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Sample records for cobas taqscreen mpx

  1. MPX: software for multiplexing hardware performance counters in multithreaded programs

    SciTech Connect

    May, J M

    2000-08-23

    Hardware performance counters are CPU registers that count data loads and stores, cache misses, and other events. Counter data can help programmers understand software performance. Although CPUs typically have multiple counters, each can monitor only one type of event at a time, and some counters can monitor only certain events. Therefore, some CPUs cannot concurrently monitor interesting combinations of events. Software multiplexing partly overcomes this limitation by using time sharing to monitor multiple events on one counter. However, counter multiplexing is harder to implement for multithreaded programs than for single-threaded ones because of certain difficulties in managing the length of the time slices. This paper describes a software library called MPX that overcomes these difficulties. MPX allows applications to gather hardware counter data concurrently for any combination of countable events. MPX data are typically within a few percent of counts recorded without multiplexing.

  2. MPX: software for multiplexing hardware performance counters in multithreaded programs

    SciTech Connect

    May, J M

    2001-01-08

    Hardware performance counters are CPU registers that count data loads and stores, cache misses, and other events. Counter data can help programmers understand software performance. Although CPUs typically have multiple counters, each can monitor only one type of event at a time, and some counters can monitor only certain events. Therefore, some CPUs cannot concurrently monitor interesting combinations of events. Software multiplexing partly overcomes this limitation by using time sharing to monitor multiple events on one counter: However; counter multiplexing is harder to implement for multithreaded programs than for single-threaded ones because of certain difficulties in managing the length of the time slices. This paper describes a software library called MPX that overcomes these difficulties. MPX allows applications to gather hardware counter data concurrently for any combination of countable events. MPX data are typically within a few percent of counts recorded without multiplexing.

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

    PubMed Central

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

    2016-01-01

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

  5. Clinical Performance of Roche Cobas 4800 HPV Test

    PubMed Central

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

    2014-01-01

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

  6. 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.

  7. 160 Mpx/Sec Laser Pattern Generator For Mask And Reticle Production

    NASA Astrophysics Data System (ADS)

    MacDonald, D. B.; Nagler, M.; Van Peski, C.; Whitney, T. R.

    1984-06-01

    A new Laser Pattern Generator (LPG) designed for reticle production was recently introduced by THE Semiconductor Equipment Corporation. The system uses HeCd laser radiation with a wavelength of 441.6 nm to expose commercial photoresist (e.g. AZ 1350J or AZ 1470). A writing rate of 160 Mpx/sec is achieved by parallel operation of sixteen (16) independently modulated channels. The binary light intensity distribution is controlled in each channel by acousto-optic modulation. The sixteen (16) independent chan-nels are brought to a common crossover and scanned simultaneously using a single acousto-optic deflector. Pattern data must be expanded into a pixel format in two steps due to the inherent writing speed of the LPG. Prior to run time, geometrical data is trans-lated from Electromask or Mann format into a compact vector format using an off-line preprocessing unit. The vector data is stored on a 300 Mbyte portable disk pack which has a nominal data transfer rate of 9.67 Mbits/sec. During run time, vector data is read from the disk and expanded in the real time processing unit to supply pixel data to the optical modulation system. The placement of data in the correct position is controlled by a laser interferometry system and a control computer. The LPG system throughput of 160 Mpx/ sec permits the writing of 100 mm x 100 mm rejicles with information equivalent to 10' optical pattern generator flashes in less than 30 minutes, independent of pat-tern complexity. Although the specified minimum geometry is 2.5 pm, patterns with 1 pm features have been resolved. The address resolution is 0.25 μm, and the individual beam spot size is 0.5 μm (FWHM). Examples of printed patterns are included.

  8. 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

  9. 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

  10. Mini review: current molecular methods for the detection and quantification of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus type 1.

    PubMed

    Albertoni, Guilherme; Castelo Girão, Manoel João Batista; Schor, Nestor

    2014-08-01

    The detection of acute human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) infection is vital for controlling the spread of HIV, HBV, and HCV to uninfected individuals. Considering that these viruses have high replication rates and are undetectable by serological markers, early detection upon transmission is crucial. Various nucleic acid assays have been developed for diagnostics and therapeutic monitoring of infections. In the past decade, rapid and sensitive molecular techniques such as PCR have revolutionized the detection of a variety of infectious viruses, including HIV, HCV, and HBV. Here, we describe two of the most commonly used licensed methods for the detection and quantification of HIV, HCV, and HBV: the cobas TaqScreen MPX (PCR) test and the Tigris System. We used transcription-mediated amplification to review and compare the development and efficiency of these technologies. PMID:24927665

  11. An in-house real-time polymerase chain reaction: standardisation and comparison with the Cobas Amplicor HBV monitor and Cobas AmpliPrep/Cobas TaqMan HBV tests for the quantification of hepatitis B virus DNA.

    PubMed

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

    2016-02-01

    This study aimed to standardise an in-house real-time polymerase chain reaction (rtPCR) to allow quantification of hepatitis B virus (HBV) DNA in serum or plasma samples, and to compare this method with two commercial assays, the Cobas Amplicor HBV monitor and the Cobas AmpliPrep/Cobas TaqMan HBV test. Samples from 397 patients from the state of São Paulo were analysed by all three methods. Fifty-two samples were from patients who were human immunodeficiency virus and hepatitis C virus positive, but HBV negative. Genotypes were characterised, and the viral load was measure in each sample. The in-house rtPCR showed an excellent success rate compared with commercial tests; inter-assay and intra-assay coefficients correlated with commercial tests (r = 0.96 and r = 0.913, p < 0.001) and the in-house test showed no genotype-dependent differences in detection and quantification rates. The in-house assay tested in this study could be used for screening and quantifying HBV DNA in order to monitor patients during therapy.

  12. 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

  13. cobU-dependent assimilation of nonadenosylated cobinamide in cobA mutants of Salmonella typhimurium.

    PubMed Central

    O'Toole, G A; Escalante-Semerena, J C

    1993-01-01

    The cobA locus of Salmonella typhimurium is involved in the assimilation of nonadenosylated cobinamide, (CN)2CBI, into cobalamin (CBL) under aerobic and anaerobic growth conditions. Aerobically, cobA mutants are unable to assimilate (CN)2CBI into CBL. However, under anaerobic conditions, cobA mutants assimilate (CN)2CBI into CBL as efficiently as cobA+ strains. On the basis of this observation, we postulated the existence of a cobA-independent pathway for the assimilation of (CN)2CBI into CBL that is functional under anaerobic growth conditions (J. C. Escalante-Semerena, S.-J. Suh, and J. R. Roth, J. Bacteriol. 172:273-280, 1990). In this paper, we report the isolation and initial genetic characterization of derivatives of cobA mutants that are unable to assimilate (CN)2CBI into CBL during anaerobic growth. As demonstrated by complementation analysis, marker rescue, and DNA sequencing data, these mutations are alleles of cobU, a gene involved in the assembly of the nucleotide loop of CBL. We have shown that the block in CBL synthesis in these cobU cobA double mutant strains can be corrected by exogenous adenosyl-CBI. Our data indicate that this new class of cobU mutations blocks CBL biosynthesis but does not destroy the putative kinase-guanylyltransferase activities of the CobU protein. We propose that this new class of cobU mutations may affect an as yet unidentified ATP:corrinoid adenosyltransferase activity of the CobU protein. Alternatively, such mutations may alter the ability of CobU to use nonadenosylated CBI as a substrate. PMID:8407805

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

    PubMed

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

    2011-01-01

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

  15. Purification and initial characterization of the ATP:corrinoid adenosyltransferase encoded by the cobA gene of Salmonella typhimurium.

    PubMed Central

    Suh, S; Escalante-Semerena, J C

    1995-01-01

    The cobA gene of Salmonella typhimurium and its product were overexpressed to approximately 20% of the total cell protein. CobA was purified to 98% homogeneity; N-terminal sequence analysis (21 residues) of homogeneous protein confirmed the predicted amino acid sequence. ATP:corrinoid adenosyltransferase activity was demonstrated in vitro to be associated with CobA. This activity was optimal at pH 8 and 37 degrees C. A quantitative preference was determined for Mn(II) cations and ATP. The apparent Km of CobA for ATP was 2.8 microM, and that for cob(I)alamin was 5.2 microM. Vmax was measured at 0.43 nmol/min. Cobinamide served as the substrate for CobA to yield adenosylcobinamide. Activity was stable at 4 degrees C for several weeks but was lost rapidly at room temperature (50% overnight). Dithiothreitol was required to maintain the enzymatic activity of CobA. PMID:7860601

  16. A new generation of companion diagnostics: cobas BRAF, KRAS and EGFR mutation detection tests.

    PubMed

    Angulo, Barbara; Lopez-Rios, Fernando; Gonzalez, David

    2014-06-01

    The cobas(®) (Roche) portfolio of companion diagnostics in oncology currently has three assays CE-marked for in vitro diagnostics. Two of these (EGFR and BRAF) are also US FDA-approved. These assays detect clinically relevant mutations that are correlated with response (BRAF, EGFR) or lack of response (KRAS) to targeted therapies such as selective mutant BRAF inhibitors in malignant melanoma, tyrosine kinases inhibitor in non-small cell lung cancer and anti-EGFR monoclonal antibodies in colorectal cancer, respectively. All these assays are run on a single platform using DNA extracted from a single 5 µm section of a formalin-fixed paraffin-embedded tissue block. The assays provide an 'end-to-end' solution from extraction of DNA to automated analysis and report on the cobas z 480. The cobas tests have shown robust and reproducible performance, with high sensitivity and specificity and low limit of detection, making them suitable as companion diagnostics for clinical use. PMID:24844134

  17. Comparison of the Cobas 4800 HPV Test and the Seeplex HPV4A ACE with the Hybrid Capture 2 Test

    PubMed Central

    Ki, Eun Young; Kim, Hee Eun; Choi, Yeong-Jin; Park, Jong-Sup; Kang, Chang Seok; Lee, Ahwon

    2013-01-01

    Background: It is well-known that persistent cervical infections with high-risk human papillomavirus (HPV) are related to the development of high-grade cervical intraepithelial neoplasia and invasive cervical cancer and that infection with HPV 16 and HPV 18 accounts for approximately 70% of all cases of invasive cervical cancer. Methods: We performed 3 HPV molecular tests―the Cobas 4800 HPV test, the Seeplex HPV4A ACE, and the hybrid capture 2 (HC2) test―in 146 cervical swab samples to compare between these three tests. Results: There was a concordance rate of 82.8% between the results of the Cobas 4800 HPV and the HC2 test and a concordance rate of 84.9% between the results of the Seeplex HPV4A ACE and the HC2 test. Between the Cobas 4800 HPV test and the Seeplex HPV4A ACE, there was a concordance rate of 89.6% in the detection of high-risk HPV between the results and a concordance rate of 98.7% in the detection of HPV 16 or 18. When an abnormal Pap test was defined as ≥low grade squamous intraepithelial lesion (LSIL), the sensitivity of the Cobas 4800 HPV test, the Seeplex HPV4A ACE and the HC2 test were 71.1%, 80.0%, and 88.9%, respectively, while their specificities were 76.4%, 74.5%, and 67.9%, respectively. Conclusions: The results of this study suggest that the Cobas 4800 HPV test and the Seeplex HPV4A ACE may be as effective as the HC2 test in detecting HR HPV and that the concordance between the results of the Cobas 4800 HPV test and the Seeplex HDV4A ACE may be higher in the detection of HPV 16 and HPV18 than concerning high-risk HPV. PMID:23329882

  18. 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

  19. 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

  20. Inter-laboratory evaluation of the COBAS INTEGRA 400 analytical system.

    PubMed

    Muser, J; Bienvenu, J; Blanckaert, N; Brandslund, I; Delattre, J; Soffiati, G; Swaminathan, R; Maggini, S; Mastall, H

    2001-06-01

    COBAS INTEGRA 400 is a random-access analytical system consolidating assays for clinical chemistry analytes, electrolytes, serum proteins, drugs of abuse and therapeutic drugs. Analytical performance and practicability of the instrument were evaluated in seven laboratories over a 2-year period in parallel with system development. Good within-run and total imprecision for all assays was observed with a few exceptions for specimen pools with low concentration or activity. The coefficients of variation for total imprecision were well below 3.0% for clinical chemistry analytes and electrolytes, and below 5.0% for serum proteins and therapeutic drugs. Method comparisons demonstrated a good agreement with the various systems used for comparison, with slopes varying typically from 0.94 to 1.05, and Spearman correlation coefficient generally > 0.975. Accuracy was verified by recovery of controls and certified reference materials within 90 to 110% of target values. Assay ranges were linear within +/- 5%. No carry-over on reagent or sample pipetting systems was observed. Manufacturer-specified interference limits and onboard stabilities of reagents were confirmed. A time study for calculating direct personnel times and total processing time was carried out in three laboratories under different conditions including consolidated, STAT and dedicated use. On a scenario-independent basis, the total working time was shorter on the COBAS INTEGRA 400 than on routine systems in all three laboratories. Personnel time, in particular, was significantly reduced when compared to routine instruments. In general, system practicability was judged very positively in all laboratories. Owing to its versatility, the instrument is best placed as a consolidated workstation in small- to medium-sized laboratories or as an instrument for special determinations such as serum proteins, drugs, urinalysis or emergency analyses in large laboratories.

  1. 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

  2. Nucleic acid testing of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus 1, 2 in blood donors in the General University Hospital, Prague.

    PubMed

    Dušková, D; Darebníček, L

    2014-01-01

    The Roche Cobas TaqScreen MPX Test v1 - multiplex reverse transcription-real time (MPX RT-Real Time) PCR, performed on Cobas s201 for HCV RNA, HBV DNA, HIV-1 RNA /group M and O/, and HIV-2 RNA was introduced as a supplement to the currently used imunoanalysis method for blood donor´s testing (Abbott CMIA - chemiluminescent microparticle imunoassay, performed on Architect i2000 for anti-HCV, hepatitis B surface antigen (HBsAg)), anti-HIV-1 /group M and O/, anti-HIV-2 and p24 HIV). The results of study could provide valuable arguments to support the discussion about the NAT implementation into the standards of blood donor´s testing in the Czech Republic. Two groups of samples were tested. In the first one, 5074 samples from consecutive blood donors, and in the second one, 5 repository preseroconverted samples from repeat blood donors, who were subsequently confirmed positive for Viral Hepatitis and/or HIV/AIDS by the National Reference Laboratory (NRL), were tested. One sample was found reactive by chemiluminescent microparticle immuno assay (CMIA) and nucleic acid test (NAT) (confirmed HBV-positive in NRL), 31 samples were CMIA-only reactive (15 anti-HCV, 4 HBsAg, 12 anti-HIV/p24, all confirmed negative in NRL) and one pool (6 samples) was found reactive (further individual NAT was negative for all samples) in the first group of samples. One sample was NAT-only reactive (confirmed HCV-positive in NRL) in the second group of samples. Our study confirmed that screening of infectious markers using NAT can reduce the risk of transmitting the monitored infections by blood transfusion in the Czech Republic, even as a country with currently good epidemiological situation.

  3. Nucleic acid testing of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus 1, 2 in blood donors in the General University Hospital, Prague.

    PubMed

    Dušková, D; Darebníček, L

    2014-01-01

    The Roche Cobas TaqScreen MPX Test v1 - multiplex reverse transcription-real time (MPX RT-Real Time) PCR, performed on Cobas s201 for HCV RNA, HBV DNA, HIV-1 RNA /group M and O/, and HIV-2 RNA was introduced as a supplement to the currently used imunoanalysis method for blood donor´s testing (Abbott CMIA - chemiluminescent microparticle imunoassay, performed on Architect i2000 for anti-HCV, hepatitis B surface antigen (HBsAg)), anti-HIV-1 /group M and O/, anti-HIV-2 and p24 HIV). The results of study could provide valuable arguments to support the discussion about the NAT implementation into the standards of blood donor´s testing in the Czech Republic. Two groups of samples were tested. In the first one, 5074 samples from consecutive blood donors, and in the second one, 5 repository preseroconverted samples from repeat blood donors, who were subsequently confirmed positive for Viral Hepatitis and/or HIV/AIDS by the National Reference Laboratory (NRL), were tested. One sample was found reactive by chemiluminescent microparticle immuno assay (CMIA) and nucleic acid test (NAT) (confirmed HBV-positive in NRL), 31 samples were CMIA-only reactive (15 anti-HCV, 4 HBsAg, 12 anti-HIV/p24, all confirmed negative in NRL) and one pool (6 samples) was found reactive (further individual NAT was negative for all samples) in the first group of samples. One sample was NAT-only reactive (confirmed HCV-positive in NRL) in the second group of samples. Our study confirmed that screening of infectious markers using NAT can reduce the risk of transmitting the monitored infections by blood transfusion in the Czech Republic, even as a country with currently good epidemiological situation. PMID:24957719

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

    PubMed

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

    2013-08-01

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

  5. [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.

  6. 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

  7. 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

  8. An Evaluation of the Cobas4800 HPV Test on Cervico-Vaginal Specimens in Liquid versus Solid Transport Media

    PubMed Central

    Luo, Hongxue; Du, Hui; Maurer, Kathryn; Belinson, Jerome L.; Wang, Guixiang; Liu, Zhihong; Zhang, Lijie; Zhou, Yanqiu; Wang, Chun; Tang, Jinlong; Qu, Xinfeng; Wu, Ruifang

    2016-01-01

    Objectives Determine the ability of the Cobas 4800 assay to detect high-risk human papillomavirus (HrHPV) and high-grade cervical lesions when using cervico-vaginal samples applied to liquid medium and solid media cards compared to a direct cervical sample. Methods Two cervico-vaginal specimens (pseudo self-collected) were obtained from 319 women. One was applied to an iFTA Card (FTA) then the brush placed in liquid-based medium (LSELF); the other was applied to a new solid media: POI card (POI). The clinical performance of Cobas4800 assay using the three aforementioned specimens was compared to direct collected endocervical specimens in liquid media (LDOC). Results The overall agreements of HrHPV detection were 84.2% (LSELF vs. LDOC), 81.0% (FTA vs. LDOC), and 82.3% (POI vs. LDOC). LSELF, FTA and POI identified 98.0%, 79.6%, and 97.5% positive cases of LDOC. Sensitivity to identify CIN2+ were 98.4% (LSELF), 73.8% (FTA), 95.1% (POI), and 93.4% (LDOC) respectively. FTA had 78.1% and 90.4% agreement with the LSELF samples for all HrHPV and HPV16/18 detection respectively, while POI had 91.6% for both. Conclusions Cobas4800 HPV test combined with cervico-vaginal specimens applied to both liquid media and POI solid card are accurate to detect HrHPV infection and high-grade cervical lesions as compared with direct endocervical samples in liquid media. PMID:26828360

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-05-01

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

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2014-08-01

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

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

    PubMed

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

    2015-01-01

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

  14. 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

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

    PubMed Central

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

    2000-01-01

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

  16. 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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    1987-11-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-06-01

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

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

    PubMed

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

    1999-01-01

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

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

    PubMed

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

    2012-07-01

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

  3. Parallel comparison of accuracy of API 20E, Vitek GNI, MicroScan Walk/Away Rapid ID, and Becton Dickinson Cobas Micro ID-E/NF for identification of members of the family Enterobacteriaceae and common gram-negative, non-glucose-fermenting bacilli.

    PubMed

    O'Hara, C M; Tenover, F C; Miller, J M

    1993-12-01

    We compared the API 20E (21 h) (API; bioMérieux Vitek, Hazelwood, Mo.), the Vitek GNI card (4 to 18 h) (Vitek; bioMérieux Vitek), the identification portion of the MicroScan Walk/Away Rapid Neg Combo 3 panel (2 h) (W/A; Baxter Diagnostics, Inc., West Sacramento, Calif.), and the Becton Dickinson Cobas Micro ID-E/NF rotor (21 h) (Cobas; Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.), versus conventional biochemicals for their abilities to identify accurately 252 strains of biochemically typical and atypical members of the family Enterobacteriaceae and common non-glucose-fermenting gram-negative bacilli. All strains used were included in the data base of each product. At the end of the initial incubation, 194 (77.0%), 213 (84.5%), 198 (78.6%), and 192 (76.2%) strains were correct to the genus and species levels with the API, Vitek, W/A, and Cobas systems, respectively. After additional biochemical tests were performed, as directed by each manufacturer's protocol, the numbers of strains correctly identified to the genus and species levels were 241 (95.6%), 234 (92.8%), 243 (96.4%), and 230 (91.3%) with the four systems, respectively. The errors were random in all systems, with the exception of two atypical Salmonella enteritidis strains, each of which was misidentified by three systems. After the initial recommended incubation period, both API and Cobas were significantly less accurate than Vitek (Yates' corrected P < 0.05). No significant differences were noted between the results of Vitek and W/A or between the results of API and W/A. After additional tests were completed, Cobas was significantly less accurate than W/A (P < 0.05) but was equal in accuracy to Vitek and API. API, Vitek, and W/A were equal in accuracy after these same additional tests. All four systems were significantly more accurate after additional biochemical testing than after the initial reporting period (194 of 252 versus 241 of 252 for API, 213 of 252 versus 234 of 252 for Vitek

  4. Parallel comparison of accuracy of API 20E, Vitek GNI, MicroScan Walk/Away Rapid ID, and Becton Dickinson Cobas Micro ID-E/NF for identification of members of the family Enterobacteriaceae and common gram-negative, non-glucose-fermenting bacilli.

    PubMed Central

    O'Hara, C M; Tenover, F C; Miller, J M

    1993-01-01

    We compared the API 20E (21 h) (API; bioMérieux Vitek, Hazelwood, Mo.), the Vitek GNI card (4 to 18 h) (Vitek; bioMérieux Vitek), the identification portion of the MicroScan Walk/Away Rapid Neg Combo 3 panel (2 h) (W/A; Baxter Diagnostics, Inc., West Sacramento, Calif.), and the Becton Dickinson Cobas Micro ID-E/NF rotor (21 h) (Cobas; Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.), versus conventional biochemicals for their abilities to identify accurately 252 strains of biochemically typical and atypical members of the family Enterobacteriaceae and common non-glucose-fermenting gram-negative bacilli. All strains used were included in the data base of each product. At the end of the initial incubation, 194 (77.0%), 213 (84.5%), 198 (78.6%), and 192 (76.2%) strains were correct to the genus and species levels with the API, Vitek, W/A, and Cobas systems, respectively. After additional biochemical tests were performed, as directed by each manufacturer's protocol, the numbers of strains correctly identified to the genus and species levels were 241 (95.6%), 234 (92.8%), 243 (96.4%), and 230 (91.3%) with the four systems, respectively. The errors were random in all systems, with the exception of two atypical Salmonella enteritidis strains, each of which was misidentified by three systems. After the initial recommended incubation period, both API and Cobas were significantly less accurate than Vitek (Yates' corrected P < 0.05). No significant differences were noted between the results of Vitek and W/A or between the results of API and W/A. After additional tests were completed, Cobas was significantly less accurate than W/A (P < 0.05) but was equal in accuracy to Vitek and API. API, Vitek, and W/A were equal in accuracy after these same additional tests. All four systems were significantly more accurate after additional biochemical testing than after the initial reporting period (194 of 252 versus 241 of 252 for API, 213 of 252 versus 234 of 252 for Vitek

  5. 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

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

    PubMed

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

    2015-12-09

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

  7. 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 Central

    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, I2 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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2000-11-01

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

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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.

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

    PubMed Central

    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

    2015-01-01

    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

  16. 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…

  17. 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…

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

    PubMed Central

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

    2016-01-01

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

  19. Does the cognitive architecture of simplex and multiplex ASD families differ?

    PubMed

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

    2016-02-01

    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 profiles, but within-family contrasts were highest in SPX families, suggesting SPX-MPX stratification may help parse etiological heterogeneity of ASD. Unaffected siblings (regardless SPX or MPX) were mostly unimpaired, suggesting that cognitive problems may be part of the defining features of ASD, rather than being an endophenotypic trait. Except for affective prosody, which appeared to be the most sensitive cognitive marker for detecting familial risk for ASD. PMID:26340958

  20. Does the cognitive architecture of simplex and multiplex ASD families differ?

    PubMed

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

    2016-02-01

    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 profiles, but within-family contrasts were highest in SPX families, suggesting SPX-MPX stratification may help parse etiological heterogeneity of ASD. Unaffected siblings (regardless SPX or MPX) were mostly unimpaired, suggesting that cognitive problems may be part of the defining features of ASD, rather than being an endophenotypic trait. Except for affective prosody, which appeared to be the most sensitive cognitive marker for detecting familial risk for ASD.

  1. 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.

  2. Orientation and effects of mastoparan X on phospholipid bicelles.

    PubMed Central

    Whiles, J A; Brasseur, R; Glover, K J; Melacini, G; Komives, E A; Vold, R R

    2001-01-01

    Mastoparan X (MPX: INWKGIAAMAKKLL-NH2) belongs to a family of ionophoric peptides found in wasp venom. Upon binding to the membrane, MPX increases the cell's permeability to cations leading to a disruption in the electrolyte balance and cell lysis. This process is thought to occur either through a membrane-thinning mechanism, where the peptide resides on the membrane surface thereby disrupting lipid packing, or through formation of an oligomeric pore. To address this issue, we have used both high-resolution and solid-state 2H NMR techniques to study the structure and orientation of MPX when associated with bicelles. NOESY and chemical shift analysis showed that in bicelles, MPX formed a well-structured amphipathic alpha-helix. In zwitterionic bicelles, the helical axis was found to rest generally perpendicular to the membrane normal, which could be consistent with the "carpet" mechanism for lytic activity. In anionic bicelles, on the other hand, the helical axis was generally parallel to the membrane normal, which is more consistent with the pore model for lytic activity. In addition, MPX caused significant disruption in lipid packing of the negatively charged phospholipids. Taken together, these results show that MPX associates differently with zwitterionic membranes, where it rests parallel to the surface, compared with negatively charged membranes, where it penetrates longitudinally. PMID:11159401

  3. 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

  4. 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

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

    SciTech Connect

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

    2008-02-15

    A multiwire proportional x-ray (MPX) detector is used on the TCV tokamak (Tokamak a 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 3-30 keV range with a radial resolution of about 5 mm - 1% of plasma diameter - and a frequency bandwidth of 50 kHz. 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.

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

    PubMed

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

    2012-08-01

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

  7. 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

  8. 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

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

    PubMed

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

    2015-10-01

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

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

    PubMed

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

    2011-10-01

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

  11. 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.

  12. 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…

  13. 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…

  14. 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.

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

    PubMed

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

    2014-07-01

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

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

    PubMed Central

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

    2016-01-01

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

  17. 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

  18. 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

  19. 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

  20. 1st HPV Test for Use with Preservative Fluid

    MedlinePlus

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

  1. Molecular Property eXplorer: a novel approach to visualizing SAR using tree-maps and heatmaps.

    PubMed

    Kibbey, Christopher; Calvet, Alain

    2005-01-01

    The tremendous increase in chemical structure and biological activity data brought about through combinatorial chemistry and high-throughput screening technologies has created the need for sophisticated graphical tools for visualizing and exploring structure-activity data. Visualization plays an important role in exploring and understanding relationships within such multidimensional data sets. Many chemoinformatics software applications apply standard clustering techniques to organize structure-activity data, but they differ significantly in their approaches to visualizing clustered data. Molecular Property eXplorer (MPX) is unique in its presentation of clustered data in the form of heatmaps and tree-maps. MPX employs agglomerative hierarchical clustering to organize data on the basis of the similarity between 2D chemical structures or similarity across a predefined profile of biological assay values. Visualization of hierarchical clusters as tree-maps and heatmaps provides simultaneous representation of cluster members along with their associated assay values. Tree-maps convey both the spatial relationship among cluster members and the value of a single property (activity) associated with each member. Heatmaps provide visualization of the cluster members across an activity profile. Unlike a tree-map, however, a heatmap does not convey the spatial relationship between cluster members. MPX seamlessly integrates tree-maps and heatmaps to represent multidimensional structure-activity data in a visually intuitive manner. In addition, MPX provides tools for clustering data on the basis of chemical structure or activity profile, displaying 2D chemical structures, and querying the data based over a specified activity range, or set of chemical structure criteria (e.g., Tanimoto similarity, substructure match, and "R-group" analysis).

  2. Effect of the aspartic acid D2 on the affinity of Polybia-MP1 to anionic lipid vesicles.

    PubMed

    Leite, Natália Bueno; Dos Santos Alvares, Dayane; de Souza, Bibiana Monson; Palma, Mário Sérgio; Ruggiero Neto, João

    2014-05-01

    Polybia-MP1 (IDWKKLLDAAKQIL-NH2), a helical peptide extracted from the venom of a Brazilian wasp, has broad-spectrum antimicrobial activities without being hemolytic or cytotoxic. This peptide has also displayed anticancer activity against cancer cell cultures. Despite its high selectivity, MP1 has an unusual low net charge (Q = +2). The aspartic residue (D2) in the N-terminal region plays an important role in its affinity and selectivity; its substitution by asparagine (D2N mutant) led to a less selective peptide. Aiming to explore the importance of this residue for the peptides' affinity, we compared the zwitterionic and anionic vesicle adsorption activity of Polybia-MP1 versus its D2N mutant and also mastoparan X (MPX). The adsorption, electrostatic, and conformational free energies were assessed by circular dichroism (CD) and fluorescence titrations using large unilamellar vesicles (LUVs) at the same conditions in association with measurement of the zeta potential of LUVs in the presence of the peptides. The adsorption free energies of the peptides, determined from the partition coefficients, indicated higher affinity of MP1 to anionic vesicles compared with the D2N mutant and MPX. The electrostatic and conformational free energies of MP1 in anionic vesicles are less favorable than those found for the D2N mutant and MPX. Therefore, the highest affinity of MP1 to anionic vesicles is likely due to other energetic contributions. The presence of D2 in MP1 makes these energetic components 1.2 and 1.5 kcal/mol more favorable compared with the D2N mutant and MPX, respectively.

  3. MASTER-ICATE constraints on the outburst time of OGLE-2012-NOVA-002

    NASA Astrophysics Data System (ADS)

    Levato, H.; Saffe, C.; Mallamaci, C.; Lopez, C.; Denisenko, F. Podest D.; Gorbovskoy, E.; Lipunov, V.; Balanutsa, P.; Tiurina, N.; Kornilov, V.; Belinski, A.; Shatskiy, N.; Chazov, V.; Kuznetsov, A.; Zimnukhov, D.; Krushinsky, V.; Zalozhnih, I.; Popov, A.; Bourdanov, A.; Punanova, A.; Ivanov, K.; Yazev, S.; Budnev, N.; Konstantinov, E.; Chuvalaev, O.; Poleshchuk, V.; Gress, O.; Parkhomenko, A.; Tlatov, A.; Dormidontov, D.; Senik, V.; Yurkov, V.; Sergienko, Y.; Varda, D.; Sinyakov, E.; Shumkov, V.; Shurpakov, S.; Podvorotny, P.

    2012-10-01

    MASTER-ICATE very wide field camera (72-mm f/1.2 lens + 11 Mpx CCD) located at Observatorio Astronomico Felix Aguilar (OAFA) near San Juan, Argentina, has observed the position of possible Nova OGLE-2012-NOVA-002 reported by L. Wyrzykowski et al. (ATel #4483) several times before 2012 May 20 and then again after 2012 July 03. MASTER-WFC is continuously imaging the areas of sky (24x16 sq. deg. field of view) with 5-sec unfiltered exposures.

  4. 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.

  5. 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

  6. 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

  7. Comparison of West African and Congo Basin Monkeypox Viruses in BALB/c and C57BL/6 Mice

    PubMed Central

    Hutson, Christina L.; Abel, Jason A.; Carroll, Darin S.; Olson, Victoria A.; Braden, Zachary H.; Hughes, Christine M.; Dillon, Michael; Hopkins, Consuelo; Karem, Kevin L.; Damon, Inger K.; Osorio, Jorge E.

    2010-01-01

    Although monkeypox virus (MPXV) studies in wild rodents and non-human primates have generated important knowledge regarding MPXV pathogenesis and inferences about disease transmission, it might be easier to dissect the importance of virulence factors and correlates of protection to MPXV in an inbred mouse model. Herein, we compared the two clades of MPXV via two routes of infection in the BALB/c and C57BL/6 inbred mice strains. Our studies show that similar to previous animal studies, the Congo Basin strain of MPXV was more virulent than West African MPXV in both mouse strains as evidenced by clinical signs. Although animals did not develop lesions as seen in human MPX infections, localized signs were apparent with the foot pad route of inoculation, primarily in the form of edema at the site of inoculation; while the Congo Basin intranasal route of infection led to generalized symptoms, primarily weight loss. We have determined that future studies with MPXV and laboratory mice would be very beneficial in understanding the pathogenesis of MPXV, in particular if used in in vivo imaging studies. Although this mouse model may not suffice as a model of human MPX disease, with an appropriate inbred mouse model, we can unravel many unknown aspects of MPX pathogenesis, including virulence factors, disease progression in rodent hosts, and viral shedding from infected animals. In addition, such a model can be utilized to test antivirals and the next generation of orthopoxvirus vaccines for their ability to alter the course of disease. PMID:20111702

  8. 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.

  9. Comparison of human immunodeficiency virus assays in window phase and elite controller samples: viral load distribution and implications for transmission risk

    PubMed Central

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

    2016-01-01

    BACKGROUND After 3 years of individual-donation nucleic acid test (ID-NAT) screening by the South African National Blood Service (SANBS), a repository of 73 human immunodeficiency virus antibody (anti-HIV)-negative window period (WP)-yield samples and 28 anti-HIV–positive, HIV-RNA–negative elite controllers (ECs) became available for comparison of a p24 antigen (p24 Ag) assay (Innogenetics), two viral load assays (Siemens branch DNA [bDNA] 3.0 and Abbott real-time polymerase chain reaction [RT-PCR]), and three triplex NAT assays (Novartis Diagnostics Ultrio and Ultrio-Plus and Roche TaqScreen) by replicate testing of dilutions. STUDY DESIGN AND METHODS Viral loads were assessed by bDNA and RT-PCR assays and if below 100 copies (cps)/mL, by Ultrio limiting dilution probit analysis. The probability of virus transmission by WP and EC donations was estimated for different levels of the 50% minimum infectious dose (ID50) using Poisson distribution statistics. RESULTS The equal distribution of WP donations plotted by log HIV-RNA levels indicated a random appearance of donors in the ramp-up phase. The HIV p24 Ag assay detected 45% of WP samples and the cutoff crossing point was estimated at 8140 (bDNA)/ 22,710 (RT-PCR) cps/mL. On replicate retesting of 40 HIV p24 Ag–negative ID-NAT WP-yield samples Ultrio minipool (MP)8, Ultrio-Plus MP8, and TaqScreen MP6 detected 79, 81, and 78%, respectively. Modeling with an estimated ID50 of 31.6 virions/RBC indicated that 15% of p24 Ag–negative ID-NAT WP-yield donations would have transmitted HIV if MP6–8 NAT had been used. Only 2% of RBC transfusions from ECs are estimated to be infectious with a worst-case ID50 estimate of 316 virions. CONCLUSION Our analysis of viremia and infectivity of WP and EC donations enables comparison of the efficacy of NAT options in preventing HIV transmission risk. PMID:23445273

  10. A mathematical approach to estimate the efficacy of individual-donation and minipool nucleic acid amplification test options in preventing transmission risk by window period and occult hepatitis B virus infections

    PubMed Central

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

    2016-01-01

    BACKGROUND Sensitivity data from a head-to-head comparison study in South Africa were used to compare the efficacy of the Ultrio Plus assay in individual-donation (ID) and minipool (MP)4 and MP8 formats with that of TaqScreen MP6 in preventing hepatitis B virus (HBV) transmission risk. STUDY DESIGN AND METHODS The replicate nucleic acid test (NAT) results on 106 HBV NAT (Ultrio)-yield samples and 29 HBV DNA (Ultrio)-negative, hepatitis B surface antigen (HBsAg)-positive samples were used to determine the viral load in copies/mL against the Eurohep HBV standard by probit analysis. Random viral load distributions were established in 32 pre-HBsAg window period (WP), 15 post-HBsAg WP, and 56 occult HBV infection (OBI) donations. Regression analysis of log viral load and Poisson distribution statistics of infectious HBV particles in blood components was used to predict infectivity and efficacy of NAT options in removing HBV transmission risk. RESULTS For red blood cell transfusions (20 mL of plasma), the modeling predicted an Ultrio Plus ID-NAT efficacy of 68 and 83% in removing WP and (antibody to hepatitis B surface antigen–negative) OBI transmission risk, respectively, compared to 52 and 49% by TaqScreen MP6. For 200 mL of fresh-frozen plasma the estimated efficacy levels by these ID- and MP6-NAT options reduced to 57 and 44% for WP and to 67 and 34% for OBI donations, respectively. CONCLUSION The efficacy of the currently available commercial NAT systems in reducing HBV transmission risk is mainly driven by the pool size and the transfusion plasma volume. The modeled OBI transmission risk and NAT efficacy levels were in line with those recently reported in three lookback studies and give more insight in the incremental safety provided by HBsAg and antibody to hepatitis B core antigen testing of ID-NAT screened blood. PMID:24749834

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

    PubMed

    Bornand, V

    1992-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2001-01-01

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

  14. Automated determination of angiotensin-converting enzyme in serum.

    PubMed

    Peters, R H; Golbach, A J; van den Bergh, F A

    1987-07-01

    This is an adaptation of the Fujirebio "ACEcolor" kit for automated measurement of angiotensin-converting enzyme (EC 3.4.15.1) in serum with the Cobas Fara centrifugal analyzer. The linear range extends to an activity of 110 U/L. Results obtained by the present method and by the manual method were identical, and correlated closely (r = 0.983) with those by Cushman's modified method. The reference interval for 77 adult blood-bank donors was 9-25 U/L (mean 17, SD 4 U/L). Within-run and between-run CVs are 1.7 and 4.0%, respectively. The present method permits rapid, precise, and economical measurement of the enzyme and allows users of a Cobas Fara centrifugal analyzer to introduce a fully automated assay for angiotensin-converting enzyme into their clinical laboratory.

  15. Early detection of Mycobacterium tuberculosis complex in BACTEC MGIT cultures using nucleic acid amplification.

    PubMed

    Lin, S Y; Hwang, S C; Yang, Y C; Wang, C F; Chen, Y H; Chen, T C; Lu, P L

    2016-06-01

    We evaluated the application of nucleic acid amplification (NAA) in liquid cultures for the early detection of Mycobacterium tuberculosis. The Cobas TaqMan MTB test, IS6110 real-time PCR, and hsp65 PCR-restriction fragment length polymorphism (RFLP) analysis were used to detect BACTEC MGIT 960 (MGIT) cultures on days 3, 5, 7, and 14. The procedure was initially tested with a reference strain, H37Rv (ATCC 27294). Subsequently, 200 clinical specimens, including 150 Acid Fast bacillus (AFB) smear-positive and 50 AFB smear-negative samples, were examined. The Cobas TaqMan MTB test and IS6110-based PCR analysis were able to detect M. tuberculosis after 1 day when the inoculum of H37Rv was >3 x 10(-2) CFU/ml. After a 5-day incubation in the MGIT system, all three NAA assays had a positive detection regardless of the inoculum size. After a 1-day incubation of the clinical specimens in the MGIT system, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the Cobas TaqMan MTB assay were 70.2%, 100%, 100%, and 82.3% respectively. For IS6110-based PCR analysis, these values were 63.1%, 100%, 100%, and 78.9%, and were 88.1%, 100%, 100%, and 92.1% respectively for hsp65 PCR-RFLP analysis. After a 3-day incubation, the specificity and PPV were 100% for all three NAA tests; the Cobas TaqMan MTB assay had the best sensitivity (97.6%) and NPV (98.3%). The sensitivity, specificity, PPV, and NPV for conventional culture analysis were 98.8%, 100%, 100%, and 99.1%. Thus, NAA may be useful for the early detection of M. tuberculosis after 3 days in MGIT.

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

    PubMed

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

    2016-06-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2014-07-01

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

  19. 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

  20. 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.

  1. 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, A.; De Sanctis, M. C.; Carrorro, F. G.; Ammannito, E.; Williams, D. A.; Mest, S. C.; Buczkowski, D.; Preusker, F.; Jaumann, R.; Roatsch, T.; Scully, J. E. C.; Raymond, C. A.; Russell, C. T.

    2015-12-01

    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 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  3. 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.

  4. 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

  5. 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

  6. 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

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

    PubMed

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

    2014-06-01

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

  8. 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

  9. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  12. 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

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

    PubMed Central

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

    2016-01-01

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

  14. Analytical performance of a PCR assay for the detection of KRAS mutations (codons 12/13 and 61) in formalin-fixed paraffin-embedded tissue samples of colorectal carcinoma.

    PubMed

    Lee, Sung; Brophy, Victoria H; Cao, Jianli; Velez, Margot; Hoeppner, Corey; Soviero, Stephen; Lawrence, H Jeffrey

    2012-02-01

    KRAS mutation testing is mandatory before prescribing anti-epidermal growth factor monoclonal antibodies in the treatment of advanced colorectal cancer. We describe the performance of a TaqMelt polymerase chain reaction (PCR) assay-the cobas® KRAS Mutation Test-designed to detect 19 mutations in codons 12, 13, and 61. The limit of detection was determined using DNA blends from cell lines, plasmids, and formalin-fixed paraffin-embedded tissue specimens. Assay performance was compared to Sanger sequencing using a panel of 188 specimens. Discordant specimens were subjected to next generation pyrosequencing (454). Assay repeatability was assessed using a panel of six specimens. A >95% correct mutation call rate was obtained in all specimen types with ~5% mutant alleles at DNA inputs of 0.8-6.3 ng per PCR reaction; 100% detection rate was observed at the recommended DNA input of 50 ng. The positive percent agreement with Sanger was 97.5% (79/81) for codons 12/13 and 85.7% (6/7) for codon 61. Negative percent agreement was 94.4% (101/107) for codon 12/13 and 99.4% (180/181) for codon 61. Nine of 10 discordant specimens yielded 454 results consistent with the cobas® results. With repeated testing, the assay showed a correct call rate of 100% (192/192) for all operators, instruments, reagent lots, and days tested. The cobas® test detects KRAS mutations in codons 12, 13, and 61 at a limit of detection of <5%. The PCR assay was more sensitive and specific than Sanger sequencing, and performance was highly reproducible. Test performance was not influenced by various endogenous interfering substances or common gut microbes.

  15. 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.

  16. 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.

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

    PubMed

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

    2009-05-14

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

  18. 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.

  19. 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

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

    PubMed

    Stefas, Ilias; Tigrett, Sylvia; 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 ApoH and

  1. 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

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

    PubMed

    Samardzic, Janko; 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). PMID:27635396

  3. 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

  4. 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).

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

    PubMed

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

    2013-03-01

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

  6. 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). PMID:27635396

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Ac-H-11 Sintana is one of 15 geologic mapping quadrangles on the dwarf planet Ceres, which are used to identify geologic units and features. The quadrangle is located in the southern hemisphere of Ceres between 21-66°S and 0-90°E Results of our geologic mapping will contribute to the understanding of the geologic history and surface-forming processes of this quadrangle. The dominant feature is an alignment of three craters in the topographically lower center of the quadrangle. These craters illustrate the diversity of crater forms, inner structures and symmetries, such as terraced walls and elongated central structures. There are numerous central peaks inside craters of different sizes. The largest craters in the quadrangle reveal more complex inner structures and flat floors. Great variation in the slopes of crater walls and degradation states of crater rims can be found, as well as mass wasting features, such as landslides. Several linear structures are evident, which will be distinguished and analyzed. Possible explanations for these structures include secondary crater chains and pit chains. A positive topography feature is found to the south of the Sintana crater. Examining aforementioned features will help to assess surface composition and local tectonics. Different ratios of color-filter images suggest a major geological boundary in the NE of the quadrangle. Visible and infrared spectroscopic data will contribute to the compositional interpretation. The mapping is based on a stereo digital terrain model, clear-filter images and images of different color-filter ratios derived from the Framing Camera onboard the Dawn spacecraft. To date, resolutions of 1.3 km/px from the approach phase in Spring 2015, and 415 m/px from the Survey Orbit, in June 2015, are used in geological mapping. Higher resolution images will be obtained during the High Altitude Mapping Orbit (140 m/px) in Fall 2015, followed by the Low Altitude Mapping Orbit (35 m/px) in the beginning of

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  11. 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

  12. 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.

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  17. 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

  18. Attenuation of monkeypox virus by deletion of genomic regions

    USGS Publications Warehouse

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

    2015-01-01

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

  19. 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

  20. 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

  1. 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}.

  2. 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

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

    PubMed

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

    2012-05-01

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

  4. 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

  5. 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

  6. 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

  7. False-negative HIV-1 polymerase chain reaction in a 15-month-old boy with HIV-1 subtype C infection.

    PubMed

    Oladokun, R; Korsman, S; Ndabambi, N; Hsiao, N; Hans, L; Williamson, C; Abrahams, M-R; Eley, B

    2015-10-01

    Polymerase chain reaction (PCR) testing is the gold standard for determining the HIV status in children <18 months of age. However, when clinical manifestations are not consistent with laboratory results, additional investigation is required. We report a 15-month-old HIV-exposed boy referred to our hospital after he had been admitted several times for infectious diseases. A rapid antibody test on the child was positive, while routine diagnostic HIV PCRs using the Roche COBAS Ampliprep/COBAS TaqMan HIV Qual Test were negative at 6 weeks, 6 months, 7 months and 15 months. In addition, the same PCR test performed on the HIV-infected mother was also negative. Alternative PCR and viral load assays using different primer sets detected HIV RNA or proviral DNA in both child and mother. Gag sequences from the child and his mother classified both infections as HIV-1 subtype C, with very rare mutations that may have resulted in PCR assay primer/probe mismatch. Consequently, the child was commenced on antiretroviral therapy and made a remarkable recovery. These findings indicate that more reliable PCR assays capable of detecting a wide range of HIV subtypes are desirable to circumvent the clinical problems created by false-negative PCR results. PMID:26636158

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  9. 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.

  10. Adaptation of methods for glutamate dehydrogenase and alcohol dehydrogenase activities to a centrifugal analyser: assessment of their clinical use in anoxic states of the liver.

    PubMed Central

    Shephard, M D; Penberthy, L A; Berry, M N

    1987-01-01

    Sensitive, precise, and rapid methods for the measurement of alcohol dehydrogenase (ADH) and glutamate dehydrogenase (GDH) were developed on the Cobas Bio centrifugal analyser. The optimal pH for ADH in caucasians was 9.8. Non-linearity of ADH enzyme activity was observed when samples were diluted in saline; linearity was restored when inactivated serum was used as diluent. ADH was shown to be a sensitive index of liver anoxia due to cardiorespiratory disturbance (clinical sensitivity 90%) and generalised anoxia. GDH exhibited sensitivity equal to that of alanine aminotransferase (ALT) but was inferior to gamma-glutamyltransferase (GGT) in the detection of specific liver disease. Both ADH and GDH were sensitive indicators of alcoholic liver disease. PMID:2890662

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

    PubMed

    Lanevschi, Anne; Kramer, John W.

    1996-01-01

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

  12. 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

  13. '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.

  14. 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).

  15. Evaluation of fully automated assays for the detection of Rubella IgM and IgG antibodies by the Elecsys(®) immunoassay system.

    PubMed

    van Helden, Josef; Grangeot-Keros, Liliane; Vauloup-Fellous, Christelle; Vleminckx, Renaud; Masset, Frédéric; Revello, Maria-Grazia

    2014-04-01

    Screening for acute rubella infection in pregnancy is an important element of antenatal care. This study compared the sensitivity, specificity and reproducibility of two new, fully automated Elecsys(®) Rubella IgM and IgG immunoassays designed for the Elecsys 2010, Modular Analytics E170, COBAS e-411 and COBAS e-601 and e602 analytical platforms, with current assays using serum from patients with primary rubella infections, vaccinated patients, patients with potentially cross-reacting infections and on routine samples in clinical laboratories in France, Germany and Italy. Both assays showed good within-run and within-laboratory precision. A sensitivity of 79.8-96.0% was demonstrated for Elecsys IgM in primary, early acute infection, consistent with existing assays. In samples obtained from routine antenatal screening, the Elecsys Rubella IgM assay revealed high specificity (98.7-99.0%). A significantly (p<0.0001) lower reactivity was demonstrated in samples from previously infected patients where acute rubella infection was excluded, and the incidence of false positives in patients with potentially cross-reacting infections was lower with Elecsys Rubella IgM compared with other. The Elecsys Rubella IgG assay exhibited a relative sensitivity of 99.9-100.0% and specificity of 97.4-100.0% in samples from routine antenatal screening. The Elecsys Rubella IgM and IgG assays allow convenient, rapid and reliable determination of anti-rubella antibodies. Sensitivity, specificity and reproducibility were comparable with existing assay systems. Assay results were available in approximately half the time required for currently employed methods and the assays are compatible with widely used analytical platforms.

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

    PubMed Central

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

    2015-01-01

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

  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. HPV infection-associated anogenital cyto-colpo-histological findings and molecular typing in HIV-positive women.

    PubMed

    Tso, F K; Rodrigues, C L L; Levi, J E; Mattosinho de Castro Ferraz, M G; Speck, N M G; Ribalta, J C L

    2015-12-21

    HIV and human papillomavirus (HPV) coinfection is increasing, especially in the anal canal (AC) and cervico-vaginal regions. We identified anal epithelium abnormalities related to high-risk HPV (HR-HPV) lesions in the lower genital tracts (LGTs) of HIV-positive women, described the HPV genotypes identified, and assessed the expression of E6/E7 oncogenes in coinfected patients. Ninety-eight women were enrolled in groups combining HIV status and presence or absence of HPV in the LGT. Anal and cervical smears were collected for cytology and HR-HPV assays using Cobas(®) and/or PapilloCheck(®). Samples with highly oncogenic HPV genotypes were confirmed by NucliSENS EasyQ(®). Forty-two HIV-positive (25-52; mean age 39.5) and 56 HIV-negative (18-58; mean age 35.7) patients were included. E2 and C1 groups presented AC alterations (P = 0.002); altered images for high-resolution anoscopy were higher in E1 and C2 (P < 0.001). Of the 29 women with alterations, 41.38% were HIV-negative and 58.62% were HIV-positive (P < 0.001). HIV-positive patients accounted for 29% of the anal high-grade squamous intraepithelial lesions (P = 0.015). The Cobas(®) positive result frequency was higher in three AC groups than in the other groups. There was variation in the number of HPV types in the cervico-vaginal samples among the study groups (P < 0.001). Anal cytology and anoscopy showed more altered findings in HIV-positive patients with HPV in the LGT. HR-HPV anal infections by various genotypes are common and are associated with cervical infections in HIV-positive patients. E6/E7 expression is apparently more common in the AC of HIV-positive women.

  19. 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

  20. 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 [

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

    PubMed

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

    2014-06-01

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

  2. Functional Genomic, Biochemical, and Genetic Characterization of the Salmonella pduO Gene, an ATP:Cob(I)alamin Adenosyltransferase Gene†

    PubMed Central

    Johnson, Celeste L. V.; Pechonick, Edith; Park, Sanghee D.; Havemann, Gregory D.; Leal, Nicole A.; Bobik, Thomas A.

    2001-01-01

    Salmonella enterica degrades 1,2-propanediol by a pathway dependent on coenzyme B12 (adenosylcobalamin [AdoCb1]). Previous studies showed that 1,2-propanediol utilization (pdu) genes include those for the conversion of inactive cobalamins, such as vitamin B12, to AdoCbl. However, the specific genes involved were not identified. Here we show that the pduO gene encodes a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is apparently the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation. Genetic tests showed that the function of the pduO gene was partially replaced by the cobA gene (a known ATP:corrinoid adenosyltransferase) but that optimal growth of S. enterica on 1,2-propanediol required a functional pduO gene. Growth studies showed that cobA pduO double mutants were unable to grow on 1,2-propanediol minimal medium supplemented with vitamin B12 but were capable of growth on similar medium supplemented with AdoCbl. The pduO gene was cloned into a T7 expression vector. The PduO protein was overexpressed, partially purified, and, using an improved assay procedure, shown to have cob(I)alamin adenosyltransferase activity. Analysis of the genomic context of genes encoding PduO and related proteins indicated that particular adenosyltransferases tend to be specialized for particular AdoCbl-dependent enzymes or for the de novo synthesis of AdoCbl. Such analyses also indicated that PduO is a bifunctional enzyme. The possibility that genes of unknown function proximal to adenosyltransferase homologues represent previously unidentified AdoCbl-dependent enzymes is discussed. PMID:11160088

  3. 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 [

  4. Investigation of sulfur-tolerant catalysts for selective synthesis of hydrocarbon liquids from coal-derived gases. Quarterly technical progress report, September 18-December 18, 1979

    SciTech Connect

    Bartholomew, C.H.

    1980-01-10

    Three catalysts were prepared: 3% Co/SiO/sub 2/, 3% Fe/SiO/sub 2/, and a 10% cobalt boride on alumina designated respectively as Co-S-101, Fe-S-100, and CoB-A-101. These catalysts were prepared in the following manner: analytically pure Co(NO/sub 3/)/sub 2/ . 6H/sub 2/O and Fe(NO/sub 3/)/sub 3/ . 9H/sub 2/O salts and commercial Cab-O-Sil silica were used to prepare the 3% silica-supported cobalt and iron catalysts. Samples were prepared by simple impregnation to incipient wetness with aqueous metal salt solutions. Several impregnations were necessary to ensure a uniform deposition of the metal salt, each followed by intermediate drying. After the final impregnation, the catalysts were dried in an oven at 355 to 375/sup 0/K for 24 h. These dried samples were then bulk reduced in flowing hydrogen at a space velocity of 2000 h/sup -1/. The temperature was raised during reduction at a rate of 1.5 to 2.0 K/min until 725/sup 0/K was attained, then held for 12 h. The reduced catalysts were next passivated with 1% air in nitrogen and crushed to a fine powder for use. The cobalt boride on alumina catalyst (CoB-A-101) was prepared under an N/sub 2/ blanket in a sealed reaction vessel to avoid the formation of boron oxide, which cannot be reduced in flowing H/sub 2/ even at 675/sup 0/K. Enough alumina was used so that if all the cobalt adhered to the support 18 wt % metal loading would result. From previous experience we estimate a loading of about 10 wt %; this is currently being checked by chemical analysis.

  5. Evaluation of Hologic Aptima HIV-1 Quant Dx Assay on the Panther System on HIV Subtypes.

    PubMed

    Manak, Mark M; Hack, Holly R; Nair, Sangeetha V; Worlock, Andrew; Malia, Jennifer A; Peel, Sheila A; Jagodzinski, Linda L

    2016-10-01

    Quantitation of the HIV-1 viral load in plasma is the current standard of care for clinical monitoring of HIV-infected individuals undergoing antiretroviral therapy. This study evaluated the analytical and clinical performances of the Aptima HIV-1 Quant Dx assay (Hologic, San Diego, CA) for monitoring viral load by using 277 well-characterized subtype samples, including 171 cultured virus isolates and 106 plasma samples from 35 countries, representing all major HIV subtypes, recombinants, and circulating recombinant forms (CRFs) currently in circulation worldwide. Linearity of the Aptima assay was tested on each of 6 major HIV-1 subtypes (A, B, C, D, CRF01_AE, and CRF02_AG) and demonstrated an R(2) value of ≥0.996. The performance of the Aptima assay was also compared to those of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 v.2 (CAP/CTM) and Abbott m2000 RealTime HIV-1 (RealTime) assays on all subtype samples. The Aptima assay values averaged 0.21 log higher than the CAP/CTM values and 0.30 log higher than the RealTime values, and the values were >0.4 log higher than CAP/CTM values for subtypes F and G and than RealTime values for subtypes C, F, and G and CRF02_AG. Two samples demonstrated results with >1-log differences from RealTime results. When the data were adjusted by the average difference, 94.9% and 87.0% of Aptima results fell within 0.5 log of the CAP/CTM and RealTime results, respectively. The linearity and accuracy of the Aptima assay in correctly quantitating all major HIV-1 subtypes, coupled with the completely automated format and high throughput of the Panther system, make this system well suited for reliable measurement of viral load in the clinical laboratory. PMID:27510829

  6. 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.

  7. 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

  8. 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

  9. Evaluation of Hologic Aptima HIV-1 Quant Dx Assay on the Panther System on HIV Subtypes.

    PubMed

    Manak, Mark M; Hack, Holly R; Nair, Sangeetha V; Worlock, Andrew; Malia, Jennifer A; Peel, Sheila A; Jagodzinski, Linda L

    2016-10-01

    Quantitation of the HIV-1 viral load in plasma is the current standard of care for clinical monitoring of HIV-infected individuals undergoing antiretroviral therapy. This study evaluated the analytical and clinical performances of the Aptima HIV-1 Quant Dx assay (Hologic, San Diego, CA) for monitoring viral load by using 277 well-characterized subtype samples, including 171 cultured virus isolates and 106 plasma samples from 35 countries, representing all major HIV subtypes, recombinants, and circulating recombinant forms (CRFs) currently in circulation worldwide. Linearity of the Aptima assay was tested on each of 6 major HIV-1 subtypes (A, B, C, D, CRF01_AE, and CRF02_AG) and demonstrated an R(2) value of ≥0.996. The performance of the Aptima assay was also compared to those of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 v.2 (CAP/CTM) and Abbott m2000 RealTime HIV-1 (RealTime) assays on all subtype samples. The Aptima assay values averaged 0.21 log higher than the CAP/CTM values and 0.30 log higher than the RealTime values, and the values were >0.4 log higher than CAP/CTM values for subtypes F and G and than RealTime values for subtypes C, F, and G and CRF02_AG. Two samples demonstrated results with >1-log differences from RealTime results. When the data were adjusted by the average difference, 94.9% and 87.0% of Aptima results fell within 0.5 log of the CAP/CTM and RealTime results, respectively. The linearity and accuracy of the Aptima assay in correctly quantitating all major HIV-1 subtypes, coupled with the completely automated format and high throughput of the Panther system, make this system well suited for reliable measurement of viral load in the clinical laboratory.

  10. Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots.

    PubMed

    Sahoo, Malaya K; Varghese, Vici; White, Elizabeth; Winslow, Meg; Katzenstein, David A; Shafer, Robert W; Pinsky, Benjamin A

    2016-10-01

    HIV-1 RNA quantitation in plasma, or virus load testing, is the primary method by which the response to antiretroviral therapy is monitored. Here we describe evaluation of the Aptima HIV-1 Quant Dx assay (Aptima) performed on the automated Panther system. The clinical performance of Aptima was compared to that of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test v2.0 (CAP/CTM) using 162 EDTA plasma samples collected from patients undergoing HIV-1 monitoring. Overall agreement was 84.0% (136/162), with a kappa statistic of 0.723 (standard error, 0.047; 95% confidence interval [CI], 0.630 to 0.815), indicating substantial agreement. Using the 86 clinical samples quantifiable by both methods, Passing-Bablok regression revealed a regression line of Y = (1.069 × X) - 0.346 (95% CI of the slope [1.003 to 1.139] and intercept [-0.666 to -0.074]), and Bland-Altman analysis demonstrated a mean difference (Aptima-CAP/CTM) of -0.075 log10 copies/ml (95% limits of agreement of -0.624 to 0.475), consistent with negative bias. Comparison of Aptima results for paired dried blood spot (DBS) and plasma specimens archived from participants in the Peninsula AIDS Research Cohort Study (PARC) demonstrated an overall agreement of 94.7% (90/95) when 1,000 copies/ml was used as the threshold. In conclusion, the Aptima HIV-1 Quant Dx assay provides a suitable alternative for HIV-1 monitoring in plasma and DBS. PMID:27535684

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  13. 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

  14. 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

  15. An automatic modular procedure to generate high-resolution earthquake catalogues: application to the Alto Tiberina Near Fault Observatory (TABOO), Italy.

    NASA Astrophysics Data System (ADS)

    Di Stefano, R.; Chiaraluce, L.; Valoroso, L.; Waldhauser, F.; Latorre, D.; Piccinini, D.; Tinti, E.

    2014-12-01

    The Alto Tiberina Near Fault Observatory (TABOO) in the upper Tiber Valley (northern Appennines) is a INGV research infrastructure devoted to the study of preparatory processes and deformation characteristics of the Alto Tiberina Fault (ATF), a 60 km long, low-angle normal fault active since the Quaternary. The TABOO seismic network, covering an area of 120 × 120 km, consists of 60 permanent surface and 250 m deep borehole stations equipped with 3-components, 0.5s to 120s velocimeters, and strong motion sensors. Continuous seismic recordings are transmitted in real-time to the INGV, where we set up an automatic procedure that produces high-resolution earthquakes catalogues (location, magnitudes, 1st motion polarities) in near-real-time. A sensitive event detection engine running on the continuous data stream is followed by advanced phase identification, arrival-time picking, and quality assessment algorithms (MPX). Pick weights are determined from a statistical analysis of a set of predictors designed to correctly apply an a-priori chosen weighting scheme. The MPX results are used to routinely update earthquakes catalogues based on a variety of (1D and 3D) velocity models and location techniques. We are also applying the DD-RT procedure which uses cross-correlation and double-difference methods in real-time to relocate events with high precision relative to a high-resolution background catalog. P- and S-onset and location information are used to automatically compute focal mechanisms, VP/VS variations in space and time, and periodically update 3D VP and VP/VS tomographic models. We present results from four years of operation, during which this monitoring system analyzed over 1.2 million detections and recovered ~60,000 earthquakes at a detection threshold of ML 0.5. The high-resolution information is being used to study changes in seismicity patterns and fault and rock properties along the ATF in space and time, and to elaborate ground shaking scenarios adopting

  16. Spectral modeling of water ice-rich areas on Ceres' surface from Dawn-VIR data analysis: abundance and grain size retrieval

    NASA Astrophysics Data System (ADS)

    Raponi, Andrea; De Sanctis, Maria Cristina; Ciarniello, Mauro; Tosi, Federico; Combe, Jean-Philippe; Frigeri, Alessandro; Zambon, Francesca; Ammannito, Eleonora; Giacomo Carrozzo, Filippo; Magni, Gianfranco; Capria, Maria Teresa; Formisano, Michelangelo; Longobardo, Andrea; Palomba, Ernesto; Pieters, Carle; Russell, Christopher T.; Raymond, Carol; Dawn/VIR Team

    2016-10-01

    Dawn spacecraft orbits around Ceres since early 2015 acquiring a huge amount of data at different spatial resolutions during the several phases of the mission. VIR, the visible and InfraRed spectrometer onboard Dawn [1] allowed to detect the principal mineralogical phases present on Ceres: a large abundance of dark component, NH4-phillosilicates and carbonates.Water has been detected in small areas on Ceres' surface by the Dawn-VIR instrument. The most obvious finding is located in Oxo crater [2]. Further detections of water have been made during the Survey observation phase (1.1 km/pixel) and High-Altitude Mapping Orbit (400 m/px) [3]. During the LAMO phase (Low Altitude Mapping Orbit), the data with increased spatial resolution (100 m/px) coming from both regions have improved the detection of water, highlighting clear diagnostic water ice absorption features. In this study, we focused on spectral modeling of VIR spectra of Oxo and another crater (lon = 227°, lat 57°), near Messor crater.The Hapke radiative transfer model [4] has been applied in order to retrieve the water ice properties. We consider two types of mixtures: areal and intimate mixing. In areal mixing, the surface is modelled as patches of pure water ice, with each photon scattered within one patch. In intimate mixing, the particles of water ice are in contact with particles of the dark terrain, and both are involved in the scattering of a single photon. The best fit with the measured spectra has been derived with the areal mixture. The water ice abundance obtained is up to 15-20% within the field of view, and the grain size retrieved is of the order of 100-200 μm. Phyllosilicates and carbonates, which are ubiquitous on Ceres surface [5], have been also detected and modeled in correspondence with the icy regions. The water ice is typically located near and within the shadows projected by the crater rims. Further analysis is required to study the thermal state of the ice and its origin

  17. 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

  18. 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

  19. 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

  20. α-Lipoic acid has anti-inflammatory and anti-oxidative properties: an experimental study in rats with carrageenan-induced acute and cotton pellet-induced chronic inflammations.

    PubMed

    Odabasoglu, Fehmi; Halici, Zekai; Aygun, Hayati; Halici, Mesut; Atalay, Fadime; Cakir, Ahmet; Cadirci, Elif; Bayir, Yasin; Suleyman, Halis

    2011-01-01

    α-Lipoic acid (ALA) has been termed the 'ideal' antioxidant, a readily absorbed and bioavailable compound capable of scavenging a number of free radicals, and it has been used for treating diseases in which oxidative stress plays a major role. The present study was designed to gain a better understanding for the positive effects of ALA on the models of acute and chronic inflammation in rats, and also determine its anti-oxidative potency. In an acute model, three doses of ALA (50, 100 and 200 mg/kg) and one dose of indomethacin (25 mg/kg) or diclofenac (25 mg/kg) were administered to rats by oral administration. The paw volumes of the animals were calculated plethysmometrically, and 0·1 ml of 1 % carrageenan (CAR) was injected into the hind paw of each animal 1 h after oral drug administration. The change in paw volume was detected as five replicates every 60 min by plethysmometry. In particular, we investigated the activities of catalase, superoxide dismutase (SOD), glutathione S-transferase (GST), glutathione peroxidase (GPx), glutathione reductase (GR), inducible NO synthase (iNOS) and myeloperoxidase (MPx), and the amounts of lipid peroxidation (LPO) or total GSH in the paw tissues of CAR-injected rats. We showed that ALA exhibited anti-inflammatory effects on both acute and chronic inflammations, and a strongly anti-oxidative potency on linoleic acid oxidation. Moreover, the administration of CAR induced oedema in the paws. ALA significantly inhibited the ability of CAR to induce: (1) the degree of acute inflammation, (2) the rise in MPx activity, (3) the increases of GST and iNOS activities and the amount of LPO and (4) the decreases of GPx, GR and SOD activities and the amount of GSH. In conclusion, these results suggest that the anti-inflammatory properties of ALA, which has a strong anti-oxidative potency, could be related to its positive effects on the antioxidant system in a variety of tissues in rats.

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

    PubMed Central

    Si, Meiru; Zhao, Chao; Zhang, Bing; Wei, Dawei; Chen, Keqi; Yang, Xu; Xiao, He; Shen, Xihui

    2016-01-01

    Mycothiol (MSH) is the dominant low-molecular-weight thiol (LMWT) unique to high-(G+C)-content Gram-positive Actinobacteria, such as Corynebacterium glutamicum, and is oxidised into its disulfide form mycothiol disulfide (MSSM) under oxidative conditions. Mycothiol disulfide reductase (Mtr), an NADPH-dependent enzyme, reduces MSSM to MSH, thus maintaining intracellular redox homeostasis. In this study, a recombinant plasmid was constructed to overexpress Mtr in C. glutamicum using the expression vector pXMJ19-His6. Mtr-overexpressing C. glutamicum cells showed increased tolerance to ROS induced by oxidants, bactericidal antibiotics, alkylating agents, and heavy metals. The physiological roles of Mtr in resistance to oxidative stresses were corroborated by decreased ROS levels, reduced carbonylation damage, decreased loss of reduced protein thiols, and a massive increase in the levels of reversible protein thiols in Mtr-overexpressing cells exposed to stressful conditions. Moreover, overexpression of Mtr caused a marked increase in the ratio of reduced to oxidised mycothiol (MSH:MSSM), and significantly enhanced the activities of a variety of antioxidant enzymes, including mycothiol peroxidase (MPx), mycoredoxin 1 (Mrx1), thioredoxin 1 (Trx1), and methionine sulfoxide reductase A (MsrA). Taken together, these results indicate that the Mtr protein functions in C. glutamicum by protecting cells against oxidative stress. PMID:27383057

  2. 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.

  3. 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.

  4. Creation and transition of digital light processing technology to defense applications

    NASA Astrophysics Data System (ADS)

    Hopper, Darrel G.

    2005-05-01

    A key challenge to defense science and technology programs is the identification of areas ripe for focused government investment so as to make impossible things possible on an accelerated schedule. The creation, transfer to commercial products, and transition to operational military systems of the Texas Instruments (TI) digital micromirror device (DMD) projection display technology from 1987-2005 is a case study in how DoD seeks invest in S&T for warfighting advantage while renewing the civil economy and enabling domestic production of key electronic components. The DoD investment in DMD reduced the risk enough to merit TI productization and resulted in the first VGA single ship color wheel prototype in 1992 (introduced as first commercial product in 1996) and in the first 2.36 Mpx 3-chip color demonstration system in 1995 (a resolution that is only now being introduced as a mass production product). The 1995 demonstrator was the world"s first 100% digital display system. The tenth anniversary of this 2005 achievement presents an appropriate occasion to review and document the success of this prior Air Force and DARPA investment as measured by the subsequent adoption in a wide range of civil and, especially, defense applications.

  5. 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.

  6. Zebrafish embryo model of Bartonella henselae infection.

    PubMed

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

    2014-10-01

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

  7. Contrast-enhanced ultrasound (CEUS) for the study of peripheral lung lesions: a preliminary study.

    PubMed

    Sperandeo, Marco; Sperandeo, Giuseppe; Varriale, Antonio; Filabozzi, Paola; Decuzzi, Marco; Dimitri, Lucia; Vendemiale, Gianluigi

    2006-10-01

    The use of contrast-enhanced ultrasound (CEUS) for the study of peripheral lung lesions has never been systematically investigated. We evaluated the CEUS patterns of 98 peripheral lung lesions before performing US-guided fine-needle biopsies (FNB). The examinations were done with an Esaote Technos MPX scanner in the harmonic mode with a mechanical index of 0.04 or less. Contrast enhancement was achieved with a 4.8 mL bolus of SonoVue (Bracco) administered via an antecubital vein. All FNBs performed under CEUS guidance were adequate for pathologic diagnosis. Seventy-eight lesions were malignant: 33 (41.9%) were adenocarcinomas, 29 (36.5%) were squamous-cell carcinomas, 13 (17.6%) were undifferentiated large-cell carcinomas and the remaining three (4.1%) were small-cell carcinomas. All presented intralesional enhancement consistent with tumor neovascularization. In some cases, there were unenhanced areas consistent with zones of necrosis and these areas were avoided during FNB. The other 20 lesions were benign (four lipomas, two fibrous lung tumor, two noncaseous granulomas, six abscesses, one rheumatoid nodule, one histiocytosis X, one chondroid hamartoma, one sclerosing hemangioma, two sarcoid nodules) and none presented intralesional enhancement. This initial and admittedly limited experience suggests that CEUS may provide diagnostically useful information on peripheral lung lesions and increase the diagnostic yield of transthoracic FNB by reducing the risk of inadequate tissue sampling.

  8. Effects of instrument settings on radiofrequency ultrasound local estimator images: a preliminary study in a gallbladder model.

    PubMed

    Wang, Jian; Kang, Chunsong; Feng, Tinghua; Xue, Jiping; Shi, Kailing; Li, Tingting; Liu, Xiaofang; Wang, Yu

    2013-10-01

    The aim of the present study was to evaluate the changes in radiofrequency ultrasound local estimator (RULES) images with different instrument settings. An Esaote Technos MPX Color Doppler Ultrasound Machine and RULES were used to capture images of a gallbladder model. The percentages of various colored areas (color filling rates) within the area of interest were calculated using different instrument gains, transducer frequencies and scan depths. Blue was predominant in the lumen of the model gallbladder, while red and green were primarily located near the inner edge of the lumen. When the depth was set at 62 mm and the gain at 105, the total color filling rates did not vary with different transducer frequencies. The blue color filling rate was greatest with a transducer frequency of 8.0 MHz, and the red and green color filling rates were greatest with a frequency of 12.5 MHz. Color variety was greatest when the transducer frequency was 12.5 MHz. When the transducer frequency was 12.5 MHz and the depth was 62 mm, the blue color filling rate was greatest with gains of 105 and 110, the red color filling rate was greatest with gains of 95 and 100 and the green color filling rate was greatest when the gain was 100. The total color filling rate was greatest at gains of 100 and 105. In conclusion, images obtained using RULES may be affected by the instrument gain and, to a certain extent, by transducer frequency.

  9. The U.S. Naval Observatory Robotic Astrometric Telescope 1st Catalog (URAT1)

    NASA Astrophysics Data System (ADS)

    Zacharias, Norbert; Finch, Charlie T.; Subasavage, John P.; Tilleman, Trudy; DiVittorio, Mike; Harris, Hugh C.; Rafferty, Ted; Wieder, Gary; Eric Ferguson, Chris Kilian, Albert Rhodes, Mike Schultheis

    2015-01-01

    The 1st USNO Robotic Astrometric Telescope Catalog (URAT1) is about tobe released. It contains accurate positions (typically 10 to 30 mas std.error) of 220 million stars, mainly on the northern hemisphere. Propermotions were obtained for 85% of these stars utilizing the 2MASS as 1stepoch. URAT1 is supplemented by 2MASS and APASS photometry. The URAT1catalog was derived from 2 years of operations (April 2012 to April 2014)of the USNO "redlens" astrograph with its 474 Mpx 4-shooter camera at theNaval Observatory Flagstaff Station (NOFS) in a joint effort betweenUSNO's Astrometry Department and NOFS. Due to a combination of longexposures and short exposures with objective grating, URAT1 observationscover the large 3 to 18.5 magnitude range in a single 680-750 nm bandpass.The catalog properties are presented together with a brief summary ofobservations and reductions methods. URAT1 has on average about 4-timesthe number of stars per square degree and is 4-times more accurate thanUCAC4. URAT1 will serve as the currently most accurate astrometric anddeep photometric optical reference star catalog until the delivery ofthe Gaia catalog.

  10. 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.

  11. 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

  12. Contact-free isolation of sperm and epithelial cells by laser microdissection and pressure catapulting.

    PubMed

    Seidl, Stephan; Burgemeister, Renate; Hausmann, Roland; Betz, Peter; Lederer, Thomas

    2005-06-01

    With the PALM MicroBeam system, precise laser microdissection of single cells from cell smears or tissue preparations is possible. Furthermore, this system uses a contact-free and therefore contamination-free laser pressure catapulting technique in which high energy generated by a focused laser pulse catapults single dissected cells into a collecting vessel. In this study, this technique was tested for forensic purposes with smear preparations from postcoital vaginal swabs, sperm swabs, and buccal cell swabs on different types of microscopic slides. Apart from super-frosted slides, cutting and catapulting of selected cells was possible in all cases. Subsequent polymerase chain reaction was performed using the genRES MPX-2 Amplification Kit. In the case of sperm cells stained with hematoxylin and eosin, fragments larger than approximately 200 bp could not be detected. Partial genetic profiles were obtained for DNA amounts originating from only two cell equivalents. Complete profiles, however, were observed with all preparations of a minimum of 10 epithelial cells, demonstrating a potential benefit of this technique for the contamination-free forensic analysis of extremely small specimens or mixed stains. PMID:25869953

  13. 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.

  14. Automated tracking of whiskers in videos of head fixed rodents.

    PubMed

    Clack, Nathan G; O'Connor, Daniel H; Huber, Daniel; Petreanu, Leopoldo; Hires, Andrew; Peron, Simon; Svoboda, Karel; Myers, Eugene W

    2012-01-01

    We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998% and identifies individual whiskers with 99.997% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px×352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.

  15. Contact-free isolation of sperm and epithelial cells by laser microdissection and pressure catapulting.

    PubMed

    Seidl, Stephan; Burgemeister, Renate; Hausmann, Roland; Betz, Peter; Lederer, Thomas

    2005-06-01

    With the PALM MicroBeam system, precise laser microdissection of single cells from cell smears or tissue preparations is possible. Furthermore, this system uses a contact-free and therefore contamination-free laser pressure catapulting technique in which high energy generated by a focused laser pulse catapults single dissected cells into a collecting vessel. In this study, this technique was tested for forensic purposes with smear preparations from postcoital vaginal swabs, sperm swabs, and buccal cell swabs on different types of microscopic slides. Apart from super-frosted slides, cutting and catapulting of selected cells was possible in all cases. Subsequent polymerase chain reaction was performed using the genRES MPX-2 Amplification Kit. In the case of sperm cells stained with hematoxylin and eosin, fragments larger than approximately 200 bp could not be detected. Partial genetic profiles were obtained for DNA amounts originating from only two cell equivalents. Complete profiles, however, were observed with all preparations of a minimum of 10 epithelial cells, demonstrating a potential benefit of this technique for the contamination-free forensic analysis of extremely small specimens or mixed stains.

  16. 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.

  17. 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

  18. Phobos spectral clustering: comparison between the 0.5-0.9 micron slope on OMEGA and CRISM data sets

    NASA Astrophysics Data System (ADS)

    Pajola, Maurizio; Roush, Ted L.; Marzo, Giuseppe

    2016-10-01

    We analyzed the MEX-OMEGA (8) and MRO-CRISM (1) visible multispectral data sets of Phobos using I/F values at 0.5 and 0.9 micron and derived spectral slope from these. The purpose is to understand surface spectral variablity on Phobos. Combining the multispectral data sets provides nearly complete coverage for Phobos surface. Different observing scales ranging from 110 to 2000 m/px, with a range of phase angles from 37° to 101°.We applied an unsupervised K-means partitioning algorithm to evaluate the variability of the two I/F values. Each resulting cluster is characterized by an average, and its associated variability. This approach has been validated by application to different Solar System objects, e.g. asteroids, Mars, and Iapetus. The algorithm is agnostic of the physical meaning of the resulting clusters, and scientific interpretation is required for their subsequent evaluation.Using this techinque, 7 clusters were identified for each of the 9 Phobos data sets. For each cluster, we calculated the 0.5-0.9 micron slope within each Phobos data set. The calculated slopes change from a minimum of 0.1% to a maximum of 14.7%. These results indicate that Phobos surface may be more variable than previously suggested, however the exact cause of these variations remains to be determined. In this context, the OMEGA and CRISM data sets are fundamental for expanding our knowledge about Phobos.

  19. The Effect of Patellar Taping on Squat Depth and the Perception of Pain in People with Anterior Knee Pain

    PubMed Central

    Clifford, Amanda M.; Harrington, Elaine

    Patellar taping is a treatment adjunct commonly used in the management of anterior knee pain. The aim of this cross sectional study was to investigate the effects of medial glide patellar taping on sagittal plane lower-limb joint kinematics and knee pain during a unilateral squat in a symptomatic population complaining of anterior knee pain. Ten participants with a history of unilateral or bilateral anterior knee pain were included in the study. Subjects were required to squat on the symptomatic leg under three conditions: placebo tape, patellar tape and no tape. Kinematic data was recorded using the CODA mpx64 motion analysis system and subjects’ pain was assessed using the Numerical Rating Scale. Patellar taping resulted in a significantly greater single-legged squat depth compared to placebo tape (p=0.008) and no tape (p=0.001) and a statistically significant reduction in pain during a squat compared to placebo tape (p=0.001) or no tape (p=0.001). Significant differences were not identified for maximum knee flexion in the patella taping compared to the no tape condition. This study may have significant clinical implications as participants reported less pain and alterations in sagittal plane movement following the application of patellar tape. PMID:24146711

  20. Use of the LIBS method in oil paintings examination based on examples of analyses conducted at the Wilanow Palace Museum

    NASA Astrophysics Data System (ADS)

    Modzelewska, ElŻbieta; Pawlak, Agnieszka; Selerowicz, Anna; Skrzeczanowski, Wojciech; Marczak, Jan

    2013-05-01

    This paper describes the preliminary results of a study of the paint layers in 17th-century paintings belonging to the collection of the Wilanow Palace Museum. The works chosen for examination are of great importance to the Museum, as they might have been painted by court artists of King John III Sobieski. The aim of the study was therefore to determine the technological structure of the paintings, to determine the scope of conservation interventions and, above all, to gather comparative material that would serve to conduct further multidisciplinary attributive research. The presentation relates to studies in which laser-induced breakdown spectroscopy (LIBS) and optical microscopy were used as diagnostic tools. LIBS is based on the evaporation of a small amount of the material under investigation, and the generation of plasma which emits continuum and line radiation. The analysis of line radiation allows us to identify the elements appearing in the sample being investigated. The microscope pictures were taken using a Bresser Digital Hand Micro 1.3Mpx and the Hirox 8700 microscopes. The results obtained have confirmed the utility of the LIBS method in the study of artworks. They have also proven that it can be used as a method to complement microchemical analysis, as well as an method to identify and examine artworks from which samples cannot be taken, as it is micro-destructive and the analysis can be conducted directly on the object, without the need to take samples.

  1. 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

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

    PubMed Central

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

    2016-01-01

    Abstract The HLA-B*57:01 allele is strongly associated with the hypersensitivity reaction to Abacavir (ABC). Therefore, treatment guidelines recommend that patients initiating ABC are preventively tested for the presence of this allele. To date, four different commercial assays based on the real-time quantitative polymerase chain reaction (Q-PCR) technique are available for the detection of HLA-B*57:01: Duplicα-RealTime Reagent Set HLA-B*57:01 by Euroclone, HLA-B*57:01 Real-TM by Sacace Biotechnologies, COBAS AmpliPrep/COBAS TaqMan HLA-B*57:01 Screening Test by Roche Diagnostic, and HLA-B*57:01 by Nuclear Laser Medicine. The study was carried out to compare the performance of the first three commercially available Q-PCR kits in a routine clinical setting. A total of 98 samples from Policlinico Umberto I Hospital were tested. Results obtained by the Duplicα-RealTime Genotyping kit and AmpliPrep/TaqMan system were 100% concordant. In contrast, genotyping by the HLA-B*57:01 Real-TM kit showed poor agreement with the other systems, that is, 12 out of 33 positive samples were detected as HLA-B*57:01 negative. To confirm the correct genotype of these discordant samples, two additional methods with rapid turnaround times and already implemented into routine clinical practice were used, that is, a PCR-based microsequence-specific primer DNA typing test and a laboratory-developed screening test in Q-PCR. All 12 discordant samples were genotyped as HLA-B*57:01-positive samples using these two additional methods in a single-blinded manner, thus confirming the low sensitivity of HLA-B*57:01 Real-TM test. These findings underline the need to compare results obtained with commercial assays before choosing a test suitable for use in a routine clinical laboratory. PMID:26750774

  3. 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

  4. 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.

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

    PubMed Central

    2013-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  7. 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

  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. 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

  10. 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

  11. 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.

  12. 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

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

    PubMed

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

    2007-03-01

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

  14. Time-Motion Analysis of Four Automated Systems for the Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Nucleic Acid Amplification Testing.

    PubMed

    Williams, James A; Eddleman, Laura; Pantone, Amy; Martinez, Regina; Young, Stephen; Van Der Pol, Barbara

    2014-08-01

    Next-generation diagnostics for Chlamydia trachomatis and Neisseria gonorrhoeae are available on semi- or fully-automated platforms. These systems require less hands-on time than older platforms and are user friendly. Four automated systems, the ABBOTT m2000 system, Becton Dickinson Viper System with XTR Technology, Gen-Probe Tigris DTS system, and Roche cobas 4800 system, were evaluated for total run time, hands-on time, and walk-away time. All of the systems evaluated in this time-motion study were able to complete a diagnostic test run within an 8-h work shift, instrument setup and operation were straightforward and uncomplicated, and walk-away time ranged from approximately 90 to 270 min in a head-to-head comparison of each system. All of the automated systems provide technical staff with increased time to perform other tasks during the run, offer easy expansion of the diagnostic test menu, and have the ability to increase specimen throughput. PMID:24196751

  15. Surface-activated microtiter-plate microarray for simultaneous CRP quantification and viral antibody detection.

    PubMed

    Viitala, Sari M; Jääskeläinen, Anne J; Kelo, Eira; Sirola, Helena; Moilanen, Kirsi; Suni, Jukka; Vaheri, Antti; Vapalahti, Olli; Närvänen, Ale

    2013-02-01

    Microarrays are widely used in high-throughput DNA and RNA hybridization tests and recently adopted to protein and small molecule interaction studies in basic research and diagnostics. Parallel detection of serum antibodies and antigens has several potential applications in epidemiologic research, vaccine development, and in the diagnosis of allergies, autoimmunity, and infectious diseases. This study demonstrates an immobilization method for immunoassay-based microarray in conventional 96-well polystyrene plates for a serologic diagnostic method combined with quantitative C-reactive protein (CRP) assay. A synthetic peptide (HIV-1), a recombinant protein (Puumala hantavirus nucleocapsid), and purified virus preparations (Sindbis and adenoviruses) were used as antigens for virus-specific antibody detection and monoclonal anti-CRP antibody for antigen detection. The microarray was based on conventional enzyme immunoassays and densitometry from photographed results. Peptide and recombinant antigens functioned well, while whole virus antigens gave discrepant results in 1 out of 23 samples from the reference method, tested with human sera with various antibody responses. The CRP results were in concordance in the concentration range 0.5-150 mg/L with 2 commercially available CRP assays: ReaScan rapid test (R(2) = 0.9975) and Cobas 6000 analyzer (R(2) =0.9595). The results indicate that microtiter plates provide a promising platform for further development of microarrays for parallel antibody and antigen detection. PMID:23219230

  16. Vulvovaginal-Swab or First-Catch Urine Specimen To Detect Chlamydia trachomatis in Women in a Community Setting?▿

    PubMed Central

    Skidmore, Sue; Horner, Paddy; Herring, Alan; Sell, Joanne; Paul, Ian; Thomas, Jane; Caul, E. Owen; Egger, Matthias; McCarthy, Anne; Sanford, Emma; Salisbury, Chris; Macleod, John; Sterne, Jonathan A. C.; Low, Nicola

    2006-01-01

    Screening for chlamydia in women is widely recommended. We evaluated the performance of two nucleic acid amplification tests for detecting Chlamydia trachomatis in self-collected vulvovaginal-swab and first-catch urine specimens from women in a community setting and a strategy for optimizing the sensitivity of an amplified enzyme immunoassay on vulvovaginal-swab specimens. We tested 2,745 paired vulvovaginal-swab and urine specimens by PCR (Roche Cobas) or strand displacement amplification (SDA; Becton Dickinson). There were 146 women infected with chlamydia. The assays detected 97.3% (95% confidence interval [CI], 93.1 to 99.2%) of infected patients with vulvovaginal-swab specimens and 91.8% (86.1 to 95.7%) with urine specimens. We tested 2,749 vulvovaginal-swab specimens with both a nucleic acid amplification test and a polymer conjugate-enhanced enzyme immunoassay with negative-gray-zone testing. The relative sensitivities obtained after retesting specimens in the negative gray zone were 74.3% (95% CI, 62.8 to 83.8%) with PCR and 58.3% (95% CI, 46.1 to 69.8%) with SDA. In community settings, both vulvovaginal-swab and first-catch urine specimens from women are suitable substrates for nucleic acid amplification tests, but enzyme immunoassays, even after negative-gray-zone testing, should not be used in screening programs. PMID:17065268

  17. COBAS® TaqMan® MTB, smear positivity grade and MGIT culture; correlation analyses of three methods for bacillary quantification.

    PubMed

    Chikamatsu, Kinuyo; Aono, Akio; Kato, Tomoko; Takaki, Akiko; Yamada, Hiroyuki; Sasaki, Yuka; Izumi, Kiyohiko; Yi, Lina; Mitarai, Satoshi

    2016-01-01

    We investigated the correlation between the cycle threshold (Ct) value of the COBAS(®) TaqMan(®) MTB (TaqMan MTB), the mycobacterial smear positivity grade, and the time to detection (TTD) in the Mycobacteria Growth Indicator Tube (MGIT) for quantification of Mycobacterium tuberculosis (MTB). For 57 sputum samples, significant correlations were observed between the Ct value, the smear positivity grade, and the MGIT TTD (Spearman's rank correlation coefficient: r(s) = -0.940, P < 0.001 and Pearson's correlation coefficient: r(p) = 0.737, P < 0.001). In addition, a correlation was observed between the number of bacteria estimated based on the smear positivity grade and the number of MTB bacilli calculated by the Ct value (r(s) = 0.930, P < 0.001). This study has demonstrated the possible estimation of the smear positivity grade and MGIT TTD using the Ct value of TaqMan MTB, which is based on a real-time PCR system, for diagnostic samples.

  18. Establishment of Biological Reference Intervals and Reference Curve for Urea by Exploratory Parametric and Non-Parametric Quantile Regression Models

    PubMed Central

    2013-01-01

    Background: The validity of the entire renal function tests as a diagnostic tool depends substantially on the Biological Reference Interval (BRI) of urea. Establishment of BRI of urea is difficult partly because exclusion criteria for selection of reference data are quite rigid and partly due to the compartmentalization considerations regarding age and sex of the reference individuals. Moreover, construction of Biological Reference Curve (BRC) of urea is imperative to highlight the partitioning requirements. Materials and Methods: This a priori study examines the data collected by measuring serum urea of 3202 age and sex matched individuals, aged between 1 and 80 years, by a kinetic UV Urease/GLDH method on a Roche Cobas 6000 auto-analyzer. Results: Mann-Whitney U test of the reference data confirmed the partitioning requirement by both age and sex. Further statistical analysis revealed the incompatibility of the data for a proposed parametric model. Hence the data was non-parametrically analysed. BRI was found to be identical for both sexes till the 2nd decade, and the BRI for males increased progressively 6th decade onwards. Four non-parametric models were postulated for construction of BRC: Gaussian kernel, double kernel, local mean and local constant, of which the last one generated the best-fitting curves. Conclusion: Clinical decision making should become easier and diagnostic implications of renal function tests should become more meaningful if this BRI is followed and the BRC is used as a desktop tool in conjunction with similar data for serum creatinine.

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

    PubMed

    Reischl, U; Straube, E; Unemo, M

    2009-01-01

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

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

    PubMed

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

    2005-01-01

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

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

    PubMed

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

    2013-08-01

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

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

    PubMed

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

    2004-08-01

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

  3. Evaluation of buprenorphine LUCIO immunoassay versus GC-MS using urines from a workplace drug testing program.

    PubMed

    Alves, Marcela Nogueira Rabelo; Piccinotti, Alberto; Tameni, Silvia; Polettini, Aldo

    2013-04-01

    The buprenorphine (BUP) LUCIO Nal Von Minden screening assay was evaluated. Urine samples from subjects enrolled in a workplace drug testing program were screened according to the manufacturer's instruction using a Roche COBAS Integra 800 analyser. For gas chromatography-mass spectrometry (GC-MS) confirmatory analysis, samples were submitted to enzymatic hydrolysis with β-glucuronidase and mixed-mode solid-phase extraction. Imprecision (coefficient of variation) for 3.0, 7.0, and 13.0 ng/mL calibrators varied within 2.8-8.7 intra-day (n = 20) and 7.7-8.6 inter-day (n = 19). Inaccuracy (bias) was between -5.6-30.5 intra-day and -13.2-4.2 inter-day. At the 5 ng/mL cut-off, the immunoassay showed 100% sensitivity and 88% specificity, with an overall agreement of 94% between immunoassay and GC-MS. Raising the cut-off to 10 ng/mL provided an identical overall agreement between immunoassay and GC-MS (94%), despite the decrease in sensitivity (90%) and the increase in specificity (100%). According to these results, the BUP LUCIO Nal Von Minden screening assay provides adequate sensitivity and specificity for BUP screening in urine samples using a cut-off concentration of 5 ng/mL.

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

    PubMed

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

    2016-12-15

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

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

    PubMed

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

    2016-12-15

    Detecting human papillomavirus (HPV) is central in diagnosing and monitoring HPV-related disease. However, limited sensitivity and the wide variability of the HPV genome pose challenges in the identification of HPV genes, particularly high-risk types. This study reports the development of polyethyleneimine-conjugated magnetic nanowires (PEI-MNWs) and their use in the isolation, identification, and analysis of multiple genotypes of HPV DNA from cervical cancer specimens. The nanowires are electrochemically doped with a high density of magnetic nanoparticles and biotin moieties during potentiostatic deposition, thereby allowing conjugating cationic branched polymers to direct the attachment of negatively charged DNA molecules with strong magnetic response. For proof of concept, the rapid and ultrasensitive isolation of HPV DNA is performed at concentrations as low as 10pg/mL with an efficiency of >95%. For clinical optimization, the analytical and clinical sensitivity of PEI-MNWs is compared with that of the Roche Cobas 4800 HPV Test and demonstrates excellent correlation for multiple HPV DNA genotypes with superior threshold cycle values. The high sensitivity, specificity, and good reproducibility of PEI-MNWs are particularly well suited for the recovery of DNA and provide significant and clinically meaningful evidence for the early detection and treatment of HPV-associated cancers. PMID:27494810

  6. [Markers of hepatitis virus].

    PubMed

    Suzuki, Fumitaka

    2008-11-01

    Hepatitis B virus (HBV) and hepatitis C virus (HCV) are the major viruses known to cause viral hepatitis. Serological markers are commonly used as diagnostic and/or prognostic indicators of acute or chronic HBV or HCV infection. The ability to detect HBV DNA in serum has been reported to have prognostic value for the outcome of chronic HBV infection. A rapid and sustained drop in HBV DNA or HCV RNA levels in patients under therapy has been shown to be a predictive factor for a favourable treatment outcome. Various techniques for detecting HBV DNA or HCV RNA have already been described; however, there are various problems with the sensitivity or detection range of those methods. New virus measuring methods have recently been reported and used. The Cobas Taq Man HCV Test is a new method to detect HBV DNA and HCV RNA with higher sensitivity and a broader range of quantitation than conventional methods. Some reports have shown that these methods improve therapy monitoring and the management of HBV or HCV infection. Moreover, hepatitis E virus (HEV) infection has been reported in Japan. The clinical features and viral markers of HEV have also been described. PMID:19086457

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

    PubMed

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

    2006-02-01

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

  8. Occurrence of Chlamydia trachomatis in military environment on the example of professional soldiers in the Polish Armed Forces.

    PubMed

    Korzeniewski, Krzysztof; Konior, Monika; Lass, Anna; Guzek, Aneta

    2014-01-01

    This article presents the results of a preliminary study concerning cases of Chlamydia trachomatis infections among professional soldiers in the Polish Armed Forces. Soldiers who declared casual sexual contact with women were investigated in this study regarding the transmission of chlamydial infections by sexual activity. In total, 66 healthy, sexually active professional Polish soldiers, aged between 27 and 44, who didn't report any symptoms of urogenital infection were investigated. Urine samples taken from these patients were investigated using molecular methods (Cobas TaqMan, real-time PCR) in March-April 2012 in the Military Institute of Medicine, Warsaw, Poland. In the investigated group of 66 Polish soldiers, two 33-34 year old men were asymptomatic carriers of Chlamydia trachomatis (3.0%). They confirmed having casual sexual activity without prevention with many women. In the examined group of Polish soldiers the relatively low level of chlamydial infections found may result from the use of preventive measures during sexual activity. According to the examined men, the common use of condoms is mainly connected with the fear of HIV infection. Screening tests for Chlamydia trachomatis in the Polish Armed Forces are not performed, therefore incidence rates of chlamydial infections remain unknown. The authors plan further investigations with a larger group of professional soldiers.

  9. 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.

  10. 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.

  11. Cxcl8-l1 and Cxcl8-l2 are required in the zebrafish defense against Salmonella Typhimurium.

    PubMed

    de Oliveira, Sofia; Lopez-Muñoz, Azucena; Martínez-Navarro, Francisco J; Galindo-Villegas, Jorge; Mulero, Victoriano; Calado, Ângelo

    2015-03-01

    In recent years zebrafish has emerged as an excellent model for studying the Cxcl8 signaling pathway in inflammation elicited upon tissue damage or infection. Zebrafish has two true homologs of mammalian CXCL8, named Cxcl8-l1 and Cxcl8-l2. Previously, we have shown that in wound-associated inflammation, these chemokines are up-regulated and are relevant for neutrophil recruitment. In infections, no such knowledge is available as most studies performed on this subject in zebrafish have mainly focused on Cxcl8-l1 even though Cxcl8-l2 shares higher homology with human CXCL8. In this study, we aimed to address the biological function of both zfCxcl8s in infection to improve our understanding of their respective roles under different inflammatory conditions. Gene expression analysis first confirmed that both Cxcl8-l1 and l2 are induced upon infection or in PAMP-elicited inflammatory processes. In addition, we also found that cxcl8-deficient larvae show higher susceptibility to Salmonella enterica serovar Typhimurium (S. Typhimurium) infection, reduced neutrophil recruitment to the infection site assayed in the line Tg(mpx:gfp), and decreased bacterial clearance. These data indicate that both zebrafish Cxcl8s play important roles in neutrophil recruitment and in the inflammatory response elicited upon infection or tissue damage, suggesting that even though the divergence of lower vertebrates and humans from a common ancestor occurred about 450 millions years ago, the basic principles of neutrophil recruitment are apparently conserved in all vertebrates.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. The CaSSIS imaging system: optical performance overview

    NASA Astrophysics Data System (ADS)

    Gambicorti, L.; Piazza, D.; Pommerol, A.; Roloff, V.; Gerber, M.; Ziethe, R.; El-Maarry, M. R.; Weigel, T.; Johnson, M.; Vernani, D.; Pelo, E.; Da Deppo, V.; Cremonese, G.; Ficai Veltroni, I.; Thomas, N.

    2016-07-01

    The Colour and Stereo Surface Imaging System (CaSSIS) is the high-resolution scientific imager on board the European Space Agency's (ESA) ExoMars Trace Gas Orbiter (TGO) which was launched on 14th March 2016 to Mars. CaSSIS will observe the Martian surface from an altitude of 400 km with an optical system based on a modified TMA telescope (Three Mirrors Anastigmatic configuration) with a 4th powered folding mirror. The camera EPD (Entrance Pupil Diameter) is 135 mm, and the expected focal length is 880 mm, giving an F# 6.5 in the wavelength range of 400- 1100 nm with a distortion designed to be less than 2%. CaSSIS will operate in a "push-frame" mode with a monolithic Filter Strip Assembly (FSA) produced by Optics Balzers Jena GmbH selecting 4 colour bands and integrated on the focal plane by Leonardo-Finmeccanica SpA (under TAS-I responsibility). The detector is a spare of the Simbio-Sys detector of the Italian Space Agency (ASI), developed by Raytheon Vision Systems. It is a 2kx2k hybrid Si-PIN array with a 10 μm pixel pitch. A scale of 4.6 m/px from the nominal orbit is foreseen to produce frames of 9.4 km × 47 km on the Martian surface. The University of Bern was in charge of the full instrument integration as well as the characterization of the focal plane and calibration of the entire instrument. The paper will present an overview of the CaSSIS telescope and FPA optical performance. The preliminary results of on-ground calibration and the first commissioning campaign (April 2016) will be described.

  19. 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

  20. [Investigation of occult hepatitis B in HIV infected patients].

    PubMed

    Altınbaş, Akif; Ergünay, Koray; Calık Başaran, Nursel; Alp, Alpaslan; Turgut, Didem; Hasçelik, Gülşen; Uzun, Ömrüm; Unal, Serhat

    2011-04-01

    Due to their shared transmission route, hepatitis B virus (HBV) or hepatitis C virus (HCV) co-infections can be observed in human immunodeficiency virus (HIV)-infected cases and are associated with more severe clinical courses. The detection of HBV DNA despite HBV surface antigen (HBsAg) seronegativity is defined as occult HBV infections. According to the current seroepidemiological data, Turkey is classified as an intermediate HBV, low HIV endemic region. Occult HBV infections have previously been reported from Turkey but has not been investigated previously in HIV infected cohorts. The aim of this study was to identify occult HBV infections in HIV-infected persons. Twenty-eight HIV-positive cases followed-up at Hacettepe University Hospital, Infectious Diseases Unit were included in the study after informed consent. For the detection of HBsAg, anti-HBs and anti-HCV, commercial ELISA tests (Architect System, Abbott Diagnostics, USA) were employed. Absolute CD4+ and CD8+ T-cell counts were determined via flow cytometry. HIV viral load was calculated via COBAS TaqMan HIV-1 Real-time PCR (Roche Diagnostics, USA) and the presence of HBV DNA was evaluated via COBAS TaqMan HBV Real-time PCR (Roche Diagnostics, USA), in addition to a nested PCR assay targeting HBV S gene. The mean age of the study group was 43.2 (range between 27-65) years, 64.3% (18/28) of them were males and the mean duration of HIV infection was 4.2 (2-11) years. Mean CD4+ ve CD8+ T-cell counts were 414 ± 267 cells/mm3 and 854 ± 293 cells/mm3, respectively. Twenty-six (92.8%) cases were under highly-active anti-retroviral therapy at the time of the study, 88.5% of which included HBV-active drugs (lamivudine or tenofovir). HIV RNA were found negative in 11 (39.3%) patients, of those nine (81.8%) were the cases who treated with HBV-active antiretroviral therapy. HBsAg were negative in all of the 28 patients, while the positivity rates of anti-HBs and anti-HCV were 39.3% (11/28) and 3.6% (1

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

    PubMed

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

    2009-10-01

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

  2. 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

  3. The Reference Level of Serum S-100B Protein for Poor Prognosis in Patients with Intracranial Extracerebral Hematoma

    PubMed Central

    Kaczmarek, J.; Jankowski, R.; Guzniczak, P.

    2011-01-01

    BACKGROUND S-100B protein, blood-brain barrier permeability marker, is one of a few biochemical indicators useful in the evaluation of traumatic brain injury. Our aim was to correlate serum concentration of S-100B with clinical condition and CT head scan findings as well as to estimate the level of the protein significant for clinical outcome prediction. METHODS The cohort of 41 subjects underwent clinical examination by the neurosurgeon, consciousness was evaluated with Glasgow Coma Scale (GCS). Diagnosis was established on the basis of CT head scans. Venous blood samples were collected before surgery. Serum concentration of S-100B protein was estimated using electrochemiluminesce immunoassays (ECLIA) on Cobas 6000 Analyzer (Roche Diagnostics). Clinical outcome was measured applying Glasgow Outcome Scale (GOS). Finally, data were analyzed with Statistica, v. 8.0 (StatSoft, Inc. 2007). RESULTS The average S-100B concentration was 0.95 ± 1.75 μg/L. Statistical analysis revealed significant correlation between S-100B and GCS, GOS and dimers–D concentration (p<0.001, Spearman correlation test). There were statistically significant differences in the S-100B concentration depending on the presence of brain oedema (1.29±2.02 vs. 0.06±0.03; p<0.01, Mann-Whitney test) or contusion foci (1.37±1.77 vs. 0.72±1.92; p<0.01) in CT scans. The S-100B concentration of 0.288 μg/L was determined as a cut-off point for unfavorable clinical outcome prediction (ROC, p<0.001). CONCLUSIONS Association between serum S-100B concentration and clinical, radiological or laboratory findings prove its usefulness as a diagnostic marker for assessment of brain trauma severity. The concentration of the protein >0.288 μg/L is associated with poor prognosis.

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

    PubMed

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

    2005-01-01

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

  5. 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

  6. Multicenter Evaluation of the Elecsys Hepatitis B Surface Antigen Quantitative Assay ▿

    PubMed Central

    Zacher, B. J.; Moriconi, F.; Bowden, S.; Hammond, R.; Louisirirotchanakul, S.; Phisalprapa, P.; Tanwandee, T.; Wursthorn, K.; Brunetto, M. R.; Wedemeyer, H.; Bonino, F.

    2011-01-01

    The Elecsys hepatitis B surface antigen (HBsAg) II quantitative assay is a new quantitative electrochemiluminescence immunoassay which uses onboard dilution and a simple algorithm to determine HBsAg levels expressed in international units (IU)/ml (standardized against the World Health Organization [WHO] Second International Standard). This study evaluated its performance using routine serum samples from a wide range of HBsAg carriers and patients with chronic hepatitis B (CHB). HBsAg levels were measured in serum samples collected independently by five centers in Europe, Australia, and Asia. Serial dilution analyses were performed to assess the recommended dilution algorithm and determine the assay range free of hook effect. Assay precision was also established. Following assessment of serial dilutions (1:100 to 1:1,000,000) of the 611 samples analyzed, 70.0% and 85.6% of samples tested with analyzers incorporating 1:100 (Elecsys 2010 and cobas e 411) and 1:400 (Modular Analytics E170) onboard dilution, respectively, fell within the linear range of the assay, providing a final result on the first test. No high-dose hook effect was seen up to the maximum HBsAg serum level tested (870,000 IU/ml) using the dilution algorithm. HBsAg levels were reliably determined across all hepatitis B virus (HBV) genotypes, phases of HBV infection, and stages of disease tested. Precision was high across all analyzers (% coefficient of variation [CV], 1.4 to 9.6; HBsAg concentrations, 0.1 to 37,300 IU/ml). The Elecsys HBsAg II quantitative assay accurately and reliably quantifies HBsAg in routine clinical samples. Onboard dilution minimizes retesting and reduces the potential for error. PMID:21880853

  7. Multicenter evaluation of the Elecsys hepatitis B surface antigen quantitative assay.

    PubMed

    Zacher, B J; Moriconi, F; Bowden, S; Hammond, R; Louisirirotchanakul, S; Phisalprapa, P; Tanwandee, T; Wursthorn, K; Brunetto, M R; Wedemeyer, H; Bonino, F

    2011-11-01

    The Elecsys hepatitis B surface antigen (HBsAg) II quantitative assay is a new quantitative electrochemiluminescence immunoassay which uses onboard dilution and a simple algorithm to determine HBsAg levels expressed in international units (IU)/ml (standardized against the World Health Organization [WHO] Second International Standard). This study evaluated its performance using routine serum samples from a wide range of HBsAg carriers and patients with chronic hepatitis B (CHB). HBsAg levels were measured in serum samples collected independently by five centers in Europe, Australia, and Asia. Serial dilution analyses were performed to assess the recommended dilution algorithm and determine the assay range free of hook effect. Assay precision was also established. Following assessment of serial dilutions (1:100 to 1:1,000,000) of the 611 samples analyzed, 70.0% and 85.6% of samples tested with analyzers incorporating 1:100 (Elecsys 2010 and cobas e 411) and 1:400 (Modular Analytics E170) onboard dilution, respectively, fell within the linear range of the assay, providing a final result on the first test. No high-dose hook effect was seen up to the maximum HBsAg serum level tested (870,000 IU/ml) using the dilution algorithm. HBsAg levels were reliably determined across all hepatitis B virus (HBV) genotypes, phases of HBV infection, and stages of disease tested. Precision was high across all analyzers (% coefficient of variation [CV], 1.4 to 9.6; HBsAg concentrations, 0.1 to 37,300 IU/ml). The Elecsys HBsAg II quantitative assay accurately and reliably quantifies HBsAg in routine clinical samples. Onboard dilution minimizes retesting and reduces the potential for error.

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

    PubMed Central

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

    2016-01-01

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

  9. 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

  10. 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

  11. 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.

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

    PubMed

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

    2001-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2006-01-01

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

  15. 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.

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

    PubMed

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

    2015-03-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2015-03-25

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    1998-06-01

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

  2. 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

  3. 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

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

    PubMed Central

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

    2016-01-01

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

  5. 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

  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. Necessity for Reassessment of Patients with Serogroup 2 Hepatitis C Virus (HCV) and Undetectable Serum HCV RNA

    PubMed Central

    Moritou, Yuki; Takeuchi, Yasuto; Seki, Hiroyuki; Nanba, Shintaro; Iwasaki, Yoshiaki; Yamamoto, Kazuhide

    2014-01-01

    We encountered a patient positive for anti-hepatitis C virus (HCV) whose serum HCV RNA was undetectable with the Roche AmpliPrep/Cobas TaqMan HCV assay (CAP/CTM) version 1 but showed a high viral load with the Abbott RealTime HCV assay (ART). Discrepancies in the detectability of serum HCV RNA were investigated among 891 consecutive patients who were positive for anti-HCV. Specific nucleotide variations causing the undetectability of HCV RNA were determined and confirmed by synthesizing RNA coding those variations. Serum samples with the discrepancies were also reassessed by CAP/CTM version 2. Among the 891 anti-HCV-positive patients, 4 patients had serum HCV RNA levels that were undetectable by CAP/CTM version 1 despite having levels of >5 log IU/ml that were detected by ART. All four patients had HCV genotype 2a and high titers of anti-HCV. Sequencing of the HCV 5′ noncoding regions revealed 2 common variations, A at nucleotide (nt) 145 and T at nt 151. Synthesized RNAs of the HCV 5′ noncoding region with standard (NCR145G151C) and variant nucleotides at nt 145 and nt 151 were quantified with CAP/CTM. RNAs of NCR145G151C and NCR145G151T were quantifiable with CAP/CTM version 1, while those of NCR145A151T and NCR145A151C went undetected. The substitution from G to A at nt 145 specifically conferred this undetectability, while this undetectability was reverted in synthesized HCV RNA with correction of this variation. Reassessment of these samples by CAP/CTM version 2 resulted in similar levels of HCV RNA being detected by ART. We conclude that HCV patients with undetectable HCV RNA by CAP/CTM version 1 should be reassessed for viral quantification. PMID:24478486

  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.

  9. 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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  12. Chemical bonding in phosphane and amine complexes of main group elements and transition metals.

    PubMed

    Bessac, Fabienne; Frenking, Gernot

    2006-08-21

    The geometries and bond dissociation energies of the main group complexes X3B-NX3, X3B-PX3, X3Al-NX3, and X3Al-PX3 (X = H, Me, Cl) and the transition metal complexes (CO)5M-NX3 and (CO)5M-PX3 (M = Cr, Mo, W) have been calculated using gradient-corrected density functional theory at the BP86/TZ2P level. The nature of the donor-acceptor bonds was investigated with an energy decomposition analysis. It is found that the bond dissociation energy is not a good measure for the intrinsic strength of Lewis acidity and basicity because the preparation energies of the fragments may significantly change the trend of the bond strength. The interaction energies between the frozen fragments of the borane complexes are in most cases larger than the interaction energies of the alane complexes. The bond dissociation energy of the alane complexes is sometimes higher than that of the borane analogues because the energy for distorting the planar equilibrium geometry of BX3 to the pyramidal from in the complexes is higher than for AlX3. Inspection of the three energy terms, DeltaE(Pauli), DeltaE(orb), and DeltaE(elstat), shows that all three of them must be considered to understand the trends of the Lewis acid and base strength. The orbital term of the donor-acceptor bonds with the Lewis bases NCl3 and PCl3 have a higher pi character than the bonds of EH3 and EMe3, but NCl3 and PCl3 are weaker Lewis bases because the lone-pair orbital at the donor atoms N and P has a high percent s character. The calculated DeltaE(int) values suggest that the trends of the intrinsic Lewis bases' strengths in the main-group complexes with BX3 and AlX3 are NMe3 > NH3 > NCl3 and PMe3 > PH3 > PCl3. The transition metal complexes exhibit a somewhat different order with NH3 > NMe3 > NCl3 and PMe3 > PH3 > PCl3. The slightly weaker bonding of NMe3 than that of NH3 comes from stronger Pauli repulsion. The bond length does not always correlate with the bond dissociation energy, nor does it always correlate with

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

    PubMed

    Giangregorio, Francesco

    2011-01-01

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

  14. 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

  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. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

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

    PubMed Central

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

    2013-01-01

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

  3. Glutathione is required for maximal transcription of the cobalamin biosynthetic and 1,2-propanediol utilization (cob/pdu) regulon and for the catabolism of ethanolamine, 1,2-propanediol, and propionate in Salmonella typhimurium LT2.

    PubMed Central

    Rondon, M R; Kazmierczak, R; Escalante-Semerena, J C

    1995-01-01

    Transcription of the cob/pdu regulon of Salmonella typhimurium is activated by the PocR regulatory protein in response to 1,2-propanediol (1,2-PDL) in the environment. Nutritional analysis and DNA sequencing confirmed that a strain defective in expression of the cob/pdu regulon in response to 1,2-PDL lacked a functional gshA gene. gshA encodes gamma-glutamylcysteine synthetase (L-glutamate:L-cysteine gamma-ligase [ADP forming]; EC 6.3.2.2), the enzyme that catalyzes the first step in the synthesis of glutathione (GSH). The DNA sequence of gshA was partially determined, and the location of gshA in the chromosome was established by two-factor crosses. P22 cotransduction of gshA with nearby markers showed 21% linkage to srl and 1% linkage to hyd; srl was 9% cotransducible with hyd. In light of these data, the gene order gshA srl hyd is suggested. The level of reduced thiols in the gshA strain was 87% lower than the levels measured in the wild-type strain in both aerobically and anaerobically grown cells. 1,2-PDL-dependent transcription of cob/pdu was studied by using M. Casadaban's Mu-lacZ fusions. In aerobically grown cells, transcription of a cbi-lacZ fusion (the cbi genes are the subset of cob genes that encode functions needed for the synthesis of the corrin ring) was 4-fold lower and transcription of a pdu-lacZ fusion was 10-fold lower in a gshA mutant than in the wild-type strain. Expression of the cob/pdu regulon in response to 1,2-PDL was restored when GSH was included in the medium. In anaerobically grown cells, cbi-lacZ transcription was only 0.4-fold lower than in the gshA+ strain; pdu-lacZ transcription was reduced only by 0.34-fold, despite the lower thiol levels in the mutant. cobA-lacZ transcription was used as negative control of gene whose transcription is not controlled by the PocR/1,2-PDL system; under both conditions, cobA transcription remained unaffected. The gshA mutant strain was unable to utilize 1,2-PDL, ethanolamine, or propionate as a

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

    PubMed

    Nakamura, Hisako

    2002-01-01

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

  5. 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

  6. The 380 kb pCMU01 Plasmid Encodes Chloromethane Utilization Genes and Redundant Genes for Vitamin B12- and Tetrahydrofolate-Dependent Chloromethane Metabolism in Methylobacterium extorquens CM4: A Proteomic and Bioinformatics Study

    PubMed Central

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

    2013-01-01

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

  7. 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

  8. 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

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

    PubMed

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

    2013-01-01

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

  10. Total Hepatitis B Core Antigen Antibody, a Quantitative Non-Invasive Marker of Hepatitis B Virus Induced Liver Disease.

    PubMed

    Yuan, Quan; Song, Liu-Wei; Cavallone, Daniela; Moriconi, Francesco; Cherubini, Beatrice; Colombatto, Piero; Oliveri, Filippo; Coco, Barbara Agata; Ricco, Gabriele; Bonino, Ferruccio; Shih, James Wai Kuo; Xia, Ning-Shao; Brunetto, Maurizia Rossana

    2015-01-01

    Non invasive immunologic markers of virus-induced liver disease are unmet needs. We tested the clinical significance of quantitative total and IgM-anti-HBc in well characterized chronic-HBsAg-carriers. Sera (212) were obtained from 111 HBsAg-carriers followed-up for 52 months (28-216) during different phases of chronic-HBV-genotype-D-infection: 10 HBeAg-positive, 25 inactive-carriers (HBV-DNA≤2000IU/ml, ALT<30U/L), 66 HBeAg-negative-CHB-patients and 10 with HDV-super-infection. In 35 patients treated with Peg-IFN±nucleos(t)ide-analogues (NUCs) sera were obtained at baseline, end-of-therapy and week-24-off-therapy and in 22 treated with NUCs (for 60 months, 42-134m) at baseline and end-of-follow-up. HBsAg and IgM-anti-HBc were measured by Architect-assays (Abbott, USA); total-anti-HBc by double-antigen-sandwich-immune-assay (Wantai, China); HBV-DNA by COBAS-TaqMan (Roche, Germany). Total-anti-HBc were detectable in all sera with lower levels in HBsAg-carriers without CHB (immune-tolerant, inactive and HDV-superinfected, median 3.26, range 2.26-4.49 Log10 IU/ml) versus untreated-CHB (median 4.68, range 2.76-5.54 Log10 IU/ml), p<0.0001. IgM-anti-HBc positive using the chronic-hepatitis-cut-off" (0.130-S/CO) were positive in 102 of 212 sera (48.1%). Overall total-anti-HBc and IgM-anti-HBc correlated significantly (p<0.001, r=0.417). Total-anti-HBc declined significantly in CHB patients with response to Peg-IFN (p<0.001) and in NUC-treated patients (p<0.001); the lowest levels (median 2.68, range 2.12-3.08 Log10 IU/ml) were found in long-term responders who cleared HBsAg subsequently. During spontaneous and therapy-induced fluctuations of CHB (remissions and reactivations) total- and IgM-anti-HBc correlated with ALT (p<0.001, r=0.351 and p=0.008, r=0.185 respectively). Total-anti-HBc qualifies as a useful marker of HBV-induced-liver-disease that might help to discriminate major phases of chronic HBV infection and to predict sustained response to antivirals.

  11. Total Hepatitis B Core Antigen Antibody, a Quantitative Non-Invasive Marker of Hepatitis B Virus Induced Liver Disease

    PubMed Central

    Cavallone, Daniela; Moriconi, Francesco; Cherubini, Beatrice; Colombatto, Piero; Oliveri, Filippo; Coco, Barbara Agata; Ricco, Gabriele; Bonino, Ferruccio; Shih, James Wai Kuo; Xia, Ning-Shao; Brunetto, Maurizia Rossana

    2015-01-01

    Non invasive immunologic markers of virus-induced liver disease are unmet needs. We tested the clinical significance of quantitative total and IgM-anti-HBc in well characterized chronic-HBsAg-carriers. Sera (212) were obtained from 111 HBsAg-carriers followed-up for 52 months (28-216) during different phases of chronic-HBV-genotype-D-infection: 10 HBeAg-positive, 25 inactive-carriers (HBV-DNA≤2000IU/ml, ALT<30U/L), 66 HBeAg-negative-CHB-patients and 10 with HDV-super-infection. In 35 patients treated with Peg-IFN±nucleos(t)ide-analogues (NUCs) sera were obtained at baseline, end-of-therapy and week-24-off-therapy and in 22 treated with NUCs (for 60 months, 42-134m) at baseline and end-of-follow-up. HBsAg and IgM-anti-HBc were measured by Architect-assays (Abbott, USA); total-anti-HBc by double-antigen-sandwich-immune-assay (Wantai, China); HBV-DNA by COBAS-TaqMan (Roche, Germany). Total-anti-HBc were detectable in all sera with lower levels in HBsAg-carriers without CHB (immune-tolerant, inactive and HDV-superinfected, median 3.26, range 2.26-4.49 Log10 IU/ml) versus untreated-CHB (median 4.68, range 2.76-5.54 Log10 IU/ml), p<0.0001. IgM-anti-HBc positive using the chronic-hepatitis-cut-off" (0.130-S/CO) were positive in 102 of 212 sera (48.1%). Overall total-anti-HBc and IgM-anti-HBc correlated significantly (p<0.001, r=0.417). Total-anti-HBc declined significantly in CHB patients with response to Peg-IFN (p<0.001) and in NUC-treated patients (p<0.001); the lowest levels (median 2.68, range 2.12-3.08 Log10 IU/ml) were found in long-term responders who cleared HBsAg subsequently. During spontaneous and therapy-induced fluctuations of CHB (remissions and reactivations) total- and IgM-anti-HBc correlated with ALT (p<0.001, r=0.351 and p=0.008, r=0.185 respectively). Total-anti-HBc qualifies as a useful marker of HBV-induced-liver-disease that might help to discriminate major phases of chronic HBV infection and to predict sustained response to antivirals. PMID

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. Reduction of Cob(III)alamin to Cob(II)alamin in Salmonella enterica Serovar Typhimurium LT2

    PubMed Central

    Fonseca, Maris V.; Escalante-Semerena, Jorge C.

    2000-01-01

    Reduction of the cobalt ion of cobalamin from the Co(III) to the Co(I) oxidation state is essential for the synthesis of adenosylcobalamin, the coenzymic form of this cofactor. A cob(II)alamin reductase activity in Salmonella enterica serovar Typhimurium LT2 was isolated to homogeneity. N-terminal analysis of the homogeneous protein identified NAD(P)H:flavin oxidoreductase (Fre) (EC 1.6.8.1) as the enzyme responsible for this activity. The fre gene was cloned, and the overexpressed protein, with a histidine tag at its N terminus, was purified to homogeneity by nickel affinity chromatography. His-tagged Fre reduced flavins (flavin mononucleotide [FMN] and flavin adenine dinucleotide [FAD]) and cob(III)alamin to cob(II)alamin very efficiently. Photochemically reduced FMN substituted for Fre in the reduction of cob(III)alamin to cob(II)alamin, indicating that the observed cobalamin reduction activity was not Fre dependent but FMNH2 dependent. Enzyme-independent reduction of cob(III)alamin to cob(II)alamin by FMNH2 occurred at a rate too fast to be measured. The thermodynamically unfavorable reduction of cob(II)alamin to cob(I)alamin was detectable by alkylation of the cob(I)alamin nucleophile with iodoacetate. Detection of the product, caboxymethylcob(III)alamin, depended on the presence of FMNH2 in the reaction mixture. FMNH2 failed to substitute for potassium borohydride in in vitro assays for corrinoid adenosylation catalyzed by the ATP:co(I)rrinoid adenosyltransferase (CobA) enzyme, even under conditions where Fre and NADH were present in the reaction mixture to ensure that FMN was always reduced. These results were interpreted to mean that Fre was not responsible for the generation of cob(I)alamin in vivo. Consistent with this idea, a fre mutant displayed wild-type cobalamin biosynthetic phenotypes. It is proposed that S. enterica serovar Typhimurium LT2 may not have a cob(III)alamin reductase enzyme and that, in vivo, nonadenosylated cobalamin and other

  19. 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

  20. Re-treatment of patients with hepatitis C who failed to respond (nonresponders) to previous treatment.

    PubMed

    Sharvadze, L G; Gogichaishvili, Sh Sh; Sakandelidze, Ts G; Zhamutashvili, M T; Chkhartishvili, N I

    2009-01-01

    The aim of four-year follow up study was evaluation of re-treatment efficacy of antiviral therapy in patients with hepatitis C who failed to respond (non responders) to previous therapy. Study enrolled 29 patients, aged 21-59 with HCV infection (15 had HCV genotype 1, and 14 had HCV non-genotype1), who previously were treated with unmodified interferon alfa (conventional interferon) 2a or 2b 5 MIU TIW plus ribavirin (1000-1200 mg/day) and who failed under this therapy. Study subjects were randomized into two groups: in group I were included 17 patients--relapsers (patient in whom HCV RNA becomes undetectable on treatment and is undetectable at the end of therapy, but is detected again after discontinuation of treatment). Group II was composed of 12 patients: 4 were non responders (patient in whom HCV RNA levels remain stable on treatment), 4--partial responders (HCV RNA levels decline by >2 logs, but never become undetectable during treatment) and 4--breakthrough non responders (HCV RNA become undetectable during treatment, but before-treatment termination again become detectable). The diagnosis of HCV infection was made based on detection of HCV antibodies by ELISA and confirmed by RIBA. Detection of HCV RNA (qualitative) and HCV RNA Viral load--by Real time PCR technique (COBAS TaqMan Test). HCV genotypes were detected by INNO-Lipa method. In group I--rapid virological response (RVR) was observed in 10 (58%) patients, early viral response (EVR) in 12 patients (70%). Among them 9 (52%) patients remained HCV RNA undetectable by the end of treatment. After 6 months sustained viral response (SVR) was received in 7 (41%) patients from group I. In group II--RVR was observed in 5 (41%), EVR in 6 (50%) patients. Among them 5 (41%) patients remained HCV RNA undetectable by the end of treatment. After 6 months Sustained Viral Response was received in 3 (25%) patients. Re-treatment with pegylated interferon and ribavirin in patients with hepatitis C who failed to responds

  1. 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

  2. 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.

  3. Application of a newly developed high-sensitivity HBsAg chemiluminescent enzyme immunoassay for hepatitis B patients with HBsAg seroclearance.

    PubMed

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

    2013-11-01

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

  4. 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

  5. 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

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

    PubMed

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

    2009-12-01

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

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

    PubMed

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

    2009-03-01

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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  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. 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

  16. Epidermal growth factor receptor tyrosine kinase (EGFR-TK) mutation testing in adults with locally advanced or metastatic non-small cell lung cancer: a systematic review and cost-effectiveness analysis.

    PubMed Central

    Westwood, Marie; Joore, Manuela; Whiting, Penny; van Asselt, Thea; Ramaekers, Bram; Armstrong, Nigel; Misso, Kate; Severens, Johan; Kleijnen, Jos

    2014-01-01

    as hazard ratios and tumour response data as relative risks, with 95% CIs. The health-economic analysis considered the long-term costs and quality-adjusted life-years (QALYs) associated with different tests followed by treatment with either standard chemotherapy or a TKI. Direct sequencing was taken as the comparator. The de novo model consisted of a decision tree and a Markov model. RESULTS The survey indicated no differences between tests in batch size, turnaround time, number of failed samples or cost. Six studies provided data on the accuracy of EGFR-TK mutation testing for predicting response to treatment with TKIs. Estimates of accuracy were similar across studies. Six analyses provided data on the clinical effectiveness of TKIs compared with standard chemotherapy. There were no clear differences in the treatment effects reported by different studies, regardless of which EGFR mutation test was used to select patients. Cost-effectiveness analysis using 'Evidence on comparative effectiveness available' and 'Linked evidence' approaches: Therascreen(®) EGFR polymerase chain reaction (PCR) Kit (Qiagen, Venlo, the Netherlands) was both less effective and less costly than direct sequencing of all exon 19-21 mutations at an incremental cost-effectiveness ratio of £32,167 (comparative) and £32,190 (linked) per QALY lost. 'Assumption of equal prognostic value' approach: the lowest total strategy cost was [commercial-in-confidence (CiC) information has been removed] [Sanger sequencing or Roche cobas EGFR Mutation Testing Kit(®) (Roche Molecular Systems, Inc., Branchburg, NJ, USA)] compared with (CiC information has been removed) for the most expensive strategy (fragment length analysis combined with pyrosequencing). LIMITATIONS The cost-effectiveness analysis assumed that the differences in outcomes between the results of the trials were solely attributable to the different mutation tests used to distinguish between patients; this assumption ignores other factors that