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Sample records for cobas ampliprep-cobas taqman

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

    Science.gov (United States)

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

    2017-01-01

    Routine HIV viral load testing is not widely accessible in most resource-limited settings, including Kenya. To increase access to viral load testing, alternative sample types like dried blood spots (DBS), which overcome the logistic barriers associated with plasma separation and cold chain shipment need to be considered and evaluated. The current study evaluated matched dried blood spots (DBS) and dried plasma spots (DPS) against plasma using the Abbott M 2000 (Abbott) and Roche Cobas Ampliprep/Cobas TaqMan (CAP/CTM) quantitative viral load assays in western Kenya. Matched plasma DBS and DPS were obtained from 200 HIV-1 infected antiretroviral treatment (ART)-experienced patients attending patient support centers in Western Kenya. Standard quantitative assay performance parameters with accompanying 95% confidence intervals (CI) were assessed at the assays lower detection limit (400cps/ml for CAP/CTM and 550cps/ml for Abbott) using SAS version 9.2. Receiver operating curves (ROC) were further used to assess viral-load thresholds with best assay performance (reference assay CAP/CTM plasma). Using the Abbott test, the sensitivity and specificity, respectively, for DPS were (97.3%, [95%CI: 93.2-99.2] and 98.1% [95%CI: 89.7-100]) and those for DBS (93.9% [95%CI: 88.8-97.2] and 88.0% [95%CI: 82.2-92.4]). The correlation and agreement using paired plasma and DPS/DBS were strong, with r2 = 90.5 and rc = 68.1. The Bland-Altman relative percent change was 95.3 for DPS, (95%CI: 90.4-97.7) and 73.6 (95%CI: 51.6-86.5) for DBS. Using the CAP/CTM assay, the sensitivity for DBS was significantly higher compared to DPS (100.0% [95% CI: 97.6-100.0] vs. 94.7% [95%CI: 89.8-97.7]), while the specificity for DBS was lower: 4%, [95% CI: 0.4-13.7] compared to DPS: 94.0%, [95% CI: 83.5-98.7]. When compared under different clinical relevant thresholds, the accuracy for the Abbott assay was 95% at the 1000cps/ml cut-off with a sensitivity and specificity of 96.6% [95% CI 91.8-98.7] and 90

  2. Improving clinical laboratory efficiency: a time-motion evaluation of the Abbott m2000 RealTime and Roche COBAS AmpliPrep/COBAS TaqMan PCR systems for the simultaneous quantitation of HIV-1 RNA and HCV RNA.

    Science.gov (United States)

    Amendola, Alessandra; Coen, Sabrina; Belladonna, Stefano; Pulvirenti, F Renato; Clemens, John M; Capobianchi, M Rosaria

    2011-08-01

    Diagnostic laboratories need automation that facilitates efficient processing and workflow management to meet today's challenges for expanding services and reducing cost, yet maintaining the highest levels of quality. Processing efficiency of two commercially available automated systems for quantifying HIV-1 and HCV RNA, Abbott m2000 system and Roche COBAS Ampliprep/COBAS TaqMan 96 (docked) systems (CAP/CTM), was evaluated in a mid/high throughput workflow laboratory using a representative daily workload of 24 HCV and 72 HIV samples. Three test scenarios were evaluated: A) one run with four batches on the CAP/CTM system, B) two runs on the Abbott m2000 and C) one run using the Abbott m2000 maxCycle feature (maxCycle) for co-processing these assays. Cycle times for processing, throughput and hands-on time were evaluated. Overall processing cycle time was 10.3, 9.1 and 7.6 h for Scenarios A), B) and C), respectively. Total hands-on time for each scenario was, in order, 100.0 (A), 90.3 (B) and 61.4 min (C). The interface of an automated analyzer to the laboratory workflow, notably system set up for samples and reagents and clean up functions, are as important as the automation capability of the analyzer for the overall impact to processing efficiency and operator hands-on time.

  3. Analytical performance of the Hologic Aptima HBV Quant Assay and the COBAS Ampliprep/COBAS TaqMan HBV test v2.0 for the quantification of HBV DNA in plasma samples

    DEFF Research Database (Denmark)

    Schønning, Kristian; Johansen, Kim; Nielsen, Lone Gilmor

    2018-01-01

    than in CAPCTMv2. Only minor differences were observed between genotype A (N = 4; average difference -0.01 Log IU/mL), B (N = 8; -0.13 Log IU/mL), C (N = 8; -0.31 Log IU/mL), D (N = 25; -0.22 Log IU/mL), and E (N = 7; -0.03 Log IU/mL). Deming regression showed that the two tests were excellently...

  4. Comparison of the Hologic Aptima HIV-1 Quant Dx Assay to the Roche COBAS Ampliprep/COBAS TaqMan HIV-1 Test v2.0 for the quantification of HIV-1 RNA in plasma samples

    DEFF Research Database (Denmark)

    Schønning, Kristian; Johansen, Kim; Landt, Bodil

    2017-01-01

    load compared to the CAPCTMv2 was observed in Bland-Altman analysis, by Deming regression (Slope 1.13) and in dilution series of clinical samples. Precision evaluated using the Acrometrix Positive Controls was similar for the High Control (CV: 1.2% vs. 1.3%; Aptima assay vs. CAPCTMv2 test, respectively...

  5. Performance evaluation of cobas HBV real-time PCR assay on Roche cobas 4800 System in comparison with COBAS AmpliPrep/COBAS TaqMan HBV Test.

    Science.gov (United States)

    Kim, Hanah; Hur, Mina; Bae, Eunsin; Lee, Kyung-A; Lee, Woo-In

    2018-02-19

    Hepatitis B virus (HBV) nucleic acid amplification testing (NAAT) is important for the diagnosis and management of HBV infection. We evaluated the analytical performance of the cobas HBV NAAT (Roche Diagnostics GmbH, Mannheim, Germany) on the cobas 4800 System in comparison with COBAS AmpliPrep/COBAS TaqMan HBV Test (CAP/CTM HBV). Precision was evaluated using three levels of cobas HBV/HCV/HIV-1 Control Kit, and linearity was evaluated across the anticipated measuring range (10.0-1.0×109 IU/mL) at seven levels using clinical samples. Detection capability, including limit of blank (LOB), limit of detection (LOD) and limit of quantitation (LOQ), was verified using the 4th WHO International Standard for HBV DNA for NAT (NIBSC code: 10/266). Correlation between the two systems was compared using 205 clinical samples (102 sera and 103 EDTA plasma). Repeatability and total imprecision (coefficient of variation) ranged from 0.5% to 3.8% and from 0.5% to 3.5%, respectively. Linearity (coefficient of determination, R2) was 0.999. LOB, LOD and LOQ were all acceptable within the observed proportion rate (85%). Correlation was very high between the two systems in both serum and plasma samples (correlation coefficient [r]=0.995). The new cobas HBV real-time PCR assay on the cobas 4800 System showed reliable analytical performances.

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

    NARCIS (Netherlands)

    S.D. Pas (Suzan); R. Molenkamp (Richard); J. Schinkel (Janke); S. Rebers; C. Copra (Cederick); S. Seven-Deniz; D. Thamke (Diana); R.J. de Knegt (Robert); B.L. Haagmans (Bart); M. Schutten (Martin)

    2013-01-01

    textabstractTo evaluate the analytical performance and explore the clinical applicability of the new Roche cobas AmpliPrep/cobas TaqMan HCV test, v2.0 (CAP/CTM v2.0), a platform comparison was performed on panels and diagnostic samples with the Roche cobas AmpliPrep/cobas TaqMan HCV test (CAP/CTM

  7. Results of the Abbott RealTime HIV-1 Assay for Specimens Yielding “Target Not Detected” Results by the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test▿

    OpenAIRE

    Babady, N. Esther; Germer, Jeffrey J.; Yao, Joseph D. C.

    2009-01-01

    No significantly discordant results were observed between the Abbott RealTime HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all nine U.S. geographic regions and previously yielding “target not detected” results by CTM.

  8. Results of the Abbott RealTime HIV-1 assay for specimens yielding "target not detected" results by the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test.

    Science.gov (United States)

    Babady, N Esther; Germer, Jeffrey J; Yao, Joseph D C

    2010-03-01

    No significantly discordant results were observed between the Abbott RealTime HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all nine U.S. geographic regions and previously yielding "target not detected" results by CTM.

  9. Performance evaluation of the Cobas TaqMan MTB assay on respiratory specimens according to clinical application

    Directory of Open Access Journals (Sweden)

    Jong Eun Park

    2017-11-01

    Full Text Available Objective: To evaluate the performance of the Cobas TaqMan MTB assay (Cobas assay with respect to its clinical application. Methods: This was a retrospective analysis of 1154 results from 1034 patients for whom mycobacterial cultures and the Cobas assay were performed simultaneously. Based on the patient medical records, two categories of clinical application were defined: (1 the diagnosis of patients with a high probability of pulmonary tuberculosis according to clinical and radiological features (n = 128, and (2 the exclusion of tuberculosis in clinically indeterminate patients (n = 1026. Standard culture was used as the reference method. Results: The sensitivity of the Cobas assay for the detection of Mycobacterium tuberculosis was 70.4% (95% confidence interval (CI 49.7–85.5% for category 1, but only 25.0% (95% CI 4.5–64.4% for category 2. The specificity was ≥95.0% for both categories. The positive predictive value was 79.2% (95% CI 57.3–92.1% for category 1 and 33.3% (95% CI 6.0–75.9% for category 2, while the negative predictive value was 92.3% (95% CI 85.0–96.4% for category 1 and 99.4% (95% CI 98.7–99.8% for category 2. Conclusions: The results of this study indicate that Cobas assay results must be interpreted carefully according to the clinical purpose of the assay. Keywords: Mycobacterium tuberculosis, Pulmonary tuberculosis, Cobas TaqMan MTB assay, Korea

  10. Performance of the cobas Hepatitis B virus (HBV) test using the cobas 4800 system and comparison of HBV DNA quantification ability between the COBAS AmpliPrep/COBAS TaqMan HBV test version 2.0 and cobas HBV test.

    Science.gov (United States)

    Shin, Kyung-Hwa; Lee, Hyun-Ji; Chang, Chulhun L; Kim, Hyung-Hoi

    2018-04-01

    Hepatitis B virus (HBV) DNA levels are used to predict the response to therapy, determine therapy initiation, monitor resistance to therapy, and establish treatment success. To verify the performance of the cobas HBV test using the cobas 4800 system for HBV DNA quantification and to compare the HBV DNA quantification ability between the cobas HBV test and COBAS AmpliPrep/COBAS TaqMan HBV version 2.0 (CAP/CTM v2.0). The precision, linearity, and limit of detection of the cobas HBV test were evaluated using the 4th World Health Organization International Standard material and plasma samples. Clinical samples that yielded quantitative results using the CAP/CTM v2.0 and cobas HBV tests were subjected to correlational analysis. Three hundred forty-nine samples were subjected to correlational analysis, among which 114 samples showed results above the lower limit of quantification. Comparable results were obtained ([cobas HBV test] = 1.038 × [CAP/CTM v2.0]-0.173, r = 0.914) in 114 samples, which yielded values above the lower limit of quantification. The results for 86.8% of the samples obtained using the cobas HBV test were within 0.5 log 10 IU/mL of the CAP/CTM v2.0 results. The total precision values against the low and high positive controls were 1.4% (mean level: 2.25 log 10 IU/mL) and 3.2% (mean level: 6.23 log 10 IU/mL), respectively. The cobas HBV test demonstrated linearity (1.15-6.75 log 10 IU/mL, y = 0.95 × 6 + 0.17, r 2  = 0.994). The cobas HBV test showed good correlation with CAP/CTM v2.0, and had good precision and an acceptable limit of detection. The cobas HBV test using the cobas 4800 is a reliable method for quantifying HBV DNA levels in the clinical setting. Copyright © 2018. Published by Elsevier B.V.

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

    Directory of Open Access Journals (Sweden)

    Yi-Ching Tung

    2015-04-01

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

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

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

    2017-04-04

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

  13. Establishing diagnostic cut-off criteria for the COBAS AmpliPrep/COBAS TaqMan HIV-1 Qualitative test through validation against the Amplicor DNA test v1.5 for infant diagnosis using dried blood spots.

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    Maritz, Jean; Preiser, Wolfgang; van Zyl, Gert U

    2012-02-01

    As antibody testing cannot confirm HIV-1 infection in children less than 18 months of age, diagnosis in these children depends on nucleic acid testing. The COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) (CAP/CTM, Roche(®) Molecular Systems, Inc., Branchburg, NJ) HIV-1 Qualitative test is a total nucleic acid real-time PCR assay utilising whole EDTA blood or dried blood spots (DBS), which recently replaced the Roche(®) AMPLICOR(®) DNA test v1.5 (Amplicor) as the diagnostic HIV PCR assay in many South African laboratories. For the Amplicor assay, stringent diagnostic criteria were previously formulated for the local population, and a comparison reported the CAP/CTM's sensitivity at 99.7% and specificity at 100% for both sample types compared to these Amplicor criteria. To validate the assay prior to introduction in our laboratory and to define stringent diagnostic cut-off criteria. Whole EDTA blood samples from patients younger than 18 months sent for routine HIV-1 diagnosis were tested by Amplicor, and positive results were confirmed from DBS. CAP/CTM assays were subsequently performed from DBS. The CAP/CTM had a sensitivity of 98.8% and a specificity of 97.1%, but a positive predictive value (PPV) of only 78.7% compared to the Amplicor assay. Samples positive by CAP/CTM but negative by Amplicor displayed poor amplification curves compared to concordant positive samples. Upon re-testing those with sufficient material available by CAP/CTM, all showed negative results. The decreased PPV may either be due to false positive CAP/CTM results, or increased sensitivity compared to the Amplicor assay. Criteria were formulated for defining presumed false-positive results. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. Evaluation of the Aptima HBV Quant assay vs. the COBAS TaqMan HBV test using the high pure system for the quantitation of HBV DNA in plasma and serum samples.

    Science.gov (United States)

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

    2018-03-28

    Proper management of patients with chronic hepatitis B virus (HBV) infection requires monitoring of plasma or serum HBV DNA levels using a highly sensitive nucleic acid amplification test. Because commercially available assays differ in performance, we compared herein the performance of the Hologic Aptima HBV Quant assay (Aptima) to that of the Roche Cobas TaqMan HBV test for use with the high pure system (HPS/CTM). Assay performance was assessed using HBV reference panels as well as plasma and serum samples from chronically HBV-infected patients. Method correlation, analytical sensitivity, precision/reproducibility, linearity, bias and influence of genotype were evaluated. Data analysis was performed using linear regression, Deming correlation analysis and Bland-Altman analysis. Agreement between the assays for the two reference panels was good, with a difference in assay values vs. target 0.98). The two assays had similar bias and precision across the different genotypes tested at low viral loads (25-1000 IU/mL). Aptima has a performance comparable with that of HPS/CTM, making it suitable for use for HBV infection monitoring. Aptima runs on a fully automated platform (the Panther system) and therefore offers a significantly improved workflow compared with HPS/CTM.

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

    Science.gov (United States)

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

    2017-08-01

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

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

    Science.gov (United States)

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

    2012-12-01

    The cobas p 630, a fully automated pre-analytical instrument for primary tube handling recently introduced to complete the Cobas(®) TaqMan systems portfolio, was evaluated in conjunction with: the COBAS(®) AmpliPrep/COBAS(®) TaqMan HBV Test, v2.0, COBAS(®) AmpliPrep/COBAS(®) TaqMan HCV Test, v1.0 and COBAS(®) AmpliPrep/COBAS(®) TaqMan HIV Test, v2.0. The instrument performance in transferring samples from primary to secondary tubes, its impact in improving COBAS(®) AmpliPrep/COBAS(®) TaqMan workflow and hands-on reduction and the risk of possible cross-contamination were assessed. Samples from 42 HBsAg positive, 42 HCV and 42 HIV antibody (Ab) positive patients as well as 21 healthy blood donors were processed with or without automated primary tubes. HIV, HCV and HBsAg positive samples showed a correlation index of 0.999, 0.987 and of 0.994, respectively. To assess for cross-contamination, high titer HBV DNA positive samples, HCV RNA and HIV RNA positive samples were distributed in the cobas p 630 in alternate tube positions, adjacent to negative control samples within the same rack. None of the healthy donor samples showed any reactivity. Based on these results, the cobas p 630 can improve workflow and sample tracing in laboratories performing molecular tests, and reduce turnaround time, errors, and risks. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Evaluation of clinical sensitivity and specificity of hepatitis B virus (HBV), hepatitis C virus, and human immunodeficiency Virus-1 by cobas MPX: Detection of occult HBV infection in an HBV-endemic area.

    Science.gov (United States)

    Ha, Jihye; Park, Younhee; Kim, Hyon-Suk

    2017-11-01

    Transfusion-transmitted infectious diseases remain a major concern for blood safety, particularly with hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV). Nucleic acid testing (NAT) in donor screening shortens the serologically negative window period and reduces virus transmission. The cobas MPX (Roche Molecular Systems, Inc., Branchburg, New Jersey) is a recently developed multiplex qualitative PCR system that enables the simultaneous detection of HBV, HCV, and HIV with improved sensitivity and throughput using cobas 6800 and 8800 instruments. The aim of this study was to conduct an evaluation of the clinical sensitivity and specificity of cobas MPX detection of HBV, HCV, and HIV in clinical specimens. Among samples referred for HBV, HCV, and HIV-1 quantification at Severance Hospital, Yonsei University College of Medicine, positive samples were selected to evaluate sensitivity. A total of 843 samples was tested using both cobas MPX and COBAS AmpliPrep/COBAS TaqMan Tests for HBV, HCV, and HIV-1 using the cobas 8800 system and a COBAS TaqMan 96 analyzer, respectively. Samples that showed discrepancies were confirmed by nested PCR. The cobas MPX achieved excellent sensitivity and specificity for the detection of HBV, HCV, and HIV-1 in clinical samples. We found that the lower limit of detection (LOD) of blood screening by NAT actually improves clinical sensitivity, and occult HBV infection prevalence among healthy employees of the hospital was rather high. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. A Simple Phosphate-Buffered-Saline-Based Extraction Method Improves Specificity of HIV Viral Load Monitoring Using Dried Blood Spots.

    Science.gov (United States)

    Makadzange, A Tariro; Boyd, F Kathryn; Chimukangara, Benjamin; Masimirembwa, Collen; Katzenstein, David; Ndhlovu, Chiratidzo E

    2017-07-01

    Although Roche COBAS Ampliprep/COBAS TaqMan (CAP/CTM) systems are widely used in sub-Saharan Africa for early infant diagnosis of HIV from dried blood spots (DBS), viral load monitoring with this system is not practical due to nonspecific extraction of both cell-free and cell-associated viral nucleic acids. A simplified DBS extraction technique for cell-free virus elution using phosphate-buffered saline (PBS) may provide an alternative analyte for lower-cost quantitative HIV virus load (VL) testing to monitor antiretroviral therapy (ART). We evaluated the CAP/CTM v2.0 assay in 272 paired plasma and DBS specimens using the cell-free virus elution method and determined the level of agreement, sensitivity, and specificity at thresholds of target not detected (TND), target below the limit of quantification (BLQ) (1,000 copies/ml, the sensitivities, specificities, positive predictive values (PPV), and negative predictive values (NPV) were 92.7%, 100%, 100%, and 94.3%, respectively. PBS elution of DBS offers a sensitive and specific method for monitoring plasma viremia among adults and children on ART at the WHO-recommended threshold of >1,000 copies/ml on the Roche CAP/CTM system. Copyright © 2017 Makadzange et al.

  19. Impact of the COBAS AmpliPrep/COBAS AMPLICOR HIV-1 MONITOR Test, Version 1.5, on Clinical Laboratory Operations▿

    Science.gov (United States)

    Germer, Jeffrey J.; Bendel, Jordan L.; Dolenc, Craig A.; Nelson, Sarah R.; Masters, Amanda L.; Gerads, Tara M.; Mandrekar, Jayawant N.; Mitchell, P. Shawn; Yao, Joseph D. C.

    2007-01-01

    The COBAS AmpliPrep/COBAS AMPLICOR HIV-1 MONITOR Test, version 1.5 (CAP/CA), and the COBAS AMPLICOR HIV-1 MONITOR Test, version 1.5, were compared. CAP/CA reduced and consolidated labor while modestly increasing assay throughput without increased failure rates or direct costs, regardless of batch size and assay format. PMID:17634308

  20. Evaluation of NGAL TestTM on Cobas 6000

    DEFF Research Database (Denmark)

    Hansen, Young B L; Damgaard, Anette; Poulsen, Jørgen H

    2014-01-01

    BACKGROUND: Neutrophil Gelatinase-Associated Lipocalin (NGAL) is a promising biomarker for acute kidney injury (AKI). Our objectives were to evaluate the NGAL Test(TM) from Bioporto for both urine NGAL and plasma NGAL on the Cobas 6000 c501 (Roche Diagnostics, Rotkreuz, Switzerland) with matched...... measurements run on Hitachi 917, the method's linearity on the Cobas 6000 in urine, EDTA and Lithium-Heparin (Li-Hep), the influence of using EDTA or Li-Hep tubes and, finally, the impact of freezing and thawing on the sample. METHODS: Forty matched samples of Li-Hep and EDTA plasma and 40 urine samples were...

  1. Body fluid matrix evaluation on a Roche cobas 8000 system.

    Science.gov (United States)

    Owen, William E; Thatcher, Mindy L; Crabtree, Karolyn J; Greer, Ryan W; Strathmann, Frederick G; Straseski, Joely A; Genzen, Jonathan R

    2015-09-01

    Chemical analysis of body fluids is commonly requested by physicians. Because most commercial FDA-cleared clinical laboratory assays are not validated by diagnostic manufacturers for "non-serum" and "non-plasma" specimens, laboratories may need to complete additional validation studies to comply with regulatory requirements regarding body fluid testing. The objective of this report is to perform recovery studies to evaluate potential body fluid matrix interferences for commonly requested chemistry analytes. Using an IRB-approved protocol, previously collected clinical body fluid specimens (biliary/hepatic, cerebrospinal, dialysate, drain, pancreatic, pericardial, peritoneal, pleural, synovial, and vitreous) were de-identified and frozen (-20°C) until experiments were performed. Recovery studies (spiking with high concentration serum, control, and/or calibrator) were conducted using 10% spiking solution by volume; n=5 specimens per analyte/body fluid investigated. Specimens were tested on a Roche cobas 8000 system (c502, c702, e602, and ISE modules). In all 80 analyte/body fluid combinations investigated (including amylase, total bilirubin, urea nitrogen, carbohydrate antigen 19-9, carcinoembryonic antigen, cholesterol, chloride, creatinine, glucose, potassium, lactate dehydrogenase, lipase, rheumatoid factor, sodium, total protein, triglycerides, and uric acid), the average percent recovery was within predefined acceptable limits (less than ±10% from the calculated ideal recovery). The present study provides evidence against the presence of any systematic matrix interference in the analyte/body fluid combinations investigated on the Roche cobas 8000 system. Such findings support the utility of ongoing body fluid validation initiatives conducted to maintain compliance with regulatory requirements. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  2. NT-proBNP on Cobas h 232 in point-of-care testing

    DEFF Research Database (Denmark)

    Gils, Charlotte; Ramanathan, R.; Breindahl, T.

    2015-01-01

    Background. NT-proBNP may be useful for ruling out heart failure in primary health care. In this study we examined the analytical quality of NT-proBNP in primary health care on the Cobas h 232 point-of-care instrument compared with measurements performed in a hospital laboratory. Materials...... and methods. Blood samples requested for NT-proBNP were collected in primary health care (n = 95) and in a hospital laboratory (n = 107). NT-proBNP was measured on-site on Cobas h 232 instruments both in primary health care centres and at the hospital laboratory and all samples were also analyzed...... with a comparison method at the hospital. Precision, trueness, accuracy, and lot-variation were determined at different concentration levels and evaluated according to acceptance criteria. Furthermore user-friendliness was assessed by questionnaires. Results. For Cobas h 232 repeatability CV was 8...

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

    NARCIS (Netherlands)

    Melchers, W.J.G.; Kuijpers, J; Sickler, J.J.; Rahamat-Langendoen, J.C.

    2017-01-01

    Rapid diagnosis of influenza A and B is important for direct treatment decisions in patient care and for the reduction of in-hospital transmissions. The new real-time PCR based molecular point-of-care (POC) assay, the cobas(R) Influenza A/B test on the cobas(R) Liat(R) System (cobas(R) Liat(R)

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

    Science.gov (United States)

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

    2010-12-01

    To evaluate the analytical performance of the Diazyme ADA assay on the Cobas® 6000 system for pleural fluid samples analysis. Imprecision, linearity, calibration curve stability, interference, and correlation studies were completed. The Diazyme ADA assay demonstrated excellent precision (CVADA assay correlated well with the Giusti method (r(2)=0.93) but exhibited a negative bias (~ -30%). The Diazyme ADA assay on the Cobas® 6000 system represents a rapid, accurate, precise and reliable method for determination of ADA activity in pleural fluid samples. Copyright © 2010 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  5. Comparison of the cobas Human Papillomavirus (HPV) Test with the Hybrid Capture 2 and Linear Array HPV DNA Tests

    Science.gov (United States)

    Sadorra, Mark; LaMere, Brandon J.; Kail, Randi; Aldrich, Carrie; Kinney, Walter; Fetterman, Barbara; Lorey, Thomas; Schiffman, Mark; Castle, Philip E.

    2012-01-01

    The cobas human papillomavirus (HPV) test (cobas) was recently approved by the U.S. Food and Drug Administration (FDA) and identifies HPV16 and HPV18 separately as well as detecting a pool of 11 HR-HPV genotypes (HPV31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -68) and also HPV66. We compared cobas, Linear Array (LA), and Hybrid Capture 2 (HC2) assays for detection of carcinogenic HPV DNA, and cobas and LA for detection of HPV16 and HPV18 DNA, among the first 1,852 women enrolled in the HPV Persistence and Progression Cohort (PaP Cohort) study. Specimens were tested by all 3 assays 1 year after an HC2-positive result. In 1,824 specimens with cobas results, cobas had an 85.9% agreement with HC2 and 91.0% agreement with LA for carcinogenic HPV detection. When results between cobas and HC2 disagreed, cobas tended to call more women HPV positive (P < 0.01). Categorizing cobas and LA results hierarchically according to cancer risk (HPV16, HPV18, other carcinogenic HPV genotypes, or carcinogen negative), there was a 90% agreement for all categories of HPV (n = 1,824). We found good agreement between the two U.S. FDA-approved HPV tests, with discrepancies between the two assays due to specific characteristics of the individual assays. Additional studies are needed to compare HC2 and cobas for detecting and predicting CIN3 to understand the clinical implications of the discrepant test results between the two tests. PMID:22075592

  6. [Determination of drug resistance mutations of NS3 inhibitors in chronic hepatitis C patients infected with genotype 1].

    Science.gov (United States)

    Şanlıdağ, Tamer; Sayan, Murat; Akçalı, Sinem; Kasap, Elmas; Buran, Tahir; Arıkan, Ayşe

    2017-04-01

    Direct-acting antiviral agents (DAA) such as NS3 protease inhibitors is the first class of drugs used for chronic hepatitis C (CHC) treatment. NS3 inhibitors (PI) with low genetic barrier have been approved to be used in the CHC genotype 1 infections, and in the treatment of compensated liver disease including cirrhosis together with pegile interferon and ribavirin. Consequently, the development of drug resistance during DAA treatment of CHC is a major problem. NS3 resistant variants can be detected before treatment as they can occurnaturally. The aim of this study was to investigate new and old generation NS3 inhibitors resistance mutations before DAA treatment in hepatitis C virus (HCV) that were isolated from CHC. The present study was conducted in 2015 and included 97 naive DAA patients infected with HCV genotype 1, who were diagnosed in Manisa and Kocaeli cities of Turkey. Magnetic particle based HCV RNA extraction and than RNA detection and quantification were performed using commercial real-time PCR assay QIASypmhony + Rotorgene Q/ArtusHCV QS-RGQ and COBAS Ampliprep/COBAS TaqMan HCV Tests. HCV NS3 viral protease genome region was amplified with PCR and mutation analysis was performed by Sanger dideoxy sequencing technique of NS3 protease codons (codon 32-185). HCV NS3 protease inhibitors; asunaprevir, boceprevir, faldaprevir, grazoprevir, pariteprevir, simeprevir and telaprevir were analysed for resistant mutations by Geno2pheno-HCV resistance tool. HCV was genotyped in all patients and 88 patients (n= 88/97, 91%) had genotype 1. Eight (n= 8/97, 8.2%) and 80 (n= 80/97, 82.4%) HCC patients were subgenotyped as 1a and 1b, respectively. Many aminoacid substitutions and resistance mutations were determined in 39/88 (44%) patients in the study group. Q80L, S122C/N, S138W were defined as potential substitutions (6/88 patients; 7%); R109K, R117C, S122G, I132V, I170V, N174S were described as potential resistance (34/88 patients; 39%); V36L, T54S, V55A, Q80H were

  7. Hybrid Capture 2 and cobas human papillomavirus assays perform similarly on SurePath samples from women with abnormalities

    DEFF Research Database (Denmark)

    Fornari, D; Rebolj, M; Bjerregaard, B

    2016-01-01

    OBJECTIVE: In two laboratories (Departments of Pathology, Copenhagen University Hospitals of Herlev and Hvidovre), we compared cobas and Hybrid Capture 2 (HC2) human papillomavirus (HPV) assays using SurePath® samples from women with atypical squamous cells of undetermined significance (ASCUS......) at ≥30 years and women after treatment of cervical intraepithelial neoplasia (CIN). METHODS: Samples from 566 women with ASCUS and 411 women after treatment were routinely tested with HC2 and, thereafter, with cobas. Histological outcomes were retrieved from the Danish Pathology Data Base. We calculated...... the overall agreement between the assays, and compared their sensitivity and specificity for ≥CIN2. RESULTS: In women with ASCUS, HC2 and cobas testing results were similar in the two laboratories. The overall agreement was 91% (95% CI, 88-93). After CIN treatment, the overall agreement was 87% (95% CI, 82...

  8. Human papillomavirus detection with genotyping by the cobas and Aptima assays: Significant differences in HPV 16 detection?

    Science.gov (United States)

    Chorny, Joseph A; Frye, Teresa C; Fisher, Beth L; Remmers, Carol L

    2018-03-23

    The primary high-risk human papillomavirus (hrHPV) assays in the United States are the cobas (Roche) and the Aptima (Hologic). The cobas assay detects hrHPV by DNA analysis while the Aptima detects messenger RNA (mRNA) oncogenic transcripts. As the Aptima assay identifies oncogenic expression, it should have a lower rate of hrHPV and genotype detection. The Kaiser Permanente Regional Reference Laboratory in Denver, Colorado changed its hrHPV assay from the cobas to the Aptima assay. The rates of hrHPV detection and genotyping were compared over successive six-month periods. The overall hrHPV detection rates by the two platforms were similar (9.5% versus 9.1%) and not statistically different. For genotyping, the HPV 16 rate by the cobas was 1.6% and by the Aptima it was 1.1%. These differences were statistically different with the Aptima detecting nearly one-third less HPV 16 infections. With the HPV 18 and HPV 18/45, there was a slightly higher detection rate of HPV 18/45 by the Aptima platform (0.5% versus 0.9%) and this was statistically significant. While HPV 16 represents a low percentage of hrHPV infections, it was detected significantly less by the Aptima assay compared to the cobas assay. This has been previously reported, although not highlighted. Given the test methodologies, one would expect the Aptima to detect less HPV 16. This difference appears to be mainly due to a significantly increased number of non-oncogenic HPV 16 infections detected by the cobas test as there were no differences in HPV 16 detection rates in the high-grade squamous intraepithelial lesions indicating that the two tests have similar sensitivities for oncogenic HPV 16. © 2018 Wiley Periodicals, Inc.

  9. The cobas® 6800/8800 System: a new era of automation in molecular diagnostics.

    Science.gov (United States)

    Cobb, Bryan; Simon, Christian O; Stramer, Susan L; Body, Barbara; Mitchell, P Shawn; Reisch, Natasa; Stevens, Wendy; Carmona, Sergio; Katz, Louis; Will, Stephen; Liesenfeld, Oliver

    2017-02-01

    Molecular diagnostics is a key component of laboratory medicine. Here, the authors review key triggers of ever-increasing automation in nucleic acid amplification testing (NAAT) with a focus on specific automated Polymerase Chain Reaction (PCR) testing and platforms such as the recently launched cobas® 6800 and cobas® 8800 Systems. The benefits of such automation for different stakeholders including patients, clinicians, laboratory personnel, hospital administrators, payers, and manufacturers are described. Areas Covered: The authors describe how molecular diagnostics has achieved total laboratory automation over time, rivaling clinical chemistry to significantly improve testing efficiency. Finally, the authors discuss how advances in automation decrease the development time for new tests enabling clinicians to more readily provide test results. Expert Commentary: The advancements described enable complete diagnostic solutions whereby specific test results can be combined with relevant patient data sets to allow healthcare providers to deliver comprehensive clinical recommendations in multiple fields ranging from infectious disease to outbreak management and blood safety solutions.

  10. Cross-reactivity profiles of hybrid capture II, cobas, and APTIMA human papillomavirus assays

    DEFF Research Database (Denmark)

    Preisler, Sarah Nørgaard; Rebolj, Matejka; Ejegod, Ditte Møller

    2016-01-01

    evaluated to what extent these can be explained by cross-reactivity, i.e. positive test results without evidence of high-risk HPV genotypes. The patterns of cross-reactivity have been thoroughly studied for hybrid capture II (HC2) but not yet for newer HPV assays although the manufacturers claimed...... no or limited frequency of cross-reactivity. In this independent study we evaluated the frequency of cross-reactivity for HC2, cobas, and APTIMA assays. Methods Consecutive routine cervical screening samples from 5022 Danish women, including 2859 from women attending primary screening, were tested...... with normal cytology and positive high-risk HPV test results were invited for repeated testing in 18 months. Results Cross-reactivity to low-risk genotypes was detected in 109 (2.2 %) out of 5022 samples on HC2, 62 (1.2 %) on cobas, and 35 (0.7 %) on APTIMA with only 10 of the samples cross-reacting on all 3...

  11. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S; Jaing, C

    2012-03-27

    The goal of this project is to develop forensic genotyping assays for select agent viruses, addressing a significant capability gap for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the Taqman signature development for South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.

  12. Validation of Method Performance of pH, PCO2, PO2, Na(+), K(+) of Cobas b121 ABG Analyser.

    Science.gov (United States)

    Nanda, Sunil Kumar; Ray, Lopamudra; Dinakaran, Asha

    2014-06-01

    The introduction of a new method or new analyser is a common occurrence in clinical biochemistry laboratory. Blood gas measurements and electrolytes are often performed in Point-of-Care (POC) settings. When a new POC analyser is obtained, the performance of the analyser should be evaluated by comparison to the measurements with the reference analyser in the laboratory. Evaluation of method performance of pH, PCO2, PO2, Na(+), K(+) of cobas b121 ABG analyser. The evaluation of method performance of pH, PO2, PCO2, Na(+), K(+) of cobas b121 ABG analyser was done by comparing the results of 50 patient samples run on cobas b121 with the results obtained from Rapid lab values (reference analyser). Correlation coefficient was calculated from the results obtained from both the analysers. Precision was calculated by running biorad ABG control samples. The correlation coefficient values obtained for parameters were close to 1.0 indicating good correlation. The CV obtained for all the parameters were less than 5 indicating good precision. The new ABG analyser, Cobas b121 correlated well with the reference ABG analyser (Rapid Lab) and could be used to run on patient samples.

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

    Science.gov (United States)

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

    2014-08-01

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

  14. Comparison of cobas HCV GT against Versant HCV Genotype 2.0 (LiPA) with confirmation by Sanger sequencing.

    Science.gov (United States)

    Yusrina, Falah; Chua, Cui Wen; Lee, Chun Kiat; Chiu, Lily; Png, Tracy Si-Yu; Khoo, Mui Joo; Yan, Gabriel; Lee, Guan Huei; Yan, Benedict; Lee, Hong Kai

    2018-05-01

    Correct identification of infecting hepatitis C virus (HCV) genotype is helpful for targeted antiviral therapy. Here, we compared the HCV genotyping performance of the cobas HCV GT assay against the Versant HCV Genotype 2.0 (LiPA) assay, using 97 archived serum samples. In the event of discrepant or indeterminate results produced by either assay, the core and NS5B regions were sequenced. Of the 97 samples tested by the cobas, 25 (26%) were deemed indeterminate. Sequencing analyses confirmed 21 (84%) of the 25 samples as genotype 6 viruses with either subtype 6m, 6n, 6v, 6xa, or unknown subtype. Of the 97 samples tested by the LiPA, thirteen (13%) were deemed indeterminate. Seven (7%) were assigned with genotype 1, with unavailable/inconclusive results from the core region of the LiPA. Notably, the 7 samples were later found to be either genotype 3 or 6 by sequencing analyses. Moreover, 1 sample by the LiPA was assigned as genotypes 4 (cobas: indeterminate) but were later found to be genotype 3 by sequencing analyses, highlighting its limitation in assigning the correct genotype. The cobas showed similar or slightly higher accuracy (100%; 95% CI 94-100%) compared to the LiPA (99%; 95% CI 92-100%). Twenty-six percent of the 97 samples tested by the cobas had indeterminate results, mainly due to its limitation in identifying genotype 6 other than subtypes 6a and 6b. This presents a significant assay limitation in Southeast Asia, where genotype 6 infection is highly prevalent. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Doubling immunochemistry laboratory testing efficiency with the cobas e 801 module while maintaining consistency in analytical performance.

    Science.gov (United States)

    Findeisen, P; Zahn, I; Fiedler, G M; Leichtle, A B; Wang, S; Soria, G; Johnson, P; Henzell, J; Hegel, J K; Bendavid, C; Collet, N; McGovern, M; Klopprogge, K

    2018-06-04

    The new immunochemistry cobas e 801 module (Roche Diagnostics) was developed to meet increasing demands on routine laboratories to further improve testing efficiency, while maintaining high quality and reliable data. During a non-interventional multicenter evaluation study, the overall performance, functionality and reliability of the new module was investigated under routine-like conditions. It was tested as a dedicated immunochemistry system at four sites and as a consolidator combined with clinical chemistry at three sites. We report on testing efficiency and analytical performance of the new module. Evaluation of sample workloads with site-specific routine request patterns demonstrated increased speed and almost doubled throughput (maximal 300 tests per h), thus revealing that one cobas e 801 module can replace two cobas e 602 modules while saving up to 44% floor space. Result stability was demonstrated by QC analysis per assay throughout the study. Precision testing over 21 days yielded excellent results within and between labs, and, method comparison performed versus the cobas e 602 module routine results showed high consistency of results for all assays under study. In a practicability assessment related to performance and handling, 99% of graded features met (44%) or even exceeded (55%) laboratory expectations, with enhanced reagent management and loading during operation being highlighted. By nearly doubling immunochemistry testing efficiency on the same footprint as a cobas e 602 module, the new module has a great potential to further consolidate and enhance laboratory testing while maintaining high quality analytical performance with Roche platforms. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  16. Real-time TaqMan polymerase chain reaction to quantify the effects ...

    African Journals Online (AJOL)

    TaqMan polymerase chain reaction was developed to quantify the number of Bifidobacterium. We used this assay to detect genomic DNA of Bifidobacterium in the intestinal tract digesta of piglets, including duodenum, jejunum, ileum, cecum and colon. Our results indicated that, developed new real-time quantitative PCR ...

  17. Development and evaluation of Taqman assays for the differentiation of Dickeya (sub)species

    NARCIS (Netherlands)

    Wolf, van der J.M.; Haas, de B.H.; Hoof, van R.A.; Haan, de E.G.; Bovenkamp, van den G.W.

    2014-01-01

    TaqMan assays were developed for the detection of seven Dickeya species, namely D. dianthicola, D. dadantii, D. paradisiaca, D. chrysanthemi, D. zeae, D. dieffenbachiae and D. solani. Sequences of the gene coding for dnaX were used for the design of primers and probes. In studies with axenic

  18. Transference of CALIPER pediatric reference intervals to biochemical assays on the Roche cobas 6000 and the Roche Modular P.

    Science.gov (United States)

    Higgins, Victoria; Chan, Man Khun; Nieuwesteeg, Michelle; Hoffman, Barry R; Bromberg, Irvin L; Gornall, Doug; Randell, Edward; Adeli, Khosrow

    2016-01-01

    The Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER) has recently established pediatric age- and sex-specific reference intervals for over 85 biochemical markers on the Abbott Architect system. Previously, CALIPER reference intervals for several biochemical markers were successfully transferred from Abbott assays to Roche, Beckman, Ortho, and Siemens assays. This study further broadens the CALIPER database by performing transference and verification for 52 biochemical assays on the Roche cobas 6000 and the Roche Modular P. Using CLSI C28-A3 and EP9-A2 guidelines, transference of the CALIPER reference intervals was attempted for 16 assays on the Roche cobas 6000 and 36 on the Modular P. Calculated reference intervals were further verified using 100 healthy CALIPER samples. Most assays showed strong correlation between assay systems and were transferable from Abbott to the Roche cobas 6000 (81%) and the Modular P (86%). Bicarbonate and magnesium were not transferable on either system and calcium and prealbumin were not transferable to the Modular P. Of the transferable analytes, 62% and 61% were verified on the cobas 6000 and the Modular P, respectively. This study extends the utility of the CALIPER database to two additional analytical systems, which facilitates the broad application of CALIPER reference intervals at pediatric centers utilizing Roche biochemical assays. Transference studies across different analytical platforms can later be collectively analyzed in an attempt to develop common reference intervals across all clinical chemistry instruments to harmonize laboratory test interpretation in diagnosis and monitoring of pediatric disease. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  19. Meticulous plasma isolation is essential to avoid false low-level viraemia in Roche Cobas HIV-1 viral load assays.

    Science.gov (United States)

    Mortier, Virginie; Vancoillie, Leen; Dauwe, Kenny; Staelens, Delfien; Demecheleer, Els; Schauvliege, Marlies; Dinakis, Sylvie; Van Maerken, Tom; Dessilly, Géraldine; Ruelle, Jean; Verhofstede, Chris

    2017-10-24

    Pre-analytical sample processing is often overlooked as a potential cause of inaccurate assay results. Here we demonstrate how plasma, extracted from standard EDTA-containing blood collection tubes, may contain traces of blood cells consequently resulting in a false low-level HIV-1 viral load when using Roche Cobas HIV-1 assays. The presence of human DNA in Roche Cobas 4800 RNA extracts and in RNA extracts from the Abbott HIV-1 RealTime assay was assessed by quantifying the human albumin gene by means of quantitative PCR. RNA was extracted from plasma samples before and after an additional centrifugation and tested for viral load and DNA contamination. The relation between total DNA content and viral load was defined. Elevated concentrations of genomic DNA were detected in 28 out of 100 Cobas 4800 extracts and were significantly more frequent in samples processed outside of the AIDS Reference Laboratory. An association between genomic DNA presence and spurious low-level viraemia results was demonstrated. Supplementary centrifugation of plasma before RNA extraction eliminated the contamination and the false viraemia. Plasma isolated from standard EDTA-containing blood collection tubes may contain traces of HIV DNA leading to false viral load results above the clinical cutoff. Supplementary centrifugation of plasma before viral load analysis may eliminate the occurrence of this spurious low-level viraemia.

  20. Measurement Differences Between Two Immunoassay Systems for LH and FSH: A Comparison of Roche Cobas e601 vs. Abbott Architect i2000sr.

    Science.gov (United States)

    Yin, Lianli; Tang, Yinghua; Chen, Xiang; Sun, Yifan

    2018-03-01

    Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) regulate the growth and reproductive activity of gonadal tissue and determine the concentration of LH is essential for the prediction of ovulation. Collectively, FSH and LH are important measurements to ascertain the causes of infertility as well as diagnosing disorders such as polycystic ovary syndrome and pituitary and gonadal dysfunction. This study compares the correlation between LH and FSH measurements during examination with two different systems, Architect i2000sr (Abbott Laboratories; Lake Bluff, IL, USA) and Cobas e601 (Roche; Geneva, Switzerland), and assesses the differences between these systems. Serum analysis was performed for 95 patients using both the Cobas e601 and Architect i2000sr systems. The method used to compare the systems was Passing-Bablok regression analysis with a Bland-Altman agreement plot. Inter-rater agreement was analyzed using a concordance correlation coefficient. Architect i2000sr and Cobas e601 have strong correlations in their LH and FSH results. However, the Bland-Altman plot shows that LH and FSH measurements in Cobas e601 are about 1.31 times and 1.26 times higher than those in Architect i2000sr, respectively. Passing-Bablok regression analysis also shows significant proportional deviation between them. The difference between the test results for LH and FSH in Cobas e601 and Architect i2000sr indicate that the results from one system cannot be directly used to evaluate the other system.

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

    Directory of Open Access Journals (Sweden)

    Hongxue Luo

    Full Text Available 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.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.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.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.

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

    Science.gov (United States)

    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

    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. 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). 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. 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.

  3. High-Throughput Testing of Urogenital and Extragenital Specimens for Detection of Chlamydia Trachomatis and Neisseria Gonorrhoeae with Cobas® CT/NG.

    Science.gov (United States)

    Marlowe, Elizabeth M; Hardy, David; Krevolin, Mark; Gohl, Peter; Bertram, Alexander; Arcenas, Rodney; Seiverth, Britta; Schneider, Tanja; Liesenfeld, Oliver

    2017-09-01

    We compared the analytical and clinical performance of cobas ® CT/NG for use on the Cobas ® 6800/8800 Systems with the Cobas ® 4800 CT/NG Test from urogenital and extragenital specimens in over 12,000 specimens from both male and female subjects in Germany and the United States. The analytical sensitivity was ≤40 EB/ml for Chlamydia trachomatis (CT) and ≤1 CFU/ml for Neisseria gonorrhoeae (NG). Using clinical specimens, the overall percent agreement with the Cobas ® 4800 CT/NG Test was >98.5%. Across urogenital specimens, there were 93 discrepant specimens; 76 (93.8%) of 81 CT discrepant specimens were 6800+/4800- and 10 (83.3%) of 12 NG discrepant specimens were 6800+/4800-. Sequencing verified CT results for 45 (61.6%) of 73 samples positive by 6800 and 1 (20%) of 5 positive by 4800. Similarly, 7 (70.0%) of 10 NG samples positive by 6800 and 1 of 2 positive by 4800 were confirmed by sequencing. Among discrepant extragenital specimens (all 6800+/4800-), 7 (50%) of 14 oropharyngeal and 23 (76.7%) of 30 anorectal CT discordant samples were confirmed as CT positive by sequencing; all 8 anorectal and 20 (90.9%) of 22 oropharyngeal NG discordant results were also confirmed as NG positive. In conclusion, Cobas ® CT/NG for use on the Cobas ® 6800/8800 Systems provides high-throughput automated solutions for sexually transmitted infection (STI) screening programs.

  4. T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory

    Directory of Open Access Journals (Sweden)

    Albion Tim

    2005-10-01

    Full Text Available Abstract Background Single Nucleotide Polymorphism (SNP genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS need tools to organize the data flow. Results We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. Conclusion We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS.

  5. T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory

    Science.gov (United States)

    Monnier, Stéphanie; Cox, David G; Albion, Tim; Canzian, Federico

    2005-01-01

    Background Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS) need tools to organize the data flow. Results We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. Conclusion We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS. PMID:16221298

  6. Verwerking en rapportage van meetgegevens verkregen met een Cobas-Bio centrifugaal-analysator m.b.v. de RIVM-computer

    NARCIS (Netherlands)

    Steentjes; G.M.; Koedam; J.C.

    1985-01-01

    Voor de verwerking van grote hoeveelheden meetgegevens is o.a. voor de Cobas-Bio centrifugaal analysator m.b.v. de RIVM computer een systeem ontwikkeld dat zowel monster (patient) identificatie, als rapportage van alle analyseresultaten verzorgt, zodat door het automatisch uitvoeren van een

  7. Comparison of COBAS AMPLICOR Neissefia gonorrhoeae PCR, including confirmation with N-gonorrhoeae-specific 16S rRNA PCR, with traditional culture

    NARCIS (Netherlands)

    Luijt, DS; Bos, PAJ; van Zwet, AA; Vader, PCV; Schirm, J

    A total of 3,023 clinical specimens were tested for Neisseria gonorrhoeae by using COBAS AMPLICOR (CA) PCR and confirmation of positives by N. gonorrhoeae-specific 16S rRNA PCR. The sensitivity of CA plus 16S rRNA PCR was 98.8%, compared to 68.2% for culture. Confirmation of CA positives increased

  8. 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.

    Science.gov (United States)

    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.

  9. 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

    Science.gov (United States)

    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

  10. 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.

    Directory of Open Access Journals (Sweden)

    Samia Mourah

    Full Text Available 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.

  11. A Laboratory-Developed TaqMan Array Card for Simultaneous Detection of 19 Enteropathogens

    Science.gov (United States)

    Liu, Jie; Gratz, Jean; Amour, Caroline; Kibiki, Gibson; Becker, Stephen; Janaki, Lalitha; Verweij, Jaco J.; Taniuchi, Mami; Sobuz, Shihab U.; Haque, Rashidul; Haverstick, Doris M.

    2013-01-01

    The TaqMan Array Card (TAC) system is a 384-well singleplex real-time PCR format that has been used to detect multiple infection targets. Here we developed an enteric TaqMan Array Card to detect 19 enteropathogens, including viruses (adenovirus, astrovirus, norovirus GII, rotavirus, and sapovirus), bacteria (Campylobacter jejuni/C. coli, Clostridium difficile, Salmonella, Vibrio cholerae, diarrheagenic Escherichia coli strains including enteroaggregative E. coli [EAEC], enterotoxigenic E. coli [ETEC], enteropathogenic E. coli [EPEC], and Shiga-toxigenic E. coli [STEC]), Shigella/enteroinvasive E. coli (EIEC), protozoa (Cryptosporidium, Giardia lamblia, and Entamoeba histolytica), and helminths (Ascaris lumbricoides and Trichuris trichiura), as well as two extrinsic controls to monitor extraction and amplification efficiency (the bacteriophage MS2 and phocine herpesvirus). Primers and probes were newly designed or adapted from published sources and spotted onto microfluidic cards. Fecal samples were spiked with extrinsic controls, and DNA and RNA were extracted using the QiaAmp Stool DNA minikit and the QuickGene RNA Tissue kit, respectively, and then mixed with Ag-Path-ID One Step real-time reverse transcription-PCR (RT-PCR) reagents and loaded into cards. PCR efficiencies were between 90% and 105%, with linearities of 0.988 to 1. The limit of detection of the assays in the TAC was within a 10-fold difference from the cognate assays performed on plates. Precision testing demonstrated a coefficient of variation of below 5% within a run and 14% between runs. Accuracy was evaluated for 109 selected clinical specimens and revealed an average sensitivity and specificity of 85% and 77%, respectively, compared with conventional methods (including microscopy, culture, and immunoassay) and 98% and 96%, respectively, compared with our laboratory-developed PCR-Luminex assays. This TAC allows fast, accurate, and quantitative detection of a broad spectrum of enteropathogens and

  12. Identification of field caught Anopheles gambiae s.s. and Anopheles arabiensis by TaqMan single nucleotide polymorphism genotyping

    Directory of Open Access Journals (Sweden)

    Bayoh Nabie M

    2007-02-01

    Full Text Available Abstract Background Identification of Anopheles gambiae s.s. and Anopheles arabiensis from field-collected Anopheles gambiae s.l. is often necessary in basic and applied research, and in operational control programmes. The currently accepted method involves use of standard polymerase chain reaction amplification of ribosomal DNA (rDNA from the 3' 28S to 5' intergenic spacer region of the genome, and visual confirmation of amplicons of predicted size on agarose gels, after electrophoresis. This report describes development and evaluation of an automated, quantitative PCR method based upon TaqMan™ single nucleotide polymorphism (SNP genotyping. Methods Standard PCR, and TaqMan SNP genotyping with newly designed primers and fluorophore-labeled probes hybridizing to sequences of complementary rDNA specific for either An. gambiae s.s. or An. arabiensis, were conducted in three experiments involving field-collected An. gambiae s.l. from western Kenya, and defined laboratory strains. DNA extraction was from a single leg, sonicated for five minutes in buffer in wells of 96-well PCR plates. Results TaqMan SNP genotyping showed a reaction success rate, sensitivity, and species specificity comparable to that of standard PCR. In an extensive field study, only 29 of 3,041 (0.95% were determined to be hybrids by TaqMan (i.e., having rDNA sequences from both species, however, all but one were An. arabiensis by standard PCR, suggesting an acceptably low (ca. 1% error rate for TaqMan genotyping in mistakenly identifying species hybrids. Conclusion TaqMan SNP genotyping proved to be a sensitive and rapid method for identification of An. gambiae s.l. and An. arabiensis, with a high success rate, specific results, and congruence with the standard PCR method.

  13. Evaluation of a third party enzymatic ammonia method for use on the Roche Cobas 6000 (c501) automated platform.

    Science.gov (United States)

    Seiden-Long, Isolde; Schnabl, Kareena; Skoropadyk, Wendy; Lennon, Nola; McKeage, Arlayne

    2014-08-01

    Adaptation of the Randox Enzymatic Manual UV Ammonia method to be used on the Roche Cobas 6000 (c501) automated analyzer platform. The Randox ammonia reagent was evaluated for precision, linearity, accuracy and interference from hemolysis, icterus and lipemia on the Roche c501 analyzer. Comparison studies were conducted for the Randox reagent between Roche c501, Siemens Vista, Ortho Vitros 250, and Beckman DxC methods. The Randox reagent demonstrates acceptable within-run (L1=65 μmol/L, CV 3.4% L2=168 μmol/L, CV 1.9%) and between-run precision (L1=29 μmol/L, CV 7.3% L2=102 μmol/L, CV 3.0%), Analytical Measurement Range (7-940 μmol/L), and accuracy. The method interference profile is superior for the Randox method (hemolysis index up to 600, icteric index up to 60, lipemic index up to 100) as compared to the Roche method (hemolysis index up to 200, icteric index up to 10, lipemic index up to 50). Comparison was very good between the Randox reagent and two other wet chemistry platforms. The Randox Enzymatic Manual UV Ammonia reagent is an available alternative to the Roche Cobas c501 reagent. The method is more robust to endogenous interferences and less prone to instrument error flags, thus allowing the majority of clinical specimens to be reported without additional sample handling at our institution. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  14. Characterization and Validation of the LT-SYS Copper Assay on a Roche Cobas 8000 c502 Analyzer.

    Science.gov (United States)

    Kraus, F Bernhard; Mischereit, Marlies; Eller, Christoph; Ludwig-Kraus, Beatrice

    2017-02-01

    Validation of the LT-SYS quantitative in vitro copper assay on a Roche Cobas 8000 c502 analyzer and comparison with a BIOMED assay on a Roche Cobas Mira analyzer. Imprecision and bias were quantified at different concentration levels (serum and plasma) over a 20-day period. Linearity was assessed covering a range from 4.08 µmol/L to 33.8 µmol/L. Limit of blank (LoB) and limit of detection (LoD) were established based on a total of 120 blank and low-level samples. The method comparison was based on 58 plasma samples. Within-run imprecision ranged from 0.7% to 1.2% and within-laboratory imprecision from 1.4% to 3.3%. Relative bias for the 2 serum pools with known target values was less than 2.5%. The assay did not deviate from linearity over the tested measuring range. LoB and LoD were 0.12 µmol/L and 0.23 µmol/L, respectively. The method comparison revealed an average deviation of 11.5% (2.016 µmol/L), and the linear regression fit was y = 1.464 + 0.795x. The LT-SYS copper assay characterized in this study showed a fully acceptable performance with good degrees of imprecision and bias, no deviation from linearity in the relevant measuring rangem, and very low LoB and LoD. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2016-08-01

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

  16. Genotyping of Hepatitis C virus isolated from hepatitis patients in Southeast of Iran by taqman realtime PCR

    International Nuclear Information System (INIS)

    Farivar, T.N.; Johari, P.

    2011-01-01

    Objectives: To check TaqMan Realtime PCR in detecting genotypes of hepatitis C virus in Iran. Methods: From July 2007 to April 2009, HCV genotyping was done on 52 patients who were referred to Research Centre for infectious Disease and Tropical Medicine, in Bou-Ali Hospital, Zahedan University of Medical Sciences. All these patients had proven hepatitis C infection. Results: Out of 52 anti HCV positive samples, 28(53.84%) had genotype 1, 2 cases (3.88 %) had genotype 2 , 12 (23.08 %) had genotype 3 and 7 (13.4 %) had genotype 4 . Mixed infection with genotypes 1 and 3 was seen in 3 cases (5.77 %). Conclusion: TaqMan probes for detecting genotyping of HCV were successful in picking genotyping of HCV infection especially those with mixed genotypes. (author)

  17. A quantitative PCR (TaqMan assay for pathogenic Leptospira spp

    Directory of Open Access Journals (Sweden)

    Symonds Meegan L

    2002-07-01

    Full Text Available Abstract Background Leptospirosis is an emerging infectious disease. The differential diagnosis of leptospirosis is difficult due to the varied and often "flu like" symptoms which may result in a missed or delayed diagnosis. There are over 230 known serovars in the genus Leptospira. Confirmatory serological diagnosis of leptospirosis is usually made using the microscopic agglutination test (MAT which relies on the use of live cultures as the source of antigen, often performed using a panel of antigens representative of local serovars. Other techniques, such as the enzyme linked immunosorbent assay (ELISA and slide agglutination test (SAT, can detect different classes of antibody but may be subject to false positive reactions and require confirmation of these results by the MAT. Methods The polymerase chain reaction (PCR has been used to detect a large number of microorganisms, including those of clinical significance. The sensitivity of PCR often precludes the need for isolation and culture, thus making it ideal for the rapid detection of organisms involved in acute infections. We employed real-time (quantitative PCR using TaqMan chemistry to detect leptospires in clinical and environmental samples. Results and Conclusions The PCR assay can be applied to either blood or urine samples and does not rely on the isolation and culture of the organism. Capability exists for automation and high throughput testing in a clinical laboratory. It is specific for Leptospira and may discriminate pathogenic and non-pathogenic species. The limit of detection is as low as two cells.

  18. Development of a Rickettsia bellii-Specific TaqMan Assay Targeting the Citrate Synthase Gene.

    Science.gov (United States)

    Hecht, Joy A; Allerdice, Michelle E J; Krawczak, Felipe S; Labruna, Marcelo B; Paddock, Christopher D; Karpathy, Sandor E

    2016-11-01

    Rickettsia bellii is a rickettsial species of unknown pathogenicity that infects argasid and ixodid ticks throughout the Americas. Many molecular assays used to detect spotted fever group (SFG) Rickettsia species do not detect R. bellii, so that infection with this bacterium may be concealed in tick populations when assays are used that screen specifically for SFG rickettsiae. We describe the development and validation of a R. bellii-specific, quantitative, real-time PCR TaqMan assay that targets a segment of the citrate synthase (gltA) gene. The specificity of this assay was validated against a panel of DNA samples that included 26 species of Rickettsia, Orientia, Ehrlichia, Anaplasma, and Bartonella, five samples of tick and human DNA, and DNA from 20 isolates of R. bellii, including 11 from North America and nine from South America. A R. bellii control plasmid was constructed, and serial dilutions of the plasmid were used to determine the limit of detection of the assay to be one copy per 4 µl of template DNA. This assay can be used to better determine the role of R. bellii in the epidemiology of tick-borne rickettsioses in the Western Hemisphere. Published by Oxford University Press on behalf of Entomological Society of America 2016. This work is written by US Government employees and is in the public domain in the US.

  19. Fluorimetric methods for the measurement of intermediate metabolites (lactate, pyruvate, alanine, β-hydroxybutyrate, glycerol) using a COBAS FARA centrifugal analyser

    OpenAIRE

    Monti, L. D.; Sandoli, P. E.; Costa, S.; Phan, V. C.; Piatti, P. M.

    1993-01-01

    Intermediate products of the metabolism of glucose, fat and amino-acid are important in the evaluation of such metabolic disorders as diabetes mellitus, liver disease and metabolic acidosis. In the present study, methods for the measurement of intermediate metabolites (lactate, pyruvate, alanine, β-hydroxybutyrate and glycerol) have been adapted to a fast centrifugal analyzer: the COBAS FARA. Correlation coeffcients rangedfrom 0.90 to 0.99, compared to established manual spectrophotometric me...

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

    Science.gov (United States)

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

    2017-02-01

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

  1. The Roche Immunoturbidimetric Albumin Method on Cobas c 501 Gives Higher Values Than the Abbott and Roche BCP Methods When Analyzing Patient Plasma Samples.

    Science.gov (United States)

    Helmersson-Karlqvist, Johanna; Flodin, Mats; Havelka, Aleksandra Mandic; Xu, Xiao Yan; Larsson, Anders

    2016-09-01

    Serum/plasma albumin is an important and widely used laboratory marker and it is important that we measure albumin correctly without bias. We had indications that the immunoturbidimetric method on Cobas c 501 and the bromocresol purple (BCP) method on Architect 16000 differed, so we decided to study these methods more closely. A total of 1,951 patient requests with albumin measured with both the Architect BCP and Cobas immunoturbidimetric methods were extracted from the laboratory system. A comparison with fresh plasma samples was also performed that included immunoturbidimetric and BCP methods on Cobas c 501 and analysis of the international protein calibrator ERM-DA470k/IFCC. The median difference between the Abbott BCP and Roche immunoturbidimetric methods was 3.3 g/l and the Roche method overestimated ERM-DA470k/IFCC by 2.2 g/l. The Roche immunoturbidimetric method gave higher values than the Roche BCP method: y = 1.111x - 0.739, R² = 0.971. The Roche immunoturbidimetric albumin method gives clearly higher values than the Abbott and Roche BCP methods when analyzing fresh patient samples. The differences between the two methods were similar at normal and low albumin levels. © 2016 Wiley Periodicals, Inc.

  2. Quantification of Parvovirus B19 DNA Using COBAS AmpliPrep Automated Sample Preparation and LightCycler Real-Time PCR

    Science.gov (United States)

    Schorling, Stefan; Schalasta, Gunnar; Enders, Gisela; Zauke, Michael

    2004-01-01

    The COBAS AmpliPrep instrument (Roche Diagnostics GmbH, D-68305 Mannheim, Germany) automates the entire sample preparation process of nucleic acid isolation from serum or plasma for polymerase chain reaction analysis. We report the analytical performance of the LightCycler Parvovirus B19 Quantification Kit (Roche Diagnostics) using nucleic acids isolated with the COBAS AmpliPrep instrument. Nucleic acids were extracted using the Total Nucleic Acid Isolation Kit (Roche Diagnostics) and amplified with the LightCycler Parvovirus B19 Quantification Kit. The kit combination processes 72 samples per 8-hour shift. The lower detection limit is 234 IU/ml at a 95% hit-rate, linear range approximately 104-1010 IU/ml, and overall precision 16 to 40%. Relative sensitivity and specificity in routine samples from pregnant women are 100% and 93%, respectively. Identification of a persistent parvovirus B19-infected individual by the polymerase chain reaction among 51 anti-parvovirus B19 IgM-negative samples underlines the importance of additional nucleic acid testing in pregnancy and its superiority to serology in identifying the risk of parvovirus B19 transmission via blood or blood products. Combination of the Total Nucleic Acid Isolation Kit on the COBAS AmpliPrep instrument with the LightCycler Parvovirus B19 Quantification Kit provides a reliable and time-saving tool for sensitive and accurate detection of parvovirus B19 DNA. PMID:14736825

  3. Novel TaqMan real-time polymerase chain reaction assay for verifying the authenticity of meat and commercial meat products from game birds.

    Science.gov (United States)

    Rojas, María; González, Isabel; Pavón, Miguel Angel; Pegels, Nicolette; Lago, Adriana; Hernández, Pablo E; García, Teresa; Martín, Rosario

    2010-06-01

    Species-specific real-time polymerase chain reaction (PCR) assays using TaqMan probes have been developed for verifying the labeling of meat and commercial meat products from game birds, including quail, pheasant, partridge, guinea fowl, pigeon, Eurasian woodcock and song thrush. The method combines the use of species-specific primers and TaqMan probes that amplify small fragments (amplicons meat products from the target species demonstrated the suitability of the assay for the detection of the target DNAs.

  4. Evaluation of a TaqMan Array Card for Detection of Central Nervous System Infections.

    Science.gov (United States)

    Onyango, Clayton O; Loparev, Vladimir; Lidechi, Shirley; Bhullar, Vinod; Schmid, D Scott; Radford, Kay; Lo, Michael K; Rota, Paul; Johnson, Barbara W; Munoz, Jorge; Oneko, Martina; Burton, Deron; Black, Carolyn M; Neatherlin, John; Montgomery, Joel M; Fields, Barry

    2017-07-01

    Infections of the central nervous system (CNS) are often acute, with significant morbidity and mortality. Routine diagnosis of such infections is limited in developing countries and requires modern equipment in advanced laboratories that may be unavailable to a number of patients in sub-Saharan Africa. We developed a TaqMan array card (TAC) that detects multiple pathogens simultaneously from cerebrospinal fluid. The 21-pathogen CNS multiple-pathogen TAC (CNS-TAC) assay includes two parasites ( Balamuthia mandrillaris and Acanthamoeba ), six bacterial pathogens ( Streptococcus pneumonia e, Haemophilus influenzae , Neisseria meningitidis , Mycoplasma pneumoniae , Mycobacterium tuberculosis , and Bartonella ), and 13 viruses (parechovirus, dengue virus, Nipah virus, varicella-zoster virus, mumps virus, measles virus, lyssavirus, herpes simplex viruses 1 and 2, Epstein-Barr virus, enterovirus, cytomegalovirus, and chikungunya virus). The card also includes human RNase P as a nucleic acid extraction control and an internal manufacturer control, GAPDH (glyceraldehyde-3-phosphate dehydrogenase). This CNS-TAC assay can test up to eight samples for all 21 agents within 2.5 h following nucleic acid extraction. The assay was validated for linearity, limit of detection, sensitivity, and specificity by using either live viruses (dengue, mumps, and measles viruses) or nucleic acid material (Nipah and chikungunya viruses). Of 120 samples tested by individual real-time PCR, 35 were positive for eight different targets, whereas the CNS-TAC assay detected 37 positive samples across nine different targets. The CNS-TAC assays showed 85.6% sensitivity and 96.7% specificity. Therefore, the CNS-TAC assay may be useful for outbreak investigation and surveillance of suspected neurological disease. Copyright © 2017 American Society for Microbiology.

  5. A quantitative TaqMan PCR assay for the detection of Ureaplasma diversum.

    Science.gov (United States)

    Marques, Lucas M; Amorim, Aline T; Martins, Hellen Braga; Rezende, Izadora Souza; Barbosa, Maysa Santos; Lobão, Tassia Neves; Campos, Guilherme B; Timenetsky, Jorge

    2013-12-27

    Ureaplasma diversum in veterinary studies is an undesirable microbe, which may cause infection in bulls and may result in seminal vesiculitis, balanopostitis, and alterations in spermatozoids, whereas in cows, it may cause placentitis, fetal alveolitis, abortion, and birth of weak calves. U. diversum is released through organic secretions, especially semen, preputial and vaginal mucus, conjunctival secretion, and milk. The aim of the present study was to develop a TaqMan probe, highly sensitive and specific quantitative PCR (qPCR) assay for the detection and quantification of U. diversum from genital swabs of bovines. Primers and probes specific to U. diversum 16S rRNA gene were designed. The specificity, detection limit, intra- and inter-assay variability of qPCR to detect this ureaplasma was compared with the results of the conventional PCR assay (cPCR). Swabs of vaginal mucus from 169 cows were tested. The qPCR assay detected as few as 10 copies of U. diversum and was 100-fold more sensitive than the cPCR. No cross-reactivity with other Mollicutes or eubacteria was observed. U. diversum was detected in 79 swabs (46.42%) by qPCR, while using cPCR it was detected in 42 (25%) samples. The difference in cPCR and qPCR ureaplasma detection between healthy and sick animals was not statistically significant. But the U. diversum load in samples from animals with genital disorders was higher than in healthy animals. The qPCR assay developed herein is highly sensitive and specific for the detection and quantification of U. diversum in vaginal bovine samples. Copyright © 2013. Published by Elsevier B.V.

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

    Science.gov (United States)

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

    2015-03-01

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

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

    DEFF Research Database (Denmark)

    Preisler, Sarah; Rebolj, Matejka; Untermann, Anette

    2013-01-01

    of the present study, Horizon, was to assess the prevalence of high-risk HPV infections in an area with a high background risk of cervical cancer, where women aged 23-65 years are targeted for cervical screening. We collected 6,258 consecutive cervical samples from the largest cervical screening laboratory......-29 years and 10% in women aged 60-65 years. HC2 assay was positive in 20% of samples, and cytology was abnormal (≥ atypical squamous cells of undetermined significance) for 7% samples. When only samples without recent abnormalities were taken into account, 24% tested positive on cobas, 19% on HC2, and 5...

  8. Tipo de respuesta según el genotipado del virus del papiloma humano según cobas 4800 en las lesiones asc-us HPV positivas

    OpenAIRE

    Kanjou Augé, Nadwa

    2016-01-01

    Objetivos: Evaluar el riesgo de patología subyacente en las pacientes ASC-US HPV positivas de nuestra área de influencia analizadas por el método COBAS 4800. Se estudió el riesgo de CIN2+ en el momento del diagnóstico de las mujeres ASC-US HPV positivas según el genotipo del virus del papiloma: HPV16, HPV18 ( ambos incluyendo coinfecciones) u otros HPV de alto riesgo (HR-HPV). El objetivo es detectar aquellas mujeres con citologías ASC-US HPV positivo con un mayor riesgo de progresión y por l...

  9. TaqMan probe real-time polymerase chain reaction assay for the quantification of canine DNA in chicken nugget.

    Science.gov (United States)

    Rahman, Md Mahfujur; Hamid, Sharifah Bee Abd; Basirun, Wan Jefrey; Bhassu, Subha; Rashid, Nur Raifana Abdul; Mustafa, Shuhaimi; Mohd Desa, Mohd Nasir; Ali, Md Eaqub

    2016-01-01

    This paper describes a short-amplicon-based TaqMan probe quantitative real-time PCR (qPCR) assay for the quantitative detection of canine meat in chicken nuggets, which are very popular across the world, including Malaysia. The assay targeted a 100-bp fragment of canine cytb gene using a canine-specific primer and TaqMan probe. Specificity against 10 different animals and plants species demonstrated threshold cycles (Ct) of 16.13 ± 0.12 to 16.25 ± 0.23 for canine DNA and negative results for the others in a 40-cycle reaction. The assay was tested for the quantification of up to 0.01% canine meat in deliberately spiked chicken nuggets with 99.7% PCR efficiency and 0.995 correlation coefficient. The analysis of the actual and qPCR predicted values showed a high recovery rate (from 87% ± 28% to 112% ± 19%) with a linear regression close to unity (R(2) = 0.999). Finally, samples of three halal-branded commercial chicken nuggets collected from different Malaysian outlets were screened for canine meat, but no contamination was demonstrated.

  10. Multiplex preamplification of specific cDNA targets prior to gene expression analysis by TaqMan Arrays

    Directory of Open Access Journals (Sweden)

    Ribal María

    2008-06-01

    Full Text Available Abstract Background An accurate gene expression quantification using TaqMan Arrays (TA could be limited by the low RNA quantity obtained from some clinical samples. The novel cDNA preamplification system, the TaqMan PreAmp Master Mix kit (TPAMMK, enables a multiplex preamplification of cDNA targets and therefore, could provide a sufficient amount of specific amplicons for their posterior analysis on TA. Findings A multiplex preamplification of 47 genes was performed in 22 samples prior to their analysis by TA, and relative gene expression levels of non-preamplified (NPA and preamplified (PA samples were compared. Overall, the mean cycle threshold (CT decrement in the PA genes was 3.85 (ranging from 2.07 to 5.01. A high correlation (r between the gene expression measurements of NPA and PA samples was found (mean r = 0.970, ranging from 0.937 to 0.994; p Conclusion We demonstrate that cDNA preamplification using the TPAMMK before TA analysis is a reliable approach to simultaneously measure gene expression of multiple targets in a single sample. Moreover, this procedure was validated in genes from degraded RNA samples and low abundance expressed genes. This combined methodology could have wide applications in clinical research, where scarce amounts of degraded RNA are usually obtained and several genes need to be quantified in each sample.

  11. Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay.

    Science.gov (United States)

    Pegels, N; González, I; Fernández, S; García, T; Martín, R

    2012-01-01

    A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79 bp fragment of the mitochondrial (mt) 12 S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18 S rRNA gene system, yielding a 77 bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.

  12. TaqMan MGB probe fluorescence real-time quantitative PCR for rapid detection of Chinese Sacbrood virus.

    Directory of Open Access Journals (Sweden)

    Ma Mingxiao

    Full Text Available Sacbrood virus (SBV is a picorna-like virus that affects honey bees (Apis mellifera and results in the death of the larvae. Several procedures are available to detect Chinese SBV (CSBV in clinical samples, but not to estimate the level of CSBV infection. The aim of this study was develop an assay for rapid detection and quantification of this virus. Primers and probes were designed that were specific for CSBV structural protein genes. A TaqMan minor groove binder (MGB probe-based, fluorescence real-time quantitative PCR was established. The specificity, sensitivity and stability of the assay were assessed; specificity was high and there were no cross-reactivity with healthy larvae or other bee viruses. The assay was applied to detect CSBV in 37 clinical samples and its efficiency was compared with clinical diagnosis, electron microscopy observation, and conventional RT-PCR. The TaqMan MGB-based probe fluorescence real-time quantitative PCR for CSBV was more sensitive than other methods tested. This assay was a reliable, fast, and sensitive method that was used successfully to detect CSBV in clinical samples. The technology can provide a useful tool for rapid detection of CSBV. This study has established a useful protocol for CSBV testing, epidemiological investigation, and development of animal models.

  13. A TaqMan Real-Time PCR Assay for Detection and Quantification of Sporisorium scitamineum in Sugarcane

    Directory of Open Access Journals (Sweden)

    Yachun Su

    2013-01-01

    Full Text Available Sporisorium scitamineum is a fungal smut pathogen epidemic in sugarcane producing areas. Early detection and proper identification of the smut are an essential requirement in its management practice. In this study, we developed a TaqMan real-time PCR assay using specific primers (bEQ-F/bEQ-R and a TaqMan probe (bEQ-P which were designed based on the bE (b East mating type gene (Genbank Accession no. U61290.1. This method was more sensitive (a detection limit of 10 ag pbE DNA and 0.8 ng sugarcane genomic DNA than that of conventional PCR (10 fg and 100 ng, resp.. Reliability was demonstrated through the positive detection of samples collected from artificially inoculated sugarcane plantlets (FN40. This assay was capable of detecting the smut pathogen at the initial stage (12 h of infection and suitable for inspection of sugarcane pathogen-free seed cane and seedlings. Furthermore, quantification of pathogen was verified in pathogen-challenged buds in different sugarcane genotypes, which suggested its feasibility for evaluation of smut resistance in different sugarcane genotypes. Taken together, this novel assay can be used as a diagnostic tool for sensitive, accurate, fast, and quantitative detection of the smut pathogen especially for asymptomatic seed cane or plants and evaluation of smut resistance of sugarcane genotypes.

  14. Measurement of Epstein-Barr virus DNA loads in whole blood and plasma by TaqMan PCR and in peripheral blood lymphocytes by competitive PCR.

    Science.gov (United States)

    Wadowsky, Robert M; Laus, Stella; Green, Michael; Webber, Steven A; Rowe, David

    2003-11-01

    Epstein-Barr virus (EBV) DNA load values were measured in samples of whole blood (n = 60) and plasma (n = 59) by TaqMan PCR and in samples of peripheral blood lymphocytes (PBLs) (n = 60) by competitive PCR (cPCR). The samples were obtained from 44 transplant recipients. The whole-blood and PBL loads correlated highly (r(2) > 0.900), whereas the plasma and PBL loads correlated poorly (r(2) = 0.512). Testing of whole blood by TaqMan PCR is an acceptable alternative to testing of PBLs by cPCR for quantifying EBV DNA load.

  15. Fluorimetric methods for the measurement of intermediate metabolites (lactate, pyruvate, alanine, beta-hydroxybutyrate, glycerol) using a COBAS FARA centrifugal analyser.

    Science.gov (United States)

    Monti, L D; Sandoli, P E; Costa, S; Phan, V C; Piatti, P M

    1993-01-01

    Intermediate products of the metabolism of glucose, fat and amino-acid are important in the evaluation of such metabolic disorders as diabetes mellitus, liver disease and metabolic acidosis. In the present study, methods for the measurement of intermediate metabolites (lactate, pyruvate, alanine, beta-hydroxybutyrate and glycerol) have been adapted to a fast centrifugal analyzer: the COBAS FARA. Correlation coeffcients rangedfrom 0.90 to 0.99, compared to established manual spectrophotometric methods. Within-run coeffcients of variation (CVs) ranged between 2.9 and 8.8% at low levels, between 1.5 and 5.7% at medium levels and between 1.2 and 5.6% at high levels. Between-run CVs were between 4.0 and 15.0% at low levels, between 1.7 and 7.0% at medium levels and between 1.3 and 2.7% at high levels. These fluorimetric assays for the determination of intermediate metabolites on COBAS FARA (Roche) have a good sensitivity and precision, are less costly than manual methods and can be used on a routine basis.

  16. CYP2D7 sequence variation interferes with TaqMan CYP2D6*15 and *35 genotyping

    Directory of Open Access Journals (Sweden)

    Amanda K Riffel

    2016-01-01

    Full Text Available TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35 which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696 SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe

  17. A TaqMan real-time PCR assay for detection of Meloidogyne hapla in root galls and in soil

    DEFF Research Database (Denmark)

    Sapkota, Rumakanta; Skantar, Andrea M.; Nicolaisen, Mogens

    2016-01-01

    . haplaand showed no significant amplification of DNA from non-target nematodes. The assay was able to detect M. haplain a background of plant and soil DNA. A dilution series of M. haplaeggs in soil showed a high correlation ( R 2 = 0 . 95 , P ...Early detection and quantification of Meloidogyne haplain soil is essential for effective disease management. The purpose of this study was to develop a real-time PCR assay for detection of M. haplain soil. Primers and a TaqMan probe were designed for M. hapladetection. The assay detected M......-knot development in carrots by testing soils before planting. The assay could be useful for management decisions in carrot cultivation....

  18. Development of a real-time TaqMan assay to detect mendocina sublineage Pseudomonas species in contaminated metalworking fluids.

    Science.gov (United States)

    Saha, Ratul; Donofrio, Robert S; Bagley, Susan T

    2010-08-01

    A TaqMan quantitative real-time polymerase chain reaction (qPCR) assay was developed for the detection and enumeration of three Pseudomonas species belonging to the mendocina sublineage (P. oleovorans, P. pseudoalcaligenes, and P. oleovorans subsp. lubricantis) found in contaminated metalworking fluids (MWFs). These microbes are the primary colonizers and serve as indicator organisms of biodegradation of used MWFs. Molecular techniques such as qPCR are preferred for the detection of these microbes since they grow poorly on typical growth media such as R2A agar and Pseudomonas isolation agar (PIA). Traditional culturing techniques not only underestimate the actual distribution of these bacteria but are also time-consuming. The primer-probe pair developed from gyrase B (gyrB) sequences of the targeted bacteria was highly sensitive and specific for the three species. qPCR was performed with both whole cell and genomic DNA to confirm the specificity and sensitivity of the assay. The sensitivity of the assay was 10(1) colony forming units (CFU)/ml for whole cell and 13.7 fg with genomic DNA. The primer-probe pair was successful in determining concentrations from used MWF samples, indicating levels between 2.9 x 10(3) and 3.9 x 10(6) CFU/ml. In contrast, the total count of Pseudomonas sp. recovered on PIA was in the range of <1.0 x 10(1) to 1.4 x 10(5) CFU/ml for the same samples. Based on these results from the qPCR assay, the designed TaqMan primer-probe pair can be efficiently used for rapid (within 2 h) determination of the distribution of these species of Pseudomonas in contaminated MWFs.

  19. Use of a Real-Time PCR TaqMan Assay for Rapid Identification and Differentiation of Burkholderia pseudomallei and Burkholderia mallei

    OpenAIRE

    U'Ren, Jana M.; Van Ert, Matthew N.; Schupp, James M.; Easterday, W. Ryan; Simonson, Tatum S.; Okinaka, Richard T.; Pearson, Talima; Keim, Paul

    2005-01-01

    A TaqMan allelic-discrimination assay designed around a synonymous single-nucleotide polymorphism was used to genotype Burkholderia pseudomallei and Burkholderia mallei isolates. The assay rapidly identifies and discriminates between these two highly pathogenic bacteria and does not cross-react with genetic near neighbors, such as Burkholderia thailandensis and Burkholderia cepacia.

  20. Comparación de los métodos de cuantificación de carga viral de VIH: COBAS® AmpliPrep/COBAS® TaqMan HIV-1 test, v 2.0, y VERSANT HIV-1 RNA 1.0 Assay (kPCR Comparison of COBAS® AmpliPrep/COBAS® TaqMan HIV-1 test, v 2.0 and VERSANT HIV-1 RNA 1.0 (kPCR assays for HIV-1 plasma viral load

    Directory of Open Access Journals (Sweden)

    María Isabel Múnera-Jaramillo

    2012-03-01

    Full Text Available Objetivo. El propósito del estudio fue evaluar el desempeño del método VERSANTHIV-1RNA 1.0 Assay® (kPCR (Siemens, para la cuantificación de la carga viral en pacientes con VIH-1, en comparación con el método COBAS® AmpliPrep/COBAS TaqMan HIV-1 test®, v2.0 (Roche Diagnostics (CAP/CTM. Métodos. Las muestras fueron tomadas en dos tubos con EDTA, de 60 pacientes remitidos por el médico tratante para pruebas de carga viral como parte de su control de rutina de VIH/sida, y fueron procesadas para la cuantificación del ARN del VIH-1 por ambas técnicas. Se hizo análisis de regresión y se calcularon los coeficientes de correlación de Pearson, y los de correlación y concordancia de Lin. Se evalúo la concordancia entre las dos técnicas mediante el método de Bland-Altman. Resultados. El promedio de la carga viral por el método CAP/CTM fue 3,2±1,4 long10 copias/ml y, por el método kPCR, 3,0±1,3 long10 copias/ml. El 86,7 % de muestras presentó diferencias entre los dos métodos, menores de 0,5 long10 copias/ml, y el 13,3 % presentó diferencias mayores. El coeficiente de correlación de Pearson entre los dos métodos fue de 0,97 (IC95% 0,95-0,99 y el índice kappa ponderado entre los dos métodos en diferentes rangos de concentración, fue de 0,91 (IC95% 0,87-0,96. El promedio de las diferencias entre las mediciones fue 0,22 long10 copias/ml (IC95% -0,45 a 0,89. Conclusión. Las dos técnicas evaluadas fueron comparables, con el método kPCR se observaron resultados más bajos.Objective: The purpose of this study was to evaluate the performance of the kPCR VERSANT (™ 440 HIV-1RNA 3.0 Assay® (Siemens method for the quantification of viral load in HIV-1 patients, compared to the COBAS AmpliPrep/COBASTaqMan HIV-1 test®, v. 2.0 (Roche Diagnostics (CAP/CTM. Methods: Samples were taken in 2 tubes with EDTA, in 60 patients referred by the attending physician for viral load tests as part of their routine control of HIV/AIDS, and were

  1. Comparison of allelic discrimination by dHPLC, HRM, and TaqMan in the detection of BRAF mutation V600E.

    Science.gov (United States)

    Carbonell, Pablo; Turpin, María C; Torres-Moreno, Daniel; Molina-Martínez, Irene; García-Solano, José; Perez-Guillermo, Miguel; Conesa-Zamora, Pablo

    2011-09-01

    The V600E mutation in the BRAF oncogene is associated with colorectal carcinomas, with mismatch-repair deficiency and, recently, with nonresponse to epidermal growth factor receptor inhibitor therapy. The use of reliable techniques for its detection is important. The aim of our study was to compare the performance characteristics in V600E detection of denaturing high-performance liquid chromatography (dHPLC) and high-resolution melting (HRM) with TaqMan allelic discrimination as well as direct-sequencing methods in a series of 195 colorectal paraffin-embedded specimens up to the age of 15 years. The effectiveness for obtaining results on mutation status was best using TaqMan (96.9%), followed by dHPLC (93.3%), HRM (88.7%), and sequencing (88.2%). In general, TaqMan was best for analyzing older tissues, whereas sequencing was the least efficient. Heterozygotic V600E was detected in 11.6%, 9.9%, 11.6%, and 9.9% of tissues using TaqMan, dHPLC, HRM, and sequencing, respectively. Result concordances between dHPLC and TaqMan or sequencing were excellent (κ = 0.9411 and κ = 0.8988, respectively); for HRM, the concordances were good (κ = 0.7973 and κ = 0.7488, respectively). By using DNA dilutions from tumor tissue, a minimum of 10% of V600E harboring cancer content was required for the analysis by dHPLC and HRM. dHPLC could detect four non-V600E mutations, whereas HRM detected one. Our results indicate that dHPLC and HRM are techniques that can be reliably used for the detection of the BRAFV600E mutation in archival paraffin-embedded tissues. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  2. Precision, accuracy, cross reactivity and comparability of serum indices measurement on Abbott Architect c8000, Beckman Coulter AU5800 and Roche Cobas 6000 c501 clinical chemistry analyzers.

    Science.gov (United States)

    Nikolac Gabaj, Nora; Miler, Marijana; Vrtarić, Alen; Hemar, Marina; Filipi, Petra; Kocijančić, Marija; Šupak Smolčić, Vesna; Ćelap, Ivana; Šimundić, Ana-Maria

    2018-04-25

    The aim of our study was to perform verification of serum indices on three clinical chemistry platforms. This study was done on three analyzers: Abbott Architect c8000, Beckman Coulter AU5800 (BC) and Roche Cobas 6000 c501. The following analytical specifications were verified: precision (two patient samples), accuracy (sample with the highest concentration of interferent was serially diluted and measured values compared to theoretical values), comparability (120 patients samples) and cross reactivity (samples with increasing concentrations of interferent were divided in two aliquots and remaining interferents were added in each aliquot. Measurements were done before and after adding interferents). Best results for precision were obtained for the H index (0.72%-2.08%). Accuracy for the H index was acceptable for Cobas and BC, while on Architect, deviations in the high concentration range were observed (y=0.02 [0.01-0.07]+1.07 [1.06-1.08]x). All three analyzers showed acceptable results in evaluating accuracy of L index and unacceptable results for I index. The H index was comparable between BC and both, Architect (Cohen's κ [95% CI]=0.795 [0.692-0.898]) and Roche (Cohen's κ [95% CI]=0.825 [0.729-0.922]), while Roche and Architect were not comparable. The I index was not comparable between all analyzer combinations, while the L index was only comparable between Abbott and BC. Cross reactivity analysis mostly showed that serum indices measurement is affected when a combination of interferences is present. There is heterogeneity between analyzers in the hemolysis, icteria, lipemia (HIL) quality performance. Verification of serum indices in routine work is necessary to establish analytical specifications.

  3. Comparison of nested-multiplex, Taqman & SYBR Green real-time PCR in diagnosis of amoebic liver abscess in a tertiary health care institute in India.

    Science.gov (United States)

    Dinoop, K P; Parija, Subhash Chandra; Mandal, Jharna; Swaminathan, R P; Narayanan, P

    2016-01-01

    Amoebiasis is a common parasitic infection caused by Entamoeba histolytica and amoebic liver abscess (ALA) is the most common extraintestinal manifestation of amoebiasis. The aim of this study was to standardise real-time PCR assays (Taqman and SYBR Green) to detect E. histolytica from liver abscess pus and stool samples and compare its results with nested-multiplex PCR. Liver abscess pus specimens were subjected to DNA extraction. The extracted DNA samples were subjected to amplification by nested-multiplex PCR, Taqman (18S rRNA) and SYBR Green real-time PCR (16S-like rRNA assays to detect E. histolytica/E. dispar/E. moshkovskii). The amplification products were further confirmed by DNA sequence analysis. Receiver operator characteristic (ROC) curve analysis was done for nested-multiplex and SYBR Green real-time PCR and the area under the curve was calculated for evaluating the accuracy of the tests to dignose ALA. In all, 17, 19 and 25 liver abscess samples were positive for E. histolytica by nested-multiplex PCR, SYBR Green and Taqman real-time PCR assays, respectively. Significant differences in detection of E. histolytica were noted in the real-time PCR assays evaluated ( Pnested-multiplex PCR, SYBR Green real-time PCR and Taqman real-time PCR evaluated showed a positivity rate of 34, 38 and 50 per cent, respectively. Based on ROC curve analysis (considering Taqman real-time PCR as the gold standard), it was observed that SYBR Green real-time PCR was better than conventional nested-multiplex PCR for the diagnosis of ALA. Taqman real-time PCR targeting the 18S rRNA had the highest positivity rate evaluated in this study. Both nested multiplex and SYBR Green real-time PCR assays utilized were evaluated to give accurate results. Real-time PCR assays can be used as the gold standard in rapid and reliable diagnosis, and appropriate management of amoebiasis, replacing the conventional molecular methods.

  4. Identification and quantification of genetically modified Moonshade carnation lines using conventional and TaqMan real-time polymerase chain reaction methods.

    Science.gov (United States)

    Li, Peng; Jia, Junwei; Bai, Lan; Pan, Aihu; Tang, Xueming

    2013-07-01

    Genetically modified carnation (Dianthus caryophyllus L.) Moonshade was approved for planting and commercialization in several countries from 2004. Developing methods for analyzing Moonshade is necessary for implementing genetically modified organism labeling regulations. In this study, the 5'-transgene integration sequence was isolated using thermal asymmetric interlaced (TAIL)-PCR. Based upon the 5'-transgene integration sequence, conventional and TaqMan real-time PCR assays were established. The relative limit of detection for the conventional PCR assay was 0.05 % for Moonshade using 100 ng total carnation genomic DNA, corresponding to approximately 79 copies of the carnation haploid genome, and the limits of detection and quantification of the TaqMan real-time PCR assay were estimated to be 51 and 254 copies of haploid carnation genomic DNA, respectively. These results are useful for identifying and quantifying Moonshade and its derivatives.

  5. A TaqMan real-time PCR-based assay for the identification of Fasciola spp.

    Science.gov (United States)

    Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Jowers, Michael J; Baños, Pablo Díez; Píriz, Ana; Fickel, Joerns; Zhu, Xing-Quan

    2011-06-30

    Real time quantitative PCR (qPCR) is one of the key technologies of the post-genome era, with clear advantages compared to normal end-point PCR. In this paper, we report the first qPCR-based assay for the identification of Fasciola spp. Based on sequences of the second internal transcribed spacers (ITS-2) of the ribosomal rRNA gene, we used a set of genus-specific primers for Fasciola ITS-2 amplification, and we designed species-specific internal TaqMan probes to identify F. hepatica and F. gigantica, as well as the hybrid 'intermediate'Fasciola. These primers and probes were used for the highly specific, sensitive, and simple identification of Fasciola species collected from different animal host from China, Spain, Niger and Egypt. The novel qPCR-based technique for the identification of Fasciola spp. may provide a useful tool for the epidemiological investigation of Fasciola infection, including their intermediate snail hosts. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Detection and Quantification of Methyl tert-Butyl Ether-Degrading Strain PM1 by Real-Time TaqMan PCR

    OpenAIRE

    Hristova, Krassimira R.; Lutenegger, Christian M.; Scow, Kate M.

    2001-01-01

    The fuel oxygenate methyl tert-butyl ether (MTBE), a widely distributed groundwater contaminant, shows potential for treatment by in situ bioremediation. The bacterial strain PM1 rapidly mineralizes and grows on MTBE in laboratory cultures and can degrade the contaminant when inoculated into groundwater or soil microcosms. We applied the TaqMan quantitative PCR method to detect and quantify strain PM1 in laboratory and field samples. Specific primers and probes were designed for the 16S ribos...

  7. Bat white-nose syndrome: A real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans

    Science.gov (United States)

    Laura K Muller; Jeffrey M. Lorch; Daniel L. Lindner; Michael O' Connor; Andrea Gargas; David S. Blehert

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The...

  8. Comparison of the RealTime HIV-1, COBAS TaqMan 48 v1.0, Easy Q v1.2, and Versant v3.0 assays for Determination of HIV-1 Viral Loads in a Cohort of Canadian Patients with Diverse HIV Subtype Infections▿

    OpenAIRE

    Church, Deirdre; Gregson, Daniel; Lloyd, Tracie; Klein, Marina; Beckthold, Brenda; Laupland, Kevin; Gill, M. John

    2010-01-01

    HIV clinics in Canada provide care to an increasing number of patients born outside of Canada with HIV-1 non-B subtype infections. Because the Easy Q HIV-1 v1.2 assay (EQ; bioMérieux) failed to detect some non-B subtype infections, a multiassay HIV-1 viral load (VL) study was conducted with patients with diverse HIV subtype infections. Patients were enrolled from the Southern Alberta HIV Clinic (SAC), Calgary, Alberta, Canada (n = 349) and the McGill HIV Clinic (MHC), Montreal, Quebec, Canada...

  9. Specific and straightforward molecular investigation of β-thalassemia mutations in the Malaysian Malays and Chinese using direct TaqMan genotyping assays.

    Science.gov (United States)

    Kho, S L; Chua, K H; George, E; Tan, J A M A

    2013-07-15

    Beta-thalassemia is a life-threatening inherited blood disorder. Rapid characterization of β-globin gene mutations is necessary because of the high frequency of Malaysian β-thalassemia carriers. A combination real-time polymerase chain reaction genotyping assay using TaqMan probes was developed to confirm β-globin gene mutations. In this study, primers and probes were designed to specifically identify 8 common β-thalassemia mutations in the Malaysian Malay and Chinese ethnic groups using the Primer Express software. "Blind tests" using DNA samples from healthy individuals and β-thalassemia patients with different genotypes were performed to determine the specificity and sensitivity of this newly designed assay. Our results showed 100% sensitivity and specificity for this novel assay. In conclusion, the TaqMan genotyping assay is a straightforward assay that allows detection of β-globin gene mutations in less than 40 min. The simplicity and reproducibility of the TaqMan genotyping assay permit its use in laboratories as a rapid and cost-effective diagnostic tool for confirmation of common β-thalassemia mutations in Malaysia.

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

    Science.gov (United States)

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

    2017-08-01

    To compare the cytologic preparations of 130 cervical specimens (from women of various ethnicities at high risk for human papillomavirus [HPV] infection) using the SurePath (SP) collection system with specimens gathered using the ThinPrep (TP) system, as processed on the Cobas 4800 analyzer, to determine which collection method more accurately identifies HPV infection. In our prospective study, specimens were collected from 130 women of various ethnicities residing in or near Bronx County, NY. The SP-collected specimen was first processed for cytologic findings; if clinical HPV testing was requested on that specimen, it was tested using Hybrid Capture II (HC2) methodology. We tested the remnant SP-collected cell concentrate using the Cobas analyzer. Then, the TP-collected and SP-collected specimens were tested in the same run on that analyzer, and the results were compared. We also compared the results with the concurrent cytologic findings. The results were concordant for overall HR-HPV status in 93.8% of cases. Also, a statistically significant lower cycle threshold value was observed with Cobas testing of specimen concentrates tested via the BD SurePath Pap Test (P = .001), suggesting higher sensitivity compared with specimens tested via the ThinPrep Pap Test. Cobas 4800 HPV testing of SP-collected specimen concentrates yields comparable results to TP-collected specimen concentrates. Based on the limited data that we derived, SP collection may be a more favorable methodology than TP collection for HPV testing of individuals at high risk in our ethnically diverse, urban patient population. © American Society for Clinical Pathology, 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  11. The potential of TaqMan Array Cards for detection of multiple biological agents by real-time PCR.

    Directory of Open Access Journals (Sweden)

    Phillip A Rachwal

    Full Text Available The TaqMan Array Card architecture, normally used for gene expression studies, was evaluated for its potential to detect multiple bacterial agents by real-time PCR. Ten PCR assays targeting five biological agents (Bacillus anthracis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis, and Yersinia pestis were incorporated onto Array Cards. A comparison of PCR performance of each PCR in Array Card and singleplex format was conducted using DNA extracted from pure bacterial cultures. When 100 fg of agent DNA was added to Array Card channels the following levels of agent detection (where at least one agent PCR replicate returned a positive result were observed: Y. pestis 100%, B. mallei & F. tularensis 93%; B. anthracis 71%; B. pseudomallei 43%. For B. mallei & pseudomallei detection the BPM2 PCR, which detects both species, outperformed PCR assays specific to each organism indicating identification of the respective species would not be reproducible at the 100 fg level. Near 100% levels of detection were observed when 100 fg of DNA was added to each PCR in singleplex format with singleplex PCRs also returning sporadic positives at the 10 fg per PCR level. Before evaluating the use of Array Cards for the testing of environmental and clinical sample types, with potential levels of background DNA and PCR inhibitors, users would therefore have to accept a 10-fold reduction in sensitivity of PCR assays on the Array Card format, in order to benefit for the capacity to test multiple samples for multiple agents. A two PCR per agent strategy would allow the testing of 7 samples for the presence of 11 biological agents or 3 samples for 23 biological agents per card (with negative control channels.

  12. Rapid detection of Enterovirus and Coxsackievirus A10 by a TaqMan based duplex one-step real time RT-PCR assay.

    Science.gov (United States)

    Chen, Jingfang; Zhang, Rusheng; Ou, Xinhua; Yao, Dong; Huang, Zheng; Li, Linzhi; Sun, Biancheng

    2017-06-01

    A TaqMan based duplex one-step real time RT-PCR (rRT-PCR) assay was developed for the rapid detection of Coxsackievirus A10 (CV-A10) and other enterovirus (EVs) in clinical samples. The assay was fully evaluated and found to be specific and sensitive. When applied in 115 clinical samples, a 100% diagnostic sensitivity in CV-A10 detection and 97.4% diagnostic sensitivity in other EVs were found. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Development of SYBR Green and TaqMan quantitative real-time PCR assays for hepatopancreatic parvovirus (HPV) infecting Penaeus monodon in India.

    Science.gov (United States)

    Yadav, Reena; Paria, Anutosh; Mankame, Smruti; Makesh, M; Chaudhari, Aparna; Rajendran, K V

    2015-12-01

    Hepatopancreatic parvovirus (HPV) infects Penaeus monodon and causes mortality in the larval stages. Further, it has been implicated in the growth retardation in cultured P. monodon. Though different geographical isolates of HPV show large sequence variations, a sensitive PCR assay specific to Indian isolate has not yet been reported. Here, we developed a sensitive SYBR Green-based and TaqMan real-time PCR for the detection and quantification of the virus. A 441-bp PCR amplicon was cloned in pTZ57 R/T vector and the plasmid copy number was estimated. A 10-fold serial dilution of the plasmid DNA from 1 × 10(9) copies to 1 copy was prepared and used as the standard. The primers were tested initially using the standard on a conventional PCR format to determine the linearity of detection. The standards were further tested on real-time PCR format using SYBR Green and TaqMan chemistry and standard curves were generated based on the Ct values from three well replicates for each dilution. The assays were found to be sensitive, specific and reproducible with a wide dynamic range (1 × 10(9) to 10 copies) with coefficient of regression (R(2)) > 0.99, calculated average slope -3.196 for SYBR Green assay whereas, for TaqMan assay it was >0.99 and -3.367, respectively. The intra- and inter-assay variance of the Ct values ranged from 0.26% to 0.94% and 0.12% to 0.81%, respectively, for SYBR Green assay, and the inter-assay variance of the Ct values for TaqMan assay ranged from 0.07% to 1.93%. The specificity of the assays was proved by testing other DNA viruses of shrimp such as WSSV, IHHNV and MBV. Standardized assays were further tested to detect and quantify HPV in the post-larvae of P. monodon. The result was further compared with conventional PCR to test the reproducibility of the test. The assay was also used to screen Litopeneaus vannamei, Macrobrachium rosenbergii and Scylla serrata for HPV. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

    Science.gov (United States)

    Nagy, Alexander; Černíková, Lenka; Vitásková, Eliška; Křivda, Vlastimil; Dán, Ádám; Dirbáková, Zuzana; Jiřincová, Helena; Procházka, Bohumír; Sedlák, Kamil; Havlíčková, Martina

    2016-01-01

    In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence. PMID:27031831

  15. Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructanstructans.

    Science.gov (United States)

    Muller, Laura K.; Lorch, Jeffrey M.; Lindner, Daniel L.; O'Connor, Michael; Gargas, Andrea; Blehert, David S.

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg of genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was further qualified by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific, and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research.

  16. Development and evaluation of novel one-step TaqMan realtime RT-PCR assays for the detection and direct genotyping of genogroup I and II noroviruses

    DEFF Research Database (Denmark)

    Schultz, Anna Charlotte; Vega, Everado; Dalsgaard, Anders

    2011-01-01

    BackgroundCurrent detection and genotyping methods of genogroup (G) I and II noroviruses (NoVs) consist of a 2-step approach including detection of viral RNA by TaqMan realtime RT-PCR (RT-qPCR) followed by conventional RT-PCR and sequencing of partial regions of ORF1 or ORF2. ObjectiveTo develop ......Man RT-qPCR assays for the sensitive detection and direct genotyping of GI and GII NoVs from clinical and environmental matrices...... novel long-template one-step TaqMan assays (L-RT-qPCR) for the rapid detection and direct genotyping of GI and GII NoVs and to evaluate the sensitivity and specificity of the assays. Study designGI and GII-specific broadly reactive L-RT-qPCR assays were developed by combining existing NoV primers...... and probes targeting the open reading frame (ORF)1–ORF2 junction as well as region C at the 5′–ORF2. The assays were validated using GI and GII RNA transcripts and a coded panel of 75 stool samples containing NoV strains representing 9 GI genotypes and 12 GII genotypes, as well as sapoviruses, astroviruses...

  17. Development and Validation of a TaqMan Real-Time PCR Assay for the Specific Detection and Quantification of Fusarium fujikuroi in Rice Plants and Seeds.

    Science.gov (United States)

    Carneiro, Greice Amaral; Matić, Slavica; Ortu, Giuseppe; Garibaldi, Angelo; Spadaro, Davide; Gullino, Maria Lodovica

    2017-07-01

    Bakanae disease, which is caused by the seedborne pathogen Fusarium fujikuroi, is found throughout the world on rice. A TaqMan real-time PCR has been developed on the TEF 1-α gene to detect F. fujikuroi in different rice tissues. Three primer/probe sets were tested. The selected set produced an amplicon of 84 bp and was specific for F. fujikuroi with respect to eight Fusarium species of rice and six other rice common pathogens. The assay was validated for specificity, selectivity, sensitivity, repeatability, and reproducibility. The detection limit was set at 27.5 fg of DNA, which is approximately equivalent to one haploid genome of F. fujikuroi. The developed TaqMan real-time assay was able to efficiently detect and quantify F. fujikuroi from rice culms, leaves, roots, and seeds. At 1 week post-germination (wpg), the pathogen was more diffused in the green tissues, while at 3 wpg it was uniformly spread also in the roots. The highest concentration of F. fujikuroi was measured in the M6 cultivar, which showed around 1,450 fungal cells/g. The assay was sufficiently sensitive to detect a few genomic equivalents in the rice seeds, corresponding to 9.89 F. fujikuroi cells/g. The assay permitted bakanae disease to be detected in asymptomatic tissues at the early rice development stages.

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

    Science.gov (United States)

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

    2017-09-01

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

  19. Comparison of real-time SYBR green dengue assay with real-time taqman RT-PCR dengue assay and the conventional nested PCR for diagnosis of primary and secondary dengue infection

    Science.gov (United States)

    Paudel, Damodar; Jarman, Richard; Limkittikul, Kriengsak; Klungthong, Chonticha; Chamnanchanunt, Supat; Nisalak, Ananda; Gibbons, Robert; Chokejindachai, Watcharee

    2011-01-01

    Background: Dengue fever and dengue hemorrhagic fever are caused by dengue virus. Dengue infection remains a burning problem of many countries. To diagnose acute dengue in the early phase we improve the low cost, rapid SYBR green real time assay and compared the sensitivity and specificity with real time Taqman® assay and conventional nested PCR assay. Aims: To develop low cost, rapid and reliable real time SYBR green diagnostic dengue assay and compare with Taqman real-time assay and conventional nested PCR (modified Lanciotti). Materials and Methods: Eight cultured virus strains were diluted in tenth dilution down to undetectable level by the PCR to optimize the primer, temperature (annealing, and extension and to detect the limit of detection of the assay. Hundred and ninety three ELISA and PCR proved dengue clinical samples were tested with real time SYBR® Green assay, real time Taqman® assay to compare the sensitivity and specificity. Results: Sensitivity and specificity of real time SYBR® green dengue assay (84% and 66%, respectively) was almost comparable to those (81% and 74%) of Taqman real time PCR dengue assay. Real time SYBR® green RT-PCR was equally sensitive in primary and secondary infection while real time Taqman was less sensitive in the secondary infection. Sensitivity of real time Taqman on DENV3 (87%) was equal to SYBR green real time PCR dengue assay. Conclusion: We developed low cost rapid diagnostic SYBR green dengue assay. Further study is needed to make duplex primer assay for the serotyping of dengue virus. PMID:22363089

  20. Comparison of the Abbott RealTime High Risk HPV test and the Roche cobas 4800 HPV test using urine samples.

    Science.gov (United States)

    Lim, Myong Cheol; Lee, Do-Hoon; Hwang, Sang-Hyun; Hwang, Na Rae; Lee, Bomyee; Shin, Hye Young; Jun, Jae Kwan; Yoo, Chong Woo; Lee, Dong Ock; Seo, Sang-Soo; Park, Sang-Yoon; Joo, Jungnam

    2017-05-01

    Human papillomavirus (HPV) testing based on cervical samples is important for use in cervical cancer screening. However, cervical sampling is invasive. Therefore, non-invasive methods for detecting HPV, such as urine samples, are needed. For HPV detection in urine samples, two real-time PCR (RQ-PCR) tests, Roche cobas 4800 test (Roche_HPV; Roche Molecular Diagnostics) and Abbott RealTime High Risk HPV test (Abbott_HPV; Abbott Laboratories) were compared to standard cervical samples. The performance of Roche_HPV and Abbott_HPV for HPV detection was evaluated at the National Cancer Center using 100 paired cervical and urine samples. The tests were also compared using urine samples stored at various temperatures and for a range of durations. The overall agreement between the Roche_HPV and Abbott_HPV tests using urine samples for any hrHPV type was substantial (86.0% with a kappa value of 0.7173), and that for HPV 16/18 was nearly perfect (99.0% with a kappa value of 0.9668). The relative sensitivities (based on cervical samples) for HPV 16/18 detection using Roche_HPV and Abbott_HPV with urine samples were 79.2% (95% CI; 57.9-92.9%) and 81.8% (95% CI; 59.7-94.8%), respectively. When the cut-off C T value for Abbott_HPV was extended to 40 for urine samples, the relative sensitivity of Abbott_HPV increased to 91.7% from 81.8% for HPV16/18 detection and to 87.0% from 68.5% for other hrHPV detection. The specificity was not affected by the change in the C T threshold. Roche_HPV and Abbott_HPV showed high concordance. However, HPV DNA detection using urine samples was inferior to HPV DNA detection using cervical samples. Interestingly, when the cut-off C T value was set to 40, Abbott_HPV using urine samples showed high sensitivity and specificity, comparable to those obtained using cervical samples. Fully automated DNA extraction and detection systems, such as Roche_HPV and Abbott_HPV, could reduce the variability in HPV detection and accelerate the standardization of HPV

  1. Improved Safety for Molecular Diagnosis of Classical Rabies Viruses by Use of a TaqMan Real-Time Reverse Transcription-PCR "Double Check" Strategy

    DEFF Research Database (Denmark)

    Hoffmann, B.; Freuling, C. M.; Wakeley, P. R.

    2010-01-01

    To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus...... sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany......), the Veterinary Laboratories Agency (VLA; United Kingdom), and the DTU National Veterinary Institute (Lindholm, Denmark), covering the global diversity of rabies virus lineages, it was shown that both the newly developed assay and a previously described one had some detection failures. This was overcome...

  2. Designing a time-effective TaqMan probe-based real-time polymerase chain reaction protocol for the identification of Yersinia enterocolitica in raw pork meat

    Directory of Open Access Journals (Sweden)

    Milena Alicja Stachelska

    2017-01-01

    Full Text Available The aim of this study was to design a time-effective method comprising a short pre-enrichment step in a non-selective broth in combination with the TaqMan probe applied in the real-time polymerase chain reaction to detect Yersinia enterocolitica strains in raw pork meat. The method enabled to detect 1 colony forming unit per 25 mg of Yersinia enterocolitica in pork meat. The specificity and reliability of the method was not diminished by the company of microflora naturally present in meat. The method was found successful to detect pathogenic Yersinia enterocolitica strains in pork meat. It is advised to be used for assessing the microbial risk and for controlling the microbial quality of meat and meat products.

  3. Development of a TaqMan Array Card for Acute-Febrile-Illness Outbreak Investigation and Surveillance of Emerging Pathogens, Including Ebola Virus.

    Science.gov (United States)

    Liu, Jie; Ochieng, Caroline; Wiersma, Steve; Ströher, Ute; Towner, Jonathan S; Whitmer, Shannon; Nichol, Stuart T; Moore, Christopher C; Kersh, Gilbert J; Kato, Cecilia; Sexton, Christopher; Petersen, Jeannine; Massung, Robert; Hercik, Christine; Crump, John A; Kibiki, Gibson; Maro, Athanasia; Mujaga, Buliga; Gratz, Jean; Jacob, Shevin T; Banura, Patrick; Scheld, W Michael; Juma, Bonventure; Onyango, Clayton O; Montgomery, Joel M; Houpt, Eric; Fields, Barry

    2016-01-01

    Acute febrile illness (AFI) is associated with substantial morbidity and mortality worldwide, yet an etiologic agent is often not identified. Convalescent-phase serology is impractical, blood culture is slow, and many pathogens are fastidious or impossible to cultivate. We developed a real-time PCR-based TaqMan array card (TAC) that can test six to eight samples within 2.5 h from sample to results and can simultaneously detect 26 AFI-associated organisms, including 15 viruses (chikungunya, Crimean-Congo hemorrhagic fever [CCHF] virus, dengue, Ebola virus, Bundibugyo virus, Sudan virus, hantaviruses [Hantaan and Seoul], hepatitis E, Marburg, Nipah virus, o'nyong-nyong virus, Rift Valley fever virus, West Nile virus, and yellow fever virus), 8 bacteria (Bartonella spp., Brucella spp., Coxiella burnetii, Leptospira spp., Rickettsia spp., Salmonella enterica and Salmonella enterica serovar Typhi, and Yersinia pestis), and 3 protozoa (Leishmania spp., Plasmodium spp., and Trypanosoma brucei). Two extrinsic controls (phocine herpesvirus 1 and bacteriophage MS2) were included to ensure extraction and amplification efficiency. Analytical validation was performed on spiked specimens for linearity, intra-assay precision, interassay precision, limit of detection, and specificity. The performance of the card on clinical specimens was evaluated with 1,050 blood samples by comparison to the individual real-time PCR assays, and the TAC exhibited an overall 88% (278/315; 95% confidence interval [CI], 84% to 92%) sensitivity and a 99% (5,261/5,326, 98% to 99%) specificity. This TaqMan array card can be used in field settings as a rapid screen for outbreak investigation or for the surveillance of pathogens, including Ebola virus. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  4. Development of a TaqMan Allelic Discrimination Assay for detection of Single Nucleotides Polymorphisms associated with anti-malarial drug resistance

    Directory of Open Access Journals (Sweden)

    Kamau Edwin

    2012-01-01

    Full Text Available Abstract Background Anti-malarial drug resistance poses a threat to current global efforts towards control and elimination of malaria. Several methods are used in monitoring anti-malarial drug resistance. Molecular markers such as single nucleotide polymorphism (SNP for example are increasingly being used to identify genetic mutations related to anti-malarial drug resistance. Several methods are currently being used in analysis of SNP associated with anti-malarial drug resistance and although each one of these methods has unique strengths and shortcoming, there is still need to improve and/or develop new methods that will close the gap found in the current methods. Methods TaqMan Allelic Discrimination assays for detection of SNPs associated with anti-malarial drug resistance were designed for analysis on Applied Biosystems PCR platform. These assays were designed by submitting SNP sequences associated with anti-malarial drug resistance to Applied Biosystems website. Eleven SNPs associated with resistance to anti-malarial drugs were selected and tested. The performance of each SNP assay was tested by creating plasmid DNAs carrying codons of interests and analysing them for analysis. To test the sensitivity and specificity of each SNP assay, 12 clinical samples were sequenced at codons of interest and used in the analysis. Plasmid DNAs were used to establish the Limit of Detection (LoD for each assay. Results Data from genetic profiles of the Plasmodium falciparum laboratory strains and sequence data from 12 clinical samples was used as the reference method with which the performance of the SNP assays were compared to. The sensitivity and specificity of each SNP assay was establish at 100%. LoD for each assay was established at 2 GE, equivalent to less than 1 parasite/μL. SNP assays performed well in detecting mixed infection and analysis of clinical samples. Conclusion TaqMan Allelic Discrimination assay provides a good alternative tool in

  5. Rapid Identification and Quantification of Aureococcus anophagefferens by qPCR Method (Taqman) in the Qinhuangdao Coastal Area: A Region for Recurrent Brown Tide Breakout in China.

    Science.gov (United States)

    Wang, Li-Ping; Lei, Kun

    2016-12-01

    Since 2009, Aureococcus anophagefferens has caused brown tide to occur recurrently in Qinhuangdao coastal area, China. Because the algal cells of A. anophagefferens are so tiny (~3 µm) that it is very hard to identify exactly under a microscope for natural water samples, it is very urgent to develop a method for efficient and continuous monitoring. Here specific primers and Taqman probe are designed to develop a real-time quantitative PCR (qPCR) method for identification and quantification continually. The algal community and cell abundance of A. anophagefferens in the study area (E 119°20'-119°50' and N 39°30'-39°50') from April to October in 2013 are detected by pyrosequencing, and are used to validate the specification and precision of qPCR method for natural samples. Both pyrosequencing and qPCR shows that the targeted cells are present only in May, June and July, and the cell abundance are July > June > May. Although there are various algal species including dinoflagellata, diatom, Cryptomonadales, Chrysophyceae and Chlorophyta living in the natural seawater simultaneously, no disturbance happens to qPCR method. This qPCR method could detect as few as 10 targeted cells, indicating it is able to detect the algal cells at pre-bloom levels. Therefore, qPCR with Taqman probe provides a powerful and sensitive method to monitor the brown tide continually in Qinhuangdao coastal area, China. The results provide a necessary technology support for forecasting the brown tide initiation, in China.

  6. TaqMan real-time PCR assays for single-nucleotide polymorphisms which identify Francisella tularensis and its subspecies and subpopulations.

    Directory of Open Access Journals (Sweden)

    Dawn N Birdsell

    Full Text Available Francisella tularensis, the etiologic agent of tularemia and a Class A Select Agent, is divided into three subspecies and multiple subpopulations that differ in virulence and geographic distribution. Given these differences, there is a need to rapidly and accurately determine if a strain is F. tularensis and, if it is, assign it to subspecies and subpopulation. We designed TaqMan real-time PCR genotyping assays using eleven single nucleotide polymorphisms (SNPs that were potentially specific to closely related groups within the genus Francisella, including numerous subpopulations within F. tularensis species. We performed extensive validation studies to test the specificity of these SNPs to particular populations by screening the assays across a set of 565 genetically and geographically diverse F. tularensis isolates and an additional 21 genetic near-neighbor (outgroup isolates. All eleven assays correctly determined the genetic groups of all 565 F. tularensis isolates. One assay differentiates F. tularensis, F. novicida, and F. hispaniensis from the more genetically distant F. philomiragia and Francisella-like endosymbionts. Another assay differentiates F. tularensis isolates from near neighbors. The remaining nine assays classify F. tularensis-confirmed isolates into F. tularensis subspecies and subpopulations. The genotyping accuracy of these nine assays diminished when tested on outgroup isolates (i.e. non F. tularensis, therefore a hierarchical approach of assay usage is recommended wherein the F. tularensis-specific assay is used before the nine downstream assays. Among F. tularensis isolates, all eleven assays were highly sensitive, consistently amplifying very low concentrations of DNA. Altogether, these eleven TaqMan real-time PCR assays represent a highly accurate, rapid, and sensitive means of identifying the species, subspecies, and subpopulation of any F. tularensis isolate if used in a step-wise hierarchical scheme. These assays

  7. High-risk Human Papillomavirus Determination in Formalin-fixed, Paraffin-embedded Cervical Tissue Using the Roche Cobas 4800 System: A Comparative Study With Liquid-based Cytology.

    Science.gov (United States)

    Tardío, Juan C; Cambero, Olivia; Sánchez-Estévez, Carolina; Sánchez-García, Ana B; Angulo, Fernando; Moreno, Amalia

    2017-11-14

    Roche cobas 4800 human papillomavirus (HPV) test is an automated real-time polymerase chain reaction-based system that allows the simultaneous detection of 14 human papillomavirus high-risk (HR-HPV) genotypes. This test is Food and Drug Administration approved since 2011 for HPV determination in liquid-based cytologic samples, but a clinically validated technique for formalin-fixed, paraffin-embedded (FFPE) tissue specimens is presently not commercially available. In our laboratory, we have developed an HPV detection procedure in FFPE tissue by cobas 4800 HPV test. In order to validate our method, we retrospectively studied 165 FFPE cervical biopsy and conization specimens with varied diagnoses from our files. In 50 of them, we contrasted the results with those obtained from simultaneous liquid-based cytologies from the same patients. Finally, seeking the possible complementary clinical usefulness of the procedure, we compared the HPV genotypes detected in cervical intraepithelial neoplasia grade 1 (CIN1)-diagnosed biopsies from 20 patients with a subsequent high-grade CIN (CIN2+) diagnosis with those from another group of 20 patients without a posterior CIN2+ diagnosis. Eighty-seven percent of the assays provided informative results. HR-HPV was detected in 28 of 32 (88%) invasive cervical squamous carcinomas. Coincidental HR-HPV genotypes were obtained in 32 of 50 (64%) cases with simultaneous cervical biopsy and liquid-based cytologic samples. A significant higher risk of progression to CIN2+ was found when HPV16 (P=0.022) or any HR-HPV genotype (P=0.037) was detected in CIN1 biopsies. The reported procedure provides an automated, technically time-saving, easy to integrate into laboratory routine, and reliable method of HR-HPV determination in FFPE specimens.

  8. Universal detection of phytoplasmas and Xylella spp. by TaqMan singleplex and multiplex real-time PCR with dual priming oligonucleotides.

    Directory of Open Access Journals (Sweden)

    Takao Ito

    Full Text Available Phytoplasmas and Xylella spp. are bacteria that cause many economically important plant diseases worldwide. TaqMan probe-based quantitative real-time polymerase chain reaction (qPCR assays have been utilized to universally detect phytoplasmas or Xylella fastidiosa. To develop a superior universal qPCR method, we used a dual priming oligonucleotide (DPO with two annealing sites as a reverse primer to target the well-conserved bacterial 16S rDNA. The new qPCR assays universally detected various species of phytoplasmas and subspecies of X. fastidiosa as well as Xylella taiwanensis, and generally showed superior threshold cycle values when amplifying specific or non-specific products compared to current universal qPCR assays. The proposed qPCR assays were integrated to develop a multiplex qPCR assay that simultaneously detected phytoplasmas, Xylella spp., and an internal plant DNA positive control within 1 hour. This assay could detect a minimum of ten bacterial cells and was compatible with crude extractions used in the rapid screening of various plants. The amplicons were of sufficient lengths to be directly sequenced for preliminary identification, and the primers could be used in universal conventional PCR assays. Additionally, reverse DPO primers can be utilized to improve other probe-based qPCR assays.

  9. Quantification of the biocontrol agent Trichoderma harzianum with real-time TaqMan PCR and its potential extrapolation to the hyphal biomass.

    Science.gov (United States)

    López-Mondéjar, Rubén; Antón, Anabel; Raidl, Stefan; Ros, Margarita; Pascual, José Antonio

    2010-04-01

    The species of the genus Trichoderma are used successfully as biocontrol agents against a wide range of phytopathogenic fungi. Among them, Trichoderma harzianum is especially effective. However, to develop more effective fungal biocontrol strategies in organic substrates and soil, tools for monitoring the control agents are required. Real-time PCR is potentially an effective tool for the quantification of fungi in environmental samples. The aim of this study consisted of the development and application of a real-time PCR-based method to the quantification of T. harzianum, and the extrapolation of these data to fungal biomass values. A set of primers and a TaqMan probe for the ITS region of the fungal genome were designed and tested, and amplification was correlated to biomass measurements obtained with optical microscopy and image analysis, of the hyphal length of the mycelium of the colony. A correlation of 0.76 between ITS copies and biomass was obtained. The extrapolation of the quantity of ITS copies, calculated based on real-time PCR data, into quantities of fungal biomass provides potentially a more accurate value of the quantity of soil fungi. Copyright 2009 Elsevier Ltd. All rights reserved.

  10. Characterization of Phytophthora nicotianae isolates in southeast Spain and their detection and quantification through a real-time TaqMan PCR.

    Science.gov (United States)

    Blaya, Josefa; Lacasa, Carmen; Lacasa, Alfredo; Martínez, Victoriano; Santísima-Trinidad, Ana B; Pascual, Jose A; Ros, Margarita

    2015-04-01

    The soil-borne pathogens Phytophthora nicotianae and P. capsici are the causal agents of root and stem rot of many plant species. Although P. capsici was considered the causal agent in one of the main pepper production areas of Spain to date, evidence of the presence of P. nicotianae was found. We aimed to survey the presence of P. nicotianae and study the variability in its populations in this area in order to improve the management of Tristeza disease. A new specific primer and a TaqMan probe were designed based on the internal transcribed spacer regions of ribosomal DNA to detect and quantify P. nicotianae. Both morphological and molecular analysis showed its presence and confirmed it to be the causal agent of the Phytophthora disease symptoms in the studied area. The genetic characterization among P. nicotianae populations showed a low variability of genetic diversity among the isolates. Only isolates of the A2 mating type were detected. Not only is a specific and early detection of P. nicotianae essential but also the study of genetic variability among isolates for the appropriate management of the disease, above all, in producing areas with favorable conditions for the advance of the disease. © 2014 Society of Chemical Industry.

  11. Development of a Taqman real-time PCR assay for rapid detection and quantification of Vibrio tapetis in extrapallial fluids of clams

    Directory of Open Access Journals (Sweden)

    Adeline Bidault

    2015-12-01

    Full Text Available The Gram-negative bacterium Vibrio tapetis is known as the causative agent of Brown Ring Disease (BRD in the Manila clam Venerupis (=Ruditapes philippinarum. This bivalve is the second most important species produced in aquaculture and has a high commercial value. In spite of the development of several molecular methods, no survey has been yet achieved to rapidly quantify the bacterium in the clam. In this study, we developed a Taqman real-time PCR assay targeting virB4 gene for accurate and quantitative identification of V. tapetis strains pathogenic to clams. Sensitivity and reproducibility of the method were assessed using either filtered sea water or extrapallial fluids of clam injected with the CECT4600T V. tapetis strain. Quantification curves of V. tapetis strain seeded in filtered seawater (FSW or extrapallial fluids (EF samples were equivalent showing reliable qPCR efficacies. With this protocol, we were able to specifically detect V. tapetis strains down to 1.125 101 bacteria per mL of EF or FSW, taking into account the dilution factor used for appropriate template DNA preparation. This qPCR assay allowed us to monitor V. tapetis load both experimentally or naturally infected Manila clams. This technique will be particularly useful for monitoring the kinetics of massive infections by V. tapetis and for designing appropriate control measures for aquaculture purposes.

  12. Association Between Stool Enteropathogen Quantity and Disease in Tanzanian Children Using TaqMan Array Cards: A Nested Case-Control Study

    Science.gov (United States)

    Platts-Mills, James A.; Gratz, Jean; Mduma, Esto; Svensen, Erling; Amour, Caroline; Liu, Jie; Maro, Athanasia; Saidi, Queen; Swai, Ndealilia; Kumburu, Happiness; McCormick, Benjamin J. J.; Kibiki, Gibson; Houpt, Eric R.

    2014-01-01

    Etiologic studies of diarrhea are limited by uneven diagnostic methods and frequent asymptomatic detection of enteropathogens. Polymerase chain reaction-based stool pathogen quantification may help distinguish clinically significant infections. We performed a nested case-control study of diarrhea in infants from a community-based birth cohort in Tanzania. We tested 71 diarrheal samples and pre-diarrheal matched controls with a laboratory-developed TaqMan Array Card for 19 enteropathogens. With qualitative detection, no pathogens were significantly associated with diarrhea. When pathogen quantity was considered, rotavirus (odds ratio [OR] = 2.70 per log10 increase, P < 0.001), astrovirus (OR = 1.49, P = 0.01), and Shigella/enteroinvasive Escherichia coli (OR = 1.47, P = 0.04) were associated with diarrhea. Enterotoxigenic E. coli (0.15 SD decline in length-for-age z score after 3 months per log10 increase, P < 0.001) and Campylobacter jejuni/C. coli (0.11 SD decline, P = 0.003) in pre-diarrheal stools were associated with poor linear growth. Quantitative analysis can help refine the association between enteropathogens and disease in endemic settings. PMID:24189366

  13. Rapid and Quantitative Detection of Leifsonia xyli subsp. xyli in Sugarcane Stalk Juice Using a Real-Time Fluorescent (TaqMan PCR Assay

    Directory of Open Access Journals (Sweden)

    Hua-Ying Fu

    2016-01-01

    Full Text Available Ratoon stunting disease (RSD of sugarcane, one of the most important diseases seriously affecting the productivity of sugarcane crops, was caused by the bacterial agent Leifsonia xyli subsp. xyli (Lxx. A TaqMan probe-based real-time quantitative polymerase chain reaction (qPCR assay was established in this study for the quantification of Lxx detection in sugarcane stalk juice. A pair of PCR primers (Pat1-QF/Pat1-QR and a fluorogenic probe (Pat1-QP targeting the Part1 gene of Lxx were used for the qPCR assay. The assay had a detection limit of 100 copies of plasmid DNA and 100 fg of Lxx genomic DNA, which was 100-fold more sensitive than the conventional PCR. Fifty (28.7% of 174 stalk juice samples from two field trials were tested to be positive by qPCR assay, whereas, by conventional PCR, only 12.1% (21/174 were tested to be positive with a published primer pair CxxITSf#5/CxxITSr#5 and 15.5% (27/174 were tested to be positive with a newly designed primer pair Pat1-F2/Pat1-R2. The new qPCR assay can be used as an alternative to current diagnostic methods for Lxx, especially when dealing with certificating a large number of healthy cane seedlings and determining disease incidence accurately in commercial fields.

  14. Quantitative Tetraplex Real-Time Polymerase Chain Reaction Assay with TaqMan Probes Discriminates Cattle, Buffalo, and Porcine Materials in Food Chain.

    Science.gov (United States)

    Hossain, M A Motalib; Ali, Md Eaqub; Sultana, Sharmin; Asing; Bonny, Sharmin Quazi; Kader, Md Abdul; Rahman, M Aminur

    2017-05-17

    Cattle, buffalo, and porcine materials are widely adulterated, and their quantification might safeguard health, religious, economic, and social sanctity. Recently, conventional polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP) assays have been documented but they are just suitable for identification, cannot quantify adulterations. We described here a quantitative tetraplex real-time PCR assay with TaqMan Probes to quantify contributions from cattle, buffalo, and porcine materials simultaneously. Amplicon-sizes were very short (106-, 90-, and 146-bp for cattle, buffalo, and porcine) because longer targets could be broken down, bringing serious ambiguity in molecular diagnostics. False negative detection was eliminated through an endogenous control (141-bp site of eukaryotic 18S rRNA). Analysis of 27 frankfurters and 27 meatballs reflected 84-115% target recovery at 0.1-10% adulterations. Finally, a test of 36 commercial products revealed 71% beef frankfurters, 100% meatballs, and 85% burgers contained buffalo adulteration, but no porcine was found in beef products.

  15. Rapid identification of tomato Sw-5 resistance-breaking isolates of Tomato spotted wilt virus using high resolution melting and TaqMan SNP Genotyping assays as allelic discrimination techniques.

    Directory of Open Access Journals (Sweden)

    Valentina di Rienzo

    Full Text Available In tomato, resistance to Tomato spotted wilt virus (TSWV is conferred by the dominant gene, designated Sw-5. Virulent Sw-5 resistance breaking (SRB mutants of TSWV have been reported on Sw-5 tomato cultivars. Two different PCR-based allelic discrimination techniques, namely Custom TaqMan™ SNP Genotyping and high-resolution melting (HRM assays, were developed and compared for their ability to distinguish between avirulent (Sw-5 non-infecting, SNI and SRB biotypes. TaqMan assays proved to be more sensitive (threshold of detection in a range of 50-70 TSWV RNA copies and more reliable than HRM, assigning 25 TSWV isolates to their correct genotype with an accuracy of 100%. Moreover, the TaqMan SNP assays were further improved developing a rapid and simple protocol that included crude leaf extraction for RNA template preparations. On the other hand, HRM assays showed higher levels of sensitivity than TaqMan when used to co-detect both biotypes in different artificial mixtures. These diagnostic assays contributed to gain preliminary information on the epidemiology of TSWV isolates in open field conditions. In fact, the presented data suggest that SRB isolates are present as stable populations established year round, persisting on both winter (globe artichoke and summer (tomato crops, in the same cultivated areas of Southern Italy.

  16. Detection of viable Salmonella in ice cream by TaqMan real-time polymerase chain reaction assay combining propidium monoazide

    Directory of Open Access Journals (Sweden)

    Yuexia Wang

    2015-09-01

    Full Text Available Real-time polymerase chain reaction (PCR allows rapid detection of Salmonella in frozen dairy products, but it might cause a false positive detection result because it might amplify DNA from dead target cells as well. In this study, Salmonella-free frozen ice cream was initially inoculated with heat-killed Salmonella Typhimurium cells and stored at −18°C. Bacterial DNA extracted from the sample was amplified using TaqMan probe-based real-time PCR targeting the invA gene. Our results indicated that DNA from the dead cells remained stable in frozen ice cream for at least 20 days, and could produce fluorescence signal for real-time PCR as well. To overcome this limitation, propidium monoazide (PMA was combined with real-time PCR. PMA treatment can effectively prevent PCR amplification from heat-killed Salmonella cells in frozen ice cream. The PMA real-time PCR assay can selectively detect viable Salmonella at as low as 103 CFU/mL. Combining 18 hours of pre-enrichment with the assay allows for the detection of viable Salmonella at 100 CFU/mL and avoiding the false-positive result of dead cells. The PMA real-time PCR assay provides an alternative specifically for detection of viable Salmonella in ice cream. However, when the PMA real-time PCR assay was evaluated in ice cream subjected to frozen storage, it obviously underestimated the contamination situation of viable Salmonella, which might lead to a false negative result. According to this result, the use of enrichment prior to PMA real-time PCR analysis remains as the more appropriate approach.

  17. TaqMan real-time polymerase chain reaction for detection of Ophidiomyces ophiodiicola, the fungus associated with snake fungal disease.

    Science.gov (United States)

    Bohuski, Elizabeth; Lorch, Jeffrey M; Griffin, Kathryn M; Blehert, David S

    2015-04-15

    Fungal skin infections associated with Ophidiomyces ophiodiicola, a member of the Chrysosporium anamorph of Nannizziopsis vriesii (CANV) complex, have been linked to an increasing number of cases of snake fungal disease (SFD) in captive snakes around the world and in wild snake populations in eastern North America. The emergence of SFD in both captive and wild situations has led to an increased need for tools to better diagnose and study the disease. We developed two TaqMan real-time polymerase chain reaction (PCR) assays to rapidly detect O. ophiodiicola in clinical samples. One assay targets the internal transcribed spacer region (ITS) of the fungal genome while the other targets the more variable intergenic spacer region (IGS). The PCR assays were qualified using skin samples collected from 50 snakes for which O. ophiodiicola had been previously detected by culture, 20 snakes with gross skin lesions suggestive of SFD but which were culture-negative for O. ophiodiicola, and 16 snakes with no clinical signs of infection. Both assays performed equivalently and proved to be more sensitive than traditional culture methods, detecting O. ophiodiicola in 98% of the culture-positive samples and in 40% of the culture-negative snakes that had clinical signs of SFD. In addition, the assays did not cross-react with a panel of 28 fungal species that are closely related to O. ophiodiicola or that commonly occur on the skin of snakes. The assays did, however, indicate that some asymptomatic snakes (~6%) may harbor low levels of the fungus, and that PCR should be paired with histology when a definitive diagnosis is required. These assays represent the first published methods to detect O. ophiodiicola by real-time PCR. The ITS assay has great utility for assisting with SFD diagnoses whereas the IGS assay offers a valuable tool for research-based applications.

  18. Detection of viable Salmonella in ice cream by TaqMan real-time polymerase chain reaction assay combining propidium monoazide.

    Science.gov (United States)

    Wang, Yuexia; Yang, Ming; Liu, Shuchun; Chen, Wanyi; Suo, Biao

    2015-09-01

    Real-time polymerase chain reaction (PCR) allows rapid detection of Salmonella in frozen dairy products, but it might cause a false positive detection result because it might amplify DNA from dead target cells as well. In this study, Salmonella-free frozen ice cream was initially inoculated with heat-killed Salmonella Typhimurium cells and stored at -18°C. Bacterial DNA extracted from the sample was amplified using TaqMan probe-based real-time PCR targeting the invA gene. Our results indicated that DNA from the dead cells remained stable in frozen ice cream for at least 20 days, and could produce fluorescence signal for real-time PCR as well. To overcome this limitation, propidium monoazide (PMA) was combined with real-time PCR. PMA treatment can effectively prevent PCR amplification from heat-killed Salmonella cells in frozen ice cream. The PMA real-time PCR assay can selectively detect viable Salmonella at as low as 10 3  CFU/mL. Combining 18 hours of pre-enrichment with the assay allows for the detection of viable Salmonella at 10 0  CFU/mL and avoiding the false-positive result of dead cells. The PMA real-time PCR assay provides an alternative specifically for detection of viable Salmonella in ice cream. However, when the PMA real-time PCR assay was evaluated in ice cream subjected to frozen storage, it obviously underestimated the contamination situation of viable Salmonella, which might lead to a false negative result. According to this result, the use of enrichment prior to PMA real-time PCR analysis remains as the more appropriate approach. Copyright © 2015. Published by Elsevier B.V.

  19. Multiplex real-time PCR (TaqMan) assay for the simultaneous detection and discrimination of potato powdery and common scab diseases and pathogens.

    Science.gov (United States)

    Qu, X S; Wanner, L A; Christ, B J

    2011-03-01

    To develop a multiplex real-time PCR assay using TaqMan probes for the simultaneous detection and discrimination of potato powdery scab and common scab, two potato tuber diseases with similar symptoms, and the causal pathogens Spongospora subterranea and plant pathogenic Streptomyces spp. Real-time PCR primers and a probe for S. subterranea were designed based on the DNA sequence of the ribosomal RNA ITS2 region. Primers and a probe for pathogenic Streptomyces were designed based on the DNA sequence of the txtAB genes. The two sets of primer pairs and probes were used in a single real-time PCR assay. The multiplex real-time PCR assay was confirmed to be specific for S. subterranea and pathogenic Streptomyces. The assay detected DNA quantities of 100 fg for each of the two pathogens and linear responses and high correlation coefficients between the amount of DNA and C(t) values for each pathogen were achieved. The presence of two sets of primer pairs and probes and of plant extracts did not alter the sensitivity and efficiency of multiplex PCR amplification. Using the PCR assay, we could discriminate between powdery scab and common scab tubers with similar symptoms. Common scab and powdery scab were detected in some tubers with no visible symptoms. Mixed infections of common scab and powdery scab on single tubers were also revealed. This multiplex real-time PCR assay is a rapid, cost efficient, specific and sensitive tool for the simultaneous detection and discrimination of the two pathogens on infected potato tubers when visual symptoms are inconclusive or not present. Accurate and quick identification and discrimination of the cause of scab diseases on potatoes will provide critical information to potato growers and researchers for disease management. This is important because management strategies for common and powdery scab diseases are very different. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

  20. Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC study

    Directory of Open Access Journals (Sweden)

    Dial Stacey L

    2008-07-01

    Full Text Available Abstract Background The MicroArray Quality Control (MAQC project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (Nat Biotechnol 24:1115-22, 2006. The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan® Gene Expression PCR Assay, Standardized (Sta RT-PCR™ and QuantiGene®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR® Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT2 Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency. Results The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes. Conclusion These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.

  1. Development of TaqMan probes targeting the four major celiac disease epitopes found in α-gliadin sequences of spelt (Triticum aestivum ssp. spelta) and bread wheat (Triticum aestivum ssp. aestivum).

    Science.gov (United States)

    Dubois, Benjamin; Bertin, Pierre; Muhovski, Yordan; Escarnot, Emmanuelle; Mingeot, Dominique

    2017-01-01

    Celiac disease (CD) is caused by specific sequences of gluten proteins found in cereals such as bread wheat ( Triticum aestivum ssp. aestivum ) and spelt ( T. aestivum ssp. spelta ). Among them, the α-gliadins display the highest immunogenicity, with four T-cell stimulatory epitopes. The toxicity of each epitope sequence can be reduced or even suppressed according to the allelic form of each sequence. One way to address the CD problem would be to make use of this allelic variability in breeding programs to develop safe varieties, but tools to track the presence of toxic epitopes are required. The objective of this study was to develop a tool to accurately detect and quantify the immunogenic content of expressed α-gliadins of spelt and bread wheat. Four TaqMan probes that only hybridize to the canonical-i.e. toxic-form of each of the four epitopes were developed and their specificity was demonstrated. Six TaqMan probes targeting stable reference genes were also developed and constitute a tool to normalize qPCR data. The probes were used to measure the epitope expression levels of 11 contrasted spelt accessions and three ancestral diploid accessions of bread wheat and spelt. A high expression variability was highlighted among epitopes and among accessions, especially in Asian spelts, which showed lower epitope expression levels than the other spelts. Some discrepancies were identified between the canonical epitope expression level and the global amount of expressed α-gliadins, which makes the designed TaqMan probes a useful tool to quantify the immunogenic potential independently of the global amount of expressed α-gliadins. The results obtained in this study provide useful tools to study the immunogenic potential of expressed α-gliadin sequences from Triticeae accessions such as spelt and bread wheat. The application of the designed probes to contrasted spelt accessions revealed a high variability and interesting low canonical epitope expression levels in the

  2. Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

    Science.gov (United States)

    Cura, Carolina I.; Duffy, Tomas; Lucero, Raúl H.; Bisio, Margarita; Péneau, Julie; Jimenez-Coello, Matilde; Calabuig, Eva; Gimenez, María J.; Valencia Ayala, Edward; Kjos, Sonia A.; Santalla, José; Mahaney, Susan M.; Cayo, Nelly M.; Nagel, Claudia; Barcán, Laura; Málaga Machaca, Edith S.; Acosta Viana, Karla Y.; Brutus, Laurent; Ocampo, Susana B.; Aznar, Christine; Cuba Cuba, Cesar A.; Gürtler, Ricardo E.; Ramsey, Janine M.; Ribeiro, Isabela; VandeBerg, John L.; Yadon, Zaida E.; Osuna, Antonio; Schijman, Alejandro G.

    2015-01-01

    Background Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR). Methods/Principal Findings The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm. Conclusions/Significance Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production. PMID:25993316

  3. [Detection of RAS genes mutation using the Cobas® method in a private laboratory of pathology: Medical and economical study in comparison to a public platform of molecular biology of cancer].

    Science.gov (United States)

    Albertini, Anne-Flore; Raoux, Delphine; Neumann, Frédéric; Rossat, Stéphane; Tabet, Farid; Pedeutour, Florence; Duranton-Tanneur, Valérie; Kubiniek, Valérie; Vire, Olivier; Weinbreck, Nicolas

    In France, determination of the mutation status of RAS genes for predictive response to anti-EGFR targeted treatments is carried out by public platforms of molecular biology of cancer created by the French National Cancer Institute. This study aims to demonstrate the feasibility of these analyses by a private pathology laboratory (MEDIPATH) as per the requirements of accreditation. We retrospectively studied the mutation status of KRAS and NRAS genes in 163 cases of colorectal metastatic cancer using the Cobas ® technique. We compared our results to those prospectively obtained through pyrosequencing and allelic discrimination by the genetic laboratory of solid tumors at the Nice University Hospital (PACA-EST regional platform). The results of both series were identical: 98.7% positive correlation; negative correlation of 93.1%; overall correlation of 95.7% (Kappa=0.92). This study demonstrates the feasibility of molecular analysis in a private pathology laboratory. As this practice requires a high level of guarantee, its accreditation, according to the NF-EN-ISO15189 quality compliance French standard, is essential. Conducting molecular analysis in this context avoids the steps of routing the sample and the result between the pathology laboratory and the platform, which reduces the overall time of rendering the result. In conclusion, the transfer of some analysis from these platforms to private pathology laboratories would allow the platforms to be discharged from a part of routine testing and therefore concentrate their efforts to the development of new analyses constantly required to access personalized medicine. Copyright © 2017. Published by Elsevier Masson SAS.

  4. Sensitive and specific detection of potentially allergenic almond (Prunus dulcis) in complex food matrices by Taqman real-time polymerase chain reaction in comparison to commercially available protein-based enzyme-linked immunosorbent assay

    Energy Technology Data Exchange (ETDEWEB)

    Roeder, Martin; Vieths, Stefan [Division of Allergology, Paul-Ehrlich-Institut, Paul-Ehrlich-Strasse 51-59, 63225 Langen (Germany); Holzhauser, Thomas, E-mail: holth@pei.de [Division of Allergology, Paul-Ehrlich-Institut, Paul-Ehrlich-Strasse 51-59, 63225 Langen (Germany)

    2011-01-24

    Currently, causative immunotherapies are lacking in food allergy. The only option to prevent allergic reactions in susceptible individuals is to strictly avoid the offending food. Thus, reliable labelling of allergenic constituents is of major importance, but can only be achieved if appropriate specific and sensitive detection techniques for foods with allergenic potential are available. Almond is an allergenic food that requires mandatory labelling on prepackaged foods and belongs to the genus Prunus. Species of this genus are phylogenetically closely related. We observed commercially available almond specific ELISA being highly cross-reactive with other foods of the Prunoideae family, resulting in a false-positive detection of up to 500,000 mg kg{sup -1} almond. Previously published PCR methods were reported to be cross-reactive with false positive results >1200 mg kg{sup -1}. We describe the development of a novel almond specific real-time PCR, based on mutated mismatch primers and sequence specific Taqman probe detection, in comparison with two quantitative commercially available ELISA. PCR sensitivity was investigated with chocolate, chocolate coating and cookies spiked between 5 and 100,000 mg kg{sup -1} almond. In all matrices almond was reproducibly detected by real-time PCR at the lowest spike level of 5 mg kg{sup -1}. Further, between 100 and 100,000 mg kg{sup -1} spiked almond, the method featured good correlation between quantified copy numbers and the amount of spiked almond. Within this range a similar relation between detectable signal and amount of almond was observed for both PCR and ELISA. In contrast to ELISA the Taqman real-time PCR method was highly specific in 59 food items with negligible cross-reactivity for a very limited number of Prunoideae foods. The real-time PCR analysis of 24 retail samples was in concordance with ELISA results: 21% (n = 5) contained undeclared almond. This is the first completely disclosed real-time PCR method for a

  5. TaqMan探针荧光定量PCR检测花生油中掺入棕榈油的研究%Determination of palm oil adulterated in peanut oil with the TaqMan probe -based RT- PCR method

    Institute of Scientific and Technical Information of China (English)

    周慧; 梁宇斌; 吴苏喜; 李晓明; 裴伟; 杨涛

    2011-01-01

    The method of Real - time fluorescence quantitative polymerase chain reaction ( RT - PCR) with TaqMan fluorescent probe was chosen to fast detect the amount of palm oil mixed in peanut oil. MT3 - B gene of palm was selected as target gene to detect palm oil from peanut oil. The primers of MT3 - B and TaqMan probe were designed, MT3 - B gene reconstructed plasmid was built as absolute quantitative criteria for quantitative RT - PCR to establish standard curve. Peanut oil blended with 1% -40% concentration gradient palm oil was extracted DNA to test palm content by RT - PCR. The result showed that the correlation coefficient (R1) of standard curve with logarithmic linear regression analysis was 0.996. When the adulteration of palm oil in peanut oil reached 5% volume, MT3 - B gene of 17.431 copies per milli-liter of mixed oil could be detected . The method showed good sensitivity, specificity and repeatability.%根据棕榈内源基因MT3 -B设计引物和TaqMan探针,采用基因重组技术构建用于检测棕榈基因MT3 -B的重组质粒作为绝对定量标准品,建立标准曲线,对花生油中掺入棕榈油1% ~40%梯度混合油品提取DNA进行棕榈成分定量检测.结果表明,重组质粒标准品荧光定量标准曲线对数线性回归分析相关系数(R2)为0.996;花生油中掺入棕榈油达到5%时,可检出每亳升混合油品中棕榈MT3 -B基因17.431 copies,检测的重复性和特异性好.

  6. Sensitive and specific detection of potentially allergenic almond (Prunus dulcis) in complex food matrices by Taqman(®) real-time polymerase chain reaction in comparison to commercially available protein-based enzyme-linked immunosorbent assay.

    Science.gov (United States)

    Röder, Martin; Vieths, Stefan; Holzhauser, Thomas

    2011-01-24

    Currently, causative immunotherapies are lacking in food allergy. The only option to prevent allergic reactions in susceptible individuals is to strictly avoid the offending food. Thus, reliable labelling of allergenic constituents is of major importance, but can only be achieved if appropriate specific and sensitive detection techniques for foods with allergenic potential are available. Almond is an allergenic food that requires mandatory labelling on prepackaged foods and belongs to the genus Prunus. Species of this genus are phylogenetically closely related. We observed commercially available almond specific ELISA being highly cross-reactive with other foods of the Prunoideae family, resulting in a false-positive detection of up to 500,000 mg kg(-1) almond. Previously published PCR methods were reported to be cross-reactive with false positive results >1200 mg kg(-1). We describe the development of a novel almond specific real-time PCR, based on mutated mismatch primers and sequence specific Taqman(®) probe detection, in comparison with two quantitative commercially available ELISA. PCR sensitivity was investigated with chocolate, chocolate coating and cookies spiked between 5 and 100,000 mg kg(-1) almond. In all matrices almond was reproducibly detected by real-time PCR at the lowest spike level of 5 mg kg(-1). Further, between 100 and 100,000 mg kg(-1) spiked almond, the method featured good correlation between quantified copy numbers and the amount of spiked almond. Within this range a similar relation between detectable signal and amount of almond was observed for both PCR and ELISA. In contrast to ELISA the Taqman(®) real-time PCR method was highly specific in 59 food items with negligible cross-reactivity for a very limited number of Prunoideae foods. The real-time PCR analysis of 24 retail samples was in concordance with ELISA results: 21% (n=5) contained undeclared almond. This is the first completely disclosed real-time PCR method for a specific and

  7. Sensitive and specific detection of potentially allergenic almond (Prunus dulcis) in complex food matrices by Taqman real-time polymerase chain reaction in comparison to commercially available protein-based enzyme-linked immunosorbent assay

    International Nuclear Information System (INIS)

    Roeder, Martin; Vieths, Stefan; Holzhauser, Thomas

    2011-01-01

    Currently, causative immunotherapies are lacking in food allergy. The only option to prevent allergic reactions in susceptible individuals is to strictly avoid the offending food. Thus, reliable labelling of allergenic constituents is of major importance, but can only be achieved if appropriate specific and sensitive detection techniques for foods with allergenic potential are available. Almond is an allergenic food that requires mandatory labelling on prepackaged foods and belongs to the genus Prunus. Species of this genus are phylogenetically closely related. We observed commercially available almond specific ELISA being highly cross-reactive with other foods of the Prunoideae family, resulting in a false-positive detection of up to 500,000 mg kg -1 almond. Previously published PCR methods were reported to be cross-reactive with false positive results >1200 mg kg -1 . We describe the development of a novel almond specific real-time PCR, based on mutated mismatch primers and sequence specific Taqman probe detection, in comparison with two quantitative commercially available ELISA. PCR sensitivity was investigated with chocolate, chocolate coating and cookies spiked between 5 and 100,000 mg kg -1 almond. In all matrices almond was reproducibly detected by real-time PCR at the lowest spike level of 5 mg kg -1 . Further, between 100 and 100,000 mg kg -1 spiked almond, the method featured good correlation between quantified copy numbers and the amount of spiked almond. Within this range a similar relation between detectable signal and amount of almond was observed for both PCR and ELISA. In contrast to ELISA the Taqman real-time PCR method was highly specific in 59 food items with negligible cross-reactivity for a very limited number of Prunoideae foods. The real-time PCR analysis of 24 retail samples was in concordance with ELISA results: 21% (n = 5) contained undeclared almond. This is the first completely disclosed real-time PCR method for a specific and

  8. New approaches for the standardization and validation of a real-time qPCR assay using TaqMan probes for quantification of yellow fever virus on clinical samples with high quality parameters.

    Science.gov (United States)

    Fernandes-Monteiro, Alice G; Trindade, Gisela F; Yamamura, Anna M Y; Moreira, Otacilio C; de Paula, Vanessa S; Duarte, Ana Cláudia M; Britto, Constança; Lima, Sheila Maria B

    2015-01-01

    The development and production of viral vaccines, in general, involve several steps that need the monitoring of viral load throughout the entire process. Applying a 2-step quantitative reverse transcription real time PCR assay (RT-qPCR), viral load can be measured and monitored in a few hours. In this context, the development, standardization and validation of a RT-qPCR test to quickly and efficiently quantify yellow fever virus (YFV) in all stages of vaccine production are extremely important. To serve this purpose we used a plasmid construction containing the NS5 region from 17DD YFV to generate the standard curve and to evaluate parameters such as linearity, precision and specificity against other flavivirus. Furthermore, we defined the limits of detection as 25 copies/reaction, and quantification as 100 copies/reaction for the test. To ensure the quality of the method, reference controls were established in order to avoid false negative results. The qRT-PCR technique based on the use of TaqMan probes herein standardized proved to be effective for determining yellow fever viral load both in vivo and in vitro, thus becoming a very important tool to assure the quality control for vaccine production and evaluation of viremia after vaccination or YF disease.

  9. Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

    Directory of Open Access Journals (Sweden)

    Puisieux Alain

    2003-10-01

    Full Text Available Abstract Background Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive. Results We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC in peripheral blood mononuclear cells; the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy. Conclusion Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting.

  10. Screening tests for Chlamydia trachomatis or Neisseria gonorrhoeae using the cobas 4800 PCR system do not require a second test to confirm: an audit of patients issued with equivocal results at a sexual health clinic in the Northwest of England, U.K.

    Science.gov (United States)

    Hopkins, Mark J; Smith, Godfrey; Hart, Ian J; Alloba, Fath

    2012-11-01

    To assess the clinical utility of supplementary PCRs following a positive cobas 4800 CT/NG PCR screening test result. Laboratory reports, for Chlamydia trachomatis or Neisseria gonorrhoeae, issued to genitourinary medicine patients between April 2010 and April 2011 were reviewed retrospectively. Positive reports were routinely confirmed by supplementary PCRs and N gonorrhoeae culture. Clinical records of patients with unconfirmed positive (equivocal) reports were retrieved to determine if the infection was confirmed by a second sample obtained at patient recall and the impact of this process on antibiotic management. Over 15 000 patients were tested during the study period. The prevalence of chlamydia and gonorrhoea was 972 (5.75%) and 76 (0.50%), respectively. A further 78 chlamydia and 2 gonorrhoea equivocal reports were issued. Only 56 (72%) patients with an equivocal chlamydia report returned to the clinic, and of these, only 41 (73%) gave a second sample to retest. Positive predictive value (PPV) of the PCR screening test was calculated at 98.0% and 97.5% for detection of chlamydia infection from urine and rectal swabs, respectively. Most patients accepted antibiotic treatment before their infection status had been confirmed. Prevalence of gonorrhoea infection was low but the PPV of the screening PCR in urine specimens remained high (98.75%). Equivocal reports introduce delays to patient management, while the risk of unnecessary antibiotic therapy appears acceptable to most patients. The cobas 4800 CT/NG PCR screening assay can achieve UK testing standards (PPV >90%) for chlamydia, and low prevalence gonorrhoea in urine without supplementary tests. A patient-led confirmation algorithm is proposed.

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

    Science.gov (United States)

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

    2004-02-01

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

  12. Smallpox and pan-Orthopox Virus Detection by Real-Time 3′-Minor Groove Binder TaqMan Assays on the Roche LightCycler and the Cepheid Smart Cycler Platforms

    Science.gov (United States)

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

    2004-01-01

    We designed, optimized, and extensively tested several sensitive and specific real-time PCR assays for rapid detection of both smallpox and pan-orthopox virus DNAs. The assays are based on TaqMan 3′-minor groove binder chemistry and were performed on both the rapid-cycling Roche LightCycler and the Cepheid Smart Cycler platforms. The hemagglutinin (HA) J7R, B9R, and B10R genes were used as targets for the variola virus-specific assays, and the HA and DNA polymerase-E9L genes were used as targets for the pan-orthopox virus assays. The five orthopox virus assays were tested against a panel of orthopox virus DNAs (both genomic and cloned) at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID). The results indicated that each assay was capable of detecting both the appropriate cloned gene and genomic DNA. The assays showed no cross-reactivity to the 78 DNAs in the USAMRIID bacterial cross-reactivity panel. The limit of detection (LOD) of each assay was determined to be between 12 and 25 copies of target DNA. The assays were also run against a blind panel of DNAs at the Centers for Disease Control and Prevention (CDC) on both the LightCycler and the Smart Cycler. The panel consisted of eight different variola virus isolates, five non-variola virus orthopox virus isolates, two varicella-zoster virus isolates, and one herpes simplex virus isolate. Each sample was tested in triplicate at 2.5 ng, 25 pg, 250 fg, and 2.5 fg, which represent 1.24 × 107, 1.24 × 105, 1.24 × 103, and 1.24 × 101 genome equivalents, respectively. The results indicated that each of the five assays was 100% specific (no false positives) when tested against both the USAMRIID panels and the CDC blind panel. With the CDC blind panel, the LightCycler was capable of detecting 96.2% of the orthopox virus DNAs and 93.8% of the variola virus DNAs. The Smart Cycler was capable of detecting 92.3% of the orthopox virus DNAs and between 75 and 93.8% of the variola virus DNAs. However

  13. Performance Evaluation of the Bioneer AccuPower® HIV-1 Quantitative RT-PCR kit: Comparison with the Roche COBAS® AmpliPrep/COBAS TaqMan® HIV-1 Test Ver.2.0 for Quantification of HIV-1 Viral Load in Indonesia.

    Science.gov (United States)

    Kosasih, Agus Susanto; Sugiarto, Christine; Hayuanta, Hubertus Hosti; Juhaendi, Runingsih; Setiawan, Lyana

    2017-08-08

    Measurement of viral load in human immunodeficiency virus type 1 (HIV-1) infected patients is essential for the establishment of a therapeutic strategy. Several assays based on qPCR are available for the measurement of viral load; they differ in sample volume, technology applied, target gene, sensitivity and dynamic range. The Bioneer AccuPower® HIV-1 Quantitative RT-PCR is a novel commercial kit that has not been evaluated for its performance. This study aimed to evaluate the performance of the Bioneer AccuPower® HIV-1 Quantitative RT-PCR kit. In total, 288 EDTA plasma samples from the Dharmais Cancer Hospital were analyzed with the Bioneer AccuPower® HIV-1 Quantitative RT-PCR kit and the Roche COBAS? AmpliPrep/COBAS® TaqMan® HIV-1 version 2.0 (CAP/CTM v2.0). The performance of the Bioneer assay was then evaluated against the Roche CAP/CTM v2.0. Overall, there was good agreement between the two assays. The Bioneer assay showed significant linear correlation with CAP/CTM v2.0 (R2=0.963, plaboratories.

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. TaqMan Real-Time Polymerase Chain Reaction and ...

    African Journals Online (AJOL)

    ISSN: 1596-5996 (print); 1596-9827 (electronic) ... Alcohol in humans is oxidized to acetaldehyde, which in turn is oxidized to .... cool to room temperature (15 - 25 oC) for at least. 5 min, and .... logical candidate gene for alcohol dependence. A.

  16. A European multicientre study on the comparison of HIV-1 viral loads between VERIS HIV-1 Assay and Roche COBAS® TAQMAN® HIV-1 test, Abbott RealTime HIV-1 Assay, and Siemens VERSANT HIV-1 Assay.

    Science.gov (United States)

    Braun, Patrick; Delgado, Rafael; Drago, Monica; Fanti, Diana; Fleury, Hervé; Hofmann, Jörg; Izopet, Jacques; Kühn, Sebastian; Lombardi, Alessandra; Mancon, Alessandro; Marcos, Mª Angeles; Mileto, Davide; Sauné, Karine; O'Shea, Siobhan; Pérez-Rivilla, Alfredo; Ramble, John; Trimoulet, Pascale; Vila, Jordi; Whittaker, Duncan; Artus, Alain; Rhodes, Daniel

    2017-07-01

    Viral load monitoring is essential for patients under treatment for HIV. Beckman Coulter has developed the VERIS HIV-1 Assay for use on the novel, automated DxN VERIS Molecular Diagnostics System. ¥ OBJECTIVES: Evaluation of the clinical performance of the new quantitative VERIS HIV-1 Assay at multiple EU laboratories. Method comparison with the VERIS HIV-1 Assay was performed with 415 specimens at 5 sites tested with COBAS ® AmpliPrep/COBAS ® TaqMan ® HIV-1 Test, v2.0, 169 specimens at 3 sites tested with RealTime HIV-1 Assay, and 202 specimens from 2 sites tested with VERSANT HIV-1 Assay. Patient monitoring sample results from 4 sites were also compared. Bland-Altman analysis showed the average bias between VERIS HIV-1 Assay and COBAS HIV-1 Test, RealTime HIV-1 Assay, and VERSANT HIV-1 Assay to be 0.28, 0.39, and 0.61 log 10 cp/mL, respectively. Bias at low end levels below 1000cp/mL showed predicted bias to be <0.3 log 10 cp/mL for VERIS HIV-1 Assay versus COBAS HIV-1 Test and RealTime HIV-1 Assay, and <0.5 log 10 cp/mL versus VERSANT HIV-1 Assay. Analysis on 174 specimens tested with the 0.175mL volume VERIS HIV-1 Assay and COBAS HIV-1 Test showed average bias of 0.39 log 10 cp/mL. Patient monitoring results using VERIS HIV-1 Assay demonstrated similar viral load trends over time to all comparators. The VERIS HIV-1 Assay for use on the DxN VERIS System demonstrated comparable clinical performance to COBAS ® HIV-1 Test, RealTime HIV-1 Assay, and VERSANT HIV-1 Assay. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2013-10-01

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

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

    Science.gov (United States)

    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.

  19. UJI COBA PENANGKAPAN MENGGUNAKAN AYUNAN DENGAN BENTUK YANG BERBEDA ((EXPERIMENTAL FISHING USING AYUNAN WITH DIFFERENT FORMS

    Directory of Open Access Journals (Sweden)

    Irhamsyah Irhamsyah

    2017-02-01

    Bamboo and rattan as materials to make the ayunan has a weakness because odor (smell is not good (bangai and therefore contributes to the catch. To overcome this weakness it is advisable to replace the wire with the basic material.

  20. UJI COBA PERANGKAP UDANG DENGAN BENTUK YANG BERBEDA (EXPERIMENTAL FISHING WITH TRAP PRAWN DIFFERENT FORM

    Directory of Open Access Journals (Sweden)

    Irhamsyah Irhamsyah

    2016-06-01

    Full Text Available Penelitian ini bertujuan untuk  mengetahui perbedaan hasil tangkapan udang dari tamba dan ayunan modifikasi dan hasil tangkapan selain udang.  Dari hasil penelitian diperoleh perlakuan A (tamba diperoleh hasil tangkapan udang sebanyak 52 ekor, dengan berat total 2.210 gram.  Perlakuan B (ayunan modifikasi lantai bambu, diperoleh hasil tangkapan udang sebanyak 29 ekor, dengan berat total  180 gram.  Total hasil tangkapan udang dengan menggunakan tamba dan ayunan modifikasi lantai bambu selama 16 hari pengamatan adalah 81 ekor dengan berat total 2.390 gram.  Jenis hasil tangkapan utama yaitu Udang Galah (Macrobrachium rosenbergii de Man dengan hasil tangkapan sampingan adalah ikan Lundu (Mystus gulio dan  ikan Sapu-Sapu (Hypostomus plecostomus. This study aims to (1 know the difference between the catch of prawns from tamba and ayunan, and (2 to determine the catch other than prawn. The results, treatment A (tamba gained as much as 52 prawns, with a total weight of 2,210 grams. Treatment B (ayunan modifications bamboo flooring, gained as much as 29 prawns, with a total weight of 180 grams. Total catch of prawns using swing modifications and addi bamboo flooring for 16 days of observation was 81 prawns with a total weight of 2,390 grams. Main types of catches fresh water prawn (Macrobrachium rosenbergii de Man with a side of the catch is Lundu (Mystus Gulio and Sapu-sapu (Hypostomus plecostomus.

  1. UJI COBA PEMULIHAN GIZI BURUK CARA KLINIK GIZI PUSLITBANG GIZI DI POSYANDU

    Directory of Open Access Journals (Sweden)

    Djoko Kartono

    2012-11-01

    Full Text Available Trial The Management of Severe Malnourished Children of Nutrition Clinic Method, The Nutrition Research and Development Centre at Village Level.Background: Managerrent of severe malnutrition recommended by WHO should be in hospital. For family with severe malnourished child, generally poor, hospitalization means spend a lot of money. The alternative method is the out patient management developed by Nutrition Clinic of the Nutrition Research ard Development Centre.Objectives: To study the effectiveneess of management for severe malnourished of Nutrition Clinic method in village level (posyandu by village cadre.Methods: The study was carried out at 4 sub-districts in Bogor and Sukabumi, West Java. Sixty under-five children for group 1 and 60 for group 2 were selected. Three to five posyandu's cadres were selected in each village. Visit schedule to posyandu for group 1 was similar to that Nutrition Clinic while group 2 was every 1 week. Nutrition package for group 1 and 2 was same. Data collection included body measurements, morbiddity and food consumption. Observation to the cadres performance include ownership and he use of guidance book.Results: Seven percent of children aged 6-11 months, 20% aged 12-17 months, 60% aged 18-35 months and 13% aged > 36 months. Around 30% of children had been grven fruit and porridge on the age 1-4 months old. Nutritional status improved variously depended on the nutritional indices. Energy consumption was low but protein consumption had reached the recommended allowance. Compliance to come to posyandu and nutrition package was high.Conclusions: Around 10% of cchildren had changed from under-weight to well-nourished, but most of severe malnourished children remained severe in 3 months. Stunted was over 75% and remained stunted in 3 months. Wasted was 50% and began to decline in 3 months. The average of weight increment in 3 months was 0,6 kg. Cadre could give simple education to mothers using the available guidance book.Recommendations: To use wasted as an indicator in the evaluation of management of severe malnutrition. Active role of health Centre is needed to have maximum effect of the implementation of Nutrition Clinic method at village level.Key words: management, severe malnutrition, nutrition clinic, out-patient, village cadre.

  2. Studi dan Uji Coba Teknologi Bluetooth sebagai Alternatif Komunikasi Data Nirkabel

    OpenAIRE

    Yulia, Yulia; Santoso, Leo Willyanto

    2004-01-01

    In Bahasa Indonesia : Bluetooth adalah suatu teknologi baru yang mulai dikenal dan digunakan. Teknologi ini memberikan Perubahan yang signifikan terhadap peralatan elektronik yang kita gunakan. Jika kita melihat sekeliling kita dimana keyboard dihubungkan pada komputer. Demikian juga halnya dengan printer, mouse, monitor dan lain sebagainya. Semua peralatan itu dihubungkan dengan menggunakan kabel. Akibatnya terjadi masalah banyak kabel yang dibutuhkan di kantor, rumah atau tempat-tempat...

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

    NARCIS (Netherlands)

    Hardon, A.; Idrus, N.I.

    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

  4. STUDI DAN UJI COBA TEKNOLOGI BLUETOOTH SEBAGAI ALTERNATIF KOMUNIKASI DATA NIRKABEL

    Directory of Open Access Journals (Sweden)

    Yulia Yulia

    2004-01-01

    Full Text Available Bluetooth is a new emerging technology. This technology gives significant changes for electronic devices that we are using. If we look around, a keyboard is connected to a computer. So does a printer, a mouse, a monitor and so on. This condition creates a problem of so many scattered wires installed in the offices, houses and other places. Another problem is how to inspect the damaging or boken wires. In this paper, we will have a discussion on specific applications of bluetooth such as services provided by the bluetooth technology; bluetooth method - how bluetooth devices make connections in a piconet; as well as investigation on bluetooth protocol stack. Bluetooth has succesfully built easy connection among devices from many vendor without using cables, with less power dan money. By using bluetooth, we can build small network or Piconet, consisting of several devices without cables. Abstract in Bahasa Indonesia : Bluetooth adalah suatu teknologi baru yang mulai dikenal dan digunakan. Teknologi ini memberikan perubahan yang signifikan terhadap peralatan elektronik yang kita gunakan. Jika kita melihat sekeliling kita dimana keyboard dihubungkan pada komputer. Demikian juga halnya dengan printer, mouse, monitor dan lain sebagainya. Semua peralatan itu dihubungkan dengan menggunakan kabel. Akibatnya terjadi masalah banyak kabel yang dibutuhkan di kantor, rumah atau tempat-tempat lainnya. Masalah lain yang ditemui adalah bagaimana menelusuri kabel-kabel yang terpasang jika ada suatu kesalahan atau kerusakan. Bluetooth memperbaiki penggunaan teknologi kabel yang cenderung menyulitkan ini dengan cara menghubungkan beberapa peralatan tanpa menggunakan kabel. Pada karya tulis ini, dibahas aplikasi spesifik bluetooth, antara lain servis-servis apa saja yang disediakan oleh teknologi bluetooth; cara kerja bluetooth yaitu bagaimana bluetooth device melakukan koneksi di dalam sebuah piconet serta bluetooth protocol stack. Bluetooth telah berhasil memudahkan koneksi antar beberapa alat dari berbagai vendor tanpa kabel dengan tenaga yang kecil serta biaya yang ringan. Dengan bluetooth dapat dibentuk sebuah jaringan kecil atau Piconet yang terdiri dari beberapa peralatan dan sekali lagi, tanpa memerlukan kabel. Kata kunci: Bluetooth, Bluetooth Protocol Stack, Piconet, Komunikasi data, Nirkabel.

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

    Science.gov (United States)

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

    2017-10-01

    Hepatitis B viral load testing is essential to treatment and monitoring decisions in patients with chronic Hepatitis B. Beckman Coulter has developed the VERIS HBV Assay (Veris) for use on the fully automated DxN VERIS Molecular Diagnostics System. 1 OBJECTIVES: To evaluate the clinical performance of the Veris HBV Assay at multiple EU laboratories STUDY DESIGN: Method comparison was performed with a total of 344 plasma specimens from HBV infected patients tested with Veris and COBAS ® TaqMan ® HBV Test (Cobas), 207 specimens tested with Veris and RealTime HBV Assay (RealTime), 86 specimens tested with Veris and VERSANT ® HBV Assay (Versant), and 74 specimens tested with Veris and artus ® HBV RG PCR kit (artus). Bland-Altman analysis showed average bias of -0.46 log 10 IU/mL between Veris and Cobas, -0.46 log 10 IU/mL between Veris and RealTime, -0.36 log 10 IU/mL between Veris and Versant, and -0.12 log 10 IU/mL between Veris and artus. Bias was consistent across the assay range. Patient monitoring results using Veris demonstrated similar viral load trends over time to Cobas, RealTime, and artus. The VERIS HBV Assay demonstrated comparable clinical performance, with varying degrees of negative bias, compared to other currently marketed assays for HBV DNA monitoring. This negative bias should be taken into consideration if switching monitoring methods to Veris. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Specificity of a novel TaqMan PCR method for detection of poultry DNA

    NARCIS (Netherlands)

    Scholtens-Toma, Ingrid; Prins, Theo W.; Raamsdonk, Van Leo W.D.

    2017-01-01

    After the Bovine Spongiform Encephalopathy (BSE) crisis emerged in 1985/1986, all processed animal proteins (PAPs) were finally banned for use in animal feed in the European Union. To partially lift this feed ban, paths for re-introduction of PAPs from species other than ruminants e.g. pig and

  7. DETECTION AND IDENTIFICATION OF PATHOGENIC CANDIDA SPECIES IN WATER USING FLOW CYTOMETRY COUPLED WITH TAQMAN PCR

    Science.gov (United States)

    As the incidence of human fungal infection increases, the ability to detect and identify pathogenic fungi in potential environmental reservoirs becomes increasingly important for disease control. PCR based assays are widely used for diagnostic purposes, but may be inadequate for...

  8. Semiautomated TaqMan PCR screening of GMO labelled samples for (unauthorised) GMOs.

    Science.gov (United States)

    Scholtens, Ingrid M J; Molenaar, Bonnie; van Hoof, Richard A; Zaaijer, Stephanie; Prins, Theo W; Kok, Esther J

    2017-06-01

    In most countries, systems are in place to analyse food products for the potential presence of genetically modified organisms (GMOs), to enforce labelling requirements and to screen for the potential presence of unauthorised GMOs. With the growing number of GMOs on the world market, a larger diversity of methods is required for informative analyses. In this paper, the specificity of an extended screening set consisting of 32 screening methods to identify different crop species (endogenous genes) and GMO elements was verified against 59 different GMO reference materials. In addition, a cost- and time-efficient strategy for DNA isolation, screening and identification is presented. A module for semiautomated analysis of the screening results and planning of subsequent event-specific tests for identification has been developed. The Excel-based module contains information on the experimentally verified specificity of the element methods and of the EU authorisation status of the GMO events. If a detected GMO element cannot be explained by any of the events as identified in the same sample, this may indicate the presence of an unknown unauthorised GMO that may not yet have been assessed for its safety for humans, animals or the environment.

  9. Semiautomated TaqMan PCR screening of GMO labelled samples for (unauthorised) GMOs

    NARCIS (Netherlands)

    Scholtens-Toma, Ingrid; Molenaar, Bonnie; Hoof, van Richard A.; Zaaijer, Stephanie; Prins, Theo W.; Kok, Esther J.

    2017-01-01

    In most countries, systems are in place to analyse food products for the potential presence of genetically modified organisms (GMOs), to enforce labelling requirements and to screen for the potential presence of unauthorised GMOs. With the growing number of GMOs on the world market, a larger

  10. Application of rapid onsite PCR (TaqMan) for Phytophthora ramorum under U.S. conditions

    Science.gov (United States)

    Kelvin Hughes; Jenny Tomlinson; Neil Boonham; Kelly Ivors; Matteo Garbelotto; Ian Barker

    2006-01-01

    Currently, diagnosis of Phytophthora ramorum involves sending samples to a laboratory for traditional isolation and morphological characterisation, and/or PCR analysis. This can take as long as 2 weeks from sampling to final diagnosis. However, the Plant Health Group, Central Science Laboratory, has produced on-site DNA extraction and real-time PCR (...

  11. Real-time PCR assays for hepatitis B virus DNA quantification may require two different targets.

    Science.gov (United States)

    Liu, Chao; Chang, Le; Jia, Tingting; Guo, Fei; Zhang, Lu; Ji, Huimin; Zhao, Junpeng; Wang, Lunan

    2017-05-12

    Quantification Hepatitis B virus (HBV) DNA plays a critical role in the management of chronic HBV infections. However, HBV is a DNA virus with high levels of genetic variation, and drug-resistant mutations have emerged with the use of antiviral drugs. If a mutation caused a sequence mismatched in the primer or probe of a commercial DNA quantification kit, this would lead to an underestimation of the viral load of the sample. The aim of this study was to determine whether commercial kits, which use only one pair of primers and a single probe, accurately quantify the HBV DNA levels and to develop an improved duplex real-time PCR assay. We developed a new duplex real-time PCR assay that used two pairs of primers and two probes based on the conserved S and C regions of the HBV genome. We performed HBV DNA quantitative detection of HBV samples and compared the results of our duplex real-time PCR assays with the COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. The target region of the discordant sample was amplified, sequenced, and validated using plasmid. The results of the duplex real-time PCR were in good accordance with the commercial COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. We showed that two samples from Chinese HBV infections underestimated viral loads when quantified by the Roche kit because of a mismatch between the viral sequence and the reverse primer of the Roche kit. The HBV DNA levels of six samples were undervalued by duplex real-time PCR assays of the C region because of mutations in the primer of C region. We developed a new duplex real-time PCR assay, and the results of this assay were similar to the results of commercial kits. The HBV DNA level could be undervalued when using the COBAS TaqMan HBV Test version 2 for Chinese HBV infections owing to a mismatch with the primer/probe. A duplex real-time PCR assay based on the S and C regions could solve this problem to some extent.

  12. Diagnostic efficacy of a real time-PCR assay for Chlamydia trachomatis infection in infertile women in north India

    Directory of Open Access Journals (Sweden)

    Benu Dhawan

    2014-01-01

    Full Text Available Background & objectives: Little is known about the prevalence of Chlamydia trachomatis infection in Indian women with infertility. To improve the diagnosis of C. trachomatis infection in developing countries, there is an urgent need to establish cost-effective molecular test with high sensitivity and specificity. This study was conducted to determine the diagnostic utility of a real time-PCR assay for detention of C. trachomatis infection in infertile women attending an infertility clinic in north India. The in house real time-PCR assay was also compared with a commercial real-time PCR based detection system. Methods: Endocervical swabs, collected from 200 infertile women were tested for C. trachomatis by three different PCR assays viz. in-house real time-PCR targeting the cryptic plasmid using published primers, along with omp1 gene and cryptic plasmid based conventional PCR assays. Specimens were also subjected to direct fluorescence assay (DFA and enzyme immunoassay (EIA Performance of in-house real time-PCR was compared with that of COBAS Taqman C. trachomatis Test, version 2.0 on all in-house real time-PCR positive sample and 30 consecutive negative samples. Results: C. trachomatis infection was found in 13.5 per cent (27/200 infertile women by in-house real time-PCR, 11.5 per cent (23/200 by cryptic plasmid and/or omp1 gene based conventional PCR, 9 per cent (18/200 by DFA and 6.5 per cent (7/200 by EIA. The in-house real time-PCR exhibited a sensitivity and specificity of 100 per cent, considering COBAS Taqman CT Test as the gold standard. The negative and positive predictive values of the in-house real time-PCR were 100 per cent. The in-house real time-PCR could detect as low as 10 copies of C. trachomatis DNA per reaction. Interpretation & conclusions: In-house real time-PCR targeting the cryptic plasmid of C. trachomatis exhibited an excellent sensitivity and specificity similar to that of COBAS Taqman CT Test, v2.0 for detection of C

  13. UJI COBA PENYEMPROTAN ULV (ULV SPRAYING INSEKTISIDA BENDIOCARB 20 % (FICAM ULV TERHADAP VEKTOR DEMAM BERDARAH DENGUE Aedes aegypti

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    Hadi Suwasono

    2012-09-01

    Full Text Available A trial was conducted using ULV spraying of Bendiocarb 20% (Ficam ULV in Salatiga municipality at a dosage of 45 ml/ha and 75 ml/ha. The trial was conducted in the morning. Two cycles were implemented at an interval of 7 days, using a vehicle-mounted ULV generator. Results revealed no significant changes in mosquito population densitities, in any of the parameters observed.

  14. UJI COBA LARVISIDA SPHERIFIX (Bacillus sphaericus VCRC B 42 TERHADAP LARVA Anopheles sundaicus Di GERUMBUL KLACES, UJUNG ALANG - KABUPATEN CILACAP

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    Umi Widyastuti

    2012-09-01

    Full Text Available A biological larvicide spherifix containing Bacillus sphaericus VCRC B 42 was investigated against Anopheles sundaicus in Klaces hamlet, Cilacap regency. This study was conducted to determine the effectivity of spherifix on An. sundaicus larvae at a dosage of 2.5 kg/Ha. Observations were conducted one day before application of the larvicide, 24, 36, 48 hours, day 4, 7, and 14 after application. The larval reduction rates were calculated using the formula of Mulia et al, 1971, and a reduction of the results were 16.69 % after 24 hours, 20.95 % after 36 hours, 34.07 % after 48 hours, 65.08 % after 4 days, 85.98 % after 7 days, and 90.81 % after 14 days. B. sphaericus has capabilities to function as a biological larvicide.

  15. Uji Coba Alat Penghasil Asap Cair Skala Laboratorium dengan Bahan Pengasap Serbuk Gergaji Kayu Jati Sabrang atau Sungkai (Peronema canescens

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    Rodiah Nurbaya Sari

    2014-05-01

    energi yang dilepas dari pembentukan asap menjadi asap cair (- 476,45 kJ/kg asap, energi yang diserap air kondensor sebesar 2,1 kJ/kg air sehingga jumlah air bersuhu 30,4oC yang dibutuhkan untuk mengembunkan 1 kg asap menjadi asap cair dengan suhu pirolisis 316,7oC adalah sebanyak 226,88 liter. Kinerja alat adalah 6,98 g/(jam. m. Komponen dominan dalam asap cair yang dihasilkan adalah senyawa 1,2-benzenedicarboxylic acid, diethyl ester (C12H14O4 sebanyak 23,61%.

  16. Rekayasa Alat Penghasil Asap Cair untuk Produksi Ikan Asap 1. Uji Coba Alat Penghasil Asap Cair Skala Laboratorium

    Directory of Open Access Journals (Sweden)

    Rodiah Nurbaya Sari

    2006-04-01

    penelitian menunjukkan bahwa pada suhu pembakaran 200-250o C, tempurung kelapa dengan kadar air 11,40% menghasilkan asap cair sebanyak 48,10%, sisa pembakaran berupa arang sebanyak 31,33%, jumlah komponen yang hilang sebanyak 20,56% dengan kinerja alat sebesar 250,52 g/jam.m kondensor. Komponen terbanyak asap cair yang dihasilkan adalah senyawa 9-octadecenoic acid (Z-, tetradecyl ester (C32H62O2 sebanyak 71,68%. Pada suhu pembakaran 300–450oC asap cair yang dihasilkan sebanyak 48,66%, sisa pembakaran berupa arangsebanyak 26,30%, komponen asap yang hilang sebanyak 25,04% dengan kinerja alat 253,44 g/jam.m kondensor. Pada suhu tersebut komponen terbanyak asap cair adalah senyawa 2-lauro-1,3-didecoinyaitu 37,53%.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Jose Eduardo Levi

    2013-06-01

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

  19. A novel duplex real-time reverse transcriptase-polymerase chain reaction assay for the detection of hepatitis C viral RNA with armored RNA as internal control

    Directory of Open Access Journals (Sweden)

    Meng Shuang

    2010-06-01

    Full Text Available Abstract Background The hepatitis C virus (HCV genome is extremely heterogeneous. Several HCV infections can not be detected using currently available commercial assays, probably because of mismatches between the template and primers/probes. By aligning the HCV sequences, we developed a duplex real-time reverse transcriptase-polymerase chain reaction (RT-PCR assay using 2 sets of primers/probes and a specific armored RNA as internal control. The 2 detection probes were labelled with the same fluorophore, namely, 6-carboxyfluorescein (FAM, at the 5' end; these probes could mutually combine, improving the power of the test. Results The limit of detection of the duplex primer/probe assay was 38.99 IU/ml. The sensitivity of the assay improved significantly, while the specificity was not affected. All HCV genotypes in the HCV RNA Genotype Panel for Nucleic Acid Amplification Techniques could be detected. In the testing of 109 serum samples, the performance of the duplex real-time RT-PCR assay was identical to that of the COBAS AmpliPrep (CAP/COBAS TaqMan (CTM assay and superior to 2 commercial HCV assay kits. Conclusions The duplex real-time RT-PCR assay is an efficient and effective viral assay. It is comparable with the CAP/CTM assay with regard to the power of the test and is appropriate for blood-donor screening and laboratory diagnosis of HCV infection.

  20. HCV infection among Saudi population: high prevalence of genotype 4 and increased viral clearance rate.

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    Ahmed S Abdel-Moneim

    Full Text Available HCV is a major etiological agent of liver disease with a high rate of chronic evolution. The virus possesses 6 genotypes with many subtypes. The rate of spontaneous clearance among HCV infected individuals denotes a genetic determinant factor. The current study was designed in order to estimate the rate of HCV infection and ratio of virus clearance among a group of infected patients in Saudi Arabia from 2008 to 2011. It was additionally designed to determine the genotypes of the HCV in persistently infected patients. HCV seroprevalence was conducted on a total of 15,323 individuals. Seropositive individuals were tested by Cobas AmpliPrep/Cobas TaqMan HCV assay to determine the ratio of persistently infected patients to those who showed spontaneous viral clearance. HCV genotyping on random samples from persistently infected patients were conducted based on the differences in the 5'untranslated region (5'UTR. Anti-HCV antibodies were detected in 7.3% of the totally examined sera. A high percentage of the HCV infected individuals experienced virus clearance (48.4%. HCV genotyping revealed the presence of genotypes 1 and 4, the latter represented 97.6% of the tested strains. Evidences of the widespread of the HCV genotype 4 and a high rate of HCV virus clearance were found in Saudi Arabia.

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

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    Pascale Ondoa

    2014-01-01

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

  2. Detection of Mycobacterium tuberculosis Complex in Paraffin-Embedded Tissues by the New Automated Abbott RealTime MTB Assay.

    Science.gov (United States)

    Fu, Yung-Chieh; Liao, I-Chuang; Chen, Hung-Mo; Yan, Jing-Jou

    2016-07-01

    The Abbott RealTime MTB assay, launched in June 2014, has been shown to have a competitive performance in the detection of the Mycobacterium tuberculosis (MTB) complex in respiratory specimens. The present study was conducted to investigate the usefulness of the Abbott MTB Realtime assay in the detection of MTB in formalin-fixed paraffin-embedded (FFPE) tissues. A total of 96 FFPE specimens obtained from microbiologically proven MTB cases (N=60) and nontuberculous Mycobacterium cases (N=36) were analyzed. The performance of the Abbott MTB Realtime assay was compared with that of the Roche Cobas TaqMan MTB assay. The overall sensitivity and specificity of the Abbott assay were 63.3% and 97.2%, respectively, compared with 11.7% and 100% for the Cobas assay. The detection rate of the Abbott assay was much higher among 37 acid-fast-positive specimens than among 23 acid-fast-negative specimens (89.3% versus 21.7%, respectively). The detection rate of the assay was higher among 29 resection specimens than among 31 small biopsy specimens (86.2% versus 41.9%, respectively). Our results suggest that the Abbott RealTime MTB assay can be used to differentiate MTB from nontuberculous mycobacterial infections in acid-fast-positive FFPE tissues. © 2016 by the Association of Clinical Scientists, Inc.

  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.

    Science.gov (United States)

    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. Intratumor genetic heterogeneity of breast carcinomas as determined by fine needle aspiration and TaqMan low density array

    DEFF Research Database (Denmark)

    Lyng, Maria B.; Laenkholm, Anne-Vibeke; Pallisgaard, Niels

    2007-01-01

    BACKGROUND: Gene expression profiling is thought to be an important tool in determining treatment strategies for breast cancer patients. Tissues for such analysis may at a preoperative stage be obtained, by fine needle aspiration (FNA) allowing initiation of neoadjuvant treatment. To evaluate the...... of breast carcinomas, as sampled by FNA, does not prohibit generation of useful gene profiles for treatment decision making. However, sampling and analysis strategies should take heterogeneity within a tumor, and varying heterogeneity amongst the single genes, into account...

  5. A real time Taqman RT-PCR for the detection of rabbit hemorrhagic disease virus 2 (RHDV2).

    Science.gov (United States)

    Duarte, Margarida Dias; Carvalho, Carina L; Barros, Silvia C; Henriques, Ana M; Ramos, Fernanda; Fagulha, Teresa; Luís, Tiago; Duarte, Elsa L; Fevereiro, Miguel

    2015-07-01

    A specific real time RT-PCR for the detection of RHDV2 was developed and validated using RHDV and RHDV2 RNA preparations from positive field samples. The system was designed to amplify a 127 nucleotide-long RNA region located within the vp60 gene, based on the alignment of six sequences originated in Portugal, obtained in our laboratory, and 11 sequences from France and Italy. The primers and probe target sequences are highly conserved in the vast majority of the RHDV2 sequences presently known. In the sequences showing variability, only one mismatch is found per strain, usually outlying the 3' end of the primer or probe hybridization sequences. The specificity of the method was demonstrated in vitro with a panel of common rabbit pathogens. Standardization was performed with RNA transcripts obtained from a recombinant plasmid harboring the target sequence. The method was able to detected nine RNA molecules with an efficiency of 99.4% and a R(2) value of 1. Repeatability and reproducibility of the method were very high, with coefficients of variation lower than 2.40%. The assay was proven a valuable tool to diagnose most of RDVH2 circulating strains, and may be also useful to monitor viral loads, and consequently, disease progression and vaccination efficacy. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Partial validation of a TaqMan real-time quantitative PCR for the detection of ranaviruses

    DEFF Research Database (Denmark)

    Stilwell, Natalie K.; Whittington, Richard J.; Hick, Paul M.

    2018-01-01

    Ranaviruses are globally emerging pathogens negatively impacting wild and cultured fish, amphibians, and reptiles. Although conventional and diagnostic real-time PCR (qPCR) assays have been developed to detect ranaviruses, these assays often have not been tested against the known diversity of ran...

  7. Rapid Detection of Chlamydia trachomatis and Typing of the Lymphogranuloma venereum associated L-Serovars by TaqMan PCR

    Directory of Open Access Journals (Sweden)

    Henrich Birgit

    2008-04-01

    Full Text Available Abstract Background Infection due to Chlamydia trachomatis is the most common sexually transmitted bacterial disease of global health significance, and especially the L-serovars causing lymphogranuloma venereum are increasingly being found in Europe in men who have sex with men. Results The design and evaluation of a rapid, multiplex, real-time PCR targeting the major outer membrane protein (omp-1 -gene and a L-serovar-specific region of the polymorphic protein H (pmp-H -gene for the detection of Chlamydia trachomatis is reported here. The PCR takes place as a single reaction with an internal control. For L1-, L2- and L3-serovar differentiation a second set of real-time PCRs was evaluated based on the amplification of serovar-specific omp-1-regions. The detection limit of each real-time PCR, multiplexed or not, was 50 genome copies per reaction with an efficiency ranging from 90,5–95,2%. In a retrospective analysis of 50 ocular, rectal and urogenital specimens formerly tested to be positive for C. trachomatis we identified six L2-serovars in rectal specimens of HIV-positive men, one in a double-infection with L3, and one L2 in a urethral specimen of an HIV-negative male. Conclusion This unique real-time PCR is specific and convenient for the rapid routine-diagnostic detection of lymphogranuloma venereum-associated L-serovars and enables the subsequent differentiation of L1, L2 and L3 for epidemiologic studies.

  8. Rapid Detection of Chlamydia trachomatis and Typing of the Lymphogranuloma venereum associated L-Serovars by TaqMan PCR

    Science.gov (United States)

    Schaeffer, Anke; Henrich, Birgit

    2008-01-01

    Background Infection due to Chlamydia trachomatis is the most common sexually transmitted bacterial disease of global health significance, and especially the L-serovars causing lymphogranuloma venereum are increasingly being found in Europe in men who have sex with men. Results The design and evaluation of a rapid, multiplex, real-time PCR targeting the major outer membrane protein (omp-1) -gene and a L-serovar-specific region of the polymorphic protein H (pmp-H) -gene for the detection of Chlamydia trachomatis is reported here. The PCR takes place as a single reaction with an internal control. For L1-, L2- and L3-serovar differentiation a second set of real-time PCRs was evaluated based on the amplification of serovar-specific omp-1-regions. The detection limit of each real-time PCR, multiplexed or not, was 50 genome copies per reaction with an efficiency ranging from 90,5–95,2%. In a retrospective analysis of 50 ocular, rectal and urogenital specimens formerly tested to be positive for C. trachomatis we identified six L2-serovars in rectal specimens of HIV-positive men, one in a double-infection with L3, and one L2 in a urethral specimen of an HIV-negative male. Conclusion This unique real-time PCR is specific and convenient for the rapid routine-diagnostic detection of lymphogranuloma venereum-associated L-serovars and enables the subsequent differentiation of L1, L2 and L3 for epidemiologic studies. PMID:18447917

  9. Optimization of a 12-hour TaqMan PCR-based method for detection of Salmonella bacteria in meat

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Krause, Michael; Hansen, F.

    2007-01-01

    no positive effects and resulted in decreased reproducibility. Increasing the amount of PCR template DNA from 5 to 20 mu l improved the threshold cycle value by approximately 2. The improved 12-h PCR method was successfully compared to a reference culture method with 100 minced meat and poultry samples...... the highest number of salmonellae. When analyzing minced meat samples, positive effects of increasing the initial sampling volume from 1 to 5 ml and increasing the amount of paramagnetic particles to 90 mu l were observed. However, washing the pellet and eluting the DNA in reduced volumes (25 and 50 mu l) had...

  10. Development of a TaqMan assay for the six major genotypes of hepatitis C virus: Comparison with commercial assays

    DEFF Research Database (Denmark)

    Engle, Ronald E; Russell, Rodney S; Purcell, Robert H

    2008-01-01

    A quantitative real-time PCR assay was developed that detects genomic RNA from reference strains representing the six major genotypes of hepatitis C virus (HCV) with equal sensitivity and accurately measured HCV RNA in JFH1 HCV-infected Huh7.5 cells. The method is indirectly calibrated to the first...

  11. Molecular detection of Phytophthora ramorum by real-time PCR using Taqman, SYBR Green and molecular beacons with three genes

    Science.gov (United States)

    G.J. Bilodeau; C.A. Lévesque; A.W.A.M. De Cock; C. Duchaine; G. Kristjansson; R.C. Hamelin

    2006-01-01

    Sudden oak death, caused by Phytophthora ramorum, is a severe disease that can affect numerous species of trees and shrubs. This pathogen has been spread via nursery stock, and quarantine measures are currently in place to prevent further spread. Molecular assays have been developed to rapidly detect and identify P. ramorum, but...

  12. Differentiation of herpes simplex virus types 1 and 2 in clinical samples by a real-time taqman PCR assay.

    Science.gov (United States)

    Corey, Lawrence; Huang, Meei-Li; Selke, Stacy; Wald, Anna

    2005-07-01

    While the clinical manifestations of HSV-1 and -2 overlap, the site of CNS infection, complications, response to antivirals, frequency of antiviral resistance, and reactivation rate on mucosal surfaces varies between HSV-1 and -2. Detection of HSV DNA by PCR has been shown to be the most sensitive method for detecting HSV in clinical samples. As such, we developed a PCR-based assay to accurately distinguish HSV-1 from HSV-2. Our initial studies indicated the assay using type specific primers was slightly less efficient for detecting HSV-1 and -2 DNA than the high throughput quantitative PCR assay we utilize that employs type common primers to gB. We subsequently evaluated the type specific assay on 3,131 specimens that had HSV DNA detected in the type common PCR assay. The typing results of these specimens were compared with the monoclonal antibody staining results of culture isolates collected from the same patients at the same time, and the HSV serologic status of the patient. The typing assay accurately identified both HSV-1 and -2 with a specificity of >99.5% and was significantly more sensitive than typing by culture and subsequent monoclonal antibody assays. Complete concordance was seen between the typing assay and HSV serologic status of the patient. Dual (HSV-1 and -2) infection in clinical samples was recognized in 2.6% of clinical samples using the new typing assay. This assay, when used in combination with the type common assay, can now accurately type almost all mucosal and visceral HSV isolates by molecular techniques. Copyright (c) 2005 Wiley-Liss, Inc.

  13. Development of a digital droplet PCR assay to measure HBV DNA in patients receiving long-term TDF treatment.

    Science.gov (United States)

    Liu, Yang; Cathcart, Andrea L; Delaney, William E; Kitrinos, Kathryn M

    2017-11-01

    The COBAS TaqMan assay has a lower limit of quantification (LLOQ) of 169 HBV copies/mL and a lower limit of detection (LLOD) of 58 copies/mL. HBV DNA below the TaqMan LLOQ is classified as target not detected (TND) (HBV DNA to 8 copies/mL. HBV DNA levels in plasma from patients with or without HBsAg seroconversion were assessed by ddPCR. For patients who did not achieve HBsAg seroconversion, the majority of TD samples (33/58, 57%) were HBV DNA positive by ddPCR while (10/37, 27%) of TND samples were positive. In contrast, for patients who achieved HBsAg seroconversion, HBV DNA was rarely detected by ddPCR after HBsAg seroconversion (1/28, 3.6%). ddPCR is a sensitive method to evaluate low-level viral replication in plasma samples. Frequent detection of HBV DNA by ddPCR among patients who did not achieve HBsAg seroconversion suggests new agents may be needed to suppress low levels of replicating HBV. Copyright © 2017. Published by Elsevier B.V.

  14. Repeat testing of low-level HIV-1 RNA: assay performance and implementation in clinical trials.

    Science.gov (United States)

    White, Kirsten; Garner, Will; Wei, Lilian; Eron, Joseph J; Zhong, Lijie; Miller, Michael D; Martin, Hal; Plummer, Andrew; Tran-Muchowski, Cecilia; Lindstrom, Kim; Porter, James; Piontkowsky, David; Light, Angela; Reiske, Heinz; Quirk, Erin

    2018-05-15

    Assess the performance of HIV-1 RNA repeat testing of stored samples in cases of low-level viremia during clinical trials. Prospective and retrospective analysis of randomized clinical trial samples and reference standards. To evaluate assay variability of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test, v2.0, three separate sources of samples were utilized: the World Health Organization (WHO) HIV reference standard (assayed using 50 independent measurements at six viral loads <200 copies/ml), retrospective analysis of four to six aliquots of plasma samples from four clinical trial participants, and prospective repeat testing of 120 samples from participants in randomized trials with low-level viremia. The TaqMan assay on the WHO HIV-1 RNA standards at viral loads <200 copies/ml performed within the expected variability according to assay specifications. However, standards with low viral loads of 36 and 18 copies/ml reported values of ≥ 50 copies/ml in 66 and 18% of tests, respectively. In participants treated with antiretrovirals who had unexpected viremia of 50-200 copies/ml after achieving <50 copies/ml, retesting of multiple aliquots of stored plasma found <50 copies/ml in nearly all cases upon retesting (14/15; 93%). Repeat testing was prospectively implemented in four clinical trials for all samples with virologic rebound of 50-200 copies/ml (n = 120 samples from 92 participants) from which 42% (50/120) had a retest result of less than 50 copies/ml and 58% (70/120) retested ≥ 50 copies/ml. The TaqMan HIV-1 RNA assay shows variability around 50 copies/ml that affects clinical trial results and may impact clinical practice. In participants with a history of viral load suppression, unexpected low-level viremia may be because of assay variability rather than low drug adherence or true virologic failure. Retesting a stored aliquot of the same sample may differentiate between assay variability and virologic failure as the source of viremia

  15. Pulmão profundo – Reacção celular ao VIH

    Directory of Open Access Journals (Sweden)

    Maria Alcide Tavares Marques

    2007-03-01

    ída terapêutica anti-retroviral, primeiro grupo, enquanto o segundo grupo incluía doentes com doença mais prolongada, com vários episódios infecciosos oportunistas e tratamento antiretroviral, para além de outros esquemas terapêuticos.Métodos: Todos os doentes após, consentimento informado, foram submetidos a exame broncoendoscópico e LBA, após anestesia local da orofaringe e cordas vocais com lidocaína a 2%, sob monitorização cárdio--respiratória. O LBA foi efectuado com base nas alterações evidenciadas pela telerradiografia do tórax: lobo médio nas lesões difusas, ou outro brônquio segmentar correspondente a alterações radiológicas localizadas A determinação das cargas virais no líquido de lavagem broncoalveolar (LLBA, em 9 doentes, foi efectuada pela quantificação do ARN-VIH1, através de PCR-RT, nas primeiras 4horas após a colheita (sendo cada amostra centrifugada, procedendo-se posteriomente nas aliquotas do sobrenadante à congelação a menos 80° C, até à extracção e amplificação dos ácidos nucleicos. Realizou--se igualmente, na totalidade da amostra, a determinação das viremias plasmáticas (14 doentes, a partir de amostras de sangue colhido em EDTA, com processamento ulterior (separação do plasma e congelamento a menos 80°C. A extração e amplificação dos ácidos nucleicos foi efectuada por um método automatizado Cobas Ampliprep/Cobas Amplicor HIV1 Monitor TM Test, version 1.5 Roche Diagnostic Systems. Este método permite a obtenção duma sequência de 155 nucleótidos situada numa região altamente conservada do gene gag. Os resultados foram observados numa escala numérica com uma variação dinâmica situada entre as 50 e 750 000 cópias de ARN VIH1/cm3, procedendo-se posteriormente à sua conversão logarítmica. No LLBA (10 doentes e no sangue (13 doentes foi efectuado um

  16. Pulmão profundo – Reacção celular ao VIH

    Directory of Open Access Journals (Sweden)

    Maria Alcide Tavares Marques

    2007-03-01

    sido instituída terapêutica anti-retroviral, primeiro grupo, enquanto o segundo grupo incluía doentes com doença mais prolongada, com vários episódios infecciosos oportunistas e tratamento anti-retroviral, para além de outros esquemas terapêuticos. Métodos: Todos os doentes após, consentimento informado, foram submetidos a exame broncoendoscó-pico e LBA, após anestesia local da orofaringe e cordas vocais com lidocaína a 2%, sob monitorização cárdio-respiratória. O LBA foi efectuado com base nas alterações evidenciadas pela telerradiografia do tórax: lobo médio nas lesões difusas, ou outro brônquio segmentar correspondente a alterações radiológicas localizadas A determinação das cargas virais no líquido de lavagem broncoalveolar (LLBA, em 9 doentes, foi efectuada pela quantificação do ARN-VIH1, através de PCR-RT, nas primeiras 4horas após a colheita (sendo cada amostra centrifugada, procedendose posteriomente nas aliquo-tas do sobrenadante à congelação a menos 80 º C, até à extracção e amplificação dos ácidos nucleicos. Realizou-se igualmente, na totalidade da amostra, a determinação das viremias plasmáticas (14 doentes, a partir de amostras de sangue colhido em EDTA, com processa-mento ulterior (separação do plasma e congelamento a menos 80 ºC. A extração e amplificação dos ácidos nucleicos foi efectuada por um método automatizado Cobas Ampliprep/Cobas Amplicor HIV1 Monitor TM Test, version 1.5 Roche Diagnostic Systems. Este método permite a obtenção duma sequência de 155 nucleótidos situada numa região altamente conservada do gene gag. Os resultados foram observados numa escala numérica com uma variação dinâmica situada entre as 50 e 750 000 cópias de ARN VIH1/cm3, procedendo-se posterior-mente à sua conversão logarítmica. No LLBA (10 doentes e no sangue

  17. Potensi Kapsul Bee Pollen Plus sebagai Food Supplement Inovatif Peningkat Stamina dalam Rangka Pencegahan Penggunaan Doping pada Atlet Makassar : Uji Coba pada Mahasiswa UKM Sepak Bola

    OpenAIRE

    Utomo, Emilia; Saidah, Lia Nurmilatun; Utami, Iin Fadhilah; Sartini, Sartini

    2017-01-01

    Doping used for stamina enhancement and athletes' performance is actually a medicine that has negative effects on health and potentially causes an addiction. Therefore, it is necessary supplements that can increase the stamina and endurance of an athlete and at the same time could minimize the possibility of doping USAge. Bee pollen is one of the products of bees which is rich nutrients. The nutrients content of Bee pollen such as carbohydrates, proteins, lipids, minerals, vitamins, and polyp...

  18. UJI COBA TEKNOLOGI BIOFILM KONSORSIUM BAKTERI PADA REAKTOR SEMIANAEROB-AEROB UNTUK PENGOLAHAN AIR LIMBAH DI INDUSTRI PENCELUPAN TEKSTIL SKALA RUMAH TANGGA

    Directory of Open Access Journals (Sweden)

    Dewa Ketut Sastrawidana

    2013-04-01

    Full Text Available Penelitian ini bertujuan untuk menganalisis efektifitas teknologi biofilm konsorsium bakteri pada  reaktor semianaerob-aerob ntuk mengolah air limbah pencelupan tekstil. Bakteri pada reaktor semianaerob terdiri dari  Aeromonas sp. Pseudomonas sp, dan Flavobacterium sp. sedangkan pada reaktor aerob terdiri dari Vibrio sp. Plesiomonas sp. dan Enterobacter sp. Perombakan proses pertumbuhan terlekat diawali dengan menumbuhkan konsorsium bakteri pada masing-masing reaktor selama 10  hari menggunakan pada batu vulkanik merah sebagai media pelekatan bakteri. Setelah terbentuk biofilm,selanjutnya digunakan untuk merombak limbah denagn waktu tinggal limbah 2 hari. Hasil penelitian menunjukkan teknologi biofilm cukup efektif diaplikasikan pada skala lapang menghasilkan efisiensi perombakan TSS, BOD dan COD secara berturut-turut sebesar 84,7%; 80,56% dan 90,40%. Uji toksisitas air limbah tekstil menggunakan ikan nila dengan waktu paparan 3 hari menunjukkan bahwa air limbah tekstil sebelum diolah berkatagori toksik ringan dengan nilai EC50 adalah 88,80% sedangkan setelah diolah dalam reaktor biofilm konsorsium bakteri sistem anaerob-aerob selama 2 hari menjadi katagori tidak toksik dengan nilai EC50 sebesar 101,64%. Dengan demikian, pengolahan limbah tektil dengan sistem kombinasi anaerob-aerob menghasilkan kualitas limbah dengan kriteria sudah memenuhi baku mutu untuk dibuang ke lingkungan.

  19. Analytical performance evaluation of the Elecsys® Cyclosporine and Elecsys® Tacrolimus assays on the cobas e411 analyzer

    Directory of Open Access Journals (Sweden)

    Maki Sasano

    2017-08-01

    Full Text Available Background: Cyclosporine (CsA and tacrolimus (TAC are immunosuppressant drugs that are often used to treat autoimmune diseases and as transplantation therapy; therefore, their concentrations need to be monitored carefully. We herein evaluated the analytical performance of the Elecsys® Cyclosporine and Elecsys® Tacrolimus assay kits, which have been newly developed to measure CsA and TAC concentrations in the whole blood. Methods: We used residual whole blood samples from autoimmune disease and transplantation patients who were being treated with CsA or TAC. CsA concentrations were measured using an affinity chrome-mediated immunoassay (ACMIA and an electrochemiluminescence immunoassay (ECLIA. TAC concentrations were measured using a chemiluminescence immunoassay (CLIA and ECLIA. We investigated assay precision, linearity, lower limit of quantitation (LOQ, stability of calibration, influence of interference substances and the hematocrit, correlation of ACMIA with ECLIA, and correlation of CLIA with ECLIA. Results: Within-assay coefficients of variation were 1.8−3.6% (CsA: 94−1238 ng/mL and 2.9−3.9% (TAC: 2.1−17.8 ng/mL, whereas day-to-day coefficients of variation ranged between 3.0−4.1% (CsA and 2.8−3.9% (TAC. The limits of quantitation were defined as the concentration at which the CV was approximately 10%. Each lower LOQ obtained was 16 ng/mL (CsA, and 0.95 ng/mL (TAC. CsA and TAC calibrations were stable for at least 21 days. Neither the presence of conjugated bilirubin, unconjugated bilirubin, chyle, and rheumatoid factor nor the hematocrit affected these assays. A method comparison using a standardized major axis regression analysis of ACMIA and ECLIA was r=0.995, y=0.924x −1.175, n=200 (CsA, while that of CLIA and ECLIA was r=0.994, y=1.080x −0.197, n=200 (TAC. Conclusions: The analytical performances of the Elecsys® Cyclosporine and Elecsys®Tacrolimus assays were acceptable. Furthermore, CyA and TAC concentrations may be simultaneously measured using a single pretreatment which is of benefit if patients have to undertake conversion between these two drugs. Additionally, it benefits the workflow in the clinical laboratory. Thus, the Elecsys® Cyclosporine and Elecsys® Tacrolimus assays may be suitable for routine therapeutic drug monitoring.

  20. The New Aptima HBV Quant Real-Time TMA Assay Accurately Quantifies Hepatitis B Virus DNA from Genotypes A to F.

    Science.gov (United States)

    Chevaliez, Stéphane; Dauvillier, Claude; Dubernet, Fabienne; Poveda, Jean-Dominique; Laperche, Syria; Hézode, Christophe; Pawlotsky, Jean-Michel

    2017-04-01

    Sensitive and accurate hepatitis B virus (HBV) DNA detection and quantification are essential to diagnose HBV infection, establish the prognosis of HBV-related liver disease, and guide the decision to treat and monitor the virological response to antiviral treatment and the emergence of resistance. Currently available HBV DNA platforms and assays are generally designed for batching multiple specimens within an individual run and require at least one full day of work to complete the analyses. The aim of this study was to evaluate the ability of the newly developed, fully automated, one-step Aptima HBV Quant assay to accurately detect and quantify HBV DNA in a large series of patients infected with different HBV genotypes. The limit of detection of the assay was estimated to be 4.5 IU/ml. The specificity of the assay was 100%. Intra-assay and interassay coefficients of variation ranged from 0.29% to 5.07% and 4.90% to 6.85%, respectively. HBV DNA levels from patients infected with HBV genotypes A to F measured with the Aptima HBV Quant assay strongly correlated with those measured by two commercial real-time PCR comparators (Cobas AmpliPrep/Cobas TaqMan HBV test, version 2.0, and Abbott RealTi m e HBV test). In conclusion, the Aptima HBV Quant assay is sensitive, specific, and reproducible and accurately quantifies HBV DNA in plasma samples from patients with chronic HBV infections of all genotypes, including patients on antiviral treatment with nucleoside or nucleotide analogues. The Aptima HBV Quant assay can thus confidently be used to detect and quantify HBV DNA in both clinical trials with new anti-HBV drugs and clinical practice. Copyright © 2017 American Society for Microbiology.

  1. Evaluation of the NucliSens EasyQ v2.0 assay in comparison with the Roche Amplicor v1.5 and the Roche CAP/CTM HIV-1 Test v2.0 in quantification of C-clade HIV-1 in plasma.

    Directory of Open Access Journals (Sweden)

    Maximilian Muenchhoff

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

  2. Hepatitis B virus DNA quantification with the three-in-one (3io) method allows accurate single-step differentiation of total HBV DNA and cccDNA in biopsy-size liver samples.

    Science.gov (United States)

    Taranta, Andrzej; Tien Sy, Bui; Zacher, Behrend Johan; Rogalska-Taranta, Magdalena; Manns, Michael Peter; Bock, Claus Thomas; Wursthorn, Karsten

    2014-08-01

    Hepatitis B virus (HBV) replicates via reverse transcription converting its partially double stranded genome into the covalently closed circular DNA (cccDNA). The long-lasting cccDNA serves as a replication intermediate in the nuclei of hepatocytes. It is an excellent, though evasive, parameter for monitoring the course of liver disease and treatment efficiency. To develop and test a new approach for HBV DNA quantification in serum and small-size liver samples. The p3io plasmid contains an HBV fragment and human β-actin gene (hACTB) as a standard. Respective TaqMan probes were labeled with different fluorescent dyes. A triplex real-time PCR for simultaneous quantification of total HBV DNA, cccDNA and hACTB could be established. Three-in-one method allows simultaneous analysis of 3 targets with a lower limit of quantification of 48 copies per 20 μl PCR reaction and a wide range of linearity (R(2)>0.99, pDNA samples from HBV infected patients. Total HBV DNA and cccDNA could be quantified in 32 and 22 of 33 FFPE preserved liver specimens, respectively. Total HBV DNA concentrations quantified by the 3io method remained comparable with Cobas TaqMan HBV Test v2.0. The three-in-one protocol allows the single step quantification of viral DNA in samples from different sources. Therefore lower sample input, faster data acquisition, a lowered error and significantly lower costs are the advantages of the method. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays.

    Science.gov (United States)

    Harvey, John J; Chester, Stephanie; Burke, Stephen A; Ansbro, Marisela; Aden, Tricia; Gose, Remedios; Sciulli, Rebecca; Bai, Jing; DesJardin, Lucy; Benfer, Jeffrey L; Hall, Joshua; Smole, Sandra; Doan, Kimberly; Popowich, Michael D; St George, Kirsten; Quinlan, Tammy; Halse, Tanya A; Li, Zhen; Pérez-Osorio, Ailyn C; Glover, William A; Russell, Denny; Reisdorf, Erik; Whyte, Thomas; Whitaker, Brett; Hatcher, Cynthia; Srinivasan, Velusamy; Tatti, Kathleen; Tondella, Maria Lucia; Wang, Xin; Winchell, Jonas M; Mayer, Leonard W; Jernigan, Daniel; Mawle, Alison C

    2016-02-01

    In this study, a multicenter evaluation of the Life Technologies TaqMan(®) Array Card (TAC) with 21 custom viral and bacterial respiratory assays was performed on the Applied Biosystems ViiA™ 7 Real-Time PCR System. The goal of the study was to demonstrate the analytical performance of this platform when compared to identical individual pathogen specific laboratory developed tests (LDTs) designed at the Centers for Disease Control and Prevention (CDC), equivalent LDTs provided by state public health laboratories, or to three different commercial multi-respiratory panels. CDC and Association of Public Health Laboratories (APHL) LDTs had similar analytical sensitivities for viral pathogens, while several of the bacterial pathogen APHL LDTs demonstrated sensitivities one log higher than the corresponding CDC LDT. When compared to CDC LDTs, TAC assays were generally one to two logs less sensitive depending on the site performing the analysis. Finally, TAC assays were generally more sensitive than their counterparts in three different commercial multi-respiratory panels. TAC technology allows users to spot customized assays and design TAC layout, simplify assay setup, conserve specimen, dramatically reduce contamination potential, and as demonstrated in this study, analyze multiple samples in parallel with good reproducibility between instruments and operators. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Interlaboratory validation of an improved U.S. Food and Drug Administration method for detection of Cyclospora cayetanensis in produce using TaqMan real-time PCR

    Science.gov (United States)

    A collaborative validation study was performed to evaluate the performance of a new U.S. Food and Drug Administration method developed for detection of the protozoan parasite, Cyclospora cayetanensis, on cilantro and raspberries. The method includes a sample preparation step in which oocysts are re...

  5. Quantification of Paratrichodorus allius in DNA extracted from soil using TaqMan probe and SYBR green real-time PCR assays

    Science.gov (United States)

    The ectoparasitic stubby root nematode Paratrichodorus allius transmits Tobacco rattle virus, which causes corky ringspot disease resulting in significant economic losses in the potato industry. This study developed a diagnostic method for direct quantification of P. allius from soil DNA using a Taq...

  6. Simultaneous detection of five different DNA targets by real-time Taqman PCR using the Roche LightCycler480: Application in viral molecular diagnostics

    NARCIS (Netherlands)

    Molenkamp, Richard; van der Ham, Alwin; Schinkel, Janke; Beld, Marcel

    2007-01-01

    One of the most interesting aspects of real-time PCR based on the detection of fluorophoric labeled oligonucleotides is the possibility of being able to detect conveniently multiple targets in the same PCR reaction. Recently, Roche Diagnostics launched a real-time PCR platform, the LightCycler480

  7. Detection and identification of six Monilinia spp. causing brown rot using TaqMan real-time PCR from pure cultures and infected apple fruit

    Science.gov (United States)

    Brown rot is a severe disease affecting stone and pome fruits. This disease was recently confirmed to be caused by the following six closely related species: Monilinia fructicola, Monilinia laxa, Monilinia fructigena, Monilia polystroma, Monilia mumecola and Monilia yunnanensis. Because of differenc...

  8. Development of a taqman-based real-time PCR assay for the rapid and specific detection of novel duck- origin goose parvovirus.

    Science.gov (United States)

    Wang, Jianchang; Wang, Jinfeng; Cui, Yuan; Nan, Huizhu; Yuan, Wanzhe

    2017-08-01

    A real-time PCR assay was developed for specific detection of novel duck-origin goose parvovirus (N-GPV), the etiological agent of duck beak atrophy and dwarfism syndrome (BADS). The detection limit of the assay was 10 2 copies. The assay was useful in the prevention and control of BADS. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Quantification of ochratoxin A-producing molds in food products by SYBR Green and TaqMan real-time PCR methods

    DEFF Research Database (Denmark)

    Rodríguez, Alicia; Rodríguez, Mar; Luque, M. Isabel

    2011-01-01

    , usually reported in food products, were used as references. All strains were tested for OTA production by mycellar electrokinetic capillary electrophoresis (MECE) and high-pressure liquid chromatography-mass spectrometry (HPLC-MS). The ability of the optimized qPCR protocols to quantify OTA......Ochratoxin A (OTA) is a mycotoxin synthesized by a variety of different fungi, most of them from the genera Penicillium and Aspergillus. Early detection and quantification of OTA producing species is crucial to improve food safety. In the present work, two protocols of real-time qPCR based on SYBR......-producing molds was evaluated in different artificially inoculated foods. A good linear correlation was obtained over the range 1 x 104 to 10 conidia/g per reaction for all qPCR assays in the different food matrices (cooked and cured products and fruits). The detection limit in all inoculated foods ranged between...

  10. Gebruik van TaqMan PCR voor het kwantificeren van Fusarium spp. en Microdochium nivale in gewassen en gewasresten van tarwe

    NARCIS (Netherlands)

    Köhl, J.; Haas, de B.H.; Kastelein, P.; Burgers, S.L.G.E.; Waalwijk, C.

    2005-01-01

    Samenvattingen van 5 presentaties: 'Heterogenity of Dutch Fusarium oxysporum strains isolated as forma specialis radicis-lycopersici';'Een proteomics benadering om eiwitten te identificeren die door Fusarium oxysporum worden uitgescheiden in xyleemsap van tomaat'; 'Ontwikkeling en implementatie van

  11. Gebruik van TaqMan PCR voor het kwantificeren van Fusarium spp. en Microdochium nivale in gewassen en gewasresten van tarwe.

    NARCIS (Netherlands)

    Köhl, J.; Haas, de B.H.; Kastelein, P.; Burgers, S.L.G.E.; Waalwijk, C.

    2005-01-01

    Infecties van tarwe door toxigene Fusarium spp. kunnen leiden tot contaminatie van graan met diverse mycotoxines. Voorkoming van mycotoxinebesmetting is uit oogpunt van voedselveiligheid, diergezondheid, maar ook bedrijfseconomisch, vereist. Voor vier Fusariumsoorten is een kwantitatieve detectie

  12. Comparative, Collaborative, and On-Site Validation of a TaqMan PCR Method as a Tool for Certified Production of Fresh, Campylobacter-Free Chickens

    DEFF Research Database (Denmark)

    Krause, Michael; Josefsen, Mathilde Hartmann; Lund, Marianne

    2006-01-01

    , a faster, real-time PCR approach was validated in comparative and collaborative trials, based on recommendations from the Nordic system for validation of alternative microbiological methods (NordVal). The comparative real-time PCR trial was performed in comparison to two reference culture protocols...... fulfilled the NordVal validation criteria and has since been implemented at a major abattoir....

  13. A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses.

    Science.gov (United States)

    Wadhwa, Ashutosh; Wilkins, Kimberly; Gao, Jinxin; Condori Condori, Rene Edgar; Gigante, Crystal M; Zhao, Hui; Ma, Xiaoyue; Ellison, James A; Greenberg, Lauren; Velasco-Villa, Andres; Orciari, Lillian; Li, Yu

    2017-01-01

    Rabies, resulting from infection by Rabies virus (RABV) and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA) test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR) based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N) coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses, its high throughput capability and its simplicity of use, which can be quickly adapted in a laboratory to enhance the capacity of rabies molecular diagnostics. The LN34 assay provides an alternative approach for rabies diagnostics, especially in rural areas and rabies endemic regions that lack the conditions and broad experience required to run the standard DFA assay.

  14. A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses.

    Directory of Open Access Journals (Sweden)

    Ashutosh Wadhwa

    2017-01-01

    Full Text Available Rabies, resulting from infection by Rabies virus (RABV and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses, its high throughput capability and its simplicity of use, which can be quickly adapted in a laboratory to enhance the capacity of rabies molecular diagnostics. The LN34 assay provides an alternative approach for rabies diagnostics, especially in rural areas and rabies endemic regions that lack the conditions and broad experience required to run the standard DFA assay.

  15. Monkeypox detection in rodents using real-time 3'minor groove binder Taqman assays on the Roche LightCycler, Laboratory Investigation 84:1200 - 1208

    National Research Council Canada - National Science Library

    Kulesh, David

    2004-01-01

    .... The rodents were euthanized and submitted for testing to the United States Army Medical Research Institute of Infectious Diseases by the Galesburg Animal Disease Laboratory, Illinois Department of Agriculture...

  16. Novel TaqMan PCR screening methods for element cry3A and construct gat/T-pinII to support detection of both known and unknown GMOs

    NARCIS (Netherlands)

    Prins, Theo W.; Hoof, van Richard A.; Scholtens, Ingrid M.J.; Kok, Esther J.

    2017-01-01

    The import and use of genetically modified organisms (GMOs) is strictly regulated in the European Union. In order to maintain the legislation on GMOs, a genetic element screening is generally applied as a first step to detect authorised as well as unauthorised GMOs. Subsequent identification of

  17. Multiplex real-time PCR (TaqMan) assay for the simultaneous detection and discrimination of potato powdery and common scab

    Science.gov (United States)

    Powdery scab caused by the protist Spongospora subterranea and common scab caused by pathogenic bacteria in the genus Streptomyces are two important potato diseases worldwide. The symptoms of the two diseases are often similar, and diagnosis of the two diseases is therefore challenging for potato r...

  18. Development of duplex real-time RT-PCR based on Taqman technology for detecting simultaneously the genome of pan-enterovirus and enterovirus 71.

    Science.gov (United States)

    Hwang, Seoyeon; Kang, Byunghak; Hong, Jiyoung; Kim, Ahyoun; Kim, Hyejin; Kim, Kisang; Cheon, Doo-Sung

    2013-07-01

    Human enterovirus (EV) 71 is the main etiological agent of hand, foot, and mouth disease (HFMD). It is associated with neurological complications, and caused fatalities during recent outbreaks in the Asia-Pacific region. Infections caused by EV71 could lead to many complications, ranging from brainstem encephalitis to pulmonary oedema, resulting in high mortality. In this study, a duplex real-time RT-PCR assay was developed in order to simultaneously detect pan-EV and EV71. EV71-specific primers and probes were designed based on the highly conserved VP1 region of EV71. Five EV71 strains were detected as positive, and no positive fluorescence signal was observed in the duplex real-time RT-PCR for other viral RNA, which showed 100% specificity for the selected panel, and no cross-reactions were observed in this duplex real-time RT-PCR. The EV71-specific duplex real-time RT-PCR was more sensitive than conventional RT-PCR, and detected viral titers that were 10-fold lower than those measured by the latter. Of the 381 HFMD clinical specimens, 196 (51.4%) cases were pan-EV-positive, of which 170 (86.7%) were EV71-positive when tested by pan-EV and EV71-specific duplex real-time RT-PCR. EV71-specific duplex real-time RT-PCR offers a rapid and sensitive method to detect EV71 from clinical specimens, and will allow quarantine measures to be taken more effectively during outbreaks. Copyright © 2013 Wiley Periodicals, Inc.

  19. Comparison of one commercial and two in-house TaqMan multiplex real-time PCR assays for detection of enteropathogenic, enterotoxigenic and enteroaggregative Escherichia coli.

    Science.gov (United States)

    Hahn, Andreas; Luetgehetmann, Marc; Landt, Olfert; Schwarz, Norbert Georg; Frickmann, Hagen

    2017-11-01

    Enteropathogenic, enterotoxigenic and enteroaggregative Escherichia coli (EPEC, ETEC, EAEC) are among the most frequent causes of diarrhoea during travel or on military deployments. Cost-efficient and reliable real-time multiplex PCR (mPCR) assays are desirable for surveillance or point prevalence studies in remote and resource-limited tropical settings. We compared one commercial PCR kit and two in-house assays without using a gold standard to estimate sensitivity and specificity of each assay. Residual materials from nucleic acid extractions of stool samples from two groups with presumably different prevalences and increased likelihood of being infected or colonised by diarrhoeagenic E. coli were included in the assessment. One group comprised samples from returnees from tropical deployments, the second group was of migrants and study participants from high-endemicity settings. Each sample was assessed with all of the PCR assays. Cycle threshold (Ct) values were descriptively compared. The calculated sensitivities for the commercial test vs. the in-house tests were for EPEC 0.84 vs. 0.89 and 0.96, for ETEC 0.83 vs. 0.76 and 0.61, and for EAEC 0.69 vs. 0.54 and 0.69. False positive results were rare - specificity was 0.94 and 0.97 for two EPEC tests and 1.0 for all other tests. Most positive samples had late Ct values corresponding to low quantities of pathogens. Discordant test results were associated with late Ct values. As commercial and in-house assays showed comparable results, in-house tests can be assumed to be safe while affording considerable savings, making them a valuable alternative for surveillance testing in resource-limited tropical areas. © 2017 John Wiley & Sons Ltd.

  20. An OPTIMIZE study retrospective analysis for management of telaprevir-treated hepatitis C virus (HCV)-infected patients by use of the Abbott RealTime HCV RNA assay.

    Science.gov (United States)

    Sarrazin, Christoph; Dierynck, Inge; Cloherty, Gavin; Ghys, Anne; Janssen, Katrien; Luo, Donghan; Witek, James; Buti, Maria; Picchio, Gaston; De Meyer, Sandra

    2015-04-01

    Protease inhibitor (PI)-based response-guided triple therapies for hepatitis C virus (HCV) infection are still widely used. Noncirrhotic treatment-naive and prior relapser patients receiving telaprevir-based treatment are eligible for shorter, 24-week total therapy if HCV RNA is undetectable at both weeks 4 and 12. In this study, the concordance in HCV RNA assessments between the Roche High Pure System/Cobas TaqMan and Abbott RealTime HCV RNA assays and the impacts of different HCV RNA cutoffs on treatment outcome were evaluated. A total of 2,629 samples from 663 HCV genotype 1 patients receiving telaprevir/pegylated interferon/ribavirin in OPTIMIZE were analyzed using the High Pure System and reanalyzed using Abbott RealTime (limits of detection, 15.1 IU/ml versus 8.3 IU/ml; limits of quantification, 25 IU/ml versus 12 IU/ml, respectively). Overall, good concordance was observed between the assays. Using undetectable HCV RNA at week 4, 34% of the patients would be eligible for shorter treatment duration with Abbott RealTime versus 72% with the High Pure System. However, using Abbott RealTime, a similar proportion (74%) would be eligible. Of the patients receiving 24-week total therapy, 87% achieved a sustained virologic response with undetectable HCV RNA by the High Pure System or Abbott RealTime; however, 92% of the patients with undetectable HCV RNA by Abbott RealTime achieved a sustained virologic response. Using undetectable HCV RNA as the cutoff, the more sensitive Abbott RealTime assay would identify fewer patients eligible for shorter treatment than the High Pure System. Our data confirm the Abbott RealTime assay, to determine eligibility for shortened PI-based HCV treatment. (The study was registered with ClinicalTrials.gov under registration no. NCT01241760.). Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. Evaluation of a high resolution genotyping method for Chlamydia trachomatis using routine clinical samples.

    Directory of Open Access Journals (Sweden)

    Yibing Wang

    2011-02-01

    Full Text Available 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.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.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.

  2. [To consider negative viral loads below the limit of quantification can lead to errors in the diagnosis and treatment of hepatitis C virus infection].

    Science.gov (United States)

    Acero Fernández, Doroteo; Ferri Iglesias, María José; López Nuñez, Carme; Louvrie Freire, René; Aldeguer Manté, Xavier

    2013-01-01

    For years many clinical laboratories have routinely classified undetectable and unquantifiable levels of hepatitis C virus RNA (HCV-RNA) determined by RT-PCR as below limit of quantification (BLOQ). This practice might result in erroneous clinical decisions. To assess the frequency and clinical relevance of assuming that samples that are BLOQ are negative. We performed a retrospective analysis of RNA determinations performed between 2009 and 2011 (Cobas/Taqman, lower LOQ: 15 IU/ml). We distinguished between samples classified as «undetectable» and those classified as «<1.50E+01IU/mL» (BLOQ). We analyzed 2.432 HCV-RNA measurements in 1.371 patients. RNA was BLOQ in 26 samples (1.07%) from 23 patients (1.68%). BLOQ results were highly prevalent among patients receiving Peg-Riba: 23 of 216 samples (10.6%) from 20 of 88 patients receiving treatment (22.7%). The clinical impact of BLOQ RNA samples was as follows: a) 2 patients initially considered to have negative results subsequently showed quantifiable RNA; b) 8 of 9 patients (88.9%) with BLOQ RNA at week 4 of treatment later showed sustained viral response; c) 3 patients with BLOQ RNA at weeks 12 and 48 of treatment relapsed; d) 4 patients with BLOQ RNA at week 24 and/or later had partial or breakthrough treatment responses, and e) in 5 patients the impact were null or could not be ascertained. This study suggests that BLOQ HCV-RNA indicates viremia and that equating a BLOQ result with a negative result can lead to treatment errors. BLOQ results are highly prevalent in on-treatment patients. The results of HCV-RNA quantification should be classified clearly, distinguishing between undetectable levels and levels that are BLOQ. Copyright © 2013 Elsevier España, S.L. and AEEH y AEG. All rights reserved.

  3. Enhanced reliability and accuracy for field deployable bioforensic detection and discrimination of Xylella fastidiosa subsp. pauca, causal agent of citrus variegated chlorosis using razor ex technology and TaqMan quantitative PCR.

    Science.gov (United States)

    Ouyang, Ping; Arif, Mohammad; Fletcher, Jacqueline; Melcher, Ulrich; Ochoa Corona, Francisco Manuel

    2013-01-01

    A reliable, accurate and rapid multigene-based assay combining real time quantitative PCR (qPCR) and a Razor Ex BioDetection System (Razor Ex) was validated for detection of Xylella fastidiosa subsp. pauca (Xfp, a xylem-limited bacterium that causes citrus variegated chlorosis [CVC]). CVC, which is exotic to the United States, has spread through South and Central America and could significantly impact U.S. citrus if it arrives. A method for early, accurate and sensitive detection of Xfp in plant tissues is needed by plant health officials for inspection of products from quarantined locations, and by extension specialists for detection, identification and management of disease outbreaks and reservoir hosts. Two sets of specific PCR primers and probes, targeting Xfp genes for fimbrillin and the periplasmic iron-binding protein were designed. A third pair of primers targeting the conserved cobalamin synthesis protein gene was designed to detect all possible X. fastidiosa (Xf) strains. All three primer sets detected as little as 1 fg of plasmid DNA carrying X. fastidiosa target sequences and genomic DNA of Xfp at as little as 1 - 10 fg. The use of Razor Ex facilitates a rapid (about 30 min) in-field assay capability for detection of all Xf strains, and for specific detection of Xfp. Combined use of three primer sets targeting different genes increased the assay accuracy and broadened the range of detection. To our knowledge, this is the first report of a field-deployable rapid and reliable bioforensic detection and discrimination method for a bacterial phytopathogen based on multigene targets.

  4. Genital herpes evaluation by quantitative TaqMan PCR: correlating single detection and quantity of HSV-2 DNA in cervicovaginal lavage fluids with cross-sectional and longitudinal clinical data

    Directory of Open Access Journals (Sweden)

    Cox Christopher

    2010-11-01

    Full Text Available Abstract Objective To evaluate the utility of a single quantitative PCR (qPCR measurement of HSV (HSV-1&2 DNA in cervicovaginal lavage (CVL specimens collected from women with predominantly chronic HSV-2 infection in assessing genital HSV shedding and the clinical course of genital herpes (GH within a cohort with semiannual schedule of follow up and collection of specimens. Methods Two previously described methods used for detection of HSV DNA in mucocutaneous swab samples were adapted for quantification of HSV DNA in CVLs. Single CVL specimens from 509 women were tested. Presence and quantity of CVL HSV DNA were explored in relation to observed cross-sectional and longitudinal clinical data. Results The PCR assay was sensitive and reproducible with a limit of quantification of ~50 copies per milliliter of CVL. Overall, 7% of the samples were positive for HSV-2 DNA with median log10 HSV-2 DNA copy number of 3.9 (IQR: 2.6-5.7. No HSV-1 was detected. Presence and quantity of HSV-2 DNA in CVL directly correlated with the clinical signs and symptoms of presence of active symptomatic disease with frequent recurrences. Conclusion Single qPCR measurement of HSV DNA in CVL fluids of women with chronic HSV-2 infection provided useful information for assessing GH in the setting of infrequent sampling of specimens. Observed positive correlation of the presence and quantity of HSV-2 DNA with the presence of active and more severe course of HSV-2 infection may have clinical significance in the evaluation and management of HSV-2 infected patients.

  5. Smallpox and pan-Orthodox Virus Detection by Real-Time 3’-Minor Groove Binder TaqMan Assays Oil the Roche LightCycler and the Cepheid Smart Cycler Platforms

    Science.gov (United States)

    2003-11-08

    Bacillus anthracis BA0068 Ames Sterne SPS 97.13.213 Bacillus cereus Bacillus coagulans Bacillus licheniformis Bacillus macerans Bacillus ...megaterium Bacillus polymyxa Bacillus sphaericus Bacillus stearothermophilus Bacillus subtilis subsp. niger Bacillus thuringiensis Bacillus popilliae...varicella- zoster virus, and Bacillus anthracis DNA by LightCycler polymerase chain reaction after autoclaving:

  6. Multicenter evaluation of the new Abbott RealTime assays for quantitative detection of human immunodeficiency virus type 1 and hepatitis C virus RNA

    NARCIS (Netherlands)

    Schutten, Martin; Peters, D; Back, N K T; Beld, M; Beuselinck, K; Foulongne, V; Geretti, A-M; Pandiani, L; Tiemann, C; Niesters, H G M

    The analytical performances of the new Abbott RealTime hepatitis C virus (HCV) and human immunodeficiency virus type 1 viral load assays were compared at nine laboratories with different competitor assays. These included the Abbott LcX, Bayer Versant bDNA, Roche COBAS Amplicor, and Roche COBAS

  7. Multicenter evaluation of the new Abbott RealTime assays for quantitative detection of human immunodeficiency virus type 1 and hepatitis C virus RNA

    NARCIS (Netherlands)

    Schutten, M.; Peters, D.; Back, N. K. T.; Beld, M.; Beuselinck, K.; Foulongne, V.; Geretti, A.-M.; Pandiani, L.; Tiemann, C.; Niesters, H. G. M.

    2007-01-01

    The analytical performances of the new Abbott RealTime hepatitis C virus (HCV) and human immunodeficiency virus type 1 viral load assays were compared at nine laboratories with different competitor assays. These included the Abbott LcX, Bayer Versant bDNA, Roche COBAS Amplicor, and Roche COBAS

  8. Zika virus RNA polymerase chain reaction on the utility channel of a commercial nucleic acid testing system.

    Science.gov (United States)

    Boujnan, Mohamed; Duits, Ashley J; Koppelman, Marco H G M

    2018-03-01

    Several countries have implemented safety strategies to reduce the risk of Zika virus (ZIKV) transmission through blood transfusion. These strategies have included nucleic acid amplification testing (NAT) of blood donations. In this study, a new real-time polymerase chain reaction (PCR) assay including internal control for the detection of ZIKV on the cobas omni Utility Channel (UC) on the cobas 6800 system is presented. PCR conditions and primer/probe concentrations were optimized on the LightCycler 480 instrument. Optimized conditions were transferred to the cobas omni UC on the cobas 6800 system. Subsequently, the limit of detection (LOD) in plasma and urine, genotype inclusivity, specificity, cross-reactivity, and clinical sensitivity were determined. The 95% LOD of the ZIKV PCR assay on the cobas 6800 system was 23.0 IU/mL (95% confidence interval [CI], 16.5-37.5) in plasma and 24.5 IU/mL (95% CI, 13.4-92.9) in urine. The assay detected African and Asian lineages of ZIKV. The specificity was 100%. The clinical concordance between the newly developed ZIKV PCR assay and the investigational Roche cobas Zika NAT test was 83% (24/29). We developed a sensitive ZIKV PCR assay on the cobas omni UC on the cobas 6800 system. The assay can be used for large-scale screening of blood donations for ZIKV or for testing of blood donors returning from areas with ZIKV to avoid temporal deferral. This study also demonstrates that the cobas omni UC on the cobas 6800 system can be used for in-house-developed PCR assays. © 2018 AABB.

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

    Science.gov (United States)

    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.

  10. Performance of the new Bayer VERSANT HCV RNA 3.0 assay for quantitation of hepatitis C virus RNA in plasma and serum: Conversion to international units and comparison with the Roche COBAS amplicor HCV monitor, version 2.0, assay

    NARCIS (Netherlands)

    Beld, Marcel; Sentjens, Roel; Rebers, Sjoerd; Weegink, Christine; Weel, Jan; Sol, Cees; Boom, René

    2002-01-01

    We have evaluated the VERSANT HCV RNA 3.0. Assay (HCV 3.0 bDNA assay) (Bayer Diagnostics, Berkeley, Calif.), which is an improved signal amplification procedure for the HCV 2.0 bDNA assay for the quantitation of hepatitis C virus (HCV) RNA in serum or plasma of HCV-infected individuals. The HCV 3.0

  11. PENGEMBANGAN MODUL SISTEM KEAMANAN JARINGAN BERBASIS SIMULASI CISCO

    Directory of Open Access Journals (Sweden)

    Zulkipli Zulkipli

    2016-03-01

    Tujuan penelitian adalah untuk menghasilkan dan menguji kelayakan modul sistem keamanan jaringan berbasis simulasi Cisco Paket Tracer untuk peserta didik SMK. Model pengembangan yang digunakan adalah model Dick, Carey & Carey dengan sembilan langkah. Pengembangan produk ini divalidasi oleh ahli materi dengan tingkat kevalidan 96%, ahli media dengan tingkat kevalidan 92.8%, ahli desain pembelajaran dengan tingkat kevalidan 83%, uji coba perorangan dengan tingkat kevalidan 92.3%, uji coba kelompok kecil dengan tingkat kevalidan 92% dan uji coba lapangan dengan tingkat kevalidan 89% dengan kualifikasi sangat layak tidak perlu revisi.

  12. PENGEMBANGAN MODEL KOLABORASI JIGSAW ROLE PLAYING SEBAGAI UPAYA PENINGKATAN KEMAMPUAN BEKERJASAMA SISWA KELAS V SD PADA PELAJARAN IPS

    Directory of Open Access Journals (Sweden)

    Ika Ari Pratiwi

    2015-11-01

    Full Text Available Penelitian bertujuan untuk mengembangkan model kolaborasi jigsaw, role playing untuk meningkatkan kemampuan bekerjasama siswa yang valid, efektif dan praktis. Metode penelitian adalah penelitian dan pengembangan (R&D. Tahap uji coba pengembangan terdiri atas uji coba ahli, uji coba skala terbatas dan uji coba skala luas. Keefektifan model kolaborasi jigsaw role playing  diperoleh rata-rata 51,83 dalam kategori baik diterapkan dalam pelajaran IPS, peningkatan kemampuan bekerjasama siswa hasil N-gain = 0,56 dengan kategori sedang, peningkatan hasil belajar IPS N-gain = 0,50 dengan kategori sedang dan hasil ketuntasan klasikal pembelajaran IPS 97,14%.  Hasil respon guru dan siswa terhadap model yang digunakan adalah berkriteria baik. Model final penelitian ini menghasilkan model kolaborasi jigsaw role playing yang dikemas dalam suatu buku pedoman.

  13. IMPLEMENTASI ALGORITMA MONTE CARLO PADA SISTEM INFORMASI PENERIMAAN PESERTA DIDIK BARU (PPDB SECARA ONLINE

    Directory of Open Access Journals (Sweden)

    Muhammad Rizki Irwanto

    2017-08-01

    Full Text Available Tujuan penelitian ini untuk mengimplementasikan algoritma pada sistem in­formasi Penerimaan Peserta Didik Baru (PPDB secara online.Metode penelitian yang digunakan dalam pengembangan sistem informasi ini adalah metode pe­ngem­bang­an Waterfall. Tahap-tahap dalam metode pengembangan Waterfall, ada­lah: (1 de­finisi kebutuhan sistem, (2 desain sistem dan perangkat lunak, (3 im­ple­men­tasi dan pengujian unit, (4 integrasi dan sistem, dan (5 operasi dan pemeliharaan. Hasil uji coba sis­tem informasi oleh ahli rekayasa web dan admin sebesar 100,00%. Data hasil uji coba sistem informasi oleh guru sebesar 84,10%. Sedangkan data hasil uji coba sis­tem informasi oleh siswa sebesar 87,20%. Dari  data hasil uji coba di atas, dapat di­sim­pulkan bahwa sistem informasi ini sudah valid dan siap digunakan di sekolah.

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

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Bonde, Jesper; Preisler, Sarah

    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...

  15. Performance of the Xpert HPV assay in women attending for cervical screening

    Directory of Open Access Journals (Sweden)

    Jack Cuzick

    2015-12-01

    Full Text Available Objectives: This study evaluated the Xpert HPV Assay in women attending screening in general practice by comparing Xpert with two established HPV tests, cytology and histology. Methods: A prospective study in women aged 20–60 years attending screening in Bristol, Edinburgh and London using residual Preservcyt cytology samples. Sample order was randomised between Roche cobas4800 and Cepheid Xpert assays with Qiagen hc2 third. Results: 3408 cases were included in the primary analysis. Positivity for Xpert was 19.6%, cobas 19.2% and hc2 19.9% with high concordance (kappa=86.8% vs cobas, 81.55 vs hc2. Xpert, cobas and hc2 showed similar sensitivity (98.7%, 97.5%, 98.7% for CIN2+. All pairwise comparisons had high concordance (Kappa ≥0.78 with any abnormal cytology. Xpert and hc2 were positive for all cases of ≥moderate dyskaryosis (N=63, cobas was negative in two. Histology was available for 172 participants. 79 reported CIN2+, 47 CIN3+. All CIN3+ was positive on Xpert and hc2 and one case negative for cobas. One case of CIN2 was negative for all assays. Conclusions: The performance of Xpert HPV Assay in a general screening population is comparable to established HPV tests. It offers simplicity of testing, flexibility with non-batching of individual samples and rapid turnaround time. Keywords: Human papillomavirus, Xpert, Cervical screening, HPV testing

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

    Science.gov (United States)

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

    2014-07-01

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

  17. Comparison of two immunoassay systems for hCGβ and PAPP-A in prenatal screening for trisomy 21, 18, and 13 in the first trimester

    Directory of Open Access Journals (Sweden)

    Anna Elise Engell

    2017-12-01

    Full Text Available Objectives: The biochemical serum markers free β-human chorionic gonadotropin (hCGβ and pregnancy associated plasma protein A (PAPP-A, used in screening for trisomy 21 (T21, trisomy 18 (T18, and trisomy 13 (T13 during the first trimester, can be measured on different laboratory instruments e.g. Kryptor (Brahms and Cobas (Roche. We compared the performance of these two analytical instruments when used for first trimester combined testing. Design and methods: Serum samples from 944 singleton pregnant women attending for first trimester combined testing were routinely assayed for hCGβ and PAPP-A on Kryptor, and re-analyzed on Cobas. In addition, serum samples from 70 pregnant women carrying a fetus affected by T21, T18 or T13, were re-assayed on Cobas. Results: For the screening population, the hCGβ and PAPP-A results in multiples of the median (MoM from Kryptor and Cobas were significantly lower on Cobas when compared to Kryptor. The number of pregnant women with a risk above 1:300 for T21 was 48 for both Cobas and Kryptor, although a few patients only had a high risk with one of the methods. Overall, the screen positive rate was 5.1% for both instruments. In the trisomy groups the calculated risks for T21, T18, and T13 agreed well between Cobas and Kryptor. Conclusions: The screen positive rate for T21 (5.1% did not differ between the two analytical platforms in our screening population, although PAPP-A measurements form Cobas were significantly lower than those from Kryptor. The calculated risks for the pregnancies affected by trisomies using hCGβ MoM and PAPP-A MoM from Kryptor agreed well with those from Cobas. Keywords: Aneuploidy, Combined first trimester screening, First trimester risk assessment, Free β-human chorionic gonadotropin (hCGβ, Pregnancy associated plasma protein-A (PAPP-A, Trisomy screening

  18. Vitamin B12 absorption judged by measurement of holotranscobalamin, active vitamin B12: evaluation of a commercially available EIA kit.

    Science.gov (United States)

    Greibe, Eva; Nexo, Ebba

    2011-11-01

    Active vitamin B12 absorption is followed by an increase in holotranscobalamin (holoTC) upon loading with a high physiological dose of the vitamin (the CobaSorb test). This study evaluates the use of a newly launched EIA kit for measurement of holoTC (active B12) in relation to the CobaSorb test. Intra-assay imprecision and linearity of the EIA kit was examined, employing serum pools of increasing holoTC concentrations. For the CobaSorb test, holoTC was measured before and after loading with 3-times 9 μg of vitamin B12 employing both the in-house ELISA and the EIA kit (n=25). The EIA kit showed an intra-assay CV between 2.2% and 5.8% for holoTC values ranging from 21 to 80 pmol/L. Employing diluted serum samples resulted in spurious high values of holoTC. The EIA kit performed well in relation to the CobaSorb test and classified the patients studied as capable of absorbing vitamin B12 (n=10) or not (n=15), as did the in-house ELISA. The Active B12 (holoTC) EIA kit proved suitable for use with the CobaSorb test, but not for analysis of diluted serum samples.

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

    Science.gov (United States)

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

    2017-07-01

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

  20. Automated processing, extraction and detection of herpes simplex virus types 1 and 2: A comparative evaluation of three commercial platforms using clinical specimens.

    Science.gov (United States)

    Binnicker, Matthew J; Espy, Mark J; Duresko, Brian; Irish, Cole; Mandrekar, Jay

    2017-04-01

    Recently, automated platforms have been developed that can perform processing, extraction and testing for herpes simplex virus (HSV) nucleic acid on a single instrument. In this study, we compared three commercially-available systems; Aptima ® /Panther (Hologic, San Diego, CA), ARIES ® (Luminex Corporation, Austin, TX), and cobas ® 4800 (Roche Molecular Systems Inc, Pleasanton, CA) for the qualitative detection of HSV-1/2 in clinical samples. Two-hundred seventy-seven specimens (genital [n=193], dermal [n=84]) were submitted for routine HSV-1/2 real-time PCR by a laboratory developed test. Following routine testing, samples were also tested by the Aptima, ARIES, and cobas HSV-1/2 assays per the manufacturer's recommendations. Results were compared to a "consensus standard" defined as the result obtained from ≥3 of the 4 assays. Following testing of 277 specimens, the cobas and ARIES assays demonstrated a sensitivity of 100% for HSV-1 (61/61) and HSV-2 (55/55). The Aptima assays showed a sensitivity of 91.8% (56/61) for HSV-1 and 90.9% (50/55) for HSV-2. Percent specificities for HSV-1 were 96.2% (202/210) by cobas, 99.5% (209/210) by ARIES and 100% (236/236) by Aptima. For HSV-2, the specificities were 98.1% (211/215) by cobas, 99.5% (215/216) by ARIES and 100% (216/216) by Aptima. The turnaround time for testing 24 samples was 2.5h by the cobas 4800, 3.1h by Aptima/Panther, and 3.9h by ARIES. The three commercial systems can perform all current functions on a single platform, thereby improving workflow and potentially reducing errors associated with manual processing of samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Comparison of three human papillomavirus DNA assays and one mRNA assay in women with abnormal cytology

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Lynge, Elsebeth; Ejegod, Ditte

    2014-01-01

    no follow-up, 232 (63%) had cancer. The sensitivity for ≥CIN3 was 95% (95% CI: 88-99) for HC2, 94% (95% CI: 87-98) for cobas, 93% (95% CI: 85-97) for CLART, and 87% (95% CI: 78-93) for APTIMA. In women of age above 30 years......, the sensitivities were 98% (95% CI: 87-100), 93% (95% CI: 80-98), 90% (95% CI: 77-97), and 93% (95% CI: 80-98), respectively. One woman with cervical cancer tested negative on CLART and one on cobas; HC2 and APTIMA were positive in all three cancer cases. The specificity for

  2. PENGEMBANGAN BUKU AJAR BIOLOGI SEL DENGAN PENDEKATAN BIOINFORMATIKA

    Directory of Open Access Journals (Sweden)

    Ardini Pangastuti

    2016-02-01

    Buku ajar merupakan buku panduan pembelajaran yang digunakan oleh siswa guna membantu mencapai tujuan pendidikan nasional. Pengembangan buku ajar merupakan salah satu cara yang dilakukan untuk memfasilitasi tercapainya indikator pembelajaran. Pengembangan buku ajar Biologi Sel dengan pendekatan Bioinformatika menggunakan model pengembangan Dick and Carey. Buku ajar yang dikembangkan divalidasi oleh ahli materi, ahli media pembelajaran, 15 mahasiswa uji coba perorangan, dan 15 mahasiswa uji coba kelompok sedang. Hasil validasi ahli materi menyatakan layak sebesar 84% dengan kategori baik. Hasil validasi ahli media pembelajaran menyatakan layak sebesar 82,4% dengan kategori baik.

  3. PENGEMBANGAN PROTOTIPE EGG BOILER SEBAGAI MEDIA PEMBELAJARAN PRAKARYA DAN KEWIRAUSAHAAN UNTUK MATERI TEKNOLOGI TEPAT GUNA KELAS XI MIA SMA NEGERI 4 SINGARAJA TAHUN AJARAN 2016/2017

    Directory of Open Access Journals (Sweden)

    Indra Kusuma Harta

    2017-07-01

    Full Text Available Penelitian ini bertujuan untuk mengembangkan Prototipe Egg Boiler (Pengkukus Telur Otomatis sebagai media pembelajaran untuk mata pelajaran Prakarya dan Kewirausahaan pada materi Teknologi Tepat Guna di Kelas XI MIA SMA Negeri 4 Singaraja. Penelitian ini dilakukan dengan menggunakan metode Penelitian dan Pengembangan dalam bidang pendidikan. Hasil uji validasi ahli media memperoleh skor sebesar 0,75 dalam kategori tinggi. Uji validasi isi dengan nilai sebesar 0,81 dalam kategori sangat tinggi.  Sedangkan hasil uji coba perorangan dengan nilai sebesar 0.93, uji coba kelompok kecil dengan nilai sebesar 0.71, dan uji coba lapangan dengan nilai sebesar 0.82. Pada uji coba lapangan juga dilakukan dengan menganalisis nilai dari kegiatan praktikum, nilai yang diperoleh 87.4 dikategorikan dengan hasil belajar tinggi. Dari hasil nilai pre-test dan post-test tersebut secara keseluruhan mengalami peningkatan. Sehingga Pototipe Egg Boiler yang telah dikembangkan sangat membantu siswa dalam memahami materi dan praktikum mata pelajaran Prakarya dan Kewirausahaan untuk materi Teknologi Tepat Guna di Kelas XI MIA SMA Negeri 4 Singaraja.

  4. PERANGKAT LUNAK "DIGITAL SIGNAGE MANAGER"

    Directory of Open Access Journals (Sweden)

    Siti Rochimah

    2006-07-01

    Full Text Available Digital signage adalah suatu alat untuk menampilkan konten multimedia kepada umum. Digital signage pada umumnya terdiri dari dua komponen penting, yaitu manager dan player. Digital Signage Manager (DSM adalah suatu perangkat lunak yang mempunyai fungsi mengelola perangkat lunak Digital Signage Player (DSP. Pengelolaan ini menyangkut pengaturan dan pengiriman konten, pengaturan DSP, dan pengaturan konten yang ada di DSP. Pada penelitian ini telah dibangun sebuah perangkat lunak DSM, yang merupakan bentuk pengembangan dari perangkat lunak yang sebelumnya telah ada yaitu BZNP-100, yang tidak lain adalah perangkat lunak untuk mengelola Sony Network Player NSP-100. DSM dibangun dengan tujuan untuk melengkapi kekurangan dan menambah beberapa fitur tambahan yang belum ada pada perangkat lunak sebelumnya, seperti: mendukung material Flash, mengirim Content Delivery Disc (CDD, menjadwalkan playlist, dan mendukung dua layar. BZNP-100 dan Sony Network Player NSP-100 merupakan digital signage yang dibuat oleh perusahaan elektronik Sony Corporation pada tahun 2003.Uji coba perangkat lunak DSM ini dilakukan dengan menjalankan skenario uji coba berdasarkan fungsionalitas masing-masing fitur. Uji coba dilakukan pada masing-masing fitur antara lain: login, konfigurasi, pembuatan material, manajemen DSP, manajemen playlist, memainkan material dan playlist, dan manajemen remote material dan playlist. Hasil uji coba menunjukkan bahwa perangkat lunak DSM telah berfungsi sesuai dengan tujuan yang diharapkan.Kata kunci: Digital signage, Digital Signage Manager (DSM, Digital Signage Player (DSP, Content Delivery Disc (CDD, plasma TV,  LCD.

  5. Comparison of the Abbott RealTime CT new formulation assay with two other commercial assays for detection of wild-type and new variant strains of Chlamydia trachomatis

    DEFF Research Database (Denmark)

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

    2010-01-01

    In an analytical methods comparison study on clinical samples, the Abbott RealTime CT new formulation assay (m2000 real-time PCR) consisting of a duplex PCR targeting different parts of the cryptic plasmid in Chlamydia trachomatis was compared with version 2 of the Roche COBAS(R) TaqMan(R) CT ass...

  6. Enzymatic assay for methotrexate in erythrocytes

    DEFF Research Database (Denmark)

    Schrøder, H; Heinsvig, E M

    1985-01-01

    Methotrexate (MTX) accumulates in erythrocytes in MTX-treated patients. We present a modified enzymatic assay measuring MTX concentrations between 10 and 60 nmol/l in erythrocytes, adapted for a centrifugal analyser (Cobas Bio). About 40 patient's samples could be analysed within 1 h. The detection...

  7. Influence of biological variations and sample handling on measured microalbuminuria in diabetic patients

    NARCIS (Netherlands)

    Vermes, I.; Spooren, P.F.M.J.

    1992-01-01

    Five immunochemical assays for determining low concentrations of albumin were investigated. These were a radioimmunoassay (RIA); turbidimetric immunoassays (TIA) both according to end-point measuring principle on a Cobas Fara and Hitachi 717 analysers, and according to kinetic measuring principle on

  8. PENGEMBANGAN ASESMEN ALTERNATIF PRAKTIKUM KIMIA DASAR II MELALUI CHEMISTRY FAIR PROJECT (CFP BERBASIS KONSERVASI DENGAN MEMANFAATKAN DAILY CHEMICAL

    Directory of Open Access Journals (Sweden)

    Indah Urwatin Wusqo

    2016-12-01

    Full Text Available Penelitian ini bertujuan untuk (1 Mengembangkan asesmen alternatif pada praktikum kimia dasar II melalui chemistry fair project berbasis konservasi dengan memanfaatkan daily chemical(2 Mengetahui tingkat kevalidan, kepraktisan dan keefektifannya. Penelitian ini merupakan penelitian pengembangan (Development Research Model pengembangan yang diterapkan Dick dan Carey (1985. Subjek uji coba terbatas maupun subjek uji coba lapangan adalah dosen dan mahasiswa Prodi Pendidikan IPA UNNES. Sampel ditentukan secara purposive, yaitu dosen pengampu dan mahasiswa yang menempuh mata kuliah Praktikum Kimia Dasar II. Data yang diperoleh dari uji coba ini adalah: (1 masukan dari pakar, untuk menentukan validitas isi dan konstruk dari fitur asesmen; (2 masukan dari sampel uji coba terbatas, untuk menentukan kepraktisan petunjuk chemistry fair project (CFP berbasis konservasi dengan memanfaatkan daily chemical ; Instrumen pengumpul data berupa angket keterbacaan petunjuk pembuatan chemistry fair project (CFP berbasis konservasi dengan memanfaatkan daily chemical, pedoman penskoran. (3 data hasil belajar siswa untuk mengetahui efektivitas asesmen. Masukan dari pakar angket mahasiswa, dan nilai chemistry fair project (CFP sampel ujicoba terbatas dianalisis secara kualitatif, dan kuantitatif. Asesmen alternative Praktikum Kimia Dasar II yang dikembangkan dikatakan berhasil baik apabila asesmen yang dikembangkan valid, praktis, dan efektif.

  9. Kepatuhan Nahkoda Melakukan Pemeriksaan Boat Berdasarkan Check- List Harian untuk Keselamatan Pelayaran di Perusahaan Pelayaran

    OpenAIRE

    B, Rinto; Shaluhiyah, Zahroh; Kurniawan, Bina

    2012-01-01

    Terdapat penyimpangan prosedur dalam pemeriksaan boat berdasarkan checklist inspeksiyang sudah ada dimana rata-rata nahkoda melakukan pencontrengan checklist tanpamelakukan uji coba alat-alat keselamatan dan mesin di dalam boat. Tujuan penelitian iniadalah untuk mengeksplorasi gambaran tentang perilaku kepatuhan nahkoda di Perusahaanpelayaran ini dalam melakukan pemeriksaan boat berdasarkan checklist. Penelitian inimenggunakan metode penelitian kualitatif dengan melakukan wawancara yang menda...

  10. BRAF mutation testing in solid tumors: a methodological comparison.

    Science.gov (United States)

    Weyant, Grace W; Wisotzkey, Jeffrey D; Benko, Floyd A; Donaldson, Keri J

    2014-09-01

    Solid tumor genotyping has become standard of care for the characterization of proto-oncogene mutational status, which has traditionally been accomplished with Sanger sequencing. However, companion diagnostic assays and comparable laboratory-developed tests are becoming increasingly popular, such as the cobas 4800 BRAF V600 Mutation Test and the INFINITI KRAS-BRAF assay, respectively. This study evaluates and validates the analytical performance of the INFINITI KRAS-BRAF assay and compares concordance of BRAF status with two reference assays, the cobas test and Sanger sequencing. DNA extraction from FFPE tissue specimens was performed followed by multiplex PCR amplification and fluorescent label incorporation using allele-specific primer extension. Hybridization to a microarray, signal detection, and analysis were then performed. The limits of detection were determined by testing dilutions of mutant BRAF alleles within wild-type background DNA, and accuracy was calculated based on these results. The INFINITI KRAS-BRAF assay produced 100% concordance with the cobas test and Sanger sequencing and had sensitivity equivalent to the cobas assay. The INFINITI assay is repeatable with at least 95% accuracy in the detection of mutant and wild-type BRAF alleles. These results confirm that the INFINITI KRAS-BRAF assay is comparable to traditional sequencing and the Food and Drug Administration-approved companion diagnostic assay for the detection of BRAF mutations. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  11. Referral population studies underestimate differences between human papillomavirus assays in primary cervical screening

    DEFF Research Database (Denmark)

    Rebolj, M.; Njor, S.; Lynge, E.

    2017-01-01

    with SurePath® cytology, and Hybrid Capture 2 (HC2), cobas, CLART and APTIMA HPV assays. Women with positive test results were offered a follow-up. For all detected HPV infections and HPV-positive high-grade cervical intraepithelial neoplasia (≥CIN2), we studied the distributions of assay-specific signal...

  12. A daunting challenge

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Bonde, Jesper; Ejegod, Ditte

    2015-01-01

    We compared cytology with Hybrid Capture 2 (HC2), cobas, CLART and APTIMA Human Papillomavirus (HPV) assays in primary cervical screening at age 23-29 years based on data from the Danish Horizon study. SurePath samples were collected from 1278 women undergoing routine cytology-based screening...

  13. Multicenter evaluation of the new Abbott Realtime assays for quantitative detection of human immunodeficiency virus type 1 and hepatitis C virus RNA

    NARCIS (Netherlands)

    M. Schutten (Martin); D. Peters (D.); N. Back (Nicole); A.W. van den Beld (Annewieke); B. Beuselinck (B.); V. Foulongne (V.); A.M. Geretti (Anna Maria); L. Pandiani (L.); M. Tiemann; H.G.M. Niesters (Bert)

    2007-01-01

    textabstractThe analytical performances of the new Abbott RealTime hepatitis C virus (HCV) and human immunodeficiency virus type 1 viral load assays were compared at nine laboratories with different competitor assays. These included the Abbott LcX, Bayer Versant bDNA, Roche COBAS Amplicor, and Roche

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

    Science.gov (United States)

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

    2014-02-01

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

  15. PENGEMBANGAN MODEL LATIHAN KARATE KIDS PADA ANAK USIA SEKOLAH DASAR KELAS ATAS

    Directory of Open Access Journals (Sweden)

    Widha Srianto

    2014-09-01

    Full Text Available Penelitian ini bertujuan untuk menghasilkan model latihan karate kids pada anak usia sekolah dasar (SD kelas atas (10-12 tahun. Penelitian pengembangan ini dilakukan dengan mengadaptasi langkah-langkah penelitian sebagai berikut: (1 pengumpulan informasi di lapangan, (2 melakukan analisis terhadap informasi yang telah dikumpulkan, (3 mengembangkan produk awal, (4 validasi ahli dan revisi, (5 uji coba lapangan skala kecil dan revisi,  (6 uji coba lapangan skala besar dan revisi, dan (7 pembuatan produk final. Uji coba skala kecil dilakukan di klub Forki Kota Yogyakarta berjumlah 7 anak. Uji coba skala besar di klub Inkanas DIY berjumlah 16 anak. Instrumen pengumpulan data yang digunakan yaitu: (1 pedoman wawancara, (2 skala nilai, (3 pedoman observasi model, (4 pedoman observasi keefektifan model, dan (5 kuesioner untuk siswa. Teknik analisis data yang dilakukan yaitu analisis deskriptif kuantitatif dan analisis deskriptif kualitatif. Hasil penelitian ini berupa model latihan karate kids pada anak usia SD kelas atas (10-12 tahun yaitu: (1 model latihan maegeri, (2 model latihan gyaku tsuki, (3 model latihan mawashigeri, dan (4 model latihan oi tsuki. Dari hasil analisis data penilaian para ahli materi dan kuesioner anak, dapat ditarik kesimpulan bahwa model latihan karate kids pada anak usia SD kelas atas (10-12 tahun ini dinilai baik dan efektif. Kata kunci: model latihan, karate kids

  16. Assessment of efficacy and tolerability of once-daily extended release metformin in patients with type 2 diabetes mellitus

    Directory of Open Access Journals (Sweden)

    S Yu Vorotnikova

    2012-09-01

    Full Text Available Реферат по статье: Assessment of efficacy and tolerability of once-daily extended release metformin in patients with type 2 diabetes mellitus Juliana Levy, Roberta A Cobas, Marilia B Gomes. Diabetol Metab Syndr. 2010 Mar 18; 2:16.

  17. Nucleic acid amplification technology screening for hepatitis C virus and human immunodeficiency virus for blood donations

    International Nuclear Information System (INIS)

    Bamaga, Mohammad S.; Bokhari, Fawzi F.; Aboud, Abdulrehman M.; Al-Malki, M.; Alenzi, Faris Q.

    2006-01-01

    To investigate the performance of the commercial Roche COBAS AmpliScreen assay, and demonstrate whether the COBAS AmpliScreen human immunodeficiency virus-1 (HIV-1) test, v1.5, and COBAS AmpliScreen hepatitis C virus (HCV) v 2.0 for screening for HIV-1 and HCV RNA in the donated blood units from which plasma mini pools were collected, by nucleic acid amplification technology (NAT), could detect the positive pools and reduce the risk of transmission of infections for those routinely tested by serological assays. The study was performed on 3288 plasma samples collected from blood donors in a period of 13 months, from August 2004 to August 2005, at Al-Hada Armed Forces Hospital, Molecular Pathology Laboratory, Taif, Kingdom of Saudi Arabia. The samples were tested by the reverse transcriptase polymerase chain reaction (RT-PCR) after RNA extraction (this represents the major method in NAT assays), in parallel with the routine serological testing to detect qualitatively for HIV-1 and HCV. The NAT assays that include an automated COBAS AmpliPrep system for RNA extraction and COBAS Amplicor Analyzer using AmpliScreen kits for RT-PCR assays, and the routine serological screening assays for the detection of the HIV-1 and HCV RNA in the plasma samples from the blood donors have shown to be a reliable combination that would meet our requirements. The collected data further confirms the results from the serological assays and enables us to decrease the residual risk of transmission to a minimum with the finding of no seronegative window period donation. The results demonstrate that out of 3288 samples, the percentages of RT-PCR (NAT) negative blood donations that were also confirmed as seronegative were 99% for HCV, and 99.1% for HIV-1. The modified combined systems (automated COBAS AmpliPrep system for RNA extraction and COBAS Amplicor Analyzer using AmpliScreen kits for RT-PCR assays) for NAT screening assays has allowed the release of all blood donations supplied in the

  18. PENGEMBANGAN MEDIA KOMIK PEMBELAJARAN MATEMATIKA MENINGKATKAN MOTIVASI DAN PRESTASI BELAJAR SISWA KELAS V

    Directory of Open Access Journals (Sweden)

    Indaryati Indaryati

    2015-01-01

    Full Text Available Penelitian ini bertujuan menghasilkan produk media berupa komik pembelajaran matematika yang dapat meningkatkan motivasi dan prestasi belajar matematika siswa kelas V SD. Penelitian ini merupakan penelitian pengembangan, yang terdiri dari: (1 penelitian dan pengumpulan data, (2 perencanaan, (3 pengembangan draft produk, (4 uji coba lapangan awal,  (5 revisi hasil uji coba, (6 uji coba lapangan, (7 penyempurnaan produk hasil uji coba lapangan, (8 uji pelaksanaan lapangan, dan (9 penyempurnaan produk akhir. Subjek uji coba adalah siswa kelas V SDN Glagah Yogyakarta. Subjek uji coba satu-satu terdiri atas tiga orang siswa. Subjek uji coba kelompok kecil terdiri atas sembilan orang siswa yang belum terlibat dalam uji coba satu-satu, dan subjek uji lapangan terdiri atas 54 orang siswa dari kelas VB dan kelas VC yang tidak ikut dalam uji coba satu-satu dan uji coba kelompok kecil. Hasil penelitian menunjukkan bahwa media yang dikembangkan ini mendapatkan penilaian dari para ahli dengan kategori “baik”, penilaian guru dan siswa yang menggunakan media komik menyatakan praktis, sehingga media pembelajaran ini layak digunakan. Hasil uji lapangan menunjukkan media komik pembelajaran matematika yang digunakan dapat meningkatkan motivasi belajar siswa sebesar 0,65 tergolong dalam kategori sedang menurut skala gain, sedangkan prestasi belajar siswa sebesar 0,73 tergolong dalam kategori tinggi menurut skala gain. ____________________________________________________________________________________________________________________________________ DEVELOPING COMIC MEDIA FOR THE TEACHING OF MATHEMATICS TO ENCHANCE THE MOTIVATION AND MATHEMATICS LEARNING OUTCOMES GRADE V ABSTRACT This research aims to produce a product in the form of mathematics teaching comics which can improve motivation and learning achievement of students of grade V of SD. This research is research and development study consisting of nine stages, namely: (1 research and data collection, (2

  19. PENGEMBANGAN MULTIMEDIA CERITA RAKYAT SEBAGAI PENUMBUHAN KARAKTER SISWA

    Directory of Open Access Journals (Sweden)

    Kusmayadi Kusmayadi

    2017-07-01

    Full Text Available This study was aimed to test feasibility multimedia appreciation folklore charged character education for student junior grade VII. The approach that was undertaken use qualitative and quantitative reseach. Subject pilot this reseach is one expert learning, one person media expert learning, practitioner, 5 (six student on trial small group, and 30 (thirty student on trial a large group. The trial court implemented in Junior High School 1 Praya Lombok Middle east. The data was undertaken through observation, charging chief, and guide documentation. Analysis quantitative data done by counting the percentage feasibility the product of the people of learning, media experts, practitioner, the results of the small group and results of the test a large group. The results of data qualitative presented in the form of exposure to. The research results show multimedia learning on all the step of experiment try is at the percentage very reasonable to be used as a media learning. Penelitian ini bertujuan untuk menguji kelayakan multimedia apresiasi cerita rakyat bermuatan pendidikan karakter untuk siswa SMP Kelas VII. Pendekatan yang dilakukan menggunakan kualitatif dan kuantitatif. Subjek uji coba penelitian ini adalah satu orang ahli pembelajaran, satu orang ahli media pembelajaran, satu orang praktisi, enam siswa pada uji coba kelompok kecil, dan tiga puluh siswa pada uji coba kelompok besar. Uji coba lapangan dilaksanakan di SMPN 1 Praya Timur Lombok Tengah. Pengambilan data dilakukan melalui observasi, pengisian angket, dan panduan dokumentasi. Analisis data kuantitatif dilakukan dengan menghitung persentase kelayakan produk dari ahli pembelajaran, ahli media, praktisi, hasil uji kelompok kecil dan hasil uji kelompok besar. Hasil data kualitatif disajikan dalam bentuk paparan. Hasil penelitian menunjukkan multimedia pembelajaran pada semua tahap uji coba berada pada persentase sangat layak untuk digunakan sebagai media pembelajaran.

  20. Sensitivity and specificity of a new automated system for the detection of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus nucleic acid in blood and plasma donations.

    Science.gov (United States)

    Galel, Susan A; Simon, Toby L; Williamson, Phillip C; AuBuchon, James P; Waxman, Dan A; Erickson, Yasuko; Bertuzis, Rasa; Duncan, John R; Malhotra, Khushbeer; Vaks, Jeffrey; Huynh, Nancy; Pate, Lisa Lee

    2018-03-01

    Use of nucleic acid testing (NAT) in donor infectious disease screening improves transfusion safety. Advances in NAT technology include improvements in assay sensitivity and system automation, and real-time viral target discrimination in multiplex assays. This article describes the sensitivity and specificity of cobas MPX, a multiplex assay for detection of human immunodeficiency virus (HIV)-1 Group M, HIV-2 and HIV-1 Group O RNA, HCV RNA, and HBV DNA, for use on the cobas 6800/8800 Systems. The specificity of cobas MPX was evaluated in samples from donors of blood and source plasma in the United States. Analytic sensitivity was determined with reference standards. Infectious window periods (WPs) before NAT detectability were calculated for current donor screening assays. The specificity of cobas MPX was 99.946% (99.883%-99.980%) in 11,203 blood donor samples tested individually (IDT), 100% (99.994%-100%) in 63,012 donor samples tested in pools of 6, and 99.994% (99.988%-99.998%) in 108,306 source plasma donations tested in pools of 96. Seven HCV NAT-yield donations and one seronegative occult HBV infection were detected. Ninety-five percent and 50% detection limits in plasma (IU/mL) were 25.7 and 3.8 for HIV-1M, 7.0 and 1.3 for HCV, and 1.4 and 0.3 for HBV. The HBV WP was 1 to 4 days shorter than other donor screening assays by IDT. cobas MPX demonstrated high specificity in blood and source plasma donations tested individually and in pools. High sensitivity, in particular for HBV, shortens the WP and may enhance detection of occult HBV. © 2017 The Authors Transfusion published by Wiley Periodicals, Inc. on behalf of AABB.

  1. Validation of a Human Papillomavirus (HPV) DNA Cervical Screening Test That Provides Expanded HPV Typing.

    Science.gov (United States)

    Demarco, Maria; Carter-Pokras, Olivia; Hyun, Noorie; Castle, Philip E; He, Xin; Dallal, Cher M; Chen, Jie; Gage, Julia C; Befano, Brian; Fetterman, Barbara; Lorey, Thomas; Poitras, Nancy; Raine-Bennett, Tina R; Wentzensen, Nicolas; Schiffman, Mark

    2018-05-01

    As cervical cancer screening shifts from cytology to human papillomavirus (HPV) testing, a major question is the clinical value of identifying individual HPV types. We aimed to validate Onclarity (Becton Dickinson Diagnostics, Sparks, MD), a nine-channel HPV test recently approved by the FDA, by assessing (i) the association of Onclarity types/channels with precancer/cancer; (ii) HPV type/channel agreement between the results of Onclarity and cobas (Roche Molecular Systems, Pleasanton, CA), another FDA-approved test; and (iii) Onclarity typing for all types/channels compared to typing results from a research assay (linear array [LA]; Roche). We compared Onclarity to histopathology, cobas, and LA. We tested a stratified random sample ( n = 9,701) of discarded routine clinical specimens that had tested positive by Hybrid Capture 2 (HC2; Qiagen, Germantown, MD). A subset had already been tested by cobas and LA ( n = 1,965). Cervical histopathology was ascertained from electronic health records. Hierarchical Onclarity channels showed a significant linear association with histological severity. Onclarity and cobas had excellent agreement on partial typing of HPV16, HPV18, and the other 12 types as a pool (sample-weighted kappa value of 0.83); cobas was slightly more sensitive for HPV18 and slightly less sensitive for the pooled high-risk types. Typing by Onclarity showed excellent agreement with types and groups of types identified by LA (kappa values from 0.80 for HPV39/68/35 to 0.97 for HPV16). Onclarity typing results corresponded well to histopathology and to an already validated HPV DNA test and could provide additional clinical typing if such discrimination is determined to be clinically desirable. This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

  2. Detection of cervical precancerous lesions with Aptima HPV assays using SurePath preservative fluid specimens

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    Max Chernesky

    2017-06-01

    Full Text Available SurePath specimens from women referred to colposcopy were treated with Aptima Transfer Solution (ATS before testing in Aptima HPV (AHPV and Aptima HPV 16, 18/45 (AHPV-GT assays. Untreated SurePath specimens were tested with the cobas HPV test. PreservCyt specimens were assessed for cytology and tested with AHPV. High-grade cervical intraepithelial neoplasia lesions served as the reference standard. Excellent agreement (95.5%; k=0.91 was observed for ATS-treated SurePath specimens between Tigris and Panther systems and between the PreservCyt and ATS-treated SurePath specimens (91.1%, k=0.81 with the AHPV assay on Tigris. Agreement between the AHPV and cobas assays with SurePath specimens was substantial (89.9%, k=0.80. AHPV sensitivity for CIN2+(n=147 was 91.2% for SurePath and PreservCyt. Cobas HPV sensitivity was 93.9% for SurePath specimens. AHPV testing of SurePath specimens was more specific (59.4% than cobas (54.7% (p<0.001. Detection and genotyping showed similar absolute and relative risks. ATS-treated SurePath specimens tested with AHPV and AHPV-GT assays showed similar performance with greater specificity than cobas HPV on SurePath specimens. Similar overall results were seen using a CIN3 disease endpoint. Keywords: Human papillomavirus, SurePath, PreservCyt, Cervical intraepithelial neoplasia, CIN2+, Aptima transfer solution (ATS

  3. A Comparative Study for Detection of EGFR Mutations in Plasma Cell-Free DNA in Korean Clinical Diagnostic Laboratories

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    Yoonjung Kim

    2018-01-01

    Full Text Available Liquid biopsies to genotype the epidermal growth factor receptor (EGFR for targeted therapy have been implemented in clinical decision-making in the field of lung cancer, but harmonization of detection methods is still scarce among clinical laboratories. We performed a pilot external quality assurance (EQA scheme to harmonize circulating tumor DNA testing among laboratories. For EQA, we created materials containing different levels of spiked cell-free DNA (cfDNA in normal plasma. The limit of detection (LOD of the cobas® EGFR Mutation Test v2 (Roche Molecular Systems was also evaluated. From November 2016 to June 2017, seven clinical diagnostic laboratories participated in the EQA program. The majority (98.94% of results obtained using the cobas assay and next-generation sequencing (NGS were acceptable. Quantitative results from the cobas assay were positively correlated with allele frequencies derived from digital droplet PCR measurements and showed good reproducibility among laboratories. The LOD of the cobas assay was 5~27 copies/mL for p.E746_A750del (exon 19 deletion, 35~70 copies/mL for p.L858R, 18~36 copies/mL for p.T790M, and 15~31 copies/mL for p.A767_V769dup (exon 20 insertion. Deep sequencing of materials (>100,000X depth of coverage resulted in detection of low-level targets present at frequencies of 0.06~0.13%. Our results indicate that the cobas assay is a reliable and rapid method for detecting EGFR mutations in plasma cfDNA. Careful interpretation is particularly important for p.T790M detection in the setting of relapse. Individual laboratories should optimize NGS performance to maximize clinical utility.

  4. Evaluation of a Multiplex Real-Time Reverse Transcriptase PCR Assay for Detection and Differentiation of Influenza Viruses A and B during the 2001-2002 Influenza Season in Israel

    Science.gov (United States)

    Hindiyeh, Musa; Levy, Virginia; Azar, Roberto; Varsano, Noemi; Regev, Liora; Shalev, Yael; Grossman, Zehava; Mendelson, Ella

    2005-01-01

    The ability to rapidly diagnose influenza virus infections is of the utmost importance in the evaluation of patients with upper respiratory tract infections. It is also important for the influenza surveillance activities performed by national influenza centers. In the present study we modified a multiplex real-time reverse transcriptase PCR (RT-PCR) assay (which uses TaqMan chemistry) and evaluated it for its ability to detect and concomitantly differentiate influenza viruses A and B in 370 patient samples collected during the 2001-2002 influenza season in Israel. The performance of the TaqMan assay was compared to those of a multiplex one-step RT-PCR with gel detection, a shell vial immunofluorescence assay, and virus isolation in tissue culture. The TaqMan assay had an excellent sensitivity for the detection of influenza viruses compared to that of tissue culture. The overall sensitivity and specificity of the TaqMan assay compared to the results of culture were 98.4 and 85.5%, respectively. The sensitivity and specificity of the TaqMan assay for the detection of influenza virus A alone were 100 and 91.1%, respectively. On the other hand, the sensitivity and specificity for the detection of influenza virus B alone were 95.7 and 98.7%, respectively. The rapid turnaround time for the performance of the TaqMan assay (4.5 h) and the relatively low direct cost encourage the routine use of this assay in place of tissue culture. We conclude that the multiplex TaqMan assay is highly suitable for the rapid diagnosis of influenza virus infections both in well-established molecular biology laboratories and in reference clinical laboratories. PMID:15695650

  5. Detection and differentiation of Cryptosporidium by real-time polymerase chain reaction in stool samples from patients in Rio de Janeiro, Brazil

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    Roberta Flávia Ribeiro Rolando

    2012-06-01

    Full Text Available This study reports the first genetic characterisation of Cryptosporidium isolates in Brazil using real-time polymerase chain reaction (RT-PCR. A total of 1,197 faecal specimens from children and 10 specimens from human immunodeficiency virus-infected patients were collected between 1999-2010 and screened using microscopy. Forty-eight Cryptosporidium oocyst-positive isolates were identified and analysed using a generic TaqMan assay targeting the 18S rRNA to detect Cryptosporidium species and two other TaqMan assays to identify Cryptosporidium hominis and Cryptosporidium parvum. The 18S rRNA assay detected Cryptosporidium species in all 48 of the stool specimens. The C. parvum TaqMan assay correctly identified five/48 stool samples, while 37/48 stool specimens were correctly amplified in the C. hominis TaqMan assay. The results obtained in this study support previous findings showing that C. hominis infections are more prevalent than C. parvum infections in Brazil and they demonstrate that the TaqMan RT-PCR procedure is a simple, fast and valuable tool for the detection and differentiation of Cryptosporidium species.

  6. A pilot evaluation of whole blood finger-prick sampling for point-of-care HIV viral load measurement: the UNICORN study.

    Science.gov (United States)

    Fidler, Sarah; Lewis, Heather; Meyerowitz, Jodi; Kuldanek, Kristin; Thornhill, John; Muir, David; Bonnissent, Alice; Timson, Georgina; Frater, John

    2017-10-20

    There is a global need for HIV viral load point-of-care (PoC) assays to monitor patients receiving antiretroviral therapy. UNICORN was the first study of an off-label protocol using whole blood finger-prick samples tested with and without a simple three minute spin using a clinic-room microcentrifuge. Two PoC assays were evaluated in 40 HIV-positive participants, 20 with detectable and 20 with undetectable plasma viral load (pVL) (<20 copies/ml). Using 100 µl finger-prick blood samples, the Cepheid Xpert HIV-1 Viral Load and HIV-1 Qual cartridges were compared with laboratory pVL assessment (TaqMan, Roche). For participants with undetectable viraemia by TaqMan, there was poor concordance without centrifugation with the TaqMan platform with only 40% 'undetectable' using Xpert VL and 25% 'not detected' using the Qual assay. After a 3 minute spin, 100% of samples were undetectable using either assay, showing full concordance with the TaqMan assay. Defining a lower limit of detection of 1000 copies/ml when including a spin, there was 100% concordance with the TaqMan platform with strong correlation (rho 0.95 and 0.94; p < 0.0001 for both assays). When including a simple microcentrifugation step, finger-prick PoC testing was a quick and accurate approach for assessing HIV viraemia, with excellent concordance with validated laboratory approaches.

  7. Short Communication: Testosterone Measured with an Automatic Immunoassay Compares Reasonbly Well to Results Obtained by LC-MS/MS

    DEFF Research Database (Denmark)

    Knudsen, Cindy Søndersø; Højskov, Carsten Schriver; Møller, Holger Jon

    2016-01-01

    Background: Previous studies have reported problems measuring testosterone with immunological assays. Here we explore an automatic second generation immunoassay compared to a LC-MS/MS method. Methods: We collected blood samples from 76 women and measured testosterone, progesterone, gender...... hormonebinding globulin (SHBG), and albumin employing Cobas e601/c501. Testosterone, androstenedione (andro), dehydroepiandrosterone sulphate (DHEAS), and 17-hydroxyprogesterone (17-OHP) concentrations were measured employing LC-MS/MS. We evaluated the difference between testosterone measured by the two methods...... and examined the potential interference from the selected steroids and bindings proteins. Results: Testosterone concentrations measured by the two methods yielded: Cobas e601 = 1.240 x (LC-MS/MS) - 0.197, r = 0.84, for testosterone concentrations between 0.22 - 4.9 nmol/L. A positive correlation was observed...

  8. PENGEMBANGAN MEDIA PEMBELAJARAN PENDIDIKAN JASMANI OLAHRAGA DAN KESEHATAN BERBASIS KOMPUTER UNTUK SMA

    Directory of Open Access Journals (Sweden)

    Suci Cahyati

    2014-04-01

    Full Text Available Penelitian ini bertujuan untuk menghasilkan produk berupa CD pembelajaran pendidikan jasmani olahraga dan kesehatan berbasis komputer untuk SMA yang valid dan efektif. Penelitian ini menggunakan metode Research and Development (R&D. Media yang dikembangkan memuat materi tentang HIV/AIDS. Pengembangan media pembelajaran ini menggunakan software Adobe Flash Cs3 Professional. Media yang telah dikembangkan melalui dua tahap penelitiannya itu validasi ahli dan uji coba lapangan. Berdasarkan validasi ahli dan uji coba lapangan hasil penelitian menunjukkan produk termasuk kriteria “Sangat baik” dengan rerata skor 4,25. Hasil tes siswa mengalami peningkatan dari rerata skor pretest 5,53 dan rerata skor posttest 7,56. Berdasarkan hasil tes tersebut dapat disimpulkan bahwa media pembelajaran pendidikan jasmani olahraga dan kesehatan efektif digunakan dalam pembelajaran di SMA. Kata kunci: Pengembangan media, penjasorkes, SMA

  9. Implementasi Algoritma Particle Swarm untuk Menyelesaikan Sistem Persamaan Nonlinear

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    Ardiana Rosita

    2012-09-01

    Full Text Available Penyelesaian sistem persamaan nonlinear merupakan salah satu permasalahan yang sulit pada komputasi numerik dan berbagai aplikasi teknik. Beberapa metode telah dikembangkan untuk menyelesaikan sistem persamaan ini dan metode Newton merupakan metode yang paling sering digunakan. Namun metode ini memerlukan perkiraan solusi awal dan memilih perkiraan solusi awal yang baik untuk sebagian besar sistem persamaan nonlinear tidaklah mudah. Pada makalah ini, algoritma Particle Swarm yang diusulkan oleh Jaberipour dan kawan-kawan[1] diimplementasikan. Algoritma ini merupakan pengembangan dari algoritma Particle Swarm Optimization (PSO. Algoritma ini meyelesaikan sistem persamaan nonlinear yang sebelumnya telah diubah menjadi permasalahan optimasi. Uji coba dilakukan terhadap beberapa fungsi dan sistem persamaan nonlinear untuk menguji kinerja dan efisiensi algoritma. Berdasarkan hasil uji coba, beberapa fungsi dan sistem persamaan nonlinear telah konvergen pada iterasi ke 10 sampai 20 dan terdapat fungsi yang konvergen pada iterasi ke 200. Selain itu, solusi yang dihasilkan algoritma Particle Swarm mendekati solusi eksak.

  10. Detection of EGFR mutations in plasma and biopsies from non-small cell lung cancer patients by allele-specific PCR assays

    DEFF Research Database (Denmark)

    Weber, Britta; Meldgaard, Peter; Hager, Henrik

    2014-01-01

    samples with allele-specific PCR assays. METHODS: Pairs of the diagnostic biopsy and plasma obtained just prior to start of erlotinib treatment were collected from 199 patients with adenocarcinoma of non-small-cell lung cancer. DNA from both sample types was isolated and examined for the presence...... of mutations in exons 18-21 of the EGFR gene, employing the cobas(®) EGFR Tissue Test and cobas(®) EGFR Blood Test (in development, Roche Molecular Systems, Inc., CA, USA). RESULTS: Test results were obtained in all 199 (100%) plasma samples and 196/199 (98%) of the biopsies. EGFR-activating mutations were...... identified in 24/199 (12%) plasma samples and 28/196 (14%) biopsy samples, and 17/196 (9%) matched pairs contained the same mutation. Six EGFR mutations were present only in plasma samples but not in the biopsy samples. The overall concordance of the EGFR gene mutations detected in plasma and biopsy tissue...

  11. Pemanfaatan Augmented Reality Pada Permainan Othello

    Directory of Open Access Journals (Sweden)

    Rendy Layman Aguston

    2016-11-01

    Full Text Available Perkembangan teknologi telah mengubah cara pengerjaan suatu pekerjaan dari cara konvensional menjadi cara yang lebih praktis. Dengan hadirnya teknologi Augmented Reality, cara bermain yang menggunakan pion dan membalikkan pion musuh secara manual menjadi lebih mudah dalam memainkan permainan selain juga dapat berinteraksi langsung. Pembuatan permainan Othello menggunakan program Unity dengan framework Vuforia untuk mewujudkan Augmented Reality pada permainan Othello. Untuk menerapkan Augmented Reality dengan baik, dibutuhkan papan permainan sebagai image target yang sesuai dengan kriteria, jenis kamera yang digunakan, jarak kamera terhadap papan permainan, intensitas cahaya yang ditangkap kamera, serta tingkat sensitivitas tombol virtual. Pada permainan Othello ini tersedia fitur komputer yang menggunakan algoritma Alpha Beta Pruning dengan 3 level kedalaman yang menggunakan perhitungan fungsi evaluasi berupa mobility, potential mobility dan penguasaan corner yang menghasilkan kemenangan mencapai 73,33% dari 15 kali uji coba terhadap aplikasi Othello serupa dan 78,34% dari 37 kali uji coba terhadap user.

  12. Concordance in BRAF V600E status over time in malignant melanoma and corresponding metastases

    DEFF Research Database (Denmark)

    Nielsen, Line Bjerrehave; Dabrosin, Nina; Sloth, Karen

    2017-01-01

    of inter-tumour heterogeneity between the primary tumour and the corresponding metastases, time as a factor was also investigated. METHODS: In total, 227 samples from 224 melanoma patients were analysed using both the Cobas® 4800 BRAF V600 Mutation test and IHC anti-BRAF V600E staining. In 82 primary......AIMS: The present study analysed the usability of an immunohistochemical (IHC) analysis compared to a frequently used mutation detection analysis and examined the extent of intra- and inter-tumour heterogeneity of BRAF V600E in primary tumours and their corresponding metastases. In the development...... tumours and 224 corresponding metastases, the extent of inter- and intra-tumour heterogeneity was investigated using IHC staining. RESULTS: In 15 cases, disagreement between IHC analysis and the Cobas test was seen. In all but one of the examined patients, homogeneity between the primary tumour...

  13. Pengembangan Modul Fisika Pokok Bahasan Hukum Newton bagi Anak Berkebutuhan Khusus (Tunanetra Di Kelas Inklusi SMA/MA Kelas X

    Directory of Open Access Journals (Sweden)

    Fitriany Yudistia R

    2014-04-01

    Full Text Available Siswa tunanetra SMA Muhammadiyah 4 Yogyakarta, MAN Maguwoharjo dan SMAN 1 Sewon belum memiliki sumber belajar mandiri berupa modul Braille khususnya pada materi Hukum Newton. Berdasarkan kenyataan ini maka dibutuhkan sebuah sumber belajar yang didesain khusus bagi siswa tunanetra di kelas Inklusi yakni modul Braille pada pokok bahasan Hukum Newton.Telah dilakukan penelitian yang bertujuan untuk: (1 mengembangkan modul fisika pokok bahasan Hukum Newton untuk siswa tunanetra SMA/MA kelas X sebagai sumber belajar mandiri, (2 mengetahui kualitas modul fisika Braille materi Hukum Newton untuk siswa tunanetra SMA/MA kelas X, (3 mengetahui respon siswa terhadap modul fisika Braille yang telah dikembangkan.Penelitian ini merupakan penelitian R & D dengan model prosedural yang mengadaptasi dari pengembangan perangkat model 4-D, yakni Define, Design, Develop, and Disseminate. Instrumen penelitian berupa angket kualitas modul yaitu menggunakan skala Likert yang dibuat dalam bentuk checklist. Instrumen untuk siswa berupa angket respon siswa yaitu menggunakan skala Guttman yang dibuat dalam bentuk checklist. Modul dinilai kualitasnya oleh 3 ahli materi, 1 ahli media, dan 2 guru fisika SMA/MA. Kelayakan modul berdasarkan respon siswa pada uji coba terbatas sebanyak 2 siswa dan uji coba luas sebanyak 8 siswa.Hasil penelitian berdasarkan penilaian dari ahli materi, ahli media dan guru fisika SMA/MA modul memiliki kategori sangat baik (SB. Persentase keidealan menurut ahli materi adalah 87,88%; persentase keidealan menurut ahli media adalah 90,00% dan persentase keidealan menurut guru Fisika SMA/MA adalah 75,00%. Respon siswa terhadap modul fisika Braille pada uji coba terbatas diperoleh persentase 97,22%; sedangkan pada uji coba luas diperoleh persentase 89,58%. Hasil penelitian ini menunjukkan bahwa modul layak dijadikan sebagai salah satu sumber belajar mandiri bagi siswa tunanetra.

  14. PENGEMBANGAN INSTRUMEN ASESMEN BERPIKIR KRITIS UNTUK SISWA SMP KELAS VII PADA MATERI INTERAKSI MAKHLUK HIDUP DENGAN LINGKUNGAN

    Directory of Open Access Journals (Sweden)

    Dharmawati Dharmawati

    2016-08-01

    Full Text Available This study aims to generate critical thinking assessment instrument for seven graders within organism interaction in an environment with an appropriate validity and reliability level. The design of this instrument is developed using stages suggested by Borg and Gall. The stages are researching and collecting information, planning, developing a preliminary product, conducting the limited examination, revising product from limited examination, field testing, revising product from field testing, and finalizing product. The result of content and construction validation shows that the level of feasibility is 88,35% and categorized as very feasible. While the degree of readability of assessment items is 93,51% and it is categorized as excellent. The coefficient of inter-rater reliability of assessment items is 0,951 and categorized as excellent. The instrument acquires reliability coefficient 0,792 for multiple choice and 0,753 for essay items. This study shows that the content, construction, and items in assessment are feasible. Penelitian ini bertujuan untuk menghasilkan instrumen asesmen berpikir kritis untuk siswa SMP kelas VII pada materi interaksi makhluk hidup dengan lingkungan dengan tingkat validitas dan reliabilitas yang memadai. Rancangan penelitian menggunakan model pengembangan menurut Borg & Gall, yang meliputi langkah-langkah: penelitian dan pengumpulan informasi, perencanaan, pengembangan produk awal, uji coba terbatas, revisi produk uji coba terbatas, uji coba lapangan, revisi uji coba produk lapangan, dan penyempurnaan produk akhir. Berdasarkan hasil validasi isi dan konstruk diperoleh tingkat kelayakan produk sebesar 88,35% berada pada kriteria sangat layak. Tingkat keterbacaan soal asesmen sebesar 93,51% dengan kategori sangat baik. Koefisien inter-rater reliability pada soal asesmen bentuk penugasan sebesar 0,951 dengan kategori sangat baik. Instrumen tersebut mempunyai koefisien reliabilitas sebesar 0,792 (soal pilihan ganda dan

  15. Evaluation of three methods for hemoglobin measurement in a blood donor setting

    Directory of Open Access Journals (Sweden)

    Jacob Rosenblit

    1999-05-01

    Full Text Available CONTEXT: The hemoglobin (Hb level is the most-used parameter for screening blood donors for the presence of anemia, one of the most-used methods for measuring Hb levels is based on photometric detection of cyanmetahemoglobin, as an alternative to this technology, HemoCue has developed a photometric method based on the determination of azide metahemoglobin. OBJECTIVE: To evaluate the performance of three methods for hemoglobin (Hb determination in a blood bank setting. DESIGN: Prospective study utilizing blood samples to compare methods for Hb determination. SETTING: Hemotherapy Service of the Hospital Israelita Albert Einstein, a private institution in the tertiary health care system. SAMPLE: Serial blood samples were collected from 259 individuals during the period from March to June 1996. MAIN MEASUREMENTS: Test performances and their comparisons were assessed by the analysis of coefficients of variation (CV, linear regression and mean differences. RESULTS: The CV for the three methods were: Coulter 0.68%, Cobas 0.82% and HemoCue 0.69%. There was no difference between the mean Hb determination for the three methods (p>0.05. The Coulter and Cobas methods showed the best agreement and the HemoCue method gave a lower Hb determination when compared to both the Coulter and Cobas methods. However, pairs of methods involving the HemoCue seem to have narrower limits of agreement (± 0.78 and ± 1.02 than the Coulter and Cobas combination (± 1.13. CONCLUSION: The three methods provide good agreement for hemoglobin determination.

  16. Pengembangan Instrumen Evaluasi Budi Pekerti Siswa SMU Negeri di Kabupaten Bantul

    Directory of Open Access Journals (Sweden)

    Esti Setiawati

    2014-07-01

    Full Text Available Penelitian ini bertujuan untuk mengembangkan instrumen evaluasi budi pekerti siswa SMU Negeri. Untuk itu perlu dirumuskan langkah-langkah pengembangan instrumen dan menyelidiki karakteristik instrumen tersebut. Subjek dalam penelitian ini adalah seluruh siswa SMU Negeri di Kabupaten Bantul. Penentuan banyaknya sampel dilakukan dengan teknik Purposive sampling sesuai dengan tujuan pengembangan. Instrumen penelitian ini adalah inventory Data dianalisis dengan analisis faktor. Hasil analisis data uji coba pengembangan Instrumen adalah: 1 Uji coba pertama dengan 85 butir, menunjukkan angka KMO and bartllets test sebesar 0,644 dengan p < 0,05. Setelah butir-butir tersebut dianalisis sejumlah, terdapat 11 butir yang tidak layak analisis yaitu butir 1, 2, 3, 5, 7, 8, 9, 10, 14, 32, dan butir 77 karena angka MSA < 0,5. Hasil pengujian ulang dengan 74 &117 butir menunjukkan angka KMO and Bartllets test sebesar 0,761 dengan p < 0,05, berarti mengalami kenaikan sebesar 0,117. Angka kumulatif muatan faktor sebesar 41,351 % dan nilai reliabilitas instrumen sebesar 0, 9656 2 Uji coba kedua dengan 85 butir hasil perbaikan instrumen uji coba pertama, menunjukkan angka KMO and Bartllets test sebesar 0,874 dengan p < 0,05. Setelah butir-butir tersebut dikenakan sejumlah pengujian, terdapat 1 butir yang tidak layak analisis yaitu butir 11 karena angka MSA < 0,5 hasil pengujian ulang dengan 84 butir menunjukkan angka KMO and Bartllets test sebesar 0,876 dengan P < 0,05, yang berarti mengalami kenaikan sebesar 0,002, sedangkan angka kumulatif muatan faktor sebesar 42,775% dan nilai reliabilitas Instrumen sebesar 0,9634. Hasil analisis data tersebut menunjukkan tingkat reliabilitas instrumen tergolong tinggi, namun validitas konstruk masih rendah. Kata kunci: pengembangan instrument, evaluasi budi pekerti.

  17. Hubungan Antara Persepsi Terhadap Beban Kerja Dengan Cyberloafing Pada Karyawan Biro Administrasi Umum Dan Keuangan Universitas Diponegoro

    OpenAIRE

    Ramadhan, Hafidz Ibnu; Nurtjahjanti, Harlina

    2017-01-01

    Penelitian ini bertujuan untuk mengetahui hubungan antara persepsi terhadap beban kerja dengan cyberloafing pada karyawan biro administrasi umum dan keuangan Universitas Diponegoro. Cyberloafing merupakan perilaku menggunakan berbagai jenis gadget, baik milik instansi ataupun milik pribadi dengan tujuan yang tidak berkaitan dengan pekerjaan yang dilakukan secara sadar oleh karyawan ditempat dan saat jam kerja. Penelitian ini memiliki sampel sebanyak 45 karyawan untuk uji coba skala dan 60 kar...

  18. PENGEMBANGAN MODEL PELATIHAN SOFT-SKILLS PADA SISWA SEKOLAH MENENGAH PERTAMA NEGERI (SMPN) DI KOTA MATARAM

    OpenAIRE

    Anik Darmiany

    2016-01-01

    Abstrak : Penelitian dan pengembangan ini bertujuan menghasilkan model pelatihan soft-skill khususnya keterampilan komunikasi dan kendali emosi siswa sekolah menengah pertama negeri (SMPN) di kota Mataram. Metode penelitian dan pengembangan dilakukan melalui tiga tahap dari sepuluh langkah Borg & Gall yaitu, (1) penelitian awal (analisis kebutuhan), (2) pengembangan model pelatihan, (3) uji coba dan evaluasi model. Hasil penelitian menunjukkan bahwa pengembangan model pelatihan soft-skill men...

  19. Benefit of Hepatitis C Virus Core Antigen Assay in Prediction of Therapeutic Response to Interferon and Ribavirin Combination Therapy

    OpenAIRE

    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) ...

  20. Usutu virus infections among blood donors, Austria, July and August 2017 - Raising awareness for diagnostic challenges.

    Science.gov (United States)

    Bakonyi, Tamás; Jungbauer, Christof; Aberle, Stephan W; Kolodziejek, Jolanta; Dimmel, Katharina; Stiasny, Karin; Allerberger, Franz; Nowotny, Norbert

    2017-10-01

    Between July and August 2017, seven of 12,047 blood donations from eastern Austria, reacted positive to West Nile virus (WNV) in the cobas test (Roche). Follow-up investigations revealed Usutu virus (USUV) nucleic acid in six of these. Retrospective analyses of four blood donors diagnosed as WNV-infected in 2016 showed one USUV positive. Blood transfusion services and public health authorities in USUV-endemic areas should be aware of a possible increase of human USUV infections.

  1. Optimized methods to measure acetoacetate, 3-hydroxybutyrate, glycerol, alanine, pyruvate, lactate and glucose in human blood using a centrifugal analyser with a fluorimetric attachment

    OpenAIRE

    Stappenbeck, R.; Hodson, A. W.; Skillen, A. W.; Agius, L.; Alberti, K. G. M. M.

    1990-01-01

    Optimized methods are described for the analysis of glucose, lactate, pyruvate, alanine, glycerol, D-3-hydroxybutyrate and acetoacetate in perchloric acid extracts of human blood using the Cobas Bio centrifugal analyser. Glucose and lactate are measured using the photometric mode and other metabolites using the fluorimetric mode. The intra-assay coefficients of variation ranged from 0.7 to 4.1%, except with very low levels of pyruvate and acetoacetate where the coefficients of variation were ...

  2. Automated 5 ' nuclease PCR assay for identification of Salmonella enterica

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey; Ahrens, Peter; Rådström, P.

    2000-01-01

    -point fluorescence (FAM) signals for the samples and positive control (TET) signals (relative sensitivity [Delta Rn], >0.6). The diagnostic specificity of the method was assessed using 120 non-Salmonella strains, which all resulted in negative FAM signals (Delta Rn, less than or equal to 0.5). All 100 rough...... Salmonella strains tested resulted in positive FAM and TET signals. In addition, it was found that the complete PCR mixture, predispensed in microwell plates, could be stored for up to 3 months at -20 degrees C, Thus, the diagnostic TaqMan assay developed can be a useful and simple alternative method......A simple and ready-to-go test based on a 5' nuclease (TaqMan) PCR technique was developed for identification of presumptive Salmonella enterica isolates. The results were compared with those of conventional methods. The TaqMan assay was evaluated for its ability to accurately detect 210 S. enterica...

  3. PENGEMBANGAN MULTIMEDIA PEMBELAJARAN PATISERI UNTUK SISWA TINGKAT XI SMK

    Directory of Open Access Journals (Sweden)

    Tri Sunarmi

    2015-02-01

    Full Text Available Penelitian ini bertujuan untuk: 1 mengembangkan multimedia pembelajaran patiseri pada standar kompetensi mengolah kue pastry kontinental untuk siswa tingkat XI SMK yang layak dari aspek pembelajaran, materi, dan media; 2 mengetahui keefektifan multimedia pembelajaran patiseri yang dikembangan terhadap penguasaan kompetensi belajar mengolah kue pastry kontinental dilihat dari peningkatan skor tes hasil belajar. Jenis penelitian ini adalah penelitian dan pengembangan. Subyek penelitian adalah 36 siswa, untuk uji coba kelompok kecil dan uji coba lapangan. Validasi produk dilakukan oleh ahli materi dan ahli media. Selanjutnya data dianalisis dengan teknik analisis deskriptif.Hasil penilaian ahli materi dan ahli media menunjukkan bahwa kualitas multimedia “baik”. Penilaian siswa pada uji coba lapangan mengenai kualitas multimedia dari aspek pembelajaran,aspek materi dan aspek media “sangat baik“, dengan rerata skor dari ketiga aspek 4,49. Hasil pretes menunjukkan rerata sebesar 63,15 sedangkan rerata pada posttes sebesar 89,07. N-gain sebesar 0,72 termasuk kategori “tinggi”. Kesimpulannya: multimedia pembelajaran patiseri hasil pengembangan layak dignakan untuk media pembelajaran dan efektif untuk meningkatkan hasil belajar siswa.

  4. Droplet digital PCR-based EGFR mutation detection with an internal quality control index to determine the quality of DNA.

    Science.gov (United States)

    Kim, Sung-Su; Choi, Hyun-Jeung; Kim, Jin Ju; Kim, M Sun; Lee, In-Seon; Byun, Bohyun; Jia, Lina; Oh, Myung Ryurl; Moon, Youngho; Park, Sarah; Choi, Joon-Seok; Chae, Seoung Wan; Nam, Byung-Ho; Kim, Jin-Soo; Kim, Jihun; Min, Byung Soh; Lee, Jae Seok; Won, Jae-Kyung; Cho, Soo Youn; Choi, Yoon-La; Shin, Young Kee

    2018-01-11

    In clinical translational research and molecular in vitro diagnostics, a major challenge in the detection of genetic mutations is overcoming artefactual results caused by the low-quality of formalin-fixed paraffin-embedded tissue (FFPET)-derived DNA (FFPET-DNA). Here, we propose the use of an 'internal quality control (iQC) index' as a criterion for judging the minimum quality of DNA for PCR-based analyses. In a pre-clinical study comparing the results from droplet digital PCR-based EGFR mutation test (ddEGFR test) and qPCR-based EGFR mutation test (cobas EGFR test), iQC index ≥ 0.5 (iQC copies ≥ 500, using 3.3 ng of FFPET-DNA [1,000 genome equivalents]) was established, indicating that more than half of the input DNA was amplifiable. Using this criterion, we conducted a retrospective comparative clinical study of the ddEGFR and cobas EGFR tests for the detection of EGFR mutations in non-small cell lung cancer (NSCLC) FFPET-DNA samples. Compared with the cobas EGFR test, the ddEGFR test exhibited superior analytical performance and equivalent or higher clinical performance. Furthermore, iQC index is a reliable indicator of the quality of FFPET-DNA and could be used to prevent incorrect diagnoses arising from low-quality samples.

  5. Pengembangan Program Macromedia Flash 8 untuk Pembelajaran Fisika di SMA

    Directory of Open Access Journals (Sweden)

    Wiji Susilowati

    2007-12-01

    Full Text Available Tujuan penelitian adalah membuat dan mengevaluasi media pembelajaran fisika SMA menggunakan program Macromedia Flash 8. Subjek coba pada penelitian ini berjumlah 40 orang yang terdiri dari 10 siswa untuk uji coba instrumen penelitian, 10 siswa untuk ujicoba kelompok kecdl, dan 20 siswa untuk uji coba lapangan. Pengumpulan data dilakukan dengan mengguna­kan kuesioner dan tes fisika (pre-test dan post-test. Evaluasi terhadap program ditinjau dari aspek pembelajaran dan aspek media. Kritik dan saran digunakan untuk memperbaiki program. Hasil penelitian menunjukkan bahwa program Macromedia Flash 8 untuk pembelajaran fisika di SMA: (1 dirancang sesuai dengan prinsip-prinsip desain pembelajaran, (2 terbukti mampu menaikkan skor rerata tes fisika siswa sebesar 55,42%, (3 memiliki efisiensi waktu yang tinggi, (4 ditinjau dari aspek media Hinilai cukup bagus/menarik (dinilai/dikategorikan sedang oleh siswa, (5 ditinjau dari aspek pembelajaran secara keseluruhan program ini dinilai tinggi/jelas dimengerti oleh siswa, (6 ditinjau dari aspek media dinilai menarik (bagus/kategori tinggi oleh guru fisika, dan (7 ditinjau dari aspek pembelajaran juga dinilai menarik (bagus/kategori tinggi oleh guru fisika. Kata kunci: media pembelajaran fisika diSMA.

  6. Validation of a new HPV self-sampling device for cervical cancer screening: The Cervical and Self-Sample In Screening (CASSIS) study.

    Science.gov (United States)

    El-Zein, Mariam; Bouten, Sheila; Louvanto, Karolina; Gilbert, Lucy; Gotlieb, Walter; Hemmings, Robert; Behr, Marcel A; Franco, Eduardo L; Liang, Victoria; Martins, Claudia; Duarte, Silvy; Sarban, Natalia; Geddes, Patricia; Massa, Ana; Samios, Kathrin; Aboufadl, Siham; Verdon, Sophie; Pereria, Cynthia; Lacroix, Isabelle

    2018-04-17

    We compared the self-sampling performance of the newly designed HerSwab™ device with a physician-collected cervical sample and another self-sample using the cobas® PCR Female swab for the detection of cervical intraepithelial neoplasia (CIN) and cancer. Women referred for colposcopy at McGill University affiliated hospital clinics collected two consecutive self-samples, one with HerSwab™ and one with cobas® swab, after receiving instructions. The order of sampling was randomized. The colposcopist then collected a cervical sample and conducted a colposcopic examination. Samples were tested for human papillomavirus (HPV) DNA. Sensitivity and specificity to detect CIN2+ and respective 95% confidence intervals (CI) were calculated to compare sampling approaches. The HPV testing agreement between samples was measured using the Kappa statistic. Of 1217 women enrolled, 1076 had complete results for HPV and cytology; 148 (13.8%) had CIN1, 147 (13.7%) had CIN2/3, and 5 (0.5%) had cancer. There was very good agreement between methods for HPV detection (HerSwab™ versus physician: kappa=0.84; cobas® swabs versus physician: kappa=0.81; HerSwab™ versus cobas® swabs: kappa=0.87). The sensitivity of HPV detection for CIN2+ was 87.6% (95%CI: 79.8-93.2) with self-sampling using HerSwab™, 88.6% (95%CI: 80.9-94.0) with self-sampling using the cobas® swab, and 92.4% (95%CI: 85.5-96.7) with physician sampling. Corresponding estimates of specificity were 58.1% (95%CI: 54.1-62.1), 55.0% (95%CI: 50.9-59.0) and 58.7% (95%CI: 54.6-62.6). Cytology (ASC-US or more severe) done on the physician-collected specimen was 80.2% (95%CI: 70.8-87.6) sensitive and 61.4% (95%CI: 57.2-65.5) specific for CIN2+. The HerSwab™ had good agreement with physician sampling in detecting HPV, and adequate performance in detecting high-grade lesions among women referred to colposcopy for abnormal cytology. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. PENGEMBANGAN SSP TEMATIK INTEGRATIF UNTUK MEMBANGUN KARAKTER KEJUJURAN DAN KEPEDULIAN SISWA SD KELAS II

    Directory of Open Access Journals (Sweden)

    Sri Hariyati Qodriyah

    2015-07-01

    Full Text Available Penelitian ini bertujuan untuk menghasilkan perangkat pembelajaran berupa SSP Tematik yang dapat mengembangkan karakter siswa kelas 2 sekolah dasar, meliputi karakter kejujuran dan kepedulian. Penelitian ini merupakan penelitian dan pengembangan yang terdiri dari tujuh tahap, yaitu studi pendahuluan, perencanaan, mengembangkan produk awal, uji coba awal, revisi produk utama, uji coba lapangan, dan revisi terhadap produk operasional. SSP yang dikembangkan dievaluasi oleh seorang ahli materi dan media untuk mengetahui validitasnya. Subjek uji coba berjumlah 90 siswa terdiri dari 23 siswa SD Sonosewu, Kasihan, Bantul, DIY sebagai subjek uji coba terbatas dan 33 siswa untuk kelas control dan 34 siswa untuk kelas eksperimen SD 1 Kadipiro, Kasihan, Bantul, DIY. Hasil penelitian ini berupa SSP yang meliputi: silabus, RPP, LKS, dan lembar penilaian. Hasil evaluasi dari ahli materi dan ahli media untuk menguji tingkat kevalidan SSP menyatakan bahwa SSP yang dikembangkan adalah valid dan berkategori “baik”. Hasil uji coba menunjukkan bahwa SSP yang dikembangkan dinyatakan layak serta memenuhi kriteria praktis dan efektif dalam mengembangkan karakter siswa. Pembelajaran dengan SSP yang dikembangkan mampu mengembangkan karakter kejujuran dan kepedulian. Kata Kunci: SSP, karakter jujur dan peduli   DEVELOPING THEMATIC INTEGRATIVE SSP FOR BUILDING THE CHARACTERS OF HONESTY AND CARE GRADE II STUDENT OF ELEMENTARY SCHOOL Abstract This study aims to produce integrated learning sets in the form of thematic SSP that can develop the characters of honesty and care of grade II students of elementary school. This was a research and development study consisting of seven steps, i.e. preliminary study, planning, preliminary product development, preliminary tryout, main product revision, field tryout, revision of operational product, operational product revision, and revision of the final product. The developed SSP was evaluated by a science subject expert to assess

  8. Comparison of Gene Expression in Human Embryonic Stem Cells, hESC-Derived Mesenchymal Stem Cells and Human Mesenchymal Stem Cells

    OpenAIRE

    Romain Barbet; Isabelle Peiffer; Antoinette Hatzfeld; Pierre Charbord; Jacques A. Hatzfeld

    2011-01-01

    We present a strategy to identify developmental/differentiation and plasma membrane marker genes of the most primitive human Mesenchymal Stem Cells (hMSCs). Using sensitive and quantitative TaqMan Low Density Arrays (TLDA) methodology, we compared the expression of 381 genes in human Embryonic Stem Cells (hESCs), hESC-derived MSCs ...

  9. Improved real-time PCR assay for detection of the quarantine potato pathogen, Synchytrium endobioticum, in zonal centrifuge extracts from soil and in plants

    NARCIS (Netherlands)

    Gent-Pelzer, van M.P.E.; Krijger, M.C.; Bonants, P.J.M.

    2010-01-01

    Real-time PCR was used for quantitative detection of the potato pathogen, Synchytrium endobioticum, in different substrates: zonal centrifuge extracts, warts and different plant parts of potato. Specific primers and a TaqMan probe, designed from the internal transcribed spacer region of the

  10. Evaluation of 5 ' nuclease assay for detection of Actinobacillus pleuropneumoniae

    DEFF Research Database (Denmark)

    Angen, Øystein; Jensen, J.; Lavritsen, D. T.

    2001-01-01

    Sequence detection by the 5' nuclease TaqMan assay uses online detection of internal fluorogenic probes in closed PCR tubes. Primers and probe were chosen from a part of the omlA gene common to all serotypes of Actinobacillus pleuropneumoniae, which gave an amplicon of 92 bp, The test was evaluat...

  11. Effects of the EVCAM chemical validation library on differentiation using marker gene expression in lmouse embryonic stem cells

    Science.gov (United States)

    The adherent cell differentiation and cytotoxicity (ACDC) assay was used to profile the effects of the ECVAM EST validation chemical library (19 compounds) on J1 mouse embryonic stem cells (mESC). PCR-based TaqMan Low Density Arrays (TLDA) provided a high-content assessment of al...

  12. Development of a non invasion real-time PCR assay for the quantitation of chicken parvovirus in fecal swabs

    Science.gov (United States)

    The present study describes the development of a real time Taqman polymerase chain reaction (PCR) assay using a fluorescent labeled probe for the detection and quantitation of chicken parvovirus (ChPV) in feces. The primers and probes were designed based on the nucleotide sequence of the non struct...

  13. Quantitative detection of Fusarium spp. and its correlation with fumonisin content in maize from South African subsistence farmers

    NARCIS (Netherlands)

    Waalwijk, C.; Koch, S.H.; Ncube, E.; Allwood, J.; Flett, B.; Vries, de P.M.; Kema, G.H.J.

    2008-01-01

    A quantitative detection tool was developed to enable the monitoring of fumonisin-producing fungi in food and feed commodities. To this end, a quantitative PCR (TaqMan) was developed that targets a conserved region in the polyketide synthase gene fum1, which is involved in the biosynthesis of

  14. Lack of association between PKLR rs3020781 and NOS1AP rs7538490 and type 2 diabetes, overweight, obesity and related metabolic phenotypes in a Danish large-scale study: case-control studies and analyses of quantitative traits

    DEFF Research Database (Denmark)

    Andreasen, Camilla Helene; Mogensen, Mette S.; Borch-Johnsen, Knut

    2008-01-01

    of the variants in relation to overweight and obesity. METHODS: PKLR rs3020781 and NOS1AP rs7538490 were genotyped, using TaqMan allelic discrimination, in a combined study sample comprising a total of 16,801 and 16,913 individuals, respectively. The participants were ascertained from four different study groups...

  15. Clinical Value of Treponema pallidum Real-Time PCR for Diagnosis of Syphilis

    NARCIS (Netherlands)

    Heymans, R.; van der Helm, J. J.; de Vries, H. J. C.; Fennema, H. S. A.; Coutinho, R. A.; Bruisten, S. M.

    2010-01-01

    The diagnosis of syphilis can be complicated when it is based on diverse clinical manifestations, dark-field microscopy, and serology. In the present study, therefore, we examined the additional clinical value of a Treponema pallidum real-time TaqMan PCR for the detection of primary and secondary

  16. Specific and sensitive diagnosis of syphilis using a real-time PCR for Treponema pallidum

    NARCIS (Netherlands)

    Koek, A. G.; Bruisten, S. M.; Dierdorp, M.; van Dam, A. P.; Templeton, K.

    2006-01-01

    A real-time PCR assay with a Taqman probe was developed that targeted the polA gene of Treponema pallidum. The test was validated using an analytical panel (n = 140) and a clinical panel of genital samples (n = 112) from patients attending a sexually transmitted infections clinic. High sensitivities

  17. Multiplex real-time PCR assays for the identification of the potato cyst and tobacco cyst nematodes

    Science.gov (United States)

    TaqMan primer-probe sets were developed for the detection and identification of potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis using two-tube, multiplex real-time PCR. One tube contained a primer-probe set specific for G. pallida (pale cyst nematode) multiplexed with another prim...

  18. Report for Detection of Biothreat Agents and Environmental Samples using the LLNL Virulence Array for DHS

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, Crystal [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gardner, Shea [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McLoughlin, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thissen, James [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Jackson, Paul [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2011-04-18

    The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. This report focuses on the design, testing and results of samples on the Virulence Array.

  19. Protamine 3 expressions in crossbred bull spermatozoa may not be ...

    African Journals Online (AJOL)

    The mRNA expression of PRM3 gene among two groups was evaluated by real time quantitative polymerase chain reaction (PCR) using TaqMan chemistry, where peptidylprolyl isomerase A (PPIA) was used as an internal control. Our finding revealed that expression of PRM3 was down regulated in poor quality semen ...

  20. EVALUATION OF A RAPID, QUANTITATIVE REAL-TIME PCR METHOD FOR ENUMERATION OF PATHOGENIC CANDIDA CELLS IN WATER

    Science.gov (United States)

    Quantitative Real-Time PCR (QRT-PCR) technology, incorporating fluorigenic 5' nuclease (TaqMan?) chemistry, was developed for the specific detection and quantification of six pathogenic species of Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, C. glabrata and C....

  1. Analysis of two susceptibility SNPs in HLA region and evidence of ...

    Indian Academy of Sciences (India)

    Yosser Achour

    2017-11-28

    Nov 28, 2017 ... was carried out using real-time PCR methods by TaqMan allelic discrimination assay. A trend of significant ... genetic risk loci with relatively high statistical power from. GWAS was .... for the Social Sciences (SPSS) ver. 17.0 for ...

  2. Pharmacogenetics of clopidogrel: comparison between a standard and a rapid genetic testing.

    Science.gov (United States)

    Saracini, Claudia; Vestrini, Anna; Galora, Silvia; Armillis, Alessandra; Abbate, Rosanna; Giusti, Betti

    2012-06-01

    CYP2C19 variant alleles are independent predictors of clopidogrel response variability and occurrence of major adverse cardiovascular events in high-risk vascular patients on clopidogrel therapy. Increasing evidence suggests a combination of platelet function testing with CYP2C19 genetic testing may be more effective in identifying high-risk individuals for alternative antiplatelet therapeutic strategies. A crucial point in evaluating the use of these polymorphisms in clinical practice, besides test accuracy, is the cost of the genetic test and rapid availability of the results. One hundred acute coronary syndrome patients were genotyped for CYP2C19*2,*3,*4,*5, and *17 polymorphisms with two platforms: Verigene(®) and the TaqMan(®) system. Genotyping results obtained by the classical TaqMan approach and the rapid Verigene approach showed a 100% concordance for all the five polymorphisms investigated. The Verigene system had shorter turnaround time with respect to TaqMan. The cost of reagents for TaqMan genotyping was lower than that for the Verigene system, but the effective manual staff involvement and the relative cost resulted in higher cost for TaqMan than for Verigene. The Verigene system demonstrated good performance in terms of turnaround time and cost for the evaluation of the clopidogrel poor metabolizer status, giving genetic information in suitable time (206 min) for a therapeutic strategy decision.

  3. Diagnostic Assay for Rickettsia japonica

    Science.gov (United States)

    Hanaoka, Nozomu; Matsutani, Minenosuke; Kawabata, Hiroki; Yamamoto, Seigo; Fujita, Hiromi; Sakata, Akiko; Azuma, Yoshinao; Ogawa, Motohiko; Takano, Ai; Watanabe, Haruo; Kishimoto, Toshio; Shirai, Mutsunori; Kurane, Ichiro

    2009-01-01

    We developed a specific and rapid detection system for Rickettsia japonica and R. heilongjiangensis, the causative agents of spotted fever, using a TaqMan minor groove binder probe for a particular open reading frame (ORF) identified by the R. japonica genome project. The target ORF was present only in R. japonica–related strains. PMID:19961684

  4. Development and Validation of a Novel Real-time Assay for the Detection and Quantification of Vibrio cholerae

    DEFF Research Database (Denmark)

    Rashid, Ridwan Bin; Ferdous, Jannataul; Tulsiani, Suhella

    2017-01-01

    is rapid since neither lengthy incubation period nor electrophoresis is required. The assay had excellent repeatability (CV%: 0.24–1.32) and remarkable reproducibility (CV%: 1.08–3.7). Amplification efficiencies in the 89–100% range were observed. The assay is more economical than Taqman-based multiplex...

  5. Effect of methotrexate combined with ginger, silymarin or propolis on ...

    African Journals Online (AJOL)

    The present study was performed to evaluate the effect of three natural antioxidants on the adverse effect of methotrexate (MTX) in normal liver cells. TaqMan RT-PCR technology was used to estimate the mRNA expression levels for three genes after rats injection with a single dose of 20 mg/kg b.w MTX or the same MTX ...

  6. Detectie van Meloidogyne spp. in grondmonsters - een vergelijking van twee technieken

    NARCIS (Netherlands)

    Veenhuizen, P.T.M.; Schoemakers, N.; Vos, J.; Versteegen, F.; Landeweert, R.; Karssen, G.

    2007-01-01

    Hier volgen de samenvattingen van de bijeenkomst van 20 maart 2007 van de KNPV-werkgroep Meloidogyne. 1) Kwantitatieve multiplexdetectie van aaltjes; 2). Meloidogyne chitwoodi en M. fallax: vergelijking visuele beoordeling en Taqman-PCR aan pootaardappelen; 3) Detectie van Meloidogyne spp. in

  7. Diagnostic PCR: Comparative sensitivity of four probe chemistries

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Löfström, Charlotta; Sommer, Helle Mølgaard

    2009-01-01

    Three probe chemistries: locked nucleic acid (LNA), minor groove binder (MGB) and Scorpion were compared with a TaqMan probe in a validated real-time PCR assay for detection of food-borne thermotolerant Campylobacter. The LNA probe produced significantly lower Ct-values and a higher proportion of...

  8. A New Diagnostic system for Ultra Sensitive and Specific Detection and Quantitation of “Candidatus Liberibacter asiaticus”, the Bacterium Associated with Citrus Huanglongbing

    Science.gov (United States)

    In this study, an ultra sensitive and quantitative diagnostic system for “Candidatus Liberibacter asiaticus” was developed. This system adapts a nested PCR and Taq-Man PCR in a single closed tube. The procedure involves two steps of PCR using the species specific outer and inner primer pairs. Differ...

  9. Comparison of Gull Feces-specific Assays Targeting the 16S rRNA Gene of Catellicoccus Marimammalium and Streptococcus spp.

    Science.gov (United States)

    Two novel gull-specific qPCR assays were developed using 16S rRNA gene sequences from gull fecal clone libraries: a SYBR-green-based assay targeting Streptococcus spp. (i.e., gull3) and a TaqMan qPCR assay targeting Catellicoccus marimammalium (i.e., gull4). The main objectives ...

  10. Determination of the species specificity of the primers for the detection of chicken and turkey meat by realtime PCR method

    Directory of Open Access Journals (Sweden)

    Lenka Maršálková

    2014-07-01

    Full Text Available The aim of this work was to use TaqMan Real-Time PCR for quantitative authentication of chicken and turkey meat. To meet this purpose, a specific pair of primers and TaqMan probe was used. The test was aimed at identifying the reaction cycle of turkey and chicken meat using by two sets of primers. With first set of primer designed for chicken we obtained the following results: Cp = 16.18 for 100% chicken DNA Cp = 29, 18 100% turkey DNA It was also amplified DNA of pig that exceeded the detection threshold fluorescence intensities in the 31.07 cycle (Cp = 31.07. Using primers designed for turkey we obtained the following results Cp = 31.16 for 100% CHDNA, Cp =16.18 100% TDNA. It was also amplified the 100% DNA of rabbit in 31.63 cycle (Cp = 31.63 and deer in cycle 32 (Cp = 32. The DNA of all other animal species was amplificated after more than 35 cycles (Cp >35. It follows that the second detection primer pair is specific enough to unrelated species of animals by 30 cycles of the reaction. Species authentication based on DNA analysis from this perspective overcomes all the shortcomings of proteins. At present, DNA analysis use different types of PCR. Is the most progressive Real-time PCR, which is suitable for the specific use of detection (primers and TaqMan probe. The TaqMan Real-time PCR is within the sensitivity and specificity, clearly one of the best methods for identifying the species of chicken and turkey meat. The specificity of this method, however, depends primarily on the specificity of the primers and TaqMan probe. The 30 cycle reaction was chosen by us as the threshold for specificity using primers for authentication chicken and turkey meat.

  11. MODEL PERMAINAN AKTIVITAS LUAR KELAS UNTUK MENGEMBANGKAN RANAH KOGNITIF, AFEKTIF, DAN PSIKOMOTORIK SISWA SMA

    Directory of Open Access Journals (Sweden)

    Hendra Setyawan

    2015-10-01

    Full Text Available Penelitian ini bertujuan menghasilkan model-model permainan Aktivitas Luar kelas (ALK yang layak digunakan sebagai materi pembelajaran penjas, serta efektif untuk mengembangkan ranah kognitif, afektif, dan psikomotorik siswa SMA. Penelitian ini dilakukan dengan langkah-langkah sebagai berikut: (1 pengumpulan informasi di lapangan, (2 menganalisis informasi yang telah dikumpulkan, (3 mengembangkan produk awal, (4 validasi ahli dan revisi, (5 uji coba skala kecil dan  revisi, (6 uji coba skala besar dan revisi, dan (7 pembuatan produk final. Uji coba skala kecil dilakukan terhadap siswa kelas X-D dan XI-IPA 4 dari SMA N I Prambanan berjumlah 66 orang. Uji coba skala besar dilakukan terhadap siswa kelas X-G, X-H, XI-IPS 3, dan XI-BHS dari SMA N I Prambanan berjumlah 132 orang. Instrumen pengumpulan data yang digunakan yaitu; (1 pedoman wawancara, (2 skala nilai, (3 pedoman observasi permainan, (4 pedoman observasi keefektifan permainan, (5 pedoman observasi terhadap guru pelaku uji coba, dan (6 rubrik penilaian siswa. Teknik analisis data dengan analisis deskriptif kuantitatif dan kualitatif. Hasil penelitian berupa tujuh model permainan yang layak dan efektif digunakan dalam pembelajaran penjas, hal ini dibuktikan dengan perolehan persentase sebesar 100% dari data hasil kuesioner skala nilai, observasi model permainan, observasi keefektifan permainan, dan observasi guru pelaku uji coba. Model permainan juga efektif untuk mengembangkan ranah kognitif, afektif, dan psikomotorik, yang dibuktikan dengan terjadinya peningkatan persentase nilai rata-rata siswa sebesar 21%. Kata kunci: model, permainan, aktivitas luar kelas, kognitif, afektif, psikomotorik THE OUTDOOR ACTIVITY GAME MODEL TO DEVELOP THE ASPECT OF COGNITIVE, AFFECTIVE, AND PSYCHOMOTOR OF THE SENIOR HIGH SCHOOL STUDENTS Abstract This study aims at producing outdoor activity game models which are proper to be used for physicall education learning and developing cognitive, affective, and

  12. PENGEMBANGAN MODEL PEMBELAJARAN MALCOLM’S MODELING UNTUK MENINGKATKAN KETERAMPILAN BERPIKIR KRITIS DAN MOTIVASI BELAJAR SISWA

    Directory of Open Access Journals (Sweden)

    Syarifah Syarifah

    2015-10-01

    Full Text Available Penelitian ini bertujuan untuk: (1 menghasilkan model pembelajaran fisika berbasis Malcom’s Modeling Method yang layak digunakan di sekolah, dan (2 mengetahui apakah model pembelajaran fisika berbasis Malcom’s Modeling Method dapat meningkatkan keterampilan berpikir kritis dan motivasi belajar siswa. Penelitian ini termasuk dalam ranah penelitian dan pengembangan (R&D. Prosedur pengembangan mengadaptasi dari prosedur pengembangan yang dikembangkan oleh Borg & Gall dengan langkah-langkah meliputi (1 penelitian dan pengumpulan data, (2 perencanaan, (3 pengembangan bentuk awal produk, (4 uji coba lapangan awal, (5 revisi hasil uji coba lapangan awal, (6 uji coba lapangan, (7 revisi hasil uji coba lapangan dan (8 diseminasi. Subjek uji coba lapangan awal terdiri atas 36 siswa kelas X MIA 6 di SMA N 7 Yogyakarta. Subjek uji coba lapangan pada kelas ekperimen terdiri atas 36 orang siswa kelas X MIA 1 dan pada kelas kontrol terdiri atas 34 orang siswa kelas X MIA 5 di SMA N 7 Yogyakarta. Instrumen pengumpulan data menggunakan soal untuk mengukur keterampilan berpikir kritis, angket untuk mengukur motivasi belajar, angket respon siswa dan lembar observasi keterlaksanaan pembelajaran. Teknik analisis data menggunakan uji MANOVA dengan taraf signifikansi 5%. Hasil penelitian menunjukkan bahwa model Malcom’s Modeling Method ditinjau dari sintaks, sistem sosial, prinsip reaksi, sistem pendukung dan dampak instruksional dan pengiring layak digunakan di sekolah dengan kategori sangat baik. Hasil uji MANOVA menunjukkan model Malcom’s Modeling Method dapat meningkatkan keterampilan berpikir kritis dan motivasi belajar siswa pada taraf signifikansi 5 %. Kata Kunci: Malcom’s Modeling Method, keterampilan berpikir kritis, motivasi belajar.   DEVELOPING A PHYSICS INSTRUCTION MODEL BASED ON MALCOLM’S MODELING TO IMPROVE CRITICAL THINKING SKILLS AND LEARNING MOTIVATION Abstract This research aims to (1 develop a physics instruction model based on

  13. Usefulness of nucleic acid testing to reduce risk of hepatitis B virus transfusion-transmitted infection in Argentina: high rate of recent infections.

    Science.gov (United States)

    Blanco, Sebastián; Balangero, Marcos César; Valle, Mildre Cledy; Montini, Oscar Luis; Carrizo, Luis Horacio; Gallego, Sandra Verónica

    2017-03-01

    Results from 10-year experience using nucleic acid test (NAT) screening in a blood bank of Córdoba are presented, showing the first data on prevalence of recent hepatitis B virus (HBV) infections and occult HBV infections (OBIs) in Argentina. Molecular screening was performed by COBAS AmpliScreen human immunodeficiency virus Type 1 (HIV-1) test Version 1.5 and COBAS AmpliScreen hepatitis C virus (HCV) test Version 2.0 and COBAS TaqScreen MPX and MPX Version 2.0 test (Roche Molecular Systems). To characterize OBI, additional molecular and serologic assays were performed. As results of NAT, 0.075% of the donors (155/205,388) tested positive for HIV, 0.05% (106/205,388) for HCV, and 0.045% (76/168,215) for HBV. Donors who tested positive for HIV or HCV by NAT were also positive by serology. There was one of 33,643 donors recently infected with HBV. At time of donation, six of 76 (7.9%) donors with confirmed HBV infection presented virologic and serologic profiles consistent with OBI. By additional studies three were OBI, two were window period infections, and one remained unclassified. NAT contributed significantly to the reduction of the potential risk of HBV transmission with a frequency of one in 56,072, detecting three in 168,215 donors without serologic evidence of infection. NAT also detected three in 168,215 OBIs. The finding of high frequency of recent infections (1/33,643), unexpected for this country, highlights the need of promoting unified effective regulations that enforce the use of NAT in all blood banks in Argentina and points out the importance of assessing the risk of HBV transmission in blood banks of other countries considered to be low-endemic. © 2016 AABB.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  15. PERANGKAT LUNAK UNTUK EKTRAKSI ISI DOKUMEN MULTIFORMAT DENGAN MENGGUNAKAN SMS DAN FAXIMILE

    Directory of Open Access Journals (Sweden)

    Ahmad Hoirul Basori

    2005-01-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Dokumen multiformat merupakan salah satu bentuk file yang disimpan dalam komputer  dan  banyak digunakan oleh  masyarakat saat ini.Setiap dokumen mempunyai karakteristik berbeda  dan memerlukan software yang berbeda untuk setiap file dokumen. Sedangkan perkembangan handphone yang semakin pesat membuat masyarakat lebih familiar menggunakan handphone daripada menggunakan komputer.proses pengambilan dokumen dapat terhambat jika user yang memerlukan dokumen multiformat tidak mempunyai keahlian komputer. Pada pengerjaan penelitian ini, teknologi yang digunakan untuk pengambilan dokumen multiformat adalah teknologi SMS dan mesin Faximile.sedangkan untuk pemodelan sistemnya teknologi yang digunakan adalah Unified Modelling Language dengan Rational Rose Enterprise 2000, serta  database Microsoft Access untuk penyimpanan data SMS. Untuk membangun aplikasi teknologi yang digunakan adalah Microsoft Visual Basic 6.0. Hal ini disebabkan dokumen multiformat pada penelitian ini kebanyakan merupakan produksi Microsoft sehingga antara teknologi yang digunakan dan dokumen multiformat saling mempunyai kesesuaian.   Uji coba dilakukan dengan cara melakukan pengiriman dokumen multiformat melalui SMS dan mengeluarkan outputnya ke dalam mesin faximile. Uji coba ini mencakup proses pembacaan data SMS, penyimpanan data SMS ke dalam database, pengiriman dokumen ke mesin fax, download page online, serta penambahan hak akses user melalui SMS. Hasil uji coba menunjukkan adanya permasalahan pada pengiriman dokumen multiformat yang berada dalam keadaan terproteksi. Permasalahan ini dapat diselesaikan dengan menghilangkan password yang ada pada dokumen multiformat.   Kata Kunci: SMS (Short Message Service, Ektraksi Dokumen, Mesin Fax.

  16. First Zika-positive donations in the continental United States.

    Science.gov (United States)

    Galel, Susan A; Williamson, Phillip C; Busch, Michael P; Stanek, Danielle; Bakkour, Sonia; Stone, Mars; Lu, Kai; Jones, Scott; Rossmann, Susan N; Pate, Lisa Lee

    2017-03-01

    Zika virus (ZIKV) has spread in the Americas, including parts of the southern United States, and infection can be associated with serious complications, including congenital brain abnormalities. Probable transfusion transmission of ZIKV has been documented in Brazil. Preemptive testing of blood donations for ZIKV RNA was implemented in southern US states at risk of local transmission using a test approved under a Food and Drug Administration (FDA) investigational new drug application, cobas Zika. Screening was expanded after issuance of an updated FDA guidance. Donations reactive on initial screening were further tested by nucleic acid and antibody tests to determine the donor status. Of 358,786 donations from US states screened by individual donation testing, 23 were initially reactive on cobas Zika. Fourteen of these represented probable ZIKV infection based on reactivity on additional nucleic acid testing or anti-Zika immunoglobulin M. Ten of the 14 donors reported travel to an identified ZIKV-active area within 90 days before donation (median time from end of travel to donation, 25 days; range, 6-71 days). Three donors with travel history also had a potential sexual exposure. Only seven of the 14 donations with probable ZIKV infection were detectable upon 1:6 dilution to simulate minipool testing. The estimated specificity of the cobas Zika test was 99.997%. Screening of donations for ZIKV RNA can interdict ZIKV-infected donors. Donor risk factors include travel more than 4 weeks before donation and sexual exposure. Minipool screening would have detected only 50% of the RNA-positive donations. © 2017 The Authors Transfusion published by Wiley Periodicals, Inc. on behalf of AABB.

  17. Evaluation of the Correlation Coefficient of Polyethylene Glycol Treated and Direct Prolactin Results and Comparability with Different Assay System Results.

    Science.gov (United States)

    Pal, Shyamali

    2017-12-01

    The presence of Macro prolactin is a significant cause of elevated prolactin resulting in misdiagnosis in all automated systems. Poly ethylene glycol (PEG) pretreatment is the preventive process but such process includes the probability of loss of a fraction of bioactive prolactin. Surprisingly, PEG treated EQAS & IQAS samples in Cobas e 411 are found out to be correlating with direct results of at least 3 immunoassay systems and treated and untreated Cobas e 411 results are comparable by a correlation coefficient. Comparison of EQAS, IQAS and patient samples were done to find out the trueness of such correlation factor. Study with patient's results have established the correlation coefficient is valid for very small concentration of prolactin also. EQAS, IQAS and 150 patient samples were treated with PEG and prolactin results of treated and untreated samples obtained from Roche Cobas e 411. 25 patient's results (treated) were compared with direct results in Advia Centaur, Architect I & Access2 systems. Correlation coefficient was obtained from trend line of the treated and untreated results. Two tailed p-value obtained from regression coefficient(r) and sample size. The correlation coefficient is in the range (0.761-0.771). Reverse correlation range is (1.289-1.301). r value of two sets of calculated results were 0.995. Two tailed p- value is zero approving dismissal of null hypothesis. The z-score of EQAS does not always assure authenticity of resultsPEG precipitation is correlated by the factor 0.761 even in very small concentrationsAbbreviationsGFCgel filtration chromatographyPEGpolyethylene glycolEQASexternal quality assurance systemM-PRLmacro prolactinPRLprolactinECLIAelectro-chemiluminescence immunoassayCLIAclinical laboratory improvement amendmentsIQASinternal quality assurance systemrregression coefficient.

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

    Science.gov (United States)

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

    2015-11-04

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

  19. PENGEMBANGAN MULTIMEDIAPEMBELAJARAN BAHASA JERMAN PELAJARAN PELAYANAN RESTORAN DI YOTABAKTI YOGYAKARTA

    Directory of Open Access Journals (Sweden)

    Melly Handayani

    2015-10-01

    Full Text Available Tujuan penelitian dan pengembangan ini adalah (1 mengembangkan multimedia yang berisi materi dan latihan untuk keterampilan berbicara bahasa Jerman, (2 mendeskripsikan proses pengem-bangannya, dan (3 mendeskripsikan hasil evaluasi dan hasil uji coba lapangan. Uji coba terbatas dilakukan pada satu orang pengajar dan empat orang peserta didik. Uji coba lapangan melibatkan 2 orang pengajar dan 10 orang peserta didik. Data dianalisis secara deskriptif kuantitatif. Langkah pengembangan multimedia pembelajaran bahasa Jerman yang digunakan adalah (1 analisis kebutuhan, (2 perencanaan, (3 pengembangan produk, (4 evaluasi produk, (5 revisi produk, (6 uji coba lapangan, dan (7 produk akhir. Kualitas multimedia pembelajaran bahasa Jerman menurut dosen ahli materi adalah sangat baik dan menurut ahli media adalah baik. Kualitas multimedia menurut dua orang pengajar bahasa Jerman adalah sangat baik dan menurut peserta didik adalah baik. Dari 10 orang peserta didik, 80% mencapai nilai KKM. 100% respon peserta didik terhadap multimedia yang dikembangkan adalah sangat baik. Kata Kunci: Pengembangan, multimedia, keterampilan berbicara, pelayanan restoran   DEVELOPING MULTIMEDIA FOR GERMAN LANGUAGE TEACHING MATERIAL FOR RESTAURANT SERVICE LESSONS IN YOTABAKTI YOGYAKARTA Abstract The objectives of this research and development are (1 to develop a learning media for German language teachers, a computer assisted media with learning materials and exercises for speaking skill, (2 to describe the process of developing Multimedia German Language Teaching Material for Restaurant Service Lessons, and ( 3 to describe the result of product evaluation and field try out. The small group tryout involved five participants, a German language teacher and four students of Yotabakti. Field try out involved two German language teachers and ten students. The data of this study were analysed descriptively and quantitatively. The procedures of developing multimedia German language

  20. Optimasi Jangkauan Jaringan 4G Menggunakan Algoritma Genetika

    Directory of Open Access Journals (Sweden)

    Garsinia Ely Riani

    2016-12-01

    Full Text Available Kemampuan dan jangkauan 4G yang lebih luas daripada teknologi generasi sebelumnya perlu dimaksimalkan. Hal ini mengingat antusiasme pengguna layanan selular dalam menyambut kehadiran teknologi internet cepat ini. Optimasi yang dilakukan memperhatikan luas area, kerapatan pengguna internet dan posisi Base Transceiver Station (BTS. Penelitian ini mengusulkan algoritma genetika sebagai algoritma optimasi yang sering digunakan untuk menyelesaikan berbagai permasalahan kompleks. Optimasi dilakukan untuk memaksimalkan jangkauan 4G  secara efektif dan efisien dari sisi penyedia (provider. Serangkaian uji coba menunjukkan bahwa algoritma genetika mampu memberikan solusi yang cukup baik untuk penentuan posisi BTS dalam permasalahan jangkauan pelanggan.

  1. PENGEMBANGAN MEDIA PAPAN PERMAINAN PANJAT PINANG

    Directory of Open Access Journals (Sweden)

    Desty Triastuti

    2017-10-01

    Full Text Available Media is a very important component in the learning process. Media can be used as a toll for learning, that can be easy for the teachers to learn of the material, and at the same time can be facilitate the students to accepting and understanding of the material.  The purpose of this study is to produce the product that are specialized media to help the process of thematic learning. This media serves as a tool for stimulate memory recall and reinforce the material in students of fifth grade in elementary school. The media called board games panjat pinang has been validated on the the content and design, next then tried out on one to one evaluation, 6 students on small group evaluation and 23 students on field trial. The results of the tryouts indicating the level of feasibility of teaching materials is very high. The average validity is 90,025, attractiveness 91,80, effectiveness of 92,75, and practicality 92,18, so that media announced eligible and effective for use in thematic learning especially for matter circulatory systems human and animal. Media memiliki peranan yang sangat penting dalam proses pembelajaran. Media dapat dijadikan sebagai alat bantu belajar yang dapat memudahkan guru dalam penyampain materi sekaligus memudahkan siswa dalam menerima dan memahami materi.  Tujuan penelitian ini adalah menghasilkan produk media papan permainan panjat pinang untuk pembelajaran tematik. Media ini berfungsi sebagai alat bantu menstimulasi daya ingat dan penguatan materi bagi siswa kelas V SD. Media divalidasi pada aspek isi dan desain, diujicobakan kepada satu orang siswa pada uji coba perorangan, enam siswa pada uji coba kelompok kecil dan 23 siswa pada uji coba lapangan. Hasil uji coba menunjukkan tingkat kevalidan sangat tinggi. Rata-rata kevalidan 87,7, kepraktisan 90,55, kemenarikan 92,22, dan keefektifan 91,0. Berdasarkan skor perolehan tersebur, media dinyatakan layak dan efektif untuk digunakan di dalam pembelajaran tematik,

  2. Evaluation, including effects of storage and repeated freezing and thawing, of a method for measurement of urinary creatinine

    DEFF Research Database (Denmark)

    Garde, A H; Hansen, Åse Marie; Kristiansen, J

    2003-01-01

    The aims of this study were to elucidate to what extent storage and repeated freezing and thawing influenced the concentration of creatinine in urine samples and to evaluate the method for determination of creatinine in urine. The creatinine method was based on the well-known Jaffe's reaction...... and measured on a COBAS Mira autoanalyser from Roche. The main findings were that samples for analysis of creatinine should be kept at a temperature of -20 degrees C or lower and frozen and thawed only once. The limit of detection, determined as 3 x SD of 20 determinations of a sample at a low concentration (6...

  3. Comparison of two automated assays of BTM (CTX and P1NP) and reference intervals in a Danish population

    DEFF Research Database (Denmark)

    Jørgensen, N R; Møllehave, L T; Hansen, Y B L

    2017-01-01

    the agreement on the two platforms. METHODS: Fasting sera from 2308 individuals (1250 males and 1058 females, age range 24-76 years) participating in the Health2006 study were analyzed for CTX and P1NP using the automated IDS-iSYS analyzer and the automated Cobas e411 analyzer. Participants in anti......-osteoporotic treatment were excluded, while subjects on hormonal contraceptives were included. RESULTS: There was significant disagreement between both the two P1NP assays with a mean difference of -3 μg/L (LoA -19 to 14) (p

  4. KOMPETENSI GURU PAUD DALAM MEMBUAT ALAT BERMAIN SAINS DARI LIMBAH

    Directory of Open Access Journals (Sweden)

    Dwi Yulianti

    2013-02-01

    Full Text Available Kegiatan pengabdian masyarakat ini bertujuan meningkatkan kompetensi guru PAUD dalam alat bermain sains (ABS dari barang-barang habis pakai atau limbah. Metode yang diterapkan berupa pelatihan dan workshop yang meliputi kuliah, praktek membuat alat dan peer teaching. ABS yang berhasil dibuat diantaranya tikar warna, pengukuran, menimbang, menakar, magnet, bunyi, pncampuran warna, gravitasi, telepon dari gelas plastik. Setelah kegiatan berlangsung terjadi peningkatan jumlah alat pada masing-masing sekolah. Terjadi pula peningkatan kompetensi guru dalam membuat alat bermain sains. Dari hasil uji coba melalui kegiatan per teaching, hasil belajar kognitif, afektif dan psikomotorik siswa meningkat secara signifikan.

  5. 25-hydroxy-Vitamin D status: limitations in comparison and clinical interpretation of serum-levels across different assay methods.

    Science.gov (United States)

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

    2014-01-01

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

  6. PENGEMBANGAN BUKU AJAR BIOTEKNOLOGI BERBASIS PENELITIAN BIOREMIDIASI LOGAM BERAT KADMIUM UNTUK MAHASISWA S1 BIOLOGI UNIVERSITAS NEGERI MALANG

    Directory of Open Access Journals (Sweden)

    Agung Pambudiono

    2016-06-01

    Tujuan penelitian ini adalah menghasilkan buku ajar berbasis penelitian tentang bioremidiasi logam berat. Penelitian ini mengadaptasi model pengembangan Dick & Carey. Kelayakan buku ajar didasarkan pada hasil uji coba produk oleh tim ahli dan kelompok kecil. Jenis data yang dikumpulkan adalah data kuantitatif dan data kualitatif. Data yang telah terkumpul dianalisis secara deskriptif kuantitatif dan kualitatif. Hasil validasi yang dilakukan oleh ahli materi memberikan nilai persentase kevalidan buku ajar sebesar 91.6%, penilaian dari ahli media sebesar 90.81%. sedangkan penilaian kelompok kecil sebesar 85.56%. Berdasarkan hasil validasi maka buku ajar yang dikembangkan dikategorikan sangat valid dan layak untuk dipergunakan.

  7. Aprendizaje cooperativo. Un recurso indispensable en la formación universitaria

    OpenAIRE

    Cobas Cobiella, María Elena; Montes Rodríguez, María Pilar; Alventosa del Río, Josefina; Guillén Catalán, Raquel; Ortega Giménez, Alfonso; Marí Farinós, Jesús; Muñoz Pérez, David; Martínez Evora, Joan; Panadero de la Cruz, Catalina Edeltrudis; Vega Cardona, Raúl José; Company Alcañiz, Mireia; Rivera Rodón, Gretchen; Ordelín Font, Jorge Luis; Febles Pozo, Nayiber; García Juncos, María Antonia

    2016-01-01

    El Libro “Aprendizaje cooperativo Un recurso indispensable en la formación universitaria”, se enmarca dentro del Proyecto de Innovación docente Finestra Oberta UV_ SFPIE GER 15-314671, bajo la dirección de la Profesora María Elena Cobas Cobiella, del Departamento de Derecho Civil, de la Facultad de Derecho de la Universidad de Valencia. Este libro contiene 19 artículos inéditos de un grupo importante de profesores y especialistas en la temática nacionales e internacionales, así como c...

  8. Pengembangan E-Modul Berbasis Adobe Flash CS6 pada Mata Pelajaran Penataan Barang Dagang

    Directory of Open Access Journals (Sweden)

    Indah Zahrotul Fauziah

    2016-09-01

    Full Text Available Abstract: The increasing of technology development gives several new things. They are both the technology development in the general aspect and in education aspect. Those developments demand the educators to develop the innovative learning. One of them is using an interactive multimedia in the form of e-module or electronic module which uses Adobe Flash CS6 application. This research uses Research and Development (R&D method with which the combination between ADDIE procedure and Borg & Gall. It consists of 5 stages: (1 Analysis (Needs Analysis, (2 Design (Media of Learning, (3 Development (Media and Materials Validation, (4 Implementation (Small-scale and Field Try-Out, and Evaluation (Three times of revision. The e-module was validated by two experts for three times containing the early product, after small-scale try-out, and after field try-out. The results of the final validation are 99.31% for media expert validation, 98.61% for materials expert validation, and 90.03% for student validation. Abstrak: Perkembangan teknologi yang sangat pesat menghasilkan hal-hal baru, baik teknologi secara umum maupun perkembangan teknologi dalam dunia pendidikan. Perkembangan teknologi tersebut menuntut pendidik untuk mengembangkan pembelajaran yang inovatif. Salah satunya menggunakan multimedia interaktif yang dikemas dalam bentuk e-modul atau modul elektronik dengan memanfaatkan aplikasi Adobe Flash CS6. Penelitian ini menggunakan metode penelitian dan pengembangan (R&D dengan Prosedur penelitian dan pengembangan (R&D ADDIE yang digabungkan dengan Borg & Gall, meliputi 5 tahap yaitu: (1 Analisis (analisis kebutuhan, (2 Design (media pembelajaran, (3 Development (validasi media dan materi, (4 Implementasi (uji coba terbatas dan uji coba lapangan dan (5 Evaluasi (revisi tiga kali. E-modul ini divalidasi oleh dua validator sebanyak tiga kali, yaitu produk awal, setelah uji coba terbatas, dan setelah uji coba lapangan. Berikut adalah hasil yang diperoleh pada

  9. Prévalence des dyslipidémies au laboratoire de biochimie du CHU ...

    African Journals Online (AJOL)

    Le cholestérol total, le cholestérol HDL, le cholestérol LDL ainsi que les triglycérides ont été dosés grâce à des méthodes enzymatiques sur un automate de Biochimie de type Cobas Integra 400 (Roche Diagnostics). Résultats: la prévalence des dyslipidémies dans notre population d'étude est de 39,30%. Les prévalences ...

  10. PENGEMBANGAN BUKU AJAR BERBASIS PENELITIAN EVOLUSI DAN FILOGENETIK MOLEKULER UNTUK MATAKULIAH EVOLUSI DI UNIVERSITAS JEMBER

    Directory of Open Access Journals (Sweden)

    Ulin Nuha

    2016-09-01

    Filogenetik molekuler merupakan salah satu kajian yang dipelajari pada matakuliah Evolusi untuk jenjang S1 Pendidikan Biologi. Kajian ini memerlukan bahan ajar yang kontekstual dan tetap mengikuti perkembangan IPTEKS. Kendala yang muncul adalah pengetahuan mahasiswa dalam ranah molekuler masih rendah. Salah satu solusi yang dapat dilakukan adalah dengan menyediakan buku ajar berbasis penelitian denan pendekatan molekuler. Buku ajar dikembangkan berdasarkan model pengembangan ADDIE. Produk divalidasi oleh ahli media, materi, praktisi pendidikan dan diujicobakan pada kelompok kecil. Hasil validasi ahli media, ahli materi, praktisi pendidikan, dan uji coba kelompok kecil secara berturut turut adalah 87,14%, 91,00%, 75,78%, dan 82,22%.

  11. Comparison of two immunoassay systems for hCGβ and PAPP-A in prenatal screening for trisomy 21, 18, and 13 in the first trimester

    DEFF Research Database (Denmark)

    Engell, Anna Elise; Carlsson, Elin Rebecka; Jørgensen, Finn Stener

    2017-01-01

    OBJECTIVES: The biochemical serum markers free β-human chorionic gonadotropin (hCGβ) and pregnancy associated plasma protein A (PAPP-A), used in screening for trisomy 21 (T21), trisomy 18 (T18), and trisomy 13 (T13) during the first trimester, can be measured on different laboratory instruments e.......g. Kryptor (Brahms) and Cobas (Roche). We compared the performance of these two analytical instruments when used for first trimester combined testing. DESIGN AND METHODS: Serum samples from 944 singleton pregnant women attending for first trimester combined testing were routinely assayed for hCGβ and PAPP...

  12. Effekten af sund skolekost på udvalgte blodparametre

    DEFF Research Database (Denmark)

    Horn, Peer Bendix; Brandslund, Ivan; Schmedes, Anne

    2009-01-01

    blood before (week 39) and after the intervention (week 49). The intervention group received a healthy meal for two months (25-30% of the daily intake of calories). Blood samples were analyzed for 17 parameters related to carbohydrate, fat and protein metabolism as well as vitamins and minerals. RESULTS......: During the intervention period, the intervention group showed a significant change in mean values for thyroid-stimulating hormone (TSH), calcium (CA) haemoglobin (HB), cobalamin (COBA) and creatinine (CREA) compared with the control group (p

  13. 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

    International Nuclear Information System (INIS)

    O’Donnell, Patrick; Shieh, Felice; Wei, Wen; Lawrence, H Jeffrey; Wu, Lin; Schilling, Robert; Bloom, Kenneth; Maltzman, Warren; Anderson, Steven; Soviero, Stephen; Ferguson, Jane; Shyu, Johnny; Current, Robert; Rehage, Taraneh; Tsai, Julie; Christensen, Mari; Tran, Ha Bich; Chien, Sean Shih-Chang

    2013-01-01

    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. 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. 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 for 11/12 tumors tested. Test

  14. MODEL PEMBELAJARAN NEUROLINGUISTIC PROGRAMMING BERORIENTASI KARAKTER BAGI PENINGKATAN KEMAMPUAN MENULIS SISWA SMP

    Directory of Open Access Journals (Sweden)

    Wikanengsih -

    2014-06-01

    Abstrak: Model Pembelajaran Neurolinguistic Programming Berorientasi Karakter untuk Mening­katkan Kemampuan Menulis Siswa. Penelitian ini bertujuan untuk mengetahui keefektifan model pem­belajaran neurolinguistik programming berorientasi karakter (MPNLPBK terhadap kemampuan menulis siswa. Metode penelitian yang digunakan metode penelitian kombinasi (mixed method jenis sequential exploratory strategy. Hasil penelitian tahap pertama (penelitian kualitatif menghasilkan model pembelajaran hipotetik. Penelitian tahap kedua merupakan uji coba penerapan model hipotetik (penelitian kuantitatif. Hasil pengujian menunjukkan bahwa pembelajaran menulis dengan menggunakan MPNLPBK dapat meningkatkan kemampuan menulis siswa kelompok eksperimen. Selain itu, berdasarkan hasil pengamatan terhadap aspek karakter komunikatif, toleran, tanggungjawab dan kreatif siswa, terdapat perkembangan pada diri siswa untuk setiap aspek tersebut.

  15. Interim Report on SNP analysis and forensic microarray probe design for South American hemorrhagic fever viruses, tick-borne encephalitis virus, henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever viruses, Rift Valley fever

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C; Gardner, S

    2012-06-05

    The goal of this project is to develop forensic genotyping assays for select agent viruses, enhancing the current capabilities for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the whole genome wide SNP analysis and microarray probe design for forensics characterization of South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.

  16. Report for the NGFA-5 project.

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C; Jackson, P; Thissen, J; Wollard, J; Gardner, S; McLoughlin, K

    2011-11-15

    The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, TaqMan PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. To effectively compare the sensitivity and specificity of the different genomic technologies, we used SNP TaqMan PCR, MLVA, microarray and high-throughput illumine and 454 sequencing to test various strains from B. anthracis, B. thuringiensis, BioWatch aerosol filter extracts or soil samples that were spiked with B. anthracis, and samples that were previously collected during DHS and EPA environmental release exercises that were known to contain B. thuringiensis spores. The results of all the samples against the various assays are discussed in this report.

  17. Pengembangan bahan Pembelajaran Berbantuan komputer (PBK untuk Memfasilitasi Active Learning dalam Mata Kuliah Landasan Kependidikan

    Directory of Open Access Journals (Sweden)

    Surtikanti Surtikanti

    2005-12-01

    Full Text Available Penelitian ini bertujuan untuk: (1 mengembangkan software PBK mata kuliah Landasan Kependidikan sebagai salah satu sumber media alternatif dalam rangka mencapai efektivitas, efisiensi dan daya tank untuk belajar; (2 menerapkan prinsip-prinsip desain pembelajaran (in­structional design dalam software pembelajaran Landasan Kependidikan; (3 Menentukan kelayakan produk pembelajaran landasan kependidikan berbantuan komputer agar dapat memfasilitasi active learning. Subjek penelitian terdiri dari 2 orang, (1 orang ahli mated dan 1 orang ahli media, 6 orang mahasiswa untuk uji coba kelompok kecil, dan 20 orang mahasiswa untuk uji coba lapangan. Data yang dijaring sesuai dengan jenisnya. Data kuantitatif dianalisis dengan statistik deskriptif sedangkan data kualitatif dengan naratif deskriptif. Hasil penelitian menunjukkan, bahwa: (1 Bahan PBK yang dirancang efektif digunakan untuk mencapai tujuan pembelajaran; (2 Bahan PBK memiliki efisiensi waktu yang tinggi dalam penyampaian isi pembelajaran; (3 Bahan PBK yang digunakan memiliki daya tarik yang tinggi; (4 isi program PBK sesuai dengan prinsip-prinsip desain pembelajaran; dan (5 program PBK ini dapat memfasilitasi strategi active learning. Kata kunci: pembelajaran berbantuan komputer, strategi active learning.

  18. Thermal annealing and pressure effects on BaFe2-xCoxAs2 single crystals.

    Science.gov (United States)

    Shin, Dongwon; Jung, Soon-Gil; Prathiba, G; Seo, Soonbeom; Choi, Ki-Young; Kim, Kee Hoon; Park, Tuson

    2017-11-26

    We investigate the pressure and thermal annealing effects on BaFe2-xCoxAs2 (Co-Ba122) single crystals with x = 0.1 and 0.17 via electrical transport measurements. The thermal annealing treatment not only enhances the superconducting transition temperature (Tc) from 9.6 to 12.7 K for x = 0.1 and from 18.1 to 21.0 K for x = 0.17, but also increases the antiferromagnetic transition temperature (TN). Simultaneous enhancement of Tc and TN by the thermal annealing treatment indicates that thermal annealing could substantially improve the quality of the Co-doped Ba122 samples. Interestingly, Tc of the Co-Ba122 compounds shows a scaling behavior with a linear dependence on the resistivity value at 290 K, irrespective of tuning parameters, such as chemical doping, pressure, and thermal annealing. These results not only provide an effective way to access the intrinsic properties of the BaFe2As2 system, but also may shed a light on designing new materials with higher superconducting transition temperature. © 2017 IOP Publishing Ltd.

  19. Evaluating new HbA1c methods for adoption by the IFCC and NGSP reference networks using international quality targets.

    Science.gov (United States)

    Lenters-Westra, Erna; English, Emma

    2017-08-28

    As a reference laboratory for HbA1c, it is essential to have accurate and precise HbA1c methods covering a range of measurement principles. We report an evaluation of the Abbott Enzymatic (Architect c4000), Roche Gen.3 HbA1c (Cobas c513) and Tosoh G11 using different quality targets. The effect of hemoglobin variants, other potential interferences and the performance in comparison to both the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) and the National Glycohemoglobin Standardization Program (NGSP) reference systems was assessed using certified evaluation protocols. Each of the evaluated HbA1c methods had CVs HbA1c. Partly based on the result of this study, the Abbott Enzymatic method on the Architect c4000 and the Roche Gen.3 HbA1c on the Cobas c513 are now official, certified IFCC and NGSP SRMPs in the IFCC and NGSP networks. Sigma metrics quality criteria presented in a graph distinguish between good and excellent performance.

  20. PENGEMBANGAN INSTRUMEN PENILAIAN KETERAMPILAN TEKNIK FOREHAND DAN BACKHAND DRIVE TENIS MEJA PADA ATLET USIA DINI

    Directory of Open Access Journals (Sweden)

    Verandita Rihtiana

    2014-09-01

    Full Text Available Penelitian ini bertujuan untuk mengembangkan instrumen penilaian keterampilan teknik forehand dan backhand drive tenis meja pada atlet usia dini. Penelitian ini menggunakan metode pene-litian dan pengembangan, dengan langkah-langkah pengembangan sebagai berikut: (1 pengumpulan informasi di lapangan, (2 melakukan analisis terhadap informasi yang dikumpulkan, (3 mengembangkan produk awal (draf model, (4 validasi ahli dan revisi, (5 uji coba skala kecil dan revisi, (6 uji coba skala besar dan revisi, (7 pembuatan produk final. Subjek penelitian atlet tenis meja usia dini. Analisis data untuk uji validitas dilakukan dengan CVR (content validity ratio dan reliabilitas dengan  menggunakan Alpha Crobanch. Penelitian ini menghasilkan buku panduan instrumen penilain keterampilan teknik forehand dan backhand drive tenis meja untuk atlet pemula  yang didalamnya berisi  petunjuk penggunaan, lembar tugas siswa, pedoman penilaian, rubrik penilaian, serta tabel penyekoran, yang memiliki validitas yang tinggi (1 dan reliabilitas yang tinggi¸forehand drive sikap awal: r = 0,975, pelaksanaan: r = 0,961, gerak lanjutan: r = 0, 955. Backhand drive sikap awal: r = 0,961, pelaksanaan r = 0,974, gerak lanjutan: r = 0, 989. Kata Kunci: instrumen penilaian teknik forehand dan backhand drive, tenis meja

  1. RANCANG BANGUN APLIKASI MONITORING DAN REKAM DATA SISTEM PENGENALAN SISTEM ISYARAT BAHASA INDONESIA BERBASIS SENSOR

    Directory of Open Access Journals (Sweden)

    Mohammad Iqbal

    2014-11-01

    Full Text Available ABSTRAK Dalam penelitian ini dikembangkan pengenalan sistem isyarat bahasa Indonesia (SIBI berbasis sensor yang diharapkan dapat memperbaiki akurasi, yaitu dengan menggunakan sensor flex untuk gerakan lekukan jari, dan menggunakan sensor accelerometer-gyroscope untuk mengetahui kemiringan/orientasi tangan. Untuk mendapatkan ekstraksi ciri dan metode pengenalan yang optimal, maka diperlukan uji coba dan analisis terhadap perbandingan ekstraksi ciri dan metode pengenalan, sehingga dapat ditentukan yang terbaik. Dalam uji coba dan analisis tersebut, maka diperlukan sampel data offline atau data yang sudah disimpan/direkam sebelumnya, sehingga diperlukan aplikasi untuk dapat merekam data (recording dan memonitoring data dari sensor-sensor yang dipasang pada sarung tangan. Dengan adanya data-data sensor tersebut, maka proses pemilihan ekstraksi ciri dan metode pengenalan yang optimal dapat dilakukan secara offline, menggunakan perangkat lunak komputasi. Capaian dapam Penelitian ini, adalah telah berhasil dikembangkan program aplikasi monitoring dan rekam data untuk sistem pengenalan SIBI. Data sensor yang dimonitoring dan direkam adalah data raw, sehingga perlu dilakukan pengolahan data untuk proses ekstraksi ciri sebelum diujicobakan pada metode pengenalan tertentu Kata kunci: SIBI, bahasa isyarat, sensor, flex, acclerometer, gyroscope, monitoring, recording.

  2. Nematic fluctuations and resonance in iron-based superconductors

    Science.gov (United States)

    Gallais, Yann

    The spontaneous appearance of nematicity, a state of matter that breaks rotation but not translation symmetry, is ubiquitous in many iron based superconductors (Fe SC), and has relevance for the cuprates as well. Here I will review recent electronic Raman scattering experiments which report the presence of critical nematic fluctuations in the charge channel in the tetragonal phase of several Fe SC systems. In electron doped Co-BaFe2As2 (Co-Ba122), these fluctuations extend over most of the superconducting dome. Their associated nematic susceptibility shows Curie-Weiss behavior, and its doping dependence suggests the presence of a nematic quantum critical point near optimal TC Similar nematic fluctuations are also observed in FeSe despite the absence of magnetic order, raising the question of the link between nematicity and magnetism in Fe SC. In FeSe I will further contrast the evolution of nematic fluctuations under isoelectronic S substitution and hydrostatic pressures up to 8 GPa, with only the former showing evidence for a nematic quantum critical point. In the superconducting state of Co-Ba122, I will show that a resonance emerges in the Raman spectra near the nematic quantum critical point. This nematic resonance is a clear fingerprint of the coupling between nematic fluctuations and Bogoliubov quasiparticles, and can be thought as the nematic counterpart of the spin resonance observed in neutron scattering experiments. Support from Agence Nationale de la Recherche via ANR Grant ''Pnictides'' is acknowledged.

  3. The analytic impact of a reduced centrifugation step on chemistry and immunochemistry assays: an evaluation of the Modular Pre-Analytics.

    Science.gov (United States)

    Koenders, Mieke M J F; van Hurne, Marco E J F; Glasmacher-Van Zijl, Monique; van der Linde, Geesje; Westerhuis, Bert W J J M

    2012-09-01

    The COBAS 6000 system can be completed by a Modular Pre-Analytics (MPA), an integrated laboratory automation system that streamlines preanalysis. For an optimal throughput, the MPA centrifuges blood collection tubes for 5 min at 1885 × g - a centrifugation time that is not in concordance with the World Health Organization guidelines which suggest centrifugation for 10/15 min at 2000-3000 × g. In this study, the analytical outcome of 50 serum and 50 plasma samples centrifuged for 5 or 10 min at 1885 × g was investigated. The study included routine chemistry and immunochemistry assays on the COBAS 6000 and the Minicap capillary electrophoresis. Deming-fit and Bland-Altman plots of the 5-min and 10-min centrifugation steps indicated a significant correlation in serum samples. The lipaemia index in plasma samples centrifuged for 5 min displayed a statistically significant variation when compared with the 10-min centrifugation. Preanalytical centrifugation can be successfully down-scaled to a duration of 5 min for most routine chemistry and immunochemistry assays in serum and plasma samples. To prevent inaccurate results in plasma samples with an increased lipaemia index from being reported, the laboratory information system was programmed to withhold results above certain lipaemia indices. The presented data support the use of a 5-min centrifugation step to improve turnaround times, thereby meeting one of the desires of the requesting clinicians.

  4. RANCANG BANGUN PROGRAM PENGEDITAN KURVA B-SPLINE MULTIRESOLUSI BERBASIS WAVELETS

    Directory of Open Access Journals (Sweden)

    Nanik Suciati

    2002-07-01

    Full Text Available Penelitian ini menyusun representasi multiresolusi untuk kurva B-spline kubik yang menginterpolasi titik-titik ujung dengan basis wavelets. Representasi multiresolusi ini digunakan untuk mendukung beberapa tipe pengeditan kurva, yaitu penghalusan kurva dengan tingkat resolusi kontinyu untuk menghilangkan detail-detail kurva yang tidak diinginkan, pengeditan bentuk keseluruhan kurva dengan tetap mempertahankan detaildetailnya, perubahan detail-detail kurva tanpa mempengaruhi bentuk keseluruhannya, dan pengeditan satubagian tertentu dari kurva melalui manipulasi secara langsung terhadap titik-titik kontrolnya. Untuk menguji kemampuan representasi multiresolusi dalam mendukung empat tipe manipulasi kurva tersebut, disusun program pengeditan kurva dengan menggunakan bahasa pemrograman Visual C++ pada komputer Pentium 133 MHz, memori 16 Mbyte, sistem operasi Windows 95, lingkungan pengembangan Microsoft DevelopmentStudio 97 dan pustaka Microsoft Foundation Class. Dari hasil uji coba program diketahui bahwa representasi multiresolusi memberikan dukungan yang sangat baik terhadap tipe-tipe pengeditan seperti yang disebutkan di atas. Representasi multiresolusi tidak membutuhkan memori penyimpan ekstra selain dari yang digunakan untuk menyimpan titik kontrol. Dari hasil uji coba program menggunakan ratusan titik kontrol, algoritma berjalan cukup cepat dan memadai berkaitan dengan tuntutan komunikasi interaktif antara user dan program.Kata kunci: B-Spline, Wavelet, Multiresolusi

  5. Perancangan Implementasi E-Learning Berbasis Moodle Dalam Matakuliah Statistika Program Studi Pendidikan Teknik Informatika Dan Komputer

    Directory of Open Access Journals (Sweden)

    Affni Syaviera Nova

    2017-06-01

    Full Text Available Penelitian dilakukan dengan tujuan merancang implementasi e-learning berbasis Moodle berupa website dalam matakuliah Statistika program studi Pendidikan Teknik Informatika dan Komputer. Sistem e-learning ini dirancang untuk diimpelementasikan pada semua matakuliah yang ada pada program studi Pendidikan Teknik Informatika dan Komputer, sehingga membantu kegiatan perkuliahan. Sebagai pengembangan awal, sistem e- learning ini diuji coba pada matakuliah statistika. Penelitian ini menggunakan desain penelitian dan pengembangan (Research and Development menurut Sugiyono (2010. Subyek penelitian yaitu dosen statistika dan mahasiswa yang telah mengikuti perkuliahan Statistika ditentukan secara purposive sampling. Data yang diambil adalah kelayakan dari segi materi dan media melalui angket, dan tanggapan mahasiswa melalui angket. Tanggapan ahli menunjukkan e-learning berbasis Moodle sangat baaik dari segi media dan bagus dari segi materi. Hasil angket tanggapan siswa pada uji coba skala kecil menunjukkan bahwa mayoritas siswa memberikan tanggapan positif terhadap kegiatan pembelajaran menggunakan media e-learning berbasis Moodle. Produk final e-learning berbasis Moodle berisi modul, video, ppt, chat, kelas virtual dan forum diskusi. Berbagai konten dan fasilitas yang dimiliki e-learning yang dikembangkan membuat pembelajaran Sistem Gerak menjadi lebih menarik. Berdasarkan hasil analisis dan pembahasan dapat disimpulkan bahwa e-learning berbasis Moodle sesuai dan layak diterapkan pada matakuliah Statistika.

  6. PENGOLAHAN LIMBAH CAIR INDUSTRI FARMASI FORMULASI DENGAN METODE ANAEROB-AEROB DAN ANAEROB-KOAGULASI

    Directory of Open Access Journals (Sweden)

    Farida Crisnaningtyas

    2016-05-01

    Full Text Available Studi ini membahas mengenai pengolahan limbah cair industri farmasi dalam skala laboratorium dengan menggunakan konsep anaerob-kimia-fisika dan anaerob-aerob. Proses anaerob dilakukan dengan menggunakan reaktor Upflow Anaerobic Sludge Bed reactor (UASBr pada kisaran OLR (Organic Loading Rate 0,5 – 2 kg COD/m3hari, yang didahului dengan proses aklimatisasi menggunakan substrat gula. Proses anaerob mampu memberikan efisiensi penurunan COD hingga 74%. Keluaran dari proses anaerob diolah lebih lanjut dengan menggunakan dua opsi proses: (1 fisika-kimia, dan (2 aerob. Koagulan alumunium sulfat dan flokulan kationik memberikan efisiensi penurunan COD tertinggi (73% pada kecepatan putaran masing-masing 100 rpm dan 40 rpm. Uji coba aerob dilakukan pada kisaran MLSS antara 4000-5000 mg/L dan mampu memberikan efisiensi penurunan COD hingga 97%. Hasil uji coba menunjukkan bahwa efisiensi penurunan COD total yang dapat dicapai dengan menggunakan teknologi anaerob-aerob adalah 97%, sedangkan kombinasi anaerob-koagulasi-flokulasi hanya mampu menurunkan COD total sebesar 72,53%. Berdasarkan hasil tersebut, kombinasi proses anaerob-aerob merupakan teknologi yang potensial untuk diaplikasikan dalam sistem pengolahan limbah cair industri farmasi. 

  7. PENGEMBANGAN MULTIMEDIA PEMBELAJARAN INTERAKTIF KOMPETENSI DASAR PEMASANGAN SISTEM PENERANGAN DAN WIRING KELISTRIKAN DI SMK

    Directory of Open Access Journals (Sweden)

    Nopriyanti Nopriyanti

    2015-06-01

    Full Text Available Penelitian ini bertujuan untuk: (1 menghasilkan multimedia pembelajaran interaktif kompetensi dasar pemasangan sistem penerangan dan wiring kelistrikan; (2 mengetahui kualitas multimedia pembelajaran interaktif; dan (3 mengetahui efektifitas multimedia pembelajaran interaktif kompetensi dasar pemasangan sistem penerangan dan wiring kelistrikan pada kelas XI SMK bidang keahlian Teknik Kendaraan Ringan. Penelitian ini merupakan penelitian dan pengembangan. Validasi multimedia dilakukan oleh ahli materi dan ahli media. Subjek uji coba penelitian ini adalah 32 siswa kelas XI SMKN 2 Depok, Sleman, Yogyakarta bidang keahlian Teknik Kendaraan Ringan. Kesimpulan dari penelitian ini adalah: (1 produk multimedia pembelajaran interaktif kompetensi dasar pemasangan sistem penerangan dan wiring kelistrikan layak digunakan; (2 kualitas multimedia interaktif ini sangat baik, hasil penilaian ahli ditinjau dari pembelajaran 66 (baik, isi sebesar 54 (baik, aspek tampilan 97 (baik, dan program 50 (baik, sedangkan hasil dari penilaian peserta didik uji coba lapangan pada aspek pembelajaran1277 (sangat baik, isi 1195 (sangat baik, tampilan 1562 (sangat baik, dan pemograman 519 (sangat baik; (3 Produk multimedia pembelajaran interaktif kompetensi dasar pemasangan sistem penerangan dan wiring kelistrikan efektif meningkatkan hasil belajar siswa. Rata-rata penilaian hasil belajar siswa ketika pretest adalah 63,75 dengan nilai terendah 50 dan nilai tertinggi 75. Sedangkan rata-rata nilai posttest sebesar 78,75 dengan nilai terendah 65 dan nilai tertinggi 90.

  8. Rancang Bangun Permainan Edukasi Matematika dan Fisika dengan Memanfaatkan Accelerometer dan Physics Engine Box2d pada Android

    Directory of Open Access Journals (Sweden)

    Putri Nikensasi

    2012-09-01

    Full Text Available Perkembangan industri permainan mobil yang semakin meningkat memotivasi para pengembang permainan mobil untuk membuat inovasi-inovasi terbaru dalam permainannya. Salah satu inovasi tersebut yaitu permainan edukasi, namun saat ini permainan edukasi kurang diminati karena aturan permainannya yang cenderung membosankan. Pengembangan permainan ini ditujukan untuk membuat sebuah permainan mobil edukasi dengan memanfaatkan teknologi mobil terbaru dalam aturan permainannya sehingga permainan tersebut tidak membosankan. Aplikasi yang dikembangkan merupakan aplikasi permainan mobil edukasi yang mengajarkan ilmu matematika dan fisika kepada pemainnya. Teknologi baru yang digunakan dalam permainan ini yaitu accelerometer pada sistem operasi Android yang diintegrasikan dengan Physics Engine Library Box2D. Selain itu, permainan ini dibangun dengan menggunakan Adobe Flash CS5.5 dan bahasa pemrograman Actionscript 3 (AS3 serta Adobe Air sebagai runtime aplikasinya. Uji coba dilakukan dengan menggunakan perangkat Android versi 2.3. Dari uji coba dapat disimpulkan bahwa Adobe Flash CS5.5 dapat digunakan untuk membuat permainan mobil edukasi pada perangkat Android dan mengakses sensor accelerometer-nya.

  9. PENERAPAN ALGORITMA C4.5 UNTUK PREDIKSI PENGGUNAAN JENIS KONTRASEPSI BERBASIS WEB

    Directory of Open Access Journals (Sweden)

    Rusda Wajhillah

    2017-09-01

    Keluarga Berencana (KB merupakan suatu program pemerintah yang dirancang untuk menyeimbangkan antara kebutuhan dan jumlah penduduk dengan menggunakan alat kontrasepsi. Kurangnya pengetahuan tentang kontrasepsi menyebabkan tidak sedikit akseptor lebih memilih menggunakan kontrasepsi berdasarkan coba-coba atau bahkan mengikuti saran dari orang lain yang kurang paham terhadap alat kontrasepsi. Oleh sebab itu, diperlukan adanya tindakan/penanganan khusus untuk mempermudah para akseptor dalam memilih kontrasepsi yang efektif dan sesuai dengan kondisi tubuhnya. Algoritma C4.5 yaitu metode pohon keputusan mengubah fakta yang sangat besar menjadi pohon keputusan yang merepresentasikan aturan. Aturan dapat dengan mudah dipahami dengan bahasa alami.Untuk itu, dalam penelitian ini akan dilakukan analisa data penggunaan jenis kontrasepsi menggunakan klasifikasi data mining yakni algoritma C4.5 dengan menggunakan beberapa parameter diantaranya usia, jumlah anak, tekanan darah dan riwayat penyakit yang akan diaplikasikan dalam bentuk web guna mempermudah para akseptor dalam mendapatkan nilai informasi yang lebih cepat dan fleksibel. Dari 130 jumlah kasus yang terdiri dari 104 kasus akseptor pengguna kontrasepsi hormonal dan 26 kasus pengguna kontrasepsi non hormonal yang didapat dari Posyandu Desa Nyangkowek Kecamatan Cicurug, maka didapatkan 14 rule yang dihasilkan dari pohon keputusan algoritma C4.5 dengan jumlah class non hormonal sebanyak 8 rule dan jumlah class hormonal sebanyak 6 rule serta dievaluasi dengan pengujian Cross Validation yangmenghasilkan tingkat akurasi sebesar 85,38%, sehingga dapat disimpulkan bahwa penelitian ini dapat membantu para akseptor KB dalam memilih jenis kontrasepsi yang efektif. Kata Kunci: Akseptor, Algoritma C4.5, Kontrasepsi, Sistem Pakar

  10. QuickASP: PEMBANGKIT KODE PROGRAM ASP UNTUK APLIKASI BASIS DATA BERBASIS WEB

    Directory of Open Access Journals (Sweden)

    Imam Kuswardayan

    2007-01-01

    Full Text Available Dalam pembuatan sistem aplikasi basis data berbasis web, perancangan antarmuka pengguna (presentation layer dan lapisan bisnis (bussiness layer merupakan tahap yang dilalui setelah pemahaman terhadap kebutuhan pengguna sistem. Adanya pola atau keteraturan dalam implementasi tahap ini menyebabkan pengembangan sistem akan lebih efisien jika menggunakan suatu aplikasi yang dapat menghasilkan kerangka dasar aplikasi web dengan cepat untuk kedua lapisan tersebut dan bahkan beserta kode programnya. Pada penelitian ini telah diimplementasikan suatu perangkat lunak yang selanjutnya disebut QuickASP. QuickASP membangkitkan kode ASP untuk membangun  homepage otomatis. Untuk membangkitkan kode ASP, QuickASP membutuhkan komponen berupa basis data dan file Cascading Style Sheets (CSS. Proses awal yang dilakukan QuickASP dalam membangkitkan kode program ASP adalah membaca informasi basis data berupa tabel-tabel, nama field dan tipe data. Setelah itu QuickASP akan membangkitkan file-file ASP beserta file-file pendukungnya berdasarkan hasil pengaturan tampilan halaman web yang dilakukan oleh pengguna.Uji coba QuickASP dilakukan pada tiga jenis basis data yaitu Microsoft Access, Microsoft SQL Server, dan Oracle. Dari hasil uji coba tersebut, QuickASP terbukti dapat membangkitkan homepage otomatis beserta fungsi–fungsi yang disediakan untuk modifikasi record dan fungsi navigasi.Kata kunci: QuickASP, file cascading style sheets, kode program ASP.

  11. PENGEMBANGAN BAHAN AJAR DENGAN MODEL MIND MAP UNTUK PEMBELAJARAN ILMU PENGETAHUAN SOSIAL SMP

    Directory of Open Access Journals (Sweden)

    Lukman Lukman

    2014-12-01

    Full Text Available Penelitian ini bertujuan untuk menghasilkan bahan ajar dengan model mind map yang layak digunakan pada pembelajaran Ilmu Pengetahuan Sosial (IPS untuk siswa SMP, serta mengetahui keefektifan bahan ajar hasil pengembangan. Penelitian ini merupakan penelitian dan pengembangan (Research and Development. Hasil penelitian adalah sebagi berikut: (1 menghasilkan bahan ajar dengan model mind map untuk pembelajaran Ilmu Pengetahuan Sosial siswa SMP yang dikemas dalam bentuk buku dengan materi “Perkembangan pada Masa Islam di Indonesia”. Produk yang dihasilkan layak digunakan untuk pembelajaran berdasarkan validasi dari ahli materi, ahli media, uji coba terbatas, serta uji coba lapangan. (2 Bahan ajar hasil pengembangan untuk siswa kelas VII di SMP N 3 Berbah ini efektif digunakan untuk pembelajaran IPS. Peningkatan skor postes pada kelas yang menggunakan bahan ajar dengan model mind map sebesar 13,87% dengan nilai gain score 0,45 dan ketuntasan siswa 100%. Sedangkan kelas yang menggunakan buku paket IPS dengan peningkatan skor postes sebesar 10,26% dengan nilai gain score 0,35 dan ketuntasan siswa 87,1%. Kata kunci: bahan ajar, mind map, ilmu pengetahuan sosial

  12. PENGEMBANGAN ALAT DESTILATOR BIOETANOL MODEL REFLUK BERTINGKAT DENGAN BAHAN BAKU SINGKONG

    Directory of Open Access Journals (Sweden)

    Rochmad Winarso

    2014-11-01

    Full Text Available ABSTRAK Penyediaan energi di masa depan merupakan permasalahan yang senantiasa menjadi perhatian bagi semua pihak. Seiring dengan meningkatnya pembangunan, kebutuhan akan energi terus meningkat. Disisi lain cadangan minyak bumi sebagai bahan bakar yang paling banyak dipakai saat ini semakin menipis karena sifatnya yang non renewable, oleh karena itu diperlukan upaya untuk mencari bahan bakar alternatif yang renewable sekaligus ramah lingkungan. Bioetanol sebagai salah satu bahan bakar alternatif sampai saat ini belum banyak digunakan. Padahal di Indonesia, banyak sekali sumber daya alam hayati yang dapat digunakan sebagai bahan baku untuk memproduksi bioetanol, salah satunya adalah ubi kayu. Penggunaan bioetanol sebagai bahan bakar didasari oleh sifatnya yang mudah terbakar dan memiliki kalor-bakar netto besar. Tujuan dari penelitian ini adalah mengembangkan alat destilator bioetanol dengan fokus pengembangan pada pengembangan menara refluk dengan sistem bertingkat sehingga diharapkan bisa lebih optimal menghasilkan bioetanol dengan kadar tinggi. Pengembangan alat distilator bioethanol ini dimulai dari proses observasi lapangan yang dilanjutkan dengan studi literatur. Tahapan selajutnya adalah proses perencanaan komponen-komponen dari peralatan tersebut dan dilanjutkan dengan proses pembuatan serta uji coba peralatan. Hasil penelitian ini telah dikembangkan alat destilator bioetanol dengan spesifikasi sebagai berikut: diameter tangki 400 mm, tinggi tangki 500 mm, terbuat dari bahan stainles steel A304 dengan ketebalan 2 mm. Kapasitas tangki yang diijinkan adalah dari volume tabung atau sebesar 40 liter. Dari hasil uji coba pada hasil proses distilasi fermentasi ketela pohon menghasilkan ethanol dengan kadar 92%. Kata kunci: bioetanol, destilator, refluk bertingkat.

  13. PENDIDIKAN KARAKTER BANGSA BERBASIS STRATEGI PEMBELAJARAN PAKEM MELALUI PERMAINAN CINCIN DI JEMPOL TANGAN (Karya Inovasi Pembelajaran Sekolah Dasar

    Directory of Open Access Journals (Sweden)

    Ani Adibatin

    2016-02-01

    Full Text Available Berhasil tidaknya pencapaian tujuan pembelajaran sangat ditentukan oleh kemampuan guru dalam mengelola kelas, mengelola siswa, memilih strategi pembelajaran, serta kebermaknaan dalam memberikan tugas pada siswa. Berkaitan dengan permasalahan tersebut, penulis sebagai pengawas mengembangkan alat permainan inovatif yang bisa dipakai oleh semua guru, baik guru kelas, guru mata pelajaran, maupun guru ekstra kurikuler. Alat permainan ini bisa dipakai oleh semua siswa dari berbagai tingkatan kelas, berbagai tingkat jenjang sekolah, dan untuk pembelajaran materi yang berbeda. Alat permainan inovatif pembelajaran ini dikembangkan dengan tujuan agar peserta didik bisa belajar sambil bermain dan bermain sambil belajar. Disamping itu, untuk membantu para guru dalam menanamkan pendidikan karakter, sehingga peserta didik menjadi anak yang berkarakter, berwatak sesuai dengan nilai-nilai Pancasila demi terwujudnya tujuan pendidikan nasional. Uji coba alat permainan inovatif ini dilakukan di 9 SD binaan Kecamatan Tuntang. Dari hasil uji coba diperoleh temuan bahwa ada perbedaan yang sangat signifikan antara pendidikan karakter pada pembelajaran tanpa alat permainan inovatif dibandingkan dengan pembela-jaran yang menggunakan alat permainan cincin akik di jempol tangan. Nilai rata-rata pembelajaran tanpa alat inovatif 76,55 %, sedangkan nilai rata-rata dengan menggunakan alat permainan cincin akik di jempol sebesar 86,88 %. Hasil pembelajaran menggunakan alat peraga inovatif ini menunjukkan bah-wa melalui strategi pembelajaran PAKEM dengan bermain cincin akik di jempol tangan dapat membangun karakter peserta didik sampai 11,33 %.

  14. Longitudinal Quantitative Detection by Real-Time PCR of Mycoplasma genitalium in First-Pass Urine of Men with Recurrent Nongonococcal Urethritis

    Science.gov (United States)

    Deguchi, Takashi; Yoshida, Takashi; Yokoi, Shigeaki; Ito, Masayasu; Tamaki, Masayoshi; Ishiko, Hiroaki; Maeda, Shin-Ichi

    2002-01-01

    By using a TaqMan assay we monitored longitudinal changes in Mycoplasma genitalium loads in five men with recurrent M. genitalium-positive nongonococcal urethritis. We observed regrowth of M. genitalium persisting in hosts after treatment and a possible association of the increase in the M. genitalium load with emergence of symptoms and signs of nongonococcal urethritis in four of these patients. PMID:12354899

  15. Allele Frequency - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nd 39 SNPs are assayed in three (POP_*) and two (RIKEN_japanese_*) panels, respectively. Derived from Flat f... assay (JBIC-allele and RIKEN_japanese_*), TaqMan assay (RIKEN-allele) or direct sequencing / allelic discri...unteers under informed consent RIKEN_japanese_normal_weight - 711 unrelated japanese normal weight volunteer...s ( body mass index RIKEN_japanese_obese - 796 unrelated japanese obese patients

  16. Development of Medical Technology for Contingency Response to Marrow Toxic Agents

    Science.gov (United States)

    2016-10-07

    Purified genomic DNA absorbed onto cotton- tipped swabs (“DNA swabs”) has proven to be successful and cost-effective alternative QC sample type...inversely correlated with the ability to achieve long range PCR amplification of the DNA obtained from the cotton tipped swab used by NMDP for donor...Harvey, C. Steward and V. Rocha 800 pairs Microsatellit es and STR Taqman In process Prognostic impact of somatic mutation and the levels of

  17. Development of Medical Technology for Contingency Response to Marrow Toxic Agents

    Science.gov (United States)

    2018-01-18

    Antigen will Result in Robust Serologic Response to H-Y Antigens in Male HSC transplantation Recipients D. Miklos 288 pairs H-Y Antigen ELISA ...Arai, D. Miklos 200 pairs Anti-body ELISA , Protein array Yes Detection of Donor- Directed, HLA-Specific Alloantibodies in Recipients of...SNPs ELISA and Taqman Yes Natural killer cell genomics and outcomes after allogeneic transplantation for lymphoma V. Bachanova, J. Miller

  18. Molecular diagnosis of lyssaviruses and sequence comparison of Australian bat lyssavirus samples.

    Science.gov (United States)

    Foord, A J; Heine, H G; Pritchard, L I; Lunt, R A; Newberry, K M; Rootes, C L; Boyle, D B

    2006-07-01

    To evaluate and implement molecular diagnostic tests for the detection of lyssaviruses in Australia. A published hemi-nested reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of all lyssavirus genotypes was modified to a fully nested RT-PCR format and compared with the original assay. TaqMan assays for the detection of Australian bat lyssavirus (ABLV) were compared with both the nested and hemi-nested RT-PCR assays. The sequences of RT-PCR products were determined to assess sequence variations of the target region (nucleocapsid gene) in samples of ABLV originating from different regions. The nested RT-PCR assay was highly analytically specific, and at least as analytically sensitive as the hemi-nested assay. The TaqMan assays were highly analytically specific and more analytically sensitive than either RT-PCR assay, with a detection level of approximately 10 genome equivalents per microl. Sequence of the first 544 nucleotides of the nucleocapsid protein coding sequence was obtained from all samples of ABLV received at Australian Animal Health Laboratory during the study period. The nested RT-PCR provided a means for molecular diagnosis of all tested genotypes of lyssavirus including classical rabies virus and Australian bat lyssavirus. The published TaqMan assay proved to be superior to the RT-PCR assays for the detection of ABLV in terms of analytical sensitivity. The TaqMan assay would also be faster and cross contamination is less likely. Nucleotide sequence analyses of samples of ABLV from a wide geographical range in Australia demonstrated the conserved nature of this region of the genome and therefore the suitability of this region for molecular diagnosis.

  19. Molecular diagnostics for the detection of Bokeloh bat lyssavirus in a bat from Bavaria, Germany.

    Science.gov (United States)

    Freuling, Conrad M; Abendroth, Björn; Beer, Martin; Fischer, Melina; Hanke, Dennis; Hoffmann, Bernd; Höper, Dirk; Just, Frank; Mettenleiter, Thomas C; Schatz, Juliane; Müller, Thomas

    2013-11-06

    A brain sample of a Natterer's bat tested positive for rabies with classical virological techniques. Molecular techniques confirmed the presence of Bokeloh bat lyssavirus (BBLV) in Germany for the second time. Sequence analysis revealed a close genetic relationship to the initial German BBLV case. Using a TaqMan RT-PCR specific for BBLV viral RNA was detected in various other organs albeit with differences in the relative viral load. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Relationship Between Genotype Variants Follicle-stimulating Hormone Receptor Gene Polymorphisms (FSHR) and Morphology of Oocytes Prior to ICSI Procedures

    OpenAIRE

    Gashi, Zafer; Elezaj, Shkelzen; Zeqiraj, Afrim; Grabanica, Driton; Shabani, Isak; Gruda, Bujar; Gashi, Fitore

    2016-01-01

    Introduction: This study investigated association of Asn680Ser FSHR polymorphism with the ovarian response in 104 women of Albanian ethnic population enrolled in ICSI program. The reason of infertility in all cases has been identified as male factor. Methods: Analysis of the Asn680Ser polymorphism was performed using TaqMan? SNP Genotyping Assay. Clinical and endocrinologic parameters were analyzed based on the genotype, age, BMI, oocyte yield, number of transferred embryos and pregnancy rate...

  1. Monitoring and improving the sensitivity of dengue nested RT-PCR used in longitudinal surveillance in Thailand.

    Science.gov (United States)

    Klungthong, Chonticha; Manasatienkij, Wudtichai; Phonpakobsin, Thipwipha; Chinnawirotpisan, Piyawan; Rodpradit, Prinyada; Hussem, Kittinun; Thaisomboonsuk, Butsaya; Ong-ajchaowlerd, Prapapun; Nisalak, Ananda; Kalayanarooj, Siripen; Buddhari, Darunee; Gibbons, Robert V; Jarman, Richard G; Yoon, In-Kyu; Fernandez, Stefan

    2015-02-01

    AFRIMS longitudinal dengue surveillance in Thailand depends on the nested RT-PCR and the dengue IgM/IgG ELISA. To examine and improve the sensitivity of the nested RT-PCR using a panel of archived samples collected during dengue surveillance. A retrospective analysis of 16,454 dengue IgM/IgG ELISA positive cases collected between 2000 and 2013 was done to investigate the sensitivity of the nested RT-PCR. From these cases, 318 acute serum specimens or extracted RNA, previously found to be negative by the nested RT-PCR, were tested using TaqMan real-time RT-PCR (TaqMan rRT-PCR). To improve the sensitivity of nested RT-PCR, we designed a new primer based on nucleotide sequences from contemporary strains found to be positive by the TaqMan rRT-PCR. Sensitivity of the new nested PCR was calculated using a panel of 87 samples collected during 2011-2013. The percentage of dengue IgM/IgG ELISA positive cases that were negative by the nested RT-PCR varied from 17% to 42% for all serotypes depending on the year. Using TaqMan rRT-PCR, dengue RNA was detected in 194 (61%) of the 318 acute sera or extracted RNA previously found to be negative by the nested RT-PCR. The newly designed DENV-1 specific primer increased the sensitivity of DENV-1 detection by the nested RT-PCR from 48% to 88%, and of all 4 serotypes from 73% to 87%. These findings demonstrate the impact of genetic diversity and signal erosion on the sensitivity of PCR-based methods. Published by Elsevier B.V.

  2. Investigation of Ureaplasma urealyticum biovars and their relationship with antimicrobial resistance

    Directory of Open Access Journals (Sweden)

    Zhu Chang-tai

    2011-01-01

    Full Text Available Purpose: To develop Taqman fluorescence quantitative polymerase chain reaction (PCR method for investigating the characteristics of the distributions of Ureaplasma urealyticum (UU biovars and to explore the relationship between UU biovars and antimicrobial resistance. Materials and Methods: By the method of culture, Ureaplasma species were detected. Taqman fluorescence quantitative PCR for detecting UU biovars were developed and UU clinical isolates were detected to distinguish biovars. The broth micro-dilution susceptibility testing methods were used to determine UU susceptibility. Results: By Taqman PCR method, UU biovars was successfully detected. Of 126 samples, biovar 1 was found in 73 (57.94%. There was a statistical difference between genital-urinary tract infection group and asymptomatic group (P<0.05. In the region, UU biovar 1 to 9 kinds of agents kept higher susceptibility rates, but biovar 2 maintained higher susceptibility rates only to tetracyclines. Compared with biovar 1, UU biovar 2 resistance rates to 7 kinds of agents were higher (P<0.05. Conclusions: (1 Our new established Taqman PCR method is a useful tool for screening UU biovars. (2 UU biovar 1 predominated in asymptomatic population; whereas in genital-urinary tract infection population UU biovar 2 had a higher proportion. (3 The characteristics of drug resistance were different between UU biovars. Overall, both two biovars remained higher susceptibility rates to tetracyclines. A majority of biovor 1 strains were sensitive to macrolides and quinolones; while only a small number of biovar 2 strains kept sensitive to roxithromycin and quinolones, a large proportion of biovar 2 strains were found in intermediate ranges.

  3. Real-time PCR for type-specific identification of herpes simplex in clinical samples: evaluation of type-specific results in the context of CNS diseases.

    Science.gov (United States)

    Meylan, Sylvain; Robert, Daniel; Estrade, Christine; Grimbuehler, Valérie; Péter, Olivier; Meylan, Pascal R; Sahli, Roland

    2008-02-01

    HSV-1 and HSV-2 cause CNS infections of dissimilar clinico-pathological characteristics with prognostic and therapeutic implications. To validate a type-specific real-time PCR that uses MGB/LNA Taqman probes and to review the virologico-clinical data of 25 eligible patients with non-neonatal CNS infections. This real-time PCR was evaluated against conventional PCR (26 CSF and 20 quality controls), and LightCycler assay (51 mucocutaneous, 8 CSF and 32 quality controls) and culture/immunofluorescence (75 mucocutaneous) to assess typing with independent methods. Taqman real-time PCR detected 240 HSV genomes per ml CSF, a level appropriate for the management of patients, and provided unambiguous typing for the 104 positive (62 HSV-1 and 42 HSV-2) out the 160 independent clinical samples tested. HSV type diagnosed by Taqman real-time PCR predicted final diagnosis (meningitis versus encephalitis/meningoencephalitis, p<0.001) in 24/25 patients at time of presentation, in contrast to clinical evaluation. Our real-time PCR, as a sensitive and specific means for type-specific HSV diagnosis, provided rapid prognostic information for patient management.

  4. Evaluation of CYP1A1 and CYP2B1/2 m-RNA induction in rat liver slices using the NanoString technology: a novel tool for drug discovery lead optimization.

    Science.gov (United States)

    Palamanda, Jairam R; Kumari, Pramila; Murgolo, Nicholas; Benbow, Larry; Lin, Xinjie; Nomeir, Amin A

    2009-08-01

    Cytochrome P450 (CYP) induction in rodents and humans is considered a liability for new chemical entities (NCEs) in drug discovery. In particular, CYP1A1 and CYP2B1/2 have been associated with the induction of liver tumors in oncogenicity studies during safety evaluation studies of potential drugs. In our laboratory, real time PCR (Taqman) has been used to quantify the induction of rat hepatic CYP1A1 and CYP2B1/2 in precision -cut rat liver slices. A novel technology that does not require m-RNA isolation or RT-PCR, (developed by NanoString Technologies) has been investigated to quantify CYP1A1 and CYP2B1/2 induction in rat liver slices. Seventeen commercially available compounds were evaluated using both Taqman and NanoString technologies. Precision-cut rat liver slices were incubated with individual compounds for 24 hr at 37 degrees C in a humidified CO(2) incubator and CYP1A1 and CYP2B1/2 m-RNA were quantified. The results from the NanoString technology were similar to those of the Taqman(R) with a high degree of correlation for both CYP isoforms (r(2)>0.85). Therefore, NanoString provides an additional new technology to evaluate the induction of CYP1A1 and 2B1/2, as well as potentially other enzymes or transporters in rat liver slices.

  5. Use of real-time qPCR to quantify members of the unculturable heterotrophic bacterial community in a deep sea marine sponge, Vetulina sp.

    Science.gov (United States)

    Cassler, M; Peterson, C L; Ledger, A; Pomponi, S A; Wright, A E; Winegar, R; McCarthy, P J; Lopez, J V

    2008-04-01

    In this report, real-time quantitative PCR (TaqMan qPCR) of the small subunit (SSU) 16S-like rRNA molecule, a universal phylogenetic marker, was used to quantify the relative abundance of individual bacterial members of a diverse, yet mostly unculturable, microbial community from a marine sponge. Molecular phylogenetic analyses of bacterial communities derived from Caribbean Lithistid sponges have shown a wide diversity of microbes that included at least six major subdivisions; however, very little overlap was observed between the culturable and unculturable microbial communities. Based on sequence data of three culture-independent Lithistid-derived representative bacteria, we designed probe/primer sets for TaqMan qPCR to quantitatively characterize selected microbial residents in a Lithistid sponge, Vetulina, metagenome. TaqMan assays included specificity testing, DNA limit of detection analysis, and quantification of specific microbial rRNA sequences such as Nitrospira-like microbes and Actinobacteria up to 172 million copies per microgram per Lithistid sponge metagenome. By contrast, qPCR amplification with probes designed for common previously cultured sponge-associated bacteria in the genera Rheinheimera and Marinomonas and a representative of the CFB group resulted in only minimal detection of the Rheiheimera in total DNA extracted from the sponge. These data verify that a large portion of the microbial community within Lithistid sponges may consist of currently unculturable microorganisms.

  6. Development of Real-Time PCR Methods for the Detection of Bacterial Meningitis Pathogens without DNA Extraction.

    Directory of Open Access Journals (Sweden)

    Jeni Vuong

    Full Text Available Neisseria meningitidis (Nm, Haemophilus influenzae (Hi, and Streptococcus pneumoniae (Sp are the lead causes of bacterial meningitis. Detection of these pathogens from clinical specimens using traditional real-time PCR (rt-PCR requires DNA extraction to remove the PCR inhibitors prior to testing, which is time consuming and labor intensive. In this study, five species-specific (Nm-sodC and -ctrA, Hi-hpd#1 and -hpd#3 and Sp-lytA and six serogroup-specific rt-PCR tests (A, B, C, W, X, Y targeting Nm capsular genes were evaluated in the two direct rt-PCR methods using PerfeCTa and 5x Omni that do not require DNA extraction. The sensitivity and specify of the two direct rt-PCR methods were compared to TaqMan traditional rt-PCR, the current standard rt-PCR method for the detection of meningitis pathogens. The LLD for all 11 rt-PCR tests ranged from 6,227 to 272,229 CFU/ml for TaqMan, 1,824-135,982 for 5x Omni, and 168-6,836 CFU/ml for PerfeCTa. The diagnostic sensitivity using TaqMan ranged from 89.2%-99.6%, except for NmB-csb, which was 69.7%. For 5x Omni, the sensitivity varied from 67.1% to 99.8%, with three tests below 90%. The sensitivity of these tests using PerfeCTa varied from 89.4% to 99.8%. The specificity ranges of the 11 tests were 98.0-99.9%, 97.5-99.9%, and 92.9-99.9% for TaqMan, 5x Omni, and PerfeCTa, respectively. PerfeCTa direct rt-PCR demonstrated similar or better sensitivity compared to 5x Omni direct rt-PCR or TaqMan traditional rt-PCR. Since the direct rt-PCR method does not require DNA extraction, it reduces the time and cost for processing CSF specimens, increases testing throughput, decreases the risk of cross-contamination, and conserves precious CSF. The direct rt-PCR method will be beneficial to laboratories with high testing volume.

  7. Detection of knockdown resistance (kdr) mutations in Anopheles gambiae: a comparison of two new high-throughput assays with existing methods

    Science.gov (United States)

    Bass, Chris; Nikou, Dimitra; Donnelly, Martin J; Williamson, Martin S; Ranson, Hilary; Ball, Amanda; Vontas, John; Field, Linda M

    2007-01-01

    Background Knockdown resistance (kdr) is a well-characterized mechanism of resistance to pyrethroid insecticides in many insect species and is caused by point mutations of the pyrethroid target site the para-type sodium channel. The presence of kdr mutations in Anopheles gambiae, the most important malaria vector in Africa, has been monitored using a variety of molecular techniques. However, there are few reports comparing the performance of these different assays. In this study, two new high-throughput assays were developed and compared with four established techniques. Methods Fluorescence-based assays based on 1) TaqMan probes and 2) high resolution melt (HRM) analysis were developed to detect kdr alleles in An. gambiae. Four previously reported techniques for kdr detection, Allele Specific Polymerase Chain Reaction (AS-PCR), Heated Oligonucleotide Ligation Assay (HOLA), Sequence Specific Oligonucleotide Probe – Enzyme-Linked ImmunoSorbent Assay (SSOP-ELISA) and PCR-Dot Blot were also optimized. The sensitivity and specificity of all six assays was then compared in a blind genotyping trial of 96 single insect samples that included a variety of kdr genotypes and African Anopheline species. The relative merits of each assay was assessed based on the performance in the genotyping trial, the length/difficulty of each protocol, cost (both capital outlay and consumable cost), and safety (requirement for hazardous chemicals). Results The real-time TaqMan assay was both the most sensitive (with the lowest number of failed reactions) and the most specific (with the lowest number of incorrect scores). Adapting the TaqMan assay to use a PCR machine and endpoint measurement with a fluorimeter showed a slight reduction in sensitivity and specificity. HRM initially gave promising results but was more sensitive to both DNA quality and quantity and consequently showed a higher rate of failure and incorrect scores. The sensitivity and specificity of AS-PCR, SSOP-ELISA, PCR Dot

  8. PENGEMBANGAN WEB INTRANET FISIKA UNTUK MENINGKATKAN PENGUASAAN KONSEP DAN KEMAMPUAN PEMECAHAN MASALAH SISWA SMK

    Directory of Open Access Journals (Sweden)

    A. Doyan

    2014-07-01

    Full Text Available Penelitian ini bertujuan untuk mengembangkan media pembelajaran web intranet fisika dan mengetahui pengaruhnya terhadap penguasaan konsep dan kemampuan pemecahan masalah siswa. Penelitian ini menggunakan desain penelitian dan pengembangan model Borg dan Gall yang dimodifikasi menjadi tiga tahap, yaitu tahap studi pendahuluan, tahap pengembangan media,dan tahap uji coba media. Tahap studi pendahuluan dilaksanakan dengan studi kepustakaan dan survei awal. Tahap pengembangan media menghasilkan draf awal media. Penelitian dilanjutkan dengan tahap implementasi uji coba terbatas dan uji coba lebih luas media pembelajaran web intranet fisika di SMKN 2 Praya Tengah. Pembelajaran materi usaha, energi, dan daya di kelas eksperimen menggunakan web intranet fisika sedangkan di kelas kontrol menggunakan pembelajaran konvensional. Kedua kelas dianalisis menggunakan uji perbedaan rata-rata (Uji t atau Uji Mann-Whitney dan skor gain ternormalisasi (N-gain. Berdasarkan hasil penelitian dapat disimpulkan bahwa pembelajaran web intranet fisika efektif meningkatkan penguasaan konsep tetapi tidak efektif meningkatkan kemampuan pemecahan masalah siswa SMK.ABSTRACTThe research was aimed at developing a learning media of physics intranet web and knowing its impacts to the student’s concept comprehension and problem solving skills. The research used a research design and development model of Borg and Gall which was modified into three stages; those were stage of preliminary study, stage of media development, and stage of media testing.The stage of preliminary study was conducted by having literature review and initial survey. Furthermore media development generated an initial draft of media. The research was continued with the stage of limited testing and more extensive testing implementation of physics intranet web learning media at SMKN 2 Praya Tengah. The learning material of work, energy and power in the experimental group used the physics intranet web, while the

  9. PENGEMBANGAN MODUL GEOGRAFI PARIWISATA BERBASIS PAKET WISATA PULAU LOMBOK SEBAGAI UPAYA MEMUPUK RASA CINTA TANAH AIR PADA MAHASISWA

    Directory of Open Access Journals (Sweden)

    Andrinata Andrinata

    2016-10-01

    Full Text Available The purpose of the study is to produce the tourism geography module based on the Lombok tourism packages that is prepared in accordance with the module design of C Michael and Stephen J. Page. This study is designed with Dick & Carey model and simplified into six steps. The quality of product is known through the lecturer’s feedback and students during the field test. The trial subjects are the students of Geography Education STKIP Hamzanwadi Selong in the sixth semester in year 2013 who have taken the course. Based on the results of validation and field trials, the numbers of scores are obtained namely: (a the assessment of the expert design towards the components of the module is 82.7%, (b the assessment of the content/materials to components of the module is 83%, (c the assessment of the language expert of language towards the module components is 76%, (d the assessment of the lecturer of the course and students towards the questionnaires is distributed associated with the products and developed each score 84.28% and 86.4%. The average value of the results of validation and field trials, the module is developed and appropriately used as learning sources with percentage 82.5%. Tujuan penelitian ini ialah menghasilkan modul Geografi Pariwisata Berbasis Paket Wisata Pulau Lombok yang disusun sesuai dengan desain modul C. Michael Hall dan Stephen J. Page. Penelitian ini didesain dengan pendekatan penelitian pengembangan model Dick & Carey yang disederhanakan menjadi enam langkah. Kualitas produk diketahui melalui hasil tanggapan dari dosen pengampu matakuliah dan mahasiswa pada saat uji lapangan. Subjek uji coba yakni mahasiswa Program Studi Pendidikan Geografi STKIP Hamzanwadi Selong pada semester VI angkatan 2013 yang telah menempuh matakuliah tersebut. Berdasarkan hasil validasi dan uji coba lapangan, jumlah skor yang didapat yakni: (a penilaian ahli desain pembelajaran terhadap komponen modul adalah 82,7, (b penilaian ahli isi

  10. Pengembangan problem based learning dengan assessment for learning berbantuan smartphone dalam pembelajaran matematika

    Directory of Open Access Journals (Sweden)

    Muhammad Ridlo Yuwono

    2017-11-01

    Full Text Available [Bahasa]: Penelitian ini bertujuan untuk menghasilkan model Problem Based Learning (PBL menggunakan penilaian Assessment for Learning (AfL berbantuan smartphone, disingkat PBL-AfL-S yang valid, praktis dan efektif untuk mendukung implementasi kurikulum 2013 di SMA. Tahap-tahap pengembangan model PBL-AfL-S terdiri dari penelitian pendahuluan, pengembangan/prototiping, dan evaluasi. Kualitas model PBL-AfL-S mengacu pada kriteria kualitas menurut Nieveen (1999 yaitu valid, praktis, dan efektif. Model PBL-AfL-S diujicobakan di SMA Negeri 3 Klaten dalam dua tahap uji coba. Uji coba tahap I dilaksanakan di kelas XI-IPA 6 dan uji coba tahap II dilaksanakan di kelas XI-IPA 7. Instrumen penelitian terdiri dari: 1 Instrumen penilaian kevalidan komponen model dan perangkat pendukung pembelajaran, 2 Instrumen kepraktisan aktivitas guru dan siswa, dan 3 Instrumen keefektifan yang meliputi angket penilaian diri, lembar penilaian proyek, tes prestasi belajar, dan lembar respon siswa. Hasil penelitian menunjukkan bahwa model PBL-AfL-S dan perangkat pembelajarannya telah memenuhi kriteria valid, praktis dan efektif. Kata kunci: Pembelajaran; Masalah; Asesmen; Smartphone [English]: This study aims to develop a Problem Based Learning (PBL model using Assessment for Learning (AFL with smartphone, abbreviated as PBL-AfL-S as valid, practical and effective to support the implementation of the 2013 curriculum in High School. The stages of developing the PBL-AfL-S model consist of preliminary research, development or prototyping, and evaluation. The quality criteria of PBL-AfL-S refer to Nieveen (1999, i.e. valid, practical, and effective. The PBL-AfL-S model was piloted in SMA Negeri 3 Klaten in two phases. Tryout 1 was conducted in class XI-IPA 6 and tryout 2 was in class XI-IPA 7. The research instruments consist of: 1 The validity instrument of the model and its learning support tools, 2 the practicality of the teacher’s and students’ activity, and 3 The

  11. PERANGKAT PEMBELAJARAN PERISTIWA ALAM DENGAN MODEL COOPERATIVE LEARNING TIPE INSIDE OUTSIDE CIRCLE

    Directory of Open Access Journals (Sweden)

    Diah Sunarsih

    2015-08-01

    Full Text Available Tujuan penelitian ini menghasilkan perangkat pembelajaran IPA dengan model pembelajaran cooperative learning tipe inside outside circle untuk dapat meningkatkan kemampuan berpikir kognitif dan menumbuhkan kemampuan komunikasi ilmiah siswa yang valid materi peristiwa alam. Uji coba skala terbatas dilakukan di SDN 02 Ambowetan. Uji coba skala luas kelas eksperimen SDN 01 Ambowetan VA, sedangkan kelas kontrol SDN 01 Ambowetan VB. Desain uji coba penelitian ini nonequivalent control group design. Prosedur pengembangan dan penelitian dikembangkan mengacu model pengembangan Dick dan Carry terdiri 4 tahap yaitu define, design, develop, dan disseminate. Hasil penelitian diperoleh pengembangan perangkat pembelajaran menerapkan model pembelajaran cooperative learning tipe inside outside circle berupa silabus, RPP, bahan ajar, lembar tes formatif, lembar observasi kemampuan komunikasi ilmiah, dan angket respon siswa valid, efektif, dan praktis diterapkan dalam pembelajaran IPA kelas V sekolah dasar materi peristiwa alam. Perangkat pembelajaran valid dengan nilai skor validitas akhir 3,43. Perangkat pembelajaran efektif terlihat peningkatan hasil uji N-gain menunjukkan hasil 0,50 pada klasifikasi tingkat sedang dan prosentase kemampuan ilmiah kelas eksperimen hasil sebesar 82%. Kriteria praktis dari nilai angket menunjukkan respon siswa kelas eksperimen lebih tinggi dibandingkan kelas kontrol (73% > 67 %.Purpose of this study is produce device the learning cooperative learning type inside outside circle to improve cognitive ability students and foster communication skills scientific a valid on material natural events. Trials limited scale in the SDN 02 Ambowetan. Trials wide scale for experimental class in the SDN 01 Ambowetan 5A, while the control class SDN 01 Ambowetan 5B. Design wide scale nonequivalent control group design. Procedures the development and developed research Dick and Carry consisting of 4 stage define, design, develop, and disseminate

  12. Preliminary study on the coconut crab (Birgus latro rearing in captive pond

    Directory of Open Access Journals (Sweden)

    . Sulistiono

    2009-01-01

    Full Text Available Preliminary study on the coconut crab (Birgus latro rearing was employed in captive pond at Citarate village, Lebak Regency (Banten from May to December 2008.  The rearing activity was done in captive pond sized 5x5x1.3 m3 divided into 22 smaller ponds sized 1x1x1.3 m3 with a hiding hole (constructed by pile stones, supported by two small ponds sized 30x40x40 cm3 for sea and fresh water stocks, respectively.  The coconut crab (N=22 individuals at cement pond I and N=18 individuals at cement pond II were reared in each small ponds (density: 1 individual/pond, feed by a piece of coconut (20-50 gram per individual in each cement pond.  The coconut and the water (sea and fresh water were replaced for 2-3 times per week. Result of the study showed that survival rate was around 82% (ponds I and 83% (ponds II, and mortality was around 18% (ponds I and 18% (ponds II. The coconut crab growth at captive ponds I and II were around 17.5 and 52 gram per month, respectively. Key words:  Preliminary study, rearing, coconut crab (Birgus latro   ABSTRAK Uji coba pemeliharaan kepiting kelapa (Birgus latro dilakukan di kolam penangkaran di Desa Citarate, Kabupaten Lebak (Banten pada Bulan Mei sampai Desember 2008.  Kegiatan pemeliharaan dilakukan pada bak semen berukuran 5x5x1.3 m2 yang terbagi menjadi 22 bak semen lebih kecil yang berukuran 1x1x1.3 m3 dilengkapi dengan tempat persembunyian (berupa tumpukan batu, serta bak kecil sebagai tempat penampungan air laut dan tawar masing-masing berukuran 30x40x40 cm3. Kepiting kelapa (N=22 ekor pada kolam I dan N=18 pada kolam II dimasukkan ke dalam setiap kolam (kepadatan 1 individu/kolam, dan diberikan pakan utama berupa potongan kelapa ukuran sekitar 20-50 gram per individu per kolam.  Penggantian kelapa dan air (tawar dan laut dilakukan 2-3 kali per minggu. Hasil uji coba pemeliharaan kepiting kelapa menunjukkan bahwa tingkat sintasan (survival rate di kolam peliharaan berkisar 82 (Kolam I dan 83% (Kolam II

  13. Pengembangan Modul Pembelajaran Fisika Berbasis Problem Based Learning (PBL pada Materi Gelombang Bunyi untuk Siswa SMA Kelas XII

    Directory of Open Access Journals (Sweden)

    Tri Anita Nur Hasanah

    2017-03-01

    dilakukan dalam tiga tahap yaitu pendefinisian (define, perancangan (design dan pengembangan (develop yang dibatasi sampa uji coba terbatas. Validasi modul oleh 4 validator dan uji coba terbatas  kepada 10 orang siswa. Dari hasil penelitan diperoleh skor segi  materi sebesar 3,59 dengan kriteria layak, segi penyajian sebesar 3,9 dengan kriteria layak, segi bahasa sebesar 3,41 dengan kriteria layak dan hasil uji coba terbatas mendapat rerata skor sebesar  3,6 dengan kriteria sesuai. Dapat disimpulkan bahwa modul pembelajaran fisika berbasis PBL pada materi Gelombang Bunyi untuk siswa SMA kelas XII layak digunakan. Kata Kunci: Modul Pembelajaran Fisika, Problem Based Learning (PBL, Gelombang Bunyi

  14. Whole blood samples for adrenocorticotrophic hormone measurement can be stored at room temperature for 4 hours

    DEFF Research Database (Denmark)

    Christensen, Mette; Madsen, Rikke Fogt; Møller, Line Rosengreen

    2016-01-01

    INTRODUCTION: The aim of this study was to investigate and compare the stability of adrenocorticotrophic hormone (ACTH) in whole blood stored on ice and at room temperature for up to 48 hours. This study differs from previous studies by a larger data material. MATERIALS AND METHODS: EDTA-blood sa......INTRODUCTION: The aim of this study was to investigate and compare the stability of adrenocorticotrophic hormone (ACTH) in whole blood stored on ice and at room temperature for up to 48 hours. This study differs from previous studies by a larger data material. MATERIALS AND METHODS: EDTA......-blood samples from 30 patients were collected, aliquoted and stored on ice or at room temperature for 0, 2, 4, 24, or 48 h before centrifugation, and the plasma was stored frozen until analysis. All samples were analyzed using an automated electrochemiluminescence immunoassay on cobas 6000 e601. The change...

  15. Duplex detection of the Mycobacterium tuberculosis complex and medically important non-tuberculosis mycobacteria by real-time PCR based on the rnpB gene.

    Science.gov (United States)

    Abdeldaim, Guma; Svensson, Erik; Blomberg, Jonas; Herrmann, Björn

    2016-11-01

    A duplex real-time PCR based on the rnpB gene was developed for Mycobacterium spp. The assay was specific for the Mycobacterium tuberculosis complex (MTB) and also detected all 19 tested species of non-tuberculous mycobacteria (NTM). The assay was evaluated on 404 clinical samples: 290 respiratory samples and 114 from tissue and other non-respiratory body sites. M. tuberculosis was detected by culture in 40 samples and in 30 samples by the assay. The MTB assay showed a sensitivity similar to Roche Cobas Amplicor MTB-PCR (Roche Molecular Systems, Pleasanton, CA, USA). There were only nine samples with non-tuberculous mycobacteria detected by culture. Six of them were detected by the PCR assay. © 2016 APMIS. Published by John Wiley & Sons Ltd.

  16. Pengembangan Model Manajemen ICT Center

    Directory of Open Access Journals (Sweden)

    Hakkun Elmunsyah

    2013-01-01

    Full Text Available Abstrak: Pengembangan Model Manajemen ICT Center. Kemendiknas telah melakukan investasi  cukup besar berupa pembangunan Jejaring komputer pendidikan nasional yang disebut Jaringan Pendidikan Nasional (Jardiknas, pada sekolah menengah kejuruan (SMK di seluruh Indonesia yang dikenal dengan nama ICT center. Penelitian ini bertujuan untuk menemukan model manajemen ICT center sesuai karakteristik SMK sehingga dapat memberikan kontribusi mutu pada SMK tersebut. Penelitian ini merupakan penelitian pengembangan atau Research and Development yang dikembangkan oleh Borg and Gall. Hasil secara keseluruhan penelitian menunjukkan berdasarkan uji coba keefektivan kinerja manajemen pada skala terbatas dan lebih luas menunjukkan bahwa model manajemen ICT center memenuhi kriteria sangat efektif. Kata-kata kunci: Jardiknas, SMK, model manajemen ICT center, kontribusi mutu

  17. Serum prolactin revisited

    DEFF Research Database (Denmark)

    Overgaard, Martin; Pedersen, Susanne Møller

    2017-01-01

    regimes across commonly used automated immunoassay platforms. METHODS: Parametric total and monomeric gender-specific reference intervals were determined for six immunoassay methods using female (n=96) and male sera (n=127) from healthy donors. The reference intervals were validated using 27...... and macroprolactinemic; n=27) showed higher discordant classification [mean=2.8; 95% confidence interval (CI) 1.2-4.4] for the monomer reference interval method compared to the post-polyethylene glycol (PEG) recovery cutoff method (mean=1.8; 95% CI 0.8-2.8). The two monomer/macroprolactin discrimination methods did...... not differ significantly (p=0.089). Among macroprolactinemic sera evaluated by both discrimination methods, the Cobas and Architect/Kryptor prolactin assays showed the lowest and the highest number of misclassifications, respectively. CONCLUSIONS: Current automated immunoassays for prolactin testing require...

  18. SURVEI PENANGANAN BROADCAST STORM PROBLEM PADA PROTOKOL ROUTING AODV DI MANET

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    Indera Zainul Muttaqien

    2015-07-01

    Full Text Available Komunikasi multi-hop pada lingkungan MANET dapat melibatkan broadcast paket dalam proses route discovery. Protokol routing pada MANET akan melakukan broadcast paket RREQ dan menjalarkannya ke node tujuan secepat dan seefisien mungkin, dimana paket RREQ dari rute yang optimal adalah paket RREQ yang terlebih dahulu sampai ke tujuan. Aktifitas broadcast yang tidak terkontrol dapat menyebabkan suatu kondisi yang disebut broadcast storm problem. Broadcast storm problem dapat berdampak pada terganggunya kinerja dari protokol routing akibat adanya packet redundancy, contention, dan collision. Broadcast storm problem dapat ditangani dengan membatasi jumlah node yang dapat melakukan broadcast. Tujuan utama dari pembuatan makalah ini adalah merangkum beberapa mekanisme terbaru yang telah diakukan oleh para peneliti untuk menangani broadcast storm problem. Kami juga menyajikan perbandingan dari mekanisme tersebut berdasarkan karakteristik dari mekanisme ditinjau dari kesesuaian dengan beberapa skema penanganan broadcast storm problem yang diajukan oleh peneliti sebelumnya, kebutuhan informasi tertentu antar node, lingkungan uji coba dan apakah mekanisme ini dapat diterapkan pada protokol routing lainnya.

  19. Sistem Identifikasi Kandungan Boraks pada Bakso Daging Sapi Berbasis Android Menggunakan Algoritma Naive Bayes Classifier

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    Sofi Dwi Purwanto

    2017-03-01

    Full Text Available Poin pertama yang menjadi fokus dalam pemenuhan keamanan adalah keamanan dalam bidang pangan (food security. Di Indonesia, masih terdapat beberapa fenomena seperti penggunaan boraks sebagai zat aktif kimia pada bakso. Hal ini masih menjadi tren yang menjadi hambatan dalam pemenuhan hak manusia dalam mewujudkan keamanan pangan. Penelitian ini mengimplementasikan metode naïve bayes classifiersebagai pendeteksi (detektor dengan melakukan grayscale dan melakukan estimasi parameter distribusi fitur objek untuk data citra proses training. Sedangkan proses testing juga akan melalui tahap grayscale, selanjutnya proses identifikasi dengan menggunakan fungsi diskriminan dan hasil estimasi parameter distribusi. Jumlah data yang digunakan dalam penelitian sebesar 840 citra meliputi 780 bakso yang dibuat secara mandiri dan 60 data diperoleh dari hasil survey dilapangan. Hasil uji coba menunjukkan hasil terbaik diperoleh dengan tingkat akurasi sebesar 82.7778%  untuk dimensi citra 3x4 dengan jumlah data yang diidentifikasi secara benar adalah sebanyak 149 dari 180 data yang digunakan.

  20. Pendeteksian Malware pada Lingkungan Aplikasi Web dengan Kategorisasi Dokumen

    Directory of Open Access Journals (Sweden)

    Fransiskus Gusti Ngurah Dwika Setiawan

    2017-03-01

    Full Text Available Jumlah aplikasi berbasis web semakin bertambah seiring dengan perkembangan teknologi informasi. Dengan bertambahnya jumlah aplikasi web, serangan-serangan yang dilakukan terhadap aplikasi-aplikasi web tersebut juga meningkat. Salah satu jenis serangan yang marak dilakukan terhadap aplikasi web adalah penyisipan malware seperti web shell yang dapat memberikan akses bebas terhadap komputer server kepada penyerang.Dalam makalah ini, dijelaskan implementasi aplikasi yang menerapkan teknik kategorisasi dokumen untuk mendeteksi malware atau kode malicious khususnya jenis web shell dengan teknik kategorisasi dokumen. Proses kategorisasi dokumen meliputi praproses dan tokenisasi kode sumber, pembuatan model classifier Multinomial Naive Bayes dan Decision Tree, dan klasifikasi dokumen menggunakan classifier yang telah dibuat. Uji coba yang dilakukan terhadap 718 file kode sumber PHP menghasilkan tingkat precision dari 72% hingga 83% dan recall 83% hingga 97%.

  1. PENGEMBANGAN PERANGKAT PEMBELAJARAN MATEMATIKA YANG MENUNJANG PENDIDIKAN KARAKTER SISWA KELAS IV SEKOLAH DASAR

    Directory of Open Access Journals (Sweden)

    Layin Fauziyah

    2014-07-01

    Full Text Available Penelitian ini bertujuan untuk menghasilkan perangkat pembelajaran matematika yang menun-jang pendidikan karakter siswa kelas V sekolah dasar yang layak. Penelitian ini adalah penelitian pengembangan dengan menggunakan model pengembangan 4-D yang dikembangkan oleh Thiagarajan, Semmel & Semmel yang telah dimodifikasi sehingga memuat tahapan define, design, dan develop. Produk yang dikembangkan adalah perangkat pembelajaran yang terdiri dari RPP, LKS, bahan ajar/buku siswa dan tes hasil belajar. Pengembangan perangkat pembelajaran dimulai dari tahap analisis awal-akhir, analisis peserta didik, analisis materi, analisis tugas, spesifikasi tujuan pembel-ajaran, pemilihan media, pemilihan format, validasi ahli, uji coba terbatas, uji coba lapangan, dan revisi. Instrumen penelitian yang digunakan terdiri dari lembar validasi, lembar observasi karakter siswa, dan lembar observasi kemampuan guru dalam mengelola pembelajaran untuk mengetahui keterlaksanaan RPP yang menunjang pendidikan karakter. Penelitian ini menghasilkan perangkat pembelajaran yang menunjang pendidikan karakter pada materi pecahan. Hasil validasi perangkat pembelajaran yang dikembangkan layak untuk digunakan dengan kategori cukup valid, praktis, dan efektif. Pembelajaran dengan menggunakan perangkat yang dikembangkan dapat membentuk karakter jujur, disiplin, dan bertanggung jawab. Berdasarkan pengamatan yang telah dilakukan, perangkat pembelajaran matematika yang dikembangkan pada uji coba terbatas dan uji coba lapangan menunjukkan peningkatan karakter siswa di setiap pertemuan. _________________________________________________________________________________________________________________________________________________________________________________________________________ DEVELOPING MATHEMATIC TEACHING KITS THAT SUPPORT THE CHARACTER EDUCATION OF THE STUDENTS IN CLASS V OF ELEMENTARY SCHOOLS ABSTRACT This research aims to develop appropriate mathematic teaching kits that support

  2. Early Biochemical Screening for Fetal Aneuploidy in the First Trimester

    DEFF Research Database (Denmark)

    Tørring, Niels

    2013-01-01

    Background Screening for fetal trisomy 21 in the first trimester includes analysis of the serological markers pregnancy-associated plasma protein A (PAPP-A) and free beta human choriogonadotropin (free βhCG). With the recent launch of the PAPP-A free βhCG and assays on the Roche Cobas and Elecsys...... assays showed slopes of 0.94 and 0.95 and Pearson’s correlation of r = 0.981 and r = 0.987 respectively. Similar comparison to AutoDELFIA PerkinElmer Perkin gave slopes of 0,83 (free βhCG) and 1.20 (PAPP-A). With a cut off at 1:300 the overall sensitivity of the first trimester screening including nuchal...

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

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Bonde, Jesper; Preisler, Sarah

    2016-01-01

    intraepithelial neoplasia (CIN) in 2.5 years after the baseline testing were determined from the national pathology register. HPV-positive women undergoing primary screening having concordant samples were more likely to harbor high-risk infections and less likely to harbor only low-risk infections than women......Laboratories can nowadays choose from >100 Human Papillomavirus (HPV) assays for cervical screening. Our previous analysis based on the data from the Danish Horizon study, however, showed that four widely used assays, Hybrid Capture 2 (HC2), cobas, CLART and APTIMA, frequently do not detect...... the same HPV infections. Here, we determined the characteristics of the concordant (all four assays returning a positive HPV test result) and discordant samples (all other HPV-positive samples) in primary cervical screening at 30-65 years (n=2859) and in a concurrent referral population from the same...

  4. PERANGKAT PEMBELAJARAN MATEMATIKA KONSTRUKTIVIS BERBASIS NILAI-NILAI KARAKTER 1 KONSERVASI BERBANTUAN E-LEARNING

    Directory of Open Access Journals (Sweden)

    Amidi Amidi

    2016-12-01

    Full Text Available Peningkatkan penguasaan konsep dan memperbaiki sikap belajar mahasiswa dengan menerapkan pembelajaran konstruktivis berbasis nilai-nilai karakter konservasi berbantuan E-learningi adalah fokus dalam penelitian ini, sebab pembelajaran E-learning dapat menyentuh aspek aktivitas dan kreativitas mahasiswa. Pengembangan yang dipilih adalah pengembangan dengan model 4D yang diadaptasi menjadi 4P, yaitu pendefinisian (analisis awal-akhir, analisis peserta didik, analisis materi, analisis tugas, dan merumuskan tujuan pembelajaran khusus, perancangan (penyusunan kriteria tes, pemilihan media, pemilihan format, dan desain awal, pengembangan (validasi ahli dan uji coba, dan penyebaran. Adapun perangkat yang dikembangkan adalah Rencana Pembelajaran Semester (RPS dan Rancangan Tatap Muka (RTM, yang dilengkapi dengan Lembar Diskusi dan E-learning. Adapun rata-rata prestasi belajar kelas eksperimen adalah 89,38 yang melebihi batas minimal nilai B, sehingga ratarata prestasi belajar kelas eksperimen lebih baik dari kelas kontrol yang rata-rata prestasi belajarnya adalah 80,50. Sehingga dapat disimpulkan pembelajaran efektif.

  5. Efficacy of combined hepatitis B immunoglobulin and hepatitis B vaccine in blocking father-infant transmission of hepatitis B viral infection.

    Science.gov (United States)

    Cao, L-H; Liu, Z-M; Zhao, P-L; Sun, S-C; Xu, D-B; Shao, M-H; Zhang, J-D

    2015-05-04

    The aim of this study was to examine the efficacy of combined immunization of hepatitis B immunoglobulin (HBIG) and hepatitis B vaccine (HBVac) in blocking father-infant transmission of hepatitis B virus (HBV). Newborns positive at birth for blood HBV sur-face antigen (HBsAg) and/or HBV DNA were selected and immunized with HBIG combination HBVac. At 7 months, HBV markers and HBV DNA of each neonate were measured using electrochemiluminescence with the Cobas-e-411 Automatic Electrochemiluminescence Immuno-assay Analyzer and fluorescence quantitative polymerase chain reaction. Among all 7-month-old subjects, the negative conversion rates of HBV DNA and HBsAg were 48/61 (78.7%) and 19/41 (46.3%), respectively. Therefore, this study demonstrated that prompt combination injection of HBIG and HBVac can protect some of the HBV DNA- and/ or HBsAg-positive newborns from HBV.

  6. PENGEMBANGAN PERANGKAT PEMBELAJARAN MATERI PECAHAN BERBASIS TEORI BRUNER DI KELAS IV SD LABSCHOOL UNESA

    Directory of Open Access Journals (Sweden)

    Lina Wijayanti

    2015-07-01

    Full Text Available Penelitian ini bertujuan untuk menghasilkan perangkat pembelajaran pada materi pecahan tema 3 berbasis teori Bruner ditinjau dari kualitas produk secara umum (kevalidan, kepraktisan, dan keefektifan dan dalam peningkatan kemampuan pemecahan masalah dan prestasi belajar peserta didik di kelas IV SD Labschool Unesa. Penelitian ini termasuk penelitian dan pengembangan yang menggunakan model yang dikembangkan oleh Borg & Gall. Subjek penelitian dalam uji coba terbatas berjumlah 4 siswa, sedangkan dalam uji coba lapangan berjumlah 8 siswa. Subjek uji coba produk operasional pada kelas eksperimen sebanyak 17 siswa dan kelas kontrol sebanyak 18 siswa. Pengumpulan data dalam penelitian ini menggunakan lembar penilaian produk perangkat pembelajaran, lembar observasi guru, lembar observasi peserta didik, tes hasil belajar, angket respon guru, dan agket respon peserta didik. Analisis data menggunakan independent sample t-test dengan taraf signifikansi 0,05. Hasil penelitian menunjukkan bahwa perangkat pembelajaran hasil pengembangan dinyatakan valid dengan kategori sebagai berikut: silabus berkategori baik, RPP berkategori sangat baik, tes hasil belajar berkategori baik, dan media berkategori sangat baik, sehingga rerata hasil semua perangkat pembelajaran adalah berkategori baik. Penerapan perangkat pembelajaran secara umum dapat terlaksana dengan baik. Berdasarkan hasil uji coba kelas eksperimen dan kelas kontrol, terdapat perbedaan yang signifikan pada ketercapaian hasil belajar sehingga perangkat pembelajaran dikatakan efektif, sedangkan untuk kemampuan pemecahan masalah dan prestasi belajar siswa yang mengikuti pembelajaran menggunakan perangkat pembelajaran berbasis teori Bruner hasil pengembangan mengalami peningkatan. Kata Kunci: perangkat pembelajaran, teori Bruner, kemampuan pemecahan masalah, prestasi belajar DEVELOPING TEACHING KIT BASED ON THE THEORY OF BRUNER IN GRADE FOUR STUDENTS OF SD LABSCHOOL UNESA Abstract This study aims to develop a

  7. Point of care testing of fecal calprotectin as a substitute for routine laboratory analysis

    DEFF Research Database (Denmark)

    Hejl, Julie; Theede, Klaus; Møllgren, Brian

    2018-01-01

    Objectives Fecal calprotectin (FC) is widely used to monitor the activity of inflammatory bowel disease (IBD) and to tailor medical treatment to disease activity. Laboratory testing of fecal samples may have a turnaround time of 1–2 weeks, whereas FC home testing allows results within hours...... and thus enables a rapid response to clinical deterioration. Design and methods Fifty-five stool samples were analyzed by the IBDoc® Calprotectin Home Testing kit and the BÜHLMANN fCAL® turbo assay on a Roche Cobas 6000 c501. The correlation between the assays was assessed using Spearman's Rho correlation...... coefficient and the intermediate imprecision of both assays was calculated. Results We found a strong correlation coefficient of 0.887 between FC measured on IBDoc® and the laboratory assay BÜHLMANN fCAL® turbo. The coefficients of variation (CVs) at three different FC levels were in the range 2...

  8. Pemanfaatan Web E-Commerce untuk Meningkatkan Strategi Pemasaran

    Directory of Open Access Journals (Sweden)

    Hani Atun Mumtahana

    2017-06-01

    Full Text Available UMKM merupakan salah satu usaha Mikoro yang memberdayakan Industri Rumahan. UMKM Indonesia meemiliki kontribusi sebersar 15.8% terhadap rantai pasok produksi global di tingkat Asean. Perkembangan UMKM dari tahun ke tahun dipengaruhi dengan pemanfaatan Teknologi Informasi dan Sistem Informasi. E-commerce merupakan salah satu teknologi yang mendukung perkembangan UMKM dan perdagangan saat ini. Penelitian ini bertujuan untuk mengetahui dampak yang pemanfaatan Teknologi E-Commerce dalam peningkatan strategi pemasaran produksi. Teknologi E-commerce dibangun dengan mengunakan aplikasi berbasis webside, sehingga para pelaku usaha dapat mempromosikan hasil usaha dengan mudah. Sasaran utama pemanfaatan Teknolohi E-commerce ini adalah UMKM Industri Kerajinan Kulit di  Magetan. Dari hasil uji coba dan evaluasi yang dilakukan pada Koperasi Mahasiswa STT Dharma Iswara Madiun, menunjukkan bahwa dengan memanfaatkan Teknologi E-commerce memenuhi strategi pemasaran produk yang dapat berdampak pada peningkatan pendapatan.

  9. FUZZY LOGIC STATIC SYNCHRONOUS COMPENSATOR (FLSTATCOM

    Directory of Open Access Journals (Sweden)

    I Made Mataram

    2016-06-01

    Full Text Available Penerapan teknik fuzzy membawa perubahan yang signifikan khusus pada perhitungan dan analisis sistem konvensional. Peranan peralatan FACTS (Flexible AC Transmission System untuk memperbaiki kualitas tegangan dari pembangkit menuju beban sangat besar. STATCOM merupakan peralatan paling berpengaruh untuk memperbaiki tegangan pada jaringan transmisi tenaga listrik. Pembahasan pada penelitian ini dikhususkan pada FLSTATCOM. Model Fuzzy Logic dengan dua input digunakan sebagai pengontrol IGBT, sehingga mampu meningkatkan unjuk kerja STATCOM konvensional. Sistem Single Machine Infinite Bus menjadi sistem uji coba penggunaan FLSTATCOM.Hasil simulasi menggunakan simulink MATLAB, diperoleh nilai tegangan pada tiap sisi terima tanpa menggunakan STATCOM menghasilkan tegangan sebesar 217,3 kV, menggunakan STATCOM menghasilkan tegangan sebesar 220 kV, dan penggunaan FLSTATCOM mampu meningkatkan tegangan menjadi 228,9 kV (5,34%

  10. Penggunaan QR Code untuk Menunjukkan Posisi dan Implementasi Algoritma Dijkstra dalam Pencarian Rute Terpendek pada Navigasi dalam Ruangan Berbasis Sistem Operasi Android

    Directory of Open Access Journals (Sweden)

    Prasetyo Prasetyo

    2017-01-01

    Full Text Available GPS memiliki kelemahan dalam menentukan posisi pengguna ketika berada di sebuah gedung bertingkat. Oleh karena itu, dikembangkan sebuah sistem yang  lebih akurat untuk navigasi dalam gedung bertingkat yang dikembangkan dengan konsep 3D Indoor Localization. Dengan menggunakan QR Code untuk menentukan posisi pengguna dalam suatu gedung bertingkat dan penggunaan algoritma Dijkstra dalam mencari rute terpendek ke suatu tujuan, maka sistem ini menyediakan sebuah layanan navigasi dalam ruangan yang lebih baik dari penggunaan GPS. Untuk mengetahui posisinya, pengguna hanya perlu melakukan pemindaian terhadap QR Code yang terdapat pada sebuah ruang. Pengguna selanjutnya dapat memilih lokasi tujuan yang dikehendaki, dan sistem akan mencari rute yang dapat ditempuh untuk sampai ke tujuan dengan jarak terpendek. Uji coba dilakukan menggunakan peta 3D dari gedung Teknik Informatika ITS. Hasil yang diperoleh menunjukkan bahwa sistem dapat melakukan semua prosesnya dengan baik, dimulai dari proses pemindaian hingga proses penunjukan rute ke tujuan. 

  11. AIRSAR South American deployment: Operation plan, version 3.0

    Science.gov (United States)

    Kobrick, M.

    1993-01-01

    The United States National Aeronautics and Space Administration (NASA) and the Brazilian Commission for Space Activities (COBAE) are undertaking a joint experiment involving NASA's DC-8 research aircraft and the Airborne Synthetic Aperture Radar (AIRSAR) system during late May and June 1993. The research areas motivating these activities are: (1) fundamental research in the role of soils, vegetation, and hydrology in the global carbon cycle; and (2) in cooperation with South American scientists, airborne remote sensing research for the upcoming NASA Spaceborne Imaging Radar (SIR)-C/X-SAR flights on the Space Shuttle. A flight schedule and plans for the deployment that were developed are included. Maps of the site locations and schematic indications of flight routes and dates, plots showing swath locations derived from the flight requests and generated by flight planning software, and, most importantly, a calendar showing which sites will be imaged each day are included.

  12. Blood glucose, lactate, pyruvate, glycerol, 3-hydroxybutyrate and acetoacetate measurements in man using a centrifugal analyser with a fluorimetric attachment.

    Science.gov (United States)

    Harrison, J; Hodson, A W; Skillen, A W; Stappenbeck, R; Agius, L; Alberti, K G

    1988-03-01

    Methods are described for the analysis of glucose, lactate, pyruvate, alanine, glycerol, 3-hydroxybutyrate and acetoacetate in perchloric acid extracts of human blood, using the Cobas Bio centrifugal analyser fitted with a fluorimetric attachment. Intra-assay and inter-assay coefficients of variation ranged from 1.9 to 7.9% and from 1.0 to 7.2% respectively. Correlation coefficients ranged from 0.96 to 0.99 against established continuous-flow and manual spectrophotometric methods. All seven metabolites can be measured using a single perchloric acid extract of 20 microliter of blood. The versatility of the assays is such that as little as 100 pmol pyruvate, 3-hydroxybutyrate or as much as 15 nmol glucose can be measured in the same 20 microliter extract.

  13. Optimized methods to measure acetoacetate, 3-hydroxybutyrate, glycerol, alanine, pyruvate, lactate and glucose in human blood using a centrifugal analyser with a fluorimetric attachment.

    Science.gov (United States)

    Stappenbeck, R; Hodson, A W; Skillen, A W; Agius, L; Alberti, K G

    1990-01-01

    Optimized methods are described for the analysis of glucose, lactate, pyruvate, alanine, glycerol, D-3-hydroxybutyrate and acetoacetate in perchloric acid extracts of human blood using the Cobas Bio centrifugal analyser. Glucose and lactate are measured using the photometric mode and other metabolites using the fluorimetric mode. The intra-assay coefficients of variation ranged from 0.7 to 4.1%, except with very low levels of pyruvate and acetoacetate where the coefficients of variation were 7.1 and 12% respectively. All seven metabolites can be measured in a perchloric acid extract of 20 mul of blood. The methods have been optimized with regard to variation in the perchloric acid content of the samples. These variations arise from the method of sample preparation used to minimize changes occurring in metabolite concentration after venepuncture.

  14. Deteksi Non-RTH(Ruang Terbuka Hijau Kota Malang Berbasis Citra Google Earth Dengan Menggunakan Naïve Bayes Classifier

    Directory of Open Access Journals (Sweden)

    Irwan Budi Santoso

    2016-01-01

    Full Text Available Banjir, polusi udara dan naiknya temperatur udara di perkotaan, dewasa ini semakin marak persoalan tersebut tidak lain bersumber dari aktifitas manusia yang tidak terkendali sehingga mengakibatkan kerusakan. Salah satu upaya yang bisa dilakukan untuk membantu menyelesaikan persoalan tersebut adalah adanya fasilitas yang dapat memantau kondisi lingkungan secara riil berupa non-Ruang Terbuka Hijau (non-RTH, melalui komputer. Penyediaan fasilitas tersebut sangatlah mungkin dilakukan dengan memanfaatkan foto satelit seperti yang disediakan oleh Google Earth. Studi kasus dalam penelitian ini adalah kota Malang, dengan metode yang digunakan untuk mendeteksi objek non-RTH dipermukaan bumi kota Malang berdasarkan image atau citra satelit adalah Naïve Bayes Classifier (NBC.Hasil uji coba dengan menggunakan sampel pengujian, menunjukkan tingkat akurasi metode tersebut dalam mendeteksi objek non-RTH kota Malang adalah 81%.

  15. MODEL PENGENALAN PERMAINAN DALAM PEMBELAJARAN LOMPAT JAUH PADA SISWA KELAS ATAS SEKOLAH DASAR

    Directory of Open Access Journals (Sweden)

    Kurnia Azis Setyawan

    2015-10-01

    Full Text Available Penelitian ini bertujuan untuk menghasilkan model pengenalan pembelajaran lompat jauh pada siswa sekolah dasar (SD kelas atas tahun pelajaran 2013/2014 di Kecamatan Srumbung, Kabupaten Magelang. Model pembelajaran yang dikembangkan diharapkan untuk digunakan guru SD sebagai salah satu bentuk pembelajaran lompat jauh yang baik dan efektif. Penelitian pengembangan ini dilakukan dengan mengadaptasi langkah-langkah penelitian pengembangan sebagai berikut: (1 pengumpulan informasi di lapangan, (2 melakukan analisis terhadap informasi yang telah dikumpul-kan, (3 mengembangkan produk awal (draf model, (4 validasi ahli dan revisi, (5 uji coba lapangan skala kecil dan revisi, (6 uji coba lapangan skala besar dan revisi, dan (7 pembuatan produk final. Uji coba skala kecil dilakukan terhadap siswa kelas 5 SD N Tegalrandu dan SD N Polengan, Kecamatan Srumbung yang berjumlah 31 siswa. Uji coba skala besar dilakukan terhadap siswa kelas 5 SD N Tegalrandu, SD N Polengan, SD N Pucanganom, SD N Pandanretno, SD N Soka 1 yang berjumlah 81 siswa. Instrumen pengumpulan data yang digunakan yaitu; (1 pedoman wawancara, (2 skala nilai, (3 pedoman observasi model pembelajaran, (4 pedoman observasi keefektifan model pembelajaran. Teknik analisis data yang dilakukan yaitu analisis deskriptif kuantitatif dan analisis deskriptif kualitatif. Hasil penelitian ini berupa buku dan video model pengenalan dalam pembelajaran lompat jauh pada SD kelas atas. Berdasarkan penilaian ahli materi cabang olahraga atletik dan guru penjasor-kes, produk model pengenalan dalam pembelajaran lompat jauh pada SD kelas atas, sudah sesuai dan layak untuk digunakan oleh guru penjasorkes dalam mengajarkan materi lompat jauh kepada siswanya dengan nilai rata-rata 98,1%. Kata kunci: pengembangan, permainan, model pengenalan pembelajaran lompat jauh   INTRODUCTION MODELS IN LEARNING GAMES OF LONG JUMP IN UPPER CLASS ELEMENTARY SCHOOL Abstract This study aims to produce introduction models of the

  16. Peraga Mikrometer Sekrup Braille untuk Siswa Tunanetra

    Directory of Open Access Journals (Sweden)

    Fithri Iradaty

    2017-06-01

    Full Text Available This research was conducted with Four D Models research design with a limited test involving three blind students at MAN Maguwoharjo, a physics teacher ath the school, and several students majoring in physics education FMIPA UNY. The result of the limited test shows that the props that have been developed can be applied as a screw micrometre model and the Braille-labeled LKS can also be used as a guide in a practicum implementation. The results of the assessment of the feasibility of the developed product are reviewed regarding several aspects which are the requirements of the measuring instrument that is validity (reliable, reliable, can be used internationally, is easy to produce, and safe. In general, Braille scarp micrometre displays are suitable for blind students. Besides, blind students strongly support the existence of braille screw micrometre displays equipped with this braille LKS as it will help them more easily understand micrometre screw gauges which in general this tool is still produced only for the non-blind. [Penelitian ini menggunakan desain Four D Models, dengan uji coba terbatas melibatkan tiga orang siswa tunanetra MAN Maguwoharjo, seorang guru fisika MAN Maguwoharjo, dan beberapa mahasiswa Jurusan Pendidikan Fisika FMIPA UNY. Hasil uji coba terbatas menunjukkan bahwa produk peraga yang telah dikembangkan dapat diterapkan sebagai peraga mikrometer sekrup dan LKS berhuruf Braille juga dapat dimanfaatkan sebagai pedoman dalam pelaksanaan praktikum. Hasil penilaian kelayakan produk peraga yang dikembangkan ditinjau dari beberapa aspek yang menjadi syarat alat ukur, yaitu valid (dapat dipercaya, reliable, dapat digunakan secara internasional, mudah diproduksi, dan aman. Secara umum, peraga mikrometer sekrup Braille layak digunakan bagi siswa tunanetra. Selain itu siswa tunanetra sangat mendukung keberadaan peraga mikrometer sekrup braille yang dilengkapi dengan LKS braille ini karena akan membantu mereka lebih mudah memahami

  17. TENDENCY OF PLAYERS IS TRIAL AND ERROR: CASE STUDY OF COGNITIVE CLASSIFICATION IN THE COGNITIVE SKILL GAMES

    Directory of Open Access Journals (Sweden)

    Moh. Aries Syufagi

    2012-07-01

    adalah coba-coba. Beberapa dari mereka memiliki kategori Ahli, dan sedikit yang termasuk dalam kelompok hati-hati. Dengan demikian, secara umum kemampuan pemain masih rendah.

  18. Comparison of Hemoglobin A1c assay performance on two different commercial systems

    Directory of Open Access Journals (Sweden)

    Jozo Ćorić

    2015-04-01

    Full Text Available Introduction: Glycated hemoglobin (HbA1c is formed by non-enzymatic binding of glucose to the free amino group of the N-terminal end of the ß-chain of hemoglobin A. HbA1c is representative of the mean blood glucose level over three months. The aim of the study was to evaluate the Hemoglobin A1c immunoturbidimetric assay performance on two different commercial systems.Methods: We evaluated the precision and trueness for determination of HbA1c in whole blood. Concentrations of total hemoglobin and HbA1c were evaluated on Dimension Xpand (Siemens and Cobas 501 (Roche analyzers. HbA1c was measured in a latex agglutination inhibition test. Commercial controls Liquichek Diabetes Control Level 1 and Liquichek Diabetes Control Level 2 (Bio Rad at two levels were used for quality control. Analytical validation of HbA1c included: within-run imprecision, between-day imprecision, inaccuracy and comparison determination on the human samples on 2 systems: Dimension Xpand and Cobas 501 analyzers. Results: Within-run imprecision on the commercially controls for Level 1 is 4.5% and Level 2 is 3.2% between-day imprecision on commercially controls is 6.1% Level 1 and 5.1% Level 2 for respectively inac- curacy on commercially controls for Level 1 is 1.8% and Level 2 is 4.8%. Method comparison on human samples shows the correlation coefficient of 0.99.Conclusion: The presented results of the analytical evaluation methods for the determination of HbA1c showed an acceptable accuracy and precision.

  19. The evaluation of Recombinant Immunoblot assay (RIBA and HCV-RNA test results in patients with low titer Anti-HCV positivity

    Directory of Open Access Journals (Sweden)

    Berrin Uzun

    2014-12-01

    Full Text Available Objectives: Laboratory diagnosis of hepatitis C virus (HCV infection is based on the detection of anti-HCV antibodies by enzyme immunoassay (EIA or chemiluminescence immunoassay (CIA techniques. However, a consensus related to the problem of low titer (Serum/Cut-off; S/C= 1.0 anti-HCV antibodies is still lacking. The study attempts to evaluate the clinical status of the patients with low titer anti-HCV antibodies detected by third generation anti-HCV tests during February 2013- May 2014 retrospectively. Methods: Serum samples were studied by Advia Centaur XP autoanalyser (Bayer-Siemens, Germany for anti-HCV, and line immunoassay (Inno-LIATM HCV Score, İnnogenetics, Belgium for anti-HCV confirmatory test, Cobas AmpliPre/Cobas AMPLICOR HCV Test (Roche diagnostics, Switzerland for HCV RNA. Results: A total of 55.631 serum samples were studied, and 55 of them were anti-HCV positive of which with low antibody levels (sample/cutoff [S/CO]. S/CO values ranged from 1.15 to 6.15. Seventeen (31% of patients who have low antibody levels were defined as positive and 2 (4% patients were intermittent and 36 (65% patients were negative with line immunoassay. HCV-RNA was not detected in any of the samples. Conclusions: It is thought that antibody positivity must be verified in cases of recurrent reactivity when considering the cost-effectiveness of molecular tests. In the study was concluded that the use of molecular tests would be appropriate diagnosis, and the effectiveness of treatment if necessary after evaluation of patients with biochemical analysis. J Clin Exp Invest 2014; 5 (4: 553-556

  20. Effects of common hemoglobin variants on HbA1c measurements in China: results for α- and β-globin variants measured by six methods.

    Science.gov (United States)

    Xu, Anping; Chen, Weidong; Xia, Yong; Zhou, Yu; Ji, Ling

    2018-04-07

    HbA1c is a widely used biomarker for diabetes mellitus management. Here, we evaluated the accuracy of six methods for determining HbA1c values in Chinese patients with common α- and β-globin chains variants in China. Blood samples from normal subjects and individuals exhibiting hemoglobin variants were analyzed for HbA1c, using Sebia Capillarys 2 Flex Piercing (C2FP), Bio-Rad Variant II Turbo 2.0, Tosoh HLC-723 G8 (ver. 5.24), Arkray ADAMS A1c HA-8180V fast mode, Cobas c501 and Trinity Ultra2 systems. DNA sequencing revealed five common β-globin chain variants and three common α-globin chain variants. The most common variant was Hb E, followed by Hb New York, Hb J-Bangkok, Hb G-Coushatta, Hb Q-Thailand, Hb G-Honolulu, Hb Ube-2 and Hb G-Taipei. Variant II Turbo 2.0, Ultra2 and Cobas c501 showed good agreement with C2FP for most samples with variants. HLC-723 G8 yielded no HbA1c values for Hb J-Bangkok, Hb Q-Thailand and Hb G-Honolulu. Samples with Hb E, Hb G-Coushatta, Hb G-Taipei and Hb Ube-2 produced significant negative biases for HLC-723 G8. HA-8180V showed statistically significant differences for Hb E, Hb G-Coushatta, Hb G-Taipei, Hb Q-Thailand and Hb G-Honolulu. HA-8180V yielded no HbA1c values for Hb J-Bangkok. All methods showed good agreement for samples with Hb New York. Some common hemoglobin variants can interfere with HbA1c determination by the most popular methods in China.

  1. Pengembangan Media Ice Breaker Talking Pen pada Mata Pelajaran PAI Kelas X SMAN 100 Jakarta

    Directory of Open Access Journals (Sweden)

    Ati Sulastri

    2017-07-01

    Full Text Available This study aims to find out how to develop media ice breaker talking pen and media feasibility on the subjects of PAI. The research method used is Borg and Gall development model which includes requirement analysis, validation test, and test phase. The result of this development research is ice breaker talking pen media product which consists of command card and music developed through data collection, planning, product development, and validation and testing. Based on the validation results obtained the average score of the material experts of 4.75 (very good, and from the media experts of 3.78 (good, and the results of student responses about this media amounted to 4.39 or very good category. Therefore the ice breaker talking media on the eyes of learning PAI class X is declared eligible for use with very good category. Keywords: Development Model  Study, Ice Breaker Talking Pen, PAI Abstrak Penelitian ini bertujuan untuk mengetahui cara mengembangkan media ice breaker talking pen dan kelayakan media tersebut pada mata pelajaran PAI. Metode yang digunakan adalah model pengembangan Borg dan Gall yang meliputi analisis kebutuhan, tahap validasi dan tahap uji coba. Hasil penelitian pengembangan ini adalah produk media ice breaker talking pen yang terdiri dari kartu perintah dan musik yang dikembangkan melalui tahap pengumpulan data, perencanaan, pengembangan produk, serta validasi dan uji coba. Berdasarkan pada hasil validasi didapat skor rata-rata dari ahli materi sebesar 4,75 (sangat baik, dan dari ahli media sebesar 3,78 (baik. Serta hasil dari tanggapan siswa mengenai media ini sebesar 4,39 atau kategori sangat baik. Maka dari itu media ice breaker talking pen pada mata pelajaran PAI kelas X dinyatakan layak untuk digunakan dengan kategori sangat baik. Kata Kunci : Pengembangan Model Pembelajaran, Ice Breaker Talking Pen, PAI

  2. SIKLUS PRAPEMBELAJARAN MODEL PENILAIAN FORMATIF WEB-BASED PADA PEMBELAJARAN FISIKA MATERI SUHU DAN KALOR UNTUK SISWA SMK KELAS X

    Directory of Open Access Journals (Sweden)

    E. Ediyanto

    2016-10-01

    Full Text Available Model penilaian formatif Web-based dibagi menjadi tiga siklus yaitu siklus prapembelajaran, siklus pembelajaran dan siklus pascapembelajaran. Penelitian kali ini mengembangkan siklus prapembelajaran model penilaian web-based pada mata pelajaran fisika materi suhu dan kalor untuk siswa SMK kelas X. Metode penelitian yang digunakan dalam penelitian ini adalah penelitian dan pengembangan. Langkah-langkah yang digunakan untuk pengembangan siklus prapembelajaran model penilaian formatif web-based yaitu 1 mengumpulkan informasi, 2 melakukan perencanaan, 3 mengembangkan bentuk produk awal, 4 melakukan uji permulaan, 5 revisi, dan 6 Uji coba. Berdasarkan hasil uji coba, ditemukan bahwa siklus prapembelajaran model penilaian formatif web-based dapat membantu guru dan siswa untuk mendapatkan umpan balik yang cepat. Umpan balik yang cepat dapat membantu siswa untuk mendapatkan pemahaman konsep dengan cepat dan dapat membantu guru untuk menemukan masalah siswa sehingga dapat dipecahkan dengan cepat.Web-based Formative Assessment Model is divided into three cycles: pre-teaching, whilst teaching, post-teaching. This research develops Pre-teaching Cycle of Formative Web-Based Assessment Model on physics material teaching: Temperature and Heat for X Grader of Vocational High School Students. The method used in this research is a Research and Development (R & D. The steps used for the development of pre-learning cycle of web-based formative assessment models: 1 collecting information, 2 conducting planning, 3 developing pre-product form, 4 conducting pre-test, 5 revision, 6 trial test. Based on the trial test, the findings show that pre-teaching cycle of formative web-based assessment model is able to assist teachers and students to get fast feedback. Fast feedback can helps students to gain fast conceptual comprehension and help teachers to find out the students’ problems so it enables to solve faster.

  3. EKSPERIMENTASI MODEL PEMBELAJARAN KOOPERATIF TIPE THINK PAIR SHARE (TPS DITINJAU DARI KEMANDIRIAN BELAJAR SISWA KELAS VIII SMP NEGERI DI KOTA YOGYAKARTA

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    Annis Deshinta Ayuningtyas

    2015-02-01

    Full Text Available Tujuan penelitian ini yaitu untuk mengetahui: (1 manakah yang memberikan prestasi belajar lebih baik diantara model pembelajaran kooperatif tipe TPSatau pembelajaran langsung, (2 manakah yang mempunyai prestasi belajar lebih baik di antara siswa yang mempunyai kemandirian belajar tinggi, sedang, atau rendah, (3 pada masing-masing tingkatan kemandirian belajar (tinggi, sedang, dan rendah, manakah yang memberikan prestasi belajar lebih baik antara model pembelajaran kooperatif tipe TPS atau pembelajaran langsung. Penelitian ini termasuk penelitian eksperimental semu dengan desain factorial 2x3. Populasi dalam penelitian ini adalah seluruh siswa kelas VIII Sekolah Menengah Pertama (SMP Negeri Se-Kota Yogyakarta Semester I tahun pelajaran 2011/2012. Teknik pengambilan sampel dilakukan dengan carastratified cluster random sampling. Banyak sampel adalah 195 siswa. Instrumen yang digunakan untuk mengumpulkan data adalah angket kemandirian belajar siswa dan tes prestasi belajar matematika. Uji coba angket meliputi validitas isi, konsistensi internal dan reliabilitas. Uji coba tes prestasi meliputi validitas isi, tingkat kesukaran, daya beda dan reliabilitas. Untuk uji normalitas menggunakan uji Lilliefors, uji homogenitas menggunakan uji barlett. Uji keseimbangan yang digunakan yaitu anava satu jalan dengan sel tak sama. Analisis tes prestasi matematika menggunakan analisis variansi dua jalan dengan sel tak sama. Dari hasil analisis diperoleh kesimpulan bahwa: (1 Prestasi belajar matematika dengan model pembelajaran kooperatiftipe TPS memberikan prestasi belajar yang lebih baik daripada model pembelajaran langsung, (2 Siswa yang kemandirian belajarnya tinggi mempunyai prestasi belajar yang lebih baik daripada siswa dengan kemandirian belajar sedang dan rendah, sedangkan siswa yang kemandirian belajarnya sedang mempunyai prestasi belajar yang sama dengan siswa dengan kemandirian belajar rendah, (3 Pada siswa yang mempunyai kemandirian belajar tinggi

  4. [Comparison of manual and automated (MagNA Pure) nucleic acid isolation methods in molecular diagnosis of HIV infections].

    Science.gov (United States)

    Alp, Alpaslan; Us, Dürdal; Hasçelik, Gülşen

    2004-01-01

    Rapid quantitative molecular methods are very important for the diagnosis of human immunodeficiency virus (HIV) infections, assessment of prognosis and follow up. The purpose of this study was to compare and evaluate the performances of conventional manual extraction method and automated MagNA Pure system, for the nucleic acid isolation step which is the first and most important step in molecular diagnosis of HIV infections. Plasma samples of 35 patients in which anti-HIV antibodies were found as positive by microparticule enzyme immunoassay and confirmed by immunoblotting method, were included in the study. The nucleic acids obtained simultaneously by manual isolation kit (Cobas Amplicor, HIV-1 Monitor Test, version 1.5, Roche Diagnostics) and automated system (MagNA Pure LC Total Nucleic Acid Isolation Kit, Roche Diagnostics), were amplified and detected in Cobas Amplicor (Roche Diagnostics) instrument. Twenty three of 35 samples (65.7%) were found to be positive, and 9 (25.7%) were negative by both of the methods. The agreement between the methods were detected as 91.4%, for qualitative results. Viral RNA copies detected by manual and MagNA Pure isolation methods were found between 76.0-7.590.000 (mean: 487.143) and 113.0-20.300.0000 (mean: 2.174.097) copies/ml, respectively. When both of the overall and individual results were evaluated, the number of RNA copies obtained with automatized system, were found higher than the manual method (p<0.05). Three samples which had low numbers of nucleic acids (113, 773, 857, respectively) with MagNA Pure, yielded negative results with manual method. In conclusion, the automatized MagNA Pure system was found to be a reliable, rapid and practical method for the isolation of HIV-RNA.

  5. Mengungkap Model Pendidikan Hindu Bali Tradisional Aguron-guron

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    Wayan Paramartha

    2017-06-01

    Full Text Available Pendidikan aguron-guron dikembangkan atas dua sub model. Model pertama dikembangkan dengan ideologi sakala ‘realis’ dengan tujuan Parartha ‘kesejahtraan’, yaitu agawe suka nikang rat ‘menjadikan siswa berkarakter dan dapat bekerja untuk kebahagiaan bersama di dunia (baca desa pakraman’. Sedangkan yang kedua adalah ideologi  niskala ‘idealis’ dengan tujuan paramartha, yaitu matutur ikang atma ri jatinya ‘menjadikan siswa sadar akan jati dirinya, bahwa ia sesungguhnya adalah roh’ atau sinar Ilahi. Model pendidikan aguron-guron merupakan kearifan lokal yang menjungjung tinggi nilai-nilai keseimbangan dan harmonisasi. Oleh karena itu terus diperhatikan dan dikembangkan untuk memelihara karakter bangsa, membangun landasan teori pendidikan dan pembelajaran berbasis budaya. Penelitian ini merupakan tahun ke dua, yang bertujuan menghasilkan bahan ajar dan VCD sebagai media pendukung pembelajaran model pendidikan Hindu Bali tradisional aguron-guron serta menguji efektivitas bahan ajar dan media VCD model pendidikan Hindu Bali tradisional aguron-guron tersebut. Penelitian dilaksanakan di Pasraman Seruling Dewata Tabanan dan  Pasraman  Griya  Kekeran  Blahbatuh  Gianyar. Metode pengumpulan data digunakan wawancara, studi kepustakaan, dokumentasi dan angket penilaian bahan ajar dan VCD. Data dianalisis dengan menggunakan analisis deskriptif kuantitatif teknik prosentase dan kualitatif. Hasil uji ahli dan uji coba pengguna perorangan serta uji coba pengguna kelompok kecil terhadap produk yang dikembangkan berupa bahan ajar dan VCD mencakup materi Ilmu Silat Bali Kuno,Tapak Suci, Tattwa dan Nilai-Nilai Pendidikan Agama Hindu  menunjukkan sangat layak dan masuk dalam kategori tidak perlu direvisi

  6. PENGEMBANGAN TARGET NET SEBAGAI ALAT PEMBELAJARAN PUKULAN BULUTANGKIS DI SEKOLAH MENENGAH PERTAMA

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    Afif Khoirul Hidayat

    2015-04-01

    Full Text Available Penelitian ini bertujuan untuk mengembangkan dan menghasilkan alat target net untuk memudahkan peserta didik SMP memelajari dan meningkatkan kemampuan teknik dasar pukulan net, smash, drive, dan short serve. Dalam penelitian pengembangan ini, langkah-langkah yang harus ditempuh meliputi: (1 potensi dan masalah, (2 pengumpulan data, (3 desain produk, (4 validasi desain dan instrument, (5 revisi desain, (6 uji coba produk, (7 revisi, dan (8 produksi/implementasi produk. Uji coba penelitian dilakukan terhadap 168 peserta didik dari SMP se-Kecamatan Piyungan, Bantul, Yogyakarta. Teknik analisis data terdiri dari teknik analisis data deskriptif kuantitatif dan teknik analisis data deskriptif kualitatif. Hasil akhir dari penelitian ini adalah sebuah produk alat pembelajaran target net dan buku manual target net yang memiliki kualitas yang sangat baik. Hal tersebut dibuktikan dengan diperolehnya rerata persentase skor penilaian kualitas produk alat pembelajaran dan buku manual target net sebesar 98,66%.   DEVELOP TARGET NET AS A TOOL FOR SHOT LEARNING IN BADMINTON AT JUNIOR HIGH SCHOOL   Abstract This research aims to produce and develop target net tools in facilitating JHS students to improve the basic techniques of net shots, smashes, drives, dan short serves. This research and development study follows the steps of: (1 the potential and problems identification, (2 data collection, (3 product design, (4 the design and validation of the instrumen, (5 revision of the design, (6 product trials, (7 revision, and (8 production/implementation of the product. The trials were conducted to 168 students from JSH in Piyungan districts, Bantul, Yogyakarta. The technique of data analysis is descriptive quantitative analysis and qualitative descriptive analysis. The result of this research is a learning tool of target net product and manual book of the target product, that have a very good quality.  Which is proved by the average percentage quality assessment

  7. Potential role of miR-9 and miR-223 in recurrent ovarian cancer

    Directory of Open Access Journals (Sweden)

    McGuinness Eamonn

    2008-04-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are small, noncoding RNAs that negatively regulate gene expression by binding to target mRNAs. miRNAs have not been comprehensively studied in recurrent ovarian cancer, yet an incurable disease. Results Using real-time RT-PCR, we obtained distinct miRNA expression profiles between primary and recurrent serous papillary ovarian adenocarcinomas (n = 6 in a subset of samples previously used in a transcriptome approach. Expression levels of top dysregulated miRNA genes, miR-223 and miR-9, were examined using TaqMan PCR in independent cohorts of fresh frozen (n = 18 and FFPE serous ovarian tumours (n = 22. Concordance was observed on TaqMan analysis for miR-223 and miR-9 between the training cohort and the independent test cohorts. Target prediction analysis for the above miRNA "recurrent metastatic signature" identified genes previously validated in our transcriptome study. Common biological pathways well characterised in ovarian cancer were shared by miR-9 and miR-223 lists of predicted target genes. We provide strong evidence that miR-9 acts as a putative tumour suppressor gene in recurrent ovarian cancer. Components of the miRNA processing machinery, such as Dicer and Drosha are not responsible for miRNA deregulation in recurrent ovarian cancer, as deluded by TaqMan and immunohistochemistry. Conclusion We propose a miRNA model for the molecular pathogenesis of recurrent ovarian cancer. Some of the differentially deregulated miRNAs identified correlate with our previous transcriptome findings. Based on integrated transcriptome and miRNA analysis, miR-9 and miR-223 can be of potential importance as biomarkers in recurrent ovarian cancer.

  8. Development and utility of an internal threshold control (ITC real-time PCR assay for exogenous DNA detection.

    Directory of Open Access Journals (Sweden)

    Weiyi Ni

    Full Text Available Sensitive and specific tests for detecting exogenous DNA molecules are useful for infectious disease diagnosis, gene therapy clinical trial safety, and gene doping surveillance. Taqman real-time PCR using specific sequence probes provides an effective approach to accurately and quantitatively detect exogenous DNA. However, one of the major challenges in these analyses is to eliminate false positive signals caused by either non-targeted exogenous or endogenous DNA sequences, or false negative signals caused by impurities that inhibit PCR. Although multiplex Taqman PCR assays have been applied to address these problems by adding extra primer-probe sets targeted to endogenous DNA sequences, the differences between targets can lead to different detection efficiencies. To avoid these complications, a Taqman PCR-based approach that incorporates an internal threshold control (ITC has been developed. In this single reaction format, the target sequence and ITC template are co-amplified by the same primers, but are detected by different probes each with a unique fluorescent dye. Sample DNA, a prescribed number of ITC template molecules set near the limit of sensitivity, a single pair of primers, target probe and ITC probe are added to one reaction. Fluorescence emission signals are obtained simultaneously to determine the cycle thresholds (Ct for amplification of the target and ITC sequences. The comparison of the target Ct with the ITC Ct indicates if a sample is a true positive for the target (i.e. Ct less than or equal to the ITC Ct or negative (i.e. Ct greater than the ITC Ct. The utility of this approach was demonstrated in a nonhuman primate model of rAAV vector mediated gene doping in vivo and in human genomic DNA spiked with plasmid DNA.

  9. Identification of G-Protein-Coupled Receptors (GPCRs) in Pulmonary Artery Smooth Muscle Cells as Novel Therapeutic Targets

    Science.gov (United States)

    2017-10-01

    who do not have pulmonary hypertension (PH) Completed 12/2015 lb. Prepare RNA and cDNA from PASMCs and use Taqman GPCR arrays to identify and quantify...expression of GPCRs with known physiologic agonists .Completed 5/2017 le. Prepare RNA and cDNA from commercially available coronary artery and...Isolate and culture PASMCs from 8 (4 male; 4 female) 3 -month old rats and mice, prepare RNA and cDNA and assess expression of GPCRs with known

  10. Association of DPP4 Gene Polymorphisms with Type 2 Diabetes Mellitus in Malaysian Subjects

    OpenAIRE

    Ahmed, Radwan H.; Huri, Hasniza Zaman; Al-Hamodi, Zaid; Salem, Sameer D.; Al-absi, Boshra; Muniandy, Sekaran

    2016-01-01

    Background Genetic polymorphisms of the Dipeptidyl Peptidase 4 (DPP4) gene may play a role in the etiology of type 2 diabetes mellitus (T2DM). This study aimed to investigate the possible association of single nucleotide polymorphisms (SNPs) of the DPP4 gene in Malaysian subjects with T2DM and evaluated whether they had an effect on the serum levels of soluble dipeptidyl peptidase 4 (sDPP-IV). Method Ten DPP4 SNPs were genotyped by TaqMan genotyping assays in 314 subjects with T2DM and 235 co...

  11. Real-time quantitative PCR for retrovirus-like particle quantification in CHO cell culture.

    Science.gov (United States)

    de Wit, C; Fautz, C; Xu, Y

    2000-09-01

    Chinese hamster ovary (CHO) cells have been widely used to manufacture recombinant proteins intended for human therapeutic uses. Retrovirus-like particles, which are apparently defective and non-infectious, have been detected in all CHO cells by electron microscopy (EM). To assure viral safety of CHO cell-derived biologicals, quantification of retrovirus-like particles in production cell culture and demonstration of sufficient elimination of such retrovirus-like particles by the down-stream purification process are required for product market registration worldwide. EM, with a detection limit of 1x10(6) particles/ml, is the standard retrovirus-like particle quantification method. The whole process, which requires a large amount of sample (3-6 litres), is labour intensive, time consuming, expensive, and subject to significant assay variability. In this paper, a novel real-time quantitative PCR assay (TaqMan assay) has been developed for the quantification of retrovirus-like particles. Each retrovirus particle contains two copies of the viral genomic particle RNA (pRNA) molecule. Therefore, quantification of retrovirus particles can be achieved by quantifying the pRNA copy number, i.e. every two copies of retroviral pRNA is equivalent to one retrovirus-like particle. The TaqMan assay takes advantage of the 5'-->3' exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 Sequence Detection System of PE Applied Biosystems (Foster City, CA, U.S.A.) for automated pRNA quantification through a dual-labelled fluorogenic probe. The TaqMan quantification technique is highly comparable to the EM analysis. In addition, it offers significant advantages over the EM analysis, such as a higher sensitivity of less than 600 particles/ml, greater accuracy and reliability, higher sample throughput, more flexibility and lower cost. Therefore, the TaqMan assay should be used as a substitute for EM analysis for retrovirus-like particle quantification in CHO cell

  12. Novel Molecular Beacon Probe-Based Real-Time RT-PCR Assay for Diagnosis of Crimean-Congo Hemorrhagic Fever Encountered in India

    Directory of Open Access Journals (Sweden)

    Aman Kamboj

    2014-01-01

    Full Text Available Crimean-Congo hemorrhagic fever (CCHF is an emerging zoonotic disease in India and requires immediate detection of infection both for preventing further transmission and for controlling the infection. The present study describes development, optimization, and evaluation of a novel molecular beacon-based real-time RT-PCR assay for rapid, sensitive, and specific diagnosis of Crimean-Congo hemorrhagic fever virus (CCHFV. The developed assay was found to be a better alternative to the reported TaqMan assay for routine diagnosis of CCHF.

  13. Molecular Detection of Leptospiral DNA in Environmental Water on St. Kitts

    Directory of Open Access Journals (Sweden)

    Julienne Rawlins

    2014-08-01

    Full Text Available Leptospirosis is an important waterborne zoonotic disease caused by pathogenic Leptospira. The pathogen is maintained in a population due to chronic colonization and shedding from renal tubules of domestic and wild animals. Humans and other animals become infected when they come in contact with urine from infected animals, either directly or through urine-contaminated surface water. In this study, we screened environmental water on the island of St. Kitts by using a TaqMan based real time quantitative polymerase chain reaction (qPCR targeting a pathogen specific leptospiral gene, lipl32. Our results indicate that around one-fifth of tested water sources have detectable leptospiral DNA.

  14. Methods for Real-Time PCR-Based Diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus Infections in an Opened Molecular Diagnostic Platform.

    Science.gov (United States)

    Opota, Onya; Brouillet, René; Greub, Gilbert; Jaton, Katia

    2017-01-01

    The advances in molecular biology of the last decades have dramatically improved the field of diagnostic bacteriology. In particular, PCR-based technologies have impacted the diagnosis of infections caused by obligate intracellular bacteria such as pathogens from the Chlamydiacae family. Here, we describe a real-time PCR-based method using the Taqman technology for the diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus infection. The method presented here can be applied to various clinical samples and can be adapted on opened molecular diagnostic platforms.

  15. Real-time PCR genotyping assay for canine progressive rod-cone degeneration and mutant allele frequency in Toy Poodles, Chihuahuas and Miniature Dachshunds in Japan

    OpenAIRE

    KOHYAMA, Moeko; TADA, Naomi; MITSUI, Hiroko; TOMIOKA, Hitomi; TSUTSUI, Toshihiko; YABUKI, Akira; RAHMAN, Mohammad Mahbubur; KUSHIDA, Kazuya; MIZUKAMI, Keijiro; YAMATO, Osamu

    2015-01-01

    Canine progressive rod-cone degeneration (PRCD) is a middle- to late-onset, autosomal recessive, inherited retinal disorder caused by a substitution (c.5G>A) in the canine PRCD gene that has been identified in 29 or more purebred dogs. In the present study, a TaqMan probe-based real-time PCR assay was developed and evaluated for rapid genotyping and large-scale screening of the mutation. Furthermore, a genotyping survey was carried out in a population of the three most popular breeds in Japan...

  16. Apolipoprotein(a) Kringle-IV Type 2 Copy Number Variation Is Associated with Venous Thromboembolism

    DEFF Research Database (Denmark)

    Sticchi, Elena; Magi, Alberto; Kamstrup, Pia R

    2016-01-01

    (a), including the kringle-IV type 2 (KIV-2) size polymorphism. Aim of the study was to investigate the role of LPA gene KIV-2 size polymorphism and single nucleotide polymorphisms (SNPs) (rs1853021, rs1800769, rs3798220, rs10455872) in modulating VTE susceptibility. Five hundred and sixteen patients with VTE...... without hereditary and acquired thrombophilia and 1117 healthy control subjects, comparable for age and sex, were investigated. LPA KIV-2 polymorphism, rs3798220 and rs10455872 SNPs were genotyped by TaqMan technology. Concerning rs1853021 and rs1800769 SNPs, PCR-RFLP assay was used. LPA KIV-2 repeat...

  17. AHSG tag single nucleotide polymorphisms associate with type 2 diabetes and dyslipidemia: studies of metabolic traits in 7,683 white Danish subjects

    DEFF Research Database (Denmark)

    Andersen, Gitte; Burgdorf, Kristoffer Sølvsten; Sparsø, Thomas

    2008-01-01

    been largely successful. We related seven frequent AHSG tag single nucleotide polymorphisms to a range of metabolic traits, including type 2 diabetes, obesity, and dyslipidemia. RESEARCH DESIGN AND METHODS: The polymorphisms were genotyped in 7,683 white Danish subjects using Taqman allelic...... with dyslipidemia (P = 0.003 and P(corr) = 0.009). Thr248Met (rs4917) tended to associate with lower fasting and post-oral glucose tolerance test serum insulin release (P = 0.02, P(corr) = 0.1 for fasting and P = 0.04, P(corr) = 0.2 for area under the insulin curve) and improved insulin sensitivity estimated...

  18. An Evaluation of Quantitative PCR Assays (TaqMan® and SYBR Green for the Detection of Babesia bigemina and Babesia bovis, and a Novel Fluorescent-ITS1-PCR Capillary Electrophoresis Method for Genotyping B. bovis Isolates

    Directory of Open Access Journals (Sweden)

    Bing Zhang

    2016-09-01

    Full Text Available Babesia spp. are tick-transmitted haemoparasites causing tick fever in cattle. In Australia, economic losses to the cattle industry from tick fever are estimated at AUD$26 Million per annum. If animals recover from these infections, they become immune carriers. Here we describe a novel multiplex TaqMan qPCR targeting cytochrome b genes for the identification of Babesia spp. The assay shows high sensitivity, specificity and reproducibility, and allows quantification of parasite DNA from Babesia bovis and B. bigemina compared to standard PCR assays. A previously published cytochrome b SYBR Green qPCR was also tested in this study, showing slightly higher sensitivity than the Taqman qPCRs but requires melting curve analysis post-PCR to confirm specificity. The SYBR Green assays were further evaluated using both diagnostic submissions and vaccinated cattle (at 7, 9, 11 and 14 days post-inoculation showed that B. bigemina can be detected more frequently than B. bovis. Due to fewer circulating parasites, B. bovis detection in carrier animals requires higher DNA input. Preliminary data for a novel fluorescent PCR genotyping based on the Internal Transcribed Spacer 1 region to detect vaccine and field alleles of B. bovis are described. This assay is capable of detecting vaccine and novel field isolate alleles in a single sample.

  19. Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus.

    Science.gov (United States)

    Mari, Viviana; Losurdo, Michele; Lucente, Maria Stella; Lorusso, Eleonora; Elia, Gabriella; Martella, Vito; Patruno, Giovanni; Buonavoglia, Domenico; Decaro, Nicola

    2016-03-01

    HoBi-like pestiviruses are emerging pestiviruses that infect cattle causing clinical forms overlapping to those induced by bovine viral diarrhea virus (BVDV) 1 and 2. As a consequence of their widespread distribution reported in recent years, molecular tools for rapid discrimination among pestiviruses infecting cattle are needed. The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. The assay was found to be sensitive, specific and repeatable, ensuring detection of as few as 10(0)-10(1) viral RNA copies. No cross-reactions between different pestiviral species were observed even in samples artificially contaminated with more than one pestivirus. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Hypothalamus transcriptome profile suggests an anorexia-cachexia syndrome in the anx/anx mouse model.

    Science.gov (United States)

    Mercader, Josep Maria; Lozano, Juan José; Sumoy, Lauro; Dierssen, Mara; Visa, Joana; Gratacòs, Mònica; Estivill, Xavier

    2008-11-12

    The anx/anx mouse displays poor appetite and lean appearance and is considered a good model for the study of anorexia nervosa. To identify new genes involved in feeding behavior and body weight regulation we performed an expression profiling in the hypothalamus of the anx/anx mice. Using commercial microarrays we detected 156 differentially expressed genes and validated 92 of those using TaqMan low-density arrays. The expression of a set of 87 candidate genes selected based on literature evidences was also quantified by TaqMan low-density arrays. Our results showed enrichment in deregulated genes involved in cell death, cell morphology, and cancer, as well as an alteration of several signaling circuits involved in energy balance including neuropeptide Y and melanocortin signaling. The expression profile along with the phenotype led us to conclude that anx/anx mice resemble the anorexia-cachexia syndrome typically observed in cancer, infection with human immunodeficiency virus or chronic diseases, rather than starvation, and that anx/anx mice could be considered a good model for the treatment and investigation of this condition.

  1. One-step multiplex quantitative RT-PCR for the simultaneous detection of viroids and phytoplasmas of pome fruit trees.

    Science.gov (United States)

    Malandraki, Ioanna; Varveri, Christina; Olmos, Antonio; Vassilakos, Nikon

    2015-03-01

    A one-step multiplex real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan chemistry was developed for the simultaneous detection of Pear blister canker viroid and Apple scar skin viroid along with universal detection of phytoplasmas, in pome trees. Total nucleic acids (TNAs) extraction was performed according to a modified CTAB protocol. Primers and TaqMan MGB probes for specific detection of the two viroids were designed in this study, whereas for phytoplasma detection published universal primers and probe were used, with the difference that the later was modified to carry a MGB quencher. The pathogens were detected simultaneously in 10-fold serial dilutions of TNAs from infected plant material into TNAs of healthy plant up to dilutions 10(-5) for viroids and 10(-4) for phytoplasmas. The multiplex real-time assay was at least 10 times more sensitive than conventional protocols for viroid and phytoplasma detection. Simultaneous detection of the three targets was achieved in composite samples at least up to a ratio of 1:100 triple-infected to healthy tissue, demonstrating that the developed assay has the potential to be used for rapid and massive screening of viroids and phytoplasmas of pome fruit trees in the frame of certification schemes and surveys. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Circumvention of normal constraints on granule protein gene expression in peripheral blood neutrophils and monocytes of patients with antineutrophil cytoplasmic autoantibody-associated glomerulonephritis.

    Science.gov (United States)

    Yang, Jia Jin; Pendergraft, William F; Alcorta, David A; Nachman, Patrick H; Hogan, Susan L; Thomas, Robin P; Sullivan, Pamela; Jennette, J Charles; Falk, Ronald J; Preston, Gloria A

    2004-08-01

    Granulopoiesis-related genes are distinctively upregulated in peripheral leukocytes of patients with antineutrophil cytoplasmic autoantibodies (ANCA)-associated glomerulonephritis. Affymetrix microarrays identified the upregulation of nine neutrophilic primary granule genes, including myeloperoxidase (MPO) and proteinase 3 (PR3), plus five secondary granule genes. Coordinate expression of granulocyte maturation marker CD35, measured by TaqMan PCR, and positive in situ staining for PR3 transcripts in polymorphic neutrophils and monocytes indicate that these genes are expressed in "mature" cells. Increased transcripts correlated with disease activity and absolute neutrophil values but not with "left shift," drug regimen, cytokine levels, hematuria, proteinuria, ANCA titer, serum creatinine, gender, or age. Upregulation of PR3 and MPO transcripts was specifically associated with ANCA disease (n = 56) as these changes were not detected in patients with ESRD (n = 25) or systemic lupus erythematosus (n = 17), as determined by TaqMan PCR. This is the first report of this phenomenon in nonneoplastic cells. The data raise the hypothesis that, in addition to the presence of anti-MPO or anti-PR3 autoantibodies, a second critical component in the cause of this disease is the reactivation of once-silenced genes leading to increased antigen availability.

  3. RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature

    Science.gov (United States)

    Viollet, Coralie; Davis, David A.; Tekeste, Shewit S.; Reczko, Martin; Pezzella, Francesco; Ragoussis, Jiannis

    2017-01-01

    Kaposi sarcoma-associated herpesvirus (KSHV) causes several tumors and hyperproliferative disorders. Hypoxia and hypoxia-inducible factors (HIFs) activate latent and lytic KSHV genes, and several KSHV proteins increase the cellular levels of HIF. Here, we used RNA sequencing, qRT-PCR, Taqman assays, and pathway analysis to explore the miRNA and mRNA response of uninfected and KSHV-infected cells to hypoxia, to compare this with the genetic changes seen in chronic latent KSHV infection, and to explore the degree to which hypoxia and KSHV infection interact in modulating mRNA and miRNA expression. We found that the gene expression signatures for KSHV infection and hypoxia have a 34% overlap. Moreover, there were considerable similarities between the genes up-regulated by hypoxia in uninfected (SLK) and in KSHV-infected (SLKK) cells. hsa-miR-210, a HIF-target known to have pro-angiogenic and anti-apoptotic properties, was significantly up-regulated by both KSHV infection and hypoxia using Taqman assays. Interestingly, expression of KSHV-encoded miRNAs was not affected by hypoxia. These results demonstrate that KSHV harnesses a part of the hypoxic cellular response and that a substantial portion of hypoxia-induced changes in cellular gene expression are induced by KSHV infection. Therefore, targeting hypoxic pathways may be a useful way to develop therapeutic strategies for KSHV-related diseases. PMID:28046107

  4. Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra.

    Science.gov (United States)

    Hwang, In Kwan; Lee, Hae Young; Kim, Min-Hee; Jo, Hyun-Su; Choi, Dong-Ho; Kang, Pil-Won; Lee, Yang-Han; Cho, Nam-Soo; Park, Ki-Won; Chae, Ho Zoon

    2015-10-01

    The mottled skate, Beringraja pulchra is one of the commercially important fishes in the market today. However, B. pulchra identification methods have not been well developed. The current study reports a novel real-time PCR method based on TaqMan technology developed for the genetic identification of B. pulchra. The mitochondrial cytochrome oxidase subunit 1 (COI) nucleotide sequences of 29 B. pulchra, 157 skates and rays reported in GenBank DNA database were comparatively analyzed and the COI sequences specific to B. pulchra was identified. Based on this information, a system of specific primers and Minor Groove Binding (MGB) TaqMan probe were designed. The assay successfully discriminated in 29 specimens of B. pulchra and 27 commercial samples with unknown species identity. For B. pulchra DNA, an average Threshold Cycle (Ct) value of 19.1±0.1 was obtained. Among 27 commercial samples, two samples showed average Ct values 19.1±0.0 and 26.7±0.1, respectively and were confirmed to be B. pulchra based on sequencing. The other samples tested showed undetectable or extremely weak signals for the target fragment, which was also consistent with the sequencing results. These results reveal that the method developed is a rapid and efficient tool to identify B. pulchra and might prevent fraud or mislabeling during the distribution of B. pulchra products. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  5. Rapid Detection of the Chlamydiaceae and Other Families in the Order Chlamydiales: Three PCR Tests

    Science.gov (United States)

    Everett, Karin D. E.; Hornung, Linda J.; Andersen, Arthur A.

    1999-01-01

    Few identification methods will rapidly or specifically detect all bacteria in the order Chlamydiales, family Chlamydiaceae. In this study, three PCR tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. Two tests exclusively recognized the Chlamydiaceae: a multiplex test targeting the ompA gene and the rRNA intergenic spacer and a TaqMan test targeting the 23S ribosomal DNA. The multiplex test was able to detect as few as 200 inclusion-forming units (IFU), while the TaqMan test could detect 2 IFU. The amplicons produced in these tests ranged from 132 to 320 bp in length. The third test, targeting the 23S rRNA gene, produced a 600-bp amplicon from strains belonging to several families in the order Chlamydiales. Direct sequence analysis of this amplicon has facilitated the identification of new chlamydial strains. These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation. PMID:9986815

  6. Identification of four squid species by quantitative real-time polymerase chain reaction.

    Science.gov (United States)

    Ye, Jian; Feng, Junli; Liu, Shasha; Zhang, Yanping; Jiang, Xiaona; Dai, Zhiyuan

    2016-02-01

    Squids are distributed worldwide, including many species of commercial importance, and they are often made into varieties of flavor foods. The rapid identification methods for squid species especially their processed products, however, have not been well developed. In this study, quantitative real-time PCR (qPCR) systems based on specific primers and TaqMan probes have been established for rapid and accurate identification of four common squid species (Ommastrephes bartramii, Dosidicus gigas, Illex argentinus, Todarodes pacificus) in Chinese domestic market. After analyzing mitochondrial genes reported in GenBank, the mitochondrial cytochrome b (Cytb) gene was selected for O. bartramii detection, cytochrome c oxidase subunit I (COI) gene for D. gigas and T. Pacificus detection, ATPase subunit 6 (ATPase 6) gene for I. Argentinus detection, and 12S ribosomal RNA (12S rDNA) gene for designing Ommastrephidae-specific primers and probe. As a result, all the TaqMan systems are of good performance, and efficiency of each reaction was calculated by making standard curves. This method could detect target species either in single or mixed squid specimen, and it was applied to identify 12 squid processed products successfully. Thus, it would play an important role in fulfilling labeling regulations and squid fishery control. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. A new QRT-PCR assay designed for the differentiation between elements provided from Agrobacterium sp. in GMOs plant events and natural Agrobacterium sp. bacteria.

    Science.gov (United States)

    Nabi, Nesrine; Chaouachi, Maher; Zellama, Mohamed Salem; Ben Hafsa, Ahmed; Mrabet, Besma; Saïd, Khaled; Fathia, Harzallah Skhiri

    2016-04-01

    The question asked in the present work was how to differentiate between contamination of field samples with and GM plants contained sequences provided from this bacterium in order to avoid false positives in the frame of the detection and the quantification of GMO. For this, new set of primers and corresponding TaqMan Minor Groove Binder (MGB) probes were designed to target Agrobacterium sp. using the tumor-morphology-shooty gene (TMS1). Final standard curves were calculated for each pathogen by plotting the threshold cycle value against the bacterial number (log (colony forming units) per milliliter) via linear regression. The method designed was highly specific and sensitive, with a detection limit of 10CFU/ml. No significant cross-reaction was observed. Results from this study showed that TaqMan real-time PCR, is potentially an effective method for the rapid and reliable quantification of Agrobacterium sp. in samples containing GMO or non GMO samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Development and application of a universal Hemoplasma screening assay based on the SYBR green PCR principle.

    Science.gov (United States)

    Willi, Barbara; Meli, Marina L; Lüthy, Ruedi; Honegger, Hanspeter; Wengi, Nicole; Hoelzle, Ludwig E; Reusch, Claudia E; Lutz, Hans; Hofmann-Lehmann, Regina

    2009-12-01

    Hemotropic mycoplasmas (hemoplasmas) are the causative agents of infectious anemia in several mammalian species. Their zoonotic potential has recently been substantiated by the identification of a feline hemoplasma isolate in an immunocompromised human patient. Although species-specific diagnostic molecular methods have been developed, their application as screening tools is limited due to the species diversity of hemoplasmas. The goals of this study were to develop a universal hemoplasma screening assay with broad specificity based on the SYBR green PCR principle, to compare the assay with hemoplasma-specific TaqMan PCR, and to analyze potential tick vectors and human blood samples to address the zoonotic potential. The newly developed PCR assay based on the 16S rRNA gene amplified feline, canine, bovine, porcine, camelid, and murine hemoplasmas, as well as Mycoplasma penetrans and Mycoplasma pneumoniae. The lower detection limit for feline and canine hemoplasmas was 1 to 10 copies/PCR. The assay exhibited 98.2% diagnostic sensitivity and 92.1% diagnostic specificity for feline hemoplasmas. All 1,950 Ixodes ticks were PCR negative, suggesting that Ixodes ticks are not relevant vectors for the above-mentioned hemoplasma species in Switzerland. None of the 414 blood samples derived from anemic or immunocompromised human patients revealed a clear positive result. The SYBR green PCR assay described here is a suitable tool to screen for known and so-far-undiscovered hemoplasma species. Positive results should be confirmed by specific TaqMan PCR or sequencing.

  9. Development of a spreadsheet for SNPs typing using Microsoft EXCEL.

    Science.gov (United States)

    Hashiyada, Masaki; Itakura, Yukio; Takahashi, Shirushi; Sakai, Jun; Funayama, Masato

    2009-04-01

    Single-nucleotide polymorphisms (SNPs) have some characteristics that make them very appropriate for forensic studies and applications. In our institute, SNPs typings were performed by the TaqMan SNP Genotyping Assays using the ABI PRISM 7500 FAST Real-Time PCR System (AppliedBiosystems) and Sequence Detection Software ver.1.4 (AppliedBiosystem). The TaqMan method was desired two positive control (Allele1 and 2) and one negative control to analyze each SNP locus. Therefore, it can be analyzed up to 24 loci of a person on a 96-well-plate at the same time. If SNPs analysis is expected to apply to biometrics authentication, 48 and over loci are required to identify a person. In this study, we designed a spreadsheet package using Microsoft EXCEL, and population data were used from our 120 SNPs population studies. On the spreadsheet, we defined SNP types using 'template files' instead of positive and negative controls. "Template files" consisted of the results of 94 unknown samples and two negative controls of each of 120 SNPs loci we had previously studied. By the use of the files, the spreadsheet could analyze 96 SNPs on a 96-wells-plate simultaneously.

  10. Detection of knockdown resistance (kdr mutations in Anopheles gambiae: a comparison of two new high-throughput assays with existing methods

    Directory of Open Access Journals (Sweden)

    Ball Amanda

    2007-08-01

    Full Text Available Abstract Background Knockdown resistance (kdr is a well-characterized mechanism of resistance to pyrethroid insecticides in many insect species and is caused by point mutations of the pyrethroid target site the para-type sodium channel. The presence of kdr mutations in Anopheles gambiae, the most important malaria vector in Africa, has been monitored using a variety of molecular techniques. However, there are few reports comparing the performance of these different assays. In this study, two new high-throughput assays were developed and compared with four established techniques. Methods Fluorescence-based assays based on 1 TaqMan probes and 2 high resolution melt (HRM analysis were developed to detect kdr alleles in An. gambiae. Four previously reported techniques for kdr detection, Allele Specific Polymerase Chain Reaction (AS-PCR, Heated Oligonucleotide Ligation Assay (HOLA, Sequence Specific Oligonucleotide Probe – Enzyme-Linked ImmunoSorbent Assay (SSOP-ELISA and PCR-Dot Blot were also optimized. The sensitivity and specificity of all six assays was then compared in a blind genotyping trial of 96 single insect samples that included a variety of kdr genotypes and African Anopheline species. The relative merits of each assay was assessed based on the performance in the genotyping trial, the length/difficulty of each protocol, cost (both capital outlay and consumable cost, and safety (requirement for hazardous chemicals. Results The real-time TaqMan assay was both the most sensitive (with the lowest number of failed reactions and the most specific (with the lowest number of incorrect scores. Adapting the TaqMan assay to use a PCR machine and endpoint measurement with a fluorimeter showed a slight reduction in sensitivity and specificity. HRM initially gave promising results but was more sensitive to both DNA quality and quantity and consequently showed a higher rate of failure and incorrect scores. The sensitivity and specificity of AS

  11. PENGEMBANGAN MODUL PEMBELAJARAN KIMIA BERVISI SETS BERORIENTASI CHEMO-ENTREPRENEURSHIP (CEP PADA MATERI LARUTAN ASAM BASA

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    M. Agus Prayitno

    2016-05-01

    Full Text Available Kimia merupakan salah satu mata pelajaran yang berkaitan dengan kehidupan sehari- hari, dari segi lingkungan teknologi, maupun masyarakat. Tujuan penelitian ini adalah menghasilkan modul pembelajaran kimia bervisi SETS berorientasi CEP pada materi larutan asam basa yang layak dan efektif digunakan dalam pembelajaran untuk meningkatkan motivasi belajar, minat wirausaha, dan hasil belajar siswa. Penelitian ini merupakan penelitian pengembangan. Uji coba kelayakan produk pada penelitian ini dilaksanakan di MA Mu’allimin Mu’allimat dengan model penelitian one group pre-test and post-test design dan di MAN Rembang dengan model penelitian pre-test and post-test control group design. Data penelitian diperoleh dengan metode validasi, observasi, dokumentasi, tes, dan skala Likert. Hasil validasi ahli materi, ahli media, dan praktisi menunjukkan bahwa modul pembelajaran kimia bervisi SETS berorientasi CEP sangat layak digunakan dalam pembelajaran kimia dengan skor ratarata pada aspek kegrafikan 95,00, aspek penyajian 95,33, aspek kebahasaan 95,00, dan aspek kegrafikan 94,44. Hasil uji coba modul di MA Mu’allimin Mu’allimat menunjukkan peningkatan motivasi 20%, minat wirausaha 25%, dan hasil belajar siswa 79%. Uji coba modul di MAN Rembang peningkatan motivasi belajar siswa, minat wirausaha, dan hasil belajar siswa kelas eksperimen sebesar 27%, 17% dan 66%, sedangkan peningkatan kelas kontrol secara berturutturut 0,4%, 11%, dan 24%.Chemistryis one of the subjects related to everyday life, in terms of environmental technology, and society. The purpose of this research is to produce visionary chemistry learning modules SETS with CEP oriented on acid-base materials which properly and effectively use in learning to improve learning motivation, entrepreneurial interest, and student learning outcomes. This research is development reaserch. Testing the product viability on the research carried out in MA Mu'allimin Mu'allimat with research model are one

  12. PENGEMBANGAN INSTRUMEN PENILAIAN HOTS BERBASIS KURIKULUM 2013 TERHADAP SIKAP DISIPLIN

    Directory of Open Access Journals (Sweden)

    Umi Pratiwi

    2015-11-01

    , et al. (1974. Uji coba lapangan dilakukan di 3 (tiga sekolah yang terdiri dari 3 (tiga sekolah, dengan teknik cluster random sampling terpilih kelas X(1 sebagai kelas uji coba instrumen penilaian. Variabel HOTS sebagai variabel independendan sikap disiplin sebagai variabel dependen. Data diperoleh melaluilembar validasi, instrumen penilaian dalam bentuk RPP. Proses pengembangan instrumen  penilaian HOTS dan sikap disiplin masing-masing terdiri dari 12 indikator dengan skor maksimal 4.00 menghasilkan: Instrumen penilaian adalah valid menurut 4 (empat validator, yaitu diperoleh rata-rata nilai validitas 3,57. Instrumen penilaian dikatakan efektif/berhasil, karena mencapai kesuksesan instrumen penilaian dengan skor HOTS 73,3% dan sikap disiplin 90% dari skor total. Instrumen penilaian ini baik digunakan untuk siswa dengan keaktifan tinggi, bekerja mandiri dan kemampuan yang kurang baik dalam menyelesaikan soal-soal fisika secara sistematis.

  13. Transfusion transmittable infections - Seroprevalence among blood donors in a tertiary care hospital of Delhi

    Directory of Open Access Journals (Sweden)

    Sangeeta Pathak

    2013-01-01

    Full Text Available Context: Transfusion transmittable infections (TTI continue to be a major threat to safe transfusion practices. Blood is one of the major sources of transmission of infectious diseases viz. human immunodeficiency virus (HIV, hepatitis B virus (HBV, hepatitis C virus (HCV, syphilis, malaria, and many other infections in India. Screening assays for the infectious diseases with excellent sensitivity and specificity helps to enhance the safety of the blood transfusions reducing the diagnostic window period as much as possible. Aims: The present study was designed to determine the seroprevalence of TTIs viz., HIV, HCV, and HBV, among the blood donors in Max Super Specialty Hospital, New Delhi, India based on dual testing strategy using high sensitive screening assays such as enhanced chemiluminescence assay and nucleic acid testing (NAT. Materials and Methods: A total of 41207 blood units collected from the donors (both voluntary and replacement donors were screened for the TTI s, viz., anti HIV 1 and 2 antibody, anti HCV antibody, anti HBcore antibody, and HBsAg by enhanced chemiluminescence assay on VITROS ® ECiQ immunodiagnostics system. NAT was performed using Roche Cobas ® TaqScreen MPX assay, which can detect simultaneously HIV 1 (groups M and O, HIV-2, HCV, and HBV on Roche Cobas ® s201 system. Results: The seroprevalence of HIV, HBsAg, anti HBcore antibody, and HCV based on enhanced chemiluminescence assay was found to be 0.25, 0.2, 7.06, and 0.7%, respectively. A total number of 6587 samples from July 2010 to December 2010 were tested on NAT, of which 3 samples were reactive for HBV in NAT; this was missed by enhanced chemiluminescence assay. Conclusions: Based on the seroprevalence study of infectious diseases viz., HIV, HBV, and HCV, we conclude that screening of blood and blood components by dual testing strategy using high sensitivity serological assay like enhanced chemiluminescence technology and NAT helps in detecting the

  14. [Utilization of self-sampling kits for HPV testing in cervical cancer screening - pilot study].

    Science.gov (United States)

    Ondryášová, H; Koudeláková, V; Drábek, J; Vaněk, P; Slavkovský, R; Hajdúch, M

    2015-12-01

    To get initial experience with alternative sampling (self-sampling) for HPV testing as the means of cervical cancer screening program. Original work. Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc. Based on expression of interest, 215 self-sampling kits were posted to women. Evalyn(®) Brush Vaginal swabs obtained by self-sampling were analyzed for the presence of HPV infection by Cobas 4800 HPV (Roche) followed by genotyping using PapilloCheck(®) HPV-Screening (Greiner Bio-One). Sixty women randomly chosen from our sample were sent a questionnaire focused on their experience with self-sampling. One hundred seventy-four of 215 (81%) distributed self-sampling devices have been delivered to analysis. All cervicovaginal swabs were sampled correctly and it was possible to analyze them by Cobas 4800 HPV test. Similarly, 98% (171/174) samples were analyzable by PapilloCheck(®) HPV-Screening.One hundred twenty-five (72%) of 174 tested samples were HPV negative. Low risk HPV infection was detected only in 7 samples (4%), and high risk HPV (hrHPV) infection was present in 42 samples (24%). The most frequently detected hrHPV genotypes were HPV16 (11/42; 26%) and HPV53 (6/42; 14%). HrHPV co-infection was detected in 10 cases, in 5 of them lrHPV infection was find also.Of the 60 questionnaires, 48 (80%) were returned. From this group, 47 (98%) women rated their experience with self-sampling device as good to excellent. User manual of self-sampling device was considered good to excellent by all women (100%). All women also rated the convenience of self-sampling device using as good to excellent. As expected, most of the women (n = 42 [88%]) preferred self-sampling to physician sampling. Cervicovaginal self-sampling leads to valid results of HPV screening using two molecular genetics methods and was accepted by Czech women very well. The self-sampling as an opportunity to participate in cervical cancer

  15. Aplikasi Promosi Perguruan Tinggi Berbasis Multimedia Interaktif

    Directory of Open Access Journals (Sweden)

    Wahyudi ,

    2017-02-01

    Full Text Available Promosi dapat digunakan untuk meningkatkan kepercayaan masyarakat kepada jaminan mutu suatu perguruan tinggi, semakin dikenalnya jaminan mutu suatu perguruan tinggi maka semakin banyak pula masyarakat pengguna jasanya. Promosi dalam bentuk teknologi komunikasi visual interaktif memiliki kemampuan untuk menyimpan data audio-visual, sebagai media untuk promosi dan pencitraan jaminan mutu, akuntabilitas dan kredibelitas perguruan tinggi. STMIK Indonesia Padang sebagai perguruan tinggi berbasis IT sangat membutuhkannya. Penelitian ini menggunakan pendekatan R & D (Research and Developmentdengan lima langkah utama (Borg & Gall, yaitu: 1 Menganalisis produk yang akan dikembangkan; 2 Pengembangkan produk awal; 3 Validasi ahli & revisi; 4 Uji coba lapangan & revisi produk; 5 Uji coba lapangan & produk akhir.Disini dilakukan analisa sejauhmana efisiensi perancangan dan pengembangan teknologi komunikasi visual interaktif aplikasi promosi bagi perguruan tinggi STMIK Indonesia Padang, mahasiswa, stakeholders serta memperkaya khasanah ilmu pengetahuan, dan teknologi. Penelitian ini bertujuan meningkatkan: kinerja/dukungan promosi; kegiatan publikasi; dan efisiensi informasi dengan memberikan informasimelalui tampilan multimedia audio visual interaktif.Hal ini akan dapat mengurangi pembiayaan dan pemborosan sumber daya manusia melalui efisiensi komunikasi, informasi, dan promosi.Kata Kunci : aplikasi promosi, interaktif, multimedia Promotion can be used to increase public confidence in the quality assurance of the higher education, the growing recognition of the quality assurance of the higher education so the more people who use its services. Promotion in the form of interactive visual communication technology has the ability to store the audio-visual data, as a medium for promotion and imaging quality assurance, accountability and credible of the higher education. STMIK Indonesia Padang as IT-based of the higher educationreally need it. This study uses the

  16. PENGHILANGAN NOISE PADA CITRA BERWARNA DENGAN METODE TOTAL VARIATION

    Directory of Open Access Journals (Sweden)

    Anny Yuniarti

    2006-01-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Saat ini multimedia telah menjadi teknologi yang cukup dominan. Tukar menukar informasi dalam bentuk citra sudah banyak dilakukan oleh masyarakat. Citra dengan kualitas yang baik sangat diperlukan dalam penyajian informasi. Citra yang memiliki noise kurang baik digunakan sebagai sarana informasi, oleh karena itu diperlukan suatu metode untuk memperbaiki kualitas citra. Metode yang digunakan dalam penelitian ini adalah metode total variation untuk penghilangan noise yang dapat diterapkan untuk model warna nonlinier, yaitu Chromaticity-Brightness (CB dan Hue-Saturation-Value (HSV. Filter total variation disebut filter yang bergantung pada data citra karena koefisien filternya diperoleh dari pemrosesan data citra dengan rumusan yang baku. Sehingga filter mask untuk masing-masing piksel memiliki kombinasi koefisien yang berbeda. Metode ini menggunakan proses iterasi untuk menyelesaikan persamaan dasar yang nonlinier. Uji coba dilakukan dengan menggunakan 30 data dengan berbagai jenis noise, yaitu gaussian, salt and pepper dan speckle. Uji coba pembandingan dengan metode filter median dan filter rata-rata. Dari percobaan ini menunjukkan bahwa metode total variation menghasilkan citra yang lebih baik daripada metode

  17. UPAYA PENUMBUHAN SIKAP TANGGAP BENCANA TSUNAMI MELALUI PEMBELAJARAN BERVISI SETS IPA KELAS V SEKOLAH DASAR

    Directory of Open Access Journals (Sweden)

    Tri Puas Restiadi

    2013-03-01

    Full Text Available AbstrakPembelajaran IPA di SD Negeri Glempangpasir 01 masih menggunakan metode ceramah dan hafalan serta kurang menekankan keterkaitan antara sains, lingkungan, teknologi dan masyarakat atau science, environment, technology, society (SETS dalam menumbuhkan sikap tanggap bencana tsunami. Penelitian ini bertujuan mengembangkan perangkat pemb- elajaran bervisi SETS IPA yang valid, efektif, dan praktis. Perangkat yang dikembangkan:  silabus, RPP, buku ajar, LKS, dan tes hasil belajar. Penelitian pengembangan (R & D ini terdiri atas 4 tahap yaitu tahap pengembangan, validasi, uji coba skala terbatas, dan uji coba skala luas. Data validitas dan kepraktisan perangkat pembelajaran dianalisis dengan deskriptif persentase. Perbedaan hasil belajar dianalisis dengan uji t-test berpasangan, sedangkan ke- tuntasan hasil belajar siswa dihitung dengan uji - z.. Hasil penelitian  menunjukkan bahwa perangkat pembelajaran berbasis SETS IPA valid dengan rerata nilai 3,69 pada kategori sangat baik. Penerapan perangkat pembelajaran berbasis SETS IPA praktis ditinjau dari rerata ket- erlaksanaan RPP 3,79 dalam kategori sangat baik, respons siswa dan respons guru mecapai kategori sangat baik. Penerapan  perangkat  pembelajaran berbasis SETS IPA efektif dalam mencapai ketuntasan hasil belajar klasikal ≥ 75% dan ketuntasan individu (KKM ≥ 70, rerata hasil belajar kelas eksperimen lebih besar dari rerata hasil belajar kelas kontrol, dan berbeda secara signifikan karena t hitung > t tabel. AbstractScience learning in elementary school Glempangpasir 01 still use the lecture method and rote and less stressed linkages between science, environment, technology and society or SETS in growing tsunami disas- ter responsiveness. This study aims to develop a vision of learning tools SETS IPA valid, effective, and practical. Device developed: syllabi, lesson plans, textbooks, worksheets, and achievement test. Research & development (R & D is composed of 4 phases: development

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

    Science.gov (United States)

    Koch, Carmo; Araújo, Fernando

    2013-01-01

    Monitoring the residual risk of transfusion-transmitted viral infections is important to evaluate the improvement achieved in the blood donation safety and to adopt policies to reduce risks. The present study calculates the incidence of the key infectious diseases, human immunodeficiency virus (HIV), hepatitis B virus (HBV) and hepatitis C virus (HCV) as well as the residual risk of transfusion-transmitted viral infections, during twelve years, 1999 through 2010. Data were analyzed over 3 periods of 4 years (1999-2002, 2003-2006 and 2007-2010). The risk estimates were compared to those previously obtained for blood donations occurred between 1991 and 1998. The study included 209 640 blood donations, from 42 634 regular, volunteers and unpaid donors. The residual risk of transfusion-transmitted infection per million donations was calculated, for each virus, through mathematical model "Incidence rate/window period", described by Schreiber et al. All donations were screened according to Portuguese legislation. In January 2001, the nucleic acid testing in minipool was implemented on all blood donations, for screening simultaneously HIV-1 and HCV ribonucleic acid (RNA) (Cobas Amplicor Ampliscreen-Roche©). This test was replaced, in January 2007, by the simultaneous screening of HBV deoxyribonucleic acid, HCV RNA and HIV-1/HIV-2 RNA, in minipool (Cobas Taqscreen MPX Test-Roche©). The residual risk of transmitting viral infections during the transfusion of blood components is very small and has declined over the years. After the implementation of the nucleic acid testing in minipool for the three viruses, the risk of giving blood during an infectious window period was estimated as follows: for human immunodeficiency virus, 1 in 1.67 million, for hepatitis C virus 1 in 3.33 million and for hepatitis B virus 1 in 526 000. During the 12 years under study, we found a decrease in residual risk for the three viruses, by a factor around five for human immunodeficiency virus

  19. PENGEMBANGAN MODEL PEMBELAJARAN MODIFIED STUDENT TEAMS ACHIEVEMENT DIVISION (MSTAD DALAM MENINGKATKAN HASIL BELAJAR SISWA PADA PEMBELAJARAN STRUKTUR ALJABAR

    Directory of Open Access Journals (Sweden)

    Kartika Sari

    2015-09-01

    Full Text Available The application of Students Team Achievement Division (STAD model in learning algebra structure indicated that the model is slow on detecting an error in understanding the material and it also need more time to completely delivered all of the course’s material. Therefore, in this study STAD was modified into Modified Students Teams Achievement Division (MSTAD. MSTAD development was carried out through three stages: developing new ideas based on previous research, developing results, and conducting trials. Trials  were performed  on  students taking  Algebra Structure 1  course in  2013/2014  and  2014/2015 academic year in one of the universities in Bali. Results showed that error in understanding the material was detected early, and every material was delivered on time. Statistical analysis also showed that class where MSTAD was applied achieve significantly better learning outcomes compared to STAD class and conventional class for 2013/2014 academic year (t= -9,339 < t0,05(41 = -2,702 as well as 2014/2015 academic year (Z0,5(1-0,01=0,4950 = 2,57.   ABSTRAK Penerapan   model   Student Team Achievement Division (STAD dalam pembelajaran Struktur Aljabar menunjukkan bahwa kesalahan dalam memahami materi lambat terdeteksi dan perlu tambahan waktu untuk menyelesaikan semua materi. Oleh karena itu, dalam penelitian ini dikembangkan modifikasi model STAD yaitu model pembelajaran Modified Student Teams Achievement Division (MSTAD.Pengembangan dilakukan melalui tiga tahap yaitu mengembangkan ide baru berdasarkan penelitian sebelumnya, mengem- bangkan hasil, dan melaksanakan uji coba. Uji coba dilakukan pada mahasiswa yang mengambil mata kuliah Struktur Aljabar 1 pada Tahun Ajaran 2013/2014 dan 2014/2015 di Jurusan Matematika salah satu Universitas di Bali. Hasil ujicoba menunjukkan bahwa kesalahan dalam memahami materi dapat terdeteksi lebih awal dan materi juga dapat diselesaikan tepat waktu. Hasil analisis statistik juga menunjukkan

  20. ANALISIS DAN PERANCANGAN ARSITEKTUR SISTEM OTENTIKASI TERINTEGRASI ANTARA PLATFORM LINUX, WINDOWS 2000, DAN NOVELL NETWARE: STUDI KASUS JURUSAN TEKNIK INFORMATIKA FTIF ITS

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    Rully Soelaiman

    2003-07-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Jurusan Teknik Infomatika merupakan suatu organisasi yang menggunakan jaringan komputer yang diakses dari beberapa domain dan menggunakan sistem operasi terpisah. Masing-masing sistem tersebut menggunakan pengelolaan autentikasi yang terpisah, dengan kenyataan bahwa seharusnya dapat diakses oleh setiap anggota organisasi ini. Kebutuhan pengguna dan pengelola jaringan akan efisiensi pemakaian informasi autentikasi menjadi permasalahan yang akan dibahasa dana makalah ini. Pada makalah ini, dilakukan analisis kemungkinan dilakukannya otentikasi terintegrasi pada jaringan komputer Teknik Informatika yang menggunakan Windows 2000, Linux, dan Novell Netware. Analisis dilakukan dengan meninjau kemampuan integrasi direktori, metode otentikasi, dan kerjasama dengan sistem lain. Dari hasil pemetaan terhadap kebutuhan dan ketersediaan sumber daya teknologi pada jurusan, dipilih solusi otentikasi menggunakan Samba dan OpenLDAP untuk melayani permintaan otentikasi dari Windows 2000 dan Linux. Uji coba telah dilakukan untuk otentikasi client Windows 2000 dan Linux , mencakup login dari masing-masing sistem operasi, domain yang berbeda, menggunakan satu username dan password. Uji coba juga dilakukan terhadap proses

  1. PEMBELAJARAN MATEMATIKA MODEL DOUBLE LOOP PROBLEM SOLVING DENGAN PENDEKATAN PMRI BERMUATAN KARAKTER UNTUK MENINGKATKAN KEMAMPUAN PEMECAHAN MASALAH

    Directory of Open Access Journals (Sweden)

    Indrati Rahayu

    2014-06-01

    Full Text Available AbstrakTujuan dari penelitian ini  adalah  untuk memperoleh hasil perangkat pembelajaran matematika model DLPS dengan pendekatan PMRI yang valid, praktis dan efektif. Perangkat pembelajaran yang dikembangkan meliputi Silabus, RPP, Buku Peserta didik, LKPD dan test kemampuan pemecahan masalah. Subyek uji coba dalam penelitian ini adalah peserta didik kelas X semester genap SMAN 4 Semarang. Variabel penelitian meliputi keaktivan (X1 dan sikap peserta didik (X2 dan kemampuan pemecahan masalah (Y. Pengembangan perangkat pembelajaran   mengacu pada model Plomp, yaitu: (1 investigasi awal (prelimenary investigation, (2 perancangan (design; (3 realisasi/ kontruksi (realization/construction, (4 pengujian, evaluasi dan revisi (test, evaluation and revision, dan (5 implementasi (implementation. Hasil Penelitian menunjukkan: (1 perangkat pembelajaran yang dikembangkan telah dinyatakan valid dan (2 uji coba perangkat menghasilkan (a secara signifikan prestasi belajar peserta didik melebihi KKM = 70 dan lebih dari 80% peserta didik mencapai KKM yaitu 93,75%. Simpulan dari penelitian ini adalah model DLPS dengan Pendekatan PMRI bermuatan karakter untuk meningkatkan kemampuan pemecahan masalah materi trigonometri kelas X merupakan model pembelajaran yang valid dan efektif, dan praktis.AbstractThe purpose of this study is to obtain the results of mathematical learning DLPS models with PMRI approachment charged   character that is valid, pratical and effective. The learning instruments which are developed include syllabus, lesson plan, student book, student work sheets, and problem solving abilities test. The subject of this study are the students of Senior High School 4 Semarang. The variable of this research include the activity as (X1 and the student’s attitudes as (X2. while the dependent variable is the problem solving abilities as (Y. The learning development refers to a model of Plomp i.e : (1 prelimenary investigation, (2 design, (3 realization

  2. Preliminary study on domestication of coconut crab (Birgus latro

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    . Sulistiono

    2007-07-01

    Full Text Available Preliminary study on domestication of coconut crab (Birgus latro had been done since June - November 2004 and December - 2005 February 2006.  Study was carried out in two locations namely Laboratory of Sekolah Tinggi Kelautan dan Perikanan, Palu to study adult crab, and Laboratory of Ecobiology of Faculty of Fisheries and Marine Science, Bogor Agricultural University to study crab in clomang stage.  Adult crabs were collected by using some fishing gears namely trap, net and directly using bamboo stick.  Domestication was done in rearing batch sized 1x1x1 m3 with artificial nests (30x15x15 cm3, and small batch for water (7x10x10 cm3.  While for clomang stage, crabs were reared in aquarium (80x40x40 cm3 with debris and small water batch.  Result showed that adult crab had a survival rate around 12.5-0%, and mortality around 50-87.5%.  A similar result was also in clomang stage, which was 12.5% for survival rate and 87.5% for mortality.  Adult coconut crab was preferred to feed coconut than other food likely vegetable and chick. Keywords: domestication, coconut crab, Birgus latro, food habit   ABSTRAK Penelitian awal mengenai kajian awal penangkaran kepiting kelapa (Birgus latro dilakukan pada bulan Juni - November 2004 dan Desember 2005 Februari 2006.  Pelaksanaan penelitian di lakukan di dua tempat, yaitu Laboratorium Sekolah Tinggi Kelautan dan Perikanan, Palu untuk percobaan kepiting dewasa, dan Laboratorium Ekobiologi Fakultas Perikanan dan Ilmu Kelautan IPB Bogor,  untuk percobaan kepiting tahap klomang.  Kepiting dewasa ditangkap dengan menggunakan beberapa peralatan a.l. perangkap, jaring dan secara langsung dengan tongkat.  Penangkaran dilakukan di bak-bak peliharaan berukuran 1x1x1 m3 yang dilengkapi dengan tempat persembunyian (30x15x15 cm3, dan bak kecil tempat air (7x10x10 cm3.  Sedangkan kepiting tahap klomang dipelihara di akuarium (80x40x40 cm3 yang diberi daun/serasah dan tempat air.  Hasil uji coba penangkaran

  3. Pengenalan Angka Pada Sistem Operasi Android Dengan Menggunakan Metode Template Matching

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    Abdi Pandu Kusuma

    2016-07-01

    Full Text Available AbstrakUsia dini merupakan usia yang efektif untuk mengembangkan berbagai potensi yang dimiliki oleh anak. Upaya pengembangan potensi dapat dilakukan melalui berbagai cara termasuk dengan cara bermain. Bermain bagi anak merupakan cara yang tepat untuk belajar. Berdasarkan fenomena tersebut, maka perlu dibuat sebuah aplikasi pengenalan angka yang interaktif dengan unsur edukasi. Aplikasi tersebut diharapkan dapat mengambil keputusan secara otomatis apa yang ditulis anak itu bernilai benar atau salah dan juga dapat membangkitkan semangat belajar anak dalam mengenal pola angka. Solusi yang sesuai agar aplikasi tersebut dapat memberikan jawaban salah atau benar digunakan satu metode yaitu template matching. Pengenalan angka dengan menggunakan metode template matching dilakukan dengan cara membandingkan citra masukan dengan citra template. Hasil template matching dihitung dari banyaknya titik pada citra masukan yang sesuai dengan citra template. Template disediakan pada database untuk memberikan contoh cara penulisan pola angka. Uji coba dilakukan pada aplikasi sebanyak 40 kali dengan pola yang berbeda. Dari hasil uji coba didapat prosentase keberhasilan aplikasi ini mencapai 75,75%.Kata kunci: Belajar, bermain, Template Matching, dan pola. AbstractEarly childhood is an effective age to develop the potential of the child. Potential development efforts can be done through various ways, including by playing. Playing for children is a great way to learn. Based on this phenomenon, it should be made an introduction to the numbers interactive application with elements of education. The application is expected to take decisions automatically what the child is written is true or false, and also can encourage a child's learning in recognizing number patterns. Appropriate solutions so that the app can give an answer right or wrong to use the methods that template matching. The introduction of the numbers by using template matching is done by comparing the

  4. PENGEMBANGAN MEDIA PEMBELAJARAN KIMIA BERBASIS ANDROID UNTUK MENINGKATKAN MOTIVASI BELAJAR DAN PRESTASI KOGNITIF PESERTA DIDIK SMA

    Directory of Open Access Journals (Sweden)

    Isma Ramadhani Lubis

    2015-10-01

    Full Text Available Penelitian ini bertujuan untuk mengembangkan media pembelajaran kimia berbasis android dan mengetahui karakteristik, kualitas dan efektifitas dari media pembelajaran berbasis android. Jenis penelitian ini merupakan penelitian dan pengembangan. Penilaian produk dilakukan oleh ahli media, ahli materi, pendidik kimia, peer reviewers dan uji coba peserta didik. Data penelitian dikumpulkan melalui angket penilaian media, angket motivasi dan tes, kemudian dianalisis dengan Manova. Hasil dari penelitian ini adalah: (1 media pembelajaran kimia berbasis android memiliki karakteristik, yaitu visualisasi menarik, praktis dan fleksibel serta evaluasi soal yang variatif, (2 media pembelajaran kimia berbasis android dinilai layak digunakan dalam pembelajaran, ditinjau dari aspek materi, aspek media dan hasil uji coba peserta didik, serta (3 terdapat peningkatan yang signifikan antara motivasi belajar dan prestasi kognitif peserta didik yang mengikuti pembelajaran menggunakan media pembelajaran kimia berbasis android dengan pembelajaran konvensional. Hasil penelitian ini menunjukkan bahwa media pembelajaran kimia berbasis android layak dan efektif digunakan dalam pembelajaran kimia. Kata Kunci: pengembangan, media pembelajaran kimia berbasis android, motivasi, prestasi kognitif.   DEVELOPING ANDROID-BASED CHEMISTRY INSTRUCTIONAL MEDIA TO IMPROVE THE LEARNING MOTIVATION AND COGNITIVE ACHIEVEMENT OF SMA STUDENTS Abstract The aims of this study are: to develop android-based chemistry instructional media and to reveal the characteristic, the quality, and the effectiveness of android-based chemistry instructional media. This research was research and development. The product assessment was conducted by a media expert, a material expert, chemistry teachers peer reviewers and students. The data collecting technique was done by using media evaluation questionnaires, motivation questionnaire and test, then it was analysed by Manova. The results of the study show that

  5. Evaluation of the human immunodeficiency virus type 1 and 2 antibodies detection in dried whole blood spots (dbs samples Pesquisa de anticorpos contra o vírus da imunodeficiência humana tipos 1 e 2 em amostras de sangue seco coletadas em papel filtro

    Directory of Open Access Journals (Sweden)

    Andréa Cauduro de Castro

    2008-06-01

    Full Text Available Human Immunodeficiency Vírus Type 1 and 2 antibodies detection was performed in 457 dried whole blood spots samples (S&S 903. Q-Preven HIV 1+2 was the screening test used. The results were compared with the gold standard serum tests by ELISA (Cobas Core e Axsym HIV1/2 gO and imunofluorescence was the definitive confirmatory test. The samples were obtained from the Hospital Nossa Senhora da Conceição in Porto Alegre, RS - Brazil, through whole blood transfer to filter paper card and sent to Caxias do Sul, RS - Brazil where the tests were performed. The dried whole blood spot stability was evaluated with two different panels. The first one was composed of five negative and five positive samples stored at room temperature, 4 ºC, -20 ºC and -70 ºC, while the second was composed of two negative and three positive samples stored at 37 ºC (humidity Foram realizados 457 testes para detectar anticorpos contra o Vírus da Imunodeficiência Humana tipos 1 e 2, em amostras de sangue total seco coletadas em papel filtro (S&S 903, com o teste de triagem Q-Preven HIV 1+2, comparando-se com os resultados dos testes de triagem no soro (Cobas Core e Axsym HIV1/2 gO, sendo a imunofluorescência indireta o teste confirmatório. As amostras foram obtidas no Hospital Conceição em Porto Alegre, pela transferência de sangue total para cartão de papel filtro e encaminhadas para Caxias do Sul para a realização dos testes. Foi analisada a estabilidade da amostra em papel filtro com a utilização de dois painéis: o primeiro com cinco amostras negativas e cinco positivas armazenadas por seis semanas à temperatura ambiente, 4 ºC, -20 ºC e -70 ºC; o segundo com duas negativas e três positivas armazenadas por seis semanas com avaliações semanais a 37 ºC (umidade <50%. Os resultados de todas as amostras testadas foram mantidos. A sensibilidade foi de 100%, a especificidade de 99,6%, o valor preditivo positivo de 99,5% e o valor preditivo negativo de 100

  6. KOMPONEN WEB DATA ANALYZER PADA IE STUDI KASUS: AKSES WEB TERFAVORIT LABORATORIUM IBS TEKNIK INFORMATIKA - ITS

    Directory of Open Access Journals (Sweden)

    Darlis Heru Murti

    2005-07-01

    Explorer. Untuk itu di dalam pelaksanaan penelitian ini, akan dilakukan perancangan dan pembuatan sebuah perangkat lunak komponen Web Data Analyzer yang melekat pada browser Internet Explorer untuk pencarian akses web terfavorit pengguna. Uji coba dan evaluasi pada penelitian ini dilakukan dengan melakukan instalasi komponen Web Data Analyzer pada sejumlah workstation di Laboratorium IBS Teknik Informatika ITS. Hasil uji coba menunjukkan bahwa komponen Web Data Analyzer mampu memonitor dan menganalisa data aktivitas browsing pengguna serta melakukan otomatisasi terhadap fitur Favorites Internet Explorer dari data aktivitas browsing pengguna yang berhasil tersimpan ke database server. Kata kunci: band object, explorer bar, browser helper object (bho, http analyzer.

  7. Pengembangan tes kemampuan literasi sains pada materi momentum dan impuls dengan Analisis Item Response Theory (IRT

    Directory of Open Access Journals (Sweden)

    Della Apriyani Kusuma Putri

    2018-04-01

    Full Text Available Kemampuan literasi sains adalah suatu kemampuan yang memungkinkan seseorang untuk membuat suatu keputusan dengan pengetahuan konsep dan proses sains yang dimilikinya. Berbagai macam permasalahan yang terjadi di era globalisasi ini menuntut siswa untuk tidak hanya cakap dalam aspek kognitif tapi juga mampu memberi keputusan untuk memecahkan permasalahan, sehingga dapat dikatakan bahwa kemampuan literasi sains adalah kemampuan yang penting dan harus dimiliki siswa. Oleh karena itu, dibutuhkan instrumen untuk mengukur kemampuan literasi sains. hal inilah yang mendasari peneliti mengembangkan instrumen kemampuan literasi sains. Tujuan penelitian ini adalah untuk mengembangkan dan mengetahui karakteristik tes kemampuan literasi sains fisika siswa SMA pada materi momentum dan impuls berdasarkan aspek literasi sains yang dikemukakan oleh Gormally. Metode penelitian yang diterapkan adalah penelitian dan pengembangan (Research and Development yaitu metode penelitian yang digunakan untuk menghasilkan produk tertentu, dan menguji keefektifan produk tersebut. Sebelum diuji coba tes telah divalidasi oleh tiga orang validator dan menghasilkan kesimpulan bahwa tes cukup baik dan dapat diuji coba. Hasil analisis menggunakan Item Response Theory menunjukkan bahwa model 3PL adalah model yang sesuai dengan karakteristik tes. Sedangkan karakteristik tes yang meliputi daya pembeda, tingkat kesukaran, dan faktor tebakan termasuk dalam kategori baik. Science literacy skills is an ability that allows one to make a decision with the knowledge of the concepts and processes of science has. A wide variety of problems that occur in a globalized world requires students to not only proficient in cognitive but also able to make a decision to solve the problem, so it can be said that the ability of science literacy is an important capability and must be owned by the students. Therefore, the instrument is required to measure the ability of science literacy. This problem is

  8. Instructional Materials Physics High School with Multi Representation Approach

    Directory of Open Access Journals (Sweden)

    Yuvita Widi Astuti

    2014-06-01

    disesuaikan dengan kebutuhan penelitian. Instrumen penelitian yang digunakan berupa angket kelayakan. Jenis data yang diperoleh adalah data kuantitatif dan data kualitatif. Hasil uji coba menunjukkan bahwa bahan ajar hasil pengembangan dapat dikategorikan sangat layak. Hasil uji coba lapangan menunjukkan bahwa: (1 sebagian besar siswa pada kelas eksperimen memperoleh hasil tes diatas KKM, (2 hasil postes kelas eksperimen lebih besar daripada kelas kontrol, sehingga bahan ajar dikatakan efektif, namun tidak signifikan untuk meningkatkan pemahaman konsep fisika. Kata kunci: bahan ajar, multi representasi, dinamika rotasi

  9. SISTEM BERBASIS PENGETAHUAN UNTUK KENAIKAN PANGKAT MILITER TNI AU

    Directory of Open Access Journals (Sweden)

    Joko Lianto Buliali

    2007-01-01

    digunakan pada implementasi sistem. Studi kasus pada penelitian ini dilakukan di Pusdiklat Hanudnas Surabaya. Uji coba dilaksanakan dengan menggunakan data yang telah diperiksa dan disetujui oleh pihak Pusdiklat Hanudnas Surabaya. Dari hasil uji coba tersebut disimpulkan bahwa sistem berjalan dengan baik yaitu bahwa hasil akhir yang diperoleh sistem sama dengan hasil perhitungan secara manual. Kata kunci: sistem berbasis pengetahuan, aturan, kenaikan pangkat, personel militer, TNI AU.

  10. PENGEMBANGAN PERANGKAT PERKULIAHAN KEGIATAN LABORATORIUM FISIKA DASAR II BERBASIS INKUIRI TERBIMBING UNTUK MENINGKATKAN KERJA ILMIAH MAHASISWA

    Directory of Open Access Journals (Sweden)

    R. Ariesta

    2012-02-01

    Full Text Available Tujuan penelitian adalah mengembangkan bentuk perangkat perkuliahan kegiatan Laboratorium Fisika Dasar II berbasis inkuiriterbimbing untuk meningkatkan kemampuan kerja ilmiah mahasiswa. Pengembangan perangkat perkuliahan ini mengikuti modelPlomp meliputi fase investigasi awal, fase desain, fase realisasi/konstruksi, fase tes, evaluasi, revisi dan fase implementasi.Analisis data meliputi analisis hasil validasi perangkat secara deskriptif kualitatif, hasil penyekoran lembar observasi dianalisissecara deskriptif kualitatif, analisis hasil tes dengan N-Gain, analisis hasil uji coba soal tes (uji validitas, reliabilitas, tingkatkesukaran, dan daya beda soal. Hasil penelitian ini ditunjukkan oleh perolehan persentase kerja ilmiah mahasiswa secara klasikalsebesar 91,67% dengan kriteria sangat baik, sikap ilmiah dengan persentase 87,50% dengan kriteria sangat baik, penyusunanlaporan oleh mahasiswa dengan persentase 76,88% dengan kriteria baik, serta peningkatan rata-rata hasil belajar (rata-rata gainpertemuan pertama 0,58(sedang, pertemuan kedua 0,56 (sedang, pertemuan ketiga 0,7 (sedang, dan pertemuan keempat 0,93(tinggi. Hasil uji coba pengembangan bentuk perangkat perkuliahan kegiatan Laboratorium Fisika Dasar II berbasis inkuiriterbimbing dapat meningkatkan kerja ilmiah mahasiswa. The research is aimed to develop teaching material of Fundamental Physics 2 Laboratory based on guided inquiry model and toincrease the students' scientific performance. The development of the teaching material is based on Plomp model, consist ofpreliminary investigation phase, design phase, construction phase, test phase, evaluation and revision phase and implementationphase. The instrument validity and scoring from observation sheets were analyzed qualitative-descriptively; the test result wasanalyzed using N-Gain; and try-out test results were analyzed using validity, reliability, item difficulty, and item discriminant test. Theanalysis results show that the

  11. Evaluation of an Improved U.S. Food and Drug Administration Method for the Detection of Cyclospora cayetanensis in Produce Using Real-Time PCR.

    Science.gov (United States)

    Murphy, Helen R; Lee, Seulgi; da Silva, Alexandre J

    2017-07-01

    Cyclospora cayetanensis is a protozoan parasite that causes human diarrheal disease associated with the consumption of fresh produce or water contaminated with C. cayetanensis oocysts. In the United States, foodborne outbreaks of cyclosporiasis have been linked to various types of imported fresh produce, including cilantro and raspberries. An improved method was developed for identification of C. cayetanensis in produce at the U.S. Food and Drug Administration. The method relies on a 0.1% Alconox produce wash solution for efficient recovery of oocysts, a commercial kit for DNA template preparation, and an optimized TaqMan real-time PCR assay with an internal amplification control for molecular detection of the parasite. A single laboratory validation study was performed to assess the method's performance and compare the optimized TaqMan real-time PCR assay and a reference nested PCR assay by examining 128 samples. The samples consisted of 25 g of cilantro or 50 g of raspberries seeded with 0, 5, 10, or 200 C. cayetanensis oocysts. Detection rates for cilantro seeded with 5 and 10 oocysts were 50.0 and 87.5%, respectively, with the real-time PCR assay and 43.7 and 94.8%, respectively, with the nested PCR assay. Detection rates for raspberries seeded with 5 and 10 oocysts were 25.0 and 75.0%, respectively, with the real-time PCR assay and 18.8 and 68.8%, respectively, with the nested PCR assay. All unseeded samples were negative, and all samples seeded with 200 oocysts were positive. Detection rates using the two PCR methods were statistically similar, but the real-time PCR assay is less laborious and less prone to amplicon contamination and allows monitoring of amplification and analysis of results, making it more attractive to diagnostic testing laboratories. The improved sample preparation steps and the TaqMan real-time PCR assay provide a robust, streamlined, and rapid analytical procedure for surveillance, outbreak response, and regulatory testing of foods for

  12. Melt analysis of mismatch amplification mutation assays (Melt-MAMA: a functional study of a cost-effective SNP genotyping assay in bacterial models.

    Directory of Open Access Journals (Sweden)

    Dawn N Birdsell

    Full Text Available Single nucleotide polymorphisms (SNPs are abundant in genomes of all species and biologically informative markers extensively used across broad scientific disciplines. Newly identified SNP markers are publicly available at an ever-increasing rate due to advancements in sequencing technologies. Efficient, cost-effective SNP genotyping methods to screen sample populations are in great demand in well-equipped laboratories, but also in developing world situations. Dual Probe TaqMan assays are robust but can be cost-prohibitive and require specialized equipment. The Mismatch Amplification Mutation Assay, coupled with melt analysis (Melt-MAMA, is flexible, efficient and cost-effective. However, Melt-MAMA traditionally suffers from high rates of assay design failures and knowledge gaps on assay robustness and sensitivity. In this study, we identified strategies that improved the success of Melt-MAMA. We examined the performance of 185 Melt-MAMAs across eight different pathogens using various optimization parameters. We evaluated the effects of genome size and %GC content on assay development. When used collectively, specific strategies markedly improved the rate of successful assays at the first design attempt from ~50% to ~80%. We observed that Melt-MAMA accurately genotypes across a broad DNA range (~100 ng to ~0.1 pg. Genomic size and %GC content influence the rate of successful assay design in an independent manner. Finally, we demonstrated the versatility of these assays by the creation of a duplex Melt-MAMA real-time PCR (two SNPs and conversion to a size-based genotyping system, which uses agarose gel electrophoresis. Melt-MAMA is comparable to Dual Probe TaqMan assays in terms of design success rate and accuracy. Although sensitivity is less robust than Dual Probe TaqMan assays, Melt-MAMA is superior in terms of cost-effectiveness, speed of development and versatility. We detail the parameters most important for the successful application of

  13. Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order.

    Science.gov (United States)

    Bilodeau, Guillaume J; Martin, Frank N; Coffey, Michael D; Blomquist, Cheryl L

    2014-07-01

    A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperatures for specificity. An amplification primer pair designed from conserved regions of the atp9 and nad9 genes produced an amplicon of ≈340 bp specific for the Phytophthora spp. tested. The TaqMan probe for the genus-specific Phytophthora test was designed from a conserved portion of the atp9 gene whereas variable intergenic spacer sequences were used for designing the species-specific TaqMan probes. Specific probes were developed for 13 species and the P. citricola species complex. In silico analysis suggests that species-specific probes could be developed for at least 70 additional described and provisional species; the use of locked nucleic acids in TaqMan probes should expand this list. A second locus spanning three tRNAs (trnM-trnP-trnM) was also evaluated for genus-specific detection capabilities. At 206 bp, it was not as useful for systematic development of a broad range of species-specific probes as the larger 340-bp amplicon. All markers were validated against a test panel that included 87 Phytophthora spp., 14 provisional Phytophthora spp., 29 Pythium spp., 1 Phytopythium sp., and 39 plant species. Species-specific probes were validated further against a range of geographically diverse isolates to ensure uniformity of detection at an intraspecific level, as well as with other species having high levels of sequence similarity to ensure specificity. Both diagnostic

  14. Prevalence of H63D, S65C and C282Y hereditary hemochromatosis gene mutations in Slovenian population by an improved high-throughput genotyping assay

    Directory of Open Access Journals (Sweden)

    Rupreht Ruth

    2007-11-01

    Full Text Available Abstract Background Hereditary hemochromatosis (HH is a common genetic disease characterized by excessive iron overload that leads to multi-organ failure. Although the most prevalent genotype in HH is homozygosity for C282Y mutation of the HFE gene, two additional mutations, H63D and S65C, appear to be associated with a milder form of HH. The aim of this study was to develop a high-throughput assay for HFE mutations screening based on TaqMan technology and to determine the frequencies of HFE mutations in the Slovenian population. Methods Altogether, 1282 randomly selected blood donors from different Slovenian regions and 21 HH patients were analyzed for the presence of HFE mutations by an in-house developed real-time PCR assay based on TaqMan technology using shorter non-interfering fluorescent single nucleotide polymorphism (SNP-specific MGB probes. The assay was validated by RFLP analysis and DNA sequencing. Results The genotyping assay of the H63D, S65C and C282Y mutations in the HFE gene, based on TaqMan technology proved to be fast, reliable, with a high-throughput capability and 100% concordant with genotypes obtained by RFLP and DNA sequencing. The observed frequency of C282Y homozygotes in the group of HH patients was only 48%, others were of the heterogeneous HFE genotype. Among 1282 blood donors tested, the observed H63D, S65C and C282Y allele frequency were 12.8% (95% confidence interval (CI 11.5 – 14.2%, 1.8% (95% CI 1.4 – 2.5% and 3.6% (95% CI 3.0 – 4.5%, respectively. Approximately 33% of the tested subjects had at least one of the three HH mutations, and 1% of them were C282Y homozygotes or compound heterozygotes C282Y/H63D or C282Y/S65C, presenting an increased risk for iron overload disease. A significant variation in H63D allele frequency was observed for one of the Slovenian regions. Conclusion The improved real-time PCR assay for H63D, S65C and C282Y mutations detection is accurate, fast, cost-efficient and ready for

  15. Accurate Digital Polymerase Chain Reaction Quantification of Challenging Samples Applying Inhibitor-Tolerant DNA Polymerases.

    Science.gov (United States)

    Sidstedt, Maja; Romsos, Erica L; Hedell, Ronny; Ansell, Ricky; Steffen, Carolyn R; Vallone, Peter M; Rådström, Peter; Hedman, Johannes

    2017-02-07

    Digital PCR (dPCR) enables absolute quantification of nucleic acids by partitioning of the sample into hundreds or thousands of minute reactions. By assuming a Poisson distribution for the number of DNA fragments present in each chamber, the DNA concentration is determined without the need for a standard curve. However, when analyzing nucleic acids from complex matrixes such as soil and blood, the dPCR quantification can be biased due to the presence of inhibitory compounds. In this study, we evaluated the impact of varying the DNA polymerase in chamber-based dPCR for both pure and impure samples using the common PCR inhibitor humic acid (HA) as a model. We compared the TaqMan Universal PCR Master Mix with two alternative DNA polymerases: ExTaq HS and Immolase. By using Bayesian modeling, we show that there is no difference among the tested DNA polymerases in terms of accuracy of absolute quantification for pure template samples, i.e., without HA present. For samples containing HA, there were great differences in performance: the TaqMan Universal PCR Master Mix failed to correctly quantify DNA with more than 13 pg/nL HA, whereas Immolase (1 U) could handle up to 375 pg/nL HA. Furthermore, we found that BSA had a moderate positive effect for the TaqMan Universal PCR Master Mix, enabling accurate quantification for 25 pg/nL HA. Increasing the amount of DNA polymerase from 1 to 5 U had a strong effect for ExTaq HS, elevating HA-tolerance four times. We also show that the average Cq values of positive reactions may be used as a measure of inhibition effects, e.g., to determine whether or not a dPCR quantification result is reliable. The statistical models developed to objectively analyze the data may also be applied in quality control. We conclude that the choice of DNA polymerase in dPCR is crucial for the accuracy of quantification when analyzing challenging samples.

  16. Clinical evaluation of a quantitative real time polymerase chain reaction assay for diagnosis of primary Epstein-Barr virus infection in children.

    Science.gov (United States)

    Pitetti, Raymond D; Laus, Stella; Wadowsky, Robert M

    2003-08-01

    Epstein-Barr virus (EBV) infectious mononucleosis is often diagnosed based on characteristic clinical features and either a positive heterophil antibody test or serology, both of which can be unreliable in young children. Real time quantitative PCR assays that measure EBV DNA load in serum or plasma are highly sensitive in young children, but serum and plasma contain inhibitors of PCR which must be removed by DNA extraction techniques. A real time TaqMan PCR assay was designed and evaluated for simultaneously measuring EBV DNA load and validating the removal of PCR inhibitors from serum samples. A serum sample was available from patients classified serologically as primary EBV infection (n = 28), EBV-seronegative (n = 25) and EBV-seropositive (n = 26). Patients were classified as having EBV infectious mononucleosis if they had specified clinical findings and > or =10% atypical lymphocytes in peripheral blood or had a positive Monospot test result. DNA was purified by a spin column method and tested in PCR reactions with primers for EBV DNA polymerase gene and internal control targets. Amplification of the two PCR products was measured in real time with separate TaqMan DNA probes labeled with various fluorescent reporters. The mean age of study patients was 9 years, 4 months. Twenty-one (75%) of the patients in the primary EBV infection group, one (4%) of the seronegatives and none of the seropositives had detectable EBV DNA. Within the primary infection group, those with detectable virus were more likely than those without detectable virus to have evidence of lymphadenopathy (14 of 16 vs.1 of 5; P = 0.011), higher mean atypical (11.7 vs.0.9%; P = 0.002) and absolute atypical (1.5 vs.0.1 x 109/l; P = 0.004) lymphocyte count, higher mean absolute lymphocyte count (4.7 vs.2.3 x 109/l; P = 0.026) and higher mean aspartate aminotransferase value (119.8 vs.37.3 IU/l; P = 0.036). Ten patients, all in the primary infection group, had EBV infectious mononucleosis, and all

  17. Deficit of Kcnma1 mRNA expression in the dentate gyrus of epileptic rats

    Science.gov (United States)

    Ermolinsky, Boris; Arshadmansab, Massoud F.; Pacheco Otalora, Luis F.; Zarei, Masoud M.; Garrido-Sanabria, Emilio R.

    2008-01-01

    Epileptogenesis in mesial temporal lobe epilepsy is determined by several factors including abnormalities in the expression and function of ion channels. Here, we report a long-lasting deficit in gene expression of Kcnma1 coding for the large-conductance calcium-activated potassium (BK, MaxiK) channel α-subunits after pilocarpine-induced status epilepticus. By using comparative real-time PCR, Taqman gene expression assays, and the delta-delta comparative threshold method we detected a significant reduction in Kcnma1 expression in microdissected dentate gyrus at different intervals after status epilepticus (24 h, 10 days, 1 month, and more than 2 months). BK channels are key regulators of neuronal excitability and transmitter release. Hence, defective Kcnma1 expression may play a critical role in the pathogenesis of mesial temporal lobe epilepsy. PMID:18695509

  18. Lack of an association of miR-938 SNP in IDDM10 with human type 1 diabetes

    Directory of Open Access Journals (Sweden)

    Mi Xiaofan

    2011-10-01

    Full Text Available Abstract MicroRNAs (miRNAs are a newly discovered type of small non-protein coding RNA that function in the inhibition of effective mRNA translation, and may serve as susceptibility genes for various disease developments. The SNP rs12416605, located in human type 1 diabetes IDDM10 locus, changes the seeding sequence (UGU[G/A]CCC of miRNA miR-938 and potentially alters miR-938 targets, including IL-16 and IL-17A. In an attempt to test whether miR-938 may be a susceptibility gene for IDDM10, we assessed the possible association of the miR-938 SNP with T1D in an American Caucasian cohort of 622 patients and 723 healthy controls by TaqMan assay. Our current data do not support the association between the SNP in miR-938 and type 1 diabetes.

  19. 8q24 sequence variants in relation to prostate cancer risk among men of African descent: A case-control study

    Directory of Open Access Journals (Sweden)

    VanCleave Tiva T

    2010-06-01

    Full Text Available Abstract Background Human chromosome 8q24 has been implicated in prostate tumorigenesis. Methods Consequently, we evaluated seven 8q24 sequence variants relative to prostate cancer (PCA in a case-control study involving men of African descent. Genetic alterations were detected in germ-line DNA from 195 incident PCA cases and 531 controls using TaqMan polymerase chain reaction (PCR. Results Inheritance of the 8q24 rs16901979 T allele corresponded to a 2.5-fold increase in the risk of developing PCA for our test group. These findings were validated using multifactor dimensionality reduction (MDR and permutation testing (p = 0.038. The remaining 8q24 targets were not significantly related to PCA outcomes. Conclusions Although compelling evidence suggests that the 8q24 rs16901979 locus may serve as an effective PCA predictor, our findings require additional evaluation in larger studies.

  20. Nucleolin is regulated both at the level of transcription and translation

    International Nuclear Information System (INIS)

    Bicknell, Katrina; Brooks, Gavin; Kaiser, Pete; Chen Hongying; Dove, Brian K.; Hiscox, Julian A.

    2005-01-01

    Nucleolin is a multi-functional protein that is located to the nucleolus. In tissue culture cells, the stability of nucleolin is related to the proliferation status of the cell. During development, rat cardiomyocytes proliferate actively with increases in the mass of the heart being due to both hyperplasia and hypertrophy. The timing of this shift in the phenotype of the myocyte from one capable of undergoing hyperplasia to one that can grow only by hypertrophy occurs within 4 days of post-natal development. Thus, cardiomyocytes are an ideal model system in which to study the regulation of nucleolin during growth in vivo. Using Western blot and quantitative RT-PCR (TaqMan) we found that the amount of nucleolin is regulated both at the level of transcription and translation during the development of the cardiomyocyte. However, in cells which had exited the cell cycle and were subsequently given a hypertrophic stimulus, nucleolin was regulated post-transcriptionally

  1. Studies of CTNNBL1 and FDFT1 variants and measures of obesity: analyses of quantitative traits and case-control studies in 18,014 Danes

    DEFF Research Database (Denmark)

    Andreasen, Camilla Helene; Mogensen, Mette Sloth; Borch-Johnsen, Knut

    2009-01-01

    of obesity-related quantitative traits, and case-control studies in large study samples of Danes. METHODS: The FDFT1 rs7001819, CTNNBL1 rs6013029 and rs6020846 were genotyped, using TaqMan allelic discrimination, in a combined study sample comprising 18,014 participants ascertained from; the population...... and a previous study. FDFT1 rs7001819 showed no association with obesity, neither when analysing quantitative traits nor when performing case-control studies of obesity.......). The most significantly associating variants within CTNNBL1 including rs6013029 and rs6020846 were additionally confirmed to associate with morbid obesity in a French Caucasian case-control sample. The aim of this study was to investigate the impact of these three variants on obesity, through analyses...

  2. A random PCR screening system for the identification of type 1 human herpes simplex virus.

    Science.gov (United States)

    Yu, Xuelian; Shi, Bisheng; Gong, Yan; Zhang, Xiaonan; Shen, Silan; Qian, Fangxing; Gu, Shimin; Hu, Yunwen; Yuan, Zhenghong

    2009-10-01

    Several viral diseases exhibit measles-like symptoms. Differentiation of suspected cases of measles with molecular epidemiological techniques in the laboratory is useful for measles surveillance. In this study, a random PCR screening system was undertaken for the identification of isolates from patients with measles-like symptoms who exhibited cytopathic effects, but who had negative results for measles virus-specific reverse transcription (RT)-PCR and indirect immunofluorescence assays. Sequence analysis of random amplified PCR products showed that they were highly homologous to type 1 human herpes simplex virus (HSV-1). The results were further confirmed by an HSV-1-specific TaqMan real-time PCR assay. The random PCR screening system described in this study provides an efficient procedure for the identification of unknown viral pathogens. Measles-like symptoms can also be caused by HSV-1, suggesting the need to include HSV-1 in differential diagnoses of measles-like diseases.

  3. The GCKR rs780094 polymorphism is associated with elevated fasting serum triacylglycerol, reduced fasting and OGTT-related insulinaemia, and reduced risk of type 2 diabetes

    DEFF Research Database (Denmark)

    Sparsø, T; Andersen, G; Nielsen, T

    2007-01-01

    to metabolic traits (mainly fasting hypertriacylglycerolaemia) and traits related to pancreatic beta cell function. METHODS: The polymorphism was genotyped in 16,853 Danes using Taqman allelic discrimination. Association was analysed in case-control studies and quantitative trait analyses. We also analysed...... the possible interactive effect between the GCK -30G>A polymorphism and the GCKR rs780094 variant on metabolic traits. RESULTS: The minor GCKR A-allele of rs780094 is associated with an increased level of fasting serum triacylglycerol (p = 6 x 10(-14)), impaired fasting (p = 0.001) and OGTT-related insulin...... release (p = 3 x 10(-6)), reduced homeostasis model assessment of insulin resistance (p = 0.0004), WHO-defined dyslipidaemia (p = 6 x 10(-9)) and a modestly decreased risk of type 2 diabetes (p = 0.01). Significantly increased fasting serum insulin concentrations were demonstrated when analysing the GCK...

  4. Attenuation of the beta-catenin/TCF4 complex in colorectal cancer cells induces several growth-suppressive microRNAs that target cancer promoting genes

    DEFF Research Database (Denmark)

    Schepeler, Troels; Holm, Anja; Halvey, P

    2012-01-01

    Aberrant activation of the Wnt signaling pathway is causally involved in the formation of most colorectal cancers (CRCs). Although detailed knowledge exists regarding Wnt-regulated protein-coding genes, much less is known about the possible involvement of non-coding RNAs. Here we used TaqMan Array......RNAs are upregulated as a consequence of forced attenuation of Wnt signaling in CRC cells, and some of these miRNAs inhibit cell growth with concomitant suppression of several growth-stimulatory cancer-related genes....... MicroRNA Cards, capable of detecting 664 unique human microRNAs (miRNAs), to describe changes of the miRNA transcriptome following disruption of beta-catenin/TCF4 activity in DLD1 CRC cells. Most miRNAs appeared to respond independent of host gene regulation and proximal TCF4 chromatin occupancy...

  5. MAVS is not a Likely Susceptibility Locus for Addison's Disease and Type 1 Diabetes.

    Science.gov (United States)

    Zurawek, Magdalena; Fichna, Marta; Kazimierska, Marta; Fichna, Piotr; Dzikiewicz-Krawczyk, Agnieszka; Przybylski, Grzegorz; Ruchala, Marek; Nowak, Jerzy

    2017-06-01

    Mitochondrial antiviral signaling (MAVS) protein is an intracellular adaptor molecule, downstream of viral sensors, retinoid acid-inducible gene I (RIG-I)-like receptors (RLRs). Impaired antiviral cell signaling might contribute to autoimmunity. Studies have recently shown variations in genes encoding RLRs as risk factors for autoimmune diseases. We investigated whether MAVS coding polymorphisms are associated with Addison's disease (AD) and type 1 diabetes (T1D) in Polish population. We genotyped 140 AD, 532 T1D patients and 600 healthy controls for MAVS rs17857295, rs7262903, rs45437096 and rs7269320. Genotyping was performed by TaqMan assays. Distribution of the MAVS genotypes and alleles did not reveal significant differences between patients and controls (p > 0.05). This analysis did not indicate the association of the MAVS locus with susceptibility to AD and T1D.

  6. SCN1A, ABCC2 and UGT2B7 gene polymorphisms in association with individualized oxcarbazepine therapy.

    Science.gov (United States)

    Ma, Chun-Lai; Wu, Xun-Yi; Jiao, Zheng; Hong, Zhen; Wu, Zhi-Yuan; Zhong, Ming-Kang

    2015-01-01

    Associations between the effects of SCN1A, SCN2A, ABCC2 and UGT2B7 genetic polymorphisms and oxcarbazepine (OXC) maintenance doses in Han Chinese epileptic patients were investigated. Genetic polymorphisms were detected in 184 epileptic patients receiving OXC monotherapy by high-resolution melting curve and TaqMan method. Carriers of the SCN1A IVS5-91G>A, UGT2B7 c.802T>C and ABCC2 c.1249G>A variant alleles required significantly higher OXC maintenance doses than noncarriers (p GA > AA. SCN1A, UGT2B7 and ABCC2 genetic polymorphisms are associated with OXC maintenance doses and may be useful for the personalization of OXC therapy in epileptic patients. Further studies are needed. Original submitted 6 June 2014; Revision submitted 5 September 2014.

  7. Age and gender differences in the influences of eNOS T-786C polymorphism on arteriosclerotic parameters in general population in Japan.

    Science.gov (United States)

    Hashimoto, Marowa; Miyai, Nobuyuki; Hattori, Sonomi; Iwahara, Akihiko; Utsumi, Miyoko; Arita, Mikio; Takeshita, Tatsuya

    2016-07-01

    The influence of T-786C polymorphism in the promoter region of endothelial nitric oxide synthase (eNOS) on arteriosclerotic parameters by age and gender were examined. Brachial-ankle pulse wave velocity (baPWV), heart-rate adjusted augmentation index (AIx@75), pulse pressure (PP) and albumin-creatinine ratio (ACR) were assessed as arteriosclerotic parameters in addition to non-high-density lipoprotein cholesterol (non-HDL-C) to HDL-C (non-HDL-C/HDL-C) ratio in 1499 participants. T-786C polymorphism (rs2070744) was screened using a TaqMan allelic discrimination assay. Analyses of covariance were carried. Women with the non-C allele showed significantly lower AIx@75 in participants aged gender differences, possibly involving antioxidative and/or endothelial signaling other than inflammatory signaling.

  8. BRIP1 (BACH1 variants and familial breast cancer risk: a case-control study

    Directory of Open Access Journals (Sweden)

    Bugert Peter

    2007-05-01

    Full Text Available Abstract Background Inactivating and truncating mutations of the nuclear BRCA1-interacting protein 1 (BRIP1 have been shown to be the major cause of Fanconi anaemia and, due to subsequent alterations of BRCA1 function, predispose to breast cancer (BC. Methods We investigated the effect of BRIP1 -64G>A and Pro919Ser on familial BC risk by means of TaqMan allelic discrimination, analysing BRCA1/BRCA2 mutation-negative index patients of 571 German BC families and 712 control individuals. Results No significant differences in genotype frequencies between BC cases and controls for BRIP1 -64G>A and Pro919Ser were observed. Conclusion We found no effect of the putatively functional BRIP1 variants -64G>A and Pro919Ser on the risk of familial BC.

  9. Direct detection of Leishmania from clinical samples.

    Science.gov (United States)

    Waitumbi, John N; Bast, Joshua; Nyakoe, Nancy; Magiri, Charles; Quintana, Miguel; Takhampunya, Ratree; Schuster, Anthony L; Van de Wyngaerde, Marshall T; McAvin, James C; Coleman, Russell E

    2017-01-01

    The ability to rapidly and accurately diagnose leishmaniasis is a military priority. Testing was conducted to evaluate diagnostic sensitivity and specificity of field-expedient Leishmania genus and visceral Leishmania specific dual-fluorogenic, hydrolysis probe (TaqMan), polymerase chain reaction assays previously established for use in vector surveillance. Blood samples of patients with confirmed visceral leishmaniasis and controls without the disease from Baringo District, Kenya, were tested. Leishmania genus assay sensitivity was 100% (14/14) and specificity was 84% (16/19). Visceral Leishmania assay sensitivity was 93% (13/14) and specificity 80% (4/5). Cutaneous leishmaniasis (CL) skin scrapes of patients from Honduras were also evaluated. Leishmania genus assay sensitivity was 100% (10/10). Visceral Leishmania assay specificity was 100% (10/10) from cutaneous leishmaniasis samples; no fluorescence above background was reported. These results show promise in a rapid, sensitive, and specific method for Leishmania direct detection from clinical samples.

  10. Comparative analysis of minor histocompatibility antigens genotyping methods

    Directory of Open Access Journals (Sweden)

    A. S. Vdovin

    2016-01-01

    Full Text Available The wide range of techniques could be employed to find mismatches in minor histocompatibility antigens between transplant recipients and their donors. In the current study we compared three genotyping methods based on polymerase chain reaction (PCR for four minor antigens. Three of the tested methods: allele-specific PCR, restriction fragment length polymorphism and real-time PCR with TaqMan probes demonstrated 100% reliability when compared to Sanger sequencing for all of the studied polymorphisms. High resolution melting analysis was unsuitable for genotyping of one of the tested minor antigens (HA-1 as it has linked synonymous polymorphism. Obtained data could be used to select the strategy for large-scale clinical genotyping.

  11. Fast real-time polymerase chain reaction for quantitative detection of Lactobacillus delbrueckii bacteriophages in milk.

    Science.gov (United States)

    Martín, Maria Cruz; del Rio, Beatriz; Martínez, Noelia; Magadán, Alfonso H; Alvarez, Miguel A

    2008-12-01

    One of the main microbiological problems of the dairy industry is the susceptibility of starter bacteria to virus infections. Lactobacillus delbrueckii, a component of thermophilic starter cultures used in the manufacture of several fermented dairy products, including yogurt, is also sensitive to bacteriophage attacks. To avoid the problems associated with these viruses, quick and sensitive detection methods are necessary. In the present study, a fast real-time quantitative polymerase chain reaction assay for the direct detection and quantification of L. delbrueckii phages in milk was developed. A set of primers and a TaqMan MGB probe was designed, based on the lysin gene sequence of different L. delbrueckii phages. The results show the proposed method to be a rapid (total processing time 30 min), specific and highly sensitive technique for detecting L. delbrueckii phages in milk.

  12. Molecular detection of oomycetes species in water courses

    Directory of Open Access Journals (Sweden)

    Oszako Tomasz

    2016-12-01

    Full Text Available In Poland, about 20% of forest nurseries use irrigation water coming from natural superficial reservoirs, presumed to be the first source of infection caused by harmful pathogens belonging to the Oomycota class, especially Phytophthora genus and Pythium genus. The forest nursery is the only place where forest managers can react before pathogens leave it with asymptomatic plants or soil attached to their roots. The aim of this research was detection and identification phytopathogens in water samples. In order to recognise genus Phytophthora or Pythium in water collected from 33 places in five different forest districts in Poland, two DNA-based approaches of identification were applied: (i the TaqMan probes, and (ii sequencing of the ITS6/4 region.

  13. Preliminary report for analysis of genome wide mutations from four ciprofloxacin resistant B. anthracis Sterne isolates generated by Illumina, 454 sequencing and microarrays for DHS

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, Crystal [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vergez, Lisa [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hinckley, Aubree [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thissen, James [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gardner, Shea [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McLoughlin, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Jackson, Paul [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ellingson, Sally [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hauser, Loren [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brettin, Tom [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Fofanov, Viacheslav [Eureka Genomics, Hercules, CA (United States); Koshinsky, Heather [Eureka Genomics, Hercules, CA (United States); Fofanov, Yuriy [Univ. of Houston, TX (United States)

    2011-06-21

    The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. As the result of a different DHS project, we have selected for and isolated a large number of ciprofloxacin resistant B. anthracis Sterne isolates. These isolates vary in the concentrations of ciprofloxacin that they can tolerate, suggesting multiple mutations in the samples. In collaboration with University of Houston, Eureka Genomics and Oak Ridge National Laboratory, we analyzed the ciprofloxacin resistant B. anthracis Sterne isolates by microarray hybridization, Illumina and Roche 454 sequencing to understand the error rates and sensitivity of the different methods. The report provides an assessment of the results and a complete set of all protocols used and all data generated along with information to interpret the protocols and data sets.

  14. Real-Time PCR Detection of Dogwood Anthracnose Fungus in Historical Herbarium Specimens from Asia.

    Science.gov (United States)

    Miller, Stephen; Masuya, Hayato; Zhang, Jian; Walsh, Emily; Zhang, Ning

    2016-01-01

    Cornus species (dogwoods) are popular ornamental trees and important understory plants in natural forests of northern hemisphere. Dogwood anthracnose, one of the major diseases affecting the native North American Cornus species, such as C. florida, is caused by the fungal pathogen Discula destructiva. The origin of this fungus is not known, but it is hypothesized that it was imported to North America with its host plants from Asia. In this study, a TaqMan real-time PCR assay was used to detect D. destructiva in dried herbarium and fresh Cornus samples. Several herbarium specimens from Japan and China were detected positive for D. destructiva, some of which were collected before the first report of the dogwood anthracnose in North America. Our findings further support that D. destructiva was introduced to North America from Asia where the fungus likely does not cause severe disease.

  15. Quantification of massively parallel sequencing libraries - a comparative study of eight methods

    DEFF Research Database (Denmark)

    Hussing, Christian; Kampmann, Marie-Louise; Mogensen, Helle Smidt

    2018-01-01

    Quantification of massively parallel sequencing libraries is important for acquisition of monoclonal beads or clusters prior to clonal amplification and to avoid large variations in library coverage when multiple samples are included in one sequencing analysis. No gold standard for quantification...... estimates followed by Qubit and electrophoresis-based instruments (Bioanalyzer, TapeStation, GX Touch, and Fragment Analyzer), while SYBR Green and TaqMan based qPCR assays gave the lowest estimates. qPCR gave more accurate predictions of sequencing coverage than Qubit and TapeStation did. Costs, time......-consumption, workflow simplicity, and ability to quantify multiple samples are discussed. Technical specifications, advantages, and disadvantages of the various methods are pointed out....

  16. Age- and Tumor Subtype-Specific Breast Cancer Risk Estimates for CHEK2*1100delC Carriers

    DEFF Research Database (Denmark)

    Schmidt, Marjanka K; Hogervorst, Frans; van Hien, Richard R

    2016-01-01

    PURPOSE: CHEK2*1100delC is a well-established breast cancer risk variant that is most prevalent in European populations; however, there are limited data on risk of breast cancer by age and tumor subtype, which limits its usefulness in breast cancer risk prediction. We aimed to generate tumor...... subtype- and age-specific risk estimates by using data from the Breast Cancer Association Consortium, including 44,777 patients with breast cancer and 42,997 controls from 33 studies genotyped for CHEK2*1100delC. PATIENTS AND METHODS: CHEK2*1100delC genotyping was mostly done by a custom Taqman assay....... Breast cancer odds ratios (ORs) for CHEK2*1100delC carriers versus noncarriers were estimated by using logistic regression and adjusted for study (categorical) and age. Main analyses included patients with invasive breast cancer from population- and hospital-based studies. RESULTS: Proportions...

  17. E112D polymorphism in the prolylcarboxypeptidase gene is associated with blood pressure response to benazepril in Chinese hypertensive patients.

    Science.gov (United States)

    Zhang, Yan; Hong, Xiu-mei; Xing, Hou-xun; Li, Jian-ping; Huo, Yong; Xu, Xi-ping

    2009-10-20

    Marked interindividual variation exists in blood pressure response to benazepril, which is considered to have genetic basis. Our objectives were to evaluate whether the E112D polymorphism in the prolylcarboxypeptidase (PRCP) gene has impact on blood pressure response to benazepril. Hypertensive patients from Huoqiu County and Yuexi County of Anhui Province received daily treatment with an oral dosage of 10 mg benazepril for 15 days. Genotypes of the E112D polymorphism in the PRCP gene were determined by TaqMan SNP genotyping assay. Multivariate linear and Logistic regressions using generalized estimating equation model were performed in a total of 1092 patients to evaluate the association of PRCP genotypes and blood pressure response to benazepril. Patients carrying ED or DD genotype had a less systolic blood pressure reduction (adjusted beta = -3.7 + or - 1.1, P benazepril treatment in hypertensive patients of Anhui Province, China.

  18. Novel reverse transcription loop-mediated isothermal amplification for rapid detection of foot-and-mouth disease virus

    DEFF Research Database (Denmark)

    Dukes, J.P.; King, D.P.; Alexandersen, Søren

    2006-01-01

    Speed is paramount in the diagnosis of foot-and-mouth disease (FMD) and simplicity is required if a test is to be deployed in the field. The development of a one-step, reverse transcription loop-mediated amplification (RT-LAMP) assay enables FMD virus (FMDV) to be detected in under an hour...... in a single tube without thermal cycling. A fragment of the 3D RNA polymerase gene of the virus is amplified at 65 degrees C in the presence of a primer mixture and both reverse transcriptase and Bst DNA polymerase. Compared with real-time RT-PCR, RT-LAMP was consistently faster, and ten copies of FMDV...... vesicular diseases and from that of genetically related picornaviruses. Diagnostic sensitivity was validated by the amplification of reference FMDV strains and archival material from field cases of FMD. In comparison with the performance of the established diagnostic TaqMan (R) assay, RT-LAMP appears...

  19. High-resolution melting analysis using unlabeled probe and amplicon scanning simultaneously detects several lactase persistence variants

    DEFF Research Database (Denmark)

    Janukonyté, Jurgita; Vestergaard, Else M; Ladefoged, Søren A

    2010-01-01

    Lactase persistence and thereby tolerance to lactose is a common trait in people of Northern European descent. It is linked to the LCT -13910C>T variant located in intron 13 of the MCM6 gene 13.9 kb upstream of the lactase (LCT) gene. In people of African and Middle Eastern descent, lactase...... persistence can be associated with other variants nearby the -13910C>T variant, limiting the use of the -13910C>T-based SNP analysis, e.g. TaqMan assays for the diagnosis of lactose intolerance. Using high-resolution melting analysis, we identified five samples that were heterozygous for the -13915T>G variant...... the -13910C>T and -13915T>G variants in addition to rarer variants surrounding the -13910 site. This new method may contribute to improve the diagnostic performance of the genetic analysis for lactose intolerance....

  20. Culture-independent identification and quantification of Gallibacterium anatis (G. anatis) by real-time quantitative PCR

    DEFF Research Database (Denmark)

    Wang, Chong; Robles, Francisco; Ramirez, Saul

    2016-01-01

    Gallibacterium is a genus within the family Pasteurellaceae characterized by a high level of phenotypic and genetic diversity. No diagnostic method has yet been described, which allows species-specific identification of Gallibacterium anatis. The aim of this study was to develop a real...... published conventional PCR method and culture-based identification, respectively. The detection rates were 97%, 78% and 34% for the current qPCR, the conventional PCR and the culture-based identification method, respectively. The qPCR assay was able to detect the gene gyrB in serial dilutions of 10......-time quantitative PCR (qPCR) method allowing species-specific identification and quantification of G. anatis. A G. anatis specific DNA sequence was identified in the gyrase subunit B gene (gyrB) and used to design a TaqMan probe and corresponding primers. The specificity of the assay was tested on 52 bacterial...

  1. Evaluation of a single-tube fluorogenic RT-PCR assay for detection of bovine respiratory syncytial virus in clinical samples

    DEFF Research Database (Denmark)

    Hakhverdyan, Mikhayil; Hägglund, Sara; Larsen, Lars Erik

    2005-01-01

    understanding of the virus. In this study, a BRSV fluorogenic reverse transcription PCR (fRT-PCR) assay, based on TaqMan principle, was developed and evaluated on a large number of clinical samples, representing various cases of natural and experimental BRSV infections. By using a single-step closed-tube format......, the turn-around time was shortened drastically and results were obtained with minimal risk for cross-contamination. According to comparative analyses, the detection limit of the fRT-PCR was on the same level as that of a nested PCR and the sensitivity relatively higher than that of a conventional PCR......, antigen ELISA (Ag-ELISA) and virus isolation (VI). Interspersed negative control samples, samples from healthy animals and eight symptomatically or genetically related viruses were all negative, confirming a high specificity of the assay. Taken together, the data indicated that the fRT-PCR assay can...

  2. SISTEM INFORMASI RENSTRA DAN RENOP JURUSAN TEKNIK ELEKTRO POLITEKNIK NEGERI SEMARANG

    Directory of Open Access Journals (Sweden)

    Alifia Choirunnisa

    2016-10-01

    Full Text Available Setiap jurusan di Politeknik Negeri Semarang mempunyai Rencana Strategi (Renstra dan Rencana Operasional (Renop untuk mengelola dan memantau perkembangan jurusannya masing-masing. Salah satu jurusannya yaitu jurusan Teknik Elektro. Dalam pengelolaan data perencanaan strategi dan operasional jurusan Teknik Elektro masih dilakukan secara manual. Dengan memanfaatkan teknologi sistem informasi, Sistem Informasi Renstra dan Renop Jurusan Teknik Elektro Berbasis Web mengubah sistem pengelolaan dari manual menjadi berbasis teknologi sistem informasi yang lebih efisien dan efektif. Tujuan dari pembuatan sistem informasi ini adalah untuk menghasilkan sebuah Sistem Informasi Renstra dan Renop Jurusan Teknik Elektro Berbasis Web serta membantu dan memberikan kemudahan dalam pengelolaan informasi Renstra dan Renop. Metode yang digunakan dalam penelitian ini adalah metodologi waterfall, dimana dalam metodologi ini setiap langkah penelitian dilakukan secara berurutan, mulai dari tahapan Analisis Kebutuhan, Desain Sistem, Implementasi dan Pengujian Unit, Integrasi dan Pengujian Sistem, serta Operasi dan Pemeliharaan. Perancangan sistem menggunakan model Data Flow Diagram (DFD. Pembangunan sistem menggunakan bahasa pemrograman PHP dan framework codeigniter serta database MySQL. Pengujian sistem menggunakan metode pengujian setiap unit fungsi dari masing-masing fitur. Hasil dari penelitian ini yaitu sebuah sistem informasi yang dapat membantu ketua jurusan, sekretaris jurusan, maupun ketua program studi dalam mengelola Renstra dan Renop. Sistem ini telah di uji coba dengan hasil tingkat kepuasan pengguna sebesar 81,2%.

  3. PEMANFATAN TEOREMA BAYES DALAM PENENTUAN PENYAKIT THT

    Directory of Open Access Journals (Sweden)

    Sri Winiarti

    2008-07-01

    Full Text Available Dalam konsep pelacakan dalam mencari solusi dengan pendekatan artificial inteligent, ada berbagai metode yang dapat diterapkan untuk mengatasi masalah ketidakpastian saat proses pelacakan terjadi. Salah satunya adalah teorema bayes. Adanya ketidakpastian pada proses pelacakan dapat terjadi karena adanya perubahan pengetahuan yang ada di dalam sistem. Untuk itu diperlukan adanya suatu metode untuk mengatasi permasalahan tersebut. Dalam penelitian ini telah diterapkan suatu metode untuk mengatasi ketidakpastian dengan teorema Bayes pada kasus pelacakan untuk mendiagnosa penyakit pada THT (Telinga,Hidung dan Tenggorokan. Subjek pada penelitian ini adalah proses pelacakan untuk menentukan penyakit THT dengan model penalaran forward chaining dan metode kepastiannya menggunakan teorema bayes dengan cara menghitung nilai probabilitas suatu penyakit dan membandingkan probabilitas setiap gejalanya. Model pengembangan perangkat lunak yang digunakan dalam penelitian ini adalah Waterfall. Metode Waterfall diawali dengan analisis data, perancangan sistem, pengkodean menggunakan Visual Basic 6.0, pengujian sistem dengan black box test dan alfa test. Dari penelitian yang dilakukan menghasilkan sebuah perangkat lunak yaitu yang mampu menentukan penyakit pada THT dengan menerapkan metode bayes untuk mengatasi ketidakpastian. Hasil uji coba sistem menujukkan bahwa aplikasi ini layak dan dapat digunakan. Kata kunci : Penyakit, THT, Teorema Bayes.

  4. PEMANFATAN TEOREMA BAYES DALAM PENENTUAN PENYAKIT THT

    Directory of Open Access Journals (Sweden)

    Sri Winiarti

    2012-05-01

    Full Text Available Dalam konsep pelacakan dalam mencari solusi dengan pendekatan artificial inteligent, ada berbagai metode  yang dapat diterapkan untuk mengatasi masalah ketidakpastian saat proses pelacakan terjadi. Salah satunya adalah teorema bayes. Adanya ketidakpastian pada proses pelacakan dapat terjadi karena adanya perubahan pengetahuan yang ada di dalam sistem. Untuk itu diperlukan adanya suatu metode untuk mengatasi permasalahan tersebut. Dalam penelitian ini telah diterapkan suatu metode untuk mengatasi ketidakpastian dengan teorema Bayes pada kasus pelacakan untuk mendiagnosa penyakit pada THT (Telinga,Hidung dan Tenggorokan.  Subjek pada penelitian ini adalah proses pelacakan untuk menentukan penyakit THT dengan model penalaran forward chaining dan metode kepastiannya menggunakan teorema bayes dengan cara menghitung nilai probabilitas suatu penyakit dan membandingkan probabilitas setiap gejalanya. Model pengembangan perangkat lunak yang digunakan dalam penelitian ini adalah Waterfall. Metode Waterfall diawali dengan analisis data, perancangan sistem, pengkodean menggunakan Visual Basic 6.0, pengujian sistem dengan black box test dan alfa test. Dari penelitian yang dilakukan menghasilkan sebuah perangkat lunak yaitu  yang mampu menentukan penyakit pada THT dengan menerapkan metode bayes untuk mengatasi ketidakpastian. Hasil uji coba sistem menujukkan bahwa aplikasi ini layak dan dapat digunakan.

  5. Implementasi Wireless Quality of Service dengan Metode Load Switching Jaringan Seluler Menggunakan Software Defined Network untuk Meningkatkan Network Reliability pada Jaringan Dinamis

    Directory of Open Access Journals (Sweden)

    Yoga Bayu Aji Pranawa

    2017-03-01

    Full Text Available Wireless Quality of Service (QOS adalah salah satu dimensi mobilitas, yaitu sebuah metode yang digunakan untuk menjaga kualitas suatu jaringan nirkabel. QOS diperlukan sebagai sebuah metode untuk memenuhi kriteria pelayanan sistem bagi pengguna, yaitu confidentiality, integrity, dan availability. Beberapa aspek yang menjadi topik utama dalam QOS adalah failure and recovery mechanism, variable bandwidth, computing distribution, discovery mechanism, variable lantency, dan performance feedback. Wireless yang dibahas pada penelitian ini dititik beratkan pada jaringan seluler yang cenderung tidak reliable pada daerah tertentu. Oleh karena itu dibutuhkan sebuah mekanisme yang dapat mengatasi tidak stabilnya jaringan seluler tersebut. mplementasi mekanisme yang diterapkan pada penelitian ini adalah dengan menerapkan load switching pada jaringan seluler dengan menggunakan beberapa provider dan menerapkan teknologi Software Defined Network (SDN. Berdasarkan hasi uji coba dapat disimpulkan bahwa sistem yang dibuat pada penelitian ini dapat menerapkan wireless quality of service dan meningkatkan network reliability sebesar 65,29% dan 83,87% lebih baik untuk penggunaan tanpa waktu tunggu dan dengan waktu tunggu pada suatu jaringan  dinamis.

  6. Quantification of the value of C-reactive protein and its relationship with periodontal disease and cardiovascular risk in a sample of patients from the Facultad de Odontologia de la Universidad de Costa Rica: preliminary study

    International Nuclear Information System (INIS)

    Bermudez Mora, Gustavo; Gonzalez Leon, Yerlin; Jimenez Hernandez, Melissa; Padron Giraldino, Lieny; Rojas Villagra, Andrea

    2013-01-01

    Plasma P-CR concentration was measured and the value obtained was related to the presence and severity of periodontal and cardiovascular disease. A cross-sectional descriptive study was carried out, with the sample of 30 patients of different gender, age, type of periodontal disease and systemic condition. A serological test was performed on the subjects and analyzed quantitatively, using the measuring parameter of the Roche / Hitachi cobas 111 device, which automatically calculates the concentration of the P-CR in each sample. The results lack a statistically significant relationship of gender, age or degree of periodontal disease. The average value of P-CR was obtained from the study (3.72 mg / L) corresponds to a high risk of cardiovascular disease based on the parameters established by the American Heart Association. The only significant factor was the presence of associated systemic diseases in patients with high levels of P-CR, in comparison with those who suffer from some type of ailment. (author) [es

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

    Science.gov (United States)

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

    2014-08-01

    Next-generation diagnostics for Chlamydia trachomatis and Neisseria gonorrhoeae are available on semi- or fully-automated platforms. These systems require less hands-on time than older platforms and are user friendly. Four automated systems, the ABBOTT m2000 system, Becton Dickinson Viper System with XTR Technology, Gen-Probe Tigris DTS system, and Roche cobas 4800 system, were evaluated for total run time, hands-on time, and walk-away time. All of the systems evaluated in this time-motion study were able to complete a diagnostic test run within an 8-h work shift, instrument setup and operation were straightforward and uncomplicated, and walk-away time ranged from approximately 90 to 270 min in a head-to-head comparison of each system. All of the automated systems provide technical staff with increased time to perform other tasks during the run, offer easy expansion of the diagnostic test menu, and have the ability to increase specimen throughput. © 2013 Society for Laboratory Automation and Screening.

  8. Assessment of real-time PCR method for detection of EGFR mutation using both supernatant and cell pellet of malignant pleural effusion samples from non-small-cell lung cancer patients.

    Science.gov (United States)

    Shin, Saeam; Kim, Juwon; Kim, Yoonjung; Cho, Sun-Mi; Lee, Kyung-A

    2017-10-26

    EGFR mutation is an emerging biomarker for treatment selection in non-small-cell lung cancer (NSCLC) patients. However, optimal mutation detection is hindered by complications associated with the biopsy procedure, tumor heterogeneity and limited sensitivity of test methodology. In this study, we evaluated the diagnostic utility of real-time PCR using malignant pleural effusion samples. A total of 77 pleural fluid samples from 77 NSCLC patients were tested using the cobas EGFR mutation test (Roche Molecular Systems). Pleural fluid was centrifuged, and separated cell pellets and supernatants were tested in parallel. Results were compared with Sanger sequencing and/or peptide nucleic acid (PNA)-mediated PCR clamping of matched tumor tissue or pleural fluid samples. All samples showed valid real-time PCR results in one or more DNA samples extracted from cell pellets and supernatants. Compared with other molecular methods, the sensitivity of real-time PCR method was 100%. Concordance rate of real-time PCR and Sanger sequencing plus PNA-mediated PCR clamping was 98.7%. We have confirmed that real-time PCR using pleural fluid had a high concordance rate compared to conventional methods, with no failed samples. Our data demonstrated that the parallel real-time PCR testing using supernatant and cell pellet could offer reliable and robust surrogate strategy when tissue is not available.

  9. Teknik Migrasi Data Lintas DBMS dengan Menggunakan Metadata

    Directory of Open Access Journals (Sweden)

    Wahyu Hidayat

    2015-11-01

    Full Text Available Proses migrasi data biasanya dibutuhkan saat adanya perubahan sistem, format, atau tipe storage. Saat ini telah dikenal beberapa teknik dan kakas untuk melakukan migrasi data, misalnya CSV file, ODBC, SQLDump dan sebagainya. Sayangnya tidak semua teknik tersebut dapat diimplementasikan untuk migrasi data antara dua DBMS yang berbeda. Dalam penelitian ini dipaparkan sebuah teknik migrasi data yang dapat digunakan untuk migrasi data lintas DBMS. Teknik migrasi data yang dipaparkan memanfaatkan metadata yang ada di masing-masing DBMS. Proses migrasi data yang dipaparkan di sini melalui tiga tahap yaitu capture, convert dan construct. Sebuah prototype dibangun untuk menguji teknik migrasi data ini. Dengan menggunakan schema HR dilakukan uji coba migrasi data lintas DBMS antara Oracle dan MySQL. Dengan menggunakan teknik ini, migrasi data full-schema membutuhkan waktu rata-rata 20,43 detik dari DBMS Oracle ke MySQL dan 12,96 detik untuk skenario sebaliknya. Adapun untuk migrasi data parsial dibutuhkan waktu rata-rata 5,95 detik dari DBMS Oracle ke MySQL dan 2,19 detik untuk skenario sebaliknya.

  10. A comparative biochemical profile of some cyprinids fish in Dukan Lake, Kurdistan-Iraq

    Science.gov (United States)

    Azeez, Darya Mohammed; Mohammed, Sarbaz Ibrahim

    2017-09-01

    The present study was carried out to demonstrate the baseline values for some serum biochemical parameters for 64 adult freshwater fish including seven species belong to family Cyprinidae, have been collected in Dukan Lake, Kurdistan region-Iraq. Fishes were weighed, measured, and collect blood for blood chemistry. Serum biochemical analyses were determined using (Cobas C 311) full automatic chemical analyzer. The result of comparative study of serum biochemical parameters of all Cyprinidae species showed that serum glucose was (459.10±106.99 mg/dl) and direct bilirubin was (0.056±0.021mg/dl) in Barbus grypus, serum total protein (3.511± 0.0484gm/dl) and HDL (133.11±0.4231mg/dl) in Cyprinus carpio, serum cholesterol (338.33±43.923 mg/dl) and LDL (86.11±11.871mg/dl) in Carassius carassius, serum triglyceride (420.0±28.8mg/dl) and ALK (113.93±20.65U/L) in Chondrostoma regium, serum AST and serum ALT in Capoeta trutta, were significantly higher when compared to other species. In a conclusion there is variation in biochemical values among species of same family.

  11. Penokohan Film Sawung Kampret Karya Dwi Koendoro (Dwi Koen Dalam Perspektif Strukturalisme

    Directory of Open Access Journals (Sweden)

    Dyah Gayatri Puspitasari

    2015-03-01

    Full Text Available Tulisan ini berisi  kajian penokohan film Sawung Kampret yang diadaptasi dari komik Le- genda Sawung Kampret. Kajian ini menarik karena dua hal. Pertama, komik dan film adaptasi- nya diciptakan dan disutradarai oleh orang yang sama, yakni Dwi Koendoro. Kedua, kajian film yang diadaptasi dari komik Indonesia merupakan yang pertama. Melalui pendekatan struktural Ferdinand de Saussure, kajian berpusat pada relasi berbagai elemen penokohan yang membentuk keutuhan struktur narasi film. Didapat beberapa temuan menarik dimana unsur kelucuan pada penokohan film Sawung Kampret direlasikan dengan sejarah, hingga mampu membentuk narasi asosiatif yang mengusung nasionalisme berdasar nilai kemanusiaan, kebe- ragaman etnis dan budaya. Fakta tersebut menunjukkan bahwa melalui film Sawung Kampret, Dwi Koendoro mampu menciptakan perspektif struktur baru dengan melakukan kritik terha- dap struktur lama. Pasangan berlawanan (binary opposition dalam sistem lama coba diperta- nyakan. Sebagai hasil akhir maka dapat disimpulkan bahwa film Sawung Kampret merupakan film parodi sejarah yang sarat akan muatan pesan moral dan nasionalisme.       Kata kunci: film, adaptasi, penokohan, struktur, relasi

  12. Sistem Navigasi Indoor Menggunakan Sinyal Wi-Fi dan Kompas Digital Berbasis Integrasi dengan Smartphone untuk Studi Kasus pada Gedung Bertingkat

    Directory of Open Access Journals (Sweden)

    Alifa Ridho Musthafa

    2017-01-01

    Full Text Available Sistem navigasi menggunakan teknologi GPS saat ini sudah sangat maju ketika digunakan di luar ruangan. Namun, sistem tersebut masih kurang akurat ketika digunakan di dalam ruangan. Hal tersebut disebabkan karena GPS tidak bekerja dengan baik ketika berada di dalam ruangan. Di sisi lain, sudah ada sistem yang dapat menggantikan GPS untuk studi kasus di dalam ruangan, salah satunya yaitu sistem indoor localization berbasis Wi-fi. Memanfaatkan sistem indoor localization berbasis Wi-fi, dibuatlah sistem navigasi yang dapat digunakan di dalam ruangan. Sistem indoor localization digunakan untuk menentukan posisi pengguna. Setelah posisi pengguna diketahui, rute terbaik menuju tujuan pengguna ditentukan dengan bantuan algoritma A* dan kompas digital digunakan untuk menentukan arah kemana pengguna harus pergi. Studi kasus ini dilakukan di kampus Teknik Informatika ITS. Sistem indoor localization yang digunakan untuk menggantikan fungsi GPS dalam menentukan posisi mampu menghasilkan presentase rata-rata akurasi pendeteksian lokasi sebesar 88,953%. Sedangkan untuk uji coba pencarian rute, sistem indoor navigation dapat memberikan rute terpendek pada semua kasus percobaan.

  13. Prototype Sistem Multi-Telemetri Wireless untuk Mengukur Suhu Udara Berbasis Mikrokontroler ESP8266 pada Greenhouse

    Directory of Open Access Journals (Sweden)

    Hanum Shirotu Nida

    2017-07-01

    Full Text Available Telemetri wireless adalah proses pengukuran parameter suatu obyek yang hasil pengukurannya dikirimkan ke tempat lain melalui proses pengiriman data tanpa menggunakan kabel (wireless, sedangkan multi telemetri adalah gabungan dari beberapa telemeteri itu sendiri. Penelitian ini merancang prototype sistem multi-telemetri wireless untuk mengukur suhu udara dan kelembaban udara pada greenhouse dengan menggunakan sensor DHT11 dan data hasil dari pembacaan sensor dikirim dengan menggunakan modul WiFi ESP8266 ke server dengan menggunakan protokol HTTP. Dalam penelitian ini diuji nilai sensor DHT11, heap memory ESP8266, jarak atau jangkauan ESP8266, uji coba data missing handling dan kestabilan jaringan. Berdasarkan hasil pengujian diketahui bahwa sensor DHT11 memiliki rata-rata kesalahan ukur suhu 0.92 oC dan kelembaban 3.1%. Modul WiFi ESP8266 mampu menyimpan dan mengirim buffer hingga 100 data dan dapat melakukan pengiriman dalam jangkauan 50 meter. Data missing handling memanfaatkan buffer untuk menyimpan data selama server sedang tidak dapat diakses oleh sensor node agar data tidak hillang. Kestabilan pengiriman data atau koneksi sensor node dengan server dipengaruhi oleh jumlah access point yang sedang berkomunikasi disekitar access point server dengan menggunakan channel yang sama.

  14. Penggunaan Accelerometer dan Magnetometer pada Sistem Real Time Tracking Indoor Position untuk Studi Kasus Pada Gedung Teknik Informatika ITS

    Directory of Open Access Journals (Sweden)

    Dinar Winia Mahandhira

    2017-01-01

    Full Text Available Indoor Positioning System (IPS menggunakan perangkat mobile seperti smartphone masih menjadi permasalahan yang menantang. Seperti GPS yang tidak bekerja secara akurat di dalam gedung, IPS juga memiliki kelemahan yaitu sangat bergantung pada infrastruktur gedung seperti sinyal WiFi yang terkadang tidak tersebar secara merata di seluruh bagian gedung, sehingga membuat sistem ini terkadang tidak dapat bekerja secara optimal dan real time di setiap bagian gedung. Untuk itulah dikembangkan IPS yang menggunakan sensor gerak seperti accelerometer dan magnetometer sebagai tambahan untuk melakukan update posisi secara real time dengan mendeteksi langkah dan arah hadap pengguna saat berjalan. Pertama, posisi awal pengguna harus ditentukan terlebih dahulu misalnya menggunakan sinyal WiFi yang diproses melalui klasifikasi. Setelah posisi pengguna telah ditentukan, sistem akan mendeteksi pergerakan pengguna secara real time menggunakan sensor gerak. Uji coba dilakukan menggunakan studi kasus gedung Teknik Informatika lantai tiga. Hasil yang diberikan pada saat pengujian memberikan performa yang cukup baik dengan rata-rata persentase akurasi untuk pendeteksian langkah dan estimasi arah hadap pengguna adalah sebesar 94,8% dan 94,48%.

  15. Hepatitis C virus genotyping of organ donor samples to aid in transplantation of HCV-positive organs.

    Science.gov (United States)

    Gentile, Caren; Van Deerlin, Vivianna M; Goldberg, David S; Reese, Peter P; Hasz, Richard D; Abt, Peter; Blumberg, Emily; Farooqi, Midhat S

    2018-02-01

    Given the availability of new highly efficacious anti-HCV therapies, some clinicians have advocated for wider use of kidneys from hepatitis C virus-positive (HCV+) donors, including transplanting them into HCV-negative recipients. As treatment regimens for HCV are commonly guided by genotype, pretransplant HCV genotyping of tissue donors would be beneficial. To our knowledge, donor HCV genotyping has never been reported. We retrieved archived frozen plasma samples for 17 previous organ donors through a local organ procurement organization. We performed HCV genotyping using the eSensor HCVg Direct Test (GenMark Diagnostics) and also by Sanger sequencing, for confirmation (Retrogen). In addition, viral loads were measured using the COBAS AmpliPrep/TaqMan system (Roche Diagnostics). We found that most of the samples (n = 14) were HCV Genotype 1a with the remainder being Genotype 2b (n = 1) or Genotype 3 (n = 2). All genotyping results were concordant with Sanger sequencing. The average HCV viral load in the sample group was ~ 1.6 million IU/mL (range: ~16 000 IU/mL to 7 million IU/mL). We demonstrate that viral RNA from organ donor plasma can be successfully genotyped for HCV. This ability suggests that transplantation of HCV+ kidneys into HCV-negative recipients, followed by genotype-guided antiviral therapy, could be feasible. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Diagnostic effectiveness of immunoassays systems for hepatitis C virus in samples from multi-transfusion patients

    International Nuclear Information System (INIS)

    Rivero Jimenez, Rene A; Merlin Linares, Julio C; Blanco de Armas, Madelin; Navea Leyva, Leonor M

    2009-01-01

    Hepatitis C virus (CHV) blood-transmission is a health problem in Cuba and in the world. Some types of diagnostic immunoassays have been developed for the blood certification and in general have a high diagnostic sensitivity and specificity in healthy donors. However, its behavior in samples from multi-transfusion patients could by less effective. To assess the diagnostic effectiveness of the UMELISA HCV third generation Cuban immunoassay (TecnoSUMA, S.A. La Habana), Cuba) in samples from multi-transfusion patients, in parallel, 335 sera from patients were processed by UBI HCV EIA 4.0 (United Biomedical, EE.UU) and UMELISA HCV third generation, and the samples with incongruous results were verified by PCR COBAS AmpliScreen HCV Test, v2 system (Roche, EE.UU.) Comparing the UMELISA HCV third generation system with the UBI HCV EIA 4.0 it was achieved a Sd of 95,8% CI(95%): 92,5-99,15 and a Ed of 100% CI (95%): 99,7-100, with IY: 0,96 (0,93-0,99) with k: 0,0582 ID (95%): 0,9276-0,9888, p = 0,000. Both immunoassay systems were satisfactory for immunodiagnosis of multi-transfusion patients

  17. IMPLEMENTASI METODE RETINEX UNTUK PENCERAHAN CITRA

    Directory of Open Access Journals (Sweden)

    Murinto Murinto

    2009-07-01

    Full Text Available Data atau informasi tidak hanya disajikan dalam bentuk teks, tetapi juga dapat berupa gambar, audio, dan video. Citra/gambar mempunyai karakteristik yang tidak dimiliki oleh teks, yaitu citra kaya dengan informasi. Dewasa ini penggunaan citra digital semakin meningkat karena kelebihan-kelebihan yang dimiliki oleh citra digital tersebut, antara lain kemudahan dalam mendapatkan gambar, memperbanyak gambar dan pengolahan gambar. Situasi dan kondisi pada saat pengambilan citra digital sangat berpengaruh terhadap hasil citra digital yang diperoleh. Kurangnya intensitas cahaya pada saat pengambilan citra dapat menyebabkan kualitas citra menjadi tidak baik, seperti citra menjadi gelap atau perubahan warna dari gambar. Perlu suatu metode untuk memperbaiki kualitas citra dengan mempertahankan warna asli citra. Penelitian ini menggunakan metode Retinex untuk meningkatkan kecerahan citra. Jenis gambar yang digunakan berekstensi *.jpg berformat 24 bit dengan ukuran pixel yang tidak dibatasi. Citra tersebut kemudian dimasukan ke dalam program lalu diproses dengan menggunakan metode Retinex. Adapun parameter yang digunakan adalah citra hasil, histogram, dan signal-to-noise (SNR. Pengujian dilakukan dengan metode White Box Tes dan Alpha Test. Penelitian yang dilakukan menghasilkan suatu aplikasi pengolahan citra untuk meningkatkan kecerahan Citra Menggunakan Metode Retinex” yang dapat bekerja untuk mencerahkan citra. Peningkatan kecerahan citra dengan menggunakan metode retinex menghasilkan citra yang lebih cerah, nilai SNR yang lebih tinggi dan histogram dengan nilai intensitas pixel yang tinggi dan terdistribusi secara merata. Hasil uji coba menunjukan bahwa aplikasi ini dapat meningkatkan kecerahan dan kualitas citra menjadi lebih baik. Kata Kunci: Pengolahan Citra, Retinex, Histogram, SNR. 

  18. IMPLEMENTASI METODE RETINEX UNTUK PENCERAHAN CITRA

    Directory of Open Access Journals (Sweden)

    Murinto Kusno

    2012-05-01

    Full Text Available Data atau informasi tidak hanya disajikan dalam bentuk teks, tetapi juga dapat berupa gambar, audio, dan video. Citra/gambar mempunyai karakteristik yang tidak dimiliki oleh teks, yaitu citra kaya dengan informasi. Dewasa ini penggunaan citra digital semakin meningkat karena kelebihan-kelebihan yang dimiliki oleh citra digital tersebut, antara lain kemudahan dalam mendapatkan gambar, memperbanyak gambar dan pengolahan gambar. Situasi dan kondisi pada saat pengambilan citra digital sangat berpengaruh terhadap hasil citra digital yang diperoleh. Kurangnya intensitas cahaya pada saat pengambilan citra dapat menyebabkan kualitas citra menjadi tidak baik, seperti citra menjadi gelap atau perubahan warna dari gambar. Perlu suatu metode untuk memperbaiki kualitas citra dengan mempertahankan warna asli citra. Penelitian ini menggunakan metode Retinex untuk meningkatkan kecerahan citra. Jenis gambar yang digunakan berekstensi *.jpg berformat 24 bit dengan ukuran pixel yang tidak dibatasi. Citra tersebut kemudian dimasukan ke dalam program lalu diproses dengan menggunakan metode Retinex. Adapun parameter yang digunakan adalah citra hasil, histogram, dan signal-to-noise (SNR. Pengujian dilakukan dengan metode White Box Tes dan Alpha Test. Penelitian yang dilakukan menghasilkan suatu aplikasi pengolahan citra untuk meningkatkan kecerahan  Citra Menggunakan Metode Retinex” yang dapat bekerja untuk mencerahkan citra. Peningkatan kecerahan citra dengan menggunakan metode retinex menghasilkan citra yang lebih cerah, nilai SNR yang lebih tinggi dan histogram dengan nilai intensitas pixel yang tinggi dan terdistribusi secara merata. Hasil uji coba menunjukan bahwa aplikasi ini dapat meningkatkan kecerahan dan kualitas citra menjadi lebih baik

  19. PENGEMBANGAN PERANGKAT PEMBELAJARAN KOMPETENSI SULIT MATEMATIKA SMA DI RIAU

    Directory of Open Access Journals (Sweden)

    Ummi Aisyah

    2014-05-01

    Full Text Available Tujuan penelitian ini adalah untuk menghasilkan perangkat pembelajaran kompetensi sulit matematika SMA di Provinsi Riau yang berkualitas baik/layak yaitu valid, praktis, dan efektif. Penelitian ini merupakan penelitian pengembangan yang mengembangkan perangkat pembelajaran kompetensi sulit matematika SMA dengan menggunakan model pengembangan 4-D yang dikembangkan oleh Thiagarajan, Semmel & Semmel yang telah dimodifikasi sehingga hanya memuat tahap pen-definisian, perancangan, dan pengembangan. Penelitian ini menghasilkan perangkat pembelajaran kompetensi sulit matematika SMA yang meliputi silabus, rencana pelaksanaan pembelajaran (RPP, lembar kegiatan siswa (LKS, dan instrumen tes. Hasil validasi menunjukkan bahwa silabus, RPP, LKS yang dikembangkan memiliki kategori sangat valid untuk masing-masing silabus, RPP, LKS, dan test instrument. Hasil uji coba lapangan menunjukkan bahwa perangkat yang dikembangkan praktis dan efektif. Kepraktisan mencapai hasil sangat baik ditinjau dari penilaian guru dan siswa. Keefektifan ditinjau dari ketuntasan belajar siswa dan hasil observasi keterlaksanaan pembelajaran. Secara klasikal ketuntasan belajar mencapai 84,38%. Secara keseluruhan, hasil penelitian menunjukkan bahwa perangkat pembelajaran yang dikembangkan adalah layak untuk digunakan. Kata Kunci: pengembangan, perangkat pembelajaran, kompetensi sulit matematika

  20. STRATEGI PEMBERDAYAAN EKONOMI KOMUNITAS WARIA MELALUI LIFE SKILL EDUCATION

    Directory of Open Access Journals (Sweden)

    Rr. Indah Mustikawati

    2013-04-01

    Full Text Available Abstrak: Strategi Pemberdayaan Ekonomi Komunitas Waria Melalui Life Skill Education. Penelitian ini bertujuan untuk mengetahui penurunan jumlah waria yang “turun ke jalan” yang berprofesi sebagai Pekerja Seks Komersial melalui life skill education dan pengaruhnya terhadap jumlah pendapatan yang diterima waria dari sumber yang “halal”, serta penurunan kemiskinan komunitas waria di Kotamadya Yogyakarta. Penelitian ini menggunakan metode Research and Development dengan empat tahapan, yaitu studi pendahuluan pengembangan, penyusunan desain, uji coba model, dan evaluasi hasil pengembangan model life skill education. Keempat tahapan tersebut dilakukan untuk menemukan model yang sesuai untuk strategi pemberdayaan ekonomi bagi komunitas waria. Hasil penelitian menunjukkan bahwa semua waria menginginkan untuk memiliki kompetensi tambahan yang dapat digunakan untuk merintis usaha sesuai dengan peminatan mereka, dan menambah penghasilan mereka, dan sebagai bekal di hari tua.   Kata Kunci: Strategi Pemberdayaan Ekonomi, Pengentasan kemiskinan, Waria   Abstract: Economy Empowerment Strategy Trough Life skill Education as Poverty Reduction of Transgender Community. Aims of this research are to determine reduction number of transgender working as prostitute through life skill education and the impact of that reduction on their halal income, to examine poverty reduction among transgender communities in Yogyakarta. This study uses four-steps of research and development approach, namely preliminary study development, design preparation, model test, life skill education model evaluations. The results show that all of the transgender involved in this study yearn for having additional skill to set new business up to increase their income.   Keywords: economic empowerment strategy, poverty eradication, transgender

  1. Biological Variation and Reference Change Value Data for Serum Neuron-Specific Enolase in a Turkish Population.

    Science.gov (United States)

    Matyar, Selcuk; Goruroglu Ozturk, Ozlem; Ziyanoglu Karacor, Esin; Yuzbasioglu Ariyurek, Sedefgul; Sahin, Gulhan; Kibar, Filiz; Yaman, Akgun; Inal, Tamer

    2016-11-01

    Neuron-specific enolase (NSE) is a recognized biomarker for the assessment of cerebral injury in neurological disorders. This study aims to report a definitive assessment of the biological variation (BV) components of this biomarker, including within-subject BV (CVI), between-subject BV (CVG), index of individuality (II), and reference change value (RCV), in a cohort of Turkish participants using an experimental protocol. Six blood specimens were collected from each of the 13 apparently healthy volunteers (seven women, six men; ranging in age from 23 to 36) on the same day, every 2 weeks for 2 months. Serum specimens were stored at -20°C until analysis. Neuron-specific enolase levels were evaluated in serum samples using an electrochemiluminescence (ECLIA) immunoassay kit with a Roche Cobas e 411 auto-analyser. ANOVA test was used to calculate the variations. The CVI and CVG for NSE were 21.5% and 28.8%, respectively. Analytical variation (CVA) was calculated as 10.2%. Additionally, II and RCV were calculated as 0.74 and 66% (95% confident interval, CI), respectively. As the performance index (PI) was found to be less than 2 (PI = 0.95), it is concluded that the NSE measurements have a desirable performance for analytical imprecision. Since the II was found to be less than 1 (II: 0.74), the reference values will be of little use. Thus, RCV would provide better information for deciding whether a significant change has occurred. © 2016 Wiley Periodicals, Inc.

  2. Chlamydia trachomatis infections in Greece: first prevalence study using nucleic acid amplification tests.

    Science.gov (United States)

    Levidiotou, S; Vrioni, G; Papadogeorgaki, H; Avdeliodi, K; Kada, H; Kaparos, G; Kouskouni, E; Fragouli, E; Legakis, N J

    2005-03-01

    The present retrospective study was initiated to determine the prevalence of Chlamydia trachomatis and to assess the risk factors for infection in adult women and men presenting to general practitioners, gynecologists, dermatologists, and family-planning centers in Greece. The study was carried out in four different Greek hospital centers using highly sensitive nucleic acid amplification techniques. Altogether, 16,834 women and 1,035 men were enrolled from October 1998 to April 2004. Two types of specimens were collected from each patient: cervical swabs from women, urethral swabs from men, and first-catch urine from women and men. All specimens were examined with the Cobas Amplicor C. trachomatis polymerase chain reaction assay (Roche Molecular Systems, Branchburg, NJ, USA) or the LC x C. trachomatis ligase chain reaction assay (Abbott Laboratories, Abbott Park, IL, USA). Demographic and behavioral data were collected by clinicians using a standardized questionnaire. A total of 704 (3.9%) patients were infected with C. trachomatis. The prevalence among female patients was 3.5% and that among male patients 11.2%. Among infected patients, 88% were under 30 years of age, 71% reported more than one sexual partner, and 91% reported a new sexual partner within the last year. In conclusion, the prevalence of C. trachomatis infection in Greece is low. Young age and new and multiple sexual partners within the last year were factors consistently associated with an increased risk of chlamydial infection.

  3. PERANCANGAN APLIKASI SISTEM REPAIR SCHEDULE PADA KAPAL PENYEBERANGAN MERAK-BAKAUHENI BERBASIS WEB MENURUT ATURAN BIRO KLASIFIKASI INDONESIA

    Directory of Open Access Journals (Sweden)

    Samuel Samuel

    2014-10-01

    Full Text Available Reparasi kapal (docking merupakan keharusan guna menjamin sertifikat kelaikan maupun keselamatan. Minimal setiap setahun sekali kapal harus docking. Saat ini di pelabuhan Merak–Bakauheni terjadi antrian yang panjang terutama pada saat high season karena kurangnya armada kapal yang disebabkan jadwal docking pada high season dan kurangnya komunikasi dan pengawasan docking kapal tersebut. Untuk menghindari hal tersebut, peneliti merancang dan membuat sistem informasi docking schedule berbasis web yang dilengkapi dengan reminder dalam bentuk email dan sms untuk memudahkan PT. ASDP sebagai pengelola transportasi di pelabuhan merak-bakauheni dalam mengatur jadwal dan melakukan pengawasan pada kapal. Pengembangan aplikasi dimulai dengan identifikasi kebutuhan sistem yang menghasilkan desain sistem, yang didefinisikan dengan Data Flow Diagram (DFD, Entity Relationship Diagram (ERD, Use case Diagram. Implementasi aplikasi berdasarkan desain sistem diterapkan pada lingkungan web dengan MySQL dan PHP dan sms gateway. Sistem penjadwalan reparasi dan survey berbasis web dengan pesan pengingat melalui Email dan SMS ini mampu  memberikan informasi jadwal repair dan survey dengan cepat dan dapat diakses kapanpun dan dimanapun dan dari hasil uji coba sistem, menunjukkan bahwa aplikasi yang dibangun telah dapat memenuhi semua kebutuhan sistem pengguna.

  4. DISAIN SIMULATOR AUTOMOTIVE AIR CONDITIONING UNTUK MENINGKATKAN KOMPETENSI MAHASISWA

    Directory of Open Access Journals (Sweden)

    Kamin Sumardi

    2015-08-01

    Full Text Available Perkembangan teknologi automotive air conditioning dan aplikasinya sangat cepat, salah satunya dengan menerapkan green technology. Penerapan green technology pada teknologi air conditioning, karena masih menggunakan refrigeran yang mengandung unsur kimia yang merusak lapisan ozon dan pemanasan global. Alih teknologi bidang air conditioning yang ramah lingkungan, belum dibarengi dengan ketersediaan tenaga kerja pada tingkat SMK dan perguruan tinggi yang memadai, baik kuantitas maupun kompetensinya. Pada level SMK dan perguruan tinggi, kompetensi akademik dan vokasional bidang automotive air conditioning harus terus ditingkatkan dan diperbaharui sesuai dengan perkembangan teknologinya. Penelitian ini bertujuan untuk menghasilkan simulator automotive air conditioner dan model pembelajaran tata udara pada otomotif berwawasan teknologi ramah lingkungan. Penelitian menggunakan metode research and development dengan langkah-langkah: studi pendahuluan, perencanaan, pengembangan melalui uji coba simulator, validasi, dan produk akhir. Simulator dibuat sesuai dengan kondisi di dunia kerja agar tidak terjadi miskonsepsi dan mala-praktek automotive air conditioning. Simulator ini dibuat secara kompak dan mobile atau dapat dipindah dan dibawa. Model pembelajaran disesuaikan dengan kebutuhan kompetensi yang dipersyaratkan. Hasil penelitian menunjukkan bahwa dengan bantuan simulator automotive air conditioner dan model pembelajaran yang tepat mahasiswa mampu menyerap konsep dan praktek lebih cepat 85%. Hasil belajar pada ranah afektif, kognitif, psikomotor dan kompetensi meningkat secara signifikan.

  5. PENJUALAN MOBIL BERBASIS WEB DAN MANAJEMEN DATA PEMBAYARAN DI SHOWROOM MOBIL XYZ

    Directory of Open Access Journals (Sweden)

    Joko Lianto Buliali

    2005-01-01

    Full Text Available The purpose of this research is to build a virtual showroom for a car showroom company which allows company to do marketing, selling, and providing payment information through Web. The system is developed based on the requirements of the users and current selling procedure in the showroom. From the investigation result, analysis, design, and implementation are carried out. Testing on the system shows that the system has fulfilled all the requirements needed by the users of the of the system Abstract in Bahasa Indonesia : Penelitian ini bertujuan untuk mengembangkan suatu sistem showroom virtual pada suatu showroom mobil sehingga dapat dilakukan pemasaran dan penjualan mobil disertai dengan informasi pembayaran customernya melalui Web. Sistem dikembangkan berdasarkan kebutuhan pengguna terhadap sistem dan prosedur penjualan pada showroom tersebut saat ini. Dari hasil tersebut, dilakukan analisis, desain, dan implementasi sistem yang dibutuhkan. Uji coba terhadap sistem yang dibuat menunjukkan bahwa sistem yang dibuat sudah memiliki seluruh fasilitas yang dibutuhkan pengguna sistem. Kata kunci: showroom virtual, pemasaran, penjualan mobil.

  6. Biochemically Investigation of the Effects of Nettle Seed Herbal Mixture on Alcohol Damaged Liver

    Directory of Open Access Journals (Sweden)

    A. ÇELİK

    2014-06-01

    Full Text Available It was experimentally investigated in this research how protective Nettle Seed Herbal Mixture is against ethanol which causes oxidative stress in rats and causes toxic effects in the liver with chronic use. 20 4-month-old female Wistar male rats were used in the study. All rats in the study were fed with normal pellet Mouse food during the experiment. 10 week application was done by dividing the rats into four equal groups. Application method is orally drinking method. First group is the control group. The second group is the alcohol group. This group was given 30% ethanol in order to cause chronic alcoholisms. The third group was the alcohol+ Nettle Seed Herbal Mixture group and the rats in this group were given liquid, which was 30% ethanol,+ Nettle Seed Herbal Mixture extract. Fourth group was Nettle Seed Herbal Mixture extract group and the rats in this group were given liquid, which was Nettle Seed Herbal Mixture extract. At the end of ten weeks, within the first 24 hours, blood species were obtained from the animals under anesthesia using appropriate techniques. Serum ALT and AST values of the obtained blood samples were studied by enzymatic methods in "Roche Cobas 6000" device.. Biochemically ALT and AST enzyme values and statistical analysis with SPSS programe were done. No significant difference was found between these four groups at the end of the analysis because p value was bigger than 0,005.

  7. The soluble receptor for vitamin B12 uptake (sCD320) increases during pregnancy and occurs in higher concentration in urine than in serum

    DEFF Research Database (Denmark)

    Abuyaman, Omar; Andreasen, Birgitte H; Kronborg, Camilla

    2013-01-01

    BACKGROUND: Cellular uptake of vitamin B12 (B12) demands binding of the vitamin to transcobalamin (TC) and recognition of TC-B12 (holoTC) by the receptor CD320, a receptor expressed in high quantities on human placenta. We have identified a soluble form of CD320 (sCD320) in serum and here we...... gestational weeks 17-41. sCD320, holoTC, total TC and complex formation between holoTC and sCD320 were measured by in-house ELISA methods, while creatinine was measured on the automatic platform Cobas 6000. Size exclusion chromatography was performed on a Superdex 200 column. RESULTS: Median (range) of serum...... was around two fold higher than in serum. Urinary sCD320/creatinine ratio correlated with serum sCD320 and reached a peak median level of 53 (30-101) pmol/mmol creatinine (week 35). sCD320 present in serum and urine showed the same elution pattern upon size exclusion chromatography. CONCLUSION: We report...

  8. PENINGKATAN KECERDASAN COMPUTER PLAYER PADA GAME PERTARUNGAN BERBASIS K-NEAREST NEIGHBOR BERBOBOT

    Directory of Open Access Journals (Sweden)

    M Ihsan Alfani Putera

    2018-02-01

    Full Text Available Salah satu teknologi komputer yang berkembang dan perubahannya cukup pesat adalah game. Tujuan dibuatnya game adalah sebagai sarana hiburan dan memberikan kesenangan bagi penggunanya. Contoh elemen dalam pembuatan game yang penting adalah adanya tantangan yang seimbang sesuai level. Dalam hal ini, adanya kecerdasan buatan atau AI merupakan salah satu unsur yang diperlukan dalam pembentukan game. Penggunaan AI yang tidak beradaptasi ke strategi lawan akan  mudah diprediksi dan repetitif. Jika AI terlalu pintar maka player akan kesulitan dalam memainkan game tersebut. Dengan keadaan seperti itu akan menurunkan tingkat enjoyment dari pemain. Oleh karena itu, dibutuhkan suatu metode AI yang dapat beradaptasi dengan kemampuan dari player yang bermain. Sehingga tingkat kesulitan yang dihadapi dapat mengikuti kemampuan pemainnya dan pengalaman enjoyment ketika bermain game terus terjaga. Pada penelitian sebelumnya, metode AI yang sering digunakan pada game berjenis pertarungan adalah K-NN. Namun metode tersebut menganggap semua atribut dalam game adalah sama sehingga hal ini mempengaruhi hasil learning AI menjadi kurang optimal.Penelitian ini mengusulkan metode untuk AI dengan menggunakan metode K-NN berbobot pada game berjenis pertarungan. Dimana, pembobotan tersebut dilakukan untuk memberikan pengaruh setiap atribut dengan bobot disesuaikan dengan aksi player. Dari hasil evaluasi yang dilakukan terhadap 50 kali pertandingan pada 3 skenario uji coba, metode yang diusulkan yaitu K-NN berbobot mampu menghasilkan tingkat kecerdasan AI dengan akurasi sebesar 51%. Sedangkan, metode sebelumnya yaitu K-NN tanpa bobot hanya menghasilkan tingkat kecerdasan AI sebesar 38% dan metode random menghasilkan tingkat kecerdasan AI sebesar 25%.

  9. Determination of Urine Albumin by New Simple High-Performance Liquid Chromatography Method.

    Science.gov (United States)

    Klapkova, Eva; Fortova, Magdalena; Prusa, Richard; Moravcova, Libuse; Kotaska, Karel

    2016-11-01

    A simple high-performance liquid chromatography (HPLC) method was developed for the determination of albumin in patients' urine samples without coeluting proteins and was compared with the immunoturbidimetric determination of albumin. Urine albumin is important biomarker in diabetic patients, but part of it is immuno-nonreactive. Albumin was determined by high-performance liquid chromatography (HPLC), UV detection at 280 nm, Zorbax 300SB-C3 column. Immunoturbidimetric analysis was performed using commercial kit on automatic biochemistry analyzer COBAS INTEGRA ® 400, Roche Diagnostics GmbH, Manheim, Germany. The HLPC method was fully validated. No significant interference with other proteins (transferrin, α-1-acid glycoprotein, α-1-antichymotrypsin, antitrypsin, hemopexin) was found. The results from 301 urine samples were compared with immunochemical determination. We found a statistically significant difference between these methods (P = 0.0001, Mann-Whitney test). New simple HPLC method was developed for the determination of urine albumin without coeluting proteins. Our data indicate that the HPLC method is highly specific and more sensitive than immunoturbidimetry. © 2016 Wiley Periodicals, Inc.

  10. Penerapan Case-Based Reasoning Pada Sistem Cerdas Untuk Pendeteksian dan Penanganan Dini Penyakit Sapi

    Directory of Open Access Journals (Sweden)

    Irlando Moggi Prakoso

    2012-09-01

    Full Text Available Penyakit sapi memberikan dampak yang signifikan terhadap penurunan produksi daging bagi para peternak sapi. Untuk meminimalisir dampak dari penyakit perlu dilakukan pendeteksian dan penanganan dini untuk mencegah tingginya kerugian yang terjadi. Sistem cerdas dapat memudahkan peternak sapi untuk mendiagnosa secara mandiri. Penelitian sebelumnya menghasilkan sistem cerdas  untuk mendiagnosa penyakit sapi menggunakan algoritma Backpropagation Artificial neural Network(ANN. Namun ANN bersifat black-box karena kita tidak dapat melihat informasi yang mendasari hasil diagnosa. Tugas akhir ini memiliki tujuan untuk menjawab permasalahan tersebut, yakni dengan membuat sistem cerdas berbasis Cased-Based Reasoning(CBR untuk menyempurnakan sistem cerdas yang sebelumnya dibuat menggunakan ANN. CBR memberikan hasil diagnosa berdasarkan permasalahan terdahulu yang dapat direvisi untuk memecahkan permasalahan terbaru. Dari ketiga uji coba dengan case didalam case memory(skenario 1, diluar case memory(skenario 2, dan gejala parsial dari case memory(skenario 3 mendapatkan hasil yang baik dengan nilai precision 100% dan 95.83% untuk skenario 1 dan 3.   Serta nilai precision yang memang kurang baik untuk skenario 2 sebesar 59.31%. Dengan demikian, sistem cerdas ini dapat memberikan hasil diagnosa yang akurat dan memudahkan peternak sapi dalam mendiagnosa secara mandiri.

  11. OPTIMASI DAYA MESIN DAN KONSUMSI BAHAN BAKAR MESIN TOYOTA SERI 5K MELALUI PENGGUNAAN PENGAPIAN BOOSTER

    Directory of Open Access Journals (Sweden)

    Mardani Ali Sera

    2015-10-01

    Full Text Available Proses pembakaran adalah proses secara fisik yang terjadi di dalam silinder. Proses pembakaran dimulai pada saat busi memercikkan bunga api hingga terjadi proses pembakaran. Dalam penelitian ini digunakan metode eksperimen yaitu membandingkan daya dan konsumsi bahan bakar antara pengapian standar dengan pengapian menggunakan booster. Berdasarkan data hasil uji coba perbandingan antara sistem pengapian standar dengan pengapian yang menggunakan booster dengan objek penelitian mesin Toyota seri 5K diketahui adanya kenaikan 2.61% daya menjadi 27.723 kW dari 27.17 kW antara sistem pengapian standar dengan pengapian yang menggunakan booster pada putaran mesin 2400 rpm. Sedangkan prosentase kenaikan rerata daya sebesar 2.79 %. Penggunaan booster juga membuat penggunaan konsumsi bahan bakar spesifik (sfc antara sistem pengapian standar dengan pengapian yang menggunakan booster. Prosentase penurunan rerata konsumsi bahan bakar spesifik (sfc sebesar 6.99%. Pada sistem pengapian yang menggunakan booster, sfc minimum sebesar 0.219 kg/kWh pada putaran mesin 2200 rpm. Pada pengapian standar sfc minimum sebesar 0.231 kg/kWh pada putaran mesin 2400 rpm.

  12. Strong negative interference of ethamsylate (Dicynone®) in serum creatinine quantification via enzymatic assay using Trinder reaction.

    Science.gov (United States)

    Wiewiorka, Ondrej; Dastych, Milan; Čermáková, Zdenka

    2013-08-01

    With discrepancies encountered as early as the verification of enzymatic method for quantification of serum creatinine, our research pointed to a later confirmed interference caused by a compound called ethamsylate present in the commonly used antihemorrhagic drug Dicynone. We measured concentrations of creatinine of 10 patients with blood taken before and 15 minutes after the intravenous administration of a 500 mg dose of Dicynone. The creatinine concentration was determined using Jaffe method and enzymatic method that utilize Trinder reaction (Roche) in analyzer Cobas c 501 (Roche AG, Basel, Switzerland). We also monitored concentration of blood creatinine in three patients before and 15 minutes after application of Dicynone (500 mg i.v.) and in the following 6th, 12th, 18th, and 24th hours. We discovered a significant negative bias in creatinine results using enzymatic assay with Trinder reaction in blood taken 15 min after i.v. application of 500 mg Dicynone to patients compared to their pre-application values (average decrease of 47%). Unlike this, the results of compensated Jaffe method yielded steady results in all samples (average deviation 0.6% from original values). However, 12 h after the drug administration comparable results were seen as before the administration. Considering the strong negative interference of ethamsylate in enzymatic assay using Trinder reaction for creatinine quantification, blood from patients with prescribed Dicynone should be taken at least 12 h after the last application of the drug for obtaining the correct creatinine values.

  13. Ethamsylate (Dicynone) interference in determination of serum creatinine, uric acid, triglycerides, and cholesterol in assays involving the Trinder reaction; in vivo and in vitro.

    Science.gov (United States)

    Dastych, Milan; Wiewiorka, Ondrej; Benovská, Miroslava

    2014-01-01

    The aim of our research was the quantification of interfering properties of the haemostatic drug Dicynone (ethamsylate) in serum creatinine, uric acid, cholesterol, and triglyceride assays using the Trinder reaction. Blood from patients was collected before and 15 minutes after administration of 500 mg Dicynone dose i.v. and the above mentioned analytes were quantified using Roche assays (Cobas 8000). In our in vitro experiment, we measured concentrations of the analytes in pooled serum aliquots with final concentrations of Dicynone additions 0, 30, 60, 150, and 300 mg/L. Aliquots with 60 mg/L Dicynone were also measured at 2, 6, and 8 hours after initial measurement when stored in 22 degrees C and 4 degrees C for comparison. Concentrations of the measured analytes in samples from patients administered with a 500 mg dose of Dicynone were lower in all cases (n = 10) when compared to values in samples taken immediately before treatment. The in vitro samples showed that considerable negative interference occurred even with the low concentrations of Dicynone additions (30 and 60 mg/L), showing the strongest negative interference in creatinine values, followed by uric acid, triglycerides, and cholesterol. Using in vitro samples, we showed strong time and temperature dependence on Dicynone interference. We found and proved significant negative interference of the drug Dicynone (ethamsylate) in the clinical analysis of blood using in vivo and in vitro experiments. Furthermore, we observed a change of this effect in serum matrix over time and at different storage temperatures.

  14. DEKOMPOSISI MORFOLOGI BENTUK BINER DUA DIMENSI MENJADI POLIGON KONVEKS DENGAN PENDEKATAN HEURISTIK

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    Nanik Suciati

    2006-07-01

    Full Text Available Dalam pengolahan citra digital dan pengenalan pola, representasi bentuk merupakan masalah yang paling mendasar. Sebuah skema representasi bentuk yang bagus dapat memberi kemudahan pada analisis bentuk untuk dikembangkan pada berbagai macam pencocokan bentuk atau tugas pengenalan.Pada Penelitian ini, dirancang perangkat lunak untuk mendekomposisi bentuk biner dua dimensi menjadi poligon konveks dengan menggunakan teori morfologi dan pendekatan secara heuristik. Proses dekomposisi dilakukan dengan menentukan aproksimasi konveks dari citra yang diolah. Penentuan aproksimasi konveks didapat dari penyusutan bentuk untuk mengambil bentuk primitif dasar, kemudian mengembangkan kembali bentuk tersebut sehingga menjadi poligon konveks. Hasil dari proses ini berupa komponen konveks dan representasinya.Hasil uji coba membuktikan bahwa komponen konveks yang dihasilkan dari bentuk dengan tepi yang tidak banyak lekukan akan lebih sedikit daripada bentuk dengan banyak lekukan pada tepinya. Selain itu jumlah komponen konveks yang dibutuhkan untuk menghasilkan pendekatan bentuk asal, lebih sedikit bila dibandingkan dengan algoritma Wang, algoritma Pitas dan Skeleton Transform.Kata Kunci : bentuk biner, poligon konveks, morfologi, komponen konveks.

  15. Teknologi Proses Pembuatan Molecular Sieve TiZA Untuk Pemekatan Asam Nitrat

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    Ali Nurdin

    2017-10-01

    Full Text Available Molecular sieve zeolit dapat memurnikan campuran larutan yang bersifat azeotrop yang tidak bisa dilakukan menggunakan metode distilasi biasa. Namun, masih memiliki kelemahan dalam half life time molecular sieve tersebut, khususnya stabilitas bahan apabila digunakan pada larutan yang bersifat korosif seperti larutan asam atau basa. Pada penelitian ini telah  dilakukan pembuatan molecular sieve zeolit A yang dimodifikasi  dengan penambahan 10% titanium. Molecular sieve titanium - zeolit A (TiZA dibuat dengan dengan metode hidrotermal pada temperatur 110 °C dan kalsinasi pada temperatur 500 °C. Karakterisasi dilakukan antara lain menggunakan X-ray Diffraction (XRD, Scanning Electron Microscopy-Energy Dispersive X-ray Spectroscopy (SEM-EDX dan karakterisasi pori dengan metode physisorption menggunakan nitrogen pada temperatur 44 K. Molecular sieve TiZA yang dihasilkan stabil terhadap temperatur tinggi, dan larutan asam. Modifikasi zeolit A dengan titanium telah mampu meningkatkan stabilitas molecular sieve Ti-zeolit A dalam larutan asam nitrat selama 24 jam. Distribusi ukuran pori BJH (Barret Joyner Halenda  yang sempit menggambarkan ukuran yang homogen dengan didominasi oleh mikro porus dengan diameter rata-rata sekitar 4Å. Uji coba pemurnian asam nitrat dengan menggunakan molecular sieve secara single stage dapat meningkatkan kemurnian asam nitrat dari 70% hingga 85%.

  16. Chlamydia trachomatis ompA genotypes in male patients with urethritis in Greece: conservation of the serovar distribution and evidence for mixed infections with Chlamydophila abortus.

    Science.gov (United States)

    Psarrakos, Panagiotis; Papadogeorgakis, Eleni; Sachse, Konrad; Vretou, Evangelia

    2011-08-01

    PCR amplification and nucleotide sequencing of the ompA gene of Chlamydia trachomatis were used to determine the prevalence and distribution of genotypes in 51 urine and urethral specimens from Greek male patients with urethritis, that were positive by the COBAS Amplicor test. A single C. trachomatis serovar was identified in 43 of the 51 amplified samples. Serovars F and E were the most prevalent (both 12, 28%), followed by D (9, 21%), G (4, 9%), B and K (both 2, 5%) and H and J (both 1, 2%). Over one third of the samples bared a variant ompA genotype that had been previously identified in other areas worldwide. Two results in this study, both observed for the first time, were of particular interest. First, the emergence of the unique variant genotype D/Ep6 (X77364.2) identified in 3 urethral samples. Second, the ompA genotype OCLH196 of the animal pathogen Chlamydophila abortus as well as a 23S rRNA gene fragment of this species detected by the assay ArrayTube™ was found in 7 urethral samples. The implications resulting from this observation for the health of the general population are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. Identification and monitoring of host cell proteins by mass spectrometry combined with high performance immunochemistry testing.

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    Katrin Bomans

    Full Text Available Biotherapeutics are often produced in non-human host cells like Escherichia coli, yeast, and various mammalian cell lines. A major focus of any therapeutic protein purification process is to reduce host cell proteins to an acceptable low level. In this study, various E. coli host cell proteins were identified at different purifications steps by HPLC fractionation, SDS-PAGE analysis, and tryptic peptide mapping combined with online liquid chromatography mass spectrometry (LC-MS. However, no host cell proteins could be verified by direct LC-MS analysis of final drug substance material. In contrast, the application of affinity enrichment chromatography prior to comprehensive LC-MS was adequate to identify several low abundant host cell proteins at the final drug substance level. Bacterial alkaline phosphatase (BAP was identified as being the most abundant host cell protein at several purification steps. Thus, we firstly established two different assays for enzymatic and immunological BAP monitoring using the cobas® technology. By using this strategy we were able to demonstrate an almost complete removal of BAP enzymatic activity by the established therapeutic protein purification process. In summary, the impact of fermentation, purification, and formulation conditions on host cell protein removal and biological activity can be conducted by monitoring process-specific host cell proteins in a GMP-compatible and high-throughput (> 1000 samples/day manner.

  18. PREDIKSI BISNIS FOREX MENGGUNAKAN MODEL NEURAL NETWORK BERBASIS ADA BOOST MENGGUNAKAN 2047 DATA

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    Suyatno Suyatno

    2016-11-01

    Full Text Available Setelah melakukan penelitian dan percobaan maka didapatkan hasil penelitian pertama yang telah dilakukan dengan menggunakan Algoritma Neural Network Backpropagatioan dengan menggunakan data sebanyak 268 menunjungkan tingkat akurasi error prediksi pada waktu prediksi per 5 menit sebesar 0.758619403, bila menggunakan data sebanyak 2047 menunjukkan tingkat akurasi error prediksi sebesar 0.500161212 dan hasil penelitian kedua yang telah dilakukan menggunakan Algoritma Optimasi Adaboost pada proses trainning dan ditambah Neural Network Backpropagation pada proses learning menunjukkan tingkat akurasi error prediksi pada waktu prediksi per 5 menit menggunakan data sebanyak 268 sebesar 0.397014925, bila menggunakan data sebanyak 2047 menunjukkan tingkat akurasi error prediksi sebesar 0.099951148. Tahap awal dalam melakukan penelitian ini sampai dengan pengujian menggunakan perhitungan prediksi nilai akurasi error menggunakan rumus MSE (Mean Sequare Error dengan menggunakan algoritma optimasi adaboost untuk memberikan jawaban atas permasalahan bahwa nilai akurasi error Algoritma Neural Network Backpropagation perlu direndahkan agar akurasi prediksi meningkat dan tahap kedua dilakukan uji coba menggunakan data yang lebih banyak dibandingan dengan tahap ke satu. Berdasarkan hasil penelitian yang telah dilakukan, dapat disimpulkan bahwa Algoritma Neural Network memiliki akurasi yang lebih rendah bila dibandingkan dengan akurasi menggunakan metode optimasi adaboost pada proses trainning ditambah dengan Neural Network, ini dapat dilihat dengan rendahnya tingkat error MSE menggunakan metode adaboost + neural network dan dapat disimpukan pula bahwa dengan menggunakan jumlah data yang lebih banyak maka dapat menurunkan tingkat akurasi error MSE sehingga berhasil meningkatkan akurasi prediksi dalam bisnis forex trading. Kata kunci: forex, trading, neural network, adaboost, central capital futures.

  19. Determinants of vitamin D status in fair-skinned women of childbearing age at northern latitudes.

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    Linnea Hedlund

    Full Text Available BACKGROUND AND OBJECTIVE: Poor vitamin D status during pregnancy has been associated with unfavorable outcomes for mother and child. Thus, adequate vitamin D status in women of childbearing age may be important. The aim of this study is to investigate the determinants of 25-hydroxyvitamin D (25(OHD serum concentrations in women of childbearing age living in Sweden, at latitude 57-58° north. METHOD: Eighty four non-pregnant, non-lactating, healthy, fair-skinned women aged between 25-40 years were included. All subjects provided blood samples, four day food records and answered questionnaires about sun exposure and lifestyle. Total serum 25(OHD was analyzed using Roche Cobas® electrochemoluminiescent immunoassay. RESULTS: Mean 25(OHD was 65.8±19.9 nmol/l and 23% of the subjects had concentrations <50 nmol/l. Only 1% had concentrations <25 nmol/l. Determinants of 25(OHD concentrations were recent sunbed use, recent travel to southern latitude, season, estrogen contraceptive use and use of supplementary vitamin D (R(2 = 0.27. CONCLUSION: Every fifth woman had 25(OHD concentrations <50 nmol/l. About 30% of the variation in vitamin D status was explained by sun exposure, use of vitamin D supplements and use of estrogen contraceptives. Cutaneous vitamin D synthesis seems to be a major contributor to vitamin D status, even at northern latitudes. Thus, recommendations on safe UV-B exposure could be beneficial for vitamin D status.

  20. Evaluation of the Hologic gen-probe PANTHER, APTIMA Combo 2 assay in a tertiary care teaching hospital.

    Science.gov (United States)

    Cheng, Annie; Kirby, James E

    2014-03-01

    To evaluate the performance of the Hologic Gen-Probe (San Diego, CA) PANTHER system. The performance of PANTHER was compared with the Hologic Gen-Probe TIGRIS and/or Roche (Indianapolis, IN) COBAS AMPLICOR systems through testing of patient specimens and the spiked-urine matrix. After discrepant resolution, PANTHER demonstrated a 99.3% (95% confidence interval [CI], 96.0%-99.9%) positive and 100% (98.5%-100.0%) negative agreement for Chlamydia trachomatis (CT) and 100% (96.6%-100.0%) positive and 100% (98.6%-100.0%) negative agreement for Neisseria gonorrhoeae (NG) for all male, female, unsexed, and NG-spiked female urine specimens combined. For other specimen types collectively, the PANTHER demonstrated 100% (95% CI, 90.6%-100.0%) positive and 100% (88.3%-100.0%) negative agreement for CT and 90.9% (62.8%-98.4%) positive and 100% (93.5%-100.0%) negative agreement for NG. Analytical sensitivity of the PANTHER in urine matrix was similar to the TIGRIS system. The PANTHER system provides an excellent new addition to options for detecting CT and NG, is appropriate for testing urine samples, and will facilitate high-throughput testing in the clinical laboratory.