to hypertension associated with T2D. Ultimately, TE plays an important role in the hypertension pathophysiology and can be considered as predictive T2D biomarkers in hypertensive patients.

  16. Evaluation of Two Techniques for Viral Load Monitoring Using Dried Blood Spot in Routine Practice in Vietnam (French National Agency for AIDS and Hepatitis Research 12338)

    PubMed Central

    Taieb, Fabien; Tram, Tran Hong; Ho, Hien Thi; Pham, Van Anh; Nguyen, Lan; Pham, Ban Hien; Tong, Linh An; Tuaillon, Edouard; Delaporte, Eric; Nguyen, Anh Tuan; Bui, Duc Duong; Do, NhanThi; Madec, Yoann

    2016-01-01

    Background. Although it is the best method to detect early therapeutic failure, viral load (VL) monitoring is still not widely available in many resource-limited settings because of difficulties in specimen transfer, personnel shortage, and insufficient laboratory infrastructures. Dried blood spot (DBS) use, which was introduced in the latest World Health Organization recommendations, can overcome these difficulties. This evaluation aimed at validating VL measurement in DBS, in a laboratory without previous DBS experience and in routine testing conditions. Methods. Human immunodeficiency virus (HIV)-infected adults were observed in a HIV care site in Hanoi, and each patient provided 2 DBS cards with whole blood spots and 2 plasma samples. Viral load was measured in DBS and in plasma using the COBAS Ampliprep/TaqMan and the Abbott RealTime assays. To correctly identify those with VL ≥ 1000 copies/mL, sensitivity and specificity were estimated. Results. A total of 198 patients were enrolled. With the Roche technique, 51 plasma VL were ≥1000 copies/mL; among these, 28 presented a VL in DBS that was also ≥1000 copies/mL (sensitivity, 54.9; 95% confidence interval [CI], 40.3–68.9). On the other hand, all plasma VL < 1000 copies/mL were also <1000 copies/mL in DBS (specificity, 100; 95% CI, 97.5–100). With the Abbott technique, 45 plasma VL were ≥1000 copies/mL; among these, 42 VL in DBS were also ≥1000 copies/mL (sensitivity, 93.3%; 95% CI, 81.7–98.6); specificity was 94.8 (95% CI, 90.0–97.7). Conclusions. The Abbott RealTime polymerase chain reaction assay provided adequate VL results in DBS, thus allowing DBS use for VL monitoring. PMID:27704001

  17. Home-based HPV self-sampling improves participation by never-screened and under-screened women: Results from a large randomized trial (iPap) in Australia.

    PubMed

    Sultana, Farhana; English, Dallas R; Simpson, Julie A; Drennan, Kelly T; Mullins, Robyn; Brotherton, Julia M L; Wrede, C David; Heley, Stella; Saville, Marion; Gertig, Dorota M

    2016-07-15

    We conducted a randomized controlled trial to determine whether HPV self-sampling increases participation in cervical screening by never- and under-screened (not screened in past 5 years) women when compared with a reminder letter for a Pap test. Never- or under-screened Victorian women aged 30-69 years, not pregnant and with no prior hysterectomy were eligible. Within each stratum (never-screened and under-screened), we randomly allocated 7,140 women to self-sampling and 1,020 to Pap test reminders. The self-sampling kit comprised a nylon tipped flocked swab enclosed in a dry plastic tube. The primary outcome was participation, as indicated by returning a swab or undergoing a Pap test; the secondary outcome, for women in the self-sampling arm with a positive HPV test, was undergoing appropriate clinical investigation. The Roche Cobas® 4800 test was used to measure presence of HPV DNA. Participation was higher for the self-sampling arm: 20.3 versus 6.0% for never-screened women (absolute difference 14.4%, 95% CI: 12.6-16.1%, p < 0.001) and 11.5 versus 6.4% for under-screened women (difference 5.1%, 95% CI: 3.4-6.8%, p < 0.001). Of the 1,649 women who returned a swab, 45 (2.7%) were positive for HPV16/18 and 95 (5.8%) were positive for other high-risk HPV types. Within 6 months, 28 (62.2%) women positive for HPV16/18 had colposcopy as recommended and nine (20%) had cytology only. Of women positive for other high-risk HPV types, 78 (82.1%) had a Pap test as recommended. HPV self-sampling improves participation in cervical screening for never- and under-screened women and most women with HPV detected have appropriate clinical investigation.

  18. Performance of the Roche second generation hemoglobin A1c immunoassay in the presence of HB-S or HB-C traits.

    PubMed

    Abadie, Jude M; Koelsch, Angela A

    2008-01-01

    Blood HbA1c determination is a powerful tool for the evaluation and management of patients with diabetes mellitus. Many HbA1c analytical methods demonstrate bias in samples from patients with hemoglobinopathies. This study evaluated the analytical performance of Roche Diagnostics' 1st and 2nd generation HbA1c assays in patients with or without hemoglobinopathies whose HbA1c levels were elevated or normal, respectively. Boronate-affinity high performance liquid chromatography (HPLC) served as the reference method. Whole blood samples were collected from 80 patients with HbS or HbC whose group mean HbA1c value was elevated and also from 80 patients without hemoglobinopathy whose HbA1c values were in the well-controlled range. Each sample was assayed for HbA1c by the Primus boronate-affinity HPLC technique and by Roche's 1st and 2nd generation immunoassays using a Cobas Integra 800 analytical system. Results by the HPLC technique were compared with the results of both Roche assays by linear regression and Bland-Altman analysis. The 1st and 2nd generation assays yielded regression lines and correlation values vs HPLC assay of y = 1.43x - 1.59; R(2) = 0.83, and y = 0.94x + 0.10; R(2) = 0.92, respectively, in the 80 patients with hemoglobinopathies. The mean difference and the +/-2SD range were greater in the 1st than in the 2nd generation assay (2.68, +/-2.07 vs -0.54, +/-0.86, respectively). The 2nd generation assay also showed better performance than the 1st generation assay in samples from the 80 patients without hemoglobinopathy. In conclusion, this study validates the accuracy of Roche's 2nd generation assay, which is substantially improved over Roche's 1st generation HbA1c assay.

  19. Boceprevir or telaprevir in hepatitis C virus chronic infection: The Italian real life experience

    PubMed Central

    CLEO Study Group; Ascione, Antonio; Adinolfi, Luigi Elio; Amoroso, Pietro; Andriulli, Angelo; Armignacco, Orlando; Ascione, Tiziana; Babudieri, Sergio; Barbarini, Giorgio; Brogna, Michele; Cesario, Francesco; Citro, Vincenzo; Claar, Ernesto; Cozzolongo, Raffaele; D’Adamo, Giuseppe; D’Amico, Emilio; Dattolo, Pellegrino; De Luca, Massimo; De Maria, Vincenzo; De Siena, Massimo; De Vita, Giuseppe; Di Giacomo, Antonio; De Marco, Rosanna; De Stefano, Giorgio; De Stefano, Giulio; Di Salvo, Sebastiano; Di Sarno, Raffaele; Farella, Nunzia; Felicioni, Laura; Fimiani, Basilio; Fontanella, Luca; Foti, Giuseppe; Furlan, Caterina; Giancotti, Francesca; Giolitto, Giancarlo; Gravina, Tiziana; Guerrera, Barbara; Gulminetti, Roberto; Iacobellis, Angelo; Imparato, Michele; Iodice, Angelo; Iovinella, Vincenzo; Izzi, Antonio; Liberti, Alfonso; Leo, Pietro; Lettieri, Gennaro; Luppino, Ileana; Marrone, Aldo; Mazzoni, Ettore; Messina, Vincenzo; Monarca, Roberto; Narciso, Vincenzo; Nosotti, Lorenzo; Pellicelli, Adriano Maria; Perrella, Alessandro; Piai, Guido; Picardi, Antonio; Pierri, Paola; Pietromatera, Grazia; Resta, Francesco; Rinaldi, Luca; Romano, Mario; Rossini, Angelo; Russello, Maurizio; Russo, Grazia; Sacco, Rodolfo; Sangiovanni, Vincenzo; Schiano, Antonio; Sciambra, Antonio; Scifo, Gaetano; Simeone, Filomena; Sullo, Annarita; Tarquini, Pierluigi; Tundo, Paolo; Vallone, Alfredo

    2016-01-01

    AIM To check the safety and efficacy of boceprevir/telaprevir with peginterferon/ribavirin for hepatitis C virus (HCV) genotype 1 in the real-world settings. METHODS This study was a non-randomized, observational, prospective, multicenter. This study involved 47 centers in Italy. A database was prepared for the homogenous collection of the data, was used by all of the centers for data collection, and was updated continuously. All of the patients enrolled in this study were older than 18 years of age and were diagnosed with chronic infection due to HCV genotype 1. The HCV RNA testing was performed using COBAS-TaqMan2.0 (Roche, LLQ 25 IU/mL). RESULTS All consecutively treated patients were included. Forty-seven centers enrolled 834 patients as follows: Male 64%; median age 57 (range 18-78), of whom 18.3% were over 65; mean body mass index 25.6 (range 16-39); genotype 1b (79.4%); diagnosis of cirrhosis (38.2%); and fibrosis F3/4 (71.2%). The following drugs were used: Telaprevir (66.2%) and PEG-IFN-alpha2a (67.6%). Patients were naïve (24.4%), relapsers (30.5%), partial responders (14.8%) and null responders (30.3%). Overall, adverse events (AEs) occurred in 617 patients (73.9%) during the treatment. Anemia was the most frequent AE (52.9% of cases), especially in cirrhotic. The therapy was stopped for 14.6% of the patients because of adverse events or virological failure (15%). Sustained virological response was achieved in 62.7% of the cases, but was 43.8% in cirrhotic patients over 65 years of age. CONCLUSION In everyday practice, triple therapy is safe but has moderate efficacy, especially for patients over 65 years of age, with advanced fibrosis, non-responders to peginterferon + ribavirin. PMID:27574549

  20. Prevalence of end of treatment RNA-positive/sustained viral response in HCV patients treated with sofosbuvir combination therapies

    PubMed Central

    Malespin, Miguel; Benyashvili, Tamara; Uprichard, Susan L.; Perelson, Alan S.; Dahari, Harel; Cotler, Scott J.

    2016-01-01

    Background: Some chronic hepatitis C virus (HCV), genotype 1 infected patients treated with direct antiviral agents (DAAs) remain viremic at end of treatment (EOT+), yet go on to achieve sustained virological response 12 weeks after completion of therapy (SVR12). The incidence of EOT+/SVR in patients with genotype 1 and other genotypes, as well as whether such patients achieve SVR24 remain in question. The aims of this study were to evaluate the frequency and durability of EOT+/SVR12&24 and other response categories in HCV genotype 1, 2, or 3 infected patients treated with DAA in clinical practice. Methods: Data from patients treated with all oral sofosbuvir-based regimens at a university hepatology practice by 1 July 2015 were reviewed retrospectively. Responses were categorized based on virus levels during and post DAA treatment. HCV RNA levels were measured by Abbott RealTime HCV (ART) or by Roche CobasTaqMan v2.0 (RCTM) assays. Results: The study population included 89 patients. Participants were 62% genotype 1, 19% genotype 2 and 19% genotype 3, 54% cirrhotic and 46% treatment-experienced. A total of 45 received sofosbuvir–simeprevir, 38 sofosbuvir–ribavirin and 6 sofosbuvir–ledipasvir. The SVR12 rate was 82%. A total of 5 patients (6%), all with genotype 1, had EOT+ by ART assay and each achieved SVR12&24. Conclusions: A total of 9% of genotype 1 patients (6% overall) treated with DAAs were EOT+ by ART and all EOT+ cases achieved SVR24. EOT+/SVR was not observed with genotype 2 or 3 or by the RCTM assay. In patients treated with DAAs, EOT+ by the ART assay does not indicate treatment failure. PMID:28286560

  1. Which high-risk HPV assays fulfil criteria for use in primary cervical cancer screening?

    PubMed

    Arbyn, M; Snijders, P J F; Meijer, C J L M; Berkhof, J; Cuschieri, K; Kocjan, B J; Poljak, M

    2015-09-01

    Several countries are in the process of switching to high-risk human papillomavirus (hrHPV) testing for cervical cancer screening. Given the multitude of available tests, validated assays which assure high-quality screening need to be identified. A systematic review was conducted to answer the question which hrHPV tests fulfil the criteria defined by an international expert team in 2009, based on reproducibility and relative sensitivity and specificity compared to Hybrid Capture-2 or GP5+/6+ PCR-enzyme immunoassay. These latter two hrHPV DNA assays were validated in large randomized trials and cohorts with a follow-up duration of 8 years or more. Eligible studies citing the 2009 guideline were retrieved from Scopus (http://www.scopus.com) and from a meta-analysis assessing the relative accuracy of new hrHPV assays versus the standard comparator tests to detect high-grade cervical intraepithelial neoplasia or cancer in primary screening. The cobas 4800 HPV test and Abbott RealTime High Risk HPV test were consistently validated in two and three studies, respectively, whereas the PapilloCheck HPV-screening test, BD Onclarity HPV assay and the HPV-Risk assay were validated each in one study. Other tests which partially fulfil the 2009 guidelines are the following: Cervista HPV HR Test, GP5+/6+ PCR-LMNX, an in-house E6/E7 RT quantitative PCR and MALDI-TOF (matrix-assisted laser desorption-ionization time-of-flight). The APTIMA HPV assay targeting E6/E7 mRNA of hrHPV was also fully validated. However, the cross-sectional equivalency criteria of the 2009 guidelines were set up for HPV DNA assays. Demonstration of a low risk of CIN3+ after a negative APTIMA test over a longer period is awaited to inform us about its utility in cervical cancer screening at 5-year or longer intervals.

  2. Performance characteristics of the HemoCue B-Glucose analyzer using whole-blood samples.

    PubMed

    Voss, E M; Cembrowski, G S

    1993-07-01

    We evaluated the HemoCue B-Glucose (HemoCue Inc, Mission Viejo, Calif) analyzer for accuracy, precision, linearity, and recovery. One hundred eighteen capillary whole-blood samples were analyzed in duplicate on the HemoCue B-Glucose and the YSI 2300 STAT Glucose/L-Lactate (Yellow Springs [Ohio] Instruments) analyzers; corresponding plasma glucose levels were measured in duplicate on the Roche Cobas MIRA (Roche Diagnostic Systems, Nutley, NJ) analyzer. Plasma glucose levels were converted to whole-blood equivalent glucose levels by using a factor of 1.11. The following regression equations were obtained: HemoCue = 1.02 (YSI) + 0.19, Sy/x = 0.52, r2 = .984; and HemoCue = 0.98 (whole-blood equivalent glucose levels) + 0.26, Sy/x = 0.55, r2 = .982. Within-run coefficients of variation were 4.0%, 3.5%, 2.2%, and 1.0% at glucose concentrations of 3.9, 5.4, 8.7, and 17.1 mmol/L (71, 97, 156, and 308 mg/dL), respectively. Between-run imprecision and total imprecision using lyopholized materials with three lot numbers of cuvettes were 4.2% and 5.6% at 2.1 mmol/L (37 mg/dL) and 2.4% and 2.7% at 5.2 mmol/L (95 mg/dL), respectively. The HemoCue B-Glucose analyzer displayed linearity between 0 and 22.2 mmol/L (0 and 400 mg/dL), and the percent recovery averaged 98.7% +/- 4.5% (mean +/- SD). The HemoCue B-Glucose analyzer is a rapid, simple, and reliable method for determinations of whole-blood glucose levels.

  3. Effect of Antiviral Therapy on Serum Activity of Angiotensin Converting Enzyme in Patients with Chronic Hepatitis C

    PubMed Central

    Husic-Selimovic, Azra; Sofic, Amela; Huskic, Jasminko; Bulja, Deniz

    2016-01-01

    Introduction: Renin-angiotenzin system (RAS) is frequently activated in patients with chronic liver disease. Angiotenzin - II (AT-II), produced by angiotenzin converting enzyme (ACE), has many physiological effects, including an important role in liver fibrogenesis. Combined antiviral therapy with PEG-IFN and ribavirin besides its antiviral effect also leads to a reduction in liver parenchyma fibrosis. Aim of the study: Determining the value of ACE in serum of patients with chronic hepatitis C before and after combined antiviral therapy, as well as the value of ACE activities in sera of the control group. Materials and methods: We studied 50 patients treated at Gastroenterohepatology Department, in the time-period of four years. Value of ACE in serum was determined by Olympus AU 400 device, with application of kit “Infinity TN ACE Liquid Stable Reagent”. HCV RNA levels in sera were measured by real time PCR. HCV RNA test was performed with modular analysis of AMPLICOR and COBAS AMPLICOR HCV MONITOR test v2.0, which has proved infection and was used for quantification of the viruses and monitoring of the patients’ response to therapy. Liver histology was evaluated in accordance with the level of necroinflammation activity and stage of fibrosis. Results: Serum activities of ACE in chronic hepatitis C patients is statistically higher than the values in the control group (p=0.02). Antiviral therapy in chronic hepatitis C patients statistically decreases serum activities of ACE (p= 0.02) and indirectly affects fibrogenesis of the liver parenchyma. Correlation between ACE and ALT activity after the therapy was proved (0.3934). Conclusion: Our findings suggest that the activity of ACE in serum is a good indirect parameter of the liver damage, and could be used as an indirect prognostic factor of the level of liver parenchyma damage. Serum activity of ACE can be used as a parameter for non-invasive assessment of intensity of liver damage. PMID:27147779

  4. Comparative evaluation of three automated systems for DNA extraction in conjunction with three commercially available real-time PCR assays for quantitation of plasma Cytomegalovirus DNAemia in allogeneic stem cell transplant recipients.

    PubMed

    Bravo, Dayana; Clari, María Ángeles; Costa, Elisa; Muñoz-Cobo, Beatriz; Solano, Carlos; José Remigia, María; Navarro, David

    2011-08-01

    Limited data are available on the performance of different automated extraction platforms and commercially available quantitative real-time PCR (QRT-PCR) methods for the quantitation of cytomegalovirus (CMV) DNA in plasma. We compared the performance characteristics of the Abbott mSample preparation system DNA kit on the m24 SP instrument (Abbott), the High Pure viral nucleic acid kit on the COBAS AmpliPrep system (Roche), and the EZ1 Virus 2.0 kit on the BioRobot EZ1 extraction platform (Qiagen) coupled with the Abbott CMV PCR kit, the LightCycler CMV Quant kit (Roche), and the Q-CMV complete kit (Nanogen), for both plasma specimens from allogeneic stem cell transplant (Allo-SCT) recipients (n = 42) and the OptiQuant CMV DNA panel (AcroMetrix). The EZ1 system displayed the highest extraction efficiency over a wide range of CMV plasma DNA loads, followed by the m24 and the AmpliPrep methods. The Nanogen PCR assay yielded higher mean CMV plasma DNA values than the Abbott and the Roche PCR assays, regardless of the platform used for DNA extraction. Overall, the effects of the extraction method and the QRT-PCR used on CMV plasma DNA load measurements were less pronounced for specimens with high CMV DNA content (>10,000 copies/ml). The performance characteristics of the extraction methods and QRT-PCR assays evaluated herein for clinical samples were extensible at cell-based standards from AcroMetrix. In conclusion, different automated systems are not equally efficient for CMV DNA extraction from plasma specimens, and the plasma CMV DNA loads measured by commercially available QRT-PCRs can differ significantly. The above findings should be taken into consideration for the establishment of cutoff values for the initiation or cessation of preemptive antiviral therapies and for the interpretation of data from clinical studies in the Allo-SCT setting.

  5. Profile of Vitamin D in patients attending at general hospital Mahad India

    PubMed Central

    Bawaskar, Parag Himatrao; Bawaskar, Himmatrao Saluba; Bawaskar, Pramodini Himmatrao; Pakhare, Abhijit Patilbuwa

    2017-01-01

    Background: Despite abundant sunshine, Vitamin D deficiency is prevalent in urban India. However, reports on analyzing Vitamin D status from rural Indian population are scanty. Here, we have evaluated Vitamin D status in patients attending outpatient department (OPD) in a rural Indian hospital setting. Methods: A hospital-based cross-sectional study was conducted at a secondary level rural hospital in patients attending medicine OPD. After obtaining informed consent, demographic information was collected from consecutive adult patients along with 3 ml blood sample for Vitamin D analysis using electro chemiluminescene on cobas elecys E411 fully automated system. Vitamin D levels were compared across various groups by using Mann–Whitney or Kruskal–Wallis tests, and multiple linear regression analysis was performed to identify the predictors of Vitamin D level. Results: A total of 640 patients were enrolled in the study, and the prevalence of Vitamin D deficiency (<20 ng/ml) was found to be 65.4% with 95% confidence interval of 61.7–69.1%. On univariate analysis, Vitamin D levels were statistically significantly lower among younger age group, those who have dark complexion, wearing Burkha (veil), and those who were not adequately exposed to sunlight. After multiple linear regressions, dark complexion, wearing Burkha, inadequate exposure to sunlight, and presence of diabetes were identified as statistically significant predictors of Vitamin D deficiency. Conclusion: We report a high prevalence of Vitamin-D deficiency in patients attending medicine OPD. Thus, patients with generalized complaints may be evaluated for serum Vitamin D levels. PMID:28217511

  6. Role for Ferredoxin:NAD(P)H Oxidoreductase (FprA) in Sulfate Assimilation and Siderophore Biosynthesis in Pseudomonads

    PubMed Central

    Glassing, Angela; Harper, Justin; Franklin, Michael J.

    2013-01-01

    Pyridine-2,6-bis(thiocarboxylate) (PDTC), produced by certain pseudomonads, is a sulfur-containing siderophore that binds iron, as well as a wide range of transition metals, and it affects the net hydrolysis of the environmental contaminant carbon tetrachloride. The pathway of PDTC biosynthesis has not been defined. Here, we performed a transposon screen of Pseudomonas putida DSM 3601 to identify genes necessary for PDTC production (Pdt phenotype). Transposon insertions within genes for sulfate assimilation (cysD, cysNC, and cysG [cobA2]) dominated the collection of Pdt mutations. In addition, two insertions were within the gene for the LysR-type transcriptional activator FinR (PP1637). Phenotypic characterization indicated that finR mutants were cysteine bradytrophs. The Pdt phenotype of finR mutants could be complemented by the known target of FinR regulation, fprA (encoding ferredoxin:NADP+ oxidoreductase), or by Escherichia coli cysJI (encoding sulfite reductase). These data indicate that fprA is necessary for effective sulfate assimilation by P. putida and that the effect of finR mutation on PDTC production was due to deficient expression of fprA and sulfite reduction. fprA expression in both P. putida and P. aeruginosa was found to be regulated by FinR, but in a manner dependent upon reduced sulfur sources, implicating FinR in sulfur regulatory physiology. The genes and phenotypes identified in this study indicated a strong dependence upon intracellular reduced sulfur/cysteine for PDTC biosynthesis and that pseudomonads utilize sulfite reduction enzymology distinct from that of E. coli and possibly similar to that of chloroplasts and other proteobacteria. PMID:23794620

  7. Oxidative stress associated with rootstock-scion interactions in pear/quince combinations during early stages of graft development.

    PubMed

    Irisarri, Patricia; Binczycki, Piotr; Errea, Pilar; Martens, Helle Juel; Pina, Ana

    2015-03-15

    Exposing a plant to stress situations, such as grafting, generally triggers antioxidant defense systems. In fruit tree grafting, quince (Cydonia oblonga) is widely used as a rootstock for pear (Pyrus communis L.), but several economically important pear cultivars are incompatible with available quince rootstocks. In this study, grafts were established using an in vitro callus graft system mimicking the events taking place in fruit trees. In vitro grown callus from pear [P. communis L. cv. 'Conference' (Co) and cv. 'William' (Wi)] and quince (C. oblonga Mill. clone 'BA29') was used to establish the compatible homografts 'Co/Co', 'Wi/Wi' and 'BA29/BA29', the compatible heterograft 'Co/BA29' and the incompatible heterograft 'Wi/BA29'. The main objective was to determine whether specific isoforms of genes involved in oxidative stress [superoxide dismutase (SOD), ascorbate peroxidase (APX) and catalase (CAT)] are differentially expressed at the graft interface from compatible and incompatible unions throughout 3 weeks after grafting. Reactive oxygen species (ROS) levels and programmed cell death were also evaluated in the course of graft development. Genes differentially expressed between compatible and incompatible heterografts were identified. Transcript levels of six antioxidant genes (SOD1, SOD3, APX3, APX6, CAT1 and CAT3) were down-regulated 10 days after grafting (DAG) in the incompatible heterograft in comparison to the compatible one. Likewise, SOD enzymatic activities were significantly higher at 1 and 10 days after wounding in the compatible cultivar 'Co' than in the incompatible one 'Wi'. These findings, together with live cell imaging of ROS-specific probes, ultrastructural mitochondrial changes and DNA fragmentation related to apoptotic processes, give indications that within incompatible rootstock/scion interfaces, either the level of ROS is increased or there is a less efficient detoxification system.

  8. Validation of Electrochemiluminiscence Immunoassay for Ovarian Steroid Determination in Rhinella arenarum.

    PubMed

    Arias Torres, Ana Josefina; Páez, José Bernardino; Zelarayán, Liliana Isabel

    2016-04-01

    In this work, we describe the validation of an electrochemiluminescence immunoassay (ECLIA) that allowed us for the first time to determine the levels of progesterone (P4 ) and testosterone (T) secreted by Rhinella arenarum follicles during the preovulatory (POP) and reproductive (RP) periods. We also verified the relation between P4 and T levels and oocyte maturation. Moreover, we demonstrated that the extraction protocol developed for the determinations of P4 and T by ECLIA proved to be efficient and reproducible since the efficacy of the extraction was above 95% in all assays conducted. The results indicate that in the validation process the variation coefficient (CV) between assays is compatible with the analytical procedures based on automated immunoassays (CV < 8%) and that the adaptation proposed for the samples allows the determination of T and P4 with the Cobas e-411 analyzer. Our results indicate that in basal conditions the levels of T released by R. arenarum follicles were higher than those of P4 during POP and RP. In these conditions, steroid secretion failed to induce germinal vesicle break down (GVBD) in the follicles. Under gonadotropin stimulation, steroidogenesis showed a remarkable increase in both periods, especially during POP. This increase was correlated with a high maturation percentage in the follicles incubated in vitro (GVBD = 72 ± 16%) during POP. During RP, human Chorionic Gonadotropin (hCG) induced 81.75 ± 9.1% GVBD. This study is the first report of the seasonal steroidogenic activity in the ovary of R. arenarum in situ using an ECLIA-modified protocol developed in our laboratory.

  9. Disagreement between Human Papillomavirus Assays: An Unexpected Challenge for the Choice of an Assay in Primary Cervical Screening

    PubMed Central

    Ejegod, Ditte Møller; Rygaard, Carsten; Lynge, Elsebeth; Bonde, Jesper

    2014-01-01

    We aimed to determine the disagreement in primary cervical screening between four human papillomavirus assays: Hybrid Capture 2, cobas, CLART, and APTIMA. Material from 5,064 SurePath samples of women participating in routine cervical screening in Copenhagen, Denmark, was tested with the four assays. Positive agreement between the assays was measured as the conditional probability that the results of all compared assays were positive given that at least one assay returned a positive result. Of all 5,064 samples, 1,679 (33.2%) tested positive on at least one of the assays. Among these, 41% tested positive on all four. Agreement was lower in women aged ≥30 years (30%, vs. 49% at <30 years), in primary screening samples (29%, vs. 38% in follow-up samples), and in women with concurrent normal cytology (22%, vs. 68% with abnormal cytology). Among primary screening samples from women aged 30–65 years (n = 2,881), 23% tested positive on at least one assay, and 42 to 58% of these showed positive agreement on any compared pair of the assays. While 4% of primary screening samples showed abnormal cytology, 6 to 10% were discordant on any pair of assays. A literature review corroborated our findings of considerable disagreement between human papillomavirus assays. This suggested that the extent of disagreement in primary screening is neither population- nor storage media-specific, leaving assay design differences as the most probable cause. The substantially different selection of women testing positive on the various human papillomavirus assays represents an unexpected challenge for the choice of an assay in primary cervical screening, and for follow up of in particular HPV positive/cytology normal women. PMID:24466262

  10. Evaluation of a High Resolution Genotyping Method for Chlamydia trachomatis Using Routine Clinical Samples

    PubMed Central

    Wang, Yibing; Skilton, Rachel J.; Cutcliffe, Lesley T.; Andrews, Emma; Clarke, Ian N.; Marsh, Pete

    2011-01-01

    Background Genital chlamydia infection is the most commonly diagnosed sexually transmitted infection in the UK. C. trachomatis genital infections are usually caused by strains which fall into two pathovars: lymphogranuloma venereum (LGV) and the genitourinary genotypes D–K. Although these genotypes can be discriminated by outer membrane protein gene (ompA) sequencing or multi-locus sequence typing (MLST), neither protocol affords the high-resolution genotyping required for local epidemiology and accurate contact-tracing. Principal Findings We evaluated variable number tandem repeat (VNTR) and ompA sequencing (now called multi-locus VNTR analysis and ompA or “MLVA-ompA”) to study local epidemiology in Southampton over a period of six months. One hundred and fifty seven endocervical swabs that tested positive for C. trachomatis from both the Southampton genitourinary medicine (GUM) clinic and local GP surgeries were tested by COBAS Taqman 48 (Roche) PCR for the presence of C. trachomatis. Samples tested as positive by the commercial NAATs test were genotyped, where possible, by a MLVA-ompA sequencing technique. Attempts were made to isolate C. trachomatis from all 157 samples in cell culture, and 68 (43%) were successfully recovered by repeatable passage in culture. Of the 157 samples, 93 (i.e. 59%) were fully genotyped by MLVA-ompA. Only one mixed infection (E & D) in a single sample was confirmed. There were two distinct D genotypes for the ompA gene. Most frequent ompA genotypes were D, E and F, comprising 20%, 41% and 16% of the type-able samples respectively. Within all genotypes we detected numerous MLVA sub-types. Conclusions Amongst the common genotypes, there are a significant number of defined MLVA sub-types, which may reflect particular background demographics including age group, geography, high-risk sexual behavior, and sexual networks. PMID:21347295

  11. Comparison of molecular tests for detection and quantification of cell-associated cytomegalovirus DNA.

    PubMed

    Caliendo, Angela M; Yen-Lieberman, Belinda; Baptista, Jovana; Andersen, Janet; Crumpacker, Clyde; Schuurman, Rob; Spector, Stephen A; Bremer, James; Lurain, Nell S

    2003-08-01

    A cell-based standard was developed to compare the COBAS Amplicor CMV Monitor test, the Hybrid Capture System CMV DNA test, and the NucliSens CMV test. The standard was prepared by infecting human foreskin fibroblasts (HFFs) with cytomegalovirus (CMV) strain AD169 at low multiplicity of infection (0.03) and harvesting the cells at 6 h postinfection. Buffy coat cells were added to produce concentrations of from 0 to 10(5) HFFs per 10(6) total cells. Five laboratories performed the Amplicor PCR test and two laboratories performed the NucliSens and Hybrid Capture tests. The Amplicor PCR test was 1.5 to 2.0 log(10) more sensitive than the Hybrid Capture test. The specificities of the Amplicor PCR and Hybrid Capture tests were 100 and 93.8%, respectively. The linear range of the Amplicor PCR and Hybrid Capture tests were 2 to 4.48 log(10) and 3.48 to at least 5.0 log(10) CMV target cells, respectively. The standard deviations of the Amplicor PCR and Hybrid Capture tests varied throughout their linear range, and for both tests the variability was greater for lower concentrations of input CMV DNA. These data allow the direct comparison of viral load values between the Amplicor and Hybrid Capture tests. The analytical sensitivity of the NucliSens test could not be determined by using the 6-h standard, because the low multiplicity of infection and short culture time did not allow for adequate transcription of pp67 late mRNA measured in the test. Extending the incubation time of the standard to 24 h increased the analytical sensitivity of the NucliSens test to 3.0 log(10) target cells.

  12. Comparison of Gen-probe transcription-mediated amplification, Abbott PCR, and Roche PCR assays for detection of wild-type and mutant plasmid strains of Chlamydia trachomatis in Sweden.

    PubMed

    Møller, Jens Kjølseth; Pedersen, Lisbeth Nørum; Persson, Kenneth

    2008-12-01

    The clinical performance of two nucleic acid amplification assays targeting the cryptic plasmid and two assays targeting rRNA molecules in Chlamydia trachomatis was examined. First-catch urine samples from Malmoe, Sweden, were tested for C. trachomatis with the Abbott real-time PCR assay m2000 and an in-house PCR for the new variant strain of C. trachomatis with a deletion in the cryptic plasmid. Aliquots of the urine samples were sent to Aarhus, Denmark, and further examined with the Roche COBAS Amplicor CT (RCA) PCR, the Gen-Probe Aptima Combo 2 assay (AC2) targeting the C. trachomatis 23S rRNA, and the Aptima C. trachomatis assay (ACT) targeting the 16S rRNA molecule. A positive prevalence of 9% (163/1,808 urine samples examined) was detected according to the combined reference standard. The clinical sensitivity and specificity of the four assays were as follows: for ACT, 100% (163/163) and 99.9% (1,643/1,645), respectively; for AC2, 100% (163/163) and 99.6% (1,640/1,645); for m2000, 68.7% (112/163) and 99.9% (1,644/1,645); for RCA, 63.8% (104/163) and 99.9% (1,643/1,645). The two Gen-Probe assays detected all mutant strains characterized by the in-house PCR as having the deletion in the cryptic plasmid, whereas the Roche and the Abbott PCRs targeting the plasmid were both unable to detect the plasmid mutant. The difference in clinical sensitivity between the plasmid PCR assays m2000 and RCA, on the one hand, and the rRNA assays AC2 and ACT, on the other, could be attributed almost exclusively to the presence of the plasmid mutant in about one-quarter of the Chlamydia-positive samples examined.

  13. The 67P/Churyumov-Gerasimenko comet: colors, albedo variations and inhomogeneity of the nucleus from the ROSETTA/OSIRIS images

    NASA Astrophysics Data System (ADS)

    Fornasier, S.; Leyrat, C.; Barucci, M. A.; Hasselmann, P. H.; Thomas, N.; Kueppers, M.; Sierks, H.; Oklay, N.; Snodgrass, C.; Tubiana, C.; Vincent, J. B.; Jorda, L.; Keller, H. U.; Hviik, S.; Magrin, S.; Massironi, M.; Besse, S.; Pajola, M.

    2014-04-01

    Rosetta is the cornerstone mission of the European Space Agency devoted to the study of the minor bodies. Launched on 2 March 2004, Rosetta has as primary target the comet 67P/Churyumov-Gerasimenko, a short period comet of the Jupiter's family. On its journey to the comet, after three Earth and one Mars gravity assist manoeuvres, Rosetta flew by two selected asteroids, 2867 Steins, in September 2008, and 21 Lutetia in July 2010. In June 2011, Rosetta was placed in hibernation for 31 months to save its power resources, and it was successfully reactivated on January 2014, before the rendez-vous maneuver to the comet at 4 AU from the Sun. The spacecraft will orbit and perform long-term exploration of the cometary nucleus and coma, including its innermost part, for more than 1 year and a half, following the comet up to its perihelion at 1.37 AU and shortly after it. A large complement of scientific experiments designed to complete the most detailed study of a comet ever attempted are on board Rosetta, including imaging cameras, spectrometers, dust analysers, radio science experiment, and the Philae lander that will land on the nucleus in November 2014. In this work we will present the results on the 67P nucleus physical-chemical properties derived from the OSIRIS images acquired during the comet approach phase and the first bound orbits in July-August 2014. OSIRIS is constituted of aWide Angle Camera (WAC) and a Narrow Angle Camera (NAC) [1]. The NAC camera will obtain high resolution images with different filters in the near UV-near IR range. Those filters are optimised for the mineralogical studies of the nucleus. The WAC camera has a wide field of view (12×12 degrees) and narrow band filters devoted to the study of the gaseous species of the coma. In the July-August 2014 timeframe, OSIRIS will map the entire surface of the comet with several filters in the 250-1000 nm range, at different phase angles (5- 50 degrees), and with a resolution up to 1 m/px with the NAC

  14. Vesta Collisional History Revealed by DAWN

    NASA Astrophysics Data System (ADS)

    Marchi, S.; McSween, H. Y.; O'Brien, D. P.; Schenk, P.; De Sanctis, M. C.; Gaskell, R.; Hiesinger, H.; Jaumann, R.; Mottola, S.; Preusker, F.; Raymond, C. A.; Roatsch, T.; Russell, C. T.; Yingst, R. A.

    2012-04-01

    Vesta is a 530 km diameter differentiated rocky body in the main asteroid belt that accreted within the first few million years after the formation of the earliest solar system solids [1,2,3]. These circumstances, along with the fact that Vesta's surface is probably sampled in meteorite collections (the so-called howardite, eucrite and diogenite (HED) meteorites), make Vesta one of the best targets for studying the early evolution of the main belt. According to current dynamical models [4,5,6], Vesta early evolution took place in an environment where collisions with other asteroids were much more frequent than today. These considerations lead us to deal with fundamental questions, such as: How much of Vesta history can be inferred from remote sensing, and in particular from cratering studies? Can this history inform us about the past evolution of the main asteroid belt and the solar system? Can radiometric ages of HEDs be used to establish a Vesta crater chronology to be compared and, possibly extend, the Apollo-based lunar crater chronology? Dawn observations of Vesta confirm and extend the range of geologic and impact processes seen on smaller asteroids. One of the obvious features emerging from these observations is that the surface of Vesta is dominated at all scales by impact craters. The lack of many of the obliteration processes that may occur on larger bodies (e.g., erosion on Mars, Venus; lava emplacement on the Moon and Mercury) allows for greater preservation of craters on Vesta. Observed crater sizes range from the resolution limit (10s of meters for the low-altitude mapping orbit) to the largest ~500-km impact basin at the south pole, called Rheasilvia. The Framing Camera on the Dawn spacecraft extensively imaged Vesta during its Survey phase, at an altitude of about 2700 km. These data have been used to build a global mosaic with a scale of 260 m/px, covering about 85% of Vesta's surface [7]. At the moment of writing, we have identified and catalogued

  15. Imaging detection of new HCCs in cirrhotic patients treated with different techniques: Comparison of conventional US, spiral CT, and 3-dimensional contrast-enhanced US with the Navigator technique (Nav 3D CEUS)().

    PubMed

    Giangregorio, F; Comparato, G; Marinone, M G; Di Stasi, M; Sbolli, G; Aragona, G; Tansini, P; Fornari, F

    2009-03-01

    Sommario INTRODUZIONE: Il sistema “Navigator” di Esaote consente di ottenere ricostruzioni 3-D di tutto il fegato (corrette volumetricamente da un sistema di guida) mediante singola acquisizione con CEUS (mediante scansione perpendicolare all'asse lungo del fegato, per una completa acquisizione 2-D del suo asse corto) e sovrappone tali ricostruzioni 3-D con quelle ottenute con la TC. SCOPO: valutare la capacità di tale sistema di diagnosticare nuovi HCC rispetto all'US e alla TC in una popolazione di HCC su cirrosi precedentemente trattati con varie metodiche. MATERIALI E METODI: Settantadue cirrotici con pregressi HCC (M/F: 38/34; tutti HCV +vi, Child A/B: 58/14, con detection di 49 nuovi noduli (N) in 34 pazienti; 10 nuovi HCC multinodulari (NMulti); 6 riprese locali di malattia (Ri) in 4 pazienti (3 riprese singole, in un paziente tre noduli con ripresa di malattia); 47 HCC trattati efficacemente (neg) in 22 pazienti + 2 pazienti con HCC multinodulare senza segni di ripresa (neg-Multi) sono stati sottoposti a 100 esami (1 esame: 48 pazienti; 2 esami: 20 pazienti; 3 esami: 4 pazienti) dal 1 novembre 2006 al novembre 2007. La Nav 3D CEUS è stata eseguita con SonoVue (BR1; Bracco) e con l'ecografo Esaote MPX collegato a un sistema “Navigator” con software di ricostruzione 3-D dedicato. La TC spirale di controllo è stata eseguita entro 30 giorni dall'esecuzione di Nav 3D CEUS. Sono stati valutati sensibilità, specificità, accuratezza diagnostica (ODA), valore predittivo positivo (PPV) e negativo (NPV). RISULTATI: La diagnosi finale fu: 34 pazienti con 49 nuove lesioni (N), 10 con HCC multiN e 6 recidive loco-regionali in 4 pazienti; 47 noduli in 24 pazienti senza nuove lesioni durante il follow-up. Gli US hanno ottenuto: 29 N (+5 multinodularN e 3 LR), 20 falsi negativi (+5 Nmulti e 3 LR) (sensibilità: 59,2, specificità: 100%; accuratezza diagnostica: 73;6; VPP: 100; VPN: 70, 1); la TC spirale ha ottenuto: 42 N (+9 multinodularN e 7 LR), 7 falsi

  16. Predictive value of time-intensity curves obtained with contrast-enhanced ultrasonography (CEUS) in the follow-up of 30 patients with Crohn's disease.

    PubMed

    Giangregorio, F; Bertone, A; Fanigliulo, L; Comparato, G; Aragona, G; Marinone, M G; Sbolli, G; Tansini, P; Fornari, F

    2009-12-01

    Sommario OBIETTIVI: La CEUS è in grado di quantificare accuratamente la microvascolarizzazione della parete intestinale nel Crohn. IPOTESI: L'infiammazione della parete intestinale non è correlata con la quantità di parete vascolarizzata (studi di pattern di vascolarizzazione - SPV), ma con il grado di flusso di parete durante un periodo di tempo (studi di intensità-tempo - SIT). Obiettivo è stato capire se gli studi SPV o quelli SIT con CEUS fossero espressione dell'infiammazione vascolare della parete intestinale e fossero correlabili con l'attività clinica di malattia (T0) o nel follow-up (tre e sei mesi: T3, T6). MATERIALI E METODI: 30 Crohn (M: 12; F: 18; età media: 41,96; terapia: 8 Pts 5-ASA; 13 steroide; 7 ANTI-TNF; 2 azatioprina) sono stati seguiti per almeno sei mesi e studiati con CEUS SPV e con CEUS SIT. È stato utilizzato come mezzo di contrasto il SonoVue (BR1, Bracco) e un ecografo dedicato (TECHNOS MPX, Esaote) con software per curve di time intensity. Quattro pattern vascolari (1: tutta la parete vascolarizzata; 2: più del 50% di parete con vascolarizzazione; 3: flusso solo all'interno della sottomucosa; 4: nessun segnale). Un'analisi semiquantitativa è stata ottenuta misurando l'area sotto la curva - AUC (cut-off tra attività ed inattività = 15), l'intensità media - MI (cut off = 10). Tutti gli esami sono stati eseguiti per 150 secondi, registrati e analizzati in modo digitale. RISULTATI: T0: cDAI <150 in 22 pts; cDAI > 150 in 8; T3: 22 pts con cDAI <150, 8 con cDAI >150. A T0 sia la CEUS SPV che la SIT hanno ottenuto bassa specificità, accuratezza diagnostica e valore predittivo negativo (p = ns); la CEUS SPV ha dato a T0: 8 VP, 15 VN, 8 FP, 0 FN (sens: 100%; spec: 68,2%; acc diagn: 69,5%; VPP: 100%; VPN: 53,3%); la CEUS SIT ha conseguito a T0: 6 VP, 18 VN, 4 FP, 2 FN (sens: 75%; spec: 81,8%; acc diagn: 75%; VPP: 60%; VPN: 90%). La CEUS SPV ha raggiunto a T3: 8 VP, 12 VN, 7 FP, 3 FN (sens: 72,7%; spec: 63,2%; acc diagn: 50%; VPP

  17. Insolation and Resulting Surface Temperatures of the Kuiper-Rudaki Study Region on Mercury.

    NASA Astrophysics Data System (ADS)

    Bauch, Karin E.; Hiesinger, Harald; D'Amore, Mario; Helbert, Jörn; Weinauer, Julia

    2016-04-01

    The imaging spectrometer MERTIS (Mercury Radiometer and Thermal Infrared Spectrometer) is part of the payload of ESA's BepiColombo mission, which is scheduled for launch in 2017 [1]. The instrument consists of an IR-spectrometer and radiometer, which observe the surface in the wavelength range of 7-14 and 7-40μm, respectively. The four scientific objectives are to a) study Mercury's surface composition, b) identify rock-forming minerals, c) globally map the surface mineralogy and d) study surface temperature and thermal inertia [1, 2]. In preparation of the MERTIS experiment, we performed detailed thermal models of the lunar surface, which we extrapolated to Mercury. In order to calculate insolation and surface temperatures, we use a numerical model, which has been described by [7]. Surface temperatures are dependent on the surface and subsurface bulk thermophysical properties, such as bulk density, heat capacity, thermal conductivity, emissivity, topography, and albedo. Lunar and Mercurian surface temperatures show the same general characteristics. Both have very steep temperature gradients at sunrise and sunset, due to the lack of an atmosphere. However, there are major differences due to the orbital characteristics. On Mercury the 3:2 resonant rotation rate and the eccentric orbit causes local noon at longitudes 0° and 180° to coincide with perihelion, which leads to "hot poles". At longitudes 90° and 270° , local noon coincides with aphelion, which results in "cold poles" [8]. At these longitudes brief secondary sunrises and sunsets are visible, when Mercury's orbital angular velocity exceeds the spin rate during perihelion [8]. Here we present diurnal temperature curves of the Kuiper-Rudaki study region, based on thermophysical estimates and MESSENGER (Mercury Surface, Space Environment, Geochemistry, and Ranging [9]) albedo data with a resolution of 1000m/px. Our study region spans more than 90° along the equator, thus allowing us to study both, hot and

  18. Cross-Correlation based relocation of deep interface seismicity of the 2010 Chile Earthquake

    NASA Astrophysics Data System (ADS)

    Methe, P.; Tilmann, F. J.; Lange, D.

    2011-12-01

    The Chile earthquake of 27 February 2010 nucleated just north of the city of Concépcion, and ruptured to the north and to the south along 350-400 km, with most slip (up to 15 m) accumulating in the northern patch. With a magnitude of 8.8, it is the sixth-strongest earthquake since the beginning of the instrumental record; rapid response teams from Chile, the US, Germany and the UK installed a dense network for monitoring aftershocks along the whole rupture zone. We analysed a subset of this network (in total 139 stations) and detected over 100000 aftershocks following the main earthquake in the period from March to September 2010 alone, using automatic detection and grid-search based phase association algorithms (binder and CMM). Picks are refined by an auto-picking algorithm (MPX) and events are relocated in a minimum-1D model. About 20000 events are designated as very well located with at least 16 high quality automatic picks and a residual rms no larger than 0.2 s. Besides crustal seismicity, the aftershock sequence is dominated by intense plate interface seismicity near and immediately downdip of the most intense coseismic rupture. We also observe a second separate band of deeper aftershocks below the downdip end of the seismogenic zone at a depth of 40-50 km and a distance to the trench of 130-180 km, with a gap of 20-30 km to the main plate interface seismicity. In this presentation we concentrate on the analysis of this deep seismic band. The seismicity in this band is not truly continuous along the rupture zone but it is present along the whole rupture zone and forms clusters elongated along strike. Focal mechanisms derived from first motion polarities show that these events tend to be thrust type events, well aligned with the plate interface. A second deep separate group of plate interface aftershocks is not known from other subduction zone aftershock sequences. To get a better idea about the distribution of these 6000 deep aftershocks (30 to 50 km), a

  19. The Colour and Stereo Surface Imaging System for ESA's Trace Gas Orbiter

    NASA Astrophysics Data System (ADS)

    Thomas, Nicolas; Cremonese, Gabriele

    2016-04-01

    The Colour and Stereo Surface Imaging System (CaSSIS) is an 11 μrad/px imaging system ready to launch on the European Space Agency's (ESA) ExoMars Trace Gas Orbiter (TGO) on 14 March 2016 from Baikonur. CaSSIS is based around an 880 mm focal length carbon-fibre reinforced polymer (CFRP) telescope with a 135 mm primary mirror and a 2k x 2k CMOS hybrid detector with 10 micron pixel pitch providing 4.6 m/px imaging from the nominal 400 km circular orbit. The telescope is a slightly modified three mirror anastigmat optical configuration with no central obscuration. The instrument is designed to operate in "push-frame" mode where 2048 x 256 images are acquired at a repetition rate which matches the ground-track velocity (~3 km/s) allowing sufficient overlap for co-registration thereby building image strips along the surface. A filter strip assembly (FSA) is mounted directly above the detector providing images in 4 wavelength bands. Two of these (480.5nm and 676.5nm prior to convolution with the rest of the instrument) correspond closely to bands used by the HiRISE instrument on the Mars Reconnaissance Orbiter [4]. Two other filters split the NIR wavelengths with centres at 838 nm and close to 985 nm. Analyses show that the filters provide good differentiation between expected surface minerals, particularly Fe-bearing phases (Tornabene et al. LPSC, 2016). CaSSIS is designed to produce stereo from images acquired ~30 s apart by using a rotation drive. The telescope points 10 degrees off-nadir. The drive aligns the telescope with the ground-track direction so that the telescope is pointing forward. After image acquisition, the telescope is rapidly rotated by 180 degrees to point in the opposite direction and the second image of the stereo pair is acquired. CaSSIS will extend the monitoring of past missions to future years allowing the tracking of longer-term changes. It will also provide contemporaneous imaging of regions that may produce unique signatures detected by

  20. First geological mapping of 67P/Churyumov-Gerasimenko nucleus from Rosetta mission

    NASA Astrophysics Data System (ADS)

    Massironi, M.; Cremonese, G.; Giacomini, L.; Pajola, M.; Marchi, S.; Besse, S.; Thomas, N.; Vincent, J.-B.; Barucci, M. A.; Bertini, I.; Ferri, F.; Fornasier, S.; Lazzarin, M.; Magrin, S.; A'Hearn, M. F.; Marzari, F.; Snodgrass, C.; Naletto, G.; Barbieri, C.; Sierks, H.

    2014-04-01

    (CAT) characterization, the foreseen spacecraft distance will be rapidly reduced down to 52 km, giving the unique opportunity to get full frame images (2048 X 2048 px) and a complete coverage of the nucleus with a scale of 90 cm/px. It is worth pointing out that such images will provide the best ever cometary surface characterization to date; on top of all that, during the close operation phase a more detailed analysis of the surface is even expected, leading to 15 cm resolution images of specific 67P regions. In this phase the OSIRIS-Wide Angle Camera (WAC) will reach its highest spatial resolution of 1 m/px, allowing a comparative analysis with the NAC images acquired during the Comet Approach Trajectory. We will present the preliminary geological map created from these images (cometary distance from the Sun spanning between 3.6 and 3.4 AU during the month of August 2014), that will be considered as the reference mapping for the following surface modifications/changes due to the incipient cometary activity. Such a detailed geological analysis of the 67P cometary nucleus will be a newcomer in the cometary science frame.

  1. Genesis and fluid source in Arabia crater mounds: mapping, fractal analysis, and impact simulations

    NASA Astrophysics Data System (ADS)

    Pozzobon, R.; Mazzarini, F.; Rossi, A.; Lucchetti, A.; Pondrelli, M.; Marinangeli, L.; Martellato, E.; Cremonese, G.; Massironi, M.

    2013-12-01

    Arabia Terra is dominated by heavily cratered terrains, and some peculiar landforms can be found mostly in craters interior. With high-resolution images from HiRISE (25 cm/px) and CTX (6 m/px) cameras pitted cones, mounds and knobs can be easily recognized. Those mounds are interpreted to have worked as pathways for subsurface fluid. It is commonly hypothesized that Arabia Terra is an area of past fluid activity, being crater central bulges a place of sulfate precipitation. In this work we investigate the presence, origin and timing of their formation as well as the the depth of the mounds fluid source. The spatial distribution of monogenic eruptive structures within volcanic areas on Earth has been linked to fracture systems that allowed an efficient hydraulic connection between surface and crustal or subcrustal magma reservoirs. Self-similarity in vent distribution is described by a power law distribution with fractal exponent D and defined over a range of lengths comprised between a lower limit (lower cutoff, Lco) and an upper limit (upper cutoff, Uco). On Earth, volcanic vents as well as mud volcanoes have shown that the Uco of their fractal distribution scales with the depth of pressurized fluid reservoirs. The same approach has been this applied to mounds mapped at Firsoff and Crommelin craters. 431 mounds were mapped on Firsoff Crater's floor, and 160 on Crommelin Crater's floor. The reslulting Uco for both craters are similar giving a source depth of 2.3 ×0.3 km from Firsoff Crater's ground floor and 2.6 ×0.5 km from Crommelin's floor. Hence it is possible to hypothesize a common regional-scale pressurized fluid level at 2.5 km of depth from craters floor. Morphogic and stratigraphical analyses of the high-resolution imagery and topography of those mounds allowed us to discern from actual mud volcano candidates and stratigraphic erosional remnants. We also studied the craters formation by simulating the impact with the hydrocode. We used iSALE shock code

  2. Spectrophotometric properties of the nucleus of comet 67P/Churyumov-Gerasimenko from the OSIRIS instrument onboard the ROSETTA spacecraft

    NASA Astrophysics Data System (ADS)

    Fornasier, S.; Hasselmann, P. H.; Barucci, M. A.; Feller, C.; Besse, S.; Leyrat, C.; Lara, L.; Gutierrez, P. J.; Oklay, N.; Tubiana, C.; Scholten, F.; Sierks, H.; Barbieri, C.; Lamy, P. L.; Rodrigo, R.; Koschny, D.; Rickman, H.; Keller, H. U.; Agarwal, J.; A'Hearn, M. F.; Bertaux, J.-L.; Bertini, I.; Cremonese, G.; Da Deppo, V.; Davidsson, B.; Debei, S.; De Cecco, M.; Fulle, M.; Groussin, O.; Güttler, C.; Hviid, S. F.; Ip, W.; Jorda, L.; Knollenberg, J.; Kovacs, G.; Kramm, R.; Kührt, E.; Küppers, M.; La Forgia, F.; Lazzarin, M.; Lopez Moreno, J. J.; Marzari, F.; Matz, K.-D.; Michalik, H.; Moreno, F.; Mottola, S.; Naletto, G.; Pajola, M.; Pommerol, A.; Preusker, F.; Shi, X.; Snodgrass, C.; Thomas, N.; Vincent, J.-B.

    2015-11-01

    Context. The Rosetta mission of the European Space Agency has been orbiting the comet 67P/Churyumov-Gerasimenko (67P) since August 2014 and is now in its escort phase. A large complement of scientific experiments designed to complete the most detailed study of a comet ever attempted are onboard Rosetta. Aims: We present results for the photometric and spectrophotometric properties of the nucleus of 67P derived from the OSIRIS imaging system, which consists of a Wide Angle Camera (WAC) and a Narrow Angle Camera (NAC). The observations presented here were performed during July and the beginning of August 2014, during the approach phase, when OSIRIS was mapping the surface of the comet with several filters at different phase angles (1.3°-54°). The resolution reached up to 2.1 m/px. Methods: The OSIRIS images were processed with the OSIRIS standard pipeline, then converted into I/F radiance factors and corrected for the illumination conditions at each pixel using the Lommel-Seeliger disk law. Color cubes of the surface were produced by stacking registered and illumination-corrected images. Furthermore, photometric analysis was performed both on disk-averaged photometry in several filters and on disk-resolved images acquired with the NAC orange filter, centered at 649 nm, using Hapke modeling. Results: The disk-averaged phase function of the nucleus of 67P shows a strong opposition surge with a G parameter value of -0.13 ± 0.01 in the HG system formalism and an absolute magnitude Hv(1,1,0) = 15.74 ± 0.02 mag. The integrated spectrophotometry in 20 filters covering the 250-1000 nm wavelength range shows a red spectral behavior, without clear absorption bands except for a potential absorption centered at ~290 nm that is possibly due to SO2 ice. The nucleus shows strong phase reddening, with disk-averaged spectral slopes increasing from 11%/(100 nm) to 16%/(100 nm) in the 1.3°-54° phase angle range. The geometric albedo of the comet is 6.5 ± 0.2% at 649 nm, with

  3. Geomorphological and Spectrophotometric Study of Philae Landing Site A

    NASA Astrophysics Data System (ADS)

    Pajola, M.; La Forgia, F.; Giacomini, L.; Oklay, N.; Massironi, M.; Bertini, I.; Simioni, E.; Marzari, F.; Barbieri, C.; Naletto, G.; Groussin, O.; Lazzarin, M.; Scholten, F.; Preusker, F.; Fornasier, S.; Vincent, J. B.; Sierks, H.

    2015-10-01

    5 finalists, this site has the unique value to provide detailed analysis of the multiple fractures present on its cliff and on the neighboring Hathor. Figure 1: Site A as imaged by the OSIRIS NAC camera on 6 August 2014 at 02:20:12 UT. The distance from the comet center is 117.24 km, the scale is 2.17 m/px. EPSC Abstracts Vol. 10, EPSC2015-526, 2015 European Planetary Science Congress 2015 c Author(s) 2015 EPSC European Planetary Science Congress We here present the geomorphological map coupled with the size-frequency distributions of boulders # 2 m located on the different types of terrains here identified, such as outcropping layered terrains, gravitational accumulation deposits, taluses and fine particle deposits. Gravitational slopes, derived through the 67P shape model by assuming uniform density, have been used to characterize and better interpret the various terrains. Moreover, we show the spectrophotometric properties of the area, studied through images taken by OSIRIS NAC with a scale of 50 cm/px. Albedo maps, as well as surface reflectance spectra have been obtained by taking advantage of the shape model and DTM in order to correct for the illumination and observing conditions of the terrain. This multidisciplinary analysis highlights that different types of deposits show different photometric properties.

  4. Geological Mapping of the Ac-H-3 Dantu Quadrangle of Ceres from NASA's Dawn Mission.

    NASA Astrophysics Data System (ADS)

    Kneissl, Thomas; Schmedemann, Nico; Neesemann, Adrian; Williams, David A.; Crown, David A.; Mest, Scott C.; Buczkowski, Debra L.; Scully, Jennifer E. C.; Frigeri, Allessandro; Ruesch, Ottaviano; Hiesinger, Harald; Walter, Sebastian H. G.; Jaumann, Ralf; Roatsch, Thomas; Preusker, Frank; Kersten, Elke; Naß, Andrea; Nathues, Andreas; Platz, Thomas; Russell, Chistopher T.

    2016-04-01

    The Dawn Science Team is conducting a geologic mapping campaign for Ceres similar to that done for Vesta [1,2], including production of a Survey- and High Altitude Mapping Orbit (HAMO)-based global map and a series of 15 Low Altitude Mapping Orbit (LAMO)-based quadrangle maps. In this abstract we discuss the geologic evolution of the Ac-H-3 Dantu Quadrangle. The current map is based on a Framing Camera (FC) clear-filter image mosaic from HAMO data (~140 m/px) as well as a digital terrain model (DTM) derived from imagery of the Survey phase [3]. Albedo variations were identified and mapped using a mosaic of photometrically corrected HAMO images provided by DLR. FC color images provided further context for map unit identification. LAMO images (35m/pixel), which have just become available at the time of writing, will be used to update the map to be presented as a poster. The quadrangle is located between 21-66°N and 90-180°E in a large-scale depression north of the impact basin Kerwan. The northern and southeastern parts of the quadrangle are characterized by cratered terrain while the south and southwest are dominated by the partially smooth ejecta blankets of craters Dantu and Gaue. East-west oriented pit/crater chains in the southern half of the quadrangle might be related to tectonic processes [4,5]. Dantu crater (d=~126 km) is a complex impact crater showing slump terraces and a partially smooth crater floor with concentric and radial fractures. Furthermore, Dantu shows a central pit structure with pitted terrain on its floor as well as several bright spots in the interior and exterior of the crater. High-resolution measurements of crater size-frequency distributions (CSFDs) superposed on Dantu indicate a formation/modification age of ~200 - 700 Ma. Most of the ejecta appear to be relatively bright and correspond to parts of the #2 high albedo region observed with the Hubble Space Telescope [6]. However, the southwestern portion of the ejecta blanket is

  5. Application of a Newly Developed High-Sensitivity HBsAg Chemiluminescent Enzyme Immunoassay for Hepatitis B Patients with HBsAg Seroclearance

    PubMed Central

    Shinkai, Noboru; Matsuura, Kentaro; Sugauchi, Fuminaka; Watanabe, Tsunamasa; Murakami, Shuko; Iio, Etsuko; Ogawa, Shintaro; Nojiri, Shunsuke; Joh, Takashi

    2013-01-01

    We modified and automated a highly sensitive chemiluminescent enzyme immunoassay (CLEIA) for surface antigen (HBsAg) detection using a combination of monoclonal antibodies, each for a specific epitope of HBsAg, and by improving an earlier conjugation technique. Of 471 hepatitis B virus (HBV) carriers seen in our hospital between 2009 and 2012, 26 were HBsAg seronegative as determined by the Abbott Architect assay. The Lumipulse HBsAg-HQ assay was used to recheck those 26 patients who demonstrated seroclearance by the Abbott Architect assay. The performance of the Lumipulse HBsAg-HQ assay was compared with that of a quantitative HBsAg detection system (Abbott Architect) and the Roche Cobas TaqMan HBV DNA assay (CTM) (lower limit of detection, 2.1 log copies/ml) using blood serum samples from patients who were determined to be HBsAg seronegative by the Abbott Architect assay. Ten patients had spontaneous HBsAg loss. Of 8 patients treated with nucleotide analogues (NAs), two were HBsAg seronegative after stopping lamivudine therapy and 6 were HBsAg seronegative during entecavir therapy. Eight acute hepatitis B (AH) patients became HBsAg seronegative. Of the 26 patients, 16 were HBsAg positive by the Lumipulse HBsAg-HQ assay but negative by the Abbott Architect assay. The differences between the two assays in terms of detectable HBsAg persisted over the long term in the spontaneous loss group (median, 10 months), the NA-treated group (2.5 months), and the AH group (0.5 months). In 9 patients, the Lumipulse HBsAg-HQ assay detected HBsAg when HBV DNA was negative by the CTM assay. HBsAg was also detected by the Lumipulse HBsAg-HQ assay in 4 patients with an anti-HBs concentration of >10 mIU/ml, 3 of whom had no HBsAg escape mutations. The automatic, highly sensitive HBsAg CLEIA Lumipulse HBsAg-HQ is a convenient and precise assay for HBV monitoring. PMID:23946517

  6. Prediction of Preeclampsia Using the Soluble fms-Like Tyrosine Kinase 1 to Placental Growth Factor Ratio

    PubMed Central

    Gaccioli, Francesca; Cook, Emma; Hund, Martin; Charnock-Jones, D. Stephen; Smith, Gordon C.S.

    2017-01-01

    We sought to assess the ratio of sFlt-1 (soluble fms-like tyrosine kinase 1) to PlGF (placental growth factor) in maternal serum as a screening test for preeclampsia in unselected nulliparous women with a singleton pregnancy. We studied 4099 women recruited to the POP study (Pregnancy Outcome Prediction) (Cambridge, United Kingdom). The sFlt-1:PlGF ratio was measured using the Roche Cobas e411 platform at ≈20, ≈28, and ≈36 weeks of gestational age (wkGA). Screen positive was defined as an sFlt-1:PlGF ratio >38, but higher thresholds were also studied. At 28 wkGA, an sFlt-1:PlGF ratio >38 had a positive predictive value (PPV) of 32% for preeclampsia and preterm birth, and the PPV was similar comparing women with low and high prior risk of disease. At 36 wkGA, an sFlt-1:PlGF ratio >38 had a PPV for severe preeclampsia of 20% in high-risk women and 6.4% in low-risk women. At 36 wkGA, an sFlt-1:PlGF ratio >110 had a PPV of 30% for severe preeclampsia, and the PPV was similar comparing low- and high-risk women. Overall, at 36 wkGA, 195 (5.2%) women either had an sFlt-1:PlGF ratio of >110 or an sFlt-1:PlGF ratio >38 plus maternal risk factors: 43% of these women developed preeclampsia, about half with severe features. Among low-risk women at 36 wkGA, an sFlt-1:PlGF ratio ≤38 had a negative predictive value for severe preeclampsia of 99.2%. The sFlt-1:PlGF ratio provided clinically useful prediction of the risk of the most important manifestations of preeclampsia in a cohort of unselected nulliparous women. PMID:28167687

  7. Prévalence des dyslipidémies au laboratoire de biochimie du CHU Aristide le Dantec de Dakar, Sénégal

    PubMed Central

    Cissé, Fatou; Agne, Fatou Diallo; Diatta, Alassane; Mbengue, Abdou Salam; Ndiaye, Arame; Samba, Abdourahmane; Thiam, Souleymane; Doupa, Dominique; Sarr, Gaston Ndéné; Sall, Niama Diop; Touré, Méissa

    2016-01-01

    Introduction L'objectif de cette étude était d'évaluer la prévalence des dyslipidémies chez les patients reçus au laboratoire de Biochimie de l'Hôpital Aristide Le Dantec pour le dosage d'un paramètre lipidique au cours de l'année 2013. Méthodes Il s'agit d'une étude rétrospective portant sur 1356 patients âgés de 10 à 94 ans reçus au laboratoire de Biochimie du CHU Le Dantec de janvier à décembre 2013. Etaient inclus dans l'étude, tous les patients ayant au moins un paramètre du bilan lipidique dont les résultats étaient enregistrés dans le registre du laboratoire. Le cholestérol total, le cholestérol HDL, le cholestérol LDL ainsi que les triglycérides ont été dosés grâce à des méthodes enzymatiques sur un automate de Biochimie de type Cobas Integra 400 (Roche Diagnostics). Résultats La prévalence des dyslipidémies dans notre population d'étude est de 39,30%. Les prévalences de l'hypercholestérolémie, l'hypoHDLémie, l'hyperLDLémie, l'hypertriglycéridémie et l'hyperlipidémie mixte étaient respectivement : 30,89% ; 7,30% ; 31,19% ; 0,51% ; 7,22%. Les sujets de 40 à 59 ans semblaient être plus exposés et on note une prédominance féminine en ce qui concerne l'hypercholestérolémie (54,17% vs 45,82%), l'hypoHDLémie (54,54% vs45, 45%), et l'hyperlipidémie mixte (51,08% vs 48,97%). Enfin les dyslipidémies étaient fortement corrélées à l'HTA et l'obésité. Conclusion La forte prévalence des dyslipidémies retrouvée dans notre étude démontre l'intérêt d'étudier la prévalence des facteurs de risque cardio-vasculaires en particulier les dyslipidémies dans la population sénégalaise. PMID:28292030

  8. Reaching the Next Generation of College Students via Their Digital Devices.

    NASA Astrophysics Data System (ADS)

    Whitmeyer, S. J.; De Paor, D. G.; Bentley, C.

    2015-12-01

    Current college students attended school during a decade in which many school districts banned cellphones from the classroom or even from school grounds. These students are used to being told to put away their mobile devices and concentrate on traditional classroom activities such as watching PowerPoint presentations or calculating with pencil and paper. However, due to a combination of parental security concerns and recent education research, schools are rapidly changing policy and embracing mobile devices for ubiquitous learning opportunities inside and outside of the classroom. Consequently, many of the next generation of college students will have expectations of learning via mobile technology. We have developed a range of digital geology resources to aid mobile-based geoscience education at college level, including mapping on iPads and other tablets, "crowd-sourced" field projects, augmented reality-supported asynchronous field classes, 3D and 4D split-screen virtual reality tours, macroscopic and microscopic gigapixel imagery, 360° panoramas, assistive devices for inclusive field education, and game-style educational challenges. Class testing of virtual planetary tours shows modest short-term learning gains, but more work is needed to ensure long-term retention. Many of our resources rely on the Google Earth browser plug-in and application program interface (API). Because of security concerns, browser plug-ins in general are being phased out and the Google Earth API will not be supported in future browsers. However, a new plug-in-free API is promised by Google and an alternative open-source virtual globe called Cesium is undergoing rapid development. It already supports the main aspects of Keyhole Markup Language and has features of significant benefit to geoscience, including full support on mobile devices and sub-surface viewing and touring. The research team includes: Heather Almquist, Stephen Burgin, Cinzia Cervato, Filis Coba, Chloe Constants, Gene

  9. The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: a proteomic and bioinformatics study.

    PubMed

    Roselli, Sandro; Nadalig, Thierry; Vuilleumier, Stéphane; Bringel, Françoise

    2013-01-01

    Chloromethane (CH3Cl) is the most abundant volatile halocarbon in the atmosphere and contributes to the destruction of stratospheric ozone. The only known pathway for bacterial chloromethane utilization (cmu) was characterized in Methylobacterium extorquens CM4, a methylotrophic bacterium able to utilize compounds without carbon-carbon bonds such as methanol and chloromethane as the sole carbon source for growth. Previous work demonstrated that tetrahydrofolate and vitamin B12 are essential cofactors of cmuA- and cmuB-encoded methyltransferases of chloromethane dehalogenase, and that the pathway for chloromethane utilization is distinct from that for methanol. This work reports genomic and proteomic data demonstrating that cognate cmu genes are located on the 380 kb pCMU01 plasmid, which drives the previously defined pathway for tetrahydrofolate-mediated chloromethane dehalogenation. Comparison of complete genome sequences of strain CM4 and that of four other M. extorquens strains unable to grow with chloromethane showed that plasmid pCMU01 harbors unique genes without homologs in the compared genomes (bluB2, btuB, cobA, cbiD), as well as 13 duplicated genes with homologs of chromosome-borne genes involved in vitamin B12-associated biosynthesis and transport, or in tetrahydrofolate-dependent metabolism (folC2). In addition, the presence of both chromosomal and plasmid-borne genes for corrinoid salvaging pathways may ensure corrinoid coenzyme supply in challenging environments. Proteomes of M. extorquens CM4 grown with one-carbon substrates chloromethane and methanol were compared. Of the 49 proteins with differential abundance identified, only five (CmuA, CmuB, PurU, CobH2 and a PaaE-like uncharacterized putative oxidoreductase) are encoded by the pCMU01 plasmid. The mainly chromosome-encoded response to chloromethane involves gene clusters associated with oxidative stress, production of reducing equivalents (PntAA, Nuo complex), conversion of tetrahydrofolate

  10. Options to Expand HIV Viral Load Testing in South Africa: Evaluation of the GeneXpert® HIV-1 Viral Load Assay

    PubMed Central

    Gous, Natasha; Scott, Lesley; Berrie, Leigh; Stevens, Wendy

    2016-01-01

    Background Expansion of HIV viral load (VL) testing services are required to meet increased targets for monitoring patients on antiretroviral treatment. South Africa currently tests >4million VLs per annum in 16 highly centralised, automated high-throughput laboratories. The Xpert HIV-1 VL assay (Cepheid) was evaluated against in-country predicates, the Roche Cobas Taqmanv2 and Abbott HIV-1RT, to investigate options for expanding VL testing using GeneXpert’s random access, polyvalent capabilities and already established footprint in South Africa with the Xpert MTB/RIF assay (207 sites). Additionally, the performance of Xpert HIV-1VL on alternative, off-label specimen types, Dried Blood Spots (DBS) and whole blood, was investigated. Method Precision, accuracy (agreement) and clinical misclassification (1000cp/ml) of Xpert HIV-1VL plasma was compared to Taqmanv2 (n = 155) and Abbott HIV-1 RT (n = 145). Misclassification of Xpert HIV-1VL was further tested on DBS (n = 145) and whole blood (n = 147). Results Xpert HIV-1VL demonstrated 100% concordance with predicate platforms on a standardised frozen, plasma panel (n = 42) and low overall percentage similarity CV of 1.5% and 0.9% compared to Taqmanv2 and Abbott HIV-1 RT, respectively. On paired plasma clinical specimens, Xpert HIV-1VL had low bias (SD 0.32–0.37logcp/ml) and 3% misclassification at the 1000cp/ml threshold compared to Taqmanv2 (fresh) and Abbott HIV-1 RT (frozen), respectively. Xpert HIV-1VL on whole blood and DBS increased misclassification (upward) by up to 14% with increased invalid rate. All specimen testing was easy to perform and compatible with concurrent Xpert MTB/RIF Tuberculosis testing on the same instrument. Conclusion The Xpert HIV-1VL on plasma can be used interchangeably with existing predicate platforms in South Africa. Whole blood and DBS testing requires further investigation, but polyvalency of the GeneXpert offers a solution to extending VL testing services. PMID:27992495

  11. Prediction of Preeclampsia Using the Soluble fms-Like Tyrosine Kinase 1 to Placental Growth Factor Ratio: A Prospective Cohort Study of Unselected Nulliparous Women.

    PubMed

    Sovio, Ulla; Gaccioli, Francesca; Cook, Emma; Hund, Martin; Charnock-Jones, D Stephen; Smith, Gordon C S

    2017-04-01

    We sought to assess the ratio of sFlt-1 (soluble fms-like tyrosine kinase 1) to PlGF (placental growth factor) in maternal serum as a screening test for preeclampsia in unselected nulliparous women with a singleton pregnancy. We studied 4099 women recruited to the POP study (Pregnancy Outcome Prediction) (Cambridge, United Kingdom). The sFlt-1:PlGF ratio was measured using the Roche Cobas e411 platform at ≈20, ≈28, and ≈36 weeks of gestational age (wkGA). Screen positive was defined as an sFlt-1:PlGF ratio >38, but higher thresholds were also studied. At 28 wkGA, an sFlt-1:PlGF ratio >38 had a positive predictive value (PPV) of 32% for preeclampsia and preterm birth, and the PPV was similar comparing women with low and high prior risk of disease. At 36 wkGA, an sFlt-1:PlGF ratio >38 had a PPV for severe preeclampsia of 20% in high-risk women and 6.4% in low-risk women. At 36 wkGA, an sFlt-1:PlGF ratio >110 had a PPV of 30% for severe preeclampsia, and the PPV was similar comparing low- and high-risk women. Overall, at 36 wkGA, 195 (5.2%) women either had an sFlt-1:PlGF ratio of >110 or an sFlt-1:PlGF ratio >38 plus maternal risk factors: 43% of these women developed preeclampsia, about half with severe features. Among low-risk women at 36 wkGA, an sFlt-1:PlGF ratio ≤38 had a negative predictive value for severe preeclampsia of 99.2%. The sFlt-1:PlGF ratio provided clinically useful prediction of the risk of the most important manifestations of preeclampsia in a cohort of unselected nulliparous women.

  12. [Determination of hepatitis C virus genotype distribution in Mersin province, Turkey].

    PubMed

    Tezcan, Seda; Ulger, Mahmut; Aslan, Gönül; Yaraş, Serkan; Altıntaş, Engin; Sezgin, Orhan; Emekdaş, Gürol; Gürer Giray, Burcu; Sungur, Mehmet Ali

    2013-04-01

    Hepatitis C virus (HCV) is a member of the Flaviviridae family and the RNA genome e x hibit high genetic heterogeneity. Six major genotypes were phylogenetically determined and each genotype contains different subtypes. The distribution of HCV genotypes varies geographically throughout the world. Determination of viral genotype has great importance in the selection of antiviral therapy, treatment duration and monitoring the response to treatment. The aim of this study was to determine the distribution of HCV genotypes in Mersin province located at the Southern part of Turkey. A total of 236 patients (137 females, 99 males; mean age: 53.28 ± 14.99 years) with chronic HCV infection who were admitted to Mersin University Hospital Microbiology Laboratory during March 2010-May 2012 period were included in the study. The patients were anti-HCV (ELISA; Abbott Laboratories, USA) and HCV-RNA (Cobas TaqMan 48, Roche Diagnostic, USA) positive. HCV genotype analysis was determined by using a commercial LiPA kit (Line Probe Assay; AMPLIQUALITY HCV-TS; AB Analitica, Italy) based on the reverse hybridization of amplification products of viral 5'-UTR region. Out of the 236 patients, genotype 1b was observed in 84.7% (n= 200), genotype 3a in 4.2% (n= 10), genotype 1 in 3.8% (n= 9), genotype 1a/1b in 2.1% (n= 5), genotype 4a in 2% (n= 2), genotype 1a in 1.7% (n= 4), genotype 2b in 1.3% (n= 3), genotype 2 in 0.4% (n= 1), genotype 2a/2c in 0.4% (n= 1) and genotype 6 in 0.4% (n= 1). In the cases infected with genotype 1b, statistically significant differences were detected between gender distribution with the mean serum ALT (46.14 IU/L in females, 63.9 IU/L in males; p= 0.029) and HCV-RNA (634 x 103 IU/L in females, 20 x 105 IU/L in males; p= 0.005) levels. This was the first study that reflected the distribution of HCV genotypes in southern Turkey region. Genotype 1b, associated with poor prognosis and which had the highest prevalence in Turkey, was also determined as the most common

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

    PubMed Central

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

    2016-01-01

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

  14. Effect of maternal and neonatal factors on cord blood thyroid stimulating hormone

    PubMed Central

    Lakshminarayana, Sheetal G.; Sadanandan, Nidhish P.; Mehaboob, A. K.; Gopaliah, Lakshminarayana R.

    2016-01-01

    Background: Congenital hypothyroidism (CH) is most common preventable cause of mental retardation in children. Cord blood Thyroid Stimulating Hormone (CBTSH) level is an accepted screening tool for CH. Objectives: To study CBTSH profile in neonates born at tertiary care referral center and to analyze the influence of maternal and neonatal factors on their levels. Design: Cross retrospective sectional study. Methods: Study population included 979 neonates (males = 506 to females = 473). The CBTSH levels were estimated using electrochemiluminescence immunoassay on Cobas analyzer. Kit based cut-offs of TSH level were used for analysis. All neonates with abnormal CBSTH levels, were started on levothyroxine supplementation 10 μg/Kg/day and TSH levels were reassessed as per departmental protocol. Results: The mean CBTSH was 7.82 μIU/mL (Range 0.112 to 81.4, SD = 5.48). The mean CBTSH level was significantly higher in first order neonates, neonates delivered by assisted vaginal delivery and normal delivery, delivered at term or preterm, neonates with APGAR score <5 and those needing advanced resuscitation after birth. The CBTSH level >16.10 and <1.0 μIU/mL was found in 4.39 % and 1.02 % neonates respectively. The prevalence rate of CBTSH level >16.1 μIU/mL was significantly higher in neonates delivered by assisted vaginal delivery and normal delivery, term and preterm neonates, APAGR score of <5, presence of fetal distress, need for resuscitation beyond initial steps and in those with birth weight of <1.5 Kg. Three neonates were confirmed to have CH after retesting of TSH level. Conclusions: The CBTSH estimation is an easy, non-invasive method for screening for CH. The cutoff level of CB TSH (μIU/mL) >16.10 and <1.0 led to a recall of 5.41% of neonates which is practicable given the scenario in our Country. The mode of delivery and perinatal stress factors have a significant impact on CBTSH levels and any rise to be seen in the light of these factors. The prevalence

  15. Electronic excitation and charge transfer processes in collisions of H{sup +}, H{sub 2}{sup +}, and H{sub 3}{sup +} ions with carbon monoxide at typical solar-wind velocities

    SciTech Connect

    Werbowy, S.; Pranszke, B.

    2014-01-10

    Luminescence in the 200-580 nm spectral region was observed in the collisions of H{sup +}, H{sub 2}{sup +}, and H{sub 3}{sup +} with CO in the 50-1000 eV projectile energy range. Using computer simulations, we have identified emission of the following products in the observed spectra: the CO{sup +}(A-X) comet-tail system, CO{sup +}(B-X) first negative system, CO{sup +}(B-A) Baldet-Johnson system, and CO(b-a) third positive system. Also, an emission from atomic hydrogen (H{sub β} line at 486nm) has been observed. From the analysis of the experimental spectra, we have determined the absolute emission cross-sections for the formation of the observed products. Computer simulations gave the excited-product population distributions over vibrational and rotational energy levels. The vibrational level distribution from the CO{sup +}(A-X) comet-tail system is compared with the data for CO excited by 100 eV electrons and extreme ultraviolet radiation (XUV) photons. We have used these data to analyze the excitation conditions in the comet Humason (1961e). From the vibrational population distributions observed in the comet, we found that this distribution can be reproduced if electrons produce 25%, protons 70%, and XUV photons produce 5% of the emitting molecules. We find that the ratio of the CO{sup +}(B-X) emission to the sum of two main emissions (CO{sup +}(A-X)+CO{sup +}(B-X)) is velocity dependent and does not depend on the projectile ion type. For small velocities (below 100 km s{sup –1}) the ratio is about 5%, while for higher velocities it increases to 30%. For these data, we have found an empirical formula that satisfactorily describes the experimental data: R = R {sub max}(1 – v {sub th}/v), (where R {sub max} = 33%, v {sub th} = 87 km s{sup –1}). This could be used to infer the velocity of ions producing the observed emission of CO{sup +} products.

  16. Primary Screening for Cervical Cancer Based on High-Risk Human Papillomavirus (HPV) Detection and HPV 16 and HPV 18 Genotyping, in Comparison to Cytology

    PubMed Central

    Constantinidis, Theocharis; Constantinidis, Theodoros C.

    2015-01-01

    Objectives The objective of the present study is to assess the performance of a high-risk human papillomavirus (HR-HPV) DNA test with individual HPV-16/HPV-18 genotyping as a method for primary cervical cancer screening compared with liquid-based cytology (LBC) in a population of Greek women taking part in routine cervical cancer screening. Methods The study, conducted by the “HEllenic Real life Multicentric cErvical Screening” (HERMES) study group, involved the recruitment of 4,009 women, aged 25–55, who took part in routine cervical screening at nine Gynecology Departments in Greece. At first visit cervical specimens were collected for LBC and HPV testing using the Roche Cobas 4800 system. Women found positive for either cytology or HPV were referred for colposcopy, whereas women negative for both tests will be retested after three years. The study is ongoing and the results of the first screening round are reported herein. Results Valid results for cytology and HPV testing were obtained for 3,993 women. The overall prevalence of HR-HPV was 12.7%, of HPV-16 2.7% and of HPV-18 1.4%. Of those referred for colposcopy, cervical intraepithelial neoplasia grade 2 or worse (CIN2+) was detected in 41 women (1.07%). At the threshold of CIN2+, cytology [atypical squamous cells of undetermined significance (ASC-US) or worse] and HPV testing showed a sensitivity of 53.7% and 100% respectively, without change between age groups. Cytology and HPV testing showed specificity of 96.8% and 90.3% respectively, which was increased in older women (≥30) in comparison to younger ones (25–29). Genotyping for HPV16/18 had similar accuracy to cytology for the detection of CIN2+ (sensitivity: 58.5%; specificity 97.5%) as well as for triage to colposcopy (sensitivity: 58.5% vs 53.7% for cytology). Conclusion HPV testing has much better sensitivity than cytology to identify high-grade cervical lesions with slightly lower specificity. HPV testing with individual HPV-16/HPV-18

  17. Distribution and Predominance of Genotype 3 in Hepatitis C Virus Carriers in the Province of Kahramanmaras, Turkey

    PubMed Central

    Caliskan, Ahmet; Kirisci, Ozlem; Ozkaya, Esra; Ozden, Sevinc; Tumer, Seray; Caglar, Serkan; Guler, Selma Ates; Senol, Hande

    2015-01-01

    Background: The hepatitis C virus (HCV) has six major genotypes and more than 100 subtypes, and the determination of the responsible genotype, collection of epidemiological data, tailoring antiviral therapy, and prediction of prognosis have an important place in disease management. Objectives: The aim of the present study was to determine the distribution of HCV genotypes across geographic regions and compare these data with those obtained from other geographic locations. Patients and Methods: The HCV genotypes were identified in HCV RNA positive blood samples, obtained from different centers. The HCV genotype was determined using molecular methods [Real-Time Polymerase Chain Reaction (RT-PCR)] in 313 patients, who were found to be positive for HCV RNA. The presence of HCV RNA was investigated using the RT-PCR method in serum samples delivered to the Microbiology Laboratory at Kahramanmaras Necip Fazıl City Hospital, Kahramanmaras, Turkey, from the centers located in Kahramanmaras City center and peripheral districts of the province, between March 2010 and August 2014. The HCV genotype analysis was performed in HCV RNA positive samples, using RT-PCR reagents kit. Urine samples from the patients were tested for amphetamine with an Amphetamines II (AMPS2) kit, cocaine was tested with a Cocaine II (COC2) kit, opiates were tested with an Opiates II (OPI2) kit, and cannabinoids were tested with a Cannabinoids II (THC2) kit in Roche/Hitachi Cobas c501 device. Results: The blood samples collected from 313 patients were included in the study. Of these patients, 212 (67.7%) were male and 101 (32.3%) were female. The mean age of the patients was 41.29 ± 20.32 years. In terms of HCV genotype distribution, 162 patients (51.7%) had genotype 1, 144 patients (46%) had genotype 3, four patients (1.3%) had genotype 2, and three patients (1%) had genotype 4. The results of urine drug tests were available in only 65 patients (20.2%). Of these, 61 (93.8%) patients had HCV genotype 3

  18. Effects of Growth Hormone/IGF-I and Exercise on Unloaded Bones

    NASA Technical Reports Server (NTRS)

    Harper, J. S.; Arnaud, S. B.; Gosselink, K. L.; Grindeland, R. E.

    1994-01-01

    Growth hormone (GH) and insulin-like growth factor-I (IGF-I) in combination with exercise prevent muscle atrophy induced by unloading in the tail-suspension rat model for space flight (Gosselink et al, FASEB J 1994). This study evaluated the effects of these treatments on bone. Hypophysectomized rats were suspended (S) and treated with 1mg/kg/day CH plus IGF-I (H) or vehicle (Sal) daily by injection and exercised (Ex) by 3 climbs up a 1m ladder carrying a load equal to 30% the initial body weight (BW) 3x/day for 10 days. Tibial epiphysis (Epi) widths were measured by micrometry and femoral Bone Mineral Content (fBMC) in excised femurs by DEXA (Lunar DPX-L). Serum calcium (Ca) and phosphorus (Pi) were measured by COBAS Autoanalyzer (Roche Diag.). Ambulatory (Amb)-H treated rats showed growth rates of 6.6+-0.9 g/day, similar to S-H-Ex and higher than S-H (3.210.6, p less than 0.05) and S-Sal (-0.711.0, p less than 0.05). Epi widths were 10% lower in S-Sal, and S-Sal-Ex, and increased 100% in all H groups. fBMC was less in S than Amb, only when all S groups are compared to both Amb groups (p less than 0.03). H treatment increased fBMC (p less than 0.05) but reduced fBMC/100g BW in all H groups (p less than 0.001). The reduced density of H bone cannot be attributed to low circulating Ca. and Pi since they were higher in H than Sal (p less than 0.001). H treatment for 10 days in doses sufficient to support normal growth in BW failed to produce normal Epi widths or fBMC, even when combined with exercise. The suspension effect observed in Epi widths was not corrected by H or Ex alone, but was improved by H plus a This regimen. although effective in preventing muscle atrophy, failed to return bone measures, Epi widths and fBMC, to normal.

  19. [Comparison of two commercial molecular assays for quantitative measurement of hepatitis B viral DNA].

    PubMed

    Zalewska, Małgorzata; Domagała, Małgorzata; Gładysz, Andrzej

    2003-12-01

    The detection and quantification of hepatitis B virus (HBV) genomes appear to be the most reliable method for monitoring HBV infection and assessing responses to antiviral treatment. For quantitative determination of HBV viremia molecular biology-based assays are used. The aim of this study was to compare and evaluate the performance of two HBV DNA detection and quantification commercial assays: hybrid-capture Digene Hybrid Capture HBV DNA assays and based on competitive polymerase chain reaction (PCR) Cobas Amplicor HBV Monitor Roche Diagnostics. Reproducibility, linearity, sensitivity were determined with 2-fold dilution series of high-titers samples and with 113 sera samples from patients with chronic HBV infection. Within-run and between-run coefficients of variation ranged from 2.4-9.7% for hybrid-capture and from 3.7-15% for PCR-based Monitor. The hybrid-capture and PCR Monitor assays appeared to be linear throughout their range of quantification: 5-2000 pg/ml and 2 x 10(2)-2 x 10(5) copies/ml respectively. The HBV DNA units used in the two assays were not comparable. Hybrid-capture and Monitor gave concordant results with 87 (82.1%) of 106 samples. The assays were both positive with 79 (74.5%) samples and were negative in 7 (7.5%) cases. Hybrid-capture and Monitor gave discordant results in 17 (17.9%) cases. The Monitor Assay was positive in 13 (61.9%) of the 21 samples negative in hybrid-capture. The competitive PCR-based Monitor assay appear to be significantly more sensitive but slightly less reproducible than the hybrid-capture. In the group of patients with seroconversion to anti-HBe PCR method should be used for measurement of viral load. In the presence of HBe antigen concentration of HBV DNA may be tested by hybrid-capture assay. Also these two assays may be used in complementary fashion in the management of HBV infected patients. It seems reasonable to use a hybrid-capture assay first, because its linear range of quantification is extended to high

  20. Analytical Interference in Serum Iron Determination Reveals Iron Versus Gadolinium Transmetallation With Linear Gadolinium-Based Contrast Agents

    PubMed Central

    Fretellier, Nathalie; Poteau, Nathalie; Factor, Cécile; Mayer, Jean-François; Medina, Christelle; Port, Marc; Idée, Jean-Marc; Corot, Claire

    2014-01-01

    Objectives The purposes of this study were to evaluate the risk for analytical interference with gadolinium-based contrast agents (GBCAs) for the colorimetric measurement of serum iron (Fe3+) and to investigate the mechanisms involved. Materials and Methods Rat serum was spiked with several concentrations of all molecular categories of GBCAs, ligands, or “free” soluble gadolinium (Gd3+). Serum iron concentration was determined by 2 different colorimetric methods at pH 4.0 (with a Vitros DT60 analyzer or a Cobas Integra 400 analyzer). Secondly, the cause of interference was investigated by (a) adding free soluble Gd3+ or Mn2+ to serum in the presence of gadobenic acid or gadodiamide and (b) electrospray ionization mass spectrometry. Results Spurious decrease in serum Fe3+ concentration was observed with all linear GBCAs (only with the Vitros DT60 technique occurring at pH 4.0) but not with macrocyclic GBCAs or with free soluble Gd3+. Spurious hyposideremia was also observed with the free ligands present in the pharmaceutical solutions of the linear GBCAs gadopentetic acid and gadodiamide (ie, diethylene triamine pentaacetic acid and calcium-diethylene triamine pentaacetic acid bismethylamide, respectively), suggesting the formation of Fe-ligand chelate. Gadobenic acid-induced interference was blocked in a concentration-dependent fashion by adding a free soluble Gd3+ salt. Conversely, Mn2+, which has a lower affinity than Gd3+ and Fe3+ for the ligand of gadobenic acid (ie, benzyloxypropionic diethylenetriamine tetraacetic acid), was less effective (interference was only partially blocked), suggesting an Fe3+ versus Gd3+ transmetallation phenomenon at pH 4.0. Similar results were observed with gadodiamide. Mass spectrometry detected the formation of Fe-ligand with all linear GBCAs tested in the presence of Fe3+ and the disappearance of Fe-ligand after the addition of free soluble Gd3+. No Fe-ligand chelate was found in the case of the macrocyclic GBCA gadoteric

  1. Evidence regarding human papillomavirus testing in secondary prevention of cervical cancer.

    PubMed

    Arbyn, Marc; Ronco, Guglielmo; Anttila, Ahti; Meijer, Chris J L M; Poljak, Mario; Ogilvie, Gina; Koliopoulos, George; Naucler, Pontus; Sankaranarayanan, Rengaswamy; Peto, Julian

    2012-11-20

    screening provides a further small gain in sensitivity at the expense of a considerable loss in specificity if positive by either test is referred to colposcopy, in comparison with HPV testing only. Randomised trials and follow-up of cohort studies consistently demonstrate a significantly lower cumulative incidence of CIN3+ and even of cancer, in women aged 30 years or older, who were at enrollment hrHPV DNA negative compared to those who were cytologically negative. The difference in cumulative risk of CIN3+ or cancer for double negative (cytology & HPV) versus only HPV-negative women is small. HC2, GP5+/6+ PCR (polymerase chain reaction), cobas(®) 4800 PCR (Roche Molecular Systems Inc., Alameda, CA, USA) and Real Time PCR (Abbott Molecular, Des Plaines, IL, USA) can be considered as clinically validated for use in primary screening. The loss in specificity associated with primary HPV-based screening can be compensated by appropriate algorithms involving reflex cytology and/or HPV genotyping for HPV16 or 18. There exists a substantial evidence base to support that HPV testing is advantageous both in triage of women with equivocal abnormal cytology, in surveillance after treatment of CIN lesions and in primary screening of women aged 30 years or older. However, the possible advantages offered by HPV-based screening require a well organised program with good compliance with screening and triage policies. This article forms part of a special supplement entitled "Comprehensive Control of HPV Infections and Related Diseases" Vaccine Volume 30, Supplement 5, 2012.

  2. Clinical applicability and cost of a 46-gene panel for genomic analysis of solid tumours: Retrospective validation and prospective audit in the UK National Health Service

    PubMed Central

    Kaur, Kulvinder; Camps, Carme; Kaisaki, Pamela; Gupta, Avinash; Talbot, Denis; Middleton, Mark; Henderson, Shirley; Cutts, Anthony; Vavoulis, Dimitrios V.; Housby, Nick; Taylor, Jenny C.; Schuh, Anna

    2017-01-01

    Background Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing. Methods and findings We validated a 46-gene hotspot cancer panel assay allowing multiple gene testing from small diagnostic biopsies. From 1 January 2013 to 31 December 2013, solid tumour samples (including non-small-cell lung carcinoma [NSCLC], colorectal carcinoma, and melanoma) were sequenced in the context of the UK National Health Service from 351 consecutively submitted prospective cases for which treating clinicians thought the patient had potential to benefit from more extensive genetic analysis. Following histological assessment, tumour-rich regions of formalin-fixed paraffin-embedded (FFPE) sections underwent macrodissection, DNA extraction, NGS, and analysis using a pipeline centred on Torrent Suite software. With a median turnaround time of seven working days, an integrated clinical report was produced indicating the variants detected, including those with potential diagnostic, prognostic, therapeutic, or clinical trial entry implications. Accompanying phenotypic data were collected, and a detailed cost analysis of the panel compared with single gene testing was undertaken to assess affordability for routine patient care. Panel sequencing was successful for 97% (342/351) of tumour samples in the prospective cohort and showed 100% concordance with known mutations (detected using cobas assays). At least one mutation was identified in 87% (296/342) of

  3. Airborne & SAR Synergy Reveals the 3D Structure of Air Bubble Entrainment in Internal Waves and Frontal Zones

    NASA Astrophysics Data System (ADS)

    da Silva, J. C. B.; Magalhaes, J. M.; Batista, M.; Gostiaux, L.; Gerkema, T.; New, A. L.

    2013-03-01

    spectral range 8-12 μm. With a nominal ground resolution of approximately 1.5 meters (at an altitude of 500 meters) it is capable to detect fine structure associated to turbulence. The LiDAR system that has been used is the Leica ALS50-II (1064nm) with a hit rate greater than 1 hit per square meter and a vertical resolution of approximately 15 cm. Both systems were available simultaneously, together with the hyperspectral system and the RCD105 39Mpx digital camera, integrated with the LiDAR navigation system. We analyse the airborne data together with a comprehensive dataset of satellite Synthetic Aperture Radar (SAR) that includes ENVISAT and TerraSAR-X images. In addition, in situ observations in the near-shore zone were obtained in a previous experiment (Project SPOTIWAVE-II POCI/MAR/57836/2004 funded by the Portuguese FCT) during the summer period in 2006. These included thermistor chain measurements along the water column that captured the vertical structure of shoaling internal (tidal) waves and ISWs close to the breaking point. The SAR and airborne images were obtained in light wind conditions, in the near-shore zone, and in the presence of ISWs. The LiDAR images revealed sub-surface structures (some 1-2 m below the sea surface) that were co-located with surface films. These film slicks were induced by the convergent fields of internal waves and upwelling fronts. Some of the sub-surface features were located over the front slopes of the internal waves, which coincides with the internal wave slick band visible in the aerial photos and hyperspectral systems. Our flight measurements revealed thermal features similar to “boils” of cold water within the wake of (admittedly breaking) internal waves. These features are consistent with the previous in situ measurements of breaking ISWs. In this paper we will show coincident multi-sensor airborne and satellite SAR observations that reveal the 3D structure of air bubble entrainment in the internal wave field and frontal