Science.gov

Sample records for cobas taqscreen mpx

  1. Luminosity monitoring in ATLAS with MPX detectors

    NASA Astrophysics Data System (ADS)

    Sopczak, A.

    2014-01-01

    The ATLAS-MPX detectors are based on the Medipix2 silicon devices designed by CERN for the detection of multiple types of radiation. Sixteen such detectors were successfully operated in the ATLAS detector at the LHC and collected data independently of the ATLAS data-recording chain from 2008 to 2013. Each ATLAS-MPX detector provides separate measurements of the bunch-integrated LHC luminosity. An internal consistency for luminosity monitoring of about 2% was demonstrated. In addition, the MPX devices close to the beam are sensitive enough to provide relative-luminosity measurements during van der Meer calibration scans, in a low-luminosity regime that lies below the sensitivity of the ATLAS calorimeter-based bunch-integrating luminometers. Preliminary results from these luminosity studies are presented for 2012 data taken at √s = 8 TeV proton-proton collisions.

  2. Luminosity Monitoring in ATLAS with MPX Detectors

    NASA Astrophysics Data System (ADS)

    Asbah, Nedaa

    2014-06-01

    The ATLAS-MPX detectors are based on the Medipix2 silicon devices designed by CERN for the detection of multiple types of radiation. Sixteen such detectors were successfully operated in the ATLAS detector at the LHC and collected data independently of the ATLAS data-recording chain from 2008 to 2013. Each ATLAS-MPX detector provides separate measurements of the bunch-integrated LHC luminosity. An internal consistency for luminosity monitoring of about 2% was demonstrated. In addition, the MPX devices close to the beam are sensitive enough to provide relative-luminosity measurements during van der Meer calibration scans, in a low-luminosity regime that lies below the sensitivity of the ATLAS calorimeter-based bunch-integrating luminometers. Preliminary results from these luminosity studies are presented for 2012 data taken at √ s = 8 TeV proton-proton collisions.

  3. Remote control of ATLAS-MPX Network and Data Visualization

    NASA Astrophysics Data System (ADS)

    Turecek, D.; Holy, T.; Pospisil, S.; Vykydal, Z.

    2011-05-01

    The ATLAS-MPX Network is a network of 15 Medipix2-based detector devices, installed in various positions in the ATLAS detector at CERN, Geneva. The aim of the network is to perform a real-time measurement of the spectral characteristics and the composition of radiation inside the ATLAS detector during its operation. The remote control system of ATLAS-MPX controls and configures all the devices from one place, via a web interface, accessible from different operating systems. The Data Visualization application, also with a web interface, has been developed in order to present measured data to the scientific community. It allows to browse through recorded frames from all devices and to search for specific frames by date and time. Charts containing the number of different types of tracks in each frame as a function of time may be rendered from the database.

  4. Measurement of the Radiation Field in Atlas with the Atlas-Mpx Detectors

    NASA Astrophysics Data System (ADS)

    Campbell, Michael; Heijne, Erik; Leroy, Claude; Martin, Jean-Pierre; Mornacchi, Giuseppe; Nessi, Marzio; Pospisil, Stanislav; Solc, Jaroslav; Soueid, Paul; Suk, Michal; Turecek, Daniel; Vykydal, Zdenek

    2012-08-01

    A network of 16 ATLAS-MPX (silicon pixelated) detectors has been installed by the ATLAS-MPX Collaboration at various positions within the ATLAS detector and its environment. The ATLAS-MPX detectors allow real-time measurements of spectral characteristics and composition of the radiation field inside and around the ATLAS detector during its operation. Results obtained with the ATLAS-MPX detectors are reported in this article. They include luminosity measurement obtained with van der Meer luminosity scans and measurement of induced radioactivity in between/after collision.

  5. 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

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

    PubMed

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

    2016-01-01

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

  7. 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. PMID:26611812

  8. TSH Comparison Between Chemiluminescence (Architect) and Electrochemiluminescence (Cobas) Immunoassays: An Indian Population Perspective.

    PubMed

    Sarkar, Rajarshi

    2014-04-01

    Although 3rd generation TSH assays are the most widely used immunoassays, credible comparison studies, specially involving Indian sub-populations are practically non-existent. To compare the TSH measurements between chemiluminescence (Architect) and electrochemiluminescence (Cobas) inmmunoassays in an urban ambulatory Indian population. 1,615 subjects were selected randomly from the usual laboratory workflow, their TSH measured in Architect and Cobas and the paired data thus generated were statistically analysed. TSH values of Cobas were observed to be higher than the Architect values by 28.7 %, with a significant proportional difference between the two, but majority of the Cobas values (above 90 %) were within the limits of agreement with Architect values. In situations where both the instruments are in use simultaneously, a standardization of the methods is imperative, in larger interest of the patient populace. PMID:24757301

  9. Laboratory evaluation of the COBAS MIRA S random access analyser.

    PubMed

    Kanluan, T; Intaramanee, S; Tangvarasittichai, S; Tangvarasittichai, O; Suwanton, L; Manochiopinij, S; Tantrarongroj, S; Leangphibul, P

    1991-01-01

    The random access analyser COBAS MIRA S (Roche Diagnostics) was evaluated for two months. The instrument is a computer-controlled discrete analyser which can be run in a combination profile and single test mode. This instrument has special features, including an automatic cuvette segment changer, a reagent rack cooling system, an external keyboard and monitor, as well as a bar-code facility for the entry of test parameters, worklists and sample identification numbers. Study of within-run and between-run precision gave values of % CV 0.54-3.37 and 0.61-3.65, respectively, for a variety of assays. Linearity testing to the upper limit of each test was also studied and were found to cover the necessary pathological range. Within the two-month period, no major problems were encountered. The instrument required minimum operator attention during operation. Correlation studies with the Hitachi 705 using six clinical chemistry tests (glucose, cholesterol, triglyceride, ALP, AST, ALT) gave correlation coefficients ranging from 0.95-0.99 and slopes of 0.91-1.17. PMID:18924890

  10. 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

  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. 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

  13. 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

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

    PubMed

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

    2015-12-01

    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

  15. 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

  16. Analytic and Clinical Performance of cobas HPV Testing in Anal Specimens from HIV-Positive Men Who Have Sex with Men

    PubMed Central

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

    2014-01-01

    Anal human papillomavirus (HPV) infections are common, and the incidence of anal cancer is high in HIV-infected men who have sex with men (MSM). To evaluate the performance of HPV assays in anal samples, we compared the cobas HPV test (cobas) to the Roche Linear Array HPV genotyping assay (LA) and cytology in HIV-infected MSM. Cytology and cobas and LA HPV testing were conducted for 342 subjects. We calculated agreement between the HPV assays and the clinical performance of HPV testing and HPV genotyping alone and in combination with anal cytology. We observed high agreement between cobas and LA, with cobas more likely than LA to show positive results for HPV16, HPV18, and other carcinogenic types. Specimens testing positive in cobas but not in LA were more likely to be positive for other markers of HPV-related disease compared to those testing negative in both assays, suggesting that at least some of these were true positives for HPV. cobas and LA showed high sensitivities but low specificities for the detection of anal intraepithelial neoplasia grade 2/3 (AIN2/3) in this population (100% sensitivity and 26% specificity for cobas versus 98.4% sensitivity and 28.9% specificity for LA). A combination of anal cytology and HPV genotyping provided the highest accuracy for detecting anal precancer. A higher HPV load was associated with a higher risk of AIN2/3 with HPV16 (Ptrend < 0.001), HPV18 (Ptrend = 0.07), and other carcinogenic types (Ptrend < 0.001). We demonstrate that cobas can be used for HPV detection in anal cytology specimens. Additional tests are necessary to identify men at the highest risk of anal cancer among those infected with high-risk HPV. PMID:24899025

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

    PubMed

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

    2016-09-01

    We assess the concordance between low level HCV values obtained using the VERSANT HCV RNA 1.0 Assay (kPCR) and COBAS AmpliPrep/COBAS TaqMan HCV Quantitative Test v2.0. The correlation between the values obtained by the two RT-PCR assays for samples with quantifiable HCV RNA levels revealed that viral load measured by kPCR significantly correlated with that of the CAP/CTM (R=0.644, P<0.0001). The results show a good concordance (n=126/144, 87%); discordant results were mainly observed in the assessment of values below the lower limit of detection of the assays. These variations may have an impact on clinical decisions for patients on HCV triple therapy or interferon- free regimens. It is therefore recommended to monitor individual patients with the same test throughout treatment. PMID:27602422

  18. Cervical Cytology Specimen Stability in Surepath Preservative and Analytical Sensitivity for HPV Testing with the cobas and Hybrid Capture 2 Tests

    PubMed Central

    Malmberg, Elisabeth; Lunt, Tatum C.; Schlaberg, Robert

    2016-01-01

    None of the commercial HPV tests are U.S. FDA-approved for testing of cervical cytology specimens in SurePath preservative. Still, ~30% of HPV testing is performed on specimens in this formalin-containing preservative. Formalin-induced DNA fragmentation and cross-linking may interfere with HPV detection. We evaluated analytical sensitivity and specimen stability of the cobas 4800 HPV (Roche) and Hybrid Capture 2 HPV (HC2, Qiagen) tests with residual cervical cytology samples in SurePath preservative available within 1 week of collection. Cobas testing was performed with and without heating samples at 120°C for 20 min diluted 1:1 in an alkaline environment (pretreatment) to revert DNA crosslinking. Stability was tested after 2 weeks of storage at ambient temperature followed by ≤10 weeks at 4°C. Analytical sensitivity and positivity rates (HC2, 18%; cobas pretreated, 46%; cobas untreated, 47%) were greater for cobas than HC2 (n = 682). After 6 weeks of storage, mean HC2 ratios were lower (mean 0.9, SD 6.3) but high variability limited statistical power to detect trends. Cobas threshold cycles (Ct’s) increased in untreated (mean 2.1) but not pretreated samples (mean 0.3; n = 110; p≤0.0001). Overall, cobas had greater analytical sensitivity for samples in SurePath preservative. Although pretreatment introduced a manual sample transfer step and 30 min of incubation times, it improved stability without negatively affecting analytical sensitivity. While awaiting results of large trials to evaluate the clinical performance of cobas, the addition of the pretreatment step may improve the detection of HPV, especially after prolonged sample storage. PMID:26905067

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

    PubMed

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

    2015-12-01

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

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

    PubMed

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

    2014-01-01

    The introduction of nucleic acid amplification techniques (NAT) in blood banks was intended to reduce the residual risk of transfusion-transmitted infections. Co-circulation of a great diversity of HIV-1 variants in Argentina portrays the need to assess the sensitivity of serological and molecular assays available for their detection. In this study, we evaluated the sensitivity of the COBAS AmpliScreen™ HIV-1 Test, version 1.5 (Roche) for the detection of HIV-1 RNA in plasma samples of infected individuals from Argentina. The results of this study reveal that this technique has high sensitivity for the detection of HIV-1 RNA under assay conditions: using mini-pool testing, pools ≥ 50 RNA copies per ml achieved ≥ 92 % sensitivity, whereas in the standard procedure, samples ≥ 207 RNA copies/ml achieved 100 % sensitivity. Moreover, the COBAS AmpliScreen™ HIV-1 Test, version 1.5 (Roche) is suitable for detecting prevailing HIV-1 variants. PMID:25444127

  1. Supplementary testing is not required in the cobas 4800 CT/NG test for Neisseria gonorrhoeae weak-positive urogenital samples.

    PubMed

    Bromhead, Collette; Liyanarachchy, Nadika; Mayes, Julia; Upton, Arlo; Balm, Michelle

    2015-01-01

    Weak-positive Neisseria gonorrhoeae nucleic acid amplification test results are difficult to interpret. We show that the frequency of unconfirmed N. gonorrhoeae results from the cobas 4800 test rises exponentially after 38.0 cycles, where the likelihood of an unconfirmed result exceeds 29%. Supplementary testing of such samples should be avoided; instead, treatment should be based on clinical pretest probability. PMID:25392357

  2. Supplementary Testing Is Not Required in the cobas 4800 CT/NG Test for Neisseria gonorrhoeae Weak-Positive Urogenital Samples

    PubMed Central

    Liyanarachchy, Nadika; Mayes, Julia; Upton, Arlo; Balm, Michelle

    2014-01-01

    Weak-positive Neisseria gonorrhoeae nucleic acid amplification test results are difficult to interpret. We show that the frequency of unconfirmed N. gonorrhoeae results from the cobas 4800 test rises exponentially after 38.0 cycles, where the likelihood of an unconfirmed result exceeds 29%. Supplementary testing of such samples should be avoided; instead, treatment should be based on clinical pretest probability. PMID:25392357

  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 Central

    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. PMID:25789737

  4. Discordance Between Cobas BRAF V600 Testing and VE1 Immunohistochemistry in a Melanoma Patient With Bone Marrow Metastases.

    PubMed

    Rapisuwon, Suthee; Busam, Klaus J; Parks, Kellie; Chapman, Paul B; Lee, Elsie; Atkins, Michael B

    2016-09-01

    False negative result remains an ongoing problem in direct gene sequencing of cancers. It is important to use the appropriate mutation detection method most appropriate to each circumstance and the available tissue. Here, we report a patient with melanoma of unknown primary with metastases to spleen and bone marrow, who was tested negative for Cobas BRAF V600E mutation, whose cancer progressed on antiprogrammed death 1 (PD1) receptor monoclonal antibody therapy. Subsequent VE1 immunohistochemistry was positive for BRAF V600E mutation, and the tumor responded dramatically to v-Raf murine sarcoma viral oncogene homolog B (BRAF)/Mitogen-activated protein kinase inhibitor combination therapy. This demonstrates how alternative BRAF testing methodology could produce results that can influence treatment choice and the outcome. PMID:27541170

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

    PubMed

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

    2010-11-01

    Laboratory analysis of blood specimens is an increasingly important tool for rapid diagnosis and control of therapy. So, miniaturization of test systems is needed, but reduced specimens might impair test quality. For rapid detection and quantitation of HBV DNA, the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV test has proved a robust instrument in routine diagnostic services. The test system has been modified recently for application of reduced samples of blood plasma and for blood serum, too. The performance of this modified COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV v2.0 (HBV v2.0 (this test is currently not available in the USA)) test was evaluated by comparison with the former COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV v1.0 (HBV v1.0) test. In this study a platform correlation of both assay versions was done including 275 HBV DNA positive EDTA plasma samples. Comparable results were obtained (R(2)=0.97, mean difference -0.03 log(10)IU/ml). The verification of equivalency of the sample matrix (plasma vs. serum samples tested in HBV v2.0 in the same run) showed comparable results for all 278 samples with a R(2)=0.99 and a mean difference of 0.06 log(10)IU/ml. In conclusion, the new test version HBV v2.0 is highly specific and reproducible and quantifies accurately HBV DNA in EDTA plasma and serum samples from patients with chronic HBV infection. PMID:20728470

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

    PubMed

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

    2016-01-01

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

  7. Comparison of Human Papillomavirus Detection by Aptima HPV and cobas HPV Tests in a Population of Women Referred for Colposcopy following Detection of Atypical Squamous Cells of Undetermined Significance by Pap Cytology

    PubMed Central

    Castle, Philip E.; Eaton, Barbara; Reid, Jennifer; Dockter, Janel

    2015-01-01

    Few studies have compared the cobas HPV test to the Aptima HPV assay (AHPV) and the Aptima HPV 16 18/45 genotype assay (AHPV GT) for high-risk human papillomavirus (hrHPV) detection, clinical performance in detecting cervical intraepithelial neoplasia grade 2 (CIN2) or more severe (CIN2+) diagnoses, and risk stratification by partial HPV genotyping. The cobas HPV test is a DNA test that separately and concurrently detects HPV16, HPV18, and a pool of 12 other hrHPV types. AHPV is an RNA test for a pool of 14 hrHPV genotypes, and AHPV GT is an RNA test run on AHPV-positive results to detect HPV16 separately from HPV18 and HPV45, which are detected together. In a population of patients (n = 988) referred for colposcopy because of a cervical Pap cytology result of atypical squamous cells of undetermined significance (ASC-US), a cervical scrape specimen was taken, placed into a ThinPrep Pap test vial containing PreservCyt liquid cytology medium, and tested in a blinded fashion with cobas and AHPV and with AHPV GT for AHPV-positive results. The final diagnoses were based on a consensus panel review of the biopsy specimen histology. AHPV and cobas were equally sensitive for CIN2+ diagnoses (89.4% each; P = 1.000), and AHPV was more specific than cobas (63.1% versus 59.3%; P ≤ 0.001). The percent total agreement, percent positive agreement, and kappa value were 90.9%, 81.1%, and 0.815, respectively. Risk stratification using partial HPV genotyping was similar for the two assays. AHPV and AHPV GT had similar sensitivity and risk stratification to cobas HPV, but they were more specific than cobas HPV. PMID:25653409

  8. Rapid colorimetric assay of urinary beta-galactosidase and N-acetyl-beta-D-glucosaminidase with Cobas Mire Auto-analyzer.

    PubMed

    Xu, G; Zhu, L; Hong, J; Cao, Y; Xia, T

    1999-01-01

    A rapid and simple colorimetric method for the assay of urinary beta-galactosidase (GAL) and N-acetyl-beta-D-glucosaminidase (NAG) using 4-nitrophenyl-glycosides as the substrates and a Cobas Mire Auto-analyzer is described. Optimal conditions for this method including substrate concentration, ionic strength, pH and incubation time were characterized. Endogenous substances in urine did not interfere with the assays. Incubation time could be shortened to 10 minutes. A small volume of an alkaline buffer to terminate the enzyme reaction achieved better sensitivity and accuracy. Buffer-substrate solutions were stable for at least one week at 4 degrees C. Normal values of the two urinary enzymes are also reported. PMID:10323472

  9. cobas 4800 HPV Test, a real-time polymerase chain reaction assay for the detection of human papillomavirus in cervical specimens.

    PubMed

    Isidean, Sandra D; Coutlée, François; Franco, Eduardo L

    2014-01-01

    Cervical cancer screening incorporating high-risk human papillomavirus (HPV) detection has become the preferred screening strategy in some countries and is increasingly more widespread in other countries with organized or opportunistic screening programs. Given knowledge that high-risk HPV genotypes differ in their oncogenic potential, commercial HPV assays with genotyping capabilities have been developed and have garnered attention in the recent literature. The cobas 4800 HPV Test is a qualitative multiplex assay that provides specific genotyping information for HPV types 16 and 18, while concurrently detecting 12 other high-risk HPV genotypes as a pooled result. It is currently the only clinically validated, US FDA-approved assay with this capability. Since HPV types 16 and 18 have been designated as conferring the greatest risk for cervical disease, their detection may prove useful in guiding patient management. PMID:24308341

  10. Limited Utility of Dried-Blood- and Plasma Spot-Based Screening for Antiretroviral Treatment Failure with Cobas Ampliprep/TaqMan HIV-1 Version 2.0

    PubMed Central

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

    2014-01-01

    The 2013 WHO antiretroviral therapy (ART) guidelines recommend dried blood spots (DBS) as an alternative specimen type for viral load (VL) monitoring. We assessed the programmatic utility of screening for antiretroviral (ARV) treatment failure (TF) at 5,000 and 1,000 copies/ml using DBS and dried plasma spots (DPS) with a commonly used VL assay, the Roche Cobas Ampliprep/Cobas TaqMan V.2.0 (CAP/CTM). Plasma, DBS, and DPS were prepared from 839 whole-blood specimens collected from patients on ART for ≥6 months at three public facilities in Namibia. Using the CAP/CTM test, VL were measured in plasma, DBS, and DPS, and the results were compared using the plasma VL as the reference standard. The clinical sensitivities, specificities, and positive (PPV) and negative predictive values (NPV) of DBS at ARV TF diagnostic thresholds of 5,000 copies/ml and 1,000 copies/ml were 0.99, 0.55, 0.33, and 0.99 and 0.99, 0.26, 0.29, and 0.99, respectively, and for DPS at TF diagnostic thresholds of 5,000 copies/ml and 1,000 copies/ml, they were 0.88, 0.98, 0.92, and 0.97 and 0.91, 0.96, 0.89, and 0.97, respectively. The prevalences of TF were overestimated in DBS by 33% and 57% at these two thresholds, respectively. A high rate of false-positive results would occur if the CAP/CTM with DBS were to be used to screen for ARV TF. WHO recommendations for DBS-based VL monitoring should be specific to the VL assay version and type. Despite the better performance of DPS, the programmatic utility for TF screening may be limited by requirements for processing the whole blood at the collection site. PMID:25143579

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

    PubMed Central

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

    2014-01-01

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

  12. 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

  13. 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

    2015-01-01

    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. PMID:26648113

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

    PubMed Central

    Speicher, Andrea; Börner, Anna; Enders, Martin

    2016-01-01

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

  15. 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. PMID:26865682

  16. The Cobas® EGFR Mutation Test v2 assay.

    PubMed

    Brown, Paul

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  19. 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

  20. 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. PMID:25175296

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

    PubMed

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

    2016-04-01

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

  2. 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. PMID:26519842

  3. Functional characterization of a mycothiol peroxidase in Corynebacterium glutamicum that uses both mycoredoxin and thioredoxin reducing systems in the response to oxidative stress.

    PubMed

    Si, Meiru; Xu, Yixiang; Wang, Tietao; Long, Mingxiu; Ding, Wei; Chen, Can; Guan, Xinmeng; Liu, Yingbao; Wang, Yao; Shen, Xihui; Liu, Shuang-Jiang

    2015-07-01

    Previous studies have identified a putative mycothiol peroxidase (MPx) in Corynebacterium glutamicum that shared high sequence similarity to sulfur-containing Gpx (glutathione peroxidase; CysGPx). In the present study, we investigated the MPx function by examining its potential peroxidase activity using different proton donors. The MPx degrades hydrogen peroxide and alkyl hydroperoxides in the presence of either the thioredoxin/Trx reductase (Trx/TrxR) or the mycoredoxin 1/mycothione reductase/mycothiol (Mrx1/Mtr/MSH) regeneration system. Mrx1 and Trx employ different mechanisms in reducing MPx. For the Mrx1 system, the catalytic cycle of MPx involves mycothiolation/demycothiolation on the Cys(36) sulfenic acid via the monothiol reaction mechanism. For the Trx system, the catalytic cycle of MPx involves formation of an intramolecular disulfide bond between Cys(36) and Cys(79) that is pivotal to the interaction with Trx. Both the Mrx1 pathway and the Trx pathway are operative in reducing MPx under stress conditions. Expression of mpx markedly enhanced the resistance to various peroxides and decreased protein carbonylation and intracellular reactive oxygen species (ROS) accumulation. The expression of mpx was directly activated by the stress-responsive extracytoplasmic function-σ (ECF-σ) factor [SigH]. Based on these findings, we propose that the C. glutamicum MPx represents a new type of GPx that uses both mycoredoxin and Trx systems for oxidative stress response. PMID:25891483

  4. Simplex and multiplex stratification in ASD and ADHD families: a promising approach for identifying overlapping and unique underpinnings of ASD and ADHD?

    PubMed

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

    2015-03-01

    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 underpinnings of the disorders. ASD and ADHD traits were measured in 56 ASD/31 ADHD SPX families, 59 ASD/171 ADHD MPX families and 203 control families. In ASD but not ADHD, behavioral traits were less elevated in SPX than MPX unaffected relatives, suggesting that SPX-MPX stratification may thus help parse ASD, but not ADHD heterogeneity. Particularly unaffected relatives from MPX ASD/ADHD families displayed elevated trait levels of both disorders, indicating shared (multifactorial) underpinnings underlying ASD and ADHD in these families. Cross-disorder traits were highest in MPX ASD unaffected siblings. PMID:25173102

  5. Human Monkeypox in the Kivus, a Conflict Region of the Democratic Republic of the Congo.

    PubMed

    McCollum, Andrea M; Nakazawa, Yoshinori; Ndongala, Guy Mutombo; Pukuta, Elisabeth; Karhemere, Stomy; Lushima, Robert Shongo; Ilunga, Benoit Kebela; Kabamba, Joelle; Wilkins, Kimberly; Gao, Jinxin; Li, Yu; Emerson, Ginny; Damon, Inger K; Carroll, Darin S; Reynolds, Mary G; Malekani, Jean; Tamfum, Jean-Jacques Muyembe

    2015-10-01

    Monkeypox (MPX) is a zoonotic Orthopoxvirus infection endemic in central and western Africa. Human MPX cases occur in the central and northern regions of the Democratic Republic of the Congo (DRC), and this is the first report of confirmed MPX cases in the forested areas of North and South Kivu Provinces, with a detailed epidemiological investigation for one case. The location of each case is within areas predicted to be suitable for MPX virus transmission based on an ecological niche model. Phylogenetic analysis places these viruses in the Congo Basin clade. PMID:26283752

  6. 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…

  7. 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…

  8. 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.

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

    PubMed

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

    2014-07-01

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

  10. A comparison of three methods for detecting KRAS mutations in formalin-fixed colorectal cancer specimens

    PubMed Central

    Gonzalez de Castro, D; Angulo, B; Gomez, B; Mair, D; Martinez, R; Suarez-Gauthier, A; Shieh, F; Velez, M; Brophy, V H; Lawrence, H J; Lopez-Rios, F

    2012-01-01

    Background: KRAS mutation testing is required to select patients with metastatic colorectal cancer (CRC) to receive anti-epidermal growth factor receptor antibodies, but the optimal KRAS mutation test method is uncertain. Methods: We conducted a two-site comparison of two commercial KRAS mutation kits – the cobas KRAS Mutation Test and the Qiagen therascreen KRAS Kit – and Sanger sequencing. A panel of 120 CRC specimens was tested with all three methods. The agreement between the cobas test and each of the other methods was assessed. Specimens with discordant results were subjected to quantitative massively parallel pyrosequencing (MPP). DNA blends were tested to determine detection rates at 5% mutant alleles. Results: Reproducibility of the cobas test between sites was 98%. Six mutations were detected by cobas that were not detected by Sanger, and five were confirmed by MPP. The cobas test detected eight mutations which were not detected by the therascreen test, and seven were confirmed by MPP. Detection rates with 5% mutant DNA blends were 100% for the cobas and therascreen tests and 19% for Sanger. Conclusion: The cobas test was reproducible between sites, and detected several mutations that were not detected by the therascreen test or Sanger. Sanger sequencing had poor sensitivity for low levels of mutation. PMID:22713664

  11. High-resolution multiwire proportional soft x-ray diagnostic measurements on TCV

    NASA Astrophysics Data System (ADS)

    Sushkov, A.; Andreev, V.; Camenen, Y.; Pochelon, A.; Klimanov, I.; Scarabosio, A.; Weisen, H.

    2008-02-01

    A multiwire proportional x-ray (MPX) detector is used on the TCV tokamak (Tokamak à configuration variable) as a high spatial and temporal resolution soft x-ray emissivity imaging diagnostic. The MPX system consists of 64 vertically viewing channels and has been designed to complement the existing TCV soft x-ray tomography system by enhancing the spatial resolution. The MPX detector is suitable for the measurement of fast and localized phenomena and can be used, for instance, for the observation of magnetohydrodynamic activity, for the characterization of transport barriers or for an improved determination of the electron cyclotron heating power deposition profile. The MPX detector operates in continuous-current mode and measures the plasma soft x-ray emission in the 3-30keV range with a radial resolution of about 5mm—1% of plasma diameter—and a frequency bandwidth of 50kHz. A detailed description of the MPX detector construction and the principle of its operation are given. The properties of the detector in photon-counting and continuous-current operation modes are studied. The implementation of the system on TCV and experimental results illustrating the potential of the diagnostic are also presented.

  12. 1st HPV Test for Use with Preservative Fluid

    MedlinePlus

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

  13. 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

  14. Human Papillomavirus Assays and Cytology in Primary Cervical Screening of Women Aged 30 Years and Above.

    PubMed

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

    2016-01-01

    In women aged ≥ 30 years, Human Papillomavirus testing will replace cytology for primary cervical screening. We compared Hybrid Capture 2 (HC2), cobas, CLART, and APTIMA HPV assays with cytology on 2869 SurePath samples from women undergoing routine screening at 30-65 years in Copenhagen, Denmark. Women with cytological abnormalities were managed according to routine recommendations, with 92% completeness. Those with cytology-normal/HPV-positive samples (on any of the four assays) were invited for repeated cytology and HPV testing in 1.5 year, and 58% had additional testing. HPV testing detected more ≥ CIN3 than cytology (HC2: 35, cobas, CLART: 37, APTIMA: 34, cytology: 31), although statistically the differences were not significant. Cobas and CLART detected significantly more ≥ CIN2 than cytology (cobas, CLART: 49, cytology: 39). The proportion of women with false-positive test results (positive test results without ≥ CIN3) varied between 3.3% with cytology and 14.9% with cobas. All HPV assays led to significantly more false-positive tests, whereas compared to HC2 cobas and CLART were associated with a significantly higher and APTIMA with a significantly lower proportion. Detection of CIN1 was particularly increased for the three DNA assays. With APTIMA combined with cytological triage, about 20% more women were referred for colposcopy than with cytology screening. With the three DNA assays, the increase was ≥ 50%. The number of women with repeated testing was twice as high with APTIMA and almost five times as high with cobas compared to cytology. To our knowledge, Horizon was the only study set in routine practice that compared more than two HPV assays in the same women while also ascertaining the histological status of women with normal cytology/HPV-positive test results. HPV-based screening of Danish women aged 30-65 detected more high-grade CIN but decreased the screening specificity, and increased the demand for additional testing. PMID:26789267

  15. Selective Acylation Enhances Membrane Charge Sensitivity of the Antimicrobial Peptide Mastoparan-X

    PubMed Central

    Etzerodt, Thomas; Henriksen, Jonas R.; Rasmussen, Palle; Clausen, Mads H.; Andresen, Thomas L.

    2011-01-01

    The partitioning of the wasp venom peptide mastoparan-X (MPX) into neutral and negatively charged lipid membranes has been compared with two new synthetic analogs of MPX where the Nα-terminal of MPX was acylated with propanoic acid (PA) and octanoic acid (OA). The acylation caused a considerable change in the membrane partitioning properties of MPX and it was found that the shorter acylation with PA gave improved affinity and selectivity toward negatively charged membranes, whereas OA decreased the selectivity. Based on these findings, we hypothesize that minor differences in the embedding and positioning of the peptide in the membrane caused by either PA or OA acylation play a critical role in the fine-tuning of the effective charge of the peptide and thereby the fine-tuning of the peptide's selectivity between neutral and negatively charged lipid membranes. This finding is unique compared to previous reports where peptide acylation enhanced membrane affinity but also resulted in impaired selectivity. Our result may provide a method of enhancing selectivity of antimicrobial peptides toward bacterial membranes due to their high negative charge—a finding that should be investigated for other, more potent antimicrobial peptides in future studies. PMID:21244836

  16. 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…

  17. 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…

  18. Distinct regulation of the anterior and posterior myeloperoxidase expression by Etv2 and Gata1 during primitive Granulopoiesis in zebrafish.

    PubMed

    Glenn, Nicole O; Schumacher, Jennifer A; Kim, Hyon J; Zhao, Emma J; Skerniskyte, Jurate; Sumanas, Saulius

    2014-09-01

    Neutrophilic granulocytes are the most abundant type of myeloid cells and form an essential part of the innate immune system. In vertebrates the first neutrophils are thought to originate during primitive hematopoiesis, which precedes hematopoietic stem cell formation. In zebrafish embryos, it has been suggested that primitive neutrophils may originate in two distinct sites, the anterior (ALPM) and posterior lateral plate mesoderm (PLPM). An ETS-family transcription factor Etsrp/Etv2/ER71 has been implicated in vasculogenesis and hematopoiesis in multiple vertebrates. However, its role during neutrophil development is not well understood. Here we demonstrate using zebrafish embryos that Etv2 has a specific cell-autonomous function during primitive neutropoiesis in the anterior lateral plate mesoderm (ALPM) but has little effect on erythropoiesis or the posterior lateral plate mesoderm (PLPM) expression of neutrophil marker myeloperoxidase mpo/mpx. Our results argue that ALPM-derived neutrophils originate from etv2-expressing cells which downregulate etv2 during neutropoiesis. We further show that Scl functions downstream of Etv2 in anterior neutropoiesis. Additionally, we demonstrate that mpx expression within the PLPM overlaps with gata1 expression, potentially marking the cells with a dual myelo-erythroid potential. Intriguingly, initiation of mpx expression in the PLPM is dependent on gata1 but not etv2 function. Our results demonstrate that mpx expression is controlled differently in the ALPM and PLPM regions and describe novel roles for etv2 and gata1 during primitive neutropoiesis. PMID:24956419

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

    PubMed

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

    2016-07-01

    Autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) frequently co-occur. Besides shared genetic factors, pre- and perinatal risk factors (PPFs) may determine if ASD, ADHD, or the combination of both disorders becomes manifest. This study aimed to test shared and unique involvement of PPFs for ASD and ADHD, using an approach that stratifies the sample into affected/unaffected offspring and single-incidence (SPX) versus multi-incidence (MPX) families. Pre- perinatal data based on retrospective parent-report were collected in 288 children (71 % males) from 31 SPX and 59 MPX ASD families, 476 children (65 % males) from 31 SPX and 171 MPX ADHD families, and 408 control children (42 % males). Except for large family size and more firstborns amongst affected offspring, no shared PFFs were identified for ASD and ADHD. PPFs predominantly related to ASD (maternal infections and suboptimal condition at birth) were more often reported in affected than unaffected siblings. PPFs associated with ADHD (low parental age, maternal diseases, smoking and stress) were shared between affected and unaffected siblings. Firstborn-ship was more frequent in SPX than MPX ASD probands. Our results suggest that the co-morbidity of ASD and ADHD is not likely explained by shared PPFs. Instead, PPFs might play a crucial role in the developmental pathways leading up to either disorder. PPFs in ADHD appear to index an increased shared risk, whereas in ASD PPFs possibly have a more determining role in the disorder. SPX-MPX stratification detected possible etiological differences in ASD families, but provided no deeper insight in the role of PPFs in ADHD. PMID:26466830

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

    PubMed

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

    2016-03-01

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

  1. 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

  2. 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

  3. High concentrations of haptocorrin interfere with routine measurement of cobalamins in human serum and milk. A problem and its solution.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Human milk and occasional serum samples contain high concentrations of unsaturated haptocorrin (apoHC), which may influence measurement of cobalamins (Cbl). Methods: Cbl in serum samples spiked with increasing amounts of apoHC were measured employing the Centaur, Cobas and Architect anal...

  4. 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. PMID:26527457

  5. The Corynebacterium glutamicum mycothiol peroxidase is a reactive oxygen species-scavenging enzyme that shows promiscuity in thiol redox control.

    PubMed

    Pedre, Brandán; Van Molle, Inge; Villadangos, Almudena F; Wahni, Khadija; Vertommen, Didier; Turell, Lucía; Erdogan, Huriye; Mateos, Luis M; Messens, Joris

    2015-06-01

    Cysteine glutathione peroxidases (CysGPxs) control oxidative stress levels by reducing hydroperoxides at the expense of cysteine thiol (-SH) oxidation, and the recovery of their peroxidatic activity is generally accomplished by thioredoxin (Trx). Corynebacterium glutamicum mycothiol peroxidase (Mpx) is a member of the CysGPx family. We discovered that its recycling is controlled by both the Trx and the mycothiol (MSH) pathway. After H2 O2 reduction, a sulfenic acid (-SOH) is formed on the peroxidatic cysteine (Cys36), which then reacts with the resolving cysteine (Cys79), forming an intramolecular disulfide (S-S), which is reduced by Trx. Alternatively, the sulfenic acid reacts with MSH and forms a mixed disulfide. Mycoredoxin 1 (Mrx1) reduces the mixed disulfide, in which Mrx1 acts in combination with MSH and mycothiol disulfide reductase as a biological relevant monothiol reducing system. Remarkably, Trx can also take over the role of Mrx1 and reduce the Mpx-MSH mixed disulfide using a dithiol mechanism. Furthermore, Mpx is important for cellular survival under H2 O2 stress, and its gene expression is clearly induced upon H2 O2 challenge. These findings add a new dimension to the redox control and the functioning of CysGPxs in general. PMID:25766783

  6. Morphologic and functional characterization of granulocytes and macrophages in embryonic and adult zebrafish.

    PubMed

    Lieschke, G J; Oates, A C; Crowhurst, M O; Ward, A C; Layton, J E

    2001-11-15

    The zebrafish is a useful model organism for developmental and genetic studies. The morphology and function of zebrafish myeloid cells were characterized. Adult zebrafish contain 2 distinct granulocytes, a heterophil and a rarer eosinophil, both of which circulate and are generated in the kidney, the adult hematopoietic organ. Heterophils show strong histochemical myeloperoxidasic activity, although weaker peroxidase activity was observed under some conditions in eosinophils and erythrocytes. Embryonic zebrafish have circulating immature heterophils by 48 hours after fertilization (hpf). A zebrafish myeloperoxidase homologue (myeloid-specific peroxidase; mpx) was isolated. Phylogenetic analysis suggested it represented a gene ancestral to the mammalian myeloperoxidase gene family. It was expressed in adult granulocytes and in embryos from 18 hpf, first diffusely in the axial intermediate cell mass and then discretely in a dispersed cell population. Comparison of hemoglobinized cell distribution, mpx gene expression, and myeloperoxidase histochemistry in wild-type and mutant embryos confirmed that the latter reliably identified a population of myeloid cells. Studies in embryos after tail transection demonstrated that mpx- and peroxidase-expressing cells were mobile and localized to a site of inflammation, indicating functional capability of these embryonic granulocytes. Embryonic macrophages removed carbon particles from the circulation by phagocytosis. Collectively, these observations have demonstrated the early onset of zebrafish granulopoiesis, have proved that granulocytes circulate by 48 hpf, and have demonstrated the functional activity of embryonic granulocytes and macrophages. These observations will facilitate the application of this genetically tractable organism to the study of myelopoiesis. PMID:11698295

  7. Human Papillomavirus Assays and Cytology in Primary Cervical Screening of Women Aged 30 Years and Above

    PubMed Central

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

    2016-01-01

    In women aged ≥30 years, Human Papillomavirus testing will replace cytology for primary cervical screening. We compared Hybrid Capture 2 (HC2), cobas, CLART, and APTIMA HPV assays with cytology on 2869 SurePath samples from women undergoing routine screening at 30–65 years in Copenhagen, Denmark. Women with cytological abnormalities were managed according to routine recommendations, with 92% completeness. Those with cytology-normal/HPV-positive samples (on any of the four assays) were invited for repeated cytology and HPV testing in 1.5 year, and 58% had additional testing. HPV testing detected more ≥CIN3 than cytology (HC2: 35, cobas, CLART: 37, APTIMA: 34, cytology: 31), although statistically the differences were not significant. Cobas and CLART detected significantly more ≥CIN2 than cytology (cobas, CLART: 49, cytology: 39). The proportion of women with false-positive test results (positive test results without ≥CIN3) varied between 3.3% with cytology and 14.9% with cobas. All HPV assays led to significantly more false-positive tests, whereas compared to HC2 cobas and CLART were associated with a significantly higher and APTIMA with a significantly lower proportion. Detection of CIN1 was particularly increased for the three DNA assays. With APTIMA combined with cytological triage, about 20% more women were referred for colposcopy than with cytology screening. With the three DNA assays, the increase was ≥50%. The number of women with repeated testing was twice as high with APTIMA and almost five times as high with cobas compared to cytology. To our knowledge, Horizon was the only study set in routine practice that compared more than two HPV assays in the same women while also ascertaining the histological status of women with normal cytology/HPV-positive test results. HPV-based screening of Danish women aged 30–65 detected more high-grade CIN but decreased the screening specificity, and increased the demand for additional testing. PMID:26789267

  8. 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.

  9. Structural insights into the mechanism of four-coordinate Cob(II)alamin formation in the active site of the Salmonella enterica ATP:Co(I)rrinoid adenosyltransferase enzyme: critical role of residues Phe91 and Trp93.

    PubMed

    Moore, Theodore C; Newmister, Sean A; Rayment, Ivan; Escalante-Semerena, Jorge C

    2012-12-01

    ATP:co(I)rrinoid adenosyltransferases (ACATs) are enzymes that catalyze the formation of adenosylcobalamin (AdoCbl, coenzyme B(12)) from cobalamin and ATP. There are three families of ACATs, namely, CobA, EutT, and PduO. In Salmonella enterica, CobA is the housekeeping enzyme that is required for de novo AdoCbl synthesis and for salvaging incomplete precursors and cobalamin from the environment. Here, we report the crystal structure of CobA in complex with ATP, four-coordinate cobalamin, and five-coordinate cobalamin. This provides the first crystallographic evidence of the existence of cob(II)alamin in the active site of CobA. The structure suggests a mechanism in which the enzyme adopts a closed conformation and two residues, Phe91 and Trp93, displace 5,6-dimethylbenzimidazole, the lower nucleotide ligand base of cobalamin, to generate a transient four-coordinate cobalamin, which is critical in the formation of the AdoCbl Co-C bond. In vivo and in vitro mutational analyses of Phe91 and Trp93 emphasize the important role of bulky hydrophobic side chains in the active site. The proposed manner in which CobA increases the redox potential of the cob(II)alamin/cob(I)alamin couple to facilitate formation of the Co-C bond appears to be analogous to that utilized by the PduO-type ACATs, where in both cases the polar coordination of the lower ligand to the cobalt ion is eliminated by placing that face of the corrin ring adjacent to a cluster of bulky hydrophobic side chains. PMID:23148601

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

    PubMed

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

    2004-01-01

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

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

    PubMed Central

    de Assis, Angela Maria

    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, negaive 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. PMID:26087285

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

    PubMed

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

    2016-06-01

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

  13. Enzymes of the antioxidant network as novel determiners of Trypanosoma cruzi virulence

    PubMed Central

    Piacenza, L.; Zago, M.P.; Peluffo, G.; Alvarez, M.N.; Basombrio, M.A.; Radi, R.

    2013-01-01

    Virulence of Trypanosoma cruzi depends on a variety of genetic and biochemical factors. It has been proposed that components of the parasites' antioxidant system may play a key part in this process by pre-adapting the pathogen to the oxidative environment encountered during host cell invasion. Using several isolates (10 strains) belonging to the two major phylogenetic lineages (T. cruzi-I and T. cruzi-II), we investigated whether there was an association between virulence (ranging from highly aggressive to attenuated isolates at the parasitemia and histopathological level) and the antioxidant enzyme content. Antibodies raised against trypanothione synthetase (TcTS), ascorbate peroxidase (TcAPX), mitochondrial and cytosolic tryparedoxin peroxidases (TcMPX and TcCPX) and trypanothione reductase (TcTR) were used to evaluate the antioxidant enzyme levels in epimastigote and metacyclic trypomastigote forms in the T. cruzi strains. Levels of TcCPX, TcMPX and TcTS were shown to increase during differentiation from the non-infective epimastigote to the infective metacyclic trypomastigote stage in all parasite strains examined. Peroxiredoxins were found to be present at higher levels in the metacyclic infective forms of the virulent isolates compared with the attenuated strains. Additionally, an increased resistance of epimastigotes from virulent T. cruzi populations to hydrogen peroxide and peroxynitrite challenge was observed. In mouse infection models, a direct correlation was found between protein levels of TcCPX, TcMPX and TcTS, and the parasitemia elicited by the different isolates studied (Pearson's coefficient: 0.617, 0.771, 0.499; respectively, P < 0.01). No correlation with parasitemia was found for TcAPX and TcTR proteins in any of the strains analyzed. Our data support that enzymes of the parasite antioxidant armamentarium at the onset of infection represent new virulence factors involved in the establishment of disease. PMID:19505468

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

    SciTech Connect

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

    2007-03-15

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

  15. Preliminary Geological Map of the Ac-H-8 Nawish Quadrangle of Ceres: An Integrated Mapping Study Using Dawn Spacecraft Data

    NASA Astrophysics Data System (ADS)

    Frigeri, Alessandro; De Sanctis, Maria Cristina; Carrozzo, Giacomo; Ammannito, Eleonora; Williams, David; Mest, Scott; Buczkowski, Debra; Preusker, Frank; Jaumann, Ralf; Roatsch, Thomas; Scully, Jennifer; Raymond, Carol; Russell, Christopher

    2016-04-01

    Herein we present the geologic mapping of the Ac-H-8 Nawish Quadrangle of dwarf planet Ceres, produced on the basis of the Dawn spacecraft data. The Ac-H-08 Nawish quadrangle is located between -22°S and 22°N and between 144°E and 216°E. At the north-east border, a polygonal, 75km-wide crater named Nawish gives the name to the whole quadrangle. An unamed, partially degraded, 100km-diameter crater is evident in the lower central sector of the quadrangle. Bright materials have been mapped and are associated with craters. For example, bright materials occur in the central peak region of Nawish crater and in the ejecta of an unnamed crater, which is located in the nearby quadrangle Ac-H-09. The topography of the area obtained from stereo-processing of imagery shows an highland in the middle of the quadrangle. Topography is lower in the northern and southern borders, with a altitude span of about 9500 meters. At the time of this writing geologic mapping was based on Framing Camera (FC) mosaics from the High Altitude Mapping Orbit (HAMO, 140 m/px) and Survey (415 m/px) orbits, including grayscale and color images and digital terrain models derived from stereo images. The first sessions of Low Altitude Mapping Orbit (LAMO, 35 m/px) images have been received as we are writing this abstract in the first half of January 2016. LAMO images represent the maximum spatial resolution images available for Ceres from the Dawn mission. 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.

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

    PubMed Central

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

    2014-01-01

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

  17. Evaluation of novel assays for the detection of human papilloma virus in self-collected samples for cervical cancer screening.

    PubMed

    Chen, Q; Du, H; Zhang, R; Zhao, J H; Hu, Q C; Wang, C; Wang, G X; Tang, J L; Wu, R F

    2016-01-01

    The aim of this study was to evaluate the performance of three new high-risk human papillomavirus (HPV) assays for primary cervical cancer screening, by using self-collected samples, and to identify an HPV assay that could overcome the major obstacles faced during large-scale population-based screening. Two hundred and ten women showing abnormal cervical cytology (and referred for a colposcopy) were recruited in this study. Self-collected samples obtained from all women were tested with the Cobas, Seq, and BioPerfectus Multiplex Real Time HPV assays; simultaneously, clinician-collected samples (from the same women) were tested with the gold-standard Cobas HPV assay. The results of all the assays were consistent. The sensitivity, positive predictive value, and negative predictive value for cervical intraepithelial neoplasia 2+ (CIN2+) and CIN3+ were comparable between the self-collected samples tested with the three new assays and the clinician-collected samples tested with the Cobas HPV assay (P > 0.05). The single-genotype HPV load per sample did not differ significantly between the self- and clinician-collected samples (P = 0.195). In conclusion, the results of this study demonstrated the applicability of the three new HPV assays for primary cervical cancer screening based on self-collection. PMID:27420961

  18. 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

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

    PubMed

    Franceschi, Valentina; Parker, Scott; Jacca, Sarah; Crump, Ryan W; Doronin, Konstantin; Hembrador, Edguardo; Pompilio, Daniela; Tebaldi, Giulia; Estep, Ryan D; Wong, Scott W; Buller, Mark R; Donofrio, Gaetano

    2015-06-01

    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

  20. 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.

  1. Clinical Evaluation of the Cartridge-Based GeneXpert Human Papillomavirus Assay in Women Referred for Colposcopy

    PubMed Central

    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.

    2014-01-01

    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. PMID:24719440

  2. 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

  3. Introduction of Monkeypox into a Community and Household: Risk Factors and Zoonotic Reservoirs in the Democratic Republic of the Congo.

    PubMed

    Nolen, Leisha Diane; Osadebe, Lynda; Katomba, Jacques; Likofata, Jacques; Mukadi, Daniel; Monroe, Benjamin; Doty, Jeffrey; Kalemba, Lem's; Malekani, Jean; Kabamba, Joelle; Bomponda, Pierre Lokwa; Lokota, Jules Inonga; Balilo, Marcel Pie; Likafi, Toutou; Lushima, Robert Shongo; Tamfum, Jean-Jacques Muyembe; Okitolonda, Emile Wemakoy; McCollum, Andrea M; Reynolds, Mary G

    2015-08-01

    An increased incidence of monkeypox (MPX) infections in the Democratic Republic of the Congo was noted by the regional surveillance system in October 2013. Little information exists regarding how MPX is introduced into the community and the factors associated with transmission within the household. Sixty-eight wild animals were collected and tested for Orthopoxvirus. Two of three rope squirrels (Funisciurus sp.) were positive for antibodies to Orthopoxviruses; however, no increased risk was associated with the consumption or preparation of rope squirrels. A retrospective cohort investigation and a case-control investigation were performed to identify risk factors affecting the introduction of monkeypox virus (MPXV) into the community and transmission within the home. School-age males were the individuals most frequently identified as the first person infected in the household and were the group most frequently affected overall. Risk factors of acquiring MPXV in a household included sleeping in the same room or bed, or using the same plate or cup as the primary case. There was no significant risk associated with eating or processing of wild animals. Activities associated with an increased risk of MPXV transmission all have potential for virus exposure to the mucosa. PMID:26013374

  4. 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

  5. Introduction of Monkeypox into a Community and Household: Risk Factors and Zoonotic Reservoirs in the Democratic Republic of the Congo

    PubMed Central

    Nolen, Leisha Diane; Osadebe, Lynda; Katomba, Jacques; Likofata, Jacques; Mukadi, Daniel; Monroe, Benjamin; Doty, Jeffrey; Kalemba, Lem's; Malekani, Jean; Kabamba, Joelle; Bomponda, Pierre Lokwa; Lokota, Jules Inonga; Balilo, Marcel Pie; Likafi, Toutou; Lushima, Robert Shongo; Tamfum, Jean-Jacques Muyembe; Okitolonda, Emile Wemakoy; McCollum, Andrea M.; Reynolds, Mary G.

    2015-01-01

    An increased incidence of monkeypox (MPX) infections in the Democratic Republic of the Congo was noted by the regional surveillance system in October 2013. Little information exists regarding how MPX is introduced into the community and the factors associated with transmission within the household. Sixty-eight wild animals were collected and tested for Orthopoxvirus. Two of three rope squirrels (Funisciurus sp.) were positive for antibodies to Orthopoxviruses; however, no increased risk was associated with the consumption or preparation of rope squirrels. A retrospective cohort investigation and a case–control investigation were performed to identify risk factors affecting the introduction of monkeypox virus (MPXV) into the community and transmission within the home. School-age males were the individuals most frequently identified as the first person infected in the household and were the group most frequently affected overall. Risk factors of acquiring MPXV in a household included sleeping in the same room or bed, or using the same plate or cup as the primary case. There was no significant risk associated with eating or processing of wild animals. Activities associated with an increased risk of MPXV transmission all have potential for virus exposure to the mucosa. PMID:26013374

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

    PubMed

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

    2016-01-12

    Holoenzymes of adenosylcobalamin-dependent diol and glycerol dehydratases undergo mechanism-based inactivation by glycerol and O2 inactivation in the absence of substrate, which accompanies irreversible cleavage of the coenzyme Co-C bond. The inactivated holodiol dehydratase and the inactive enzyme·cyanocobalamin complex were (re)activated by incubation with NADH, ATP, and Mg(2+) (or Mn(2+)) in crude extracts of Klebsiella oxytoca, suggesting the presence of a reactivating system in the extract. The reducing system with NADH could be replaced by FMNH2. When inactivated holoenzyme or the enzyme·cyanocobalamin complex, a model of inactivated holoenzyme, was incubated with purified recombinant diol dehydratase-reactivase (DD-R) and an ATP:cob(I)alamin adenosyltransferase in the presence of FMNH2, ATP, and Mg(2+), diol dehydratase activity was restored. Among the three adenosyltransferases (PduO, EutT, and CobA) of this bacterium, PduO and CobA were much more efficient for the reactivation than EutT, although PduO showed the lowest adenosyltransfease activity toward free cob(I)alamin. These results suggest that (1) diol dehydratase activity is maintained through coenzyme recycling by a reactivating system for diol dehydratase composed of DD-R, PduO adenosyltransferase, and a reducing system, (2) the releasing factor DD-R is essential for the recycling of adenosycobalamin, a tightly bound, prosthetic group-type coenzyme, and (3) PduO is a specific adenosylating enzyme for the DD reactivation, whereas CobA and EutT exert their effects through free synthesized coenzyme. Although FMNH2 was mainly used as a reductant in this study, a natural reducing system might consist of PduS cobalamin reductase and NADH. PMID:26704729

  7. Performance of the new automated Abbott RealTime MTB assay for rapid detection of Mycobacterium tuberculosis complex in respiratory specimens.

    PubMed

    Chen, J H K; She, K K K; Kwong, T-C; Wong, O-Y; Siu, G K H; Leung, C-C; Chang, K-C; Tam, C-M; Ho, P-L; Cheng, V C C; Yuen, K-Y; Yam, W-C

    2015-09-01

    The automated high-throughput Abbott RealTime MTB real-time PCR assay has been recently launched for Mycobacterium tuberculosis complex (MTBC) clinical diagnosis. This study would like to evaluate its performance. We first compared its diagnostic performance with the Roche Cobas TaqMan MTB assay on 214 clinical respiratory specimens. Prospective analysis of a total 520 specimens was then performed to further evaluate the Abbott assay. The Abbott assay showed a lower limit of detection at 22.5 AFB/ml, which was more sensitive than the Cobas assay (167.5 AFB/ml). The two assays demonstrated a significant difference in diagnostic performance (McNemar's test; P = 0.0034), in which the Abbott assay presented significantly higher area under curve (AUC) than the Cobas assay (1.000 vs 0.880; P = 0.0002). The Abbott assay demonstrated extremely low PCR inhibition on clinical respiratory specimens. The automated Abbott assay required only very short manual handling time (0.5 h), which could help to improve the laboratory management. In the prospective analysis, the overall estimates for sensitivity and specificity of the Abbott assay were both 100 % among smear-positive specimens, whereas the smear-negative specimens were 96.7 and 96.1 %, respectively. No cross-reactivity with non-tuberculosis mycobacterial species was observed. The superiority in sensitivity of the Abbott assay for detecting MTBC in smear-negative specimens could further minimize the risk in MTBC false-negative detection. The new Abbott RealTime MTB assay has good diagnostic performance which can be a useful diagnostic tool for rapid MTBC detection in clinical laboratories. PMID:26071001

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

    PubMed

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

    2016-03-15

    A polymerase chain reaction (PCR)-free technique for the effective detection of genomic length hepatitis B virus (HBV) DNA is described in this study. The honeycomb-like barrier layer of an anodic aluminum oxide (AAO) film having a uniform nanohemisphere array was used as the substrate of the sensing electrode. A 30-nm gold film was sputtered onto the AAO barrier layer surface as the electrode, followed by electrochemical deposition of gold nanoparticles (GNPs) on the hemisphere surface. A specially designed single-strand 96-mer gene fragment of the target genomic DNA of HBV based on the genome sequences of HBV was immobilized on the nanostructured electrode as the capture probe. Target HBV DNA obtained from clinical samples was hybridized to the sensing probes. Detection results illustrate two dynamic linear ranges, 10(2)-10(3) and 10(3)-10(5.1) copies/mL, having R(2) values of 0.801 and 0.996 could be obtained, respectively. The detection limit of the proposed sending scheme was measured to be 111 copies/mL. The total of 45 target samples, including 20 samples with HBV concentration being lower than 10(2) copies/mL and 25 samples with HBV concentration being in the range of 10(3)-10(5.1) copies/mL, were used for real test. The concentration of these 45 HBV DNA samples was measured by the COBAS Ampliprep system. Comparing the measured results of the COBAS Ampliprep and our system, it was illustrated that the HBV DNA concentrations measured by the proposed method in this study had a high linear correlation with the COBAS Ampliprep, having R(2) values of 0.983. The proposed sensing scheme is highly feasible for future clinical applications. PMID:26479905

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

    PubMed Central

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

    2015-01-01

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

  10. Discrepant amplification results during the development of an assay leads to reclassification of two AIDS reagent repository HIV-2 isolates as HIV-1.

    PubMed

    Jagodzinski, Linda L; Liu, Ying; Hack, Holly R; Kibirige, Catherine; Peel, Sheila A; Manak, Mark M

    2014-01-01

    The development and verification of HIV-2 assays depends in part on the availability of well-characterized samples, including those from reagent repositories. During the development of an HIV-2 RNA quantification assay, two HIV-2 viral isolates (CDC 301340 and CDC 301342) obtained from the NIAID AIDS Reagent and Reference Repository were not detected leading to an investigation. Two HIV-2 primers/probe sets of known performance in real-time viral RNA quantification assays, targeting different regions of the virus, also failed to generate RT-PCR products for these two isolates. These isolates were tested in the HIV-1 specific COBAS AmpliPrep/COBAS TaqMan HIV-1 Test v2.0 (Roche Molecular Diagnostics) and were quantified at high copy number. Other HIV-2 isolates tested were not amplified in the COBAS HIV-1 TaqMan assay. Furthermore, the discrepant isolates were highly reactive in an HIV-1 p24 antigen test while the other HIV-2 isolates showed very weak, if any, cross-reactivity with the HIV-1 p24 assay. Phylogenetic tree analysis of sequences from the protease-reverse transcriptase regions of the discrepant HIV-2 isolates mapped with HIV-1 Group M, Subtype CRF02_AG confirming these isolates were of HIV-1 origin and had been misclassified as HIV-2. The use of misclassified isolates in the verification of molecular and immunological assays can lead to misinterpretation of test results, misdirection of efforts into assay redesign and increased development costs. The results of this study were shared with the NIAID AIDS Reagent Program, leading to the reclassification of the two discrepant isolates as HIV-1. PMID:24797800

  11. Evaluating HPV-negative CIN2+ in the ATHENA trial.

    PubMed

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

    2016-06-15

    A post hoc analysis of the ATHENA study was performed to determine whether true HPV-negative cervical lesions occur and whether they have clinical relevance. The ATHENA database was searched for all CIN2 or worse (CIN2+) cases with cobas HPV-negative results and comparison was made with Linear Array (LA) and Amplicor to detect true false-negative HPV results. Immunostaining with p16 was performed on these cases to identify false-positive histology results. H&E slides were re-reviewed by the study pathologists with knowledge of patient age, HPV test results and p16 immunostaining. Those with positive p16 immunostaining and/or a positive histopathology review underwent whole tissue section HPV PCR by the SPF10/LiPA/RHA system. Among 46,887 eligible women, 497 cases of CIN2+ were detected, 55 of which tested negative by the cobas(®) HPV Test (32 CIN2, 23 CIN3/ACIS). By LA and/or Amplicor, 32 CIN2+ (20 CIN2, 12 CIN3/ACIS) were HPV positive and categorized as false-negatives by cobas HPV; nine of 12 false-negative CIN3/ACIS cases were p16+. There were 23 cases (12 CIN2, 11 CIN3/ACIS) negative by all HPV tests; seven of 11 CIN3/ACIS cases were p16+. H&E slides were available for six cases for re-review and all were confirmed as CIN3/ACIS. Tissue PCR was performed on the six confirmed CIN3/ACIS cases (and one without confirmation): four were positive for HPV types not considered oncogenic, two were positive for oncogenic genotypes and one was indeterminate. In summary, subanalysis of a large cervical cancer screening study did not identify any true CIN3/ACIS not attributable to HPV. PMID:26851121

  12. Analytic performance studies and clinical reproducibility of a real-time PCR assay for the detection of epidermal growth factor receptor gene mutations in formalin-fixed paraffin-embedded tissue specimens of non-small cell lung cancer

    PubMed Central

    2013-01-01

    Background Epidermal growth factor receptor (EGFR) gene mutations identify patients with non-small cell lung cancer (NSCLC) who have a high likelihood of benefiting from treatment with anti-EGFR tyrosine kinase inhibitors. Sanger sequencing is widely used for mutation detection but can be technically challenging, resulting in longer turn-around-time, with limited sensitivity for low levels of mutations. This manuscript details the technical performance verification studies and external clinical reproducibility studies of the cobas EGFR Mutation Test, a rapid multiplex real-time PCR assay designed to detect 41 mutations in exons 18, 19, 20 and 21. Methods The assay’s limit of detection was determined using 25 formalin-fixed paraffin-embedded tissue (FFPET)-derived and plasmid DNA blends. Assay performance for a panel of 201 specimens was compared against Sanger sequencing with resolution of discordant specimens by quantitative massively parallel pyrosequencing (MPP). Internal and external reproducibility was assessed using specimens tested in duplicate by different operators, using different reagent lots, instruments and at different sites. The effects on the performance of the cobas EGFR test of endogenous substances and nine therapeutic drugs were evaluated in ten FFPET specimens. Other tests included an evaluation of the effects of necrosis, micro-organisms and homologous DNA sequences on assay performance, and the inclusivity of the assay for less frequent mutations. Results A >95% hit rate was obtained in blends with >5% mutant alleles, as determined by MPP analysis, at a total DNA input of 150 ng. The overall percent agreement between Sanger sequencing and the cobas test was 96.7% (negative percent agreement 97.5%; positive percent agreement 95.8%). Assay repeatability was 98% when tested with two operators, instruments, and reagent lots. In the external reproducibility study, the agreement was > 99% across all sites, all operators and all reagent lots

  13. 25-hydroxy-Vitamin D status: limitations in comparison and clinical interpretation of serum-levels across different assay methods.

    PubMed

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

    2014-01-01

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

  14. Different Vancomycin Immunoassays Contribute to the Variability in Vancomycin Trough Measurements in Neonates

    PubMed Central

    Smits, Anne; Spriet, Isabel; Soldatovic, Ivan; Atkinson, Andrew; Bajcetic, Milica; Van Den Anker, John N.; Allegaert, Karel

    2016-01-01

    Substantial interassay variability (up to 20%) has been described for vancomycin immunoassays in adults, but the impact of neonatal matrix is difficult to quantify because of blood volume constraints in neonates. However, we provide circumstantial evidence for a similar extent of variability. Using the same vancomycin dosing regimens and confirming similarity in clinical characteristics, vancomycin trough concentrations measured by PETINIA (2011-2012, n = 400) were 20% lower and the mean difference was 1.93 mg/L compared to COBAS (2012–2014, n = 352) measurements. The impact of vancomycin immunoassays in neonatal matrix was hereby suggested, supporting a switch to more advanced techniques (LC-MS/MS).

  15. 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. PMID:26423658

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

    PubMed Central

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

    2015-01-01

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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  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. Attenuation of Monkeypox Virus by Deletion of Genomic Regions

    PubMed Central

    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 vivo studies 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. PMID:25462353

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

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  5. 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}.

  6. 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.

  7. 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

  8. Structure and properties of electrodeposited Fe Ni W alloys with different levels of tungsten content: A comparative study

    NASA Astrophysics Data System (ADS)

    He, Fengjiao; Yang, Juan; Lei, Tongxin; Gu, Chunyan

    2007-07-01

    Fe-Ni-W alloys with 18 wt%, 35 wt% and 55 wt% tungsten have been obtained by electrodeposition from an ammoniacal citrate bath. The deposits are smooth, of nice appearance, and adhere well to iron and steel. The morphology and structure of Fe-Ni-W alloys were studied by SEM and XRD, respectively. The structure of the as-plated deposits changed from crystalline to amorphous with increasing tungsten content. The amorphous structure crystallized under heat treatment condition. The wear and corrosion resistance of the deposits were tested by MPX-2000 wear-tear equipment and neutral salt spray test (NSS), respectively. The alloys with 55 wt% tungsten, after heat treatment at proper temperatures, appear to have good wear resistance and hardness. The alloys with 18 wt% tungsten are very corrosion-resistant.

  9. 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

  10. 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

  11. The Tectonics of Mercury: The View from Orbit

    NASA Astrophysics Data System (ADS)

    Watters, T. R.; Byrne, P. K.; Klimczak, C.; Enns, A. C.; Banks, M. E.; Walsh, L. S.; Ernst, C. M.; Robinson, M. S.; Gillis-Davis, J. J.; Solomon, S. C.; Strom, R. G.; Gwinner, K.

    2011-12-01

    Flybys of Mercury by the Mariner 10 and MESSENGER spacecraft revealed a broad distribution of contractional tectonic landforms, including lobate scarps, high-relief ridges, and wrinkle ridges. Among these, lobate scarps were seen as the dominant features and have been interpreted as having formed as a result of global contraction in response to interior cooling. Extensional troughs and graben, where identified, were generally confined to intermediate- to large-scale impact basins. However, the true global spatial distribution of tectonic landforms remained poorly defined because the flyby observations were limited in coverage and spatial resolution, and many flyby images were obtained under lighting geometries far from ideal for the detection and identification of morphologic features. With the successful insertion of MESSENGER into orbit in March 2011, we are exploiting the opportunity to characterize the tectonics of Mercury in unprecedented detail using images at high resolution and optimum lighting, together with topographic data obtained from Mercury Laser Altimeter (MLA) profiles and stereo imaging. We are digitizing all of Mercury's major tectonic landforms in a standard geographic information system format from controlled global monochrome mosaics (mean resolution 250 m/px), complemented by high-resolution targeted images (up to ~10 m/px), obtained by the Mercury Dual Imaging System (MDIS) cameras. On the basis of an explicit set of diagnostic criteria, we are mapping wrinkle ridges, high-relief ridges, lobate scarps, and extensional troughs and graben in separate shapefiles and cataloguing the segment endpoint positions, length, and orientation for each landform. The versatility of digital mapping facilitates the merging of this tectonic information with other MESSENGER-derived map products, e.g., volcanic units, surface color, geochemical variations, topography, and gravity. Results of this mapping work to date include the identification of extensional

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  13. Utilization of hepatitis C antibody-positive livers: genotype dominance is virally determined

    PubMed Central

    O’Leary, Jacqueline G.; Neri, Michael A.; Trotter, James F.; Davis, Gary L.; Klintmalm, Göran B.; Annette, C.; Simmons, Harold C.

    2015-01-01

    Summary Because of the unrelenting donor shortage, utilization of all potential liver donors is essential. However, when utilizing marginal donors it is critical to precisely characterize the risks, inform recipients of those risks, and allocate these higher risk organs to appropriate candidates. Towards this goal, we need to determine the safety and potential consequences, if any, of utilizing hepatitis C (HCV) antibody-positive donors in HCV infected recipients. To further characterize HCV antibody-positive donors, we analyzed prospectively collected serum samples from HCV antibody-positive donors transplanted into HCV RNA-positive recipients from 5/1993 to 10/2008 for HCV viral load (Roche Cobas AmpliPrep/Cobas Taqman HCV Assay) and genotype (Siemens Versant 2.0 LiPA HCV 5’ UTR/Core Assay). Seventeen of 32 (53%) HCV antibodypositive donors were RNA negative. Fifteen patients received an HCV RNA-positive donor and nine donor–recipient pairs had different genotypes or subtypes for analysis. When genotype 1 competed with a non-1 genotype, it was found in 5/6 recipients. In 2/3 cases of mismatched genotype 1 subtypes, genotype 1a dominated. Kaplan–Meier analysis of patient and graft survival and fibrosis progression did not reveal differences between patients who received an HCV antibody-positive donor that was viremic or aviremic. In conclusion, approximately half of HCV antibody-positive donors were aviremic. Viral dominance in viremic donor–recipient pairs seems virally determined. PMID:22643162

  14. Evaluation of a novel saliva‐based epidermal growth factor receptor mutation detection for lung cancer: A pilot study

    PubMed Central

    Pu, Dan; Liang, Hao; Wei, Fang; Akin, David; Feng, Ziding; Yan, QingXiang; Li, Yin; Zhen, Yan; Xu, Lin; Dong, Gaochao; Wan, Huajing; Dong, Jingsi; Qiu, Xiaoming; Qin, Changlong; Zhu, Daxing; Wang, Xi; Sun, Tong; Zhang, Wenbiao; Li, Canjun; Tang, Xiaojun; Qiao, Youlin

    2016-01-01

    Background This article describes a pilot study evaluating a novel liquid biopsy system for non‐small cell lung cancer (NSCLC) patients. The electric field‐induced release and measurement (EFIRM) method utilizes an electrochemical biosensor for detecting oncogenic mutations in biofluids. Methods Saliva and plasma of 17 patients were collected from three cancer centers prior to and after surgical resection. The EFIRM method was then applied to the collected samples to assay for exon 19 deletion and p.L858 mutations. EFIRM results were compared with cobas results of exon 19 deletion and p.L858 mutation detection in cancer tissues. Results The EFIRM method was found to detect exon 19 deletion with an area under the curve (AUC) of 1.0 in both saliva and plasma samples in lung cancer patients. For L858R mutation detection, the AUC of saliva was 1.0, while the AUC of plasma was 0.98. Strong correlations were also found between presurgery and post‐surgery samples for both saliva (0.86 for exon 19 and 0.98 for L858R) and plasma (0.73 for exon 19 and 0.94 for L858R). Conclusion Our study demonstrates the feasibility of utilizing EFIRM to rapidly, non‐invasively, and conveniently detect epidermal growth factor receptor mutations in the saliva of patients with NSCLC, with results corresponding perfectly with the results of cobas tissue genotyping. PMID:27385985

  15. 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

    2016-09-01

    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. PMID:27602416

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

    PubMed Central

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

    2014-01-01

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

  17. [Testosterone assays using non recommended methods lead to misdiagnosis in women].

    PubMed

    Taibi, Ludmia; Giton, Frank; Moutereau, Stéphane; Fiet, Jean; Guéchot, Jérôme

    2010-01-01

    French and US endocrine societies recommend using GC-MS or RIA after purification (extraction + chromatography) to assess blood levels of testosterone in women. However, most of laboratories use automatized methods that have to be reserved to measure testosterone levels in men. The aim of this study was to show the consequences of analytical discrepancies of some immunological methods on the diagnostics values of testosterone levels assayed in women. Compared to GC-MS the correlations of the assayed levels varied (Spearman's rank correlation coefficients: 0.935; 0.793; 0.841; 0.852 respectively for RIA Immunotech™ with extraction and chromatographic purification; Testosterone Access-DxI800®; Testosterone Immulite 2000®; Testosterone II Cobas E601®). The testosterone levels allowed an accurate conclusion in 95.2 %; 75.8 %; 77.4 %; 89.8 % of patients, respectively. The agreement with GC-MS results was very good for RIA method (κ=0,840), moderate for DxI800® method (κ=0,414), moderate for Immulite® method (κ=0,467), good for Cobas® method (κ=0,667). Most of discordances are false hypertestosteronemia. The use of non recommended methods may leads to nosological errors (misclassification rates of 10 to 25% with automatized methods) that causes loss of chance in part of female patients. PMID:21159578

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

    PubMed Central

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

    2016-01-01

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

  19. Performance and logistical challenges of alternative HIV-1 virological monitoring options in a clinical setting of Harare, Zimbabwe.

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  1. Promising Effects of Afatinib on Leptomeningeal Carcinomatosis Derived from Erlotinib-resistant Lung Adenocarcinoma.

    PubMed

    Sekine, Akimasa; Kato, Terufumi; Iwasawa, Tae; Baba, Tomohisa; Suido, Akihiro; Sakuranaka, Haruyasu; Futaki, Masaaki; Ogura, Takashi

    2016-01-01

    We herein report a case of a 67-year-old woman previously treated with erlotinib for adenocarcinoma with an epidermal growth factor receptor (EGFR) mutation in exon 19, which rapidly developed to progressive symptomatic leptomeningeal carcinomatosis. The primary tumor and lung metastases also worsened and the performance status (PS) score declined to 3. With a re-biopsy from the pulmonary metastases, the T790M mutation was detected by the cobas EGFR mutation test, but not the cycleave test, although an exon 19 deletion was detected by both of the tests. A week after afatinib initiation, the neurological symptoms disappeared and the PS improved to 1 with a radiological response in all disease sites. Chest physicians should consider the use of afatinib for patients with leptomeningeal carcinomatosis from 1st-generation EGFR-TKI resistant adenocarcinoma, regardless of the PS score and the presence of the T790M mutation in the extracranial lesion. PMID:27580550

  2. 'Tetl' Rock

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image, taken by the panoramic camera on NASA's Mars Exploration Rover Spirit during the rover's trek through the 'Columbia Hills' at 'Gusev Crater,' shows the horizontally layered rock dubbed 'Tetl.' Scientists hope to investigate this rock in more detail, aiming to determine whether the rock's layering is volcanic or sedimentary in origin. If for some reason this particular rock is not favorably positioned for grinding and examination by the toolbox of instruments on the rover's robotic arm, Spirit will be within short reach of another similar rock, dubbed 'Coba.' Spirit took this image on its 264th martian day, or sol (Sept. 29, 2004). This is a false-color composite image generated from the panoramic camera's 750-, 530-, and 430-nanometer filters.

  3. Layered Rock Ahead

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Now that solar conjunction is over so that communication between Earth and Mars is no longer blocked by the Sun, NASA's Mars Exploration Rover Spirit is continuing its trek through the 'Columbia Hills' in Gusev Crater. Straight ahead, in the foreground of this image, is a horizontally layered rock dubbed 'Tetl,' which scientists hope to investigate. Layering can be either volcanic or sedimentary in origin; researchers aim to determine which of these processes created this rock. If for some reason this particular rock is not favorably positioned for grinding and examination by the toolbox of instruments on the rover's robotic arm, Spirit will be within short reach of another similar rock, dubbed 'Coba,' just to the right, toward the middle of this image. Spirit took this image with its navigation camera on its 263rd martian day, or sol (Sept. 28, 2004).

  4. Urinary microalbumin measurement using a homogeneous liposomal immunoassay.

    PubMed

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

    1996-08-14

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

  5. 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.

  6. 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

  7. 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 [

  8. Hepatitis C Virus RNA Real-Time Quantitative RT-PCR Method Based on a New Primer Design Strategy.

    PubMed

    Chen, Lida; Li, Wenli; Zhang, Kuo; Zhang, Rui; Lu, Tian; Hao, Mingju; Jia, Tingting; Sun, Yu; Lin, Guigao; Wang, Lunan; Li, Jinming

    2016-01-01

    Viral nucleic acids are unstable when improperly collected, handled, and stored, resulting in decreased sensitivity of currently available commercial quantitative nucleic acid testing kits. Using known unstable hepatitis C virus RNA, we developed a quantitative RT-PCR method based on a new primer design strategy to reduce the impact of nucleic acid instability on nucleic acid testing. The performance of the method was evaluated for linearity, limit of detection, precision, specificity, and agreement with commercial hepatitis C virus assays. Its clinical application was compared to that of two commercial kits--Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) and Kehua. The quantitative RT-PCR method delivered a good performance, with a linearity of R(2) = 0.99, a total limit of detection (genotypes 1 to 6) of 42.6 IU/mL (95% CI, 32.84 to 67.76 IU/mL), a CV of 1.06% to 3.34%, a specificity of 100%, and a high concordance with the CAP/CTM assay (R(2) = 0.97), with a means ± SD value of -0.06 ± 1.96 log IU/mL (range, -0.38 to 0.25 log IU/mL). The method was superior to commercial assays in detecting unstable hepatitis C virus RNA (P < 0.05). This quantitative RT-PCR method can effectively eliminate the influence of RNA instability on nucleic acid testing. The principle of primer design strategy may be applied to the detection of other RNA or DNA viruses. PMID:26612712

  9. 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

  10. Measuring blood glucose in neonatal units: how does hemocue compare?

    PubMed Central

    Deshpande, S A; Matthews, J N; Platt, M P

    1996-01-01

    Rapid and reliable determination of blood glucose concentration is essential during the neonatal period to prevent adverse neurodevelopmental outcome from hypoglycaemia. Despite their unreliability, reagent strip methods continue to be used extensively in neonatal nurseries due to their rapidity and convenience. Recently, a new portable laboratory standard technique has been introduced (HemoCue B-Glucose system) for whole blood glucose determination. It is particularly suitable for near-patient testing in neonatal units. This new method, as well as other established methods of whole blood (Yellow Springs Instrument (YSI) and a hexokinase method on Cobas Bio), and plasma (Kodak Ektachem) glucose measurement, were therefore evaluated for their accuracy and concordance of measurements taken in the neonatal period. There were substantial discrepancies among the four methods of glucose measurement with wide limits of agreement between these methods. The glucose concentrations measured by HemoCue and YSI (n = 206), HemoCue and hexokinase (n = 113), HemoCue and plasma glucose on Ektachem (n = 69) and hexokinase and Ektachem (n = 66) were likely to differ by -29 to +61%, -23 to +56%, -36 to +65%, and -19 to +30%, respectively. Even the laboratory methods of blood glucose determination, therefore, can not be used interchangeably. Using a model based approach, the probabilities of "discordant" classification as hypo- or normo-glycaemia were estimated to be 6.8%, 6.5%, and 7.1% between HemoCue and YSI, HemoCue and hexokinase on Cobas Bio, and HemoCue and Ektachem analysers, respectively. In view of these low probabilities of discordant classification with other glucose analysers, the HemoCue system may offer a reasonable compromise between bedside and laboratory blood glucose estimations in neonates. PMID:8976688

  11. BRAF V600 mutations and pathological features in Japanese melanoma patients

    PubMed Central

    Tanaka, Ryota; Tsutsumida, Arata; Namikawa, Kenjiro; Eguchi, Hironobu; Omata, Wataru; Oashi, Kohei; Ogawa, Toru; Hayashi, Amiko; Nakamura, Noriyuki; Tsuta, Koji

    2015-01-01

    Ultraviolet radiation is a risk factor for BRAF V600 mutations frequently found in melanomas that cause constitutive BRAF activation. Primary sites of melanoma and the frequency of BRAF mutations might differ between races. Melanoma is rare in Japan (1500–2000 cases/year compared with 132 000/year worldwide) and the frequency and distribution of BRAF V600 mutations are unknown. We aimed to investigate the frequency of BRAF V600 mutations in a cohort of Japanese patients with melanoma and determine the relationship between mutations and clinical/pathologic features. DNA was extracted from 80 formalin-fixed, paraffin-embedded tumours from individuals diagnosed with melanoma. BRAF V600 mutations were detected using the Cobas 4800 System with z480 Analyzer and Cobas 4800 BRAF V600 Mutation Test reagents. BRAF V600 mutations were detected in 41.8% of tested tumours, with an invalid rate of 1.3%. The mutation rate was more than 60% in patients aged less than 60 years and more than 36% in patients with stage III/IV disease. No sex difference in the mutation rate was observed. BRAF V600 mutations were detected in 18.8% of acral lentiginous melanomas (ALMs), 64.7% of superficial spreading melanomas, 50.0% of lentigo maligna melanomas and 20.0% of nodular melanomas. Although the mutation rate was low in ALMs, 36.4% were mutation positive at stage III/IV compared with 9.5% at stage I/II. This study confirmed associations among BRAF V600 mutations, pathological features and subtypes of melanoma. BRAF V600 mutations were more frequent in late-stage ALMs than in early-stage ALMs. Superficial spreading melanomas had similar mutation rates at all stages. These insights suggest improved treatment predictions for stage III/IV melanoma patients. PMID:25051202

  12. BRAF V600 mutations and pathological features in Japanese melanoma patients.

    PubMed

    Yamazaki, Naoya; Tanaka, Ryota; Tsutsumida, Arata; Namikawa, Kenjiro; Eguchi, Hironobu; Omata, Wataru; Oashi, Kohei; Ogawa, Toru; Hayashi, Amiko; Nakamura, Noriyuki; Tsuta, Koji

    2015-02-01

    Ultraviolet radiation is a risk factor for BRAF V600 mutations frequently found in melanomas that cause constitutive BRAF activation. Primary sites of melanoma and the frequency of BRAF mutations might differ between races. Melanoma is rare in Japan (1500-2000 cases/year compared with 132 000/year worldwide) and the frequency and distribution of BRAF V600 mutations are unknown. We aimed to investigate the frequency of BRAF V600 mutations in a cohort of Japanese patients with melanoma and determine the relationship between mutations and clinical/pathologic features. DNA was extracted from 80 formalin-fixed, paraffin-embedded tumours from individuals diagnosed with melanoma. BRAF V600 mutations were detected using the Cobas 4800 System with z480 Analyzer and Cobas 4800 BRAF V600 Mutation Test reagents. BRAF V600 mutations were detected in 41.8% of tested tumours, with an invalid rate of 1.3%. The mutation rate was more than 60% in patients aged less than 60 years and more than 36% in patients with stage III/IV disease. No sex difference in the mutation rate was observed. BRAF V600 mutations were detected in 18.8% of acral lentiginous melanomas (ALMs), 64.7% of superficial spreading melanomas, 50.0% of lentigo maligna melanomas and 20.0% of nodular melanomas. Although the mutation rate was low in ALMs, 36.4% were mutation positive at stage III/IV compared with 9.5% at stage I/II. This study confirmed associations among BRAF V600 mutations, pathological features and subtypes of melanoma. BRAF V600 mutations were more frequent in late-stage ALMs than in early-stage ALMs. Superficial spreading melanomas had similar mutation rates at all stages. These insights suggest improved treatment predictions for stage III/IV melanoma patients. PMID:25051202

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

    PubMed

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

    2015-12-01

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

  14. BRAF mutation testing with a rapid, fully integrated molecular diagnostics system.

    PubMed

    Janku, Filip; Claes, Bart; 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

    2015-09-29

    Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTMBRAF 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 IdyllaTMBRAF 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

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

    PubMed Central

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

    2004-01-01

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

  16. 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

  17. Evaluation of a Novel PCR-Based Assay for Detection and Identification of Chlamydia trachomatis Serovars in Cervical Specimens▿

    PubMed Central

    Quint, Koen; Porras, Carolina; Safaeian, Mahboobeh; González, Paula; Hildesheim, Allan; Quint, Wim; van Doorn, Leen-Jan; Silva, Sandra; Melchers, Willem; Schiffman, Mark; Rodríguez, Ana Cecilia; Wacholder, Sholom; Freer, Enrique; Cortes, Bernal; Herrero, Rolando

    2007-01-01

    The aims of this study were to compare a novel PCR-based Chlamydia trachomatis detection and genotyping (Ct-DT) assay with the FDA-approved, commercially available C. trachomatis detection Hybrid Capture 2 (HC2) assay and to investigate the C. trachomatis serovar distribution among young women in a rural Costa Rican study population. A total of 5,828 sexually active women participating in a community-based trial in Costa Rica were tested for C. trachomatis by HC2. A sample of 1,229 specimens consisting of 100% HC2 C. trachomatis-positive specimens (n = 827) and a random sample of 8% HC2 C. trachomatis-negative specimens (n = 402) were tested with the Ct-DT assay. Agreement between the two assays was determined by the unweighted kappa statistic. Discrepant specimens were tested with a second commercially available test (COBAS TaqMan). The Ct-DT-positive specimens were further analyzed with the Ct-DT genotyping step to investigate the distribution of 14 different C. trachomatis serovars (A, B/Ba, C, D/Da, E, F, G/Ga, H, I/Ia, J, K, L1, L2/L2a, and L3). After accounting for the sampling fraction selected for Ct-DT testing, crude agreement with the HC2 assay was 98% and the kappa was 0.92 (95% confidence interval [CI], 0.89 to 0.97). The 33 discordant samples that were further analyzed with the COBAS TaqMan test showed better agreement with the Ct-DT assay (31/33, P < 0.001). Among the 806 Ct-DT-positive samples, serovar E was the most common serovar (31%), followed by serovars F and D (both 21%) and serovar I (15%). In conclusion, the novel Ct-DT assay permits reliable detection and identification of C. trachomatis serovars. PMID:17959760

  18. Evaluation of the Whole-Blood Alere Q NAT Point-of-Care RNA Assay for HIV-1 Viral Load Monitoring in a Primary Health Care Setting in Mozambique.

    PubMed

    Jani, Ilesh V; Meggi, Bindiya; Vubil, Adolfo; Sitoe, Nádia E; Bhatt, Nilesh; Tobaiwa, Ocean; Quevedo, Jorge I; Loquiha, Osvaldo; Lehe, Jonathan D; Vojnov, Lara; Peter, Trevor F

    2016-08-01

    Viral load testing is the WHO-recommended monitoring assay for patients on HIV antiretroviral therapy (ART). Point-of-care (POC) assays may help improve access to viral load testing in resource-limited settings. We compared the performance of the Alere Q NAT POC viral load technology (Alere Technologies, Jena, Germany), measuring total HIV RNA using finger prick capillary whole-blood samples collected in a periurban health center, with that of a laboratory-based plasma RNA test (Roche Cobas Ampliprep/Cobas TaqMan v2) conducted on matched venous blood samples. The whole-blood Alere Q NAT POC assay produced results with a bias of 0.8593 log copy/ml compared to the laboratory-based plasma assay. However, at above 10,000 copies/ml, the bias was 0.07 log copy/ml. Using the WHO-recommended threshold to determine ART failure of 1,000 copies/ml, the sensitivity and specificity of the whole-blood Alere Q NAT POC assay were 96.83% and 47.80%, respectively. A cutoff of 10,000 copies/ml of whole blood with the Alere Q NAT POC assay appears to be a better predictor of ART failure threshold (1,000 copies/ml of plasma), with a sensitivity of 84.0% and specificity of 90.3%. The precision of the whole-blood Alere Q NAT POC assay was comparable to that observed with the laboratory technology (5.4% versus 7.5%) between detectable paired samples. HIV POC viral load testing is feasible at the primary health care level. Further research on the value of whole-blood viral load to monitor antiretroviral therapy is warranted. PMID:27252459

  19. Cross-Platform Analysis of HIV-1 RNA Data Generated by a Multicenter Assay Validation Study with Wide Geographic Representation

    PubMed Central

    Harty, Brian; Granger, Suzanne; Wager, Carrie; Crump, John A.; Fiscus, Susan A.; Bremer, James W.

    2012-01-01

    HIV-1 RNA quantitation continues to be extremely important for monitoring patients infected with HIV-1, and a number of assays have been utilized for this purpose. Differences in assay performance with respect to log10 recovery and HIV-1 subtype specificity have been well documented for commercially available assays, although comparisons are usually limited to one or two assay platforms. Two new FDA-approved assays, the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test (RT) and the Abbott RealTime HIV-1 assay (AR), that utilize real-time PCR have replaced previous HIV-1 RNA platforms. Inadequate detection of some strains of HIV-1 resulted in the addition of a new primer/probe set and the introduction of a second version of the RT assay. In this study, comparisons of assay performance between the different FDA-approved HIV-1 RNA assay platforms (both new and existing) were performed by using validation data that included both well-characterized virus stock and locally collected clinical samples. Laboratories across diverse geographical regions performed the validation testing and submitted data to the Virology Quality Assurance program (VQA) for analysis. Correlation values for clinical sample testing varied across the assay platforms (r = 0.832 to 0.986), and average log10 recoveries for HIV-1 RNA controls (compared to the nominal value) ranged from −0.215 to 0.181. These data demonstrate the need for use of one assay platform for longitudinal patient monitoring, but the data also reinforce the notion that no one assay is superior and that testing across platforms may be required for discordance reconciliation. PMID:22692747

  20. 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

  1. 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

  2. Performance evaluation of ExiStation HBV diagnostic system for hepatitis B virus DNA quantitation.

    PubMed

    Cha, Young Joo; Yoo, Soo Jin; Sohn, Yong-Hak; Kim, Hyun Soo

    2013-11-01

    The performance of a recently developed real-time PCR system, the ExiStation HBV diagnostic system, for quantitation of hepatitis B virus (HBV) in human blood was evaluated. The detection limit, reproducibility, cross-reactivity, and interference were evaluated as measures of analytical performance. For the comparison study, 100 HBV-positive blood samples and 100 HBV-negative samples from Korean Blood Bank Serum were used, and the results of the ExiStation HBV system showed good correlation with those obtained using the Cobas TaqMan (r2=0.9931) and Abbott real-time PCR systems (r2=0.9894). The lower limit of detection was measured as 9.55 IU/mL using WHO standards and the dynamic range was linear from 6.68 to 6.68×10(9) IU/mL using cloned plasmids. The within-run coefficient of variation (CV) was 9.4%, 2.1%, and 1.1%, and the total CV was 11.8%, 3.6%, and 1.7% at a concentration of 1.92 log10 IU/mL, 3.88 log10 IU/mL, and 6.84 log10 IU/mL, respectively. No cross-reactivity or interference was detected. The ExiStation HBV diagnostic system showed satisfactory analytical sensitivity, excellent reproducibility, no cross-reactivity, no interference, and high agreement with the Cobas TaqMan and Abbott real-time PCR systems, and is therefore a useful tool for the detection and monitoring of HBV infection. PMID:23892129

  3. 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

    2015-01-01

    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. PMID:26782408

  4. Automatic P- and S-Phase Picker for High-Resolution Local Source Tomography: Application to the Alpine Region

    NASA Astrophysics Data System (ADS)

    Diehl, T.; Kissling, E.; Husen, S.; Deichmann, N.; Aldersons, F.

    2008-12-01

    Resolution and reliability of tomographic velocity models strongly depend on quality and consistency of available travel-time data. Arrival times routinely picked by network analysts on a day-to-day basis often yield a high level of noise due to mispicks and other inconsistencies, particularly in error assessment. Furthermore, tomographic studies at regional scales require merging of phase picks of several networks. Since a common quality assessment is usually not available for phase data provided by different networks, additional inconsistencies are introduced by the merging process. Considerable improvement in the quality of phase data can only be achieved by massive re-picking of seismograms. Considering the amount of data necessary for regional high-resolution tomography, algorithms combining accurate picking with an automated error assessment represent the best tool to derive large suitable data sets. In this work, we present algorithms for automatic P- and S-phase picking at local to regional distances including consistent picking error assessment. These algorithms are tested and applied to a waveform data set of the greater Alpine region. The MPX software is used to derive high-quality P-phase arrival times and the quality-attributed automatic picks are inverted for regional 1-D and 3-D P-wave models of the greater Alpine region. The comparison with a tomographic model based on standard routine phase data extracted from the ISC Bulletin illustrates effects on tomographic results due to consistency and reliability of our high- quality data set. In our proposed S-wave picking approach, we combine three commonly used phase detection and picking methods to a robust automated picking procedure. Information from the different techniques provides an 'in- situ' estimate of timing uncertainty and phase identification of the automatic S-phase pick. The average accuracy of automatic picks and their classification is comparable with manually picked reference picks, even

  5. 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

  6. Comet 67P/C-G: Surface Temperatures as Derived by Rosetta/VIRTIS in the Mapping Phase

    NASA Astrophysics Data System (ADS)

    Tosi, F.; Capria, M. T.; Capaccioni, F.; Filacchione, G.; De Sanctis, M. C.; Erard, S.; Leyrat, C.; Bockelée-Morvan, D.; Kuhrt, E.

    2014-12-01

    We show spatially-resolved temperature maps of comet 67P/Churyumov-Gerasimenko, main target of the ESA Rosetta spacecraft, as derived from infrared hyperspectral images acquired by the VIRTIS imaging spectrometer onboard the Rosetta Orbiter in the Mapping phase carried out in August and September 2014. These data were obtained during the Mapping phase, at variable spatial resolution (from roughly 100 m/px down to ~10 m/px), illumination conditions, and heliocentric distances (spanning the range from 3.6 to 3.4 AU). VIRTIS infrared spectra in the range longward of ~4 μm are affected by the thermal emission of the comet, hence the measured radiance in that spectral region can be used to determine surface temperatures and spectral emissivities by means of temperature-retrieval algorithms. We use a Bayesian approach that was previously applied to Rosetta/VIRTIS data obtained during the close flybys of asteroids 2678 Steins and 21 Lutetia, as well as to the entire dataset of infrared data acquired by the VIR mapping spectrometer aboard the Dawn spacecraft during its orbital phase at asteroid Vesta in 2011-2012. The VIRTIS instrument onboard Rosetta is not sensitive to physical temperatures on the nightside of the comet, where the signal is considerably low. Typically, ~170 K is the minimum temperature that allows one to retrieve surface temperatures while preserving high accuracies. On the other hand, for a given local solar time, the maximum temperature depends on the solar incidence angle and on surface properties such as thermal inertia and albedo. The availability of spatially-resolved, accurate temperature observations, significantly spaced out in local solar time, provides clues to the physical structure of specific surface units, which complements the mineralogical investigation based on imaging spectroscopy data collected at shorter wavelengths. AcknowledgementsThis work is supported by the Italian Space Agency (ASI), ASI-INAF Contract n. I/024/12/0. We

  7. 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

  8. High-Throughput Serum 25-Hydroxy Vitamin D Testing with Automated Sample Preparation.

    PubMed

    Stone, Judy

    2016-01-01

    Serum from bar-coded tubes, and then internal standard, are pipetted to 96-well plates with an 8-channel automated liquid handler (ALH). The first precipitation reagent (methanol:ZnSO4) is added and mixed with the 8-channel ALH. A second protein precipitating agent, 1 % formic acid in acetonitrile, is added and mixed with a 96-channel ALH. After a 4-min delay for larger precipitates to settle to the bottom of the plate, the upper 36 % of the precipitate/supernatant mix is transferred with the 96-channel ALH to a Sigma Hybrid SPE(®) plate and vacuumed through for removal of phospholipids and precipitated proteins. The filtrate is collected in a second 96-well plate (collection plate) which is foil-sealed, placed in the autosampler (ALS), and injected into a multiplexed LC-MS/MS system running AB Sciex Cliquid(®) and MPX(®) software. Two Shimadzu LC stacks, with multiplex timing controlled by MPX(®) software, inject alternately to one AB Sciex API-5000 MS/MS using positive atmospheric pressure chemical ionization (APCI) and a 1.87 min water/acetonitrile LC gradient with a 2.1 × 20 mm, 2.7 μm, C18 fused core particle column (Sigma Ascentis Express). LC-MS/MS through put is ~44 samples/h/LC-MS/MS system with dual-LC channel multiplexing. Plate maps are transferred electronically from the ALH and reformatted into LC-MS/MS sample table format using the Data Innovations LLC (DI) Instrument Manager middleware application. Before collection plates are loaded into the ALS, the plate bar code is manually scanned to download the sample table from the DI middleware to the LC-MS/MS. After acquisition-LC-MS/MS data is analyzed with AB Sciex Multiquant(®) software using customized queries, and then results are transferred electronically via a DI interface to the LIS. 2500 samples/day can be extracted by two analysts using four ALHs in 4-6 h. LC-MS/MS analysis of those samples on three dual-channel LC multiplexed LC-MS/MS systems requires 19-21 h and data analysis can be

  9. Overexpression of Mycothiol Disulfide Reductase Enhances Corynebacterium glutamicum Robustness by Modulating Cellular Redox Homeostasis and Antioxidant Proteins under Oxidative Stress.

    PubMed

    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

  10. Observational bias and the apparent distribution of ponds on Eros

    NASA Astrophysics Data System (ADS)

    Roberts, James H.; Barnouin, Olivier S.; Kahn, Eliezer G.; Prockter, Louise M.

    2014-10-01

    Over 300 “ponds” have been identified on 433 Eros: smooth deposits that sharply embay the bounding depressions in which they lie. The known ponds are largely concentrated near the equator at the ends of the long axis of the asteroid. Here, we examine the pixel scale of images available at the pond locations, and compare the observed distribution of ponds on Eros to that of the image pixel scale. We find that the majority (60%) of ponds are found in the regions covered by images with pixel scales less than 2 m/px, a total of only 13% of the surface area. The correlation between pond density and image pixel scale suggests a significant observational bias in the identification of small ponds. These findings suggest that the distribution of ponds on Eros may not be as clear-cut as previously reported, and that it may be best not to use this distribution to assess existing models regarding their formation of these landforms.

  11. Optical design and stray light analysis for the JANUS camera of the JUICE space mission

    NASA Astrophysics Data System (ADS)

    Greggio, D.; Magrin, D.; Munari, M.; Zusi, M.; Ragazzoni, R.; Cremonese, G.; Debei, S.; Friso, E.; Della Corte, V.; Palumbo, P.; Hoffmann, H.; Jaumann, R.; Michaelis, H.; Schmitz, N.; Schipani, P.; Lara, L. M.

    2015-09-01

    The JUICE (JUpiter ICy moons Explorer) satellite of the European Space Agency (ESA) is dedicated to the detailed study of Jupiter and its moons. Among the whole instrument suite, JANUS (Jovis, Amorum ac Natorum Undique Scrutator) is the camera system of JUICE designed for imaging at visible wavelengths. It will conduct an in-depth study of Ganymede, Callisto and Europa, and explore most of the Jovian system and Jupiter itself, performing, in the case of Ganymede, a global mapping of the satellite with a resolution of 400 m/px. The optical design chosen to meet the scientific goals of JANUS is a three mirror anastigmatic system in an off-axis configuration. To ensure that the achieved contrast is high enough to observe the features on the surface of the satellites, we also performed a preliminary stray light analysis of the telescope. We provide here a short description of the optical design and we present the procedure adopted to evaluate the stray-light expected during the mapping phase of the surface of Ganymede. We also use the results obtained from the first run of simulations to optimize the baffle design.

  12. Methods for calibrating the gain and offset of the DSSC detector for the European XFEL using X-ray line sources

    NASA Astrophysics Data System (ADS)

    Schlee, S.; Weidenspointner, G.; Moch, D.; Kuster, M.; Porro, M.

    2016-01-01

    The DSSC (DEPFET Sensor with Signal Compression) will be a silicon based, 2d 1 Mpx imaging detector for the European X-ray Free Electron Laser Facility (XFEL.EU) in Hamburg, Germany. The DSSC is foreseen for soft X-radiation from 0.5 keV up to 6 keV . Driven by its scientific requirements, the design goals of the detector system are single photon detection, high dynamic range and a high frame rate of up to 4.5 MHz. Signal compression and amplification will be performed in the silicon sensor pixels yielding a low signal noise. Utilizing an in-pixel active filtering stage and an 8/9-bit ADC, the detector will provide parallel read-out of all pixels. In order to calibrate offset and gain, the procedure currently under investigation relies on determining peak positions in measurements with calibration line sources such as 55Fe. Here the status of studies of the stability and performance of a parameterized fit function designed for this task will be presented.

  13. 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.

  14. 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.

  15. Zebrafish Embryo Model of Bartonella henselae Infection

    PubMed Central

    Lima, Amorce; Cha, Byeong J.; Amin, Jahanshah; Smith, Lisa K.

    2014-01-01

    Abstract Bartonella henselae (Bh) is an emerging zoonotic pathogen that has been associated with a variety of human diseases, including bacillary angiomatosis that is characterized by vasoproliferative tumor-like lesions on the skin of some immunosuppressed individuals. The study of Bh pathogenesis has been limited to in vitro cell culture systems due to the lack of an animal model. Therefore, we wanted to investigate whether the zebrafish embryo could be used to model human infection with Bh. Our data showed that Tg(fli1:egfp)y1 zebrafish embryos supported a sustained Bh infection for 7 days with >10-fold bacterial replication when inoculated in the yolk sac. We showed that Bh recruited phagocytes to the site of infection in the Tg(mpx:GFP)uwm1 embryos. Infected embryos showed evidence of a Bh-induced angiogenic phenotype and an increase in the expression of genes encoding pro-inflammatory factors and pro-angiogenic markers. However, infection of zebrafish embryos with a deletion mutant in the major adhesin (BadA) resulted in little or no bacterial replication and a diminished host response, providing the first evidence that BadA is critical for in vivo infection. Thus, the zebrafish embryo provides the first practical model of Bh infection that will facilitate efforts to identify virulence factors and define molecular mechanisms of Bh pathogenesis. PMID:25026365

  16. A novel optical design for planetary surface stereo-imaging: preliminary design of the stereoscopic imaging channel of SIMBIOSYS for the BepiColombo ESA mission

    NASA Astrophysics Data System (ADS)

    Da Deppo, Vania; Naletto, Giampiero; Cremonese, Gabriele; Debei, Stefano; Flamini, Enrico

    2006-06-01

    The optical design of the STereoscopic imaging Channel (STC) of the imaging/spectroscopic system SIMBIOSYS for the ESA BepiColombo mission is presented. The main aim of this system is the global stereo mapping of planet Mercury surface during the BepiColombo mission lifetime. The instrument consists of two identical cameras looking at +/-20° from nadir which are sharing some optical components and the detector. The instrument has a 23"/pixel scale factor, corresponding to 50 m/px at 400 km from the surface, on a 4°x 4° FoV; imaging in four different spectral bands, between 540 nm and 890 nm, is foreseen. The STC optical characteristics guarantee global stereo mapping of the whole Mercury surface with all the filters. The coupling of an achromatic air-spaced doublet with a relay lens system allows good aberration balancing over all the field of view: the diffraction Ensquared Energy inside one pixel of the detector is of the order of 80%. In addition, an intermediate field stop gives the possibility of designing an efficient baffling system for straylight rejection. To cope with the hazardous radiation environment in which the spacecraft will be immersed in during the mission, all the glasses selected for the design are rad-hard type. A preliminary tolerance analysis has also been undertaken showing a low criticality level for manufacturing, alignment and stability of the system.

  17. 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.

  18. 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.

  19. 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

  20. Smyd5 plays pivotal roles in both primitive and definitive hematopoiesis during zebrafish embryogenesis

    PubMed Central

    Fujii, Tomoaki; Tsunesumi, Shin-ichiro; Sagara, Hiroshi; Munakata, Miyo; Hisaki, Yoshihiro; Sekiya, Takao; Furukawa, Yoichi; Sakamoto, Kazuhiro; Watanabe, Sumiko

    2016-01-01

    Methylation of histone tails plays a pivotal role in the regulation of a wide range of biological processes. SET and MYND domain-containing protein (SMYD) is a methyltransferase, five family members of which have been identified in humans. SMYD1, SMYD2, SMYD3, and SMYD4 have been found to play critical roles in carcinogenesis and/or the development of heart and skeletal muscle. However, the physiological functions of SMYD5 remain unknown. To investigate the function of Smyd5 in vivo, zebrafish were utilised as a model system. We first examined smyd5 expression patterns in developing zebrafish embryos. Smyd5 transcripts were abundantly expressed at early developmental stages and then gradually decreased. Smyd5 was expressed in all adult tissues examined. Loss-of-function analysis of Smyd5 was then performed in zebrafish embryos using smyd5 morpholino oligonucleotide (MO). Embryos injected with smyd5-MO showed normal gross morphological development, including of heart and skeletal muscle. However, increased expression of both primitive and definitive hematopoietic markers, including pu.1, mpx, l-plastin, and cmyb, were observed. These phenotypes of smyd5-MO zebrafish embryos were also observed when we introduced mutations in smyd5 gene with the CRISPR/Cas9 system. As the expression of myeloid markers was elevated in smyd5 loss-of-function zebrafish, we propose that Smyd5 plays critical roles in hematopoiesis. PMID:27377701

  1. Smyd5 plays pivotal roles in both primitive and definitive hematopoiesis during zebrafish embryogenesis.

    PubMed

    Fujii, Tomoaki; Tsunesumi, Shin-Ichiro; Sagara, Hiroshi; Munakata, Miyo; Hisaki, Yoshihiro; Sekiya, Takao; Furukawa, Yoichi; Sakamoto, Kazuhiro; Watanabe, Sumiko

    2016-01-01

    Methylation of histone tails plays a pivotal role in the regulation of a wide range of biological processes. SET and MYND domain-containing protein (SMYD) is a methyltransferase, five family members of which have been identified in humans. SMYD1, SMYD2, SMYD3, and SMYD4 have been found to play critical roles in carcinogenesis and/or the development of heart and skeletal muscle. However, the physiological functions of SMYD5 remain unknown. To investigate the function of Smyd5 in vivo, zebrafish were utilised as a model system. We first examined smyd5 expression patterns in developing zebrafish embryos. Smyd5 transcripts were abundantly expressed at early developmental stages and then gradually decreased. Smyd5 was expressed in all adult tissues examined. Loss-of-function analysis of Smyd5 was then performed in zebrafish embryos using smyd5 morpholino oligonucleotide (MO). Embryos injected with smyd5-MO showed normal gross morphological development, including of heart and skeletal muscle. However, increased expression of both primitive and definitive hematopoietic markers, including pu.1, mpx, l-plastin, and cmyb, were observed. These phenotypes of smyd5-MO zebrafish embryos were also observed when we introduced mutations in smyd5 gene with the CRISPR/Cas9 system. As the expression of myeloid markers was elevated in smyd5 loss-of-function zebrafish, we propose that Smyd5 plays critical roles in hematopoiesis. PMID:27377701

  2. 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

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

    PubMed

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

    2014-09-01

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

  4. Comparative Analysis of Real-Time Polymerase Chain Reaction Methods to Typing HLA-B*57:01 in HIV-1-Positive Patients.

    PubMed

    Falasca, Francesca; Dello Russo, Cinzia; Mora, Barbara; Pirazzoli, Antonella; Fantauzzi, Alessandra; Navarra, Pierluigi; Pizzuti, Antonio; De Vito, Corrado; Antonelli, Guido; Turriziani, Ombretta

    2016-07-01

    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. Clinical efficacy of the highly sensitive hepatitis C virus RNA quantitative assay in patients with relapse following interferon-based therapy with second-generation direct-acting antivirals

    PubMed Central

    ISHIKAWA, TORU; ABE, SATOSHI; WATANABE, TAKAYUKI; NOZAWA, YUJIRO; SANO, TOMOE; IWANAGA, AKITO; SEKI, KEIICHI; HONMA, TERASU; YOSHIDA, TOSHIAKI

    2016-01-01

    For refractory chronic hepatitis C, interferon (IFN)-based triple-agent combination therapy with second-generation direct-acting antivirals (DAAs) has been established as the standard treatment method. The rate of decrease in the viral load and the negative conversion of hepatitis C virus (HCV) RNA in the early phase following treatment initiation are considered important factors for predicting the therapeutic outcome. In the present study, the Roche Cobas AmpliPrep/COBAS TaqMan (CAP/CTM) HCV v2.0 assay and the AccuGENE m-HCV RNA quantitative assay [Abbott RealTime HCV (ART) assay] were analyzed for their clinical efficacy and ability to predict therapeutic outcomes in the early phase in patients with relapse following IFN-based second-generation DAA therapy. Of the 56 patients who received IFN-based second-generation DAA therapy since December 2013, 6 achieved an end-of-treatment response (ETR), but subsequently experienced relapse. In these 6 patients, fluctuations in viral loads in the early phase detected by the CAP/CTM and ART assays were compared. At 4 weeks after treatment initiation, 4 of the 6 patients were diagnosed as negative by the CAP/CTM assay, whereas 2 of these 4 patients were not identified as negative by the ART assay. Of the 2 patients, one was signal-positive with an HCV RNA load <1.08 Log IU/ml, and the other patient had a viral load of 1.12 Log IU/ml. At 8 weeks after treatment initiation, 1 patient was found to be negative by the CAP/CTM assay, but signal-positive with a viral load <1.08 Log IU/ml by the ART assay. From 4 to 8 weeks after treatment initiation, 3 of the 6 patients appeared to be discrepant cases. In conclusion, of the 6 patients who achieved an ETR, 4 were determined to have achieved a rapid virological response (RVR) by the CAP/CTM assay, but may not have actually become negative. The ART assay is highly sensitive, has a wide measurement range, may be suitable for monitoring HCV RNA loads, and is expected to have an

  6. [Investigation of the correlation between anti-HCV levels (S/Co) with HCV-RNA in the diagnosis of hepatitis C virus (HCV) infection].

    PubMed

    Şanlıdağ, Tamer; Akçalı, Sinem; Ecemiş, Talat; Süer, Kaya; Erbay Dündar, Pınar; Arıkan, Ayşe; Güvenir, Meryem; Güler, Emrah

    2016-07-01

    Detection of borderline and/or low positive anti-HCV results by enzyme immunoassay (EIA) leads to severe problems in routine laboratories and needs confirmation with nucleic acid amplification tests which can increase the cost. In EIA tests, if the ratio of sample to cut-off (S/Co) is ≥ 1, the sample is accepted as positive according to the manufacturers' instructions. Although over the last decade the application of S/Co values have also applied to HCV-RNA readings, the current study aims to determine whether the S/Co value is adequate and applicable for the anti-HCV EIA test, and to determine whether a correlation exists between HCV-RNA and HCV infections. A total of 658 cases (402 female, 256 male; mean age: 49.4 ± 17.0 years) who were found anti-HCV positive between January 2011-July 2013 were included in the study. Anti-HCV tests were performed by chemiluminescent EIA (Architect i2000SR, Abbott, USA and LiaisonXL Murex, DiaSorin, Italy) and HCV-RNA by real-time PCR (Cobas Ampliprep/Cobas TaqMan HCV, Roche, USA). The mean S/Co value of the cases was 7.3 ± 4.8 (range: 1.00-17.59) and mean HCV-RNA value was 2.3x105 ± 2.1x106 copies/ml. When the anti-HCV S/Co value of varying ranges was compared with HCV-RNA readings a particular trend was noted. In the anti-HCV S/Co values of 1.0-4.0; 4.1-7.0; 7.1-10.0; 10.1-13.0; 13.1-16.0 and ³16.1, HCV-RNA positivity rates were detected as 1.9%, 24.7%,37.1%, 46.7%, 56.4% and 75%, respectively. Statistical analysis indicated an intermediate positive correlation (r= 0.454) between anti-HCV ve HCV-RNA readings (p= 0.000). An adequate S/Co value was accepted as 5.0 based on the ROC analysis, and this value gave a performance confidence level of 95.6% when determining whether a patient is HCV positive. Based on the data of this study it became evident that further EIA testing is not required if the S/Co value is ≥ 5.0, however if the S/Co value is less than 5.0, then further clinical analysis and revaluation of the patient

  7. 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

  8. 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.

  9. Effets de rayonnement sur les detecteurs au silicium a pixels du detecteur ATLAS

    NASA Astrophysics Data System (ADS)

    Lebel, Celine

    Two detection systems are using pixel silicon detectors in the ATLAS detector: the Pixel, which is the subdetector closest to the interaction point, and the MPX network. The activation of the materials present in the Pixel produced by radiation has been measured in two experiments which we performed at CERF (CERN) and NPI-ASCR (Czech Republic). These experimental studies of activation are compared with GEANT4 simulations. The results of these comparisons show that the simulation can predict the activities with a precision of an order of magnitude. They also show that GEANT4 fails to produce certain radioisotopes seen in the experimental activation studies. The contribution to background and the residual doses due to the desintegration of the radioisotopes produced by fast neutrons (category in which falls the expected average neutron energy of 1 MeV in ATLAS) are extrapolated to ATLAS conditions. It is found that this background in the ATLAS Pixel subdetector will be negligible and that the doses are well below safety concerns for detector manipulation during maintenance and repair periods. The radiation field also inflicts damages to the silicon detectors thus reducing their detection efficiency. A modified Hecht model is presented using an electric field description which includes the double junction effect and a small exponential component in areas usually considered without electric field. This model allows the description of the detection efficiency as a function of applied bias voltage and irradiation fluence for several types of silicon detectors irradiated by particles of different types and energies. On top of validating the Hecht model proposed in this thesis, the studies of the radiation damage on silicon detectors has allowed to conclude that the N1EL hypothesis has to be revised (study with different energies). Using the variation with irradiation fluence of the effective doping concentration and of the leakage current, it is shown that silicon

  10. 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

  11. 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

  12. Consistent phase picking for regional tomography models: application to the greater Alpine region

    NASA Astrophysics Data System (ADS)

    Diehl, T.; Kissling, E.; Husen, S.; Aldersons, F.

    2009-02-01

    The resolution and reliability of tomographic velocity models strongly depends on quality and consistency of available traveltime data. Arrival times routinely picked by network analysts on a day-to-day basis often yield a high level of noise due to mispicks and other inconsistencies, particularly in error assessment. Furthermore, tomographic studies at regional scales require merging of phase picks from several networks. Since a common quality assessment is not usually available for phase data provided by different networks, additional inconsistencies are introduced by the merging process. Considerable improvement in the quality of phase data can only be achieved through complete repicking of seismograms. Considering the amount of data necessary for regional high-resolution tomography, algorithms combining accurate picking with an automated error assessment represent the best tool to derive large suitable data sets. In this work, we present procedures for consistent automated and routine picking of P-wave arrival times at local to regional scales including consistent picking error assessment. Quality-attributed automatic picks are derived from the MPX picking system. The application to earthquakes in the greater Alpine region demonstrates the potential of such a repicking approach. The final data set consists of more than 13000 high-quality first-arrivals and it is used to derive regional 1-D and preliminary 3-D P-wave models of the greater Alpine region. The comparison with a tomographic model based on routine phase data extracted from the ISC Bulletin illustrates effects on tomographic results due to consistency and reliability of our high-quality data set.

  13. Lab-scale tests and numerical simulations for in situ treatment of polluted groundwater.

    PubMed

    Careghini, A; Saponaro, S; Sezenna, E; Daghio, M; Franzetti, A; Gandolfi, I; Bestetti, G

    2015-04-28

    Methyl tert-butyl ether (MTBE) is used at significant percentages as an additive of unleaded gasoline. The physical-chemical properties of the substance (water solubility, soil organic carbon-water partition coefficient) cause high mobility and high concentrations in groundwater. Laboratory scale batch and column tests and mathematical modeling were performed to study the feasibility of a biobarrier (BB), that is an in situ permeable biological barrier with or without inoculation, for the remediation of MTBE and other gasoline-derived pollutants (benzene, toluene, ethylbenzene, o-xylene and m+p-xylenes, BTEXs) polluted groundwater and to estimate kinetic constants. The experimental results showed simultaneous biodegradation of MTBE and BTEXs, with similar removals in the uninoculated and the inoculated systems. Ranges for the first order kinetic removal were obtained for MTBE ((0.18±0.02)/(0.28±0.11d(-1))), B ((0.39±0.12)/(0.56±0.12d(-1))), T ((0.51±0.03)/(0.78±0.15d(-1))), E ((0.46±0.18)/(1.57±0.21d(-1))), o-X ((0.24±0.08)/(0.64±0.09d(-1))) and m+p-X ((0.20±0.04)/(1.21±0.04d(-1))). The results of the laboratory tests allowed to improve mathematical modeling in order to design a full-scale BB at a gasoline-contaminated site. PMID:25644032

  14. Spectral heterogeneity on Phobos and Deimos: HiRISE observations and comparisons to Mars Pathfinder results

    NASA Astrophysics Data System (ADS)

    Thomas, N.; Stelter, R.; Ivanov, A.; Bridges, N. T.; Herkenhoff, K. E.; McEwen, A. S.

    2011-10-01

    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, 536-556,1996) 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, 9055-9068, 1999). The spectral gradients of the blue and red units on Phobos bracket the results from IMP.

  15. 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.

  16. 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.

  17. 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.

  18. Multilocus Sequence Typing (MLST) for Lineage Assignment and High Resolution Diversity Studies in Trypanosoma cruzi

    PubMed Central

    Yeo, Matthew; Mauricio, Isabel L.; Messenger, Louisa A.; Lewis, Michael D.; Llewellyn, Martin S.; Acosta, Nidia; Bhattacharyya, Tapan; Diosque, Patricio; Carrasco, Hernan J.; Miles, Michael A.

    2011-01-01

    Background Multilocus sequence typing (MLST) is a powerful and highly discriminatory method for analysing pathogen population structure and epidemiology. Trypanosoma cruzi, the protozoan agent of American trypanosomiasis (Chagas disease), has remarkable genetic and ecological diversity. A standardised MLST protocol that is suitable for assignment of T. cruzi isolates to genetic lineage and for higher resolution diversity studies has not been developed. Methodology/Principal Findings We have sequenced and diplotyped nine single copy housekeeping genes and assessed their value as part of a systematic MLST scheme for T. cruzi. A minimum panel of four MLST targets (Met-III, RB19, TcGPXII, and DHFR-TS) was shown to provide unambiguous assignment of isolates to the six known T. cruzi lineages (Discrete Typing Units, DTUs TcI-TcVI). In addition, we recommend six MLST targets (Met-II, Met-III, RB19, TcMPX, DHFR-TS, and TR) for more in depth diversity studies on the basis that diploid sequence typing (DST) with this expanded panel distinguished 38 out of 39 reference isolates. Phylogenetic analysis implies a subdivision between North and South American TcIV isolates. Single Nucleotide Polymorphism (SNP) data revealed high levels of heterozygosity among DTUs TcI, TcIII, TcIV and, for three targets, putative corresponding homozygous and heterozygous loci within DTUs TcI and TcIII. Furthermore, individual gene trees gave incongruent topologies at inter- and intra-DTU levels, inconsistent with a model of strict clonality. Conclusions/Significance We demonstrate the value of systematic MLST diplotyping for describing inter-DTU relationships and for higher resolution diversity studies of T. cruzi, including presence of recombination events. The high levels of heterozygosity will facilitate future population genetics analysis based on MLST haplotypes. PMID:21713026

  19. 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.

  20. 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.

  1. Comparison of monkeypox viruses pathogenesis in mice by in vivo imaging

    USGS Publications Warehouse

    Osorio, J.E.; Iams, K.P.; Meteyer, C.U.; Rocke, T.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.

  2. Selenium status in soil, water and essential crops of Iran.

    PubMed

    Nazemi, Lyly; Nazmara, Shahrokh; Eshraghyan, Mohammad Reza; Nasseri, Simin; Djafarian, Kurosh; Yunesian, Masoud; Sereshti, Hassan; Moameni, Aziz; Shahtaheri, Seyed Jamaleddin

    2012-01-01

    As a contributing factor to health, the trace element selenium (Se) is an essential nutrient of special interest for humans and all animals. It is estimated that 0.5 to 1 billion people worldwide suffer from Se deficiency. In spite of the important role of Se, its concentrations in soil, water and essential crops have not been studied in Iran. Therefore, the main aim of the current study was to determine the Se content of soil, water, and essential crops (rice in North, wheat in Center, date, and pistachio in South) of different regions of Iran. Sampling was performed in the North, South, and Central regions of Iran. In each selected area in the three regions, 17 samples of surface soil were collected; samples of water and essential crops were also collected at the same sampling points. Upon preliminary preparation of all samples, the Se concentrations were measured by ICP-OES Model Varian Vista-MPX. The amount of soil-Se was found to be in the range between 0.04 and 0.45 ppm in the studied areas; the Se content of soil in the central region of Iran was the highest compared to other regions (p<0.0001). The average Se concentration in irrigation water of different areas was less than 0.01 mg/L, and the mean concentrations of Se in the rice, wheat, date, and pistachio samples were 0.95, 0.74, 0.46, and 0.40 ppm, respectively. Although Se-soil and water-Se level in different regions were low, the typical levels of Se in the essential crops were relatively high. PMID:23369199

  3. 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

  4. Comparison of serum procalcitonin in respiratory infections and bloodstream infections

    PubMed Central

    Zhu, Yanhui; Yuan, Yulin; Huang, Huayi

    2015-01-01

    Purpose: This study observed the relationship between procalcitonin (PCT) and results of sputum culture, the relationship between PCT and results of blood culture to evaluate and compare the value of PCT in respiratory and bloodstream infections. Methods: We analyzed 1616 patients in which PCT and sputum culture were concurrently ordered and analyzed, and 1096 patients in which PCT and blood culture were concurrently ordered and analyzed from January 2014 to May 2015. PCT concentrations were measured by on a Roche Cobas E601 ECL analyzer. Results: The average values of PCT from patients with sputum culture positive and negative were 0.42 (0.17-2.16) and 0.12 (0.06-0.57) ng/ml respectively, and the average values of PCT from patients with blood culture positive and negative were 9.54 (2.10-48.47) and 0.28 (0.10-1.23) ng/ml respectively. In sputum culture, positive rate of PCT in cases with growth of pathogens was 47.1%. In blood culture, positive rate of PCT in cases with growth of pathogens was 89.2%. Conclusions: PCT is useful in early diagnosis of respiratory infections and bloodstream infections, but the specificity of PCT in diagnosing respiratory infections is not as high as it is in bloodstream infections. PMID:26885109

  5. [Hemolysis influence on twenty-two biochemical parameters measurement].

    PubMed

    Ali, Damien; Sacchetto, Emilie; Dumontet, Erwan; Le Carrer, Didier; Orsonneau, Jean-Luc; Delaroche, Odile; Bigot-Corbel, Edith

    2014-01-01

    The study of the influence of hemolysis was determined experimentally for twenty two biochemical parameters on the analyzer Cobas 6000 ce (Roche Diagnostics). The addition method of hemolysate was used to create an increasing concentration of hemoglobin ranging from 0 to 2000 μmol/L. The limit of 10% variation was chosen to define the influence of hemolysis on the measurement. The parameters studied were classified into several categories: the parameters for which hemolysis does not influence the measurement: albumin, uric acid, calcium, C-reactive protein, myoglobin, NT -pro BNP, S100 protein, and urea; parameters impacted positively leading to an overestimation of the result: aspartate aminotransferase, total cholesterol, creatine kinase, creatinine, lactate dehydrogenase, magnesium, magnesium, total protein, triglycerides; and negatively impacted settings so causing an underestimation of the result: alanine amino- transferase, gamma glutamyl transferase, lipase, alkaline phosphatase, troponin T hypersensitive. Certain parameters influence of hemolysis varies depending on the magnitude of the measured parameter this interference being observed for normal values but disappearing for pathological values: creatinine, cholesterol, alkaline phosphatase, triglycerides, or the inverse interference is greater than for conventional pathological values: lipase, alanine amino-transferase. Knowledge of this variability interference allows the biologist to adapt its methods of reporting in the case of haemolysed samples. PMID:24876141

  6. Description of an Automated Method for Urea Nitrogen Determination in Bronchoalveolar Lavage Fluid (BALF) of Neonates and Infants.

    PubMed

    Pocino, Krizia; Minucci, Angelo; Manieri, Rocco; Conti, Giorgio; De Luca, Daniele; Capoluongo, Ettore Domenico

    2015-12-01

    Bronchoalveolar lavage (BAL) partially recovers both the instilled saline and the alveolar fluid, so-called epithelial lining fluid (ELF), but a correction for the dilution due to the BAL technique itself is needed to know the amount of recovered ELF. In this regard, urea nitrogen may be useful and has been proposed to calculate ELF. The aim of the present study was to develop and validate a new method to measure urea nitrogen in BAL fluid (BALF). We used 19 BALF samples obtained from neonates and infants with different respiratory conditions. The urea nitrogen assay was carried out on Cobas c311 analyzer (Roche Diagnostics). A validation study shows that the method is perfectly linear (R(2) = 0.999), sensitive (limit of detection = 0.055 mg/dL; limit of quantification = 0.16 mg/dL), repeatable (low = 0.15 ± 0.02, 13.3%; high = 1.80 ± 0.02, 1.1%), reproducible (low = 0.14 ± 0.02, 14.2 %; high = 1.76 ± 0.04, 2.2 %) with accuracy ranging between 93-96%. Our results support the robustness of validated procedure since the described method appears simple, precise, rapid, and suitable for routine analysis. Thus, it may be used to correct concentration of various noncellular BAL components and calculate their ELF amounts in neonates and infants. PMID:25586999

  7. High-throughput and sensitive next-generation droplet digital PCR assay for the quantitation of the hepatitis C virus mutation at core amino acid 70.

    PubMed

    Mukaide, Motokazu; Sugiyama, Masaya; Korenaga, Masaaki; Murata, Kazumoto; Kanto, Tatsuya; Masaki, Naohiko; Mizokami, Masashi

    2014-10-01

    The next-generation droplet digital polymerase chain reaction (ddPCR) assay employs an emulsion-based endpoint to quantitate the amount of target DNA and is more robust than real-time PCR when analyzing sequence variations. However, no studies have applied this technique to quantitate mutations in polymorphic viral genomes. To develop this approach, a ddPCR-based assay was designed to quantitate with high-throughput and sensitivity mutations and their frequencies in codon 70 of the hepatitis C virus (HCV) gene that encodes the Core protein. The assay was linear from 2.5 to 10(5) copies per assay, and the limit of detection of mutants in the presence of a 20,000-fold excess of wild type was 0.005%. The results correlated well with those obtained using the COBAS(®) TaqMan(®) HCV Test, which is a real-time PCR assay for the quantitative detection of HCV RNA in human serum (n=87; range, 2.3-7.7log10IU/mL; Pearson's R(2)=0.9120; p<0.0001). The median frequencies of mutations by ddPCR were 0.262% (n=55; range, 0-37.951%) and 99.687% (n=32; range, 52.191-100%) for the wild-type and mutant sequences, respectively, by direct sequencing. The ddPCR assay should be useful for quantitating mutations in other polymorphic viral genomes. PMID:25019167

  8. Hematologic and biochemical reference intervals for specific pathogen free 6-week-old Hampshire-Yorkshire crossbred pigs

    PubMed Central

    2014-01-01

    Background Hematologic and biochemical reference intervals depend on many factors, including age. A review of the literature highlights the lack of reference intervals for 6-wk-old specific pathogen free (SPF) Hampshire-Yorkshire crossbred pigs. For translational research, 6-wk-old pigs represent an important animal model for both human juvenile colitis and diabetes mellitus type 2 given the similarities between the porcine and human gastrointestinal maturation process. The aim of this study was to determine reference intervals for hematological and biochemical parameters in healthy 6-wk-old crossbred pigs. Blood samples were collected from 66 clinically healthy Hampshire-Yorkshire pigs. The pigs were 6 wks old, represented both sexes, and were housed in a SPF facility. Automated hematological and biochemical analysis were performed using an ADVIA 120 Hematology System and a Cobas 6000 C501 Clinical Chemistry Analyzer. Results Reference intervals were calculated using both parametric and nonparametric methods. The mean, median, minimum, and maximum values were calculated. Conclusion As pigs are used more frequently as medical models of human disease, having reference intervals for commonly measured hematological and biochemical parameters in 6-wk-old pigs will be useful. The reference intervals calculated in this study will aid in the diagnosis and monitoring of both naturally occurring and experimentally induced disease. In comparison to published reference intervals for older non SPF pigs, notable differences in leukocyte populations, and in levels of sodium, potassium, glucose, protein, and alkaline phosphatase were observed. PMID:24410946

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

    PubMed Central

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

    2014-01-01

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

  10. 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. PMID:23115954

  11. Coproporphyrin Excretion and Low Thiol Levels Caused by Point Mutation in the Rhodobacter sphaeroides S-Adenosylmethionine Synthetase Gene ▿ †

    PubMed Central

    Sabaty, Monique; Adryanczyk, Géraldine; Roustan, Chloë; Cuiné, Stephan; Lamouroux, Christine; Pignol, David

    2010-01-01

    A spontaneous mutant of Rhodobacter sphaeroides f. sp. denitrificans IL-106 was found to excrete a large amount of a red compound identified as coproporphyrin III, an intermediate in bacteriochlorophyll and heme synthesis. The mutant, named PORF, is able to grow under phototrophic conditions but has low levels of intracellular cysteine and glutathione and overexpresses the cysteine synthase CysK. The expression of molybdoenzymes such as dimethyl sulfoxide (DMSO) and nitrate reductases is also affected under certain growth conditions. Excretion of coproporphyrin and overexpression of CysK are not directly related but were both found to be consequences of a diminished synthesis of the key metabolite S-adenosylmethionine (SAM). The wild-type phenotype is restored when the gene metK encoding SAM synthetase is supplied in trans. The metK gene in the mutant strain has a mutation leading to a single amino acid change (H145Y) in the encoded protein. This point mutation is responsible for a 70% decrease in intracellular SAM content which probably affects the activities of numerous SAM-dependent enzymes such as coproporphyrinogen oxidase (HemN); uroporphyrinogen III methyltransferase (CobA), which is involved in siroheme synthesis; and molybdenum cofactor biosynthesis protein A (MoaA). We propose a model showing that the attenuation of the activities of SAM-dependent enzymes in the mutant could be responsible for the coproporphyrin excretion, the low cysteine and glutathione contents, and the decrease in DMSO and nitrate reductase activities. PMID:20038586

  12. Magnesium concentration in amniotic fluid in the early weeks of the second trimester of pregnancy

    PubMed Central

    2011-01-01

    Background We analyse magnesium levels in amniotic fluid to establish normal values for the 14th to 18th week of pregnancy and establish critical values that could be useful diagnostic and therapeutic guidelines for possible complications. Findings Ninety-two samples of amniotic fluid obtained by amniocentesis as well as the corresponding serum samples of pregnant women were analysed. The gestational age (mean ± SD) at which the amniotic fluid sample was obtained was 16.13 ± 1.87 weeks. Magnesium levels were determined by colorimetric assay with chlorophosphonazo-III using the the Cobas c 501 analyser (Roche Diagnostics). Statistical treatment of data was performed using the SPSS program, version 15.0. Results revealed a mean magnesium value of 1.65 ± 0.16 mg/dL in amniotic fluid and 1.97 ± 0.23 mg/dL in serum. Conclusions It would be interesting to extend the study to a larger number of pregnant women to determine variations in normal magnesium values in the three trimesters of pregnancy. PMID:21672230

  13. Prognostic role of serum concentrations of high-sensitivity C-reactive protein in patients with metastatic colorectal cancer: results from the ITACa trial.

    PubMed

    Casadei Gardini, Andrea; Carloni, Silvia; Scarpi, Emanuela; Maltoni, Paolo; Dorizzi, Romolo M; Passardi, Alessandro; Frassineti, Giovanni Luca; Cortesi, Pietro; Giannini, Maria Benedetta; Marisi, Giorgia; Amadori, Dino; Lucchesi, Alessandro

    2016-03-01

    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

  14. 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

  15. Automation of o-dianisidine assay for ceruloplasmin activity analyses: usefulness of investigation in Wilson's disease and in hepatic encephalopathy.

    PubMed

    Siotto, Mariacristina; Pasqualetti, Patrizio; Marano, Massimo; Squitti, Rosanna

    2014-10-01

    Ceruloplasmin (Cp) is a serum ferroxidase that plays an essential role in iron metabolism. It is routinely tested by immunoturbidimetric assays that quantify the concentration of the protein both in its active and inactive forms. Cp activity is generally analyzed manually; the process is time-consuming, has a limited repeatability, and is not suitable for a clinical setting. To overcome these inconveniences, we have set the automation of the o-dianisidine Cp activity assay on a Cobas Mira Plus apparatus. The automation was rapid and repeatable, and the data were provided in terms of IU/L. The assay was adapted for human sera and showed a good precision [coefficient of variation (CV) 3.7 %] and low limit of detection (LoD 11.58 IU/L). The simultaneous analysis of Cp concentration and activity in the same run allowed us to calculate the Cp-specific activity that provides a better index of the overall Cp status. To test the usefulness of this automation, we tested this assay on 104 healthy volunteers and 36 patients with Wilson's disease, hepatic encephalopathy, and chronic liver disease. Cp activity and specific activity distinguished better patients between groups with respect to Cp concentration alone, and providing support for the clinical investigation of neurological diseases in which liver failure is one of the clinical hallmarks. PMID:24663495

  16. Comparison of Six Automated Treponema-Specific Antibody Assays.

    PubMed

    Park, Borae G; Yoon, Jihoon G; Rim, John Hoon; Lee, Anna; Kim, Hyon-Suk

    2016-01-01

    Six different Treponema (TP)-specific immunoassays were compared to the fluorescent treponemal antibody absorption (FTA-ABS) test. A total of 615 samples were tested. The overall percent agreement, analytical sensitivity, and analytical specificity of each assay compared to the FTA-ABS test were as follows: Architect Syphilis TP, 99.2%, 96.8%, and 100%; Cobas Syphilis, 99.8%, 99.4%, and 100%; ADVIA Centaur Syphilis, 99.8%, 99.4%, and 100%; HISCL Anti-TP assay kit, 99.7%, 98.7%, and 100%; Immunoticles Auto3 TP, 99.0%, 97.5%, and 99.6%; Mediace TPLA, 98.0%, 98.1%, and 98.0%. All results that were discrepant between the TP-specific assays were associated with samples from noninfectious cases (11 immunoassay false positives and 7 from previous syphilis cases). Our study demonstrated that TP-specific immunoassays generally showed high sensitivities, specificities, and percentages of agreement compared to FTA-ABS, with rare cases of false-positive or false-negative results. Therefore, most TP-specific immunoassays are acceptable for use in screening for syphilis. However, it is important to perform a thorough review of a patient's clinical and treatment history for interpreting the results of syphilis serology. PMID:26560543

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

    PubMed

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

    2006-01-01

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

  18. [Evaluation of the renal function in type 2 diabetes: clearance calculation or cystatin C?].

    PubMed

    Dhia, Rym Ben; Hellara, Ilhem; Harzallah, Olfa; Neffati, Fadoua; Khochtali, Ines; Mahjoub, Sylvia; Najjar, Mohamed Fadhel

    2012-01-01

    Screening for diabetic nephropathy is usually done by albuminuria/24h and the use of creatinine clearance. The objective of this study was to evaluate the renal function in Type 2 diabetes by using different formulas of creatinine clearance and to assess the contribution of cystatin C; 83 adults with type 2 diabetes (23 men and 60 women) and 83 adult controls (40 men and 43 women) were studied. Biochemical parameters were determinated on Coba 6000™ (Roche diagnostics). Diabetics showed a significant increase in blood glucose, cholesterol, triglycerides, LDLc, the ApoB, Lp(a), urea, uric acid, creatinine and cystatin C and lower HDLc. Cystatin was increased in patients with degenerative complications and in hypertensive patients. We found strong correlations of cystatin C with creatinine (r = 0.9454), urea (r = 0.8999) and uric acid (r = 0.8325). We found a significant exponentially increase of creatinine and cystatin C from one stage to another. Cystatin C has a strong association with MDRD (r = 0.8086) and CG (r = 0.7915) and a low one with creatinine clearance (r = 0.1044). In conclusion, the use of cystatin C for screening and early treatment of incipient diabetic nephropathy appears to be adequate. CG and MDRD formulas still hold their place, in regards to the classical determination of creatinine clearance, to monitor patients. PMID:22565176

  19. Association between serum cystatin C levels and cardiovascular disease in type 2 diabetic patients.

    PubMed

    Triki, Sonia; Fekih, Ons; Hellara, Ilhem; Neffati, Fadoua; Douki, Wahiba; Hamda, Khaldoun Ben; Maatouk, Faouzi; Najjar, Mohamed Fadhel

    2013-01-01

    Serum cystatin C concentration was recently reported as a marker of cardiovascular disease (CVD). In the present study, we evaluated the association between the increase of serum cystatin C levels and the risk of CVD in type 2 diabetes. 42 patients with type 2 diabetes were included in the present study; 27 of them have CVD. The control group consisted of 30 healthy adults. Cystatin C, creatinine, microalbuminuria and CRP were measured on Cobas 6000(TM). Cystatine C level was significantly higher in patients with CVD. A significant difference in serum cystatin C was found in patients with and without CVD among albuminuria. No difference in serum cystatin C levels was found according to number of affected vessels. A cystatin C level above 1.10 mg/L was associated with increase of risk of CVD with significant difference (OR = 42.52; IC 95% 1.455 to 1242.827 and p = 0.029). Our results suggested that the increase of serum cystatin C concentrations is a potential marker for CVD in diabetes. PMID:23906571

  20. [Pseudocholinesterase activity in type 1 bipolar patients].

    PubMed

    Ezzaher, Asma; Haj Mouhamed, Dhouha; Mechri, Anwar; Neffati, Fadoua; Douki, Wahiba; Gaha, Lotfi; Najjar, Mohamed Fadhel

    2012-01-01

    This study aims to investigate the variation of pseudocholinesterase activity (BuChE) in bipolar patients and to explore its relation to the clinical and therapeutic characteristics of this disease. Our study included 105 patients with bipolar disorder and 100 control subjects aged 38.7 ± 12.2 and 36.4 ± 15.7 y, respectively. BuChE was determined by kinetic methods on Cobas Integra 400 plus™. Compared with controls, patients had a significantly higher pseudocholinesterase activity. Moreover, this increase was significantly associated (p = 0.001) with bipolar disorder with sensibility of 58% and specificity of 62% at threshold of 7392 IU/L. There was no significant change in pseudocholinesterase activity in relation to illness episodes and treatment, whereas the lowest values of this activity were seen in euthymic patients and those taking psychotics. Therefore, this activity is a real interest in the biological monitoring of patients as a risk factor for neurodegenerative diseases associated with bipolar disorder. But it would be most useful to evaluate their interest as a predictor of bipolar disorder in patients at risk. PMID:22294139

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

    PubMed

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

    2010-05-01

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

  2. Chlamydia trachomatis Infection in HIV-Infected Women: Need for Screening by a Sensitive and Specific Test

    PubMed Central

    Bhattar, Sonali; Chadha, Sanjim; Tripathi, Reva; Kaur, Ravinder; Sardana, Kabir

    2013-01-01

    Reproductive tract infection (RTIs)/sexually transmitted infections (STIs) are recognized as a major public health problem, particularly due to their relationship with HIV infection. Early detection and treatment of Chlamydia trachomatis infection (CTI) among HIV-infected and HIV-uninfected women may impact heterosexual HIV transmission. A total of 120 participants were enrolled: 30 HIV seropositive women with symptoms of RTIs, 30 HIV seropositive women without symptoms of RTIs, 30 HIV seronegative women with symptoms of RTIs, and 30 HIV seronegative women without symptoms of RTIs. One endocervical swab was collected from all participants and CTI was detected by real-time PCR (COBAS TaqMan CT Test, v2.0). CTI was detected in 4 (6.67%) HIV-infected women and in 1 (1.67%) HIV-uninfected woman (OR 4.214; 95% CI 0.457–38.865). Vaginal discharge was present in almost half of HIV-infected and HIV-uninfected women; lower abdominal pain was present in 11 (18.3%) of HIV-infected and in 9 (15%) of HIV-uninfected women. This study showed that CTI is more prevalent among HIV-infected females as compared to HIV-uninfected females. As the use of real-time PCR is not feasible in most hospitals, efforts should be made to develop a simple, sensitive, and specific test to identify women with CTI for prevention of sequelae and HIV transmission. PMID:24382941

  3. 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)]. PMID:26977436

  4. Use of a Rapid Ethylene Glycol Assay: a 4-Year Retrospective Study at an Academic Medical Center.

    PubMed

    Rooney, Sydney L; Ehlers, Alexandra; Morris, Cory; Drees, Denny; Davis, Scott R; Kulhavy, Jeff; Krasowski, Matthew D

    2016-06-01

    Ethylene glycol (EG) is a common cause of toxic ingestions. Gas chromatography (GC)-based laboratory assays are the gold standard for diagnosing EG intoxication. However, GC requires specialized instrumentation and technical expertise that limits feasibility for many clinical laboratories. The objective of this retrospective study was to determine the utility of incorporating a rapid EG assay for management of cases with suspected EG poisoning. The University of Iowa Hospitals and Clinics core clinical laboratory adapted a veterinary EG assay (Catachem, Inc.) for the Roche Diagnostics cobas 8000 c502 analyzer and incorporated this assay in an osmolal gap-based algorithm for potential toxic alcohol/glycol ingestions. The main limitation is that high concentrations of propylene glycol (PG), while readily identifiable by reaction rate kinetics, can interfere with EG measurement. The clinical laboratory had the ability to perform GC for EG and PG, if needed. A total of 222 rapid EG and 24 EG/PG GC analyses were documented in 106 patient encounters. Of ten confirmed EG ingestions, eight cases were managed entirely with the rapid EG assay. PG interference was evident in 25 samples, leading to 8 GC analyses to rule out the presence of EG. Chart review of cases with negative rapid EG assay results showed no evidence of false negatives. The results of this study highlight the use of incorporating a rapid EG assay for the diagnosis and management of suspected EG toxicity by decreasing the reliance on GC. Future improvements would involve rapid EG assays that completely avoid interference by PG. PMID:26553280

  5. 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

  6. 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

  7. Analysis of PIK3CA Mutations and Activation Pathways in Triple Negative Breast Cancer

    PubMed Central

    Muroni, Maria Rosaria; Sanges, Francesca; Sotgiu, Giovanni; Ena, Sara; Pira, Giovanna; Murgia, Luciano; Manca, Alessandra; Uras, Maria Gabriela; Sarobba, Maria Giuseppina; Urru, Silvana; De Miglio, Maria Rosaria

    2015-01-01

    Background Triple Negative Breast Cancer (TNBC) accounts for 12–24% of all breast carcinomas, and shows worse prognosis compared to other breast cancer subtypes. Molecular studies demonstrated that TNBCs are a heterogeneous group of tumors with different clinical and pathologic features, prognosis, genetic-molecular alterations and treatment responsivity. The PI3K/AKT is a major pathway involved in the regulation of cell survival and proliferation, and is the most frequently altered pathway in breast cancer, apparently with different biologic impact on specific cancer subtypes. The most common genetic abnormality is represented by PIK3CA gene activating mutations, with an overall frequency of 20–40%. The aims of our study were to investigate PIK3CA gene mutations on a large series of TNBC, to perform a wider analysis on genetic alterations involving PI3K/AKT and BRAF/RAS/MAPK pathways and to correlate the results with clinical-pathologic data. Materials and Methods PIK3CA mutation analysis was performed by using cobas® PIK3CA Mutation Test. EGFR, AKT1, BRAF, and KRAS genes were analyzed by sequencing. Immunohistochemistry was carried out to identify PTEN loss and to investigate for PI3K/AKT pathways components. Results PIK3CA mutations were detected in 23.7% of TNBC, whereas no mutations were identified in EGFR, AKT1, BRAF, and KRAS genes. Moreover, we observed PTEN loss in 11.3% of tumors. Deregulation of PI3K/AKT pathways was revealed by consistent activation of pAKT and p-p44/42 MAPK in all PIK3CA mutated TNBC. Conclusions Our data shows that PIK3CA mutations and PI3K/AKT pathway activation are common events in TNBC. A deeper investigation on specific TNBC genomic abnormalities might be helpful in order to select patients who would benefit from current targeted therapy strategies. PMID:26540293

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

    PubMed

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

    2005-01-01

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

  9. 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

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

    PubMed

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

    2015-11-15

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

  11. 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. PMID:25936581

  12. Hepatic Dimethylarginine-Dimethylaminohydrolase1 is Reduced in Cirrhosis and is a Target for Therapy in Portal Hypertension

    PubMed Central

    Mookerjee, Rajeshwar P; Mehta, Gautam; Balasubramaniyan, Vairappan; Mohamed, Fatma; Davies, Nathan; Sharma, Vikram; Iwakiri, Yasuko; Jalan, Rajiv

    2015-01-01

    Background and Aims Portal hypertension is characterized by reduced hepatic eNOS activity. Asymmetric-dimethylarginine (ADMA), an eNOS inhibitor, is elevated in cirrhosis and correlates with severity of portal hypertension. Dimethylargininedimethylaminohydrolase-1 (DDAH-1) is the key enzyme metabolizing hepatic ADMA. This study characterized DDAH-1 in cirrhosis, and explored hepatic DDAH-1 reconstitution through FXR agonism and DDAH-1 gene therapy. Methods DDAH-1 Immunohistochemistry was conducted on human cirrhosis and healthy liver tissue. Subsequently, sham-operated or bile-duct-ligated (BDL) cirrhosis rats were treated with FXR agonist Obeticholic acid (OA, 5mg/kg) or vehicle for 5 days. Further animals underwent hydrodynamic injection with DDAH-1-expressing plasmid or saline control. Groups: Sham+saline, BDL+saline, BDL+DDAH-1-plasmid. Portal pressure (PP) measurements were performed. Plasma ALT was measured by Cobas-Integra; DDAH-1 expression by qPCR and Western blot; eNOS activity by radiometric assay. Results Immunohistochemistry and Western-blotting confirmed hepatic DDAH-1 was restricted to hepatocytes, and expression decreased significantly in cirrhosis. In BDL rats, reduced DDAH-1 expression was associated with elevated hepatic ADMA, reduced eNOS activity and high PP. OA treatment significantly increased DDAH-1 expression, reduced hepatic tissue ADMA, and increased liver NO generation. PP was significantly reduced in BDL+OA vs. BDL+vehicle (8±1 vs. 13.5±0.6 mmHg; p<0.01) with no change in MAP. Similarly, DDAH-1 hydrodynamic injection significantly increased hepatic DDAH-1 gene and protein expression, and significantly reduced PP in BDL+DDAH-1 vs. BDL+ saline (p<0.01). Conclusion This study demonstrates DDAH-1 is a specific molecular target for portal pressure reduction, through actions on ADMA-mediated regulation of eNOS activity. Our data support translational studies targeting DDAH-1 in cirrhosis and portal hypertension. PMID:25152204

  13. Role of Doppler Ultrasonography and C-Reactive Protein in Patients with Acute Scrotum.

    PubMed

    Mohammed, Abdulwahid G; Elkhader, Bahaaedin A; Saade, Charbel; Fagiri, Maram A; Mahmoud, Mustafa Z

    2016-01-01

    This research was designate with an intention to find the role of Doppler ultrasonography (DUS) and C-reactive protein (CRP) in patients with acute scrotum. A sum of 80 (mean age 23±2.1 years) consequential patients were recruited for a period of six months between July 2015 and January 2016 in this prospective study. Collected data confined age, medical history, and clinical symptoms. DUS was performed with a linear array transducer (10-15 MHz) connected to HI vision Avius ultrasound unit; Hitachi. CRP was measured using turbidimetric analysis through the Cobas Integra analyzer system (Test CRPL2, 0-293); Roche Diagnostics. Statistical analysis was accomplished using the standard Statistical Package for the Social Sciences version 20 for Windows; Microsoft. Fitted achievement values for DUS in the diagnosis of testicular torsion, epididymo-orchitis, and varicocele were respectively 100%, 91% and 88% for sensitivity, 92%, 71%, and 90% for specificity, and 94%, 83%, and 89% for accuracy. An increased in the serum CRP level (63.2±40.2 mg/L) was seen in an inflammatory cause of the acute scrotum. In contrast, there was no increase in CRP level (8±3.1 mg/L) in the non-inflammatory cases (P < 0.0001). Scrotal DUS is a highly precise preoperative diagnostic instrument, thereby confirm its course application in the incipient triage of patients with acute scrotum. Serum level of CRP can afford useful advice for differentiation between inflammatory and other reasons of the acute scrotum. PMID:27530575

  14. Spectroscopic Studies of the Salmonella enterica Adenosyltransferase Enzyme SeCobA: Molecular-Level Insight into the Mechanism of Substrate Cob(II)alamin Activation

    PubMed Central

    2015-01-01

    CobA from Salmonella enterica (SeCobA) is a member of the family of ATP:Co(I)rrinoid adenosyltransferase (ACAT) enzymes that participate in the biosynthesis of adenosylcobalamin by catalyzing the transfer of the adenosyl group from an ATP molecule to a reactive Co(I)rrinoid species transiently generated in the enzyme active site. This reaction is thermodynamically challenging, as the reduction potential of the Co(II)rrinoid precursor in solution is far more negative than that of available reducing agents in the cell (e.g., flavodoxin), precluding nonenzymic reduction to the Co(I) oxidation state. However, in the active sites of ACATs, the Co(II)/Co(I) redox potential is increased by >250 mV via the formation of a unique four-coordinate (4c) Co(II)rrinoid species. In the case of the SeCobA ACAT, crystallographic and kinetic studies have revealed that the phenylalanine 91 (F91) and tryptophan 93 (W93) residues are critical for in vivo activity, presumably by blocking access to the lower axial ligand site of the Co(II)rrinoid substrate. To further assess the importance of the F91 and W93 residues with respect to enzymatic function, we have characterized various SeCobA active-site variants using electronic absorption, magnetic circular dichroism, and electron paramagnetic resonance spectroscopies. Our data provide unprecedented insight into the mechanism by which SeCobA converts the Co(II)rrinoid substrate to 4c species, with the hydrophobicity, size, and ability to participate in offset π-stacking interactions of key active-site residues all being critical for activity. The structural changes that occur upon Co(II)rrinoid binding also appear to be crucial for properly orienting the transiently generated Co(I) “supernucleophile” for rapid reaction with cosubstrate ATP. PMID:25423616

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

    PubMed

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

    2011-12-01

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

  16. 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

  17. [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. PMID:27029728

  18. Preanalytical management: serum vacuum tubes validation for routine clinical chemistry

    PubMed Central

    Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Picheth, Geraldo; Guidi, Gian Cesare

    2012-01-01

    Introduction The validation process is essential in accredited clinical laboratories. Aim of this study was to validate five kinds of serum vacuum tubes for routine clinical chemistry laboratory testing. Materials and methods: Blood specimens from 100 volunteers in five diff erent serum vacuum tubes (Tube I: VACUETTE®, Tube II: LABOR IMPORT®, Tube III: S-Monovette®, Tube IV: SST® and Tube V: SST II®) were collected by a single, expert phlebotomist. The routine clinical chemistry tests were analyzed on cobas® 6000 module. The significance of the diff erences between samples was assessed by paired Student’s t-test after checking for normality. The level of statistical significance was set at P < 0.005. Finally, the biases from Tube I, Tube II, Tube III, Tube IV and Tube V were compared with the current desirable quality specifications for bias (B), derived from biological variation. Results and conclusions: Basically, our validation will permit the laboratory or hospital managers to select the brand’s vacuum tubes validated according him/her technical or economical reasons, in order to perform the following laboratory tests: glucose, total cholesterol, high density lipoprotein-cholesterol, triglycerides, total protein, albumin, blood urea nitrogen, uric acid, alkaline phosphatise, aspartate aminotransferase, gamma-glutamyltransferase, lactate dehydrogenase, creatine kinase, total bilirubin, direct bilirubin, calcium, iron, sodium and potassium. On the contrary special attention will be required if the laboratory already performs creatinine, amylase, phosphate and magnesium determinations and the quality laboratory manager intend to change the serum tubes. We suggest that laboratory management should both standardize the procedures and frequently evaluate the quality of in vitro diagnostic devices. PMID:22838184

  19. 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

  20. 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

  1. Deletion of the carbonic anhydrase-like gene NCE103 of the yeast Saccharomyces cerevisiae causes an oxygen-sensitive growth defect.

    PubMed

    Götz, R; Gnann, A; Zimmermann, F K

    1999-07-01

    The yeast protein Nce103p encoded by the gene NCE103 (YNL036w) was described by Cleves et al. (1996) as a substrate of the non-classical export pathway which acts independently of the classical pathway through the ER and the Golgi compartments. However, the predicted amino acid sequence of Nce103p shows high levels of identities to carbonic anhydrases of pro- and eukaryotes. A nce103-Delta deletion strain did not grow on a rich peptone-yeast extract-glucose medium under normal aerobic conditions at pH values of 3.0-8.0, but grew like wild-type in an oxygen-free nitrogen or oxygen-reduced atmosphere over this pH range, and was more sensitive to H(2)O(2) than wild-type. No carbonic anhydrase activity could be detected in crude extracts prepared from wild-type, nce103-Delta mutants or in strains transformed with a multicopy plasmid carrying the NCE103 gene. Expression of the Medicago sativa carbonic anhydrase gene (Coba de la Peña et al., 1997), in a yeast expression cassette on a multicopy plasmid, complemented the growth defects caused by the nce103-Delta deletion and carbonic anhydrase activity could be readily detected in the crude extract. The ability of the nce103-Delta deletion strain to grow like wild-type under anaerobic conditions suggests that the protein encoded by NCE103 is required for protection against certain products of an oxidative metabolism and can be replaced in this function by the Medicago sativa carbonic anhydrase. A NCE103 promoter-LacZ fusion in a wild-type background showed that NCE103 is poorly transcribed under aerobic conditions and at an undetectable level under anaerobic conditions. PMID:10407265

  2. Response Prediction and Treatment Tailoring for Chronic Hepatitis C Virus Genotype 1 Infection▿

    PubMed Central

    Lindh, Magnus; Alestig, Erik; Arnholm, Birgitta; Eilard, Anders; Hellstrand, Kristoffer; Lagging, Martin; Wahlberg, Thomas; Wejstål, Rune; Westin, Johan; Norkrans, Gunnar

    2007-01-01

    We monitored early viral response during the treatment of hepatitis C virus (HCV) infection with the aim of identifying predictors of treatment outcome. We studied 53 patients with genotype 1 infection who received 180 μg/week pegylated interferon alfa-2a and 1,000 or 1,200 mg/day ribavirin depending on body weight and serially assessed HCV RNA in serum, using the Cobas TaqMan assay. Thirty-one patients (58%) achieved sustained viral response (SVR). SVR was obtained in 100% (10/10) of patients with pretreatment viremia concentrations below 400,000 IU/ml, in 100% (14/14) of patients with more than 1.5 log reduction of HCV RNA after 4 days of treatment, and in 95% (22/23) of patients with a rate of decline in viremia higher than 0.70 log units/week during the second phase. Non-SVR was seen in all patients with a second-phase decline rate lower than 0.35 log units/week. Patients with slopes between 0.50 and 0.80 log units/week achieved SVR (4/4) unless the treatment dose was modified (3/3). We conclude that the second-phase slope appears to be an accurate and useful predictor of treatment response. On the basis of these findings, we propose a model of tailored treatment which takes into account the second-phase slope and the amount of HCV RNA after 21 days of treatment. PMID:17581934

  3. Inter-laboratory Variability of Current Immunoassay Methods for Tacrolimus among Japanese Hospitals.

    PubMed

    Miura, Masatomo; Masuda, Satohiro; Egawa, Hiroto; Yuzawa, Kenji; Matsubara, Kazuo

    2016-08-01

    The aim of this study was to assess inter-hospital laboratory variability (coefficient of variation; CV) of immunoassay methods for tacrolimus and the comparability of control samples and results obtained by immunoassay measurements. One hundred seven hospital laboratories routinely performing therapeutic drug monitoring (TDM) of tacrolimus participated in the study. Thirteen spiked samples with known tacrolimus concentrations in the range of 0-26.0 ng/mL were prepared. Each spiked sample was analyzed according to the manufacturer's instructions using an affinity column-mediated immunoassay (ACMIA) on a Dimension(®) analyzer, the enzyme multiplied immunoassay technique (EMIT) on a Viva-E(®) analyzer, a chemiluminescent enzyme immunoassay (CLIA) on the Architect(®) system, and the electro-chemiluminescence immunoassay (ECLIA) on a cobas(®) analyzer. The 20% coefficient of variation values for the CLIA, ACMIA, EMIT, and ECLIA assays in the hospital laboratories were 1.82, 5.36, 4.59, and 0.89 ng/mL, respectively. CLIA and ECLIA had positive biases at concentrations of tacrolimus above 12 ng/mL relative to the spiked concentration, whereas the assay bias for ACMIA tended to be more negative at concentrations of tacrolimus above 6 ng/mL. EMIT had positive biases over the wide concentration range of 0.0-26.0 ng/mL (mean of mean errors 1.224). CLIA and ECLIA provided adequate precision at the target tacrolimus concentration of 3.0 ng/mL, whereas ACMIA and EMIT were unable to respond to target concentrations between 3.0 and 5.0 ng/mL for renal transplant recipients. Appropriate assessment of tacrolimus concentration by an assay having higher sensitivity, precision, and accuracy is necessary to ensure long-term survival of transplant recipients receiving tacrolimus. PMID:27263473

  4. Cardiovascular risk score in Rheumatoid Arthritis

    PubMed Central

    Wagan, Abrar Ahmed; Mahmud, Tafazzul E Haque; Rasheed, Aflak; Zafar, Zafar Ali; Rehman, Ata ur; Ali, Amjad

    2016-01-01

    Objective: To determine the 10-year Cardiovascular risk score with QRISK-2 and Framingham risk calculators in Rheumatoid Arthritis and Non Rheumatoid Arthritis subjects and asses the usefulness of QRISK-2 and Framingham calculators in both groups. Methods: During the study 106 RA and 106 Non RA patients age and sex matched participants were enrolled from outpatient department. Demographic data and questions regarding other study parameters were noted. After 14 hours of fasting 5 ml of venous blood was drawn for Cholesterol and HDL levels, laboratory tests were performed on COBAS c III (ROCHE). QRISK-2 and Framingham risk calculators were used to get individual 10-year CVD risk score. Results: In this study the mean age of RA group was (45.1±9.5) for Non RA group (43.7±8.2), with female gender as common. The mean predicted 10-year score with QRISK-2 calculator in RA group (14.2±17.1%) and Non RA group was (13.2±19.0%) with (p-value 0.122). The 10-year score with Framingham risk score in RA group was (12.9±10.4%) and Non RA group was (8.9±8.7%) with (p-value 0.001). In RA group QRISK-2 (24.5%) and FRS (31.1%) cases with predicted score were in higher risk category. The maximum agreement scores between both calculators was observed in both groups (Kappa = 0.618 RA Group; Kappa = 0.671 Non RA Group). Conclusion: QRISK-2 calculator is more appropriate as it takes RA, ethnicity, CKD, and Atrial fibrillation as factors in risk assessment score. PMID:27375684

  5. 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

  6. 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

  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. PMID:25543953

  8. Comet 67P: surface temperature maps as derived by Rosetta/VIRTIS in the early Mapping phase

    NASA Astrophysics Data System (ADS)

    Tosi, Federico; Capria, Maria Teresa; Capaccioni, Fabrizio; Filacchione, Gianrico; De Sanctis, Maria Cristina; Erard, Stéphane; Leyrat, Cedric; Bockelee-Morvan, Dominique; Kuehrt, Ekkehard

    2014-11-01

    We show spatially-resolved temperature maps of comet 67P/Churyumov-Gerasimenko, main target of the ESA Rosetta spacecraft, as obtained from infrared hyperspectral images acquired by the VIRTIS imaging spectrometer onboard the Rosetta Orbiter in the early Mapping phase carried out in August 2014.VIRTIS infrared spectra in the range longward of about 4 μm are affected by the thermal emission of the comet, hence the measured radiance in that spectral region can be used to determine surface temperatures and spectral emissivities by means of temperature-retrieval algorithms.The VIRTIS instrument onboard Rosetta is not sensitive to physical temperatures on the nightside of the comet, where the signal is considerably low. Typically, ~170 K is the minimum temperature that allows one to retrieve surface temperatures while preserving small formal errors (<1 K on retrieved temperatures). On the other hand, for a given local solar time (LST), the maximum temperature depends on the solar incidence angle and on surface properties such as thermal inertia and albedo.Here we show surface temperature maps of comet 67P at a spatial resolution of 20-25 m/px, and under variable phase angles, illumination conditions, and heliocentric distances (spanning the range from 3.62 to 3.45 AU). We focus both on regional maps and on peculiar sites of interest seen at the local scale, with a special emphasis on the expected location of the landing site.The availability of spatially-resolved, accurate temperature observations, significantly spaced out in local solar time, provides clues to the physical structure of specific surface units, which complements the mineralogical investigation based on imaging spectroscopy data collected at shorter wavelengths.AcknowledgementsThis work is supported by the Italian Space Agency (ASI), ASI-INAF Contract n. I/024/12/0. We acknowledge funding from the French Space Agency (CNES) and the German Aerospace Center (DLR). Support of the Rosetta and VIRTIS Science

  9. 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

  10. 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

  11. The topography of Ceres and implications for the formation of linear surface structures

    NASA Astrophysics Data System (ADS)

    Buczkowski, D.; Otto, K.; Ruesch, O.; Scully, J. E. C.; Williams, D. A.; Mest, S. C.; Schenk, P.; Jaumann, R.; Nathues, A.; Preusker, F.; Park, R. S.; Raymond, C. A.; Russell, C. T.

    2015-12-01

    NASA's Dawn spacecraft began orbiting the dwarf planet Ceres in April 2015. Framing Camera data from the Approach (1.3 km/px) and Survey (415 m/px) orbits include digital terrain models derived from processing stereo images. These models have supported various scientific studies of the surface. The eastern hemisphere of Ceres is topographically higher than the western hemisphere. Some of linear structures on Ceres (which include grooves, pit crater chains, fractures and troughs) appear to be radial to the large basins Urvara and Yalode, and most likely formed due to impact processes. However, set of regional linear structures (RLS) that do not have any obvious relationship to impact craters are found on the eastern hemisphere topographic high region. Many of the longer RLS are comprised of smaller structures that have linked together, suggestive of en echelon fractures. Polygonal craters, theorized to form when pervasive subsurface fracturing affects crater formation [1], are widespread on Ceres [2], and those proximal to the RLS have straight crater rims aligned with the grooves and troughs, suggesting that the RLS are fracture systems. A cross-section of one RLS is displayed in FC images of the Occator crater wall. Comparing these images to the digital terrain models show 1) that the structure dips ~60º and 2) there is downward motion on the hanging wall, implying normal faulting. The digital terrain models also reveal the presence of numerous positive relief features with sub-circular shapes. These dome-like features have been tentatively interpreted as volcanic/magmatic features [3]; other possibilities include salt domes. Analog models of domal uplift in areas of regional extension [4] predict patterns of linear structures similar to those observed in the RLS near Occator. Utilizing topography data provided by the Ceres digital terrain models, we assess the relationship between the RLS and nearby domes and topographic high regions to determine the mechanism

  12. 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

  13. 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.

  14. 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.

  15. Regional surface morphology of comet 67P/Churyumov-Gerasimenko from Rosetta/OSIRIS images

    NASA Astrophysics Data System (ADS)

    El-Maarry, M. R.; Thomas, N.; Giacomini, L.; Massironi, M.; Pajola, M.; Marschall, R.; Gracia-Berná, A.; Sierks, H.; Barbieri, C.; Lamy, P. L.; Rodrigo, R.; Rickman, H.; Koschny, D.; Keller, H. U.; Agarwal, J.; A'Hearn, M. F.; Auger, A.-T.; Barucci, M. A.; Bertaux, J.-L.; Bertini, I.; Besse, S.; Bodewits, D.; Cremonese, , G.; Da Deppo, V.; Davidsson, B.; De Cecco, M.; Debei, S.; Güttler, C.; Fornasier, S.; Fulle, M.; Groussin, O.; Gutierrez, P. J.; Hviid, S. F.; Ip, W.-H.; Jorda, L.; Knollenberg, J.; Kovacs, G.; Kramm, J.-R.; Kührt, E.; Küppers, M.; La Forgia, F.; Lara, L. M.; Lazzarin, M.; Lopez Moreno, J. J.; Marchi, S.; Marzari, F.; Michalik, H.; Naletto, G.; Oklay, N.; Pommerol, A.; Preusker, F.; Scholten, F.; Tubiana, C.; Vincent, J.-B.

    2015-11-01

    Aims: The OSIRIS camera onboard the Rosetta spacecraft has been acquiring images of the comet 67P/Churyumov-Gerasimenko (67P)'s nucleus at spatial resolutions down to ~0.17 m/px ever since Aug. 2014. These images have yielded unprecedented insight into the morphological diversity of the comet's surface. This paper presents an overview of the regional morphology of comet 67P. Methods: We used the images that were acquired at orbits ~20-30 km from the center of the comet to distinguish different regions on the surface and introduce the basic regional nomenclature adopted by all papers in this Rosetta special feature that address the comet's morphology and surface processes. We used anaglyphs to detect subtle regional and topographical boundaries and images from close orbit (~10 km from the comet's center) to investigate the fine texture of the surface. Results: Nineteen regions have currently been defined on the nucleus based on morphological and/or structural boundaries, and they can be grouped into distinctive region types. Consolidated, fractured regions are the most common region type. Some of these regions enclose smooth units that appear to settle in gravitational sinks or topographically low areas. Both comet lobes have a significant portion of their surface covered by a dusty coating that appears to be recently placed and shows signs of mobilization by aeolian-like processes. The dusty coatings cover most of the regions on the surface but are notably absent from a couple of irregular large depressions that show sharp contacts with their surroundings and talus-like deposits in their interiors, which suggests that short-term explosive activity may play a significant role in shaping the comet's surface in addition to long-term sublimation loss. Finally, the presence of layered brittle units showing signs of mechanical failure predominantly in one of the comet's lobes can indicate a compositional heterogeneity between the two lobes. Tables 2 and 3 and Appendix A

  16. 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

  17. Geomorphological and mineralogical mapping of Hebes Chasma, Mars

    NASA Astrophysics Data System (ADS)

    Hauber, E.; Gwinner, K.; Gendrin, A.; Fueten, F.; Stesky, R.; Pelkey, S.; Zegers, T.; Bibring, J. P.; Jaumann, R.; Neukum, G.

    Despite more than three decades of analysis, the origin of the Interior Layered Deposits (ILD) in the Valles Marineris (VM) trough system is still unknown. The advance of new remote sensing data obtained by the recent planetary missions Mars Global Surveyor (MGS), Mars Odyssey (MO), and Mars Express (MEX) allow investigation of the morphology and composition in unprecedented detail. This study focusses on Hebes Chasma in the central VM, which is unique because it contains a huge mesa of ILD in a completely closed depression. We used topographic data from the HRSC camera onboard MEX to analyze the geometry of layering in Hebes Mensa with the Orion structural analysis software. Strike and dip were measured in 50m/px gridded Digital Elevation Models and corresponding orthoimages. These data have a higher spatial resolution than those used in an earlier study. We find that the layers dip gently in the downslope direction. These results are in agreement with our earlier results in Hebes Chasma and with our similar ILD studies in western Candor and Ophir Chasmata, also based on HRSC topography. A mineralogic map indicating concentrations of polyhydrated sulfates, kieserite, and oxides was produced from OMEGA spectral data. It shows that these alteration minerals are only observed in low-lying areas, which are not covered by landslides. We consider a lacustrine origin of the ILD in Hebes Chasma as unlikely. The downslope dipping of ILD layers is in agreement with a draping process, e.g., pyroclastic fall deposits from a W-E trending volcanic vent, or a series of WNW-ESE trending vents in an en echelon alignment. Thin, finely layered deposits on top of the plateaus surrounding vm (e.g., west of Juventae or south of Ius ChasmaTA) could represent that portion of the pyroclastics which escaped the troughs and were distributed on the adjacent high plains. The occurrence of alteration minerals only in very deep portions of Hebes Chasma also argues against a deposition in a deep

  18. 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

  19. Global geologic mapping of Jupiter's moon Io: First steps

    NASA Astrophysics Data System (ADS)

    Williams, D.; Keszthelyi, L.; Crown, D.; Geissler, P.; Rathbun, J.; Jaeger, W.

    We have been funded by NASA's Outer Planets Research program to produce a global geologic map of Jupiter's volcanic moon, Io, that takes advantage of the complementary global coverage obtained by the 1979 Voyager flybys and by repeated flybys of the 1995-2003 Galileo orbiter. To this end the USGS produced a series of global mosaics (completed February 2006), with a spatial resolution of 1 km/px, that combine the Galileo and Voyager data. These mosaics include the highest quality global color imaging by Galileo at uniform phase angle, and highest quality monochrome imaging (both high and low sun observations) of the subjovian (Voyager) and antijovian (Galileo) hemispheres. We have formatted these mosaics (in various projections) in ArcGIS software (by ESRI) to produce the map. Based on image analyses, Io has 5 primary types of surface materials: plains (various textures and colors), patera floors (dark and bright), flows (dark and bright), mountains (lineated, mottled, tholus), and diffuse deposits (yellow, white, black, red, and green). A range of structural features are visible only in low-sun images, including ridges, grooves, scarps, lineaments, graben, and pits. No impact craters have been seen on Io at any resolution. Based on our previous experience mapping Io using medium resolution (few 100 m/px) Galileo images, we have developed the following strategy for mapping Io using the new global mosaics: 1) Map diffuse deposits first using the Galileo global color data; 2) Map mountains, surrounding plateaus, and structural features using the monochrome mosaics supplemented by available low-sun images; 3) Map vents and paterae using the monochrome mosaics; 4) Map lava flow fields using the monochrome mosaics; 5) Map plains last. An additional complication for Io are the changes caused by active volcanism, which have been observed between the Voyager and Galileo missions and between individual Galileo flybys of Io. To address this complication we are assembling a

  20. New Time-independent and Time-dependent Seismic Source Models for the Calabria Region (Italy) for the Probabilistic Seismic Hazard Maps

    NASA Astrophysics Data System (ADS)

    Akinci, Aybige; Burrato, Pierfrancesco; Falcone, Giuseppe; Mariucci, Maria Teresa; Murru, Maura; Tiberti, Mara Monica; Vannoli, Paola

    2015-04-01

    The present study is carried out in the framework of the S2-2014 COBAS Project "Constraining Observations into Seismic Hazard" co-funded by the Civil Protection Department of the Presidency of Council of Ministers (DPC) within the general agreement DPC-INGV for the period 2012-2021. The two areas identified as priority areas in the first phase of the activities by the 2012- 2021 Agreement DPC-INGV, namely the Po Plain and the Southern Apennines from Molise-Lazio to Basilicata-Calabria borders, require different strategies for calculating "the best seismic hazard". In this study we develop new time-independent and time-dependent seismic source models for the Calabria region starting from the new version of the DISS (Database of Individual Seismogenic Sources). This version of the Database DISS contains remarkable and notable new data and information on the seismogenic sources and their parameterizations in the Calabria region. The probability of the earthquake occurrences is calculated by developing models of seismicity-derived hazard sources, and models of earthquakes on faults/seismogenic sources. Mainly the four different classes of earthquake source models are developed to be included into the PSHA maps: (1) shallow crustal background seismicity (2) special zone that account for deep background seismicity (many earthquakes deeper than 30 kilometers occur beneath the Calabrian Arc and may have caused considerable damage in the Calabria region; these earthquakes have different ground-motion properties than shallow earthquakes) (3) uniform background source zones (4) finite faults/seismogenic sources as defined in the previous activity. The first three models are based on the earthquake catalog and characterize the hazard from earthquakes Mw>4.7. In most cases, the faults contribute most to the hazard for earthquakes larger than Mw5.5. The earthquake occurrence for the faults are modeled both as a Poisson time-independent process and introducing the various renewal

  1. 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

  2. Early predictive efficacy of core antigen on antiviral outcomes in genotype 1 hepatitis C virus infected patients.

    PubMed

    Feng, Bo; Yang, Rui-Feng; Zhang, Hai-Ying; Luo, Bi-Fen; Kong, Fan-Yun; Rao, Hui-Ying; Jin, Qian; Cong, Xu; Wei, Lai

    2015-01-01

    Response-guided therapy is of limited use in developing countries because hepatitis C virus RNA detection by sensitive molecular methods is time- and labor-consuming and expensive. We evaluated early predictive efficacy of serum hepatitis C virus core antigen kinetics on sustained virologic response in patients with genotype 1 hepatitis C virus during pegylated interferon plus ribavirin treatment. For 478 patients recruited, hepatitis C virus RNAs were detected at baseline, and at weeks 4, 12, 24, 48, and 72 using Cobas TaqMan. Architect hepatitis C virus core antigen was performed at baseline, and weeks 4 and 12. Predictive values of hepatitis C virus core antigen on sustained virologic response were compared to hepatitis C virus RNA. In the first 12 weeks after treatment initiation the dynamic patterns of serum hepatitis C virus core antigen and hepatitis C virus RNA levels were similar in sustained virologic response, relapse, and null response patients groups. Although areas under the receiver operating characteristics curves of hepatitis C virus core antigen were lower than those of hepatitis C virus RNA at the same time points, modeling analysis showed that undetectable hepatitis C virus core antigen (rapid virological response based on hepatitis C virus core antigen) had similar positive predictive value on sustained virologic response to hepatitis C virus RNA at week 4 (90.4% vs 93.3%), and hepatitis C virus core antigen decrease greater than 1log10IU/mL (early virological response based on hepatitis C virus core antigen) had similar negative predictive value to hepatitis C virus RNA at week 12 (94.1% vs 95.2%). Analysis on the validation group demonstrated a positive predictive value of 97.5% in rapid virological response based on hepatitis C virus core antigen and a negative predictive value of 100% in early virological response based on hepatitis C virus core antigen. In conclusion, hepatitis C virus core antigen is comparable to hepatitis C virus RNA in

  3. 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.

  4. 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

  5. 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.

  6. Performance evaluation of the PelvoCheck CT/NG test kit for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae

    PubMed Central

    Meyer, Thomas; Klos, Christian; Kofler, Regina; Kilic, Annett; Hänel, Kristina

    2016-01-01

    Objective Assessment of the performance of the PelvoCheck CT/NG test (Greiner-Bio-One GmbH) to detect Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) in first-void urine (FVU) of females. Design A cross-sectional study to compare the PelvoCheck CT/NG with COBAS TaqMan CT Test V.2.0 (Roche) for the detection of CT and with an in-house porA-based PCR for the detection of NG in FVU specimens. In addition, pools of 5 FVU specimens containing only CT-negative or 1 CT-positive and 4 CT-negative samples were tested. Abbott RealTime CT/NG was used as an additional test to resolve discordant results. Setting Samples sent from six laboratories were tested at the University Medical Center Hamburg. Participants Urine samples were from 1622 female patients attending gynaecological practices for chlamydia screening, another 120 urine samples were from patients pretested for NG at Synlab, Medical Service Center, Weiden GmbH. In addition, 50 urine samples spiked with various concentrations of reference material were used. Results For the detection of CT and NG, the sensitivity and specificity of the PelvoCheck CT/NG test were 98.8% and 100%, and 98.3% and 98.2%, respectively. The data obtained with the PelvoCheck CT/NG for pooled urine specimens resulted in a positive agreement of 90.9% and a negative agreement of 100%. Conclusions The PelvoCheck CT/NG assay is a suitable test method for the detection of CT and NG in female FVU samples, with sensitivity and specificity comparable with other Food and Drug Administration approved CT/NG nucleic acid amplification tests. To the best of our knowledge, this is the first commercial test system validated for the analysis of pooled urine specimens. No false-positive or invalid result was observed in 55 analysed pools. Nevertheless, 5 samples were false negative due to a target concentration below the limit of detection of the PelvoCheck CT/NG test as a consequence of pooling-associated dilution. PMID:26729391

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

    PubMed Central

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

    1999-01-01

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

  8. 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. PMID:26850941

  9. Treatment of sulfur mustard (HD)-induced lung injury.

    PubMed

    Anderson, D R; Byers, S L; Vesely, K R

    2000-12-01

    An in vivo sulfur mustard (HD) vapor exposure model followed by bronchoalveolar lavage was developed previously in this laboratory to study biochemical indicators of HD-induced lung injury. This model was used to test two treatment compounds--niacinamide (NIA) and N-acetyl cysteine (NAC)--for their ability to ameliorate HD-induced biochemical changes. Anesthetized rats were intratracheally intubated and exposed to 0.35 mg of HD in 0.1 ml of ethanol or ethanol alone for 50 min. At the beginning of the exposure (t = 0), the rats were treated with either NIA (750 mg kg(-1)) or NAC (816 mg kg(-1)), i.p. At 24 h post-exposure, rats were euthanized and the lungs were lavaged with saline (three 5-ml washes). One milliliter of the recovered lavage fluid was analyzed for cellular components. The remaining fluid was centrifuged (10 min at 300 g) and the supernatant was assayed on a Cobas FARA clinical analyzer for lactate dehydrogenase (LDH), gamma-glutamyltransferase (GGT), albumin (ALB), total protein (TP) and glutathione peroxidase (GP). The HD alone and HD+NIA treatment caused significant increases in all of the biochemical parameters compared with control levels. The NAC treatment yielded LDH, ALB and TP values that, although elevated, were not significantly different from the control. The GP levels were significantly higher than the control but significantly lower than the HD alone levels, indicating some protection compared with the HD alone group. The GGT levels were unaffected by NAC compared with HD alone. Cytological analysis of lavage fluid showed that the percentages of neutrophils were 5.3 +/- 1.0 (mean +/- SEM) for control, 46.6 +/- 4.5 for HD, 31.4 +/- 4.7 for HD + NIA and 21.6 +/- 4.7 for HD + NAC, respectively. The neutrophil counts were significantly higher for the three HD-exposed groups vs controls; however, the NAC-treated group had neutrophil counts lower than HD alone, indicating decreased inflammatory response. These results show that NAC may be

  10. Interaction between castanospermine an immunosuppressant and cyclosporin A in rat cardiac transplantation

    PubMed Central

    Hibberd, Adrian D; Clark, David A; Trevillian, Paul R; Mcelduff, Patrick

    2016-01-01

    AIM: To investigate the interaction between castanospermine and cyclosporin A (CsA) and to provide an explanation for it. METHODS: The alkaloid castanospermine was prepared from the seeds of Castanospermum austral consistently achieving purity. Rat heterotopic cardiac transplantation and mixed lymphocyte reactivity were done using genetically inbred strains of PVG (donor) and DA (recipient). For the mixed lymphocyte reaction stimulator cells were irradiated with 3000 rads using a linear accelerator. Cyclosporin A was administered by gavage and venous blood collected 2 h later (C2). The blood levels of CsA (Neoral) were measured by immunoassay which consisted of a homogeneous enzyme assay (EMIT) on Cobas Mira. Statistical analyses of interactions were done by an accelerated failure time model with Weibull distribution for allograft survival and logistic regression for the mixed lymphocyte reactivity. RESULTS: Castanospermine prolonged transplant survival times as a function of dose even at relatively low doses. Cyclosporin A also prolonged transplant survival times as a function of dose particularly at doses above 2 mg/kg. There were synergistic interactions between castanospermine and CsA in the prolongation of cardiac allograft survival for dose ranges of CsA by castanospermine of (0 to 2) mg/kg by (0 to 200) mg/kg (HR = 0.986; 95%CI: 0.981-0.992; P < 0.001) and (0 to 3) mg/kg by (0 to 100) mg/kg (HR = 0.986; 95%CI: 0.981-0.992; P < 0.001) respectively. The addition of castanospermine did not significantly increase the levels of cyclosporin A on day 3 or day 6 for all doses of CsA. On the contrary, cessation of castanospermine in the presence of CsA at 2 mg/kg significantly increased the CsA level (P = 0.002). Castanospermine inhibited mixed lymphocyte reactivity in a dose dependent manner but without synergistic interaction. CONCLUSION: There is synergistic interaction between castanospermine and CsA in rat cardiac transplantation. Neither the mixed lymphocyte

  11. 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

  12. 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

  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. Point-Counterpoint: Cervical Cancer Screening Should Be Done by Primary Human Papillomavirus Testing with Genotyping and Reflex Cytology for Women over the Age of 25 Years.

    PubMed

    Stoler, Mark H; Austin, R Marshall; Zhao, Chengquan

    2015-09-01

    Screening for cervical cancer with cytology testing has been very effective in reducing cervical cancer in the United States. For decades, the approach was an annual Pap test. In 2000, the Hybrid Capture 2 human papillomavirus (HPV) test was approved by the U.S. Food and Drug Administration (FDA) for screening women who have atypical squamous cells of underdetermined significance (ASCUS) detected by Pap test to determine the need for colposcopy. In 2003, the FDA approved expanding the use of the test to include screening performed in conjunction with a Pap test for women over the age of 30 years, referred to as "cotesting." Cotesting allows women to extend the testing interval to 3 years if both tests have negative results. In April of 2014, the FDA approved the use of an HPV test (the cobas HPV test) for primary cervical cancer screening for women over the age of 25 years, without the need for a concomitant Pap test. The approval recommended either colposcopy or a Pap test for patients with specific high-risk HPV types detected by the HPV test. This was based on the results of the ATHENA trial, which included more than 40,000 women. Reaction to this decision has been mixed. Supporters point to the fact that the primary-screening algorithm found more disease (cervical intraepithelial neoplasia 3 or worse [CIN3+]) and also found it earlier than did cytology or cotesting. Moreover, the positive predictive value and positive-likelihood ratio of the primary-screening algorithm were higher than those of cytology. Opponents of the decision prefer cotesting, as this approach detects more disease than the HPV test alone. In addition, the performance of this new algorithm has not been assessed in routine clinical use. Professional organizations will need to develop guidelines that incorporate this testing algorithm. In this Point-Counterpoint, Dr. Stoler explains why he favors the primary-screening algorithm, while Drs. Austin and Zhao explain why they prefer the cotesting

  15. Bacterial vaginosis, aerobic vaginitis, vaginal inflammation and major Pap smear abnormalities.

    PubMed

    Vieira-Baptista, P; Lima-Silva, J; Pinto, C; Saldanha, C; Beires, J; Martinez-de-Oliveira, J; Donders, G

    2016-04-01

    The purpose of this investigation was to evaluate the impact of the vaginal milieu on the presence of abnormal Pap smears and a positive human papilloma virus (HPV) test. A cross-sectional study was conducted between June 2014 and May 2015, evaluating the vaginal discharge by fresh wet mount microscopy and comparing these data with Pap smear findings. Wet mount slides were scored for bacterial vaginosis (BV), aerobic vaginitis (AV), presence of Candida and Trichomonas vaginalis. Cytologic evaluation was done on all Pap smears according to the Bethesda criteria. The cobas© HPV Test (Roche) was performed for HPV detection. A total of 622 cases were evaluated. The mean age of the patients was 41.6 ± 10.65 years (range 21-75). Eighty-three women (13.3 %) had a cytology result worse than low-grade squamous intraepithelial lesion (LSIL). When comparing this group with the one with normal or minor [atypical squamous cells of undetermined significance (ASC-US) or LSIL] Pap smear abnormalities, there were no differences in the presence of Candida (32.5 % vs. 33.2 %, p = 1.0), absence of lactobacilli (38.6 % vs. 32.5 %, p = 0.32) or BV (20.5 % vs. 13.2 %, p = 0.09). On the other hand, moderate or severe inflammation (msI) (41.0 % vs. 28.8 %, p = 0,04), moderate or severe AV (msAV) (16.9 % vs. 7.2 %, p = 0.009) and msAV/BV (37.3 % vs. 20.0 %, p = 0.001) were more common in women with such major cervical abnormalities. No significant association was found between deviations of the vaginal milieu and high-risk HPV infection. The presence of msI or msAV, but not BV, is independently associated with an increased risk of major cervical cytological abnormalities, but not with HPV infection. PMID:26810061

  16. Field Evaluation of a Prototype Paper-Based Point-of-Care Fingerstick Transaminase Test

    PubMed Central

    Pollock, Nira R.; McGray, Sarah; Colby, Donn J.; Noubary, Farzad; Nguyen, Huyen; Nguyen, The Anh; Khormaee, Sariah; Jain, Sidhartha; Hawkins, Kenneth; Kumar, Shailendra; Rolland, Jason P.; Beattie, Patrick D.; Chau, Nguyen V.; Quang, Vo M.; Barfield, Cori; Tietje, Kathy; Steele, Matt; Weigl, Bernhard H.

    2013-01-01

    Monitoring for drug-induced liver injury (DILI) via serial transaminase measurements in patients on potentially hepatotoxic medications (e.g., for HIV and tuberculosis) is routine in resource-rich nations, but often unavailable in resource-limited settings. Towards enabling universal access to affordable point-of-care (POC) screening for DILI, we have performed the first field evaluation of a paper-based, microfluidic fingerstick test for rapid, semi-quantitative, visual measurement of blood alanine aminotransferase (ALT). Our objectives were to assess operational feasibility, inter-operator variability, lot variability, device failure rate, and accuracy, to inform device modification for further field testing. The paper-based ALT test was performed at POC on fingerstick samples from 600 outpatients receiving HIV treatment in Vietnam. Results, read independently by two clinic nurses, were compared with gold-standard automated (Roche Cobas) results from venipuncture samples obtained in parallel. Two device lots were used sequentially. We demonstrated high inter-operator agreement, with 96.3% (95% C.I., 94.3–97.7%) agreement in placing visual results into clinically-defined “bins” (<3x, 3–5x, and >5x upper limit of normal), >90% agreement in validity determination, and intraclass correlation coefficient of 0.89 (95% C.I., 0.87–0.91). Lot variability was observed in % invalids due to hemolysis (21.1% for Lot 1, 1.6% for Lot 2) and correlated with lots of incorporated plasma separation membranes. Invalid rates <1% were observed for all other device controls. Overall bin placement accuracy for the two readers was 84% (84.3%/83.6%). Our findings of extremely high inter-operator agreement for visual reading–obtained in a target clinical environment, as performed by local practitioners–indicate that the device operation and reading process is feasible and reproducible. Bin placement accuracy and lot-to-lot variability data identified specific targets for

  17. Hepatitis B Virus Core Promoter Mutations in Patients With Chronic Hepatitis B and Hepatocellular Carcinoma in Bucharest, Romania

    PubMed Central

    Constantinescu, Ileana; Dinu, Andrei-Antoniu; Boscaiu, Voicu; Niculescu, Marius

    2014-01-01

    Background: Accurate and personalized molecular virological diagnosis of hepatitis B virus (HBV) infection is crucial for individualized selection of patients for antiviral therapy in Romania. Objectives: We aimed to investigate HBV mutations in Romanian patients with chronic HBV infection, also to match HBV genotypes with HBV mutations identified and clinical outcomes. Patients and Methods: This was a cross-sectional study. A total of 484 Romanian patients with chronic HBV infection and hepatocellular carcinoma (HCC) were investigated. This was performed in Fundeni Clinical Institute, Bucharest, Romania during January 2005 to August 2010. HBsAg positive patients with chronic HBV infection admitted to Fundeni Clinical Institute were randomly enrolled in the study. Analysis was performed in the Centre for Immunogenetics and Virology, Fundeni Clinical Institute, Bucharest, Romania. Indirect diagnosis was performed with enhanced chemiluminescence method using Architect i2000SR and HBV-DNA was quantified with COBAS TaqMan HBV PCR. Direct sequencing of the PCR-products was performed with the PCR-product sequencing kit. HBV genotyping was performed with INNO-LiPA DR Amplification and INNO-LiPA HBV precore-core. Results: We detected two HBV genotypes; A (8.1%) and D (60.5%), and a mixture of genotypes A and D (31.4%) (P < 0.001). Basal core promoter (BCP) A1762T/G1764A and precore (PC) G1896A mutations were detected in these Romanian patients with chronic HBV infection. HBV chronic carriers had mainly genotype D (54.4%) and HBV WT (64.0%). BCP A1762T, G1764A and PC G1896A were significantly associated with HCC-tissue HBV sequencing (75.3%) (P < 0.001). PC G1896A alone was detected in HCC-serum HBV sequencing group (66.7%). Conclusions: Genotype D was the main genotype detected in Romanian patients with chronic HBV infection. Genotype D presented both BCP and PC mutations more frequently. PMID:25477976

  18. BRAF, PIK3CA, and HER2 Oncogenic Alterations According to KRAS Mutation Status in Advanced Colorectal Cancers with Distant Metastasis

    PubMed Central

    Koh, Jiwon; Kwak, Yoonjin; Seo, An Na; Park, Kyoung Un; Kim, Duck-Woo; Kang, Sung-Bum; Kim, Woo Ho; Lee, Hye Seung

    2016-01-01

    Background Anti-EGFR antibody–based treatment is an important therapeutic strategy for advanced colorectal cancer (CRC); despite this, several mutations—including KRAS, BRAF, and PIK3CA mutations, and HER2 amplification—are associated with the mechanisms underlying the development of resistance to anti-EGFR therapy. The aim of our study was to investigate the frequencies and clinical implications of these genetic alterations in advanced CRC. Methods KRAS, BRAF, and PIK3CA mutations were determined by Cobas real-time polymerase chain reaction (PCR) in 191 advanced CRC patients with distant metastasis. Microsatellite instability (MSI) status was determined by a fragmentation assay and HER2 amplification was assessed by silver in situ hybridization. In addition, KRAS mutations were investigated by the Sanger sequencing method in 97 of 191 CRC cases. Results Mutations in KRAS, BRAF, and PIK3CA were found in 104 (54.5%), 6 (3.1%), and 25 (13.1%) cases of advanced CRC, respectively. MSI-high status and HER2 amplification were observed in 3 (1.6%) and 16 (8.4%) cases, respectively. PIK3CA mutations were more frequently found in KRAS mutant type (18.3%) than KRAS wild type (6.9%) (P = 0.020). In contrast, HER2 amplifications and BRAF mutations were associated with KRAS wild type with borderline significance (P = 0.052 and 0.094, respectively). In combined analyses with KRAS, BRAF and HER2 status, BRAF mutations or HER2 amplifications were associated with the worst prognosis in the wild type KRAS group (P = 0.004). When comparing the efficacy of detection methods, the results of real time PCR analysis revealed 56 of 97 (57.7%) CRC cases with KRAS mutations, whereas Sanger sequencing revealed 49 cases (50.5%). Conclusions KRAS mutations were found in 54.5% of advanced CRC patients. Our results support that subgrouping using PIK3CA and BRAF mutation or HER2 amplification status, in addition to KRAS mutation status, is helpful for managing advanced CRC patients. PMID

  19. The clinical value of HPV genotyping in triage of women with high-risk-HPV-positive self-samples.

    PubMed

    Ebisch, Renée M F; de Kuyper-de Ridder, Gabriëlle M; Bosgraaf, Remko P; Massuger, Leon F A G; IntHout, Joanna; Verhoef, Viola M J; Heideman, Daniëlle A M; Snijders, Peter J F; Meijer, Chris J L M; van Kemenade, Folkert J; Bulten, Johan; Siebers, Albert G; Bekkers, Ruud L M; Melchers, Willem J G

    2016-08-01

    Cytology alone, or combined with HPV16/18 genotyping, might be an acceptable method for triage in hrHPV-cervical cancer screening. Previously studied HPV-genotype based triage algorithms are based on cytology performed without knowledge of hrHPV status. The aim of this study was to explore the value of hrHPV genotyping combined with cytology as triage tool for hrHPV-positive women. 520 hrHPV-positive women were included from a randomised controlled self-sampling trial on screening non-attendees (PROHTECT-3B). Eighteen baseline triage strategies were evaluated for cytology and hrHPV genotyping (Roche Cobas 4800) on physician-sampled triage material. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), referral rate, and number of referrals needed to diagnose (NRND) were calculated for CIN2+ and CIN3+. A triage strategy was considered acceptable if the NPV for CIN3+ was ≥98%, combined with maintenance or improvement of sensitivity and an increase in specificity in reference to the comparator, being cytology with a threshold of atypical cells of undetermined significance (ASC-US). Three triage strategies met the criteria: HPV16+ and/or ≥LSIL; HPV16+ and/or ≥HSIL; (HPV16+ and/or HPV18+) and/or ≥HSIL. Combining HPV16+ and/or ≥HSIL yielded the highest specificity (74.9%, 95% CI 70.5-78.9), with a sensitivity (94.4%, 95% CI 89.0-97.7) similar to the comparator (93.5%, 95% CI 87.7-97.1), and a decrease in referral rate from 52.2% to 39.5%. In case of prior knowledge of hrHPV presence, triage by cytology testing can be improved by adjusting its threshold, and combining it with HPV16/18 genotyping. These strategies improve the referral rate and specificity for detecting CIN3+ lesions, while maintaining adequate sensitivity. PMID:26991464

  20. Field evaluation of a prototype paper-based point-of-care fingerstick transaminase test.

    PubMed

    Pollock, Nira R; McGray, Sarah; Colby, Donn J; Noubary, Farzad; Nguyen, Huyen; Nguyen, The Anh; Khormaee, Sariah; Jain, Sidhartha; Hawkins, Kenneth; Kumar, Shailendra; Rolland, Jason P; Beattie, Patrick D; Chau, Nguyen V; Quang, Vo M; Barfield, Cori; Tietje, Kathy; Steele, Matt; Weigl, Bernhard H

    2013-01-01

    Monitoring for drug-induced liver injury (DILI) via serial transaminase measurements in patients on potentially hepatotoxic medications (e.g., for HIV and tuberculosis) is routine in resource-rich nations, but often unavailable in resource-limited settings. Towards enabling universal access to affordable point-of-care (POC) screening for DILI, we have performed the first field evaluation of a paper-based, microfluidic fingerstick test for rapid, semi-quantitative, visual measurement of blood alanine aminotransferase (ALT). Our objectives were to assess operational feasibility, inter-operator variability, lot variability, device failure rate, and accuracy, to inform device modification for further field testing. The paper-based ALT test was performed at POC on fingerstick samples from 600 outpatients receiving HIV treatment in Vietnam. Results, read independently by two clinic nurses, were compared with gold-standard automated (Roche Cobas) results from venipuncture samples obtained in parallel. Two device lots were used sequentially. We demonstrated high inter-operator agreement, with 96.3% (95% C.I., 94.3-97.7%) agreement in placing visual results into clinically-defined "bins" (<3x, 3-5x, and >5x upper limit of normal), >90% agreement in validity determination, and intraclass correlation coefficient of 0.89 (95% C.I., 0.87-0.91). Lot variability was observed in % invalids due to hemolysis (21.1% for Lot 1, 1.6% for Lot 2) and correlated with lots of incorporated plasma separation membranes. Invalid rates <1% were observed for all other device controls. Overall bin placement accuracy for the two readers was 84% (84.3%/83.6%). Our findings of extremely high inter-operator agreement for visual reading-obtained in a target clinical environment, as performed by local practitioners-indicate that the device operation and reading process is feasible and reproducible. Bin placement accuracy and lot-to-lot variability data identified specific targets for device

  1. 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

  2. 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

  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. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. [Monitoring of cytomegalovirus-specific CD4(+) and CD8(+) T cell responses by cytokine flow cytometry in renal transplant recipients].

    PubMed

    Kılınçkaya Doğan, Hafize; Mutlu, Esvet; Köksoy, Sadi; Yılmaz, Vural T; Koçak, Hüseyin; Çolak, Dilek; Mutlu, Derya; Günseren, Filiz; Dinçkan, Ayhan; Aliosmanoğlu, İbrahim; Süleymanlar, Gültekin; Gültekin, Meral

    2016-04-01

    In spite of the improvements in the clinical management of solid organ transplant (SOT) recipients provided by immunosuppresion and universal prophylaxis, human cytomegalovirus (CMV) infections continue to be one of the most leading causes of morbidity and mortality. Cell-mediated immunity specific to CMV (CMV-CMI) plays an important role in the control of CMV replication. Therefore, monitoring of CMV-specific T-cell response can be used to predict individuals at increased risk of CMV disease. The aim of this study was to investigate the levels of CMV-specific interferon (IFN)-γ producing CD4+ and CD8+ T cells in kidney transplant recipients before and after the transplantation, by cytokine flow cytometry. A total of 21 kidney transplant recipients (14 male, 7 female; age range: 18-66 years, mean age: 34.5 ± 9.9) who were all CMV seropositive have been evaluated in the study. Blood samples from the patients were obtained before and at the 1st, 3rd and 6th months after transplantation. CMV seropositive healthy kidney donors (n= 20) constituted the control group. The main stages of our procedure were as follows; isolation of peripheral blood mononuclear cells from whole blood, freezing and storing of the samples, later on thawing the samples, ex vivo stimulation of lymphocytes with pooled CMV peptides and counting CMV-specific IFN- producing CD4+ and CD8+ T cells by flow cytometry following surface and intracellular cytokine staining. Monitoring of the viral load (CMV-DNA) was performed in 10 days intervals in the first 3 months followed by 3 week intervals until 6 months using COBAS AmpliPrep/COBAS TaqMan CMV test system (Roche Diagnostics, USA). The frequencies of pretransplant CMV-specific IFN-γ producing CD8+ T cells in patient (3.53 ± 4.35/µl) and control (4.52 ± 5.17/µl) groups were not statistically different (p= 0.266). The difference between the number of virus-specific CD4+ T cells in patients (8.84 ± 9.56/µl) and those in the control group (8

  11. Clinical validation of hrHPV testing on vaginal and urine self-samples in primary cervical screening (cross-sectional results from the Papillomavirus Dumfries and Galloway—PaVDaG study)

    PubMed Central

    Stanczuk, Grazyna; Currie, Heather; Lawrence, James; Cuschieri, Kate; Wilson, Allan; Arbyn, Marc

    2016-01-01

    Objectives Papillomavirus Dumfries and Galloway (PaVDaG) assessed the performance of a high-risk human papillomavirus (hrHPV) PCR-based assay to detect high-grade cervical intraepithelial neoplasia (CIN2+) in self-collected vaginal and urine samples. Setting Women attending routine cervical screening in primary care. Participants 5318 women aged 20–60 years provided self-collected random urine and vaginal samples for hrHPV testing and a clinician-collected liquid-based cytology (LBC) sample for cytology and hrHPV testing. Interventions HrHPV testing. All samples were tested for hrHPV using the PCR-based cobas 4800 assay. Colposcopy was offered to women with high-grade or repeated borderline/low-grade cytological abnormalities; also to those who were LBC negative but hrHPV 16/18 positive. Primary and secondary outcome measures The self-tests' absolute sensitivity and specificity for CIN2+ were assessed on all biospecimens; also, their relative sensitivity and specificity compared with clinician-taken samples. Interlaboratory and intralaboratory performance of the hrHPV assay in self-collected samples was also established. Results HrHPV prevalence was 14.7%, 16.6% and 11.6% in cervical, vaginal and urine samples, respectively. Sensitivity for detecting CIN2+ was 97.7% (95% to 100%), 94.6% (90.7% to 98.5%) and 63.1% (54.6% to 71.7%) for cervical, vaginal and urine hrHPV detection, respectively. The corresponding specificities were 87.3% (86.4% to 88.2%), 85.4% (84.4% to 86.3%) and 89.8% (89.0% to 90.7%). There was a 38% (24% to 57%) higher HPV detection rate in vaginal self-samples from women over 50 years compared with those ≤29 years. Relative sensitivity and specificity of hrHPV positivity for the detection of CIN2+ in vaginal versus cervical samples were 0.97 (0.94 to 1.00) and 0.98 (0.97 to 0.99); urine versus cervical comparisons were 0.53 (0.42 to 0.67) and 1.03 (1.02 to 1.04). The intralaboratory and interlaboratory agreement for hrHPV positivity in

  12. [Distribution of hepatitis C virus genotypes among patients with chronic hepatitis C infection in Akdeniz University Hospital, Antalya, Turkey: a five-year evaluation].

    PubMed

    Sağlik, İmran; Mutlu, Derya; Öngut, Gözde; İnan, Dilara; Öğünç, Dilara; Can Sarinoğlu, Rabia; Özhak Baysan, Betil; Gültekin, Meral; Çolak, Dilek

    2014-07-01

    Hepatitis C virus (HCV) is one of the major causes of chronic hepatitis. It is important to know the genotypes of HCV in the decision of the HCV related chronic hepatitis therapy. The aim of this study was to evaluate the HCV genotypes determined at the Microbiology Laboratory of Akdeniz University Hospital, and to evaluate the changes in the distribution of the genotypes within the last five years. A total of 422 blood samples from HCV-RNA positive chronic hepatitis C patients (219 male, 203 female; age range: 8-79 yrs, mean age 46.3 ± 15.5 yrs) which were sent to our laboratory for genotyping between 2009-2013 period, were analyzed retrospectively. HCV-RNA extractions were performed in an automated system (EZ1 Virus Mini Kit v2.0, Qiagen, Germany), and a commercial reverse hybridization line probe-based assay (LIPA; GEN-C RT-PCR, Italy) was carried out for genotyping, For viral load determinations, a real-time PCR method (Cobas TaqMan HCV, Roche Diagnostics, Germany) was used. Demographic data of the patients were obtained from the hospital information systems and electronic patients' files. Out of the 422 patients, genotype 1b was detected in 63.3% (n= 267), genotype 1a in 14.7% (n= 62), genotype 3a in 11.1% (n= 47), genotype 2b in 0.9% (n= 4), genotype 4e in 0.2% (n= 1). The subtypes couldn't be determined for 5.4% (n= 23), 2.6% (n= 11) and 1.4% (n= 6) of the patients infected with genotype 1, 2 and 4, respectively. One (0.2%) patient, was coinfected with genotype 1 and 4. Of the patients, 40 were foreign-born (16 cases from Russia; 4 of each from Ukraine and Georgia; 3 of each from Turkmenistan, Kyrgyzstan, and Germany; one of each from Tajikistan, Azerbaijan, Uzbekistan, Chechnya, Moldova, Switzerland and Romania) and among these patients genotype 3a (19/40; 47.5%) was the most common genotype followed by genotype 1b (17/40; 42.5%). Median values of HCV viral load were 668.500 IU/ml (range: 2.000-9.630.000) in the whole group; while it was 732.000 IU

  13. Retrospective Study to Determine Diagnostic Utility of 6 Commonly Used Lung Cancer Biomarkers Among Han and Uygur Population in Xinjiang Uygur Autonomous Region of People's Republic of China.

    PubMed

    Yang-Chun, Feng; Min, Feng; Di, Zhang; Yan-Chun, Huang

    2016-05-01

    Early diagnosis was the main way to improve the survival rate of lung cancer patients. At present, the methods to diagnose lung cancer were varied, but early diagnosis of lung cancer was still difficult. In experimental and clinical studies, lung cancer related tumor markers were helpful to the early diagnosis of lung cancer. So far, there were many studies about lung cancer related tumor markers in China, but the subjects in these studies were almost the Han population. There were few studies about the Uygur population. Xinjiang was a multi-ethnic region in China, the ratios of Han and Uygur population were 40% and 45%, respectively. Xinjiang also was a high incidence area of lung cancer in China. The purpose of this study was to research the application of 6 tumor markers in Uygur and Han lung cancer patients in XinJiang, China.The study collected 342 cases who were diagnosed as lung cancer in Tumor Hospital Affiliated to XinJiang Medical University from May 2012 to December 2012. Serum concentrations of squamous cell carcinoma (SCC), cytokeratin fragment 19 (CYFRA21-1), carcino-embryonic antigen (CEA), carbohydrate antigen 125 (CA125), precursor of gastrin-releasing peptide (Pro-GRP), and neuron-specific enolase (NSE) were tested for every patient before radiation, chemotherapy, or surgery. The serum concentrations of SCC, CYFRA21-1, CEA, CA125, and Pro-GRP were assayed using the micro-particle luminescence analysis testing by the Abbott ARHCITECT i2000SR immunoanalyzer. NSE was assayed by the electrochemical luminescence analysis testing using Roche Cobas E601 electrochemical luminescence analyzer.Serum levels of SCC were different between 2 ethnic populations, smoking should be the influence factor to create the difference. Cluster analysis showed that the NSE and Pro-GRP were helpful to identify small cell lung cancer (SCLC), and CEA, CA125, SCC, CYFRA21-1 were beneficial to diagnose non-small cell lung cancer (NSCLC). The compare of diagnosis value about

  14. Retrospective Study to Determine Diagnostic Utility of 6 Commonly Used Lung Cancer Biomarkers Among Han and Uygur Population in Xinjiang Uygur Autonomous Region of People's Republic of China

    PubMed Central

    Yang-Chun, Feng; Min, Feng; Di, Zhang; Yan-Chun, Huang

    2016-01-01

    Abstract Early diagnosis was the main way to improve the survival rate of lung cancer patients. At present, the methods to diagnose lung cancer were varied, but early diagnosis of lung cancer was still difficult. In experimental and clinical studies, lung cancer related tumor markers were helpful to the early diagnosis of lung cancer. So far, there were many studies about lung cancer related tumor markers in China, but the subjects in these studies were almost the Han population. There were few studies about the Uygur population. Xinjiang was a multi-ethnic region in China, the ratios of Han and Uygur population were 40% and 45%, respectively. Xinjiang also was a high incidence area of lung cancer in China. The purpose of this study was to research the application of 6 tumor markers in Uygur and Han lung cancer patients in XinJiang, China. The study collected 342 cases who were diagnosed as lung cancer in Tumor Hospital Affiliated to XinJiang Medical University from May 2012 to December 2012. Serum concentrations of squamous cell carcinoma (SCC), cytokeratin fragment 19 (CYFRA21-1), carcino-embryonic antigen (CEA), carbohydrate antigen 125 (CA125), precursor of gastrin-releasing peptide (Pro-GRP), and neuron-specific enolase (NSE) were tested for every patient before radiation, chemotherapy, or surgery. The serum concentrations of SCC, CYFRA21-1, CEA, CA125, and Pro-GRP were assayed using the micro-particle luminescence analysis testing by the Abbott ARHCITECT i2000SR immunoanalyzer. NSE was assayed by the electrochemical luminescence analysis testing using Roche Cobas E601 electrochemical luminescence analyzer. Serum levels of SCC were different between 2 ethnic populations, smoking should be the influence factor to create the difference. Cluster analysis showed that the NSE and Pro-GRP were helpful to identify small cell lung cancer (SCLC), and CEA, CA125, SCC, CYFRA21-1 were beneficial to diagnose non-small cell lung cancer (NSCLC). The compare of diagnosis

  15. Updates on the mineralogical analysis of dark materials in Martian craters

    NASA Astrophysics Data System (ADS)

    Tirsch, D.; Jaumann, R.; Poulet, F.; Roach, L. H.; Mustard, J. L.; Bibring, J.-P.; Neukum, G.

    2008-09-01

    Introduction: A refinement of the mineralogical analysis of dark materials in Martian craters is presented here. 70 localities of dark material deposits, including dunes, dune fields, and sand sheets, were examined by using near infrared spectra from the MarsExpress/OMEGA spectrometer [1]. Additionally, near-infrared MRO/CRISM data [2] with a spatial resolution of up to 18m/px were used to derive spectral information of dark layers exposed at impact crater walls. These layers are supposed to be a local source for the material inside the craters [3, 4]. A similar mineralogical composition would prove this suggestion. Methodology: For every location, we analyzed at least two different OMEGA orbits. The data were corrected for solar irradiance and atmospheric absorptions. The mineral detection was done using an IDL routine that applies a ratioing technique to the geometrically and atmospherically corrected OMEGA data. The applied technique was developed and described in detail by [5]. The spectral parameters used for the mineral detection were derived from [5] as well. They include the typical absorption features for every mineral of interest. Using these different spectral criteria, the distribution of high- and lowcalcium pyroxenes, olivine, and hydrated minerals could be mapped. For this analysis, the spectral range from 1-2.5 μm was considered. CRISM targeted observations covering dark layers are rare so that only a few observations could be analyzed yet. Spectral ratios were use to enhance the spectral signature of the present minerals. Results: The method outputs are images comprising the absorption band depths for the minerals of interest. The overlay of these absorption depth images onto the original OMEGA images allows the mapping of mineral absorption depths on the surface. Figure 1 reflects a typical result for the analyzed localities. The major part of the dark material shows pyroxene absorptions, whereas olivine can (if existing at all) solely be

  16. 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