Clinical performance of a new hepatitis B surface antigen quantitative assay with automatic dilution

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Ta-Wei Liu

2015-01-01

Full Text Available Hepatitis B virus surface antigen (HBsAg levels reflect disease status and can predict the clinical response to antiviral treatment; however, the emergence of HBsAg mutant strains has become a challenge. The Abbott HBsAg quantification assay provides enhanced detection of HBsAg and HBsAg mutants. We aimed to evaluate the performance of the Abbott HBsAg quantification assay with automatic sample dilutions (shortened as automatic Architect assay, compared with the Abbott HBsAg quantification assay with manual sample dilutions (shortened as manual Architect assay and the Roche HBsAg quantification assay with automatic sample dilutions (shortened as Elecsys. A total of 130 sera samples obtained from 87 hepatitis B virus (HBV-infected patients were collected to assess the correlation between the automatic and manual Architect assays. Among the 87 patients, 41 provided 42 sera samples to confirm the linearity and reproducibility of the automatic Architect assay, and find out the correlation among the Elecsys and two Architect assays. The coefficients of variation (0.44–9.53% and R2 = 0.996–1, which were both determined using values obtained from the automatic Architect assay, showed good reproducibility and linearity. Results of the two Architect assays demonstrated a feasible correlation (n = 130 samples; R = 0.898, p  0.93 in all cases. In conclusion, the correlation between the automatic and manual dilution Architect assays was feasible, particularly in the HBeAg-negative and low DNA groups. With lower labor costs and less human error than the manual version, the Abbott automatic dilution Architect assay provided a good clinical performance with regard to the HBsAg levels.

A Rapid Zika Diagnostic Assay to Measure Neutralizing Antibodies in Patients

Directory of Open Access Journals (Sweden)

Chao Shan

2017-03-01

Full Text Available The potential association of microcephaly and other congenital abnormalities with Zika virus (ZIKV infection during pregnancy underlines the critical need for a rapid and accurate diagnosis. Due to the short duration of ZIKV viremia in infected patients, a serologic assay that detects antibody responses to viral infection plays an essential role in diagnosing patient specimens. The current serologic diagnosis of ZIKV infection relies heavily on the labor-intensive Plaque Reduction Neutralization Test (PRNT that requires more than one-week turnaround time and represents a major bottleneck for patient diagnosis. To overcome this limitation, we have developed a high-throughput assay for ZIKV and dengue virus (DENV diagnosis that can attain the “gold standard” of the current PRNT assay. The new assay is homogeneous and utilizes luciferase viruses to quantify the neutralizing antibody titers in a 96-well format. Using 91 human specimens, we showed that the reporter diagnostic assay has a higher dynamic range and maintains the relative specificity of the traditional PRNT assay. Besides the improvement of assay throughput, the reporter virus technology has also shortened the turnaround time to less than two days. Collectively, our results suggest that, along with the viral RT-PCR assay, the reporter virus-based serologic assay could be potentially used as the first-line test for clinical diagnosis of ZIKV infection as well as for vaccine clinical trials.

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.

Time dependent analysis of assay comparability: a novel approach to understand intra- and inter-site variability over time

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Winiwarter, Susanne; Middleton, Brian; Jones, Barry; Courtney, Paul; Lindmark, Bo; Page, Ken M.; Clark, Alan; Landqvist, Claire

2015-09-01

We demonstrate here a novel use of statistical tools to study intra- and inter-site assay variability of five early drug metabolism and pharmacokinetics in vitro assays over time. Firstly, a tool for process control is presented. It shows the overall assay variability but allows also the following of changes due to assay adjustments and can additionally highlight other, potentially unexpected variations. Secondly, we define the minimum discriminatory difference/ratio to support projects to understand how experimental values measured at different sites at a given time can be compared. Such discriminatory values are calculated for 3 month periods and followed over time for each assay. Again assay modifications, especially assay harmonization efforts, can be noted. Both the process control tool and the variability estimates are based on the results of control compounds tested every time an assay is run. Variability estimates for a limited set of project compounds were computed as well and found to be comparable. This analysis reinforces the need to consider assay variability in decision making, compound ranking and in silico modeling.

Augmentation of Deglutitive Thyrohyoid Muscle Shortening by the Shaker Exercise

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Mepani, Rachel; Antonik, Stephen; Massey, Benson; Kern, Mark; Logemann, Jerilyn; Pauloski, Barbara; Rademaker, Alfred; Easterling, Caryn

2010-01-01

Earlier studies of the effect of 6 weeks of the Shaker Exercise have shown significant increase in UES opening and anterior excursion of larynx and hyoid during swallowing in patients with upper esophageal sphincter (UES) dysfunction, resulting in elimination of aspiration and resumption of oral intake. This effect is attributed to strengthening of the suprahyoid muscles, as evidenced by comparison of electromyographic changes in muscle fatigue before and after completion of the exercise regime. The effect of this exercise on thyrohyoid muscle shortening is unknown. Therefore the aim of this study was to determine the effect of the exercise on thyrohyoid muscle shortening. We studied 11 dysphagic patients with UES dysfunction. Six were randomized to traditional swallowing therapy and five to the Shaker Exercise. Videofluoroscopy was used to measure deglutitive thyrohyoid shortening before and after completion of assigned therapy regimen. Maximum thyrohyoid muscle shortening occurred at close temporal proximity to the time of maximal thyroid cartilage excursion. The percent change in thyrohyoid distance from initiation of deglutition to maximal anterior/superior hyoid excursion showed no statistically significant difference between the two groups prior to either therapy (p = 0.54). In contrast, after completion of therapy, the percent change in thyrohyoid distance in the Shaker Exercise group was significantly greater compared to the traditional therapy (p = 0.034). The Shaker Exercise augments the thyrohyoid muscle shortening in addition to strengthening the suprahyoid muscles. The combination of increased thyrohyoid shortening and suprahyoid strengthening contributes to the Shaker Exercise outcome of deglutitive UES opening augmentation. PMID:18685891

Normalization methods in time series of platelet function assays

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Van Poucke, Sven; Zhang, Zhongheng; Roest, Mark; Vukicevic, Milan; Beran, Maud; Lauwereins, Bart; Zheng, Ming-Hua; Henskens, Yvonne; Lancé, Marcus; Marcus, Abraham

2016-01-01

Abstract Platelet function can be quantitatively assessed by specific assays such as light-transmission aggregometry, multiple-electrode aggregometry measuring the response to adenosine diphosphate (ADP), arachidonic acid, collagen, and thrombin-receptor activating peptide and viscoelastic tests such as rotational thromboelastometry (ROTEM). The task of extracting meaningful statistical and clinical information from high-dimensional data spaces in temporal multivariate clinical data represented in multivariate time series is complex. Building insightful visualizations for multivariate time series demands adequate usage of normalization techniques. In this article, various methods for data normalization (z-transformation, range transformation, proportion transformation, and interquartile range) are presented and visualized discussing the most suited approach for platelet function data series. Normalization was calculated per assay (test) for all time points and per time point for all tests. Interquartile range, range transformation, and z-transformation demonstrated the correlation as calculated by the Spearman correlation test, when normalized per assay (test) for all time points. When normalizing per time point for all tests, no correlation could be abstracted from the charts as was the case when using all data as 1 dataset for normalization. PMID:27428217

An Attempt to Shorten Loading Time of Epirubicin into DC Beads® Using Vibration and a Sieve

International Nuclear Information System (INIS)

Sonoda, Akinaga; Nitta, Norihisa; Yamamoto, Takefumi; Tomozawa, Yuki; Ohta, Shinichi; Watanabe, Shobu; Murata, Kiyoshi

2017-01-01

PurposeWe investigated the possibility of shortening the time required for loading epirubicin into calibrated polyvinyl alcohol-based hydrogel beads (DC Beads ® ) to be used for transarterial chemoembolization.MethodAfter separating the beads suspended in phosphate-buffered saline (PBS) solution by the use of a sieve (clearance 75 µm), epirubicin hydrochloride (EH) was loaded for 20, 30, or 60 s under vibration into DC beads. The EH loading rate into conventionally prepared (control) beads, i.e., beads loaded for 30 min without vibration, and vibration-loaded beads were calculated from the residual EH concentration in the bead-depleted EH solution. The amount of EH eluted from conventionally and vibration-loaded samples into a PBS solution (pH 7.0) was measured at 15 and 30 min and 1, 2, 6, 12, and 24 h. We also recorded the inhibitory effect of the PBS solution on the loading time. Using frozen sections, the EH load in the beads was evaluated visually under a fluorescence microscope.ResultsSpectrophotometry (495 nm) showed that the loading rate was 98.98 ± 0.34, 99.02 ± 0.32, and 99.50 ± 0.11 % with 20-, 30-, and 60-s vibration, respectively. The eluted rate was statistically similar between vibration- and statically loaded (control) beads. The PBS solution hampered EH loading into the beads. Visually, the distribution of EH in conventionally and vibration-loaded DC beads was similar.DiscussionThe use of vibration and the removal of PBS solution when epirubicin hydrochloride was loaded into DC beads dramatically shortened the loading time of epirubicin hydrochloride into DC beads.

Multiplex real-time PCR assay for Legionella species.

Science.gov (United States)

Kim, Seung Min; Jeong, Yoojung; Sohn, Jang Wook; Kim, Min Ja

2015-12-01

Legionella pneumophila serogroup 1 (sg1) accounts for the majority of infections in humans, but other Legionella species are also associated with human disease. In this study, a new SYBR Green I-based multiplex real-time PCR assay in a single reaction was developed to allow the rapid detection and differentiation of Legionella species by targeting specific gene sequences. Candidate target genes were selected, and primer sets were designed by referring to comparative genomic hybridization data of Legionella species. The Legionella species-specific groES primer set successfully detected all 30 Legionella strains tested. The xcpX and rfbA primers specifically detected L. pneumophila sg1-15 and L. pneumophila sg1, respectively. In addition, this assay was validated by testing clinical samples and isolates. In conclusion, this novel multiplex real-time PCR assay might be a useful diagnostic tool for the rapid detection and differentiation of Legionella species in both clinical and epidemiological studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Shortening Delivery Times of Intensity Modulated Proton Therapy by Reducing Proton Energy Layers During Treatment Plan Optimization

Energy Technology Data Exchange (ETDEWEB)

Water, Steven van de, E-mail: s.vandewater@erasmusmc.nl [Department of Radiation Oncology, Erasmus MC Cancer Institute, Rotterdam (Netherlands); Kooy, Hanne M. [F. H. Burr Proton Therapy Center, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts (United States); Heijmen, Ben J.M.; Hoogeman, Mischa S. [Department of Radiation Oncology, Erasmus MC Cancer Institute, Rotterdam (Netherlands)

2015-06-01

Purpose: To shorten delivery times of intensity modulated proton therapy by reducing the number of energy layers in the treatment plan. Methods and Materials: We have developed an energy layer reduction method, which was implemented into our in-house-developed multicriteria treatment planning system “Erasmus-iCycle.” The method consisted of 2 components: (1) minimizing the logarithm of the total spot weight per energy layer; and (2) iteratively excluding low-weighted energy layers. The method was benchmarked by comparing a robust “time-efficient plan” (with energy layer reduction) with a robust “standard clinical plan” (without energy layer reduction) for 5 oropharyngeal cases and 5 prostate cases. Both plans of each patient had equal robust plan quality, because the worst-case dose parameters of the standard clinical plan were used as dose constraints for the time-efficient plan. Worst-case robust optimization was performed, accounting for setup errors of 3 mm and range errors of 3% + 1 mm. We evaluated the number of energy layers and the expected delivery time per fraction, assuming 30 seconds per beam direction, 10 ms per spot, and 400 Giga-protons per minute. The energy switching time was varied from 0.1 to 5 seconds. Results: The number of energy layers was on average reduced by 45% (range, 30%-56%) for the oropharyngeal cases and by 28% (range, 25%-32%) for the prostate cases. When assuming 1, 2, or 5 seconds energy switching time, the average delivery time was shortened from 3.9 to 3.0 minutes (25%), 6.0 to 4.2 minutes (32%), or 12.3 to 7.7 minutes (38%) for the oropharyngeal cases, and from 3.4 to 2.9 minutes (16%), 5.2 to 4.2 minutes (20%), or 10.6 to 8.0 minutes (24%) for the prostate cases. Conclusions: Delivery times of intensity modulated proton therapy can be reduced substantially without compromising robust plan quality. Shorter delivery times are likely to reduce treatment uncertainties and costs.

Occlusal stability in shortened dental arches.

NARCIS (Netherlands)

Witter, D.J.; Creugers, N.H.J.; Kreulen, C.M.; Haan, A. de

2001-01-01

Shortened dental arches consisting of anterior and premolar teeth have been shown to meet oral functional demands. However, the occlusal stability may be at risk as a result of tooth migration. The aim of this nine-year study was to investigate occlusal stability in shortened dental arches as a

Comparison of Parasite Burden Using Real-Time Polymerase Chain Reaction Assay and Limiting Dilution Assay in Leishma-nia major Infected Mouse

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Somayeh GHOTLOO

2015-12-01

Full Text Available Background:Limiting dilution assay is considered as the gold standard method for quantifying the number of parasites in the animal model of Leishmania infection. Nowadays, real-time PCR is being increasingly applied to quantify infectious agents. In the present study, a real-time PCR assay was developed to estimate para­site burdens in lymph nodes of Leishmania major infected BALB/C mice. Enumera­tion of parasites was also performed by limiting dilution assay and compared with the results of real-time PCR based quantification.Methods:The SYBR Green based real- time PCR assay was performed to amplify a 75 bp fragment of superoxide dismutase B1 gene in the lymph nodes of L. major infected BALB/C mice 8 weeks post infection. Mice were infected subcutaneously at the base of their tail with 2 × 105L. major promastigotes in the stationary phase of growth. To compare parasite burdens obtained by real-time PCR assay with those of limiting dilution assay, twelve 8-fold serial dilutions of the lymph node homoge­nates were prepared in the Schneider medium and incubated at 26°C.After 7 days, wells containing motile parasites were identified by direct observation under an inverted light microscope and the total number of parasites was estimated using the ELIDA software.Results:Spearman's correlation coefficient of the parasite burdens between real-time PCR and limiting dilution assay was 0.72 (Pvalue = 0.008.Conclusion:Real-time PCR assay is an appropriate replacement to existing limit­ing dilution assay in quantifying parasite burden in the experimental model of Leishma­nia infection.

Olanzapine induced Q-Tc shortening.

Science.gov (United States)

Shoja Shafti, Saeed; Fallah Jahromi, Parisa

2014-12-01

Prolongation of Q-Tc interval is commonly accepted as a surrogate marker for the ability of a drug to cause torsade de pointes. In the present study, safety of olanzapine versus risperidone was compared among a group of patients with schizophrenia to see the frequency of the electrocardiographic alterations induced by those atypical antipsychotics. Two hundred and sixty-eight female inpatients with schizophrenia entered in one of the two parallel groups to participate in an open study for random assignment to olanzapine (n = 148) or risperidone (n = 120). Standard 12-lead surface electrocardiogram (ECG) was taken from each patient at baseline, before initiation of treatment, and then at the end of management, just before discharge. The parameters that were assessed included heart rate (HR), P-R interval, QRS interval, Q-T interval (corrected = Q-Tc), ventricular activation time (VAT), ST segment, T wave, axis of QRS, and finally, interventricular conduction process. A total of 37.83% of cases in the olanzapine group and 30% in the risperidone group showed some Q-Tc changes; 13.51% and 24.32% of the patients in the olanzapine group showed prolongation and shortening of the Q-Tc, respectively, while changes in the risperidone group were restricted to only prolongation of Q-Tc. Comparison of means showed a significant increment in Q-Tc by risperidone (p = 0.02). Also, comparison of proportions in the olanzapine group showed significantly more cases with shortening of Q-Tc versus its prolongation (p = 0.01). No significant alterations with respect to other variables were evident. Olanzapine and risperidone had comparable potentiality for induction of Q-Tc changes, while production of further miscellaneous alterations in ECG was more observable in the olanzapine group compared with the risperidone group. Also shortening of Q-Tc was specific to olanzapine.

Field monitoring of column shortenings in a high-rise building during construction.

Science.gov (United States)

Choi, Se Woon; Kim, Yousok; Kim, Jong Moon; Park, Hyo Seon

2013-10-24

The automatic monitoring of shortenings of vertical members in high-rise buildings under construction is a challenging issue in the high-rise building construction field. In this study, a practical system for monitoring column shortening in a high-rise building under construction is presented. The proposed monitoring system comprises the following components: (1) a wireless sensing system and (2) the corresponding monitoring software. The wireless sensing system comprises the sensors and energy-efficient wireless sensing units (sensor nodes, master nodes, and repeater nodes), which automate the processes for measuring the strains of vertical members and transmitting the measured data to the remote server. The monitoring software enables construction administrators to monitor real-time data collected by the server via an Internet connection. The proposed monitoring system is applied to actual 66-floor and 72-floor high-rise buildings under construction. The system enables automatic and real-time measurements of the shortening of vertical members, which can result in more precise construction.

Preoperative management of surgical patients by "shortened fasting time": a study on the amount of total body water by multi-frequency impedance method.

Science.gov (United States)

Taniguchi, Hideki; Sasaki, Toshio; Fujita, Hisae

2012-01-01

Preoperative fasting is an established procedure to be practiced for patients before surgery, but optimal preoperative fasting time still remains controversial. The aim of this study was to investigate the effect of "shortened preoperative fasting time" on the change in the amount of total body water (TBW) in elective surgical patients. TBW was measured by multi-frequency impedance method. The patients, who were scheduled to undergo surgery for stomach cancer, were divided into two groups of 15 patients each. Before surgery, patients in the control group were managed with conventional preoperative fasting time, while patients in the "enhanced recovery after surgery (ERAS)" group were managed with "shortened preoperative fasting time" and "reduced laxative medication." TBW was measured on the day before surgery and the day of surgery before entering the operating room. Defecation times and anesthesia-related vomiting and aspiration were monitored. TBW values on the day of surgery showed changes in both groups as compared with those on the day before surgery, but the rate of change was smaller in the ERAS group than in the control group (2.4±6.8% [12 patients] vs. -10.6±4.6% [14 patients], pfasting time" and "reduced administration of laxatives" is effective in the maintenance of TBW in elective surgical patients.

An Attempt to Shorten Loading Time of Epirubicin into DC Beads{sup ®} Using Vibration and a Sieve

Energy Technology Data Exchange (ETDEWEB)

Sonoda, Akinaga, E-mail: akinagasonoda@yahoo.co.jp; Nitta, Norihisa [Shiga University of Medical Science, Department of Radiology (Japan); Yamamoto, Takefumi [Shiga University of Medical Science, Central Research Laboratory (Japan); Tomozawa, Yuki; Ohta, Shinichi; Watanabe, Shobu; Murata, Kiyoshi [Shiga University of Medical Science, Department of Radiology (Japan)

2017-04-15

PurposeWe investigated the possibility of shortening the time required for loading epirubicin into calibrated polyvinyl alcohol-based hydrogel beads (DC Beads{sup ®}) to be used for transarterial chemoembolization.MethodAfter separating the beads suspended in phosphate-buffered saline (PBS) solution by the use of a sieve (clearance 75 µm), epirubicin hydrochloride (EH) was loaded for 20, 30, or 60 s under vibration into DC beads. The EH loading rate into conventionally prepared (control) beads, i.e., beads loaded for 30 min without vibration, and vibration-loaded beads were calculated from the residual EH concentration in the bead-depleted EH solution. The amount of EH eluted from conventionally and vibration-loaded samples into a PBS solution (pH 7.0) was measured at 15 and 30 min and 1, 2, 6, 12, and 24 h. We also recorded the inhibitory effect of the PBS solution on the loading time. Using frozen sections, the EH load in the beads was evaluated visually under a fluorescence microscope.ResultsSpectrophotometry (495 nm) showed that the loading rate was 98.98 ± 0.34, 99.02 ± 0.32, and 99.50 ± 0.11 % with 20-, 30-, and 60-s vibration, respectively. The eluted rate was statistically similar between vibration- and statically loaded (control) beads. The PBS solution hampered EH loading into the beads. Visually, the distribution of EH in conventionally and vibration-loaded DC beads was similar.DiscussionThe use of vibration and the removal of PBS solution when epirubicin hydrochloride was loaded into DC beads dramatically shortened the loading time of epirubicin hydrochloride into DC beads.

Radiation-induced life shortening. Annex K

International Nuclear Information System (INIS)

1982-01-01

The purpose of this Annex is to review the cumulative evidence in the field of non-neoplastic long-term effects of whole-body irradiation. In particular, the existence and extent of life-span shortening in irradiated animals and man, and the relationships of life shortening to the physical and biological variables which may influence this effect of radiation are examined.

Binge-type behavior in rats consuming trans-fat-free shortening.

Science.gov (United States)

Wojnicki, F H E; Charny, G; Corwin, R L W

2008-07-05

Studies from this and another laboratory involving an animal model of binge-type behavior have used vegetable shortening containing trans-fats. Due to reformulations by vegetable shortening manufacturers to remove trans-fats from their products, only trans-fat-free shortenings are now available. The goal of the present study was to assess binge-type behavior in rats with trans-fat and trans-free vegetable shortening. Trans-fat-free shortening was provided to three different groups of non-food-deprived male Sprague Dawley rats on different schedules of access: continuous access (24 h/day-7 days/week), daily access (1 h every day), and intermittent access (1 h on Mondays, Wednesdays, Fridays). Trans-fat shortening was provided to a fourth group on the intermittent access schedule. A fifth group had no shortening access (chow only). Both intermittent groups (trans-fat-free and trans-fat) consumed significantly more shortening during the 1-h period of availability than did the daily group, and there was no difference in shortening intakes between the intermittent groups. These results are identical to previous reports of binge-type behavior in rats using this model. Thus, binge-type behavior in the present behavioral model depends upon the schedule of access, not the presence of trans-fats in the shortening.

Respiratory acidosis prolongs, while alkalosis shortens, the duration and recovery time of vecuronium in humans.

Science.gov (United States)

Yamauchi, Masanori; Takahashi, Hiromi; Iwasaki, Hiroshi; Namiki, Akiyoshi

2002-03-01

To determine the effects of respiratory acidosis and alkalosis by mechanical ventilation on the onset, duration, and recovery times of vecuronium. Randomized, prospective study. Operating rooms in the Sapporo Medical University Hospital and Kitami Red Cross Hospital. 90 ASA physical status I and II patients undergoing lower abdominal surgery. Patients were randomly allocated to one of three groups by arterial carbon dioxide tension level (PaCO2; mmHg) after induction: hyperventilation group (PaCO2 = 25-35), normoventilation group (PaCO2 = 35-45), and hypoventilation group (PaCO2 = 45-55). Anesthesia was maintained by spinal block with inhalation of 50% to 66% nitrous oxide in oxygen and intermittent intravenous administration of fentanyl and midazolam with tracheal intubation. After vecuronium 0.08 mg/kg was given, onset, duration, and recovery time were measured by mechanomyography (Biometer Myograph 2,000, Odense, Denmark). There were significant differences in the duration and recovery time of vecuronium among the normoventilation group (12.7 +/- 3.3 min and 11.8 +/- 2.8 min, respectively), the hyperventilation group (10.6 +/- 3.5 min and 9.2 +/- 2.7 min, respectively; p respiratory acidosis and shortened in respiratory alkalosis.

Shortening treatment time in robotic radiosurgery using a novel node reduction technique

Energy Technology Data Exchange (ETDEWEB)

Water, Steven van de; Hoogeman, Mischa S.; Breedveld, Sebastiaan; Heijmen, Ben J. M. [Department of Radiation Oncology, Erasmus MC-Daniel den Hoed Cancer Center, Groene Hilledijk 301, 3075 EA Rotterdam (Netherlands)

2011-03-15

Purpose: The fraction duration of robotic radiosurgery treatments can be reduced by generating more time-efficient treatment plans with a reduced number of node positions, beams, and monitor units (MUs). Node positions are preprogramed locations where the robot can position the focal spot of the x-ray beam. As the time needed for the robot to travel between node positions takes up a large part of the treatment time, the aim of this study was to develop and evaluate a node reduction technique in order to reduce the treatment time per fraction for robotic radiosurgery. Methods: Node reduction was integrated into the inverse planning algorithm, developed in-house for the robotic radiosurgery modality. It involved repeated inverse optimization, each iteration excluding low-contribution node positions from the planning and resampling new candidate beams from the remaining node positions. Node reduction was performed until the exclusion of a single node position caused a constraint violation, after which the shortest treatment plan was selected retrospectively. Treatment plans were generated with and without node reduction for two lung cases of different complexity, one oropharyngeal case and one prostate case. Plan quality was assessed using the number of node positions, beams and MUs, and the estimated treatment time per fraction. All treatment plans had to fulfill all clinical dose constraints. Extra constraints were added to maintain the low-dose conformality and restrict skin doses during node reduction. Results: Node reduction resulted in 12 residual node positions, on average (reduction by 77%), at the cost of an increase in the number of beams and total MUs of 28% and 9%, respectively. Overall fraction durations (excluding patient setup) were shortened by 25% (range of 18%-40%), on average. Dose distributions changed only little and dose in low-dose regions was effectively restricted by the additional constraints. Conclusions: The fraction duration of robotic

Shortening treatment time in robotic radiosurgery using a novel node reduction technique

International Nuclear Information System (INIS)

Water, Steven van de; Hoogeman, Mischa S.; Breedveld, Sebastiaan; Heijmen, Ben J. M.

2011-01-01

Purpose: The fraction duration of robotic radiosurgery treatments can be reduced by generating more time-efficient treatment plans with a reduced number of node positions, beams, and monitor units (MUs). Node positions are preprogramed locations where the robot can position the focal spot of the x-ray beam. As the time needed for the robot to travel between node positions takes up a large part of the treatment time, the aim of this study was to develop and evaluate a node reduction technique in order to reduce the treatment time per fraction for robotic radiosurgery. Methods: Node reduction was integrated into the inverse planning algorithm, developed in-house for the robotic radiosurgery modality. It involved repeated inverse optimization, each iteration excluding low-contribution node positions from the planning and resampling new candidate beams from the remaining node positions. Node reduction was performed until the exclusion of a single node position caused a constraint violation, after which the shortest treatment plan was selected retrospectively. Treatment plans were generated with and without node reduction for two lung cases of different complexity, one oropharyngeal case and one prostate case. Plan quality was assessed using the number of node positions, beams and MUs, and the estimated treatment time per fraction. All treatment plans had to fulfill all clinical dose constraints. Extra constraints were added to maintain the low-dose conformality and restrict skin doses during node reduction. Results: Node reduction resulted in 12 residual node positions, on average (reduction by 77%), at the cost of an increase in the number of beams and total MUs of 28% and 9%, respectively. Overall fraction durations (excluding patient setup) were shortened by 25% (range of 18%-40%), on average. Dose distributions changed only little and dose in low-dose regions was effectively restricted by the additional constraints. Conclusions: The fraction duration of robotic

[Extension of (extremely) shortened dental arches by fixed or removable partial dentures

NARCIS (Netherlands)

Witter, D.J.; Hoefnagel, R.A.; Snoek, P.A.; Creugers, N.H.J.

2009-01-01

Whether a shortened dental arch needs to be extended depends on the degree of the shortening. Four categories of shortened dental arches can be distinguished: 1. slightly shortened dental arches; 2. moderately shortened dental arches; 3. extremely shortened dental arches; and 4. asymmetrical

Palliative Sedation in Advanced Cancer Patients: Does it Shorten Survival Time? - A Systematic Review.

Science.gov (United States)

Barathi, B; Chandra, Prabha S

2013-01-01

Patients with advanced cancer often suffer from multiple refractory symptoms in the terminal phase of their life. Palliative sedation is one of the few ways to relieve this refractory suffering. This systematic review investigated the effect of palliative sedation on survival time in terminally ill cancer patients. Six electronic databases were searched for both prospective and retrospective studies which evaluated the effect of palliative sedation on survival time. Only those studies which had a comparison group that did not receive palliative sedation were selected for the review. Abstracts of all retrieved studies were screened to include the most relevant studies and only studies which met inclusion criteria were selected. References of all retrieved studies were also screened for relevant studies. Selected studies were assessed for quality and data extraction was done using the structured data extraction form. Eleven studies including four prospective and seven retrospective studies were identified. Mean survival time (MST) was measured as the time from last admission until death. A careful analysis of the results of all the 11 studies indicated that MST of sedated and non-sedated group was not statistically different in any of the studies. This systematic review supports the fact that palliative sedation does not shorten survival in terminally ill cancer patients. However, this conclusion needs to be taken with consideration of the methodology, study design, and the population studied of the included studies in this review.

Palliative sedation in advanced cancer patients: Does it shorten survival time? - A systematic review

Directory of Open Access Journals (Sweden)

B Barathi

2013-01-01

Full Text Available Background: Patients with advanced cancer often suffer from multiple refractory symptoms in the terminal phase of their life. Palliative sedation is one of the few ways to relieve this refractory suffering. Objectives: This systematic review investigated the effect of palliative sedation on survival time in terminally ill cancer patients. Materials and Methods: Six electronic databases were searched for both prospective and retrospective studies which evaluated the effect of palliative sedation on survival time. Only those studies which had a comparison group that did not receive palliative sedation were selected for the review. Abstracts of all retrieved studies were screened to include the most relevant studies and only studies which met inclusion criteria were selected. References of all retrieved studies were also screened for relevant studies. Selected studies were assessed for quality and data extraction was done using the structured data extraction form. Results: Eleven studies including four prospective and seven retrospective studies were identified. Mean survival time (MST was measured as the time from last admission until death. A careful analysis of the results of all the 11 studies indicated that MST of sedated and non-sedated group was not statistically different in any of the studies. Conclusion: This systematic review supports the fact that palliative sedation does not shorten survival in terminally ill cancer patients. However, this conclusion needs to be taken with consideration of the methodology, study design, and the population studied of the included studies in this review.

Accelerated Telomere Shortening in Acromegaly; IGF-I Induces Telomere Shortening and Cellular Senescence.

Science.gov (United States)

Matsumoto, Ryusaku; Fukuoka, Hidenori; Iguchi, Genzo; Odake, Yukiko; Yoshida, Kenichi; Bando, Hironori; Suda, Kentaro; Nishizawa, Hitoshi; Takahashi, Michiko; Yamada, Shozo; Ogawa, Wataru; Takahashi, Yutaka

2015-01-01

Patients with acromegaly exhibit reduced life expectancy and increased prevalence of age-related diseases, such as diabetes, hypertension, and cardiovascular disease. However, the underlying mechanism has not been fully elucidated. Telomere shortening is reportedly associated with reduced life expectancy and increased prevalence of these age-related diseases. We measured telomere length in patients with acromegaly using quantitative PCR method. The effect of GH and IGF-I on telomere length and cellular senescence was examined in human skin fibroblasts. Patients with acromegaly exhibited shorter telomere length than age-, sex-, smoking-, and diabetes-matched control patients with non-functioning pituitary adenoma (0.62 ± 0.23 vs. 0.75 ± 0.35, respectively, P = 0.047). In addition, telomere length in acromegaly was negatively correlated with the disease duration (R2 = 0.210, P = 0.003). In vitro analysis revealed that not GH but IGF-I induced telomere shortening in human skin fibroblasts. Furthermore, IGF-I-treated cells showed increased senescence-associated β-galactosidase activity and expression of p53 and p21 protein. IGF-I-treated cells reached the Hayflick limit earlier than GH- or vehicle-treated cells, indicating that IGF-I induces cellular senescence. Shortened telomeres in acromegaly and cellular senescence induced by IGF-I can explain, in part, the underlying mechanisms by which acromegaly exhibits an increased morbidity and mortality in association with the excess secretion of IGF-I.

A one-step, real-time PCR assay for rapid detection of rhinovirus.

Science.gov (United States)

Do, Duc H; Laus, Stella; Leber, Amy; Marcon, Mario J; Jordan, Jeanne A; Martin, Judith M; Wadowsky, Robert M

2010-01-01

One-step, real-time PCR assays for rhinovirus have been developed for a limited number of PCR amplification platforms and chemistries, and some exhibit cross-reactivity with genetically similar enteroviruses. We developed a one-step, real-time PCR assay for rhinovirus by using a sequence detection system (Applied Biosystems; Foster City, CA). The primers were designed to amplify a 120-base target in the noncoding region of picornavirus RNA, and a TaqMan (Applied Biosystems) degenerate probe was designed for the specific detection of rhinovirus amplicons. The PCR assay had no cross-reactivity with a panel of 76 nontarget nucleic acids, which included RNAs from 43 enterovirus strains. Excellent lower limits of detection relative to viral culture were observed for the PCR assay by using 38 of 40 rhinovirus reference strains representing different serotypes, which could reproducibly detect rhinovirus serotype 2 in viral transport medium containing 10 to 10,000 TCID(50) (50% tissue culture infectious dose endpoint) units/ml of the virus. However, for rhinovirus serotypes 59 and 69, the PCR assay was less sensitive than culture. Testing of 48 clinical specimens from children with cold-like illnesses for rhinovirus by the PCR and culture assays yielded detection rates of 16.7% and 6.3%, respectively. For a batch of 10 specimens, the entire assay was completed in 4.5 hours. This real-time PCR assay enables detection of many rhinovirus serotypes with the Applied Biosystems reagent-instrument platform.

Multicenter Evaluation of a New Shortened Peptide Nucleic Acid Fluorescence In Situ Hybridization Procedure for Species Identification of Select Gram-Negative Bacilli from Blood Cultures▿

Science.gov (United States)

Morgan, Margie; Marlowe, Elizabeth; Della-Latta, Phyllis; Salimnia, Hossein; Novak-Weekley, Susan; Wu, Fann; Crystal, Benjamin S.

2010-01-01

A shortened protocol for two peptide nucleic acid fluorescence in situ hybridization (PNA FISH) assays for the detection of Gram-negative bacilli from positive blood cultures was evaluated in a multicenter trial. There was 100% concordance between the two protocols for each assay (368 of 368 and 370 of 370 results) and 99.7% (367 of 368 and 369 of 370 results) agreement with routine laboratory techniques. PMID:20357212

The role of nonlinear viscoelasticity on the functionality of laminating shortenings

Energy Technology Data Exchange (ETDEWEB)

Macias-Rodriguez, Braulio A.; Peyronel, Fernanda; Marangoni, Alejandro G.

2017-11-01

The rheology of fats is essential for the development of homogeneous and continuous layered structures of doughs. Here, we define laminating shortenings in terms of rheological behavior displayed during linear-to-nonlinear shear deformations, investigated by large amplitude oscillatory shear rheology. Likewise, we associate the rheological behavior of the shortenings with structural length scales elucidated by ultra-small angle x-ray scattering and cryo-electron microscopy. Shortenings exhibited solid-like viscoelastic and viscoelastoplastic behaviors in the linear and nonlinear regimes respectively. In the nonlinear region, laminating shortenings dissipated more viscous energy (larger normalized dynamic viscosities) than a cake bakery shortening. The fat solid-like network of laminating shortening displayed a three-hierarchy structure and layered crystal aggregates, in comparison to two-hierarchy structure and spherical-like crystal aggregates of a cake shortening. We argue that the observed rheology, correlated to the structural network, is crucial for optimal laminating performance of shortenings.

Shortened preoperative fasting time to allow oral rehydration solution clear liquid up to two hours before elective major surgery in adults

International Nuclear Information System (INIS)

Shah, J.N.; Maharjan, S.; Curung, R.

2018-01-01

To generate evidence of feasibility to allow clear liquid 2 hours before elective surgery. Study Design: Cross-sectional observational study. Place and Duration of Study: The Department of Surgery, Patan Hospital, Patan Academy of Health Sciences, Nepal, from October to December 2016. Methodology: One hundred consecutive adult elective major surgery patients of American Society of Anesthesiologist criteria 1 or 2 were enrolled. The protocol was discussed with patients, nurses, anesthetists and surgeons to allow 500 ml clear liquid (ORS) up to 0600 hours on the day of surgery to maintain minimum of 2 hours (h) nil per os (NPO) before surgery. Compliance, discomfort, nausea and vomiting were observed. Institutional review committee approved the study. Microsoft excel was used for descriptive analysis. Results: All 100 patients completed the protocol of shortened fasting time. Two patients had incomplete records and were excluded from analysis. Among the 98 patients analysed, age was 48 +-12.38 years with 74 females (75.51% of 98). There were 68 gastrointestinal, 20 urosurgery and 10 others surgeries. There was no discomfort, nausea or vomiting reported due to ORS 2-h before elective surgery. Conclusion: Preoperative clear liquid up to 2-h before elective surgery in adults is feasible and safe in our set-up to shorten the fasting time. (author)

Accelerated Telomere Shortening in Acromegaly; IGF-I Induces Telomere Shortening and Cellular Senescence.

Directory of Open Access Journals (Sweden)

Ryusaku Matsumoto

Full Text Available Patients with acromegaly exhibit reduced life expectancy and increased prevalence of age-related diseases, such as diabetes, hypertension, and cardiovascular disease. However, the underlying mechanism has not been fully elucidated. Telomere shortening is reportedly associated with reduced life expectancy and increased prevalence of these age-related diseases.We measured telomere length in patients with acromegaly using quantitative PCR method. The effect of GH and IGF-I on telomere length and cellular senescence was examined in human skin fibroblasts.Patients with acromegaly exhibited shorter telomere length than age-, sex-, smoking-, and diabetes-matched control patients with non-functioning pituitary adenoma (0.62 ± 0.23 vs. 0.75 ± 0.35, respectively, P = 0.047. In addition, telomere length in acromegaly was negatively correlated with the disease duration (R2 = 0.210, P = 0.003. In vitro analysis revealed that not GH but IGF-I induced telomere shortening in human skin fibroblasts. Furthermore, IGF-I-treated cells showed increased senescence-associated β-galactosidase activity and expression of p53 and p21 protein. IGF-I-treated cells reached the Hayflick limit earlier than GH- or vehicle-treated cells, indicating that IGF-I induces cellular senescence.Shortened telomeres in acromegaly and cellular senescence induced by IGF-I can explain, in part, the underlying mechanisms by which acromegaly exhibits an increased morbidity and mortality in association with the excess secretion of IGF-I.

Accelerated Telomere Shortening in Acromegaly; IGF-I Induces Telomere Shortening and Cellular Senescence

Science.gov (United States)

Matsumoto, Ryusaku; Fukuoka, Hidenori; Iguchi, Genzo; Odake, Yukiko; Yoshida, Kenichi; Bando, Hironori; Suda, Kentaro; Nishizawa, Hitoshi; Takahashi, Michiko; Yamada, Shozo; Ogawa, Wataru; Takahashi, Yutaka

2015-01-01

Objective Patients with acromegaly exhibit reduced life expectancy and increased prevalence of age-related diseases, such as diabetes, hypertension, and cardiovascular disease. However, the underlying mechanism has not been fully elucidated. Telomere shortening is reportedly associated with reduced life expectancy and increased prevalence of these age-related diseases. Methods We measured telomere length in patients with acromegaly using quantitative PCR method. The effect of GH and IGF-I on telomere length and cellular senescence was examined in human skin fibroblasts. Results Patients with acromegaly exhibited shorter telomere length than age-, sex-, smoking-, and diabetes-matched control patients with non-functioning pituitary adenoma (0.62 ± 0.23 vs. 0.75 ± 0.35, respectively, P = 0.047). In addition, telomere length in acromegaly was negatively correlated with the disease duration (R 2 = 0.210, P = 0.003). In vitro analysis revealed that not GH but IGF-I induced telomere shortening in human skin fibroblasts. Furthermore, IGF-I-treated cells showed increased senescence-associated β-galactosidase activity and expression of p53 and p21 protein. IGF-I-treated cells reached the Hayflick limit earlier than GH- or vehicle-treated cells, indicating that IGF-I induces cellular senescence. Conclusion Shortened telomeres in acromegaly and cellular senescence induced by IGF-I can explain, in part, the underlying mechanisms by which acromegaly exhibits an increased morbidity and mortality in association with the excess secretion of IGF-I. PMID:26448623

Real‑time, fast neutron detection for stimulated safeguards assay

International Nuclear Information System (INIS)

Joyce, Malcolm J.; Adamczyk, Justyna; Plenteda, Romano; Aspinall, Michael D.; Cave, Francis D.

2015-01-01

The advent of low‑hazard organic liquid scintillation detectors and real‑time pulse‑shape discrimination (PSD) processing has suggested a variety of modalities by which fast neutrons, as opposed to neutrons moderated prior to detection, can be used directly to benefit safeguards needs. In this paper we describe a development of a fast‑neutron based safeguards assay system designed for the assessment of 235 U content in fresh fuel. The system benefits from real‑time pulse‑shape discrimination processing and auto‑calibration of the detector system parameters to ensure a rapid and effective set‑up protocol. These requirements are essential in optimising the speed and limit of detection of the fast neutron technique, whilst minimising the intervention needed to perform the assay.

Comparative study of ß-glucan induced respiratory burst measured by nitroblue tetrazolium assay and real-time luminol-enhanced chemiluminescence assay in common carp (Cyprinus carpio L.)

DEFF Research Database (Denmark)

Jiménez, Natalia Ivonne Vera; Pietretti, D.; Wiegertjes, G. F.

2013-01-01

kidney cells of carp. However, whereas the NBT assay was shown to detect the production of only superoxide anions, the real-time luminol-enhanced assay could detect the production of both superoxide anions and hydrogen peroxide. Only the chemiluminescence assay could reliably record the production of ROS......-point measurement based on the intracellular reduction of nitroblue tetrazolium (NBT) and a real-time luminol-enhanced assay based on the detection of native chemiluminescence. Both assays allowed for detection of dose-dependent changes in magnitude of the respiratory burst response induced by β-glucans in head...... on a real-time scale at frequent and continual time intervals for time course experiments, providing more detailed information on the respiratory burst response. The real-time chemiluminescence assay was used to measure respiratory burst activity in macrophage and neutrophilic granulocyte-enriched head...

Challenges in Shortening New Product Introduction in the Pharmaceutical Industry

DEFF Research Database (Denmark)

Hansen, Klaus Reinholdt Nyhuus; Grunow, Martin

2010-01-01

Drug developing companies are forced to utilize the effective protection of the patent by focusing on shortening the new product introduction [NPI] process measured as Time-to-Market [TTM]. Here the NPI process is considered and the trade-offs, which have to be address in the future are identifie...

Bone shortening of clavicular fractures

DEFF Research Database (Denmark)

Thorsmark, A H; Muhareb Udby, P; Ban, I

2017-01-01

BACKGROUND: The indication for operative treatment of clavicular fractures with bone shortening over 2 cm is much debated. Correct measurement of clavicular length is essential, and reliable measures of clavicular length are therefore highly requested by clinical decision-makers. The aim of this ......BACKGROUND: The indication for operative treatment of clavicular fractures with bone shortening over 2 cm is much debated. Correct measurement of clavicular length is essential, and reliable measures of clavicular length are therefore highly requested by clinical decision-makers. The aim......-fracture bone lengthening that indicated methodological problems. The Hill et al. and Silva et al. methods had high minimal detectable change, making their use unreliable. CONCLUSION: As all three measurement methods had either reliability or methodological issues, we found it likely that differences...

Shortening of construction period of nuclear power plant. Activities of construction industry on construction period shortening

International Nuclear Information System (INIS)

Kamata, Hirofumi

2011-01-01

Total construction period could be shorten by prefabricating structures efficiently in another yard and reducing working hours on site, which would reduce work at height or congestion work and also upgrade safety at work. Construction period shortening would surely reduce expenses during work and advance operation start of electric utilities. Construction of reactor building, turbine building, water intake and drainage canal was performed on a relatively large scale and a big share of whole schedule. This article summarized basic technologies to shorten construction period for reactor building/turbine building and water intake and drainage canal. Advanced methods of reactor building/turbine building; (1) modularization of equipment and skeleton, (2) utilization of concrete mold, reinforcing bar and steel frame, (3) precedent steel frame method and (4) steel plate reinforced concrete (SC) method, were outlined and their application examples were shown to reduce work on site and improve work efficiency. As for water intake and drainage canal construction, (1) precast concrete method, (2) SC method and (3) steel plate shell method were described with application examples. Construction procedures and problems using mega block method for water intake and drainage canal were also introduced. (T. Tanaka)

Physico-chemical properties and performance of high oleic and palm-based shortenings.

Science.gov (United States)

Ramli, Muhamad Roddy; Lin, Siew Wai; Yoo, Cheah Kien; Idris, Nor Aini; Sahri, Miskandar Mat

2008-01-01

Solid fat from fractionation of palm-based products was converted into cake shortening at different processing conditions. High oleic palm stearin with an oleic content of 48.2 % was obtained from fractionation of high oleic palm oil which was produced locally. Palm product was blended with different soft oils at pre-determined ratio and further fractionated to obtain the solid fractions. These fractions were then converted into cake shortenings named as high oleic, N1 and N2 blends. The physico-chemical properties of the experimental shortenings were compared with those of control shortenings in terms of fatty acid composition (FAC), iodine value (IV), slip melting point (SMP), solid fat content (SFC) and polymorphic forms. Unlike the imported commercial shortenings as reported by other studies and the control, experimental shortenings were trans-free. The SMP and SFC of experimental samples, except for the N2 sample, fell within the ranges of commercial and control shortenings. The IV was higher than those of domestic shortenings but lower when compared to imported and control shortenings. They were also observed to be beta tending even though a mixture of beta and beta' was observed in the samples after 3 months of storage. The shortenings were also used in the making of pound cake and sensory evaluation showed the good performance of high oleic sample as compared to the other shortenings.

Consequences of crown shortening canine teeth in Greenland sled dogs

DEFF Research Database (Denmark)

Kortegaard, H E; Anthony Knudsen, T; Dahl, S

2015-01-01

OBJECTIVES: To evaluate the consequences of crown shortening, focusing on the prevalence of pulp exposure and periapical pathology in Greenland sled dogs that had had their canine crowns shortened at an early age. METHODS: Five cadaver heads and 54 sled dogs underwent an oral examination for dental...... fractures and pulp exposure of canines. All canines were radiographed and evaluated for periapical pathology. RESULTS: The prevalence of canine pulp exposure in 12 (5 heads and 7 dogs) crown shortened dogs was 91 · 7%, and 21 · 3% in 47 not-crown shortened dogs. A significant (P pulp...... exposure of the canines in the crown shortened group compared to the not-crown shortened group was seen with a relative risk of 4 · 3 on a dog basis and a relative risk of 12 · 2 on a tooth basis. In dogs with pulp exposure of canines (n = 51) the prevalence of periapical pathology was 82 · 4%, but only 0...

A MIQE-compliant real-time PCR assay for Aspergillus detection.

Directory of Open Access Journals (Sweden)

Gemma L Johnson

Full Text Available The polymerase chain reaction (PCR is widely used as a diagnostic tool in clinical laboratories and is particularly effective for detecting and identifying infectious agents for which routine culture and microscopy methods are inadequate. Invasive fungal disease (IFD is a major cause of morbidity and mortality in immunosuppressed patients, and optimal diagnostic criteria are contentious. Although PCR-based methods have long been used for the diagnosis of invasive aspergillosis (IA, variable performance in clinical practice has limited their value. This shortcoming is a consequence of differing sample selection, collection and preparation protocols coupled with a lack of standardisation of the PCR itself. Furthermore, it has become clear that the performance of PCR-based assays in general is compromised by the inadequacy of experimental controls, insufficient optimisation of assay performance as well as lack of transparency in reporting experimental details. The recently published "Minimum Information for the publication of real-time Quantitative PCR Experiments" (MIQE guidelines provide a blueprint for good PCR assay design and unambiguous reporting of experimental detail and results. We report the first real-time quantitative PCR (qPCR assay targeting Aspergillus species that has been designed, optimised and validated in strict compliance with the MIQE guidelines. The hydrolysis probe-based assay, designed to target the 18S rRNA DNA sequence of Aspergillus species, has an efficiency of 100% (range 95-107%, a dynamic range of at least six orders of magnitude and limits of quantification and detection of 6 and 0.6 Aspergillus fumigatus genomes, respectively. It does not amplify Candida, Scedosporium, Fusarium or Rhizopus species and its clinical sensitivity is demonstrated in histological material from proven IA cases, as well as concordant PCR and galactomannan data in matched broncho-alveolar lavage and blood samples. The robustness

Time-resolved immunofluorometric assay of serum ferritin

Energy Technology Data Exchange (ETDEWEB)

Yan, Yao [China Inst. of Atomic Energy, Beijing (China)

2007-06-15

This assay is a solid phase, two-site fluoroimmunometric assay based on the direct sandwish technique. Standards or samples containing ferritin are first reacted with immobilized anti-ferritin antibodies. Then the europium-lablled antibodies are reacted with the bound antigen. The range of this assay is 2-1000 ng/mL. The analytical sentivity is better than 0.05 ng/mL. The intra-assay variation and inter-assay variation are both below 5%; This kit was compared with Wallac DELFIA kit. The correlation is r=0.96. (authors)

[Quantitative fluorogenic real-time PCR assay for respiratory syncytial virus detection].

Science.gov (United States)

Zhang, Qi-wei; You, Shang-you; Sun, Ji-min; Wu, Qi; Yu, Chun-hua; Zhang, Chu-yu

2005-07-01

To Establish a rapid and objective quantitative fluorogenic real-time PCR assay for early detection of human respiratory syncytial virus (hRSV). Two pairs of primers and one TaqMan Fluorogenic probe that are specific for the recognition of the most conservative N gene of hRSV for virus detection with LighCycler PCR in 93 nasopharyngeal secretion specimens collected from infants and young children. The assay was compared with virus isolation, routine PCR, nested PCR, and enzyme-linked immunosorbent assay (ELISA). This TaqMan assay had a sensitivity of 1 x 10(2) cDNA copies/microl with a dynamic range between 1 x 10(2) and 1 x 10(7) cDNA copies/microl, which was the same as that of nested PCR, but 10 times more sensitive than routine PCR. The specificity of the assay was evaluated by comparing hRSV with polivirus type 1, coxsackie virus type 2, influenza A, influenza B and adenovirus type 7. A PCR product of the expected size (195 bp) was produced and fluorescence signal detected for hRSV, but not for any of the other viruses. The results in LightCycler and Rotor-Gene instrument were consistent. Forty-four specimens (43.9%) were hRSV-positive with this assay and 4 (4/93,4.3%) were hRSV-positive with ELISA, showing rather low correlation between the two methods. No visible relation was found between the concentration of hRSV RNA and severity of the disease. This assay is rapid, sensitive, specific and quantitative, and has the potential of wide application for early diagnosis of hRSV infection and evaluation of the therapeutic effect.

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.

Development of a Rapid Insulin Assay by Homogenous Time-Resolved Fluorescence.

Directory of Open Access Journals (Sweden)

Zachary J Farino

Full Text Available Direct measurement of insulin is critical for basic and clinical studies of insulin secretion. However, current methods are expensive and time-consuming. We developed an insulin assay based on homogenous time-resolved fluorescence that is significantly more rapid and cost-effective than current commonly used approaches. This assay was applied effectively to an insulin secreting cell line, INS-1E cells, as well as pancreatic islets, allowing us to validate the assay by elucidating mechanisms by which dopamine regulates insulin release. We found that dopamine functioned as a significant negative modulator of glucose-stimulated insulin secretion. Further, we showed that bromocriptine, a known dopamine D2/D3 receptor agonist and newly approved drug used for treatment of type II diabetes mellitus, also decreased glucose-stimulated insulin secretion in islets to levels comparable to those caused by dopamine treatment.

A study on occlusal stability in shortened dental arches.

Science.gov (United States)

Sarita, Paulo T N; Kreulen, Cees M; Witter, Dick J; van't Hof, Martin; Creugers, Nico H J

2003-01-01

The aim of this study was to verify the hypothesis that shortened dental arches constitute a risk to occlusal stability. Using cluster samples, 725 subjects with shortened dental arches comprising intact anterior regions and zero to eight occluding pairs of posterior teeth and 125 subjects with complete dental arches were selected. Subjects with shortened dental arches were classified into eight categories according to arch length and symmetry. Parameters for occlusal stability were interdental spacing, occlusal tooth wear, occlusal contact of incisors in intercuspal position, and vertical and horizontal overlap. Additionally, tooth mobility and overeruption of unopposed teeth were assessed. Influence of independent variables (dental arch category, age, gender, and residence) on the parameters for occlusal stability was assessed by one-way ANOVA and Tukey's multiple range tests. Extreme shortened dental arches (zero to two pairs of occluding premolars) had significantly more interdental spacing, occlusal contact of incisors, and vertical overlap compared to complete dental arches. Occlusal wear and prevalence of mobile teeth were highest in these categories. The category with three to four occluding premolars had significantly more interdental spacing and, for the older age group, more anterior teeth in occlusal contact compared to complete dental arches. Age was consistently associated with increased changes in occlusal integrity. Signs of increased risk to occlusal stability seemed to occur in extreme shortened dental arches, whereas no such evidence was found for intermediate categories of shortened dental arches.

Graphene oxide-loaded shortening as an environmentally friendly heat transfer fluid with high thermal conductivity

Directory of Open Access Journals (Sweden)

Vongsetskul Thammasit

2017-01-01

Full Text Available Graphene oxide-loaded shortening (GOS, an environmentally friendly heat transfer fluid with high thermal conductivity, was successfully prepared by mixing graphene oxide (GO with a shortening. Scanning electron microscopy revealed that GO particles, prepared by the modified Hummer’s method, dispersed well in the shortening. In addition, the latent heat of GOS decreased while their viscosity and thermal conductivity increased with increasing the amount of loaded GO. The thermal conductivity of the GOS with 4% GO was higher than that of pure shortening of ca. three times, from 0.1751 to 0.6022 W/mK, and increased with increasing temperature. The GOS started to be degraded at ca. 360°C. After being heated and cooled at 100°C for 100 cycles, its viscosity slightly decreased and no chemical degradation was observed. Therefore, the prepared GOS is potentially used as environmentally friendly heat transfer fluid at high temperature.

Is the time between onset of pain and restoration of patency of infarct-related artery shortened in patients with myocardial infarction? The effects of the Kielce Region System for Optimal Management of Acute Myocardial Infarction

Directory of Open Access Journals (Sweden)

Marcin Sadowski

2014-09-01

Full Text Available Introduction : The importance of delay in the restoration of infarct-related artery patency in patients with myocardial infarction was discussed, and actions were undertaken in the Kielce Region aimed at shortening this time within the System for Optimal Management of Acute Myocardial Infarction. Aim of the research: To evaluate the effectiveness of shortening time delays during transport of patients and diagnostics of myocardial infarction in the Kielce Region. Material and methods: Time delays were analysed in 5,934 patients with ST-segment elevation myocardial infarction (STEMI, hospitalised in cardiology wards with interventional cardiology on 24-hour duty, during the period 2008–2012. Time delays were analysed between the onset of myocardial infarction pain and undertaking treatment – T1 and T2 time – within which a patient with myocardial infarction, after admission to hospital, has intervention performed on infarct-related coronary artery. Results : During the period 2008–2012, the median T1 time was successfully shortened from 355 to 203 min, and the T2 time from 101 to 48 min. Conclusions: The effectiveness of the system was confirmed, and the necessity for further improvement of the system indicated.

Monte carlo feasibility study of an active neutron assay technique for full-volume UF{sub 6} cylinder assay using a correlated interrogation source

Energy Technology Data Exchange (ETDEWEB)

Miller, Karen A., E-mail: kamiller@lanl.gov [Los Alamos National Laboratory, Los Alamos, P.O. Box 1663 MS E540, NM 87545 (United States); Menlove, Howard O.; Swinhoe, Martyn T.; Marlow, Johnna B. [Los Alamos National Laboratory, Los Alamos, P.O. Box 1663 MS E540, NM 87545 (United States)

2013-03-01

Uranium cylinder assay plays an important role in the nuclear material accounting at gas centrifuge enrichment plants. The Passive Neutron Enrichment Meter (PNEM) was designed to determine uranium mass and enrichment in 30B and 48Y cylinders using total neutron and coincidence counting in the passive mode. 30B and 48Y cylinders are used to hold bulk UF{sub 6} feed, product, and tails at enrichment plants. In this paper, we report the results of a Monte-Carlo-based feasibility study for an active uranium cylinder assay system based on the PNEM design. There are many advantages of the active technique such as a shortened count time and a more direct measure of {sup 235}U content. The active system is based on a modified PNEM design and uses a {sup 252}Cf source as the correlated, active interrogation source. We show through comparison with a random AmLi source of equal strength how the use of a correlated driver significantly boosts the active signal and reduces the statistical uncertainty. We also discuss ways in which an active uranium cylinder assay system can be optimized to minimize background from {sup 238}U fast-neutron induced fission and direct counts from the interrogation source.

A temperature control method for shortening thermal cycling time to achieve rapid polymerase chain reaction (PCR) in a disposable polymer microfluidic device

DEFF Research Database (Denmark)

Bu, Minqiang; Perch-Nielsen, Ivan R.; Sørensen, Karen Skotte

2013-01-01

steps to achieve a rapid ramping between the temperature steps for DNA denaturation, annealing and extension. The temperature dynamics within the microfluidic PCR chamber was characterized and the overshooting and undershooting parameters were optimized using the temperature-dependent fluorescence......We present a temperature control method capable of effectively shortening the thermal cycling time of polymerase chain reaction (PCR) in a disposable polymer microfluidic device with an external heater and a temperature sensor. The method employs optimized temperature overshooting and undershooting...

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.

Matrix effects on the crystallization behaviour of butter and roll-in shortening in laminated bakery products.

Science.gov (United States)

Mattice, Kristin D; Marangoni, Alejandro G

2017-06-01

Two hydrogenated roll-in shortenings (A & B), one non-hydrogenated roll-in shortening and butter were used to prepare croissants. The impact of the laminated dough matrix on fat crystallization was then investigated using powder X-ray diffraction (XRD), pulsed nuclear magnetic resonance (p-NMR) and differential scanning calorimetry (DSC). The fat contained within a croissant matrix has never before been analyzed using these techniques. In each case, XRD revealed that the polymorphism of a roll-in fat will be different when baked within the dough matrix than when simply heated and cooled on its own. Both hydrogenated roll-in shortenings and butter experienced only minor changes, largely retaining their β' polymorphs, but the non-hydrogenated shortening experienced significant conversion from β' to the β form. However, this conversion did not take place immediately upon cooling, but after approximately 24h of storage time. The fat contained within the croissants exhibited a significantly lower SFC than the same fats in bulk. Further, DSC results demonstrated that a greater temperature was required to completely melt all of the fat in a croissant than the same fat in bulk, observed visually as broader peaks in the melting endotherms. Analysis of croissant firmness over storage time, measured as the maximum force required to cut a croissant was used as an indication of potential sensory consequences. Results suggested that only croissants prepared with non-hydrogenated shortening experienced significant changes in firmness over one week of storage. These results indicate that there is an interaction between the shortenings and the ingredients of the croissant matrix, and given the differences observed between roll-in fats used, the extent of interaction is potentially influenced by the composition of the roll-in fat itself. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synergistic nonuniform shortening of atrial refractory period induced by autonomic stimulation.

Science.gov (United States)

Takei, M; Furukawa, Y; Narita, M; Ren, L M; Karasawa, Y; Murakami, M; Chiba, S

1991-12-01

We investigated the nonuniform effects of autonomic nerve stimulation of the effective refractory period (ERP) of the right atrium in the anesthetized dog. Stimulation of the discrete intracardiac sympathetic nerves to the sinoatrial (SA) nodal region uniformly shortened ERPs at three sites in the right atrium after administration of atropine. Right ansa subclavia (RS) stimulation similarly shortened ERPs in the absence of atropine. Stimulation of the discrete intracardiac parasympathetic nerves to the SA nodal region (SAP stimulation) shortened ERPs of the right atrium in a nonuniform manner. Simultaneous RS and SAP stimulation additively shortened ERPs at each site and decreased sinus rate much more than SAP stimulation alone. Shortening of ERP induced by SAP stimulation was greater than that induced by RS stimulation at similar absolute changes in heart rate. These results suggest that simultaneous activation of sympathetic and parasympathetic nerves nonuniformly shortens the ERP in the right atrium as the algebraic sum of the individual responses to each stimulation. However, parasympathetics exert the principal neural control over atrial ERP.

Emerging Technologies and Generic Assays for the Detection of Anti-Drug Antibodies

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Michael A. Partridge

2016-01-01

Full Text Available Anti-drug antibodies induced by biologic therapeutics often impact drug pharmacokinetics, pharmacodynamics response, clinical efficacy, and patient safety. It is critical to assess the immunogenicity risk of potential biotherapeutics in producing neutralizing and nonneutralizing anti-drug antibodies, especially in clinical phases of drug development. Different assay methodologies have been used to detect all anti-drug antibodies, including ELISA, radioimmunoassay, surface plasmon resonance, and electrochemiluminescence-based technologies. The most commonly used method is a bridging assay, performed in an ELISA or on the Meso Scale Discovery platform. In this report, we aim to review the emerging new assay technologies that can complement or address challenges associated with the bridging assay format in screening and confirmation of ADAs. We also summarize generic anti-drug antibody assays that do not require drug-specific reagents for nonclinical studies. These generic assays significantly reduce assay development efforts and, therefore, shorten the assay readiness timeline.

Instability during bunch shortening of an electron-cooled beam

Directory of Open Access Journals (Sweden)

M. Takanaka

2003-10-01

Full Text Available Bunch shortening causes an electron-cooled beam to be space charge dominated at low energies. Instability during the bunch shortening has been studied using a particle-tracking program where the 3D space-charge field due to the beam is calculated with a simplifying model.

A Shortened Stress Measure in Military Nursing Personnel

Science.gov (United States)

2017-10-17

REPORT TYPE 3. DATES COVERED (From- To) 10/17/2017 Abstract 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER A Shortened Stress Measure in Military...Psychology 14. ABSTRACT A Shortened Stress Measure with Military Nursing Personnel Abstract Stress is a psychological construct with important...consequences for human health. A substantial number of stress measures are available that vary in length and dimensionality. The purpose of this study was to

Shortened protocol in practical [11C]SA4503-PET studies for sigma1 receptor quantification

International Nuclear Information System (INIS)

Sakata, Muneyuki; Kimura, Yuichi; Ishikawa, Masatomo; Oda, Keiichi; Ishii, Kenji; Ishiwata, Kiichi; Naganawa, Mika; Hashimoto, Kenji; Chihara, Kunihiro

2008-01-01

In practical positron emission tomography (PET) diagnosis, a shortened protocol is preferred for patients with brain disorders. In this study, the applicability of a shortened protocol as an alternative to the 90-min PET scan with [ 11 C]SA4503 for quantitative sigma 1 receptor measurement was investigated. Tissue time-activity curves of 288 regions of interest in the brain from 32 [ 11 C]SA4503-PET scans of 16 healthy subjects prior to and following administration of a selective serotonin reuptake inhibitor (fluvoxamine or paroxetine) were applied to two algorithms of quantitative analysis; binding potential (BP) was derived from compartmental analysis based on nonlinear estimation, and total distribution volume (tDV) was derived from Logan plot analysis. As a result, although both BP and tDV tended to be underestimated by the shortened method, the estimates from the shortened protocol had good linear relationships with those of the full-length protocol. In conclusion, if approximately 10% differences in the estimated results are acceptable for a specific purpose, then a 60-min measurement protocol is capable of providing reliable results. (author)

A novel temperature control method for shortening thermal cycling time to achieve rapid polymerase chain reaction (PCR) in a disposable polymer microfluidic device

DEFF Research Database (Denmark)

Bu, Minqiang; R. Perch-Nielsen, Ivan; Sørensen, Karen Skotte

steps to achieve a rapid ramping between the temperature steps for DNA denaturation, annealing and extension. The temperature dynamics within the microfluidic PCR chamber was characterized and the overshooting and undershooting parameters were optimized using the temperature dependent fluorescence......We present a new temperature control method capable of effectively shortening the thermal cycling time of polymerase chain reaction (PCR) in a disposable polymer microfluidic device with external heater and temperature sensor. The method employs optimized temperature overshooting and undershooting...

Investigation on shortening fabrication process of instrumented irradiation capsule of JMTR

International Nuclear Information System (INIS)

Nagata, Hiroshi; Inoue, Shuichi; Yamaura, Takayuki; Tsuchiya, Kunihiko; Nagao, Yoshiharu

2013-06-01

Refurbishment of The Japan Materials Testing Reactor (JMTR) was completed in FY2010. For damage caused by the 2011 off the Pacific coast of Tohoku Earthquake, the repair of facilities was completed in October 2012. Currently, the JMTR is in preparation for restart. Irradiation tests for LWRs safety research, science and technologies and production of RI for medical diagnosis medicine, etc. are expected after the JMTR restart. On the other hand, aiming at the attractive irradiation testing reactor, the usability improvement has been discussed. As a part of the usability improvement, shortening of turnaround time to get irradiation results from an application for irradiation use was discussed focusing on the fabrication process of irradiation capsules, where the fabrication process was analyzed and reviewed by referring a trial fabrication of the mockup capsule. As a result, it was found that the turnaround time can be shortened 2 months from fabrication period of 6 months with communize of irradiation capsule parts, application of ready-made instrumentation including the sheath heater, reconsideration of inspection process, etc. (author)

Comparative study of β-glucan induced respiratory burst measured by nitroblue tetrazolium assay and real-time luminol-enhanced chemiluminescence assay in common carp (Cyprinus carpio L.).

Science.gov (United States)

Vera-Jimenez, N I; Pietretti, D; Wiegertjes, G F; Nielsen, M E

2013-05-01

The respiratory burst is an important feature of the immune system. The increase in cellular oxygen uptake that marks the initiation of the respiratory burst is followed by the production of reactive oxygen species (ROS) such as superoxide anion and hydrogen peroxide which plays a role in the clearance of pathogens and tissue regeneration processes. Therefore, the respiratory burst and associated ROS constitute important indicators of fish health status. This paper compares two methods for quantitation of ROS produced during the respiratory burst in common carp: the widely used, single-point measurement based on the intracellular reduction of nitroblue tetrazolium (NBT) and a real-time luminol-enhanced assay based on the detection of native chemiluminescence. Both assays allowed for detection of dose-dependent changes in magnitude of the respiratory burst response induced by β-glucans in head kidney cells of carp. However, whereas the NBT assay was shown to detect the production of only superoxide anions, the real-time luminol-enhanced assay could detect the production of both superoxide anions and hydrogen peroxide. Only the chemiluminescence assay could reliably record the production of ROS on a real-time scale at frequent and continual time intervals for time course experiments, providing more detailed information on the respiratory burst response. The real-time chemiluminescence assay was used to measure respiratory burst activity in macrophage and neutrophilic granulocyte-enriched head kidney cell fractions and total head kidney cell suspensions and proved to be a fast, reliable, automated multiwell microplate assay to quantitate fish health status modulated by β-glucans. Copyright © 2013 Elsevier Ltd. All rights reserved.

Do right-ventricular trabeculae gain energetic advantage from having a greater velocity of shortening?

Science.gov (United States)

Pham, Toan; Han, June-Chiew; Taberner, Andrew; Loiselle, Denis

2017-10-15

We designed a study to test whether velocity of shortening in right-ventricular tissue preparations is greater than that of the left side under conditions mimicking those encountered by the heart in vivo. Our experiments allowed us to explore whether greater velocity of shortening results in any energetic advantage. We found that velocity of shortening was higher in the rat right-ventricular trabeculae. These results at the tissue level seem paradoxical to the velocity of ventricular ejection at the organ level, and are not always in accord with shortening of unloaded cells. Despite greater velocity of shortening in right-ventricular trabeculae, they neither gained nor lost advantage with respect to both mechanical efficiency and the heat generated during shortening. Our study aimed to ascertain whether the interventricular difference of shortening velocity, reported for isolated cardiac tissues in vitro, affects interventricular mechano-energetic performance when tested under physiological conditions using a shortening protocol designed to mimic those in vivo. We isolated trabeculae from both ventricles of the rat, mounted them in a calorimeter, and performed experiments at 37°C and 5 Hz stimulus frequency to emulate conditions of the rat heart in vivo. Each trabecula was subjected to two experimental protocols: (i) isotonic work-loop contractions at a variety of afterloads, and (ii) isometric contractions at a variety of preloads. Velocity of shortening was calculated from the former protocol during the isotonic shortening phase of the contraction. Simultaneous measurements of force-length work and heat output allowed calculation of mechanical efficiency. The shortening-dependent thermal component was quantified from the difference in heat output between the two protocols. Our results show that both extent of shortening and velocity of shortening were higher in trabeculae from the right ventricle. Despite these differences, trabeculae from both ventricles

Improvement of a real-time RT-PCR assay for the detection of enterovirus RNA

Directory of Open Access Journals (Sweden)

Bruynseels Peggy

2009-07-01

Full Text Available Abstract We describe an improvement of an earlier reported real-time RT-PCR assay for the detection of enterovirus RNA, based on the 5' exonuclease digestion of a dual-labeled fluorogenic probe by Taq DNA polymerase. A different extraction method, real-time RT-PCR instrument and primer set were evaluated. Our data show that the optimized assay yields a higher sensitivity and reproducibility and resulted in a significant reduced hands-on time per sample.

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...

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.

Shortening a loop can increase protein native state entropy.

Science.gov (United States)

Gavrilov, Yulian; Dagan, Shlomi; Levy, Yaakov

2015-12-01

Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. © 2015 Wiley Periodicals, Inc.

Interdependence of initial cell density, drug concentration and exposure time revealed by real-time impedance spectroscopic cytotoxicity assay

DEFF Research Database (Denmark)

Caviglia, Claudia; Zor, Kinga; Canepa, Silvia

2015-01-01

We investigated the combined effect of the initial cell density (12 500, 35 000, 75 000, and 100 000 cells cm−2) and concentration of the anti-cancer drug doxorubicin on HeLa cells by performing timedependent cytotoxicity assays using real-time electrochemical impedance spectroscopy. A correlation...... between the rate of cell death and the initial cell seeding density was found at 2.5 μM doxorubicin concentration, whereas this was not observed at 5 or 100 μM. By sensing the changes in the cell–substrate interaction using impedance spectroscopy under static conditions, the onset of cytotoxicity...... was observed 5 h earlier than when using a standard colorimetric end-point assay (MTS) which measures changes in the mitochondrial metabolism. Furthermore, with the MTS assay no cytotoxicity was observed after 15 h of incubation with 2.5 μM doxorubicin, whereas the impedance showed at this time point cell...

Tetraplex PCR assay involving double gene-sites discriminates beef and buffalo in Malaysian meat curry and burger products.

Science.gov (United States)

Hossain, M A Motalib; Ali, Md Eaqub; Hamid, Sharifah Bee Abd; Hossain, S M Azad; Asing; Nizar, Nina Naquiah Ahmad; Uddin, Mohammad Nasir; Ali, Lokman; Asaduzzaman, Md; Akanda, Md Jahurul Haque

2017-06-01

Replacement of beef by buffalo and vice versa is frequent in global markets, but their authentication is challenging in processed foods due to the fragmentation of most biomarkers including DNA. The shortening of target sequences through use of two target sites might ameliorate assay reliability because it is highly unlikely that both targets will be lost during food processing. For the first time, we report a tetraplex polymerase chain reaction (PCR) assay targeting two different DNA regions in beef (106 and 120-bp) and buffalo (90 and 138-bp) mitochondrial genes to discriminate beef and buffalo in processed foods. All targets were stable under boiling, autoclaving and microwave cooking conditions. A survey in Malaysian markets revealed 71% beef curries contained buffalo but there was no buffalo in beef burgers. The assay detected down to 0.01ng DNA and 1% meat in admixed and burger products. Copyright © 2016 Elsevier Ltd. All rights reserved.

Leucocyte Telomere Shortening in relation to Newly Diagnosed Type 2 Diabetic Patients with Depression

Directory of Open Access Journals (Sweden)

Zhelong Liu

2014-01-01

Full Text Available The goal of this study is to investigate the association between oxidative stress and telomere length shortening in the comorbid depression and diabetes. Therefore, 71 patients with newly diagnosed type 2 diabetes (T2D and 52 subjects with normal glycemic level (control, Ctrl were enrolled. Depressive status was identified with the Depression Subscale of Hospital Anxiety and Depression Scale (HADS-D. Leukocyte telomere length ratio (T/S ratio was determined with quantitative PCR. Oxidative stress status was evaluated with 8-hydroxy-desoxyguanosine (8-OHdG assay kit. Some other biochemical blood testing was also performed. The data showed that T2D patients had higher proportion of depression evaluated by the HADS-D (x2=4.196, P=0.041. T/S ratio was significantly negatively correlated with 8-OHdG, HADS-D, age, HbA1c, FPG, and HOMA-IR. In addition, HADS-D was significantly positively correlated with HbA1c, FPG, HOMA-IR, and 8-OHdG. Both HADS-D and 8-OHdG were the major independent predictors for T/S ratio. This study indicates that oxidative stress contributes to both telomere length shortening and depression development in newly diagnosed type 2 diabetic patients, while in depression status, some other mechanisms besides oxidative stress may also affect the telomere length.

Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens.

Science.gov (United States)

Rheem, Insoo; Park, Joowon; Kim, Tae-Hyun; Kim, Jong Wan

2012-11-01

In this study, we evaluated the analytical performance and clinical potential of a one-step multiplex real-time PCR assay for the simultaneous detection of 14 types of respiratory viruses using the AdvanSure RV real-time PCR Kit (LG Life Sciences, Korea). Three hundred and twenty clinical specimens were tested with the AdvanSure RV real-time PCR Kit and conventional multiplex reverse transcription (RT)-PCR assay. The assay results were analyzed and the one-step AdvanSure RV real-time PCR Kit was compared with the conventional multiplex RT-PCR assay with respect to the sensitivity and specificity of the detection of respiratory viruses. The limit of detection (LOD) was 1.31 plaque-forming units (PFU)/mL for human rhinoviruses (hRVs), 4.93 PFU/mL for human coronavirus HCoV-229E/NL63, 2.67 PFU/mL for human coronavirus HCoV-OC43, 18.20 PFU/mL for parainfluenza virus 1 (PIV)-1, 24.57 PFU/mL for PIV-2, 1.73 PFU/mL for PIV-3, 1.79 PFU/mL for influenza virus group (Flu) A, 59.51 PFU/mL for FluB, 5.46 PFU/mL for human respiratory syncytial virus (hRSV)-A, 17.23 PFU/mL for hRSV-B, 9.99 PFU/mL for human adenovirus (ADVs). The cross-reactivity test for this assay against 23 types of non-respiratory viruses showed negative results for all viruses tested. The agreement between the one-step AdvanSure multiplex real-time PCR assay and the conventional multiplex RT-PCR assay was 98%. The one-step AdvanSure RV multiplex real-time PCR assay is a simple assay with high potential for specific, rapid and sensitive laboratory diagnosis of respiratory viruses compared to conventional multiplex RT-PCR.

Limb shortening osteotomy in a patient with achondroplasia and leg length difference after total hip arthroplasty

Directory of Open Access Journals (Sweden)

Christian L. Galata

2013-07-01

Full Text Available Introduction: Achondroplasia is the most common reason for disproportionate short stature. Normally, orthopedic limb lengthening procedures must be discussed in the course of this genetic disorder and have been successful in numerous achondroplastic patients in the past. In some cases, the disease may lead to leg length differences with need for surgical correction. Case Report: We report a case of achondroplastic dysplastic coxarthrosis with symptomatic leg length difference after bilateral total hip arthroplasty in a 52-year-old female patient, in which a distal femoral shortening osteotomy was successfully performed. Conclusion: Femoral shortening osteotomy is very uncommon in patients with achondroplasia. We conclude, however, that in rare cases it can be indicated and provide the advantage of shorter operation time, less perioperative complications and faster recovery compared to leg lengthening procedures. Keywords: Achondroplasia, dysplastic coxarthrosis, limb shortening, distal femur osteotomy.

Rapid bioassay-guided screening of toxic substances in vegetable oils that shorten the life of SHRSP rats

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Lewandowski Paul

2010-02-01

Full Text Available Abstract It has been consistently reported that vegetable oils including canola oil have a life shortening effect in Stroke-Prone Spontaneously Hypertensive Rats (SHRSP and this toxic effect is not due to the fatty acid composition of the oil. Although it is possible that the phytosterol content or type of phytosterol present in vegetable oils may play some role in the life shortening effect observed in SHRSP rats this is still not completely resolved. Furthermore supercritical CO2 fractionation of canola oil with subsequent testing in SHRSP rats identified safe and toxic fractions however, the compounds responsible for life shortening effect were not characterised. The conventional approach to screen toxic substances in oils using rats takes more than six months and involves large number of animals. In this article we describe how rapid bioassay-guided screening could be used to identify toxic substances derived from vegetable oils and/or processed foods fortified with vegetable oils. The technique incorporates sequential fractionation of oils/processed foods and subsequent treatment of human cell lines that can be used in place of animal studies to determine cytotoxicity of the fractions with structural elucidation of compounds of interest determined via HPLC-MS and GC-MS. The rapid bioassay-guided screening proposed would require two weeks to test multiple fractions from oils, compared with six months if animal experiments were used to screen toxic effects. Fractionation of oil before bio-assay enhances the effectiveness of the detection of active compounds as fractionation increases the relative concentration of minor components.

Technical note: Time-resolved immunofluorometric assay for growth hormone in ruminants

DEFF Research Database (Denmark)

Løvendahl, P.; Adamsen, J.; Lund, Regina Teresa

2003-01-01

for 4 h at 25degreesC. Plates were then washed six times, incubated for 5 to 10 min with 250 muL of enhancement solution, and fluorescence read with a time-resolved fluorometer. The sensitivity of the assay was 0.1 ng/mL, and the working range was 0.2 to 200 ng/mL. Recovery of quantitative amounts...

A real time chemotaxis assay unveils unique migratory profiles amongst different primary murine macrophages.

Directory of Open Access Journals (Sweden)

Asif J Iqbal

Full Text Available Chemotaxis assays are an invaluable tool for studying the biological activity of inflammatory mediators such as CC chemokines, which have been implicated in a wide range of chronic inflammatory diseases. Conventional chemotaxis systems such as the modified Boyden chamber are limited in terms of the data captured given that the assays are analysed at a single time-point. We report the optimisation and validation of a label-free, real-time cell migration assay based on electrical cell impedance to measure chemotaxis of different primary murine macrophage populations in response to a range of CC chemokines and other chemoattractant signalling molecules. We clearly demonstrate key differences in the migratory behavior of different murine macrophage populations and show that this dynamic system measures true macrophage chemotaxis rather than chemokinesis or fugetaxis. We highlight an absolute requirement for Gαi signaling and actin cytoskeletal rearrangement as demonstrated by Pertussis toxin and cytochalasin D inhibition. We also studied the chemotaxis of CD14(+ human monocytes and demonstrate distinct chemotactic profiles amongst different monocyte donors to CCL2. This real-time chemotaxis assay will allow a detailed analysis of factors that regulate macrophage responses to chemoattractant cytokines and inflammatory mediators.

A Real Time Chemotaxis Assay Unveils Unique Migratory Profiles amongst Different Primary Murine Macrophages

Science.gov (United States)

Iqbal, Asif J.; Regan-Komito, Daniel; Christou, Ivy; White, Gemma E.; McNeill, Eileen; Kenyon, Amy; Taylor, Lewis; Kapellos, Theodore S.; Fisher, Edward A.; Channon, Keith M.; Greaves, David R.

2013-01-01

Chemotaxis assays are an invaluable tool for studying the biological activity of inflammatory mediators such as CC chemokines, which have been implicated in a wide range of chronic inflammatory diseases. Conventional chemotaxis systems such as the modified Boyden chamber are limited in terms of the data captured given that the assays are analysed at a single time-point. We report the optimisation and validation of a label-free, real-time cell migration assay based on electrical cell impedance to measure chemotaxis of different primary murine macrophage populations in response to a range of CC chemokines and other chemoattractant signalling molecules. We clearly demonstrate key differences in the migratory behavior of different murine macrophage populations and show that this dynamic system measures true macrophage chemotaxis rather than chemokinesis or fugetaxis. We highlight an absolute requirement for Gαi signaling and actin cytoskeletal rearrangement as demonstrated by Pertussis toxin and cytochalasin D inhibition. We also studied the chemotaxis of CD14+ human monocytes and demonstrate distinct chemotactic profiles amongst different monocyte donors to CCL2. This real-time chemotaxis assay will allow a detailed analysis of factors that regulate macrophage responses to chemoattractant cytokines and inflammatory mediators. PMID:23516549

Rapid enzyme-linked immunosorbent assay (ELISA) for Aspergillus fumigatus antibodies.

OpenAIRE

Richardson, M D; Stubbins, J M; Warnock, D W

1982-01-01

A rapid enzyme-linked immunosorbent assay (ELISA) where component incubation periods were shortened to one hour, was compared with agar gel double diffusion (AGDD) and a standard ELISA procedure for detecting antibodies to Aspergillus fumigatus in 28 asthmatic patients with suspected allergic aspergillosis. Using two A fumigatus antigens the rapid ELISA compared well with AGDD and the standard ELISA method. Eleven sera that reacted with both antigens in AGDD were all positive against antigen ...

Development and validation of a real-time PCR assay for the detection of anguillid herpesvirus 1.

Science.gov (United States)

van Beurden, S J; Voorbergen-Laarman, M A; Roozenburg, I; van Tellingen, J; Haenen, O L M; Engelsma, M Y

2016-01-01

Anguillid herpesvirus 1 (AngHV1) causes a haemorrhagic disease with increased mortality in wild and farmed European eel, Anguilla anguilla (L.) and Japanese eel Anguilla japonica, Temminck & Schlegel). Detection of AngHV1 is currently based on virus isolation in cell culture, antibody-based typing assays or conventional PCR. We developed, optimized and concisely validated a diagnostic TaqMan probe based real-time PCR assay for the detection of AngHV1. The primers and probe target AngHV1 open reading frame 57, encoding the capsid protease and scaffold protein. Compared to conventional PCR, the developed real-time PCR is faster, less labour-intensive and has a reduced risk of cross-contamination. The real-time PCR assay was shown to be analytically sensitive and specific and has a high repeatability, efficiency and r(2) -value. The diagnostic performance of the assay was determined by testing 10% w/v organ suspensions and virus cultures from wild and farmed European eels from the Netherlands by conventional and real-time PCR. The developed real-time PCR assay is a useful tool for the rapid and sensitive detection of AngHV1 in 10% w/v organ suspensions from wild and farmed European eels. © 2015 John Wiley & Sons Ltd.

The development and application of the two real-time RT-PCR assays to detect the pathogen of HFMD.

Directory of Open Access Journals (Sweden)

Aili Cui

Full Text Available Large-scale Hand, Foot, and Mouth Disease (HFMD outbreaks have frequently occurred in China since 2008, affecting more than one million children and causing several hundred children deaths every year. The pathogens of HFMD are mainly human enteroviruses (HEVs. Among them, human enterovirus 71 (HEV71 and coxsackievirus A16 (CVA16 are the most common pathogens of HFMD. However, other HEVs could also cause HFMD. To rapidly detect HEV71 and CVA16, and ensure detection of all HEVs causing HFMD, two real-time hybridization probe-based RT-PCR assays were developed in this study. One is a multiplex real-time RT-PCR assay, which was developed to detect and differentiate HEV71 specifically from CVA16 directly from clinical specimens within 1-2 h, and the other is a broad-spectrum real-time RT-PCR assay, which targeted almost all HEVs. The experiments confirmed that the two assays have high sensitivity and specificity, and the sensitivity was up to 0.1 TCID50/ml for detection of HEVs, HEV71, and CVA16, respectively. A total of 213 clinical specimens were simultaneously detected by three kinds of assays, including the two real-time RT-PCR assays, direct conventional RT-PCR assay, and virus isolation assay on human rhabdomyosarcoma cells (RD cells. The total positive rate of both HEV71 and CVA16 was 69.48% with real-time RT-PCR assay, 47.42% with RT-PCR assay, and 34.58% with virus isolation assay. One HFMD clinical specimen was positive for HEV, but negative for HEV71 or CVA16, which was identified as Echovirus 11 (Echo11 by virus isolation, RT-PCR, and sequencing for the VP1 gene. The two real-time RT-PCR assays had been applied in 31 provincial HFMD labs to detect the pathogens of HFMD, which has contributed to the rapid identification of the pathogens in the early stages of HFMD outbreaks, and helped to clarify the etiologic agents of HFMD in China.

Compatibility of selected plant-based shortening as lard substitute: microstructure, polymorphic forms and textural properties

Directory of Open Access Journals (Sweden)

N. A.M. Yanty

2017-03-01

Full Text Available A study was carried out to determine the compatibility of three plant-based shortening mixtures to lard shortening (LD in terms of microstructure, polymorphic forms, and textural properties. The shortenings of binary, ternary, and quaternary fat mixtures were prepared according to a standard procedure by blending mee fat (MF with palm stearin (PS in a 99:1 (w/w ratio; avocado fat (Avo with PS and cocoa butter (CB in a 84:7:9 (w/w ratio; palm oil (PO with PS, soybean oil (SBO and CB in a 38:5:52:5 (w/w ratio, respectively. The triacylglycerol composition, polymorphic forms, crystal morphology, and textural properties of the shortening were evaluated. This study found that all three plant-based shortenings and LD shortening were similar with respect to their consistency, hardness and compression and adhesiveness values. However, all plant-based shortening was found to be dissimilar to LD shortening with respect to microstructure.

Compatibility of selected plant-based shortening as lard substitute: microstructure, polymorphic forms and textural properties

International Nuclear Information System (INIS)

Yanty, N.A.M.; Marikkar, J.M.N.; Miskandar, M.S.; Bockstaele, F. Van; Dewettinck, K.; Nusantoro, B.P.

2017-01-01

A study was carried out to determine the compatibility of three plant-based shortening mixtures to lard shortening (LD) in terms of microstructure, polymorphic forms, and textural properties. The shortenings of binary, ternary, and quaternary fat mixtures were prepared according to a standard procedure by blending mee fat (MF) with palm stearin (PS) in a 99:1 (w/w) ratio; avocado fat (Avo) with PS and cocoa butter (CB) in a 84:7:9 (w/w) ratio; palm oil (PO) with PS, soybean oil (SBO) and CB in a 38:5:52:5 (w/w) ratio, respectively. The triacylglycerol composition, polymorphic forms, crystal morphology, and textural properties of the shortening were evaluated. This study found that all three plant-based shortenings and LD shortening were similar with respect to their consistency, hardness and compression and adhesiveness values. However, all plant-based shortening was found to be dissimilar to LD shortening with respect to microstructure. [es

Quantitative Real-Time PCR using the Thermo Scientific Solaris qPCR Assay

Science.gov (United States)

Ogrean, Christy; Jackson, Ben; Covino, James

2010-01-01

The Solaris qPCR Gene Expression Assay is a novel type of primer/probe set, designed to simplify the qPCR process while maintaining the sensitivity and accuracy of the assay. These primer/probe sets are pre-designed to >98% of the human and mouse genomes and feature significant improvements from previously available technologies. These improvements were made possible by virtue of a novel design algorithm, developed by Thermo Scientific bioinformatics experts. Several convenient features have been incorporated into the Solaris qPCR Assay to streamline the process of performing quantitative real-time PCR. First, the protocol is similar to commonly employed alternatives, so the methods used during qPCR are likely to be familiar. Second, the master mix is blue, which makes setting the qPCR reactions easier to track. Third, the thermal cycling conditions are the same for all assays (genes), making it possible to run many samples at a time and reducing the potential for error. Finally, the probe and primer sequence information are provided, simplifying the publication process. Here, we demonstrate how to obtain the appropriate Solaris reagents using the GENEius product search feature found on the ordering web site (www.thermo.com/solaris) and how to use the Solaris reagents for performing qPCR using the standard curve method. PMID:20567213

Effects of rapid shortening on rate of force regeneration and myoplasmic [Ca2+] in intact frog skeletal muscle fibres

Science.gov (United States)

Vandenboom, R; Claflin, D R; Julian, F J

1998-01-01

The effect of rapid shortening on rate of force regeneration (dF/dtR) was examined in single, intact frog (Rana temporaria) skeletal muscle fibres (3·0 °C). Step releases leading to unloaded shortening were applied after 500 ms of stimulation, during the plateau of an isometric tetanus. Initial mean sarcomere length ranged from 2·05 to 2·35 μm; force regeneration after shortening was at 2·00 μm.Values for dF/dtR following a 25 nm half-sarcomere−1 release were 3·17 ± 0·17 (mean ± s.e.m., n= 8) times greater than the initial rate of rise of force before release (dF/dtI). As release size was increased from 25 to 175 nm half-sarcomere−1, the relationship between release size and dF/dtR decreased sharply before attaining a plateau value that was 1·34 ± 0·09 times greater than dF/dtI. Despite wide variations in dF/dtR, the velocity of unloaded shortening remained constant (2·92 ± 0·08 μm half-sarcomere−1 s−1; n= 8) for the different release amplitudes used in this study.To investigate its role in the attenuation of dF/dtR with increased shortening, the effects of rapid ramp (constant velocity) shortening on intracellular free Ca2+ concentration ([Ca2+]i) were monitored using the Ca2+-sensitive fluorescent dye furaptra. Compared with an isometric contraction, rapid fibre shortening was associated with a transient increase in [Ca2+]i while force regeneration after shortening was associated with a transient reduction in [Ca2+]i. The greatest reductions in [Ca2+]i were associated with the largest amplitude ramps.Cross-bridge-mediated modifications of the Ca2+ affinity of troponin C (TnC) may explain the fluctuations in [Ca2+]i observed during and after ramps. Associated fluctuations in TnC Ca2+ occupancy could play a role in the reduction of dF/dtR with increasing release size. PMID:9679172

Cortical T2 signal shortening in amyotrophic lateral sclerosis is not due to iron deposits

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Hecht, M.J.; Neundoerfer, B. [University of Erlangen-Nurenberg, Department of Neurology, Erlangen (Germany); Fellner, C.; Fellner, F.A. [University of Erlangen-Nurenberg, Institute of Diagnostic Radiology, Erlangen (Germany); Landes-Nervenklinik Wagner-Jauregg, Institute of Radiology, Linz (Austria); Schmid, A. [University of Erlangen-Nurenberg, Institute of Diagnostic Radiology, Erlangen (Germany)

2005-11-01

Signal shortening of the motor cortex in T2-weighted MR images is a frequent finding in patients with amyotrophic lateral sclerosis (ALS). The cause of signal shortening in ALS is unknown, although iron deposits have been suggested. To test this hypothesis, we acquired T2*-weighted gradient-echo (GRE) MR images in addition to T2-weighted turbo spin-echo in 69 patients with ALS. Signal shortening in T2-weighted images was found in 31 patients. In T2*-weighted GRE images, only three patients had signal shortening. One patient with additional bifrontal haemorrhage had frontal but no motor cortex signal shortening. Iron deposits do not cause cortical signal shortening in patients with ALS predominantly. Other factors are presumably more important in the generation of cortical T2 shortening in ALS. (orig.)

Cortical T2 signal shortening in amyotrophic lateral sclerosis is not due to iron deposits

International Nuclear Information System (INIS)

Hecht, M.J.; Neundoerfer, B.; Fellner, C.; Fellner, F.A.; Schmid, A.

2005-01-01

Signal shortening of the motor cortex in T2-weighted MR images is a frequent finding in patients with amyotrophic lateral sclerosis (ALS). The cause of signal shortening in ALS is unknown, although iron deposits have been suggested. To test this hypothesis, we acquired T2*-weighted gradient-echo (GRE) MR images in addition to T2-weighted turbo spin-echo in 69 patients with ALS. Signal shortening in T2-weighted images was found in 31 patients. In T2*-weighted GRE images, only three patients had signal shortening. One patient with additional bifrontal haemorrhage had frontal but no motor cortex signal shortening. Iron deposits do not cause cortical signal shortening in patients with ALS predominantly. Other factors are presumably more important in the generation of cortical T2 shortening in ALS. (orig.)

Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

Science.gov (United States)

Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

2015-01-01

The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

Analytical and clinical evaluation of the Abbott RealTime hepatitis B sequencing assay.

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Huh, Hee Jae; Kim, Ji-Youn; Lee, Myoung-Keun; Lee, Nam Yong; Kim, Jong-Won; Ki, Chang-Seok

2016-12-01

Long-term nucleoside analogue (NA) treatment leads to selection for drug-resistant mutations in patients undergoing hepatitis B virus (HBV) therapy. The Abbott RealTime HBV Sequencing assay (Abbott assay; Abbott Molecular Inc., Des Plaines, IL, USA) targets the reverse transcriptase region of the polymerase gene and as such has the ability to detect NA resistance-associated mutations in HBV. We evaluated the analytical performance of the Abbott assay and compared its diagnostic performance to that of a laboratory-developed nested-PCR and sequencing method. The analytical sensitivity of the Abbott assay was determined using a serially-diluted WHO International Standard. To validate the clinical performances of the Abbott assay and the laboratory-developed assay, 89 clinical plasma samples with various levels of HBV DNA were tested using both assays. The limit of detection of the Abbott assay, was 210IU/ml and it successfully detected mutations when the mutant types were present at levels ≥20%. Among 89 clinical specimens, 43 and 42 were amplification positive in the Abbott and laboratory-developed assays, respectively, with 87.6% overall agreement (78/89; 95% confidence interval [CI], 78.6-93.4). The Abbott assay failed to detect the minor mutant populations in two specimens, and therefore overall concordance was 85.3% (76/89), and the kappa value was 0.79 (95% CI, 0.67-0.90). The Abbott assay showed comparable diagnostic performance to laboratory-developed nested PCR followed by direct sequencing, and may be useful as a routine method for detecting HBV NA resistance-associated mutations in clinical laboratory settings. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA.

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Majid, Farjana; Jahan, Munira; Lutful Moben, Ahmed; Tabassum, Shahina

2014-01-01

Both real-time-polymerase chain reaction (PCR) and hybrid capture 2 (HC2) assay can detect and quantify hepatitis B virus (HBV) DNA. However, real-time-PCR can detect a wide range of HBV DNA, while HC2 assay could not detect lower levels of viremia. The present study was designed to detect and quantify HBV DNA by real-time-PCR and HC2 assay and compare the quantitative data of these two assays. A cross-sectional study was conducted in between July 2010 and June 2011. A total of 66 serologically diagnosed chronic hepatitis B (CHB) patients were selected for the study. Real-time-PCR and HC2 assay was done to detect HBV DNA. Data were analyzed by statistical Package for the social sciences (SPSS). Among 66 serologically diagnosed chronic hepatitis B patients 40 (60.61%) patients had detectable and 26 (39.39%) had undetectable HBV DNA by HC2 assay. Concordant results were obtained for 40 (60.61%) out of these 66 patients by real-time-PCR and HC2 assay with mean viral load of 7.06 ± 1.13 log 10 copies/ml and 6.95 ± 1.08 log 10 copies/ml, respectively. In the remaining 26 patients, HBV DNA was detectable by real-time-PCR in 20 patients (mean HBV DNA level was 3.67 ± 0.72 log 10 copies/ml. However, HBV DNA could not be detectable in six cases by the both assays. The study showed strong correlation (r = 0.915) between real-time-PCR and HC2 assay for the detection and quantification of HBV DNA. HC2 assay may be used as an alternative to real-time-PCR for CHB patients. How to cite this article: Majid F, Jahan M, Moben AL, Tabassum S. Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA. Euroasian J Hepato-Gastroenterol 2014;4(1):31-35.

Non-contrast-enhanced hepatic MR angiography: Do two-dimensional parallel imaging and short tau inversion recovery methods shorten acquisition time without image quality deterioration?

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Shimada, Kotaro, E-mail: kotaro@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507 (Japan); Isoda, Hiroyoshi, E-mail: sayuki@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507 (Japan); Okada, Tomohisa, E-mail: tomokada@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507 (Japan); Kamae, Toshikazu, E-mail: toshi13@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507 (Japan); Arizono, Shigeki, E-mail: arizono@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507 (Japan); Hirokawa, Yuusuke, E-mail: yuusuke@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507 (Japan); Shibata, Toshiya, E-mail: ksj@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507 (Japan); Togashi, Kaori, E-mail: ktogashi@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Graduate School of Medicine, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507 (Japan)

2011-01-15

Objective: To study whether shortening the acquisition time for selective hepatic artery visualization is feasible without image quality deterioration by adopting two-dimensional (2D) parallel imaging (PI) and short tau inversion recovery (STIR) methods. Materials and methods: Twenty-four healthy volunteers were enrolled. 3D true steady-state free-precession imaging with a time spatial labeling inversion pulse was conducted using 1D or 2D-PI and fat suppression by chemical shift selective (CHESS) or STIR methods. Three groups of different scan conditions were assigned and compared: group A (1D-PI factor 2 and CHESS), group B (2D-PI factor 2 x 2 and CHESS), and group C (2D-PI factor 2 x 2 and STIR). The artery-to-liver contrast was quantified, and the quality of artery visualization and overall image quality were scored. Results: The mean scan time was 9.5 {+-} 1.0 min (mean {+-} standard deviation), 5.9 {+-} 0.8 min, and 5.8 {+-} 0.5 min in groups A, B, and C, respectively, and was significantly shorter in groups B and C than in group A (P < 0.01). The artery-to-liver contrast was significantly better in group C than in groups A and B (P < 0.01). The scores for artery visualization and overall image quality were worse in group B than in groups A and C. The differences were statistically significant (P < 0.05) regarding the arterial branches of segments 4 and 8. Between group A and group C, which had similar scores, there were no statistically significant differences. Conclusion: Shortening the acquisition time for selective hepatic artery visualization was feasible without deterioration of the image quality by the combination of 2D-PI and STIR methods. It will facilitate using non-contrast-enhanced MRA in clinical practice.

Non-contrast-enhanced hepatic MR angiography: Do two-dimensional parallel imaging and short tau inversion recovery methods shorten acquisition time without image quality deterioration?

International Nuclear Information System (INIS)

Shimada, Kotaro; Isoda, Hiroyoshi; Okada, Tomohisa; Kamae, Toshikazu; Arizono, Shigeki; Hirokawa, Yuusuke; Shibata, Toshiya; Togashi, Kaori

2011-01-01

Objective: To study whether shortening the acquisition time for selective hepatic artery visualization is feasible without image quality deterioration by adopting two-dimensional (2D) parallel imaging (PI) and short tau inversion recovery (STIR) methods. Materials and methods: Twenty-four healthy volunteers were enrolled. 3D true steady-state free-precession imaging with a time spatial labeling inversion pulse was conducted using 1D or 2D-PI and fat suppression by chemical shift selective (CHESS) or STIR methods. Three groups of different scan conditions were assigned and compared: group A (1D-PI factor 2 and CHESS), group B (2D-PI factor 2 x 2 and CHESS), and group C (2D-PI factor 2 x 2 and STIR). The artery-to-liver contrast was quantified, and the quality of artery visualization and overall image quality were scored. Results: The mean scan time was 9.5 ± 1.0 min (mean ± standard deviation), 5.9 ± 0.8 min, and 5.8 ± 0.5 min in groups A, B, and C, respectively, and was significantly shorter in groups B and C than in group A (P < 0.01). The artery-to-liver contrast was significantly better in group C than in groups A and B (P < 0.01). The scores for artery visualization and overall image quality were worse in group B than in groups A and C. The differences were statistically significant (P < 0.05) regarding the arterial branches of segments 4 and 8. Between group A and group C, which had similar scores, there were no statistically significant differences. Conclusion: Shortening the acquisition time for selective hepatic artery visualization was feasible without deterioration of the image quality by the combination of 2D-PI and STIR methods. It will facilitate using non-contrast-enhanced MRA in clinical practice.

Monitoring Acidophilic Microbes with Real-Time Polymerase Chain Reaction (PCR) Assays

Energy Technology Data Exchange (ETDEWEB)

Frank F. Roberto

2008-08-01

Many techniques that are used to characterize and monitor microbial populations associated with sulfide mineral bioleaching require the cultivation of the organisms on solid or liquid media. Chemolithotrophic species, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, or thermophilic chemolithotrophs, such as Acidianus brierleyi and Sulfolobus solfataricus can grow quite slowly, requiring weeks to complete efforts to identify and quantify these microbes associated with bioleach samples. Real-time PCR (polymerase chain reaction) assays in which DNA targets are amplified in the presence of fluorescent oligonucleotide primers, allowing the monitoring and quantification of the amplification reactions as they progress, provide a means of rapidly detecting the presence of microbial species of interest, and their relative abundance in a sample. This presentation will describe the design and use of such assays to monitor acidophilic microbes in the environment and in bioleaching operations. These assays provide results within 2-3 hours, and can detect less than 100 individual microbial cells.

Nondestructive assay technology and automated ''real-time'' materials control

International Nuclear Information System (INIS)

Keepin, G.R.

1977-01-01

Significant advances in nondestructive assay techniques and instrumentation now enable rapid, accurate and direct in-plant measurement of nuclear material on a continuous or ''real-time'' basis as it progresses through a nuclear facility. A variety of passive and active assay instruments are required for the broad range of materials measurement problems encountered by safeguards inspectors and facility operators in various types of nuclear plants. Representative NDA techniques and instruments are presented and reviewed with special attention to their assay capabilities and areas of applicability in the nuclear fuel cycle. An advanced system of materials control - called ''DYMAC'', for Dynamic Materials Control - is presently under development by the U.S. Energy Research and Development Administration; the DYMAC program integrates new nondestructive assay instrumentation and modern data-processing methods, with the overall objective of demonstrating a workable, cost-effective system of stringent safeguards and materials control in various generic types of facilities found in the nuclear fuel cycle. Throughout the program, emphasis will be placed on devloping practical solutions to generic measurement problems so that resulting techniques and instrumentation will have widespread utility. Projected levels of safeguards assurance, together with other vital - and cost-sensitive - plant operational factors such as process and quality control, criticality safety and waste management are examined in an evaluation of the impact of future advanced materials control systems on overall plant operations, efficiency and productivity. The task of implementing effective and stringent safeguards includes the transfer of new safeguards technology to the nuclear industry. Clearly the training of inspectors (both IAEA and national), plant people, etc., in the effective use of new NDA equipment is of paramount importance; thus in the United States, the Energy Research and Development

The effect of varying incubation times for hypotonic treatment of lymphocytes in dicentric assay technique

International Nuclear Information System (INIS)

Noraisyah Yusof; Noriah Jamal; Rahimah Abdul Rahim; Juliana Mahamad Napiah

2010-01-01

The International Atomic Energy Agency (IAEA) has recommended that incubation time for the hypotonic treatment of lymphocytes in dicentric assay technique to be between 15 to 20 minutes. Incubation time will effect the hypotonic treatment of lymphocytes and thus, the breakage of cytoplasmic membrane. The objective of this study is to examine the effect of varying incubation times for hypotonic treatment of lymphocytes in dicentric assay technique. In this study, we choose to use our standard protocol for dicentric assay technique. However, for the hypotonic treatment of lymphocytes, the incubation times were varied from 10, 15, 20, 25 and 30 minutes respectively. Lymphocytes were then fixed and stained with Giemsa. The cells were then analyzed for clear background that indicates good metaphases. We found that incubation time of 30 minutes gives the best metaphase images. This incubation time is longer than what has been recommended by the IAEA. This maybe explained by the fact that our country's climate is of higher humidity compared with the European countries. (author)

Real-time multiplex PCR assay for detection of Yersinia pestis and Yersinia pseudotuberculosis.

Science.gov (United States)

Matero, Pirjo; Pasanen, Tanja; Laukkanen, Riikka; Tissari, Päivi; Tarkka, Eveliina; Vaara, Martti; Skurnik, Mikael

2009-01-01

A multiplex real-time polymerase chain reaction (PCR) assay was developed for the detection of Yersinia pestis and Yersinia pseudotuberculosis. The assay includes four primer pairs, two of which are specific for Y. pestis, one for Y. pestis and Y. pseudotuberculosis and one for bacteriophage lambda; the latter was used as an internal amplification control. The Y. pestis-specific target genes in the assay were ypo2088, a gene coding for a putative methyltransferase, and the pla gene coding for the plasminogen activator. In addition, the wzz gene was used as a target to specifically identify both Y. pestis and the closely related Y. pseudotuberculosis group. The primer and probe sets described for the different genes can be used either in single or in multiplex PCR assays because the individual probes were designed with different fluorochromes. The assays were found to be both sensitive and specific; the lower limit of the detection was 10-100 fg of extracted Y. pestis or Y. pseudotuberculosis total DNA. The sensitivity of the tetraplex assay was determined to be 1 cfu for the ypo2088 and pla probe labelled with FAM and JOE fluorescent dyes, respectively.

A Multiplex RT-PCR Assay for S. aureus, L. monocytogenes, and Salmonella spp. Detection in Raw Milk with Pre-enrichment

Directory of Open Access Journals (Sweden)

Tian Ding

2017-05-01

Full Text Available This study firstly developed a multiplex real-time PCR (RT-PCR technique combined with a pre-enrichment step to simultaneously detect Staphylococcus aureus (S. aureus, Listeria monocytogenes (L. monocytogenes and Salmonella spp. in raw milk and the dairy farm environment (feces, soil, feed, water in one reaction. Brain heart infusion (BHI broth was selected for the enrichment step to increase the density of the target bacteria by using an incubation of 4 h before multiplex RT-PCR. The results showed that the detection limit of the multiplex real-time assay was approximately 102 CFU/mL for pure cultures and artificially contaminated milk without enrichment, while 12, 14, and 10 CFU/25 mL, respectively, for S. aureus, L. monocytogenes, and Salmonella spp. after pre-enrichment. The newly developed multiplex RT-PCR assay was applied to 46 dairy farm environmental samples and raw milk samples covering a wide variety of sample types. The results demonstrated that the multiplex RT-PCR assay coupled with the BHI enrichment broth was suitable for the simultaneous screening of S. aureus, L. monocytogenes, and Salmonella spp. in the pasture environment and in raw milk. The multiplex RT-PCR assay clearly and successfully shortened the total detection time and reduced labor compared to conventional culture-based methods for testing natural samples.

A Comparison of Real-Time and Endpoint Cell Viability Assays for Improved Synthetic Lethal Drug Validation.

Science.gov (United States)

Single, Andrew; Beetham, Henry; Telford, Bryony J; Guilford, Parry; Chen, Augustine

2015-12-01

Cell viability assays fulfill a central role in drug discovery studies. It is therefore important to understand the advantages and disadvantages of the wide variety of available assay methodologies. In this study, we compared the performance of three endpoint assays (resazurin reduction, CellTiter-Glo, and nuclei enumeration) and two real-time systems (IncuCyte and xCELLigence). Of the endpoint approaches, both the resazurin reduction and CellTiter-Glo assays showed higher cell viabilities when compared directly to stained nuclei counts. The IncuCyte and xCELLigence real-time systems were comparable, and both were particularly effective at tracking the effects of drug treatment on cell proliferation at sub-confluent growth. However, the real-time systems failed to evaluate contrasting cell densities between drug-treated and control-treated cells at full growth confluency. Here, we showed that using real-time systems in combination with endpoint assays alleviates the disadvantages posed by each approach alone, providing a more effective means to evaluate drug toxicity in monolayer cell cultures. Such approaches were shown to be effective in elucidating the toxicity of synthetic lethal drugs in an isogenic pair of MCF10A breast cell lines. © 2015 Society for Laboratory Automation and Screening.

Lateral mobility of minibasins during shortening: Insights from the SE Precaspian Basin, Kazakhstan

Science.gov (United States)

Duffy, Oliver B.; Fernandez, Naiara; Hudec, Michael R.; Jackson, Martin P. A.; Burg, George; Dooley, Tim P.; Jackson, Christopher A.-L.

2017-04-01

Minibasin provinces are widespread and can be found in all types of salt tectonic settings, many of which are prone to shortening. Previous studies of how minibasin provinces shorten assume that the salt between the minibasins is homogeneous and that the base of salt is flat or of low relief, such that minibasins are free to move laterally. Here we investigate how minibasin provinces respond to shortening when the lateral mobility of the minibasins is restricted by intra-salt sediment bodies, in order to gain a greater understanding of the controls on the structural styles and modes of tectono-stratigraphic evolution exhibited in minibasin provinces. We examine a borehole-constrained, 3D seismic reflection dataset from the SE Precaspian Basin (onshore western Kazakhstan). The study area is characterised by large, supra-salt minibasins and an array of smaller intra-salt sediment packages distributed between these larger minibasins. We first outline the evidence of episodic shortening between the Late Triassic and present, after the onset of supra-salt minibasin subsidence. Next, we document spatial variations in shortening style, showing how these relate to the concentration of intra-salt sediment packages. Finally, we develop synoptic models showing how intra-salt sediment packages influence both the lateral mobility of minibasins during shortening and the resultant structural style, and we compare and contrast our findings with existing models and other natural examples of shortened minibasin provinces. We conclude that minibasin provinces may have different degrees of lateral mobility depending on the presence, or absence, of intrasalt barriers, and that these variations provide a first-order control on basin-shortening style and tectono-stratigraphic evolution.

Lactose tolerance test shortened to 30 minutes: an exploratory study of its feasibility and impact

Directory of Open Access Journals (Sweden)

José Luis Domínguez-Jiménez

2014-06-01

Full Text Available Introduction: Lactose malabsorption (LM is a very common condition with a high prevalence in our setting. Lactose tolerance test (LTT is a basic, affordable test for diagnosis that requires no complex technology. It has been recently shown that this test can be shortened to 3 measurements (baseline, 30 min, 60 min with no impact on final results. The purpose of our study was to assess the feasibility and benefits of LTT simplification and shortening to 30 min, as well as the financial impact entailed. Material and methods: A multicenter, observational study of consecutive patients undergoing LTT for LM suspicion. Patients received 50 g of lactose following a fasting period of 12 h, and had blood collected from a vein at all 3 time points for the measurement of blood glucose (mg/dl. Differences between the shortened and complete test forms were analyzed using McNemar's test. A comparison of blood glucose levels between patients with normal and abnormal results was performed using Student's T-test for independent mean values. Consistency was assessed using the kappa index. A p < 0.05 was considered to be statistically significant. Results: A total of 270 patients (69.6% females were included, with a mean age of 39.9 ± 16 years. LTT was abnormal for 151 patients (55.9%. We observed no statistically significant differences in baseline blood glucose levels between patients with normal and abnormal LTT results (p = 0.13; however, as was to be expected, such differences were obvious for the remaining time points (p < 0.01. Deleting blood glucose measurements at 60 minutes only led to overdiagnose LM (false positive results in 6 patients (2.22 %, with a kappa index of 0.95 (95% CI: 0.92-0.99 (p < 0.001 versus the complete test. Suppressing measurements at 60 min would have saved at least € 7,726. Conclusion: The shortening of LTT to only 2 measurements (baseline and 30-min hardly leads to any differences in final results, and would entail savings in

Evaluation of four endogenous reference genes and their real-time PCR assays for common wheat quantification in GMOs detection.

Science.gov (United States)

Huang, Huali; Cheng, Fang; Wang, Ruoan; Zhang, Dabing; Yang, Litao

2013-01-01

Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs) detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L.) DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat.

Evaluation of four endogenous reference genes and their real-time PCR assays for common wheat quantification in GMOs detection.

Directory of Open Access Journals (Sweden)

Huali Huang

Full Text Available Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L. DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat.

Evaluation of Four Endogenous Reference Genes and Their Real-Time PCR Assays for Common Wheat Quantification in GMOs Detection

Science.gov (United States)

Huang, Huali; Cheng, Fang; Wang, Ruoan; Zhang, Dabing; Yang, Litao

2013-01-01

Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs) detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L.) DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat. PMID:24098735

Spine biomechanics associated with the shortened, modern one-plane golf swing.

Science.gov (United States)

Dale, R Barry; Brumitt, Jason

2016-06-01

The purpose of this study was to compare kinetic, kinematic, and performance variables associated with full and shortened modern backswings in a skilled group of modern swing (one-plane) golfers. Shortening the modern golf backswing is proposed to reduce vertebral spine stress, but supporting evidence is lacking and performance implications are unknown. Thirteen male golfers performed ten swings of each swing type using their own 7-iron club. Biomechanical-dependent variables included the X-Factor kinematic data and spine kinetics. Performance-related dependent variables included club head velocity (CHV), shot distance, and accuracy (distance from the target line). Data were analysed with repeated measures ANOVA with an a priori alpha of 0.05 (SPSS 22.0, IBM, Armonk, NY, USA). We found significant reductions for the X-Factor (p < 0.05) between the full and shortened swings. The shortened swing condition ameliorated vertebral compression force from 7.6 ± 1.4 to 7.0 ± 1.7 N (normalised to body weight, p = 0.01) and significantly reduced CHV (p < 0.05) by ~2 m/s with concomitant shot distance diminution by ~10 m (p < 0.05). Further research is necessary to examine the applicability of a shortened swing for golfers with low back pain.

Neutralization Assay for Zika and Dengue Viruses by Use of Real-Time-PCR-Based Endpoint Assessment.

Science.gov (United States)

Wilson, Heather L; Tran, Thomas; Druce, Julian; Dupont-Rouzeyrol, Myrielle; Catton, Michael

2017-10-01

The global spread and infective complications of Zika virus (ZKV) and dengue virus (DENV) have made them flaviviruses of public health concern. Serological diagnosis can be challenging due to antibody cross-reactivity, particularly in secondary flavivirus infections or when there is a history of flavivirus vaccination. The virus neutralization assay is considered to be the most specific assay for measurement of anti-flavivirus antibodies. This study describes an assay where the neutralization endpoint is measured by real-time PCR, providing results within 72 h. It demonstrated 100% sensitivity (24/24 ZKV and 15/15 DENV) and 100% specificity (11/11 specimens) when testing well-characterized sera. In addition, the assay was able to determine the correct DENV serotype in 91.7% of cases. The high sensitivity and specificity of the real-time PCR neutralization assay makes it suitable to use as a confirmatory test for sera that are reactive in commercial IgM/IgG enzyme immunoassays. Results are objective and the PCR-based measurement of the neutralization endpoint lends itself to automation so that throughput may be increased in times of high demand. Copyright © 2017 American Society for Microbiology.

Development and application of two independent real-time PCR assays to detect clinically relevant Mucorales species.

Science.gov (United States)

Springer, Jan; Goldenberger, Daniel; Schmidt, Friderike; Weisser, Maja; Wehrle-Wieland, Elisabeth; Einsele, Hermann; Frei, Reno; Löffler, Jürgen

2016-03-01

PCR-based detection of Mucorales species could improve diagnosis of suspected invasive fungal infection, leading to a better patient outcome. This study describes two independent probe-based real-time PCR tests for detection of clinically relevant Mucorales, targeting specific fragments of the 18S and the 28S rRNA genes. Both assays have a short turnaround time, allow fast, specific and very sensitive detection of clinically relevant Mucorales and have the potential to be used as quantitative tests. They were validated on various clinical samples (fresh and formalin-fixed paraffin-embedded specimens, mainly biopsies, n = 17). The assays should be used as add-on tools to complement standard techniques; a combined approach of both real-time PCR assays has 100 % sensitivity. Genus identification by subsequent sequencing is possible for amplicons of the 18S PCR assay. In conclusion, combination of the two independent Mucorales assays described in this study, 18S and 28S, detected all clinical samples associated with proven Mucorales infection (n = 10). Reliable and specific identification of Mucorales is a prerequisite for successful antifungal therapy as these fungi show intrinsic resistance to voriconazole and caspofungin.

The Hybrid II assay: a sensitive and specific real-time hybridization assay for the diagnosis of Theileria parva infection in Cape buffalo (Syncerus caffer) and cattle.

Science.gov (United States)

Pienaar, Ronel; Potgieter, Fred T; Latif, Abdalla A; Thekisoe, Oriel M M; Mans, Ben J

2011-12-01

Corridor disease is an acute, fatal disease of cattle caused by buffalo-adapted Theileria parva. This is a nationally controlled disease in South Africa and strict control measures apply for the movement of buffalo, which includes mandatory testing for the presence of T. parva and other controlled diseases. Accurate diagnosis of the T. parva carrier state in buffalo using the official real-time hybridization PCR assay (Sibeko et al. 2008), has been shown to be affected by concurrent infection with T. sp. (buffalo)-like parasites. We describe the Hybrid II assay, a real-time hybridization PCR method, which compares well with the official hybridization assay in terms of specificity and sensitivity. It is, however, not influenced by mixed infections of T. sp. (buffalo)-like parasites and is as such a significant improvement on the current hybridization assay.

Development of a panel of seven duplex real-time PCR assays for detecting 13 streptococcal superantigens.

Science.gov (United States)

Yang, Peng; Peng, Xiaomin; Cui, Shujuan; Shao, Junbin; Zhu, Xuping; Zhang, Daitao; Liang, Huijie; Wang, Quanyi

2013-07-30

Streptococcal superantigens (SAgs) are the major virulence factors of infection in humans for group A Streptococcus (GAS) bacteria. A panel consisting of seven duplex real-time PCR assays was developed to simultaneously detect 13 streptococcal SAgs and one internal control which may be important in the control of GAS-mediated diseases. Primer and probe sequences were selected based on the highly conserved region from an alignment of nucleotide sequences of the 13 streptococcal SAgs. The reaction conditions of the duplex real-time PCR were optimized and the specificity of the duplex assays was evaluated using SAg positive strains. The limit of detection of the duplex assays was determined by using 10-fold serial dilutions of the DNA of 13 streptococcal SAgs and compared to a conventional polymerase chain reaction (PCR) method for evaluating the duplex assays sensitivity. Using the duplex assays, we were able to differentiate between 13 SAgs from Streptococcus strains and other non-Streptococcus bacteria without cross-reaction. On the other hand, the limit of detection of the duplex assays was at least one or two log dilutions lower than that of the conventional PCR. The panel was highly specific (100%) and the limit of detection of these duplex groups was at least ten times lower than that obtained by using a conventional PCR method.

Telomere Shortening in Neurological Disorders: An Abundance of Unanswered Questions

OpenAIRE

Eitan, Erez; Hutchison, Emmette R.; Mattson, Mark P.

2014-01-01

Telomeres, ribonucleoprotein complexes that cap eukaryotic chromosomes, typically shorten in leukocytes with aging. Aging is a primary risk factor for neurodegenerative disease (ND), and a common assumption has arisen that leukocyte telomere length (LTL) can serve as a predictor of neurological disease. However, the evidence for shorter LTL in Alzheimer’s and Parkinson’s patients is inconsistent. The diverse causes of telomere shortening may explain variability in LTL between studies and indi...

Dissolvable fluidic time delays for programming multi-step assays in instrument-free paper diagnostics.

Science.gov (United States)

Lutz, Barry; Liang, Tinny; Fu, Elain; Ramachandran, Sujatha; Kauffman, Peter; Yager, Paul

2013-07-21

Lateral flow tests (LFTs) are an ingenious format for rapid and easy-to-use diagnostics, but they are fundamentally limited to assay chemistries that can be reduced to a single chemical step. In contrast, most laboratory diagnostic assays rely on multiple timed steps carried out by a human or a machine. Here, we use dissolvable sugar applied to paper to create programmable flow delays and present a paper network topology that uses these time delays to program automated multi-step fluidic protocols. Solutions of sucrose at different concentrations (10-70% of saturation) were added to paper strips and dried to create fluidic time delays spanning minutes to nearly an hour. A simple folding card format employing sugar delays was shown to automate a four-step fluidic process initiated by a single user activation step (folding the card); this device was used to perform a signal-amplified sandwich immunoassay for a diagnostic biomarker for malaria. The cards are capable of automating multi-step assay protocols normally used in laboratories, but in a rapid, low-cost, and easy-to-use format.

Ultrasensitive time-resolved immunofluorometric assay of pepsinogen I

International Nuclear Information System (INIS)

Huang Biao; Xiao Hualong; Zhang Xiangrui; Zhu Lan; Jiang Menjun

2004-01-01

Purpose: To construct a two-site sandwich-type assay for pepsinogen I with time-resolved fluoroimmunoassay (TRFIA) as a detection technique. Methods: On the noncompetitive assay, one monoclonal antibody (McAb) coating on wells directed against a specific antigenic site on the pepsinogen I, the europium-labelled McAb which was prepared by with helpful of the europium-chelate of N-(p-isothiocyanatobenzyl)- diethylenetriamine-N, N, N, N-tetraacetic acid directed against a different antigenic site on the pepsinogen I molecule we called labelling McAb. The luminescent enhancement system was enhancement solution which contained mainly 2-naphthoyltrifluoroacetone. 25μl of Calibrators or samples and 200 μl of the assay buffer were pipetted into coated microtiter wells. The plates were incubated with mechanical shaking for 1 h at 25 degree C, washed two times, then added 100 μl Eu3+- McAb solution diluted 50-fold in assay buffer. The plates were incubated again with mechanical shaking for 1 h at 25 degree C,After six washings, 200 μl of enhancement solution were dispense into each well. The plates were shaken for 5 min and fluorescence readings. All the proceeding were done by auto DELFIA1235, software was designed by our lab. The calibration curve and calculation of the concentrations in the unknown samples were performed automatically by using Multicalc software program, where a spline algorithm on logarithmically transformed data was employed. Results: The average labelling yield is 8.6 Eu3+/McAb giving high sensitivity with low background(<1000 cps). The measurement range was 3.5-328 μ g /L with ED25, ED50, ED80 of 11.34 ±0.2 μ g/L, 38.73±0.8 μ g /L and 132,3±2.9 μ g/L. The detection limit, defined as the concentration of PGI corresponding to the fluorescence of the zero calibrators plus two SDs, is 0..05μg/L. Within-run and between-run precision was l.9% and 4.7% which assessed at various PGI concentrations between 5 and 300 μg/L. We checked for cross

Development of a novel real-time qPCR assay for the dual detection of canine and phocine distemper virus

DEFF Research Database (Denmark)

Nielsen, Linette Buxbom; Hjulsager, Charlotte Kristiane; Larsen, Helene

conventional PCR assays with real-time PCR assays to obtain a uniform assay palette. The present work describes the development of a novel real-time RT-qPCR assay for the dual detection of canine and phocine distemper virus. The assay is relevant for the future detection of outbreaks of canine distemper virus...... in e.g. in farmed mink and wildlife and phocine distemper in seals. A set of primers and dual labelled probe was designed based on an alignment of distemper sequences in GenBank from various species and in-house sequences from recent outbreaks in Danish farmed mink. The assay amplifies a segment of 151...... bp in the Phosphoprotein (P) gene of the distemper virus genome. The dynamic range and PCR efficiency (E) was experimentally determined using 10-fold dilutions of a specially designed distemper DNA-oligo in addition to extracted RNA from clinical samples. E of the real-time assay was shown to range...

Evaluation of Elecsys Syphilis Assay for Routine and Blood Screening and Detection of Early Infection.

Science.gov (United States)

Kremastinou, J; Polymerou, V; Lavranos, D; Aranda Arrufat, A; Harwood, J; Martínez Lorenzo, M J; Ng, K P; Queiros, L; Vereb, I; Cusini, M

2016-09-01

Treponema pallidum infections can have severe complications if not diagnosed and treated at an early stage. Screening and diagnosis of syphilis require assays with high specificity and sensitivity. The Elecsys Syphilis assay is an automated treponemal immunoassay for the detection of antibodies against T. pallidum The performance of this assay was investigated previously in a multicenter study. The current study expands on that evaluation in a variety of diagnostic settings and patient populations, at seven independent laboratories. The samples included routine diagnostic samples, blood donation samples, samples from patients with confirmed HIV infections, samples from living organ or bone marrow donors, and banked samples, including samples previously confirmed as syphilis positive. This study also investigated the seroconversion sensitivity of the assay. With a total of 1,965 syphilis-negative routine diagnostic samples and 5,792 syphilis-negative samples collected from blood donations, the Elecsys Syphilis assay had specificity values of 99.85% and 99.86%, respectively. With 333 samples previously identified as syphilis positive, the sensitivity was 100% regardless of disease stage. The assay also showed 100% sensitivity and specificity with samples from 69 patients coinfected with HIV. The Elecsys Syphilis assay detected infection in the same bleed or earlier, compared with comparator assays, in a set of sequential samples from a patient with primary syphilis. In archived serial blood samples collected from 14 patients with direct diagnoses of primary syphilis, the Elecsys Syphilis assay detected T. pallidum antibodies for 3 patients for whom antibodies were not detected with the Architect Syphilis TP assay, indicating a trend for earlier detection of infection, which may have the potential to shorten the time between infection and reactive screening test results. Copyright © 2016 Kremastinou et al.

Evaluation of Elecsys Syphilis Assay for Routine and Blood Screening and Detection of Early Infection

Science.gov (United States)

Kremastinou, J.; Polymerou, V.; Lavranos, D.; Aranda Arrufat, A.; Harwood, J.; Martínez Lorenzo, M. J.; Ng, K. P.; Queiros, L.; Vereb, I.

2016-01-01

Treponema pallidum infections can have severe complications if not diagnosed and treated at an early stage. Screening and diagnosis of syphilis require assays with high specificity and sensitivity. The Elecsys Syphilis assay is an automated treponemal immunoassay for the detection of antibodies against T. pallidum. The performance of this assay was investigated previously in a multicenter study. The current study expands on that evaluation in a variety of diagnostic settings and patient populations, at seven independent laboratories. The samples included routine diagnostic samples, blood donation samples, samples from patients with confirmed HIV infections, samples from living organ or bone marrow donors, and banked samples, including samples previously confirmed as syphilis positive. This study also investigated the seroconversion sensitivity of the assay. With a total of 1,965 syphilis-negative routine diagnostic samples and 5,792 syphilis-negative samples collected from blood donations, the Elecsys Syphilis assay had specificity values of 99.85% and 99.86%, respectively. With 333 samples previously identified as syphilis positive, the sensitivity was 100% regardless of disease stage. The assay also showed 100% sensitivity and specificity with samples from 69 patients coinfected with HIV. The Elecsys Syphilis assay detected infection in the same bleed or earlier, compared with comparator assays, in a set of sequential samples from a patient with primary syphilis. In archived serial blood samples collected from 14 patients with direct diagnoses of primary syphilis, the Elecsys Syphilis assay detected T. pallidum antibodies for 3 patients for whom antibodies were not detected with the Architect Syphilis TP assay, indicating a trend for earlier detection of infection, which may have the potential to shorten the time between infection and reactive screening test results. PMID:27358468

Lengthening of the shortened first metatarsal after Wilson's osteotomy for hallux valgus.

Science.gov (United States)

Singh, D; Dudkiewicz, I

2009-12-01

Metatarsalgia is a recognised complication following iatrogenic shortening of the first metatarsal in the management of hallux valgus. The traditional surgical treatment is by shortening osteotomies of the lesser metatarsals. We describe the results of lengthening of iatrogenic first brachymetatarsia in 16 females. A Scarf-type osteotomy was used in the first four cases and a step-cut of equal thicknesses along the axis of the first metatarsal was performed in the others. The mean follow-up was 21 months (19 to 26). Relief of metatarsalgia was obtained in the six patients in whom 10 mm of lengthening had been achieved, compared to only 50% relief in those where less than 8 mm of lengthening had been gained. One-stage step-cut lengthening osteotomy of the first metatarsal may be preferable to shortening osteotomies of the lesser metatarsals in the treatment of metatarsalgia following surgical shortening of the first metatarsal.

Time-kill assay and Etest evaluation for synergy with polymyxin B and fluconazole against Candida glabrata.

Science.gov (United States)

Pankey, George; Ashcraft, Deborah; Kahn, Heather; Ismail, Abdulrahim

2014-10-01

Fluconazole-resistant Candida glabrata is an emerging pathogen that causes fungemia. Polymyxin B, a last-resort antibiotic used to treat multidrug-resistant Gram-negative bacterial infections, has been found to possess in vitro fungicidal activity and showed synergy with fluconazole against a single strain of C. glabrata. Since both agents may be used simultaneously in intensive care unit (ICU) patients, this study was performed to test for possible synergy of this combination against 35 C. glabrata blood isolates, using 2 methods: a time-kill assay and an experimental MIC-MIC Etest method. Thirty-five genetically unique C. glabrata bloodstream isolates were collected from 2009 to 2011, identified using an API 20C system, and genotyped by repetitive sequence-based PCR (rep-PCR). MICs were determined by Etest and broth microdilution methods. Synergy testing was performed using a modified bacterial Etest synergy method and time-kill assay, with final results read at 24 h. The Etest method showed synergy against 19/35 (54%) isolates; the time-kill assay showed synergy against 21/35 (60%) isolates. Isolates not showing drug synergy had an indifferent status. Concordance between methods was 60%. In vitro synergy of polymyxin B and fluconazole against the majority of C. glabrata isolates was demonstrated by both methods. The bacterial Etest synergy method adapted well when used with C. glabrata. Etest was easier to perform than time-kill assay and may be found to be an acceptable alternative to time-kill assay with antifungals. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Crustal balance and crustal flux from shortening estimates in the Central Andes

Science.gov (United States)

Hindle, David; Kley, Jonas; Oncken, Onno; Sobolev, Stephan

2005-01-01

The Central Andes of South America form the second largest high elevation plateau on earth. Extreme elevations have formed on a noncollisional margin with abundant associated arc magmatism. It has long been thought that the crustal thickness necessary to support Andean topography was not accounted for by known crustal shortening alone. We show that this may in part be due to a two-dimensional treatment of the problem. A three-dimensional analysis of crustal shortening and crustal thickness shows that displacement of material towards the axis of the bend in the Central Andes has added a significant volume of crust not accounted for in previous comparisons. We find that present-day crustal thickness between 12°S and 25°S is accounted for (∼-10% to ∼+3%)with the same shortening estimates, and the same assumed initial crustal thickness as had previously led to the conclusion of a ∼25-35% deficit in shortening relative to volume of crustal material. We suggest that the present-day measured crustal thickness distribution may not match that predicted due to shortening, and substantial redistribution of crust may have occurred by both erosion and deposition at the surface and lower crustal flow in regions of the thermally weakened middle and lower crust.

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.

Comparison of Microtox and Xenoassay Light as a Near Real Time River Monitoring Assay for Heavy Metals

Directory of Open Access Journals (Sweden)

M. I. E. Halmi

2014-01-01

Full Text Available Luminescence-based assays for toxicants such as Microtox, ToxAlert, and Biotox have been used extensively worldwide. However, the use of these assays in near real time conditions is limited due to nonoptimal assay temperature for the tropical climate. An isolate that exhibits a high luminescence activity in a broad range of temperatures was successfully isolated from the mackerel, Rastrelliger kanagurta. This isolate was tentatively identified as Photobacterium sp. strain MIE, based on partial 16S rDNA molecular phylogeny. Optimum conditions that support high bioluminescence activity occurred between 24 and 30°C, with pH 5.5 to 7.5, 10 to 20 g/L of sodium chloride, 30 to 50 g/L of tryptone, and 4 g/L of glycerol as the carbon source. Assessment of near real time capability of this bacterial system, Xenoassay light to monitor heavy metals from a contaminated river running through the Juru River Basin shows near real time capability with assaying time of less than 30 minutes per samples. Samples returned to the lab were tested with a standard Microtox assay using Vibrio fishceri. Similar results were obtained to Xenoassay light that show temporal variation of copper concentration. Thus, this strain is suitable for near real time river monitoring of toxicants especially in the tropics.

Rapid detection and typing of pathogenic nonpneumophila Legionella spp. isolates using a multiplex real-time PCR assay.

Science.gov (United States)

Benitez, Alvaro J; Winchell, Jonas M

2016-04-01

We developed a single tube multiplex real-time PCR assay that allows for the rapid detection and typing of 9 nonpneumophila Legionella spp. isolates that are clinically relevant. The multiplex assay is capable of simultaneously detecting and discriminating L. micdadei, L. bozemanii, L. dumoffii, L. longbeachae, L. feeleii, L. anisa, L. parisiensis, L. tucsonensis serogroup (sg) 1 and 3, and L. sainthelensis sg 1 and 2 isolates. Evaluation of the assay with nucleic acid from each of these species derived from both clinical and environmental isolates and typing strains demonstrated 100% sensitivity and 100% specificity when tested against 43 other Legionella spp. Typing of L. anisa, L. parisiensis, and L. tucsonensis sg 1 and 3 isolates was accomplished by developing a real-time PCR assay followed by high-resolution melt (HRM) analysis targeting the ssrA gene. Further typing of L. bozemanii, L. longbeachae, and L. feeleii isolates to the serogroup level was accomplished by developing a real-time PCR assay followed by HRM analysis targeting the mip gene. When used in conjunction with other currently available diagnostic tests, these assays may aid in rapidly identifying specific etiologies associated with Legionella outbreaks, clusters, sporadic cases, and potential environmental sources. Published by Elsevier Inc.

CO2 laser pulse shortening by laser ablation of a metal target

International Nuclear Information System (INIS)

Donnelly, T.; Mazoyer, M.; Lynch, A.; O'Sullivan, G.; O'Reilly, F.; Dunne, P.; Cummins, T.

2012-01-01

A repeatable and flexible technique for pulse shortening of laser pulses has been applied to transversely excited atmospheric (TEA) CO 2 laser pulses. The technique involves focusing the laser output onto a highly reflective metal target so that plasma is formed, which then operates as a shutter due to strong laser absorption and scattering. Precise control of the focused laser intensity allows for timing of the shutter so that different temporal portions of the pulse can be reflected from the target surface before plasma formation occurs. This type of shutter enables one to reduce the pulse duration down to ∼2 ns and to remove the low power, long duration tails that are present in TEA CO 2 pulses. The transmitted energy is reduced as the pulse duration is decreased but the reflected power is ∼10 MW for all pulse durations. A simple laser heating model verifies that the pulse shortening depends directly on the plasma formation time, which in turn is dependent on the applied laser intensity. It is envisaged that this plasma shutter will be used as a tool for pulse shaping in the search for laser pulse conditions to optimize conversion efficiency from laser energy to useable extreme ultraviolet (EUV) radiation for EUV source development.

Influence of muscle geometry on shortening speed of fibre, aponeurosis and muscle

NARCIS (Netherlands)

Zuurbier, C. J.; Huijing, P. A.

1992-01-01

The influence of muscle geometry on muscle shortening of the gastrocnemius medialis muscle (GM) of the rat was studied. Using cinematography, GM geometry was studied during isokinetic concentric activity at muscle lengths ranging from 85 to 105% of the optimum muscle length. The shortening speed of

Clinical efficacy comparison of flabby skin excision combined orbicularis oculi muscle shortening surgery in patients with senile entropion

Directory of Open Access Journals (Sweden)

Qing-Liang Xu

2015-07-01

Full Text Available AIM: To observe the clinical effect of slack skin excision combined with orbicularis oculi muscle shortening and orbicularis muscle shortening in the treatment of elderly patients with lower eyelid entropion, and provide the reference for the clinical treatment.METHODS: Eighty-two(126 eyesclinical diagnosis's elderly patients with lower eyelid entropion were collected from our department, then randomly divided into excised relaxing skin and orbicularis oculi muscle shortening treatment group and the orbicularis muscle shortening treatment group.The general data of the two groups, long term curative effect and short-term curative effect were compared. RESULTS: The age, sex, proportion of patients with the first time operation, course of disease were no statistical significance between the observation group and the control group(P>0.05. The short-term effective rate of the observation group was 95.2%, while the short-term effective rate of the control group was 77.8%, the short-term efficiency differences between the two groups was statistical significance(χ2=4.100, P=0.043. The long-term cure rate of the observation group was 82.5%(34 cases, 52 eyes, recurrence rate was 17.5%(7 cases, 11 eyes, while the cure rate of the control group was 60.3%(25 cases, 38 eyes, recurrence rate was 39.7%(16 cases, 25 eyes, the difference of long term cure rate was statistical significance between the two groups(PCONCLUSION: The clinical curative effect of slack skin excision combined with orbicularis oculi muscle shortening in the treatment of senile inferior entropion is better than orbicularis muscle shortening operation, recommending application in the clinical.

Superimposed extension and shortening in the southern Salinas Basin and La Panza Range, California: A guide to Neogene deformation in the Salinian block of the central California Coast Ranges

Science.gov (United States)

Colgan, Joseph P.; McPhee, Darcy K.; McDougall, Kristin; Hourigan, Jeremy K.

2013-01-01

We synthesized data from geologic maps, wells, seismic-reflection profiles, potential-field interpretations, and low-temperature thermochronology to refine our understanding of late Cenozoic extension and shortening in the Salinian block of the central California Coast Ranges. Data from the La Panza Range and southern Salinas Basin document early to middle Miocene extension, followed by Pliocene and younger shortening after a period of little deformation in the late Miocene. Extension took place on high-angle normal faults that accommodated ∼2% strain at the scale of the ∼50-km-wide Salinian block (oriented perpendicular to the San Andreas fault). Shortening was accommodated by new reverse faults, reactivation of older normal faults, and strike-slip faulting that resulted in a map-view change in the width of the Salinian block. The overall magnitude of shortening was ∼10% strain, roughly 4–5 times greater than the amount of extension. The timing and magnitude of deformation in our study area are comparable to that documented in other Salinian block basins, and we suggest that the entire block deformed in a similar manner over a similar time span. The timing and relative magnitude of extension and shortening may be understood in the context of central Coast Range tectonic boundary conditions linked to rotation of the western Transverse Ranges at the south end of the Salinian block. Older models for Coast Range shortening based on balanced fault-bend fold-style cross sections are a poor approximation of Salinian block deformation, and may lead to mechanically improbable fault geometries that overestimate the amount of shortening.

Shortened stapedius tendon: a rare cause of conductive hearing loss.

Science.gov (United States)

Zawawi, F; Varshney, R; Schloss, M D

2014-01-01

Anomalies of the stapedius tendon have been reported to cause conductive hearing loss; in theory, such anomalies limit the movement of the stapes. To demonstrate a rare cause of conductive hearing loss resulting from anomaly of the stapedius tendon and to compare the clinical findings of this patient to other stapedius tendon anomalies reported in the literature. Case report of a single case of shortened stapedius tendon and a review of the English literature on stapedius tendon anomalies. This is a case report of a 15-year-old boy with shortened stapedius tendon causing unilateral hearing loss, accompanied by a review of the literature. Contrary to other reported cases, this patient did not have an ossified tendon, but rather an extremely short tendon. The boy regained normal hearing following excision of the stapedius tendon. A shortened stapedius tendon is a very rare diagnosis, yet it should be considered as a possible cause of conductive hearing loss.

Considering Time in Orthophotography Production: from a General Workflow to a Shortened Workflow for a Faster Disaster Response

Science.gov (United States)

Lucas, G.

2015-08-01

orthophoto production faster. The shortened workflow reduces the production time by more than three whereas the positional error increases from 1 GSD to 1.5 GSD. The examination of time allocation through the production process shows that it is worth sparing time in the post-processing phase.

Renal function and plasma dabigatran level measured at trough by diluted thrombin time assay

Directory of Open Access Journals (Sweden)

Marta E. Martinuzzo

2017-02-01

Full Text Available Dabigatran etexilate (direct thrombin inhibitor is effective in preventing embolic stroke in patients with atrial fibrillation. It does not require laboratory control, but given the high renal elimination, its measurement in plasma is important in renal failure. The objectives of the study were to verify the analytical quality of the diluted thrombin time assay for measurement of dabigatran plasma concentration (cc, correlate cc with classic coagulation assays, prothrombin time (PT and activated partial thromboplastin time (APTT, and evaluate them according to the creatinine clearance (CLCr. Forty plasma samples of patients (34 consecutive and 6 suspected of drug accumulation receiving dabigatran at 150 (n = 19 or 110 (n = 21 mg/12 hours were collected. Blood samples were drawn at 10-14 hours of the last intake. Dabigatran concentration was determined by diluted thrombin time (HemosIl DTI, Instrumentation Laboratory (IL. PT and APTT (IL were performed on two fotooptical coagulometers, ACL TOP 300 and 500 (IL. DTI presented intra-assay coefficient of variation < 5.4% and inter-assay < 6%, linearity range 0-493 ng/ml. Patients' cc: median 83 (4-945 ng/ml. Individuals with CLCr in the lowest tertile (22.6-46.1 ml/min showed significantly higher median cc: 308 (49-945, compared to the average 72 (12-190 and highest tertile, 60 (4-118 ng/ml. Correlation between cc and APTT or PT were moderate, r2 = 0.59 and -0.66, p < 0.0001, respectively. DTI test allowed us to quantify plasma dabigatran levels, both in patients with normal or altered renal function, representing a useful tool in clinical situations such as renal failure, pre surgery or emergencies

An in-house assay for BK polyomavirus quantification using the Abbott m2000 RealTime system.

Science.gov (United States)

Muldrew, Kenneth L; Lovett, Jennie L

2013-11-01

BK polyomavirus (BKPyV) quantification is useful for monitoring renal transplant patient response to therapy. The Abbott m2000 RealTime System employed by some clinical laboratories to perform US Food and Drug Administration-approved assays can also be used to develop in-house assays such as the one presented here. This study aimed to validate an in-house quantitative real-time PCR assay targeting the BKPyV major capsid VP1 gene for assessment of viral load using the Abbott m2000 RealTime System. BKPyV load was measured in 95 urine and plasma samples previously tested for BKPyV by one of three laboratories (46 BKPyV-positive samples consisting of 35 plasma and 11 urine samples; 49 samples negative for BKPyV consisting of 47 plasma and two urine samples). Two additional plasma specimens from the College of American Pathologists proficiency testing survey were also analysed. Precision studies were performed by diluting a high-viral-titre patient sample into BKPyV-negative pooled plasma to create high-positive (6.16 log10 copies ml(-1)) and low-positive (3.16 log10 copies ml(-1)) samples. For precision studies of inter-assay variability, a high-positive (7.0 log10 copies ml(-1)) and a low-positive (3.0 log10 copies ml(-1)) sample were measured in 20 separate runs. The assay's limit of quantification and limit of detection were 2.70 and 2.25 log10 copies ml(-1), respectively. The assay was linear from 2.70 to 9.26 log10 copies ml(-1). Of the 48 known positives, 43 were detected as positive, with three reported by the reference laboratory as values lower than the limit of detection. Two known positives at 3.27 and 3.80 log10 copies ml(-1) tested negative by the m2000 BKPyV assay. Of the 49 known negative samples, 48 were negative by the m2000 BKPyV load assay, with one sample confirmed positive by a reference laboratory. Qualitative analysis prior to discrepancy testing demonstrated a sensitivity of 89.58 % and a specificity of 97.96 %. Precision studies

Comparison of vegetable shortening and cocoa butter as vehicles for cortisol manipulation in Salmo trutta

DEFF Research Database (Denmark)

Birnie-Gauvin, Kim; Peiman, K. S.; Larsen, M. H.

2018-01-01

This study demonstrates that vegetable shortening and cocoa butter are two effective vehicles for intraperitoneal cortisol implants in juvenile teleosts, specifically brown trout Salmo trutta, residing in north temperate freshwater environments. Each vehicle showed a different pattern of cortisol...... elevation. Vegetable shortening was found to be a more suitable vehicle for long-term cortisol elevation [elevated at 3, 6 and 9 days post treatment (dpt)], while cocoa butter may be better suited for short-term cortisol elevation (only elevated at 3 dpt). Additionally, plasma cortisol levels were higher...... with cortisol–vegetable shortening than with cortisol–cocoa butter implants. Plasma glucose levels were elevated 6 and 9 dpt for fishes injected with cortisol–vegetable shortening, but did not change relative to controls and shams in cortisol–cocoa butter fishes. In conclusion, vegetable shortening and cocoa...

Deposition, clearance, and shortening of Kevlar para-aramid fibrils in acute, subchronic, and chronic inhalation studies in rats.

Science.gov (United States)

Kelly, D P; Merriman, E A; Kennedy, G L; Lee, K P

1993-10-01

The deposition and clearance of lung-deposited Kevlar para-aramid fibrils (subfibers) have been investigated as part of a subchronic and chronic inhalation toxicity testing program. Fibrils recovered from lung tissue in para-aramid-exposed Sprague-Dawley rats were microscopically counted and measured after exposures to airborne fibrils which were about 12 microns median length (ML) and < 0.3 micron median diameter. In each of three studies lung-recovered fibrils were progressively shorter with increasing residence time in the lungs. Twenty-eight days after a single 6-hr exposure at 400 respirable fibrils per cubic centimeter (f/cm3) the ML of recovered fibrils decreased to about 5 microns. Twenty-four months after a 3-week exposure to 25 or 400 f/cm3, fibrils reached about 2 microns ML. After 2 years of continuous exposure at 2.5, 25, or 100 f/cm3 or 1 year exposure plus 1 year recovery at 400 f/cm3, fibril ML approached 4 microns. In the 2-year study, the lung-fiber accumulation rate/exposure concentration was similar for the three highest concentrations and was about 3 x greater than that seen at 2.5 f/cm3, indicating that concentrations of about 25 f/cm3 or more may overwhelm clearance mechanisms. Time required for fibrils to be reduced to < 5 microns in the lung was markedly less at lower exposure concentration and shorter exposure time. The primary shortening mechanism is proposed to be long fibril cutting by enzymatic attack at fibril defects. However, length-selective fibril deposition and clearance may contribute to shortening in the first few days after exposure. The enzymatic cutting hypothesis is supported by measured increases in numbers of short fibers following cessation of exposures, continued shortening of the fibril length distribution up to 2 years following exposure, and in vitro fibril shortening after 3 months in a proteolytic enzyme preparation. The conclusion is that para-aramid fibrils are less durable in the lungs of rats than expected from

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.

How does ulnar shortening osteotomy influence morphologic changes in the triangular fibrocartilage complex?

Science.gov (United States)

Yamanaka, Yoshiaki; Nakamura, Toshiyasu; Sato, Kazuki; Toyama, Yoshiaki

2014-11-01

Ulnar shortening osteotomy often is indicated for treatment of injuries to the triangular fibrocartilage complex (TFCC). However, the effect of ulnar shortening osteotomy on the changes in shape of the TFCC is unclear. In our study, quantitative evaluations were performed using MRI to clarify the effect of ulnar shortening on triangular fibrocartilage (TFC) thickness attributable to disc regeneration of the TFC and TFC angle attributable to the suspension effect of ulnar shortening on the TFC. The purposes of this study were (1) to compare preoperative and postoperative TFC thickness and TFC angle on MR images to quantitatively evaluate the effect of ulnar shortening osteotomy on disc regeneration and the suspension effect on the TFC; and (2) to assess whether changes in TFC thickness and TFC angle correlated with the Mayo wrist score. Between 1995 and 2008, 256 patients underwent ulnar shortening osteotomy for TFCC injuries. The minimum followup was 24 months (mean, 51 months; range, 24-210 months). A total of 79 patients (31%) with complete followup including preoperative and postoperative MR images and the Mayo wrist score was included in this retrospective study. Evaluation of the postoperative MR images and the Mayo wrist score were performed at the final followup. The remaining 177 patients did not undergo postoperative MRI, or they had a previous fracture, large tears of the disc proper, or were lost to followup. Two orthopaedists, one of whom performed the surgeries, measured the TFC thickness and the TFC angle on coronal MR images before and after surgery for each patient. Correlations of the percent change in the TFC thickness and the magnitude of TFC angle change with age, sex, postoperative MR images, extent of ulnar shortening, preoperative ulnar variance, and postoperative Mayo wrist score were assessed. Stepwise regression analysis showed a correlation between the percent change in TFC thickness and preoperative ulnar variance (R2=0.21; β=-0.33; 95

Utility of the Abbott RealTime HCV Genotype Plus RUO assay used in combination with the Abbott RealTime HCV Genotype II assay.

Science.gov (United States)

He, Chao; Germer, Jeffrey J; Ptacek, Elizabeth R; Bommersbach, Carl E; Mitchell, P Shawn; Yao, Joseph D C

Hepatitis virus C (HCV) genotype (GT) determination and subtype (ST) differentiation (1a versus 1b) remain important for the selection of appropriate direct-acting antiviral (DAA) therapy. This study is a retrospective comparison of HCV GT and ST result distribution when using the Abbott RealTime HCV Genotype II assay (HCVGT II) alone and in combination with the Abbott RealTime HCV Genotype Plus RUO assay (HCVGT Plus) for routine testing of clinical serum specimens at a reference laboratory. HCVGT II results of specimens tested from June 2014 through January 2016 (period 1) were compared with combined results from HCVGT II and HCVGT Plus (HCVGT II/Plus) performed from January 2016 through January 2017 (period 2). A total of 44,127 and 25,361 specimens were tested during periods 1 and 2, respectively. Use of HCVGT II/Plus significantly reduced the frequency of GT 1 results without ST (0.4%) when compared to preliminary HCVGT II results during period 2 (5.3%; p < 0.01) and final HCVGT II results in period 1 (5.5%; p < 0.01). HCVGT II/Plus also resulted in GT 6 reactivity in 38 specimens with results of "HCV detected" (n = 17) or GT 1 (n = 21) following initial HCVGT II testing during period 2. When compared to the use of HCVGT II alone, HCVGT II/Plus significantly reduced the frequency of GT 1 without ST results observed in a large reference laboratory, while also enabling the identification of HCV GT 6. Copyright © 2018 Elsevier B.V. All rights reserved.

Masticatory Efficiency of Shortened Dental Arch Subjects with ...

African Journals Online (AJOL)

2017-05-16

May 16, 2017 ... of shortened dental arch subjects with removable partial denture: A comparative ... at the post- and pre-treatment phases was statistically significant (P = 0.001). The .... after the delivery of metal-based RPD with the denture in.

Potential improvement of CANDU NPP safety margins by shortening the response time of shutdown systems using FPGA based implementation

Energy Technology Data Exchange (ETDEWEB)

Jingke She, E-mail: jshe2@uwo.ca [Department of Electrical and Computer Engineering, University of Western Ontario, London, Ontario N6A 5B9 (Canada); Jin Jiang, E-mail: jjiang@eng.uwo.ca [Department of Electrical and Computer Engineering, University of Western Ontario, London, Ontario N6A 5B9 (Canada)

2012-03-15

Highlights: Black-Right-Pointing-Pointer Quantitative analysis of the safety margin improvement through thermalhydraulic simulation and analysis. Black-Right-Pointing-Pointer Hardware-in-the-loop simulation of realizing the improvement by an FPGA-based SDS1. Black-Right-Pointing-Pointer Verification of potential operating power upgrade without endangering the plant safety. - Abstract: The relationship between the peak values of critical reactor variables, such as neutronic power, inside a CANDU reactor and the speed of the response of its shutdown system has been analyzed in the event of a large loss of coolant accident (LOCA). The advantage of shortening the response time of the shutdown action has been demonstrated in term of the improved safety margin. A field programmable gate array (FPGA) platform has been chosen to implement such a shutdown system. Hardware-in-the-loop (HIL) simulations have been performed to demonstrate the feasibility of this concept. Furthermore, connections between the speed of response of the shutdown system and the nominal operating power level of the reactor have been drawn to support for potential power upgrade for existing power plants.

Evaluation of the PrimerDesign™ genesig real-time reverse transcription-polymerase chain reaction assay and the INFINITI® Respiratory Viral Panel Plus assay for the detection of human metapneumovirus in Kuwait.

Science.gov (United States)

Al-Turab, Mariam; Chehadeh, Wassim; Al-Mulla, Fahd; Al-Nakib, Widad

2012-04-01

Human metapneumovirus (hMPV) is a respiratory pathogen that was discovered in 2001 and is considered a major cause of both upper and lower respiratory tract infections. A sensitive, fast, and high-throughput diagnostic test is needed for the detection of hMPV that may assist in the clinical management as well as in the reduction of inappropriate therapy. Therefore, a comparison assessment was performed in this study between the PrimerDesign™ genesig real-time reverse transcription-polymerase chain reaction (RT-PCR) Assay and the INFINITI(®) Respiratory Viral Panel Plus Assay (RVP-Plus) for the detection of hMPV infection in patients with respiratory tract infections. A total of 200 respiratory samples were collected from 185 hospitalized patients, during the winter season in Kuwait. Of 185 patients, 10 (5.4%) were positive for hMPV RNA by the in-house RT-PCR assay, while 7 (4%) were positive for hMPV RNA by the real-time RT-PCR assay and 9 (5%) were positive for hMPV RNA by the INFINITI(®) RVP-Plus assay. The high incidence rate (60%) of hMPV infection was in January 2011. The sensitivity of the real-time RT-PCR and INFINITI(®) RVP-Plus assays was 70% and 90%, respectively, with specificity of 100% for both assays. hMPV types A and B could be identified in this study; however, discordant genotyping results were found between the direct sequencing method and the INFINITI(®) RVP-Plus assay in 33% of hMPV-positive patients. Copyright © 2012 Elsevier Inc. All rights reserved.

A Shortened versus Standard Matched Postpartum Magnesium ...

African Journals Online (AJOL)

Magnesium sulphate is currently the most ideal drug for the treatment of eclampsia but its use in Nigeria is still limited due its cost and clinicians inexperience with the drug. The purpose of this study was to determine whether a shortened postpartum course of magnesium sulphate is as effective as the standard Pritchard ...

Telomere shortening and survival in free-living corvids

NARCIS (Netherlands)

Salomons, H.M.; Mulder, G.A.; Zande, L. van de; Haussmann, M.F.; Linskens, M.H.K.; Verhulst, S.

2009-01-01

Evidence accumulates that telomere shortening reflects lifestyle and predicts remaining lifespan, but little is known of telomere dynamics and their relation to survival under natural conditions. We present longitudinal telomere data in free-living jackdaws (Corvus monedula) and test hypotheses on

In ovo exposure quail assay for risk assessment of endocrine disrupting chemicals.

Science.gov (United States)

Kamata, Ryo; Takahashi, Shinji; Shimizu, Akira; Morita, Masatoshi; Shiraishi, Fujio

2006-12-01

Although there are in vivo assays using various organisms for the risk assessment of chemicals with endocrine disrupting properties, effective experimental methods for avian species are still under debate. We have developed an in ovo exposure assay using Japanese quail eggs, aimed at assessing disrupting effects on avian reproductive development and function. Hybrid eggs from Brazilian Brown male and White Egg female quails, which can be genetically sexed by their plumage color after hatching, were prepared, and test materials dissolved in olive oil were injected into the air-chamber on day 10 of incubation. After sexual maturation of hatched chicks, we observed egg production by females and the egg quality and male-typical reproductive behavior, and then examined reproductive system morphology and serum steroid concentrations in both sexes. Treatment with a synthetic estrogen, diethylstilbestrol (DES, 0.5-50 ng/g egg), dose-dependently reduced the eggshell thickness and strength of eggs. A few females treated with 5 ng/g DES per egg produced soft-shelled/ unmarked eggs, and all laying females treated with 50 ng/g egg produced eggs completely lacking shells. DES also induced shortening of the left oviduct and abnormal development of the right oviduct in a dose-dependent manner, while testis weight was reduced symmetrically. In addition, 2,2',4',6'-tetrachlorobiphenyl-4-ol (10-1,000 ng/g egg), which previously showed relatively high estrogenic activity in vitro, caused dose-dependent shortening of the left oviduct and reduction in testis weight. The methods for evaluating endocrine disrupting effects and preparing experimental birds proposed in the present study are expected to facilitate assays for avian reproductive toxicology.

Shortening and Thickening of Metropolitan Los Angeles Measured and Inferred Using Geodesy

Science.gov (United States)

Argus, D.; Heflin, M.; Donnellan, A.; Webb, F.; Dong, D.; Hurst, K.; Jefferson, D.; Lyzenga, G.; Watkins, M.; Zumberge, J.

1999-01-01

Geodetic measurements using the Global Positioning System and other techniques show north-south shortening near Los Angeles to be fastest across the northern part of the metropolitan area, where an ESE-striking, 5- to 40-km-wide belt lying to the south of San Gabriel Mountains and to the north of downtown and West Los Angeles is shortening at 5 mm/yr.

Comparison of Batch Assay and Random Assay Using Automatic Dispenser in Radioimmunoassay

Energy Technology Data Exchange (ETDEWEB)

Moon, Seung Hwan; Jang, Su Jin; Kang, Ji Yeon; Lee, Dong Soo; Chung, June Key; Lee, Myung Chul [Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul (Korea, Republic of); Lee, Ho Young; Shin, Sun Young; Min, Gyeong Sun; Lee, Hyun Joo [Seoul National University college of Medicine, Seoul (Korea, Republic of)

2009-08-15

Radioimmunoassay (RIA) was usually performed by the batch assay. To improve the efficiency of RIA without increase of the cost and time, random assay could be a choice. We investigated the possibility of the random assay using automatic dispenser by assessing the agreement between batch assay and random assay. The experiments were performed with four items; Triiodothyronine (T3), free thyroxine (fT4), Prostate specific antigen (PSA), Carcinoembryonic antigen (CEA). In each item, the sera of twenty patients, the standard, and the control samples were used. The measurements were done 4 times with 3 hour time intervals by random assay and batch assay. The coefficient of variation (CV) of the standard samples and patients' data in T3, fT4, PSA, and CEA were assessed. ICC (Intraclass correlation coefficient) and coefficient of correlation were measured to assessing the agreement between two methods. The CVs (%) of T3, fT4, PSA, and CEA measured by batch assay were 3.2+-1.7%, 3.9+-2.1%, 7.1+-6.2%, 11.2+-7.2%. The CVs by random assay were 2.1+-1.7%, 4.8+-3.1%, 3.6+-4.8%, and 7.4+-6.2%. The ICC between the batch assay and random assay were 0.9968 (T3), 0.9973 (fT4), 0.9996 (PSA), and 0.9901 (CEA). The coefficient of correlation between the batch assay and random assay were 0.9924(T3), 0.9974 (fT4), 0.9994 (PSA), and 0.9989 (CEA) (p<0.05). The results of random assay showed strong agreement with the batch assay in a day. These results suggest that random assay using automatic dispenser could be used in radioimmunoassay

Comparison of Batch Assay and Random Assay Using Automatic Dispenser in Radioimmunoassay

International Nuclear Information System (INIS)

Moon, Seung Hwan; Jang, Su Jin; Kang, Ji Yeon; Lee, Dong Soo; Chung, June Key; Lee, Myung Chul; Lee, Ho Young; Shin, Sun Young; Min, Gyeong Sun; Lee, Hyun Joo

2009-01-01

Radioimmunoassay (RIA) was usually performed by the batch assay. To improve the efficiency of RIA without increase of the cost and time, random assay could be a choice. We investigated the possibility of the random assay using automatic dispenser by assessing the agreement between batch assay and random assay. The experiments were performed with four items; Triiodothyronine (T3), free thyroxine (fT4), Prostate specific antigen (PSA), Carcinoembryonic antigen (CEA). In each item, the sera of twenty patients, the standard, and the control samples were used. The measurements were done 4 times with 3 hour time intervals by random assay and batch assay. The coefficient of variation (CV) of the standard samples and patients' data in T3, fT4, PSA, and CEA were assessed. ICC (Intraclass correlation coefficient) and coefficient of correlation were measured to assessing the agreement between two methods. The CVs (%) of T3, fT4, PSA, and CEA measured by batch assay were 3.2±1.7%, 3.9±2.1%, 7.1±6.2%, 11.2±7.2%. The CVs by random assay were 2.1±1.7%, 4.8±3.1%, 3.6±4.8%, and 7.4±6.2%. The ICC between the batch assay and random assay were 0.9968 (T3), 0.9973 (fT4), 0.9996 (PSA), and 0.9901 (CEA). The coefficient of correlation between the batch assay and random assay were 0.9924(T3), 0.9974 (fT4), 0.9994 (PSA), and 0.9989 (CEA) (p<0.05). The results of random assay showed strong agreement with the batch assay in a day. These results suggest that random assay using automatic dispenser could be used in radioimmunoassay

Accelerated telomere shortening: Tracking the lasting impact of early institutional care at the cellular level.

Science.gov (United States)

Humphreys, Kathryn L; Esteves, Kyle; Zeanah, Charles H; Fox, Nathan A; Nelson, Charles A; Drury, Stacy S

2016-12-30

Studies examining the association between early adversity and longitudinal changes in telomere length within the same individual are rare, yet are likely to provide novel insight into the subsequent lasting effects of negative early experiences. We sought to examine the association between institutional care history and telomere shortening longitudinally across middle childhood and into adolescence. Buccal DNA was collected 2-4 times, between the ages of 6 and 15 years, in 79 children enrolled in the Bucharest Early Intervention Project (BEIP), a longitudinal study exploring the impact of early institutional rearing on child health and development. Children with a history of early institutional care (n=50) demonstrated significantly greater telomere shortening across middle childhood and adolescence compared to never institutionalized children (n=29). Among children with a history of institutional care, randomization to high quality foster care was not associated with differential telomere attrition across development. Cross-sectional analysis of children randomized to the care as usual group indicated shorter telomere length was associated with greater percent of the child's life spent in institutional care up to age 8. These results suggest that early adverse care from severe psychosocial deprivation may be embedded at the molecular genetic level through accelerated telomere shortening. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Pre-Clinical Testing of Real-Time PCR Assays for Diarrheal Disease Agents of Genera Escherichia and Shigella

Science.gov (United States)

2014-05-16

FOR DIARRHEAL DISEASE AGENTS OF GENERA ESCHERICHIA AND SHIGELLA May 16, 2014 Reporting Period: October 1, 2010 to September 30, 2013...10-2010 - 30-09-2013 PRE-CLINICAL TESTING OF REAL-TIME PCR ASSAYS FOR DIARRHEAL DISEASE AGENTS OF GENERA ESCHERICHIA AND SHIGELLA ...Texas (MOA 2007 - 2013. Agreement No.: DODI 4000.19; AFI 25-201). Pre-clinical test results qualify ETEC and Shigella real-time PCR assays as lead

Shortened duration of untreated first episode of psychosis

DEFF Research Database (Denmark)

Larsen, Tor Ketil; McGlashan, T H; Johannessen, Jan Olav

2001-01-01

OBJECTIVE: This study examined whether duration of untreated psychosis can be shortened in patients with first episodes of DSM-IV schizophrenia spectrum disorders and whether shorted duration alters patient appearance at treatment. METHOD: Two study groups were ascertained in the same Norwegian h...

A Highly Sensitive Chemiluminometric Assay for Real-Time Detection of Biological Hydrogen Peroxide Formation.

Science.gov (United States)

Zhu, Hong; Jia, Zhenquan; Trush, Michael A; Li, Y Robert

2016-05-01

Hydrogen peroxide (H 2 O 2 ) is a major reactive oxygen species (ROS) produced by various cellular sources, especially mitochondria. At high levels, H 2 O 2 causes oxidative stress, leading to cell injury, whereas at low concentrations, this ROS acts as an important second messenger to participate in cellular redox signaling. Detection and measurement of the levels or rates of production of cellular H 2 O 2 are instrumental in studying the biological effects of this major ROS. While a number of assays have been developed over the past decades for detecting and/or quantifying biological H 2 O 2 formation, none has been shown to be perfect. Perhaps there is no perfect assay for sensitively and accurately quantifying H 2 O 2 as well as other ROS in cells, wherein numerous potential reactants are present to interfere with the reliable measurement of the specific ROS. In this context, each assay has its own advantages and intrinsic limitations. This article describes a highly sensitive assay for real-time detection of H 2 O 2 formation in cultured cells and isolated mitochondria. This assay is based on the luminol/horseradish peroxidase-dependent chemiluminescence that is inhibitable by catalase. The article discusses the usefulness and shortcomings of this chemiluminometric assay in detecting biological H 2 O 2 formation induced by beta-lapachone redox cycling with both cells and isolated mitochondria.

Quantitation of hepatitis B virus DNA in plasma using a sensitive cost-effective "in-house" real-time PCR assay

Directory of Open Access Journals (Sweden)

Daniel Hubert Darius

2009-01-01

Full Text Available Background: Sensitive nucleic acid testing for the detection and accurate quantitation of hepatitis B virus (HBV is necessary to reduce transmission through blood and blood products and for monitoring patients on antiviral therapy. The aim of this study is to standardize an "in-house" real-time HBV polymerase chain reaction (PCR for accurate quantitation and screening of HBV. Materials and Methods: The "in-house" real-time assay was compared with a commercial assay using 30 chronically infected individuals and 70 blood donors who are negative for hepatitis B surface antigen, hepatitis C virus (HCV antibody and human immunodeficiency virus (HIV antibody. Further, 30 HBV-genotyped samples were tested to evaluate the "in-house" assay′s capacity to detect genotypes prevalent among individuals attending this tertiary care hospital. Results: The lower limit of detection of this "in-house" HBV real-time PCR was assessed against the WHO international standard and found to be 50 IU/mL. The interassay and intra-assay coefficient of variation (CV of this "in-house" assay ranged from 1.4% to 9.4% and 0.0% to 2.3%, respectively. Virus loads as estimated with this "in-house" HBV real-time assay correlated well with the commercial artus HBV RG PCR assay ( r = 0.95, P < 0.0001. Conclusion: This assay can be used for the detection and accurate quantitation of HBV viral loads in plasma samples. This assay can be employed for the screening of blood donations and can potentially be adapted to a multiplex format for simultaneous detection of HBV, HIV and HCV to reduce the cost of testing in blood banks.

Real-Time PCR Assay To Detect Smallpox Virus

Science.gov (United States)

Sofi Ibrahim, M.; Kulesh, David A.; Saleh, Sharron S.; Damon, Inger K.; Esposito, Joseph J.; Schmaljohn, Alan L.; Jahrling, Peter B.

2003-01-01

We developed a highly sensitive and specific assay for the rapid detection of smallpox virus DNA on both the Smart Cycler and LightCycler platforms. The assay is based on TaqMan chemistry with the orthopoxvirus hemagglutinin gene used as the target sequence. With genomic DNA purified from variola virus Bangladesh 1975, the limit of detection was estimated to be approximately 25 copies on both machines. The assay was evaluated in a blinded study with 322 coded samples that included genomic DNA from 48 different isolates of variola virus; 25 different strains and isolates of camelpox, cowpox, ectromelia, gerbilpox, herpes, monkeypox, myxoma, rabbitpox, raccoonpox, skunkpox, vaccinia, and varicella-zoster viruses; and two rickettsial species at concentrations mostly ranging from 100 fg/μl to 1 ng/μl. Contained within those 322 samples were variola virus DNA, obtained from purified viral preparations, at concentrations of 1 fg/μl to 1 ng/μl. On the Smart Cycler platform, 2 samples with false-positive results were detected among the 116 samples not containing variola virus tested; i.e., the overall specificity of the assay was 98.3%. On the LightCycler platform, five samples with false-positive results were detected (overall specificity, 95.7%). Of the 206 samples that contained variola virus DNA ranging in concentrations from 100 fg/μl to 1 ng/μl, 8 samples were considered negative on the Smart Cycler platform and 1 sample was considered negative on the LightCycler platform. Thus, the clinical sensitivities were 96.1% for the Smart Cycler instrument and 99.5% for the LightCycler instrument. The vast majority of these samples were derived from virus-infected cell cultures and variola virus-infected tissues; thus, the DNA material contained both viral DNA and cellular DNA. Of the 43 samples that contained purified variola virus DNA ranging in concentration from 1 fg/μl to 1 ng/μl, the assay correctly detected the virus in all 43 samples on both the Smart Cycler

A time-resolved luminescent competitive assay to detect L-selectin using aptamers as recognition elements

International Nuclear Information System (INIS)

Cywiński, Piotr J.; Olejko, Lydia; Löhmannsröben, Hans-Gerd

2015-01-01

L-selectin is a protein with potential importance for numerous diseases and clinical disorders. In this paper, we present a new aptamer-based luminescent assay developed to detect L-selectin. The sensing system working principle is based on Förster Resonance Energy Transfer (FRET) from a donor terbium complex (TbC) to an acceptor cyanine dye (Cy5). In the present approach, the biotinylated aptamer is combined with Cy5-labelled streptavidin (Cy5-Strep) to yield an aptamer-based acceptor construct (Apta-Cy5-Strep), while L-selectin is conjugated using luminescent TbC. Upon aptamer binding to the TbC-labelled L-selectin (L-selectin-TbC), permanent donor-acceptor proximity is established which allows for radiationless energy transfer to occur. However, when unlabelled L-selectin is added, it competes with the L-selectin-TbC and the FRET signal decreases as the L-selectin concentration increases. FRET from the TbC to Cy5 was observed with time-gated time-resolved luminescence spectroscopy. A significant change in the corrected luminescence signal was observed in the dynamic range of 10–500 ng/mL L-selectin, the concentration range relevant for accelerated cognitive decline of Alzheimer's disease, with a limit of detection (LOD) equal to 10 ng/mL. The aptasensor-based assay is homogeneous and can be realized within one hour. Therefore, this method has the potential to become an alternative to tedious heterogeneous analytical methods, e.g. based on enzyme-linked immunosorbent assay (ELISA). - Highlights: • Tb-based FRET assay with aptamers toward a protein is presented for the first time. • L-selectin can be detected in concentrations relevant for the Alzheimer's Disease. • The assay can be realized in one hour with the LOD equal to 10 ng/ml

A time-resolved luminescent competitive assay to detect L-selectin using aptamers as recognition elements

Energy Technology Data Exchange (ETDEWEB)

Cywiński, Piotr J., E-mail: piotr.cywinski@iap.fraunhofer.de [Functional Materials and Devices, Fraunhofer Institute for Applied Polymer Research, Geiselberstr.69, 14476 Potsdam-Golm (Germany); Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm (Germany); Olejko, Lydia; Löhmannsröben, Hans-Gerd [Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm (Germany)

2015-08-05

L-selectin is a protein with potential importance for numerous diseases and clinical disorders. In this paper, we present a new aptamer-based luminescent assay developed to detect L-selectin. The sensing system working principle is based on Förster Resonance Energy Transfer (FRET) from a donor terbium complex (TbC) to an acceptor cyanine dye (Cy5). In the present approach, the biotinylated aptamer is combined with Cy5-labelled streptavidin (Cy5-Strep) to yield an aptamer-based acceptor construct (Apta-Cy5-Strep), while L-selectin is conjugated using luminescent TbC. Upon aptamer binding to the TbC-labelled L-selectin (L-selectin-TbC), permanent donor-acceptor proximity is established which allows for radiationless energy transfer to occur. However, when unlabelled L-selectin is added, it competes with the L-selectin-TbC and the FRET signal decreases as the L-selectin concentration increases. FRET from the TbC to Cy5 was observed with time-gated time-resolved luminescence spectroscopy. A significant change in the corrected luminescence signal was observed in the dynamic range of 10–500 ng/mL L-selectin, the concentration range relevant for accelerated cognitive decline of Alzheimer's disease, with a limit of detection (LOD) equal to 10 ng/mL. The aptasensor-based assay is homogeneous and can be realized within one hour. Therefore, this method has the potential to become an alternative to tedious heterogeneous analytical methods, e.g. based on enzyme-linked immunosorbent assay (ELISA). - Highlights: • Tb-based FRET assay with aptamers toward a protein is presented for the first time. • L-selectin can be detected in concentrations relevant for the Alzheimer's Disease. • The assay can be realized in one hour with the LOD equal to 10 ng/ml.

Detection of 12 respiratory viruses by duplex real time PCR assays in respiratory samples.

Science.gov (United States)

Arvia, Rosaria; Corcioli, Fabiana; Ciccone, Nunziata; Della Malva, Nunzia; Azzi, Alberta

2015-12-01

Different viruses can be responsible for similar clinical manifestations of respiratory infections. Thus, the etiological diagnosis of respiratory viral diseases requires the detection of a large number of viruses. In this study, 6 duplex real-time PCR assays, using EvaGreen intercalating dye, were developed to detect 12 major viruses responsible for respiratory diseases: influenza A and B viruses, enteroviruses (including enterovirus spp, and rhinovirus spp), respiratory syncytial virus, human metapneumovirus, coronaviruses group I (of which CoV 229E and CoV NL63 are part) and II (including CoV OC43 and CoV HKU1), parainfluenza viruses type 1, 2, 3 and 4, human adenoviruses and human bocaviruses. The 2 target viruses of each duplex reaction were distinguishable by the melting temperatures of their amplicons. The 6 duplex real time PCR assays were applied for diagnostic purpose on 202 respiratory samples from 157 patients. One hundred fifty-seven samples were throat swabs and 45 were bronchoalveolar lavages. The results of the duplex PCR assays were confirmed by comparison with a commercial, validated, assay; in addition, the positive results were confirmed by sequencing. The analytical sensitivity of the duplex PCR assays varied from 10(3) copies/ml to 10(4) copies/ml. For parainfluenza virus 2 only it was 10(5) copies/ml. Seventy clinical samples (35%) from 55 patients (30 children and 25 adults) were positive for 1 or more viruses. In adult patients, influenza A virus was the most frequently detected respiratory virus followed by rhinoviruses. In contrast, respiratory syncytial virus was the most common virus in children, followed by enteroviruses, influenza A virus and coronavirus NL63. The small number of samples/patients does not allow us to draw any epidemiological conclusion. Altogether, the results of this study indicate that the 6 duplex PCR assays described in this study are sensitive, specific and cost-effective. Thus, this assay could be

Human Sperm Bioassay for Reprotoxicity Testing in Embryo Culture Media: Some Practical Considerations in Reducing the Assay Time

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Amjad Hossain

2010-01-01

Full Text Available Human sperm assay (HSA is a preferred in house quality control and proficiency test (PT practiced in fertility laboratories. HSA is performed over varying durations, apparently without following set criteria. To better understand the assay time required for reprotoxicity testing in embryo culture media, we compared American-Association-of-Bioanalysts-(AAB- administered HSA data to our own assay performed using PT samples obtained from AAB. Participating laboratories were required to culture sperm for 48 hours to determine media acceptability. Conclusions drawn from 48- and 24-hour observations were the same, suggesting that HSA could identify reprotoxic media in less time than required by AAB. Our assay revealed that changes in motility grade in adulterated media are significantly different from those in control media. Furthermore, grade changes can be identified earlier than differences in motility loss between samples. Analyzing motility and motility quality together provides a method for establishing an optimal time for HSA.

Comparison of vegetable shortening and cocoa butter as vehicles for cortisol manipulation in Salmo trutta.

Science.gov (United States)

Birnie-Gauvin, K; Peiman, K S; Larsen, M H; Aarestrup, K; Gilmour, K M; Cooke, S J

2018-01-01

This study demonstrates that vegetable shortening and cocoa butter are two effective vehicles for intraperitoneal cortisol implants in juvenile teleosts, specifically brown trout Salmo trutta, residing in north temperate freshwater environments. Each vehicle showed a different pattern of cortisol elevation. Vegetable shortening was found to be a more suitable vehicle for long-term cortisol elevation [elevated at 3, 6 and 9 days post treatment (dpt)], while cocoa butter may be better suited for short-term cortisol elevation (only elevated at 3 dpt). Additionally, plasma cortisol levels were higher with cortisol-vegetable shortening than with cortisol-cocoa butter implants. Plasma glucose levels were elevated 6 and 9 dpt for fishes injected with cortisol-vegetable shortening, but did not change relative to controls and shams in cortisol-cocoa butter fishes. In conclusion, vegetable shortening and cocoa butter are both viable techniques for cortisol manipulation in fishes in temperate climates, providing researchers with different options depending on study objectives. © 2017 The Fisheries Society of the British Isles.

GLUTAMIN MEMPERCEPAT WAKTU PEMULIHAN JUMLAH SEL LIMFOSIT LIEN SETELAH AKTIVITAS FISIK MAKSIMAL PADA MENCIT (GLUTAMINE SHORTENS RECOVERY TIME OF LIEN LYMPHOCYTES AFTER EXCESSIVE PHYSICAL ACTIVITY IN MICE

Directory of Open Access Journals (Sweden)

I Made Jawi

2007-06-01

Full Text Available The immunologic? system? of the body requires? suitable recovery time after? excessive physical? activity. The recovery? time of spleen lymphocytes after? excessive? physical activity? in one? investigation was? 3? days. The? aim? of this? research is to identify?the role of? glutamine? in shortening? the recovery time of? spleen? lymphocytes? after?excessive physical activity. The? study? was conducted? on? 70? adults? Balb/c mice which? were? divided? into? 7? groups, with? a randomized control? group post-test? only design. In this? study? an observation? was made on? spleen? lymphocytes? of control, after? excessive? physical activity(in the the? form of swimming? until? near? drowning with glutamine,? without glutamine ?and? after? the? recovery time of 1 and 2 days? of? each of? the 10 mice. Spleen? lymphocytes? were? counted in spleen preparation by mikroskop. The data obtained were tested? by? one way Anova. The findings? showed? that the number of spleen? lymphocytes significantly decrease after? excessive? physical activity?? in the?glutamine? and? non glutamine groups ( p < 0,05.The number of spleen? lymphocytes? was? not different as compered to control group or returned? to normal after recovery? time? of 1? day? in? the? glutamine group (p > 0,05 .?In the nonglutamine group the number of spleen lymphocytes was different from control group until 2 days (p<0,05 . From this finding it can be concluded that glutamine? shortens the recovery time of spleen lymphocytes? after? excessive? physical activity in mice.

Shortened Lifespan and Lethal Hemorrhage in a Hemophilia A Mouse Model.

Science.gov (United States)

Staber, Janice M; Pollpeter, Molly J

2016-01-01

Hemophilia A animal models have helped advance our understanding of factor VIII deficiency. Previously, factor VIII deficient mouse models were reported to have a normal life span without spontaneous bleeds. However, the bleeding frequency and survival in these animals has not been thoroughly evaluated. To investigate the survival and lethal bleeding frequency in two strains of E-16 hemophilia A mice. We prospectively studied factor VIII deficient hemizygous affected males (n = 83) and homozygous affected females (n = 55) for survival and bleeding frequency. Animals were evaluated for presence and location of bleeds as potential cause of death. Hemophilia A mice had a median survival of 254 days, which is significantly shortened compared to wild type controls (p hemophilia A mice experienced hemorrhage in several tissues. This previously-underappreciated shortened survival in the hemophilia A murine model provides new outcomes for investigation of therapeutics and also reflects the shortened lifespan of patients if left untreated.

Molecular detection and confirmation of Neisseria gonorrhoeae in urogenital and extragenital specimens using the Abbott CT/NG RealTime assay and an in-house assay targeting the porA pseudogene.

LENUS (Irish Health Repository)

Walsh, A

2011-04-01

Culture for detection of Neisseria gonorrhoeae (NG) is being replaced by molecular assays, but difficulties are observed with false positive and negatives results, especially for extragenital samples. This study evaluates the Abbott CT\\/NG Real-Time assay and a real-time porA pseudogene assay. Samples (n = 600) from a mixed prevalence Irish population include 164 male urines with corresponding urethral swabs, 58 endocervical swabs, 173 male pharyngeal swabs, 205 male rectal swabs, 36 NG clinical isolates and 26 commensal Neisseria species isolates. There was a 100% concordance between the Abbott CT\\/NG Real-Time and the porA assay. The positivity rate was 1.2%, 1.7%, 8.1% and 5.8% for FVU\\/urethral swabs, endocervical, pharyngeal and rectal swabs, respectively. These results were compared to culture and discrepancies were found with nine pharyngeal and three rectal swabs. Seven of the 12 discrepant positive samples were sequenced and were confirmed "true positives". The sensitivity and specificity of the molecular assays was 100%. The sensitivity of the culture-based testing was 100% for urogenital samples but 36% and 75% for pharyngeal and rectal swabs, respectively. The combined Abbott CT\\/NG and porA assays provide a valuable alternative to culture and also generate a significant increase in the diagnosis of pharyngeal and rectal NG infection.

Stochastic variation in telomere shortening rate causes heterogeneity of human fibroblast replicative life span.

Science.gov (United States)

Martin-Ruiz, Carmen; Saretzki, Gabriele; Petrie, Joanne; Ladhoff, Juliane; Jeyapalan, Jessie; Wei, Wenyi; Sedivy, John; von Zglinicki, Thomas

2004-04-23

The replicative life span of human fibroblasts is heterogeneous, with a fraction of cells senescing at every population doubling. To find out whether this heterogeneity is due to premature senescence, i.e. driven by a nontelomeric mechanism, fibroblasts with a senescent phenotype were isolated from growing cultures and clones by flow cytometry. These senescent cells had shorter telomeres than their cycling counterparts at all population doubling levels and both in mass cultures and in individual subclones, indicating heterogeneity in the rate of telomere shortening. Ectopic expression of telomerase stabilized telomere length in the majority of cells and rescued them from early senescence, suggesting a causal role of telomere shortening. Under standard cell culture conditions, there was a minor fraction of cells that showed a senescent phenotype and short telomeres despite active telomerase. This fraction increased under chronic mild oxidative stress, which is known to accelerate telomere shortening. It is possible that even high telomerase activity cannot fully compensate for telomere shortening in all cells. The data show that heterogeneity of the human fibroblast replicative life span can be caused by significant stochastic cell-to-cell variation in telomere shortening.

Real-time pcr (qpcr) assay for rhizoctonia solani anastomoses group ag2-2 iiib

International Nuclear Information System (INIS)

Abbas, S.J.; Ahmad, B.

2014-01-01

Rhizoctonia solani anastomosis group AG2-2 IIIB is a severe sugar beet and maize pathogen. It causes crown and root rot disease which leads to yield losses world-wide. The soil-borne pathogen is difficult to detect and quantify by conventional methods. We developed a real-time PCR (qPCR) assay for the quantification of genomic DNA of Rhizoctonia solani AG2-2 IIIB based on the ITS region of rDNA genes. The limit of quantification of the assay is 1.8 pg genomic DNA. The amplification efficiency was 96.4. The assay will be helpful in the diagnoses of Rhizoctonia solani infection of sugar beet and maize roots and in the quantification of R. solani AG2-2 IIIB inoculum in plant debris and soil. (author)

Shortening of culture time in conventional cytogenetic dosimetry

International Nuclear Information System (INIS)

Lamadrid, Ana I.; Gonzalez, Jorge E.; Romero, Ivonne; Garcia, Omar; Roy, Laurence

2008-01-01

Conventional cytogenetic dosimetry based on chromosome aberration in metaphases is a 'gold standard' of bio-dosimetry techniques for radiation dose assessment. This method is laborious and time consuming, the culturing process requires about 48 hours to obtain a satisfactory number of lymphocytes in mitosis. The current approach to reduce the dose estimation time by cytogenetic dosimetry is the preliminary estimation of dose counting only 50 metaphases. Another possibility is to reduce the culture time. The possibility of reduce the culture time under 48 hours adding Calyculin A has been suggested recently. In the present study we tested shorter times using Calyculin A and considering the G2/M-PCC index as culture quality indicator. Peripheral blood from healthy individuals was irradiated and then maintained at 37 C degrees for 2 hours allowing to act the cellular reparation mechanisms, lymphocytes were culture in RPMI 1640 supplemented with foetal calf serum and phytohemagglutinin. Colcemid was added 24 hours after cultures started and Calyculin A was added for the last hour. The cells were collected by centrifugation between 30 to 48 hours. The cells were treated with a hypotonic solution and the fixed cells dropped onto slides. The slides were stained with Giemsa. The incidence of metaphases with chromosomes well defined was scored. Two operators participated to the scoring according the same criteria. The results were analyzed to comparing the G2/M-PCC index relatives to achieve the shortest culture duration. The culture time reduction to 40 hours gives enough G2/M-PCC cells for dose estimation analysis. Lower culture times produced very low G2/M-PCC index. (author)

On the shortening of Indian summer monsoon season in a warming scenario

Science.gov (United States)

Sabeerali, C. T.; Ajayamohan, R. S.

2018-03-01

Assessing the future projections of the length of rainy season (LRS) has paramount societal impact considering its potential to alter the seasonal mean rainfall over the Indian subcontinent. Here, we explored the projections of LRS using both historical and Representative Concentration Pathways 8.5 (RCP8.5) simulations of the Coupled Model Intercomparison Project Phase5 (CMIP5). RCP8.5 simulations project shortening of the LRS of Indian summer monsoon by altering the timing of onset and withdrawal dates. Most CMIP5 RCP8.5 model simulations indicate a faster warming rate over the western tropical Indian Ocean compared to other regions of the Indian Ocean. It is found that the pronounced western Indian Ocean warming and associated increase in convection results in warmer upper troposphere over the Indian Ocean compared to the Indian subcontinent, reducing the meridional gradient in upper tropospheric temperature (UTT) over the Asian summer monsoon (ASM) domain. The weakening of the meridional gradient in UTT induces weakening of easterly vertical wind shear over the ASM domain during first and last phase of monsoon, facilitate delayed (advanced) monsoon onset (withdrawal) dates, ensues the shortening of LRS of the Indian summer monsoon in a warming scenario.

Molecular-dynamics simulation of crystalline 18-crown-6: thermal shortening of covalent bonds

NARCIS (Netherlands)

van Eerden, J.; Harkema, Sybolt; Feil, D.

1990-01-01

Molecular-dynamics simulations of crystalline 18-crown-6 have been performed in a study of the apparent thermal shortening of covalent bonds observed in crystal structures. At 100 K, a shortening of 0.006 _+ 0.001 A for C----C and C----O bonds was obtained. This result was found to be independent of

Duplex Real-Time PCR Assay Distinguishes Aedes aegypti From Ae. albopictus (Diptera: Culicidae) Using DNA From Sonicated First-Instar Larvae.

Science.gov (United States)

Kothera, Linda; Byrd, Brian; Savage, Harry M

2017-11-07

Aedes aegypti (L.) and Ae. albopictus (Skuse) are important arbovirus vectors in the United States, and the recent emergence of Zika virus disease as a public health concern in the Americas has reinforced a need for tools to rapidly distinguish between these species in collections made by vector control agencies. We developed a duplex real-time PCR assay that detects both species and does not cross-amplify in any of the other seven Aedes species tested. The lower limit of detection for our assay is equivalent to ∼0.03 of a first-instar larva in a 60-µl sample (0.016 ng of DNA per real-time PCR reaction). The assay was sensitive and specific in mixtures of both species that reflected up to a 2,000-fold difference in DNA concentration. In addition, we developed a simple protocol to extract DNA from sonicated first-instar larvae, and used that DNA to test the assay. Because it uses real-time PCR, the assay saves time by not requiring a separate visualization step. This assay can reduce the time needed for vector control agencies to make species identifications, and thus inform decisions about surveillance and control. Published by Oxford University Press on behalf of Entomological Society of America 2017 This work is written by US Government employees and is in the public domain in the US.

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

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

Evaluation of a real-time PCR assay based on the single-copy SAG1 gene for the detection of Toxoplasma gondii.

Science.gov (United States)

Yu, Haijie; Huang, Bin; Zhuo, Xunhui; Chen, Xueqiu; Du, Aifang

2013-11-08

Real-time PCR-based detection of Toxoplasma gondii is very sensitive and convenient for diagnosing toxoplasmosis. However, the performance of the PCR assays could be influenced by the target gene chosen. Here we evaluate a real-time PCR assay using double-stranded DNA dyes (SYBR(®) Green I assay) with a new set of primers targeting the SAG1 gene for the fast and specific detection of T. gondii. The assay showed higher sensitivity than conventional PCR protocols using T. gondii DNA as template. The detection limit of the developed real-time PCR assay was in the order of 1 tachyzoite. The assay was also assessed by experimentally infected mice and showed positive results for blood (25%), spleen (50%) and lung (50%) as early as 1 dpi. The specificity of the assay was confirmed by using DNA from Neospora caninum, Escherichia coli, Babesia bovis, Trypanosoma brucei, Cryptosporidium parvum, and Toxocara canis. Assay applicability was successfully tested in blood samples collected from slaughtered pigs. These results indicate that, based on SYBR(®) green I, the quantitative SAG1 assay may also be useful in the study of the pathogenicity, immunoprophylaxis, and treatment of T. gondii. Copyright © 2013 Elsevier B.V. All rights reserved.

Rapid identification of ST131 Escherichia coli by a novel multiplex real-time allelic discrimination assay.

Science.gov (United States)

François, Patrice; Bonetti, Eve-Julie; Fankhauser, Carolina; Baud, Damien; Cherkaoui, Abdessalam; Schrenzel, Jacques; Harbarth, Stephan

2017-09-01

Escherichia coli sequence type 131 is increasingly described in severe hospital infections. We developed a rapid real-time allelic discrimination assay for the rapid identification of E. coli ST131 isolates. This rapid assay represents an affordable alternative to sequence-based strategies before completing characterization of potentially highly virulent isolates of E. coli. Copyright © 2017 Elsevier B.V. All rights reserved.

Common Patterns of Congenital Lower Extremity Shortening: Diagnosis, Classification, and Follow-up.

Science.gov (United States)

Bedoya, Maria A; Chauvin, Nancy A; Jaramillo, Diego; Davidson, Richard; Horn, B David; Ho-Fung, Victor

2015-01-01

Congenital lower limb shortening is a group of relatively rare, heterogeneous disorders. Proximal focal femoral deficiency (PFFD) and fibular hemimelia (FH) are the most common pathologic entities in this disease spectrum. PFFD is characterized by variable degrees of shortening or absence of the femoral head, with associated dysplasia of the acetabulum and femoral shaft. FH ranges from mild hypoplasia to complete absence of the fibula with variable shortening of the tibia. The development of the lower limb requires complex and precise gene interactions. Although the etiologies of PFFD and FH remain unknown, there is a strong association between the two disorders. Associated congenital defects in the lower extremity are found in more than 50% of patients with PFFD, ipsilateral FH being the most common. FH also has a strong association with shortening and bowing of the tibia and with foot deformities such as absence of the lateral rays of the foot. Early diagnosis and radiologic classification of these abnormalities are imperative for appropriate management and surgical planning. Plain radiography remains the main diagnostic imaging modality for both PFFD and FH, and appropriate description of the osseous abnormalities seen on radiographs allows accurate classification, prognostic evaluation, and surgical planning. Minor malformations may commonly be misdiagnosed. ©RSNA, 2015.

L-Carnosine reduces telomere damage and shortening rate in cultured normal fibroblasts

International Nuclear Information System (INIS)

Shao Lan; Li Qinghuan; Tan Zheng

2004-01-01

Telomere is the repetitive DNA sequence at the end of chromosomes, which shortens progressively with cell division and limits the replicative potential of normal human somatic cells. L-Carnosine, a naturally occurring dipeptide, has been reported to delay the replicative senescence, and extend the lifespan of cultured human diploid fibroblasts. In this work, we studied the effect of carnosine on the telomeric DNA of cultured human fetal lung fibroblast cells. Cells continuously grown in 20 mM carnosine exhibited a slower telomere shortening rate and extended lifespan in population doublings. When kept in a long-term nonproliferating state, they accumulated much less damages in the telomeric DNA when cultured in the presence of carnosine. We suggest that the reduction in telomere shortening rate and damages in telomeric DNA made an important contribution to the life-extension effect of carnosine

Real-time RPA assay for rapid detection and differentiation of wild-type pseudorabies and gE-deleted vaccine viruses.

Science.gov (United States)

Wang, Jianchang; Liu, Libing; Wang, Jinfeng; Pang, Xiaoyu; Yuan, Wanzhe

2018-02-15

The objective of this study was to develop a dual real-time recombinase polymerase amplification (RPA) assay using exo probes for the detection and differentiation of pseudorabies virus (PRV). Specific RPA primers and probes were designed for gB and gE genes of PRV within the conserved region of viral genome. The reaction process can be completed in 20 min at 39 °C. The dual real-time RPA assay performed in the single tube was capable of specific detecting and differentiating of the wild-type PRV and gE-deleted vaccine strains, without cross-reactions with other non-targeted pig viruses. The analytical sensitivity of the assay was 10 2 copies for gB and gE genes. The dual real-time RPA demonstrated a 100% diagnostic agreement with the real-time PCR on 4 PRV strains and 37 clinical samples. Through the linear regression analysis, the R 2 value of the real-time RPA and the real-time PCR for gB and gE was 0.983 and 0.992, respectively. The dual real-time RPA assay provides an alternative useful tool for rapid, simple, and reliable detection and differentiation of PRV, especially in remote and rural areas. Copyright © 2017 Elsevier Inc. All rights reserved.

Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples.

Science.gov (United States)

Leach, L; Zhu, Y; Chaturvedi, S

2018-02-01

Candida auris is an emerging multidrug-resistant yeast causing invasive health care-associated infection with high mortality worldwide. Rapid identification of C. auris is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan-based real-time PCR assay targeting the internal transcribed spacer 2 ( ITS 2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive, with the detection limit of 1 C. auris CFU/PCR. The performance of the C. auris real-time PCR assay was evaluated by using 623 surveillance samples, including 365 patient swabs and 258 environmental sponges. Real-time PCR yielded positive results from 49 swab and 58 sponge samples, with 89% and 100% clinical sensitivity with regard to their respective culture-positive results. The real-time PCR also detected C. auris DNA from 1% and 12% of swab and sponge samples with culture-negative results, indicating the presence of dead or culture-impaired C. auris The real-time PCR yielded results within 4 h of sample processing, compared to 4 to 14 days for culture, reducing turnaround time significantly. The new real-time PCR assay allows for accurate and rapid screening of C. auris and can increase effective control and prevention of this emerging multidrug-resistant fungal pathogen in health care facilities. Copyright © 2018 Leach et al.

Compression and Combining Based on Channel Shortening and Rank Reduction Technique for Cooperative Wireless Sensor Networks

KAUST Repository

Ahmed, Qasim Zeeshan

2013-12-18

This paper investigates and compares the performance of wireless sensor networks where sensors operate on the principles of cooperative communications. We consider a scenario where the source transmits signals to the destination with the help of L sensors. As the destination has the capacity of processing only U out of these L signals, the strongest U signals are selected while the remaining (L?U) signals are suppressed. A preprocessing block similar to channel-shortening is proposed in this contribution. However, this preprocessing block employs a rank-reduction technique instead of channel-shortening. By employing this preprocessing, we are able to decrease the computational complexity of the system without affecting the bit error rate (BER) performance. From our simulations, it can be shown that these schemes outperform the channel-shortening schemes in terms of computational complexity. In addition, the proposed schemes have a superior BER performance as compared to channel-shortening schemes when sensors employ fixed gain amplification. However, for sensors which employ variable gain amplification, a tradeoff exists in terms of BER performance between the channel-shortening and these schemes. These schemes outperform channel-shortening scheme for lower signal-to-noise ratio.

Evaluation of performance of human immunodeficiency virus antigen/antibody combination assays in Taiwan.

Science.gov (United States)

Chang, Chun-Kai; Kao, Cheng-Feng; Lin, Pi-Han; Huang, Hui-Lin; Ho, Shu-Yuan; Wong, Kuo-Chen; Lin, Bo-Chang; Yeh, Chang-Ching; Lee, Chia-Yeh; Kao, Chuan-Liang; Lee, Chun-Nan; Chang, Sui-Yuan; Yang, Jyh-Yuan

2017-08-01

The fourth-generation human immunodeficiency virus (HIV) combination assay, which can simultaneously detect the presence of anti-HIV antibody and HIV antigen, has been shown to shorten the window period in HIV diagnosis compared with the third-generation HIV antibody immunoassay. This study was aimed to determine the performance of HIV combination assays in Taiwan, where the HIV-1 seroprevalence is 0.007% and HIV-2 infection has never been reported. Performance of three fourth-generation HIV Ag/Ab combination assays (Dia.Pro, Wantai, and Bio-Rad) and one third-generation HIV Ab immunoassay (AxSYM HIV 1/2 gO) was assessed. A total of 152 specimens, including 86 confirmed HIV-seropositive and 66 HIV-seronegative samples, were used in the study. The sensitivity of four assays varied from 98.8% to 100%, and specificity varied from 98.5% to 100%. Performance of the 75 equivocal samples, the HIV status of which was confirmed later, in terms of negative prediction varied from 81.8% to 87.5%. The Bio-Rad and Dia.Pro assays exhibited higher sensitivity for the detection of p24 antigen among the three fourth-generation HIV combination assays. The three fourth-generation HIV Ag/Ab combination assays exhibited better sensitivity, specificity, and negative prediction than the third-generation HIV Ab immunoassay. Copyright © 2015. Published by Elsevier B.V.

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

Life-shortening and carcinogenesis in mice irradiated neonatally with x rays

International Nuclear Information System (INIS)

Sasaki, S.; Kasuga, T.

1981-01-01

The characteristics of life-shortening and carcinogenesis were investigated in x-irradiated neonatal B6WFr mice. Animals were irradiated with 24 hr after birth and allowed to complete their normal life span. Mean life span was shortened linearly with doses at a rate of 9.1% per 100 R for females and 9.8% for males. The spectrum of neoplastic diseases was apparently modulated by x irradiation, showing neonatal B6WFr mice to be highly susceptible to the induction of thymic lymphoma, liver tumor, and pituitary tumor. The dose-response relationship for thymice lymphoma could be described by a linear-quadratic model, and linearity could be rejected. Thymic lymphoma developed after a short latent period, resulting in death between 100 and 450 days of age. Liver and pituitary tumors increased with increasing dose up to 400 R and decreased thereafter. The latent period for liver tumor development was apparently shortened with increasing doses. Pituitary tumor developed in excess only in females after a long latent period

Mastication in subjects with extremely shortened dental arches rehabilitated with removable partial dentures.

Science.gov (United States)

Arce-Tumbay, Jackelyn; Sanchez-Ayala, Alfonso; Sotto-Maior, Bruno Salles; Senna, Plinio Mendes; Campanha, Nara Hellen

2011-01-01

Mastication was evaluated in subjects presenting extremely shortened dental arches (ESDAs) rehabilitated with mandibular free-end removable partial dentures (RPDs). Subjects were divided into four groups (n = 10): those with a complete dentition, those with ESDAs, and those with ESDAs who were rehabilitated with an RPD, who were evaluated both with and without their prostheses. Mastication was measured through masticatory performance, time, and ability. RPD wearers showed higher masticatory performance (P mastication in ESDA subjects but without achieving normal mastication levels.

Masticatory efficiency of shortened dental arch subjects with ...

African Journals Online (AJOL)

Objective: The objective of this study was to compare the masticatory efficiency in subjects with shortened dental arch (SDA) before and after restoration with removable partial denture (RPD). Materials and Methods: This was a prospective study carried out on 36 consecutive patients. The subjects were asked to chew 5 g of ...

Two quantitative real-time PCR assays for the detection of penaeid shrimp and blue crab, crustacean shellfish allergens.

Science.gov (United States)

Eischeid, Anne C; Kim, Bang-hyun; Kasko, Sasha M

2013-06-19

Food allergen detection methods must be able to specifically detect minute quantities of an allergenic food in a complex food matrix. One technique that can be used is real-time PCR. For the work described here, real-time PCR assays were developed to detect penaeid shrimp and blue crab, crustacean shellfish allergens. The method was tested using shrimp meat and crab meat spiked into several types of foods, including canned soups, deli foods, meat, seafood, and prepared seafood products. Foods were spiked with either shrimp or crab at levels ranging from 0.1 to 10⁶ parts per million (ppm) and analyzed either raw or cooked by a variety of methods. Real-time PCR data were used to generate linear standard curves, and assays were evaluated with respect to linear range and reaction efficiency. Results indicate that both assays performed well in a variety of food types. High reaction efficiencies were achieved across a linear range of 6-8 orders of magnitude. Limits of detection were generally between 0.1 and 1 ppm. Cooking methods used to simulate thermal processing of foods had little effect on assay performance. This work demonstrates that real-time PCR can be a valuable tool in the detection of crustacean shellfish.

Cucurbiturils: molecular nanocapsules for time-resolved fluorescence-based assays.

Science.gov (United States)

Marquez, Cesar; Huang, Fang; Nau, Werner M

2004-03-01

A new fluorescent host-guest system based on the inclusion of the fluorophore 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) into the cavity of the molecular container compound cucurbit[7]uril (CB7) has been designed which possesses an exceedingly long-lived emission (690 ns in aerated water). The large binding constant of (4 +/- 1) x 10(5) M(-1) along with the resistance of the CB7.DBO complex toward external fluorescence quenchers allow the use of CB7 as an enhancer in time-resolved fluorescence-based assays, e.g., to screen enzyme activity or inhibition by using DBO-labeled peptides as substrates. The response of CB7.DBO to different environmental conditions and possible quenchers are described.

Effect of shortening replacement with oleogels on the rheological and tomographic characteristics of aerated baked goods.

Science.gov (United States)

Lim, Jeongtaek; Jeong, Sungmin; Lee, JaeHwan; Park, Sungkwon; Lee, Jonggil; Lee, Suyong

2017-08-01

A great deal of effort has been made to reduce the use of shortening owing to the high level of saturated fats as well as the presence of trans fats. Grape seed oil high in unsaturated fats was structured with candelilla wax to form solid-like oleogels that were utilized as a shortening replacer in aerated baked goods, specifically muffins. Muffin batters with greater amounts of oleogels exhibited lower viscosity, greater shear-thinning behavior and less elastic nature. The shortening replacement with oleogels significantly increased the specific gravity of the batters, consequently affecting the muffin volume after baking. X-ray tomography indicated a lower fragmentation index (i.e. a more connected solid structure) in the oleogel-incorporated muffins, which was correlated with more enclosed and isolated air cells. A stress relaxation test showed that the shortening replacement with oleogels produced muffins with a firmer and springier texture. Based on fatty acid compositions, the ratio of saturated to unsaturated fatty acids was significantly reduced from 2.81 to 0.41. Use of the oleogels as a shortening replacer at a ratio of 1:3 by weight was effective in producing muffins with comparable quality attributes to the control with shortening. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

The pivotal role of multimodality reporter sensors in drug discovery: from cell based assays to real time molecular imaging.

Science.gov (United States)

Ray, Pritha

2011-04-01

Development and marketing of new drugs require stringent validation that are expensive and time consuming. Non-invasive multimodality molecular imaging using reporter genes holds great potential to expedite these processes at reduced cost. New generations of smarter molecular imaging strategies such as Split reporter, Bioluminescence resonance energy transfer, Multimodality fusion reporter technologies will further assist to streamline and shorten the drug discovery and developmental process. This review illustrates the importance and potential of molecular imaging using multimodality reporter genes in drug development at preclinical phases.

Shortening of primary operators in N-extended $SCFT_{4}$ and harmonic-superspace analyticity

CERN Document Server

Andrianopoli, L.; Sokatchev, E.; Zupnik, B.

1999-01-01

We present the analysis of all possible shortenings which occur for composite gauge invariant conformal primary superfields in SU(2,2/N) invariant gauge theories. These primaries have top-spin range N/2 \\leq J_{max} < N with J_{max} = J_1 + J_2, (J_1,J_2) being the SL(2,C) quantum numbers of the highest spin component of the superfield. In Harmonic superspace, analytic and chiral superfields give J_{max}= N/2 series while intermediate shortenings correspond to fusion of chiral with analytic in N=2, or analytic with different analytic structures in N=3,4. In the AdS/CFT language shortenings of UIR's correspond to all possible BPS conditions on bulk states. An application of this analysis to multitrace operators, corresponding to multiparticle supergravity states, is spelled out.

Genotyping three SNPs affecting warfarin drug response by isothermal real-time HDA assays.

Science.gov (United States)

Li, Ying; Jortani, Saeed A; Ramey-Hartung, Bronwyn; Hudson, Elizabeth; Lemieux, Bertrand; Kong, Huimin

2011-01-14

The response to the anticoagulant drug warfarin is greatly affected by genetic polymorphisms in the VKORC1 and CYP2C9 genes. Genotyping these polymorphisms has been shown to be important in reducing the time of the trial and error process for finding the maintenance dose of warfarin thus reducing the risk of adverse effects of the drug. We developed a real-time isothermal DNA amplification system for genotyping three single nucleotide polymorphisms (SNPs) that influence warfarin response. For each SNP, real-time isothermal Helicase Dependent Amplification (HDA) reactions were performed to amplify a DNA fragment containing the SNP. Amplicons were detected by fluorescently labeled allele specific probes during real-time HDA amplification. Fifty clinical samples were analyzed by the HDA-based method, generating a total of 150 results. Of these, 148 were consistent between the HDA-based assays and a reference method. The two samples with unresolved HDA-based test results were repeated and found to be consistent with the reference method. The HDA-based assays demonstrated a clinically acceptable performance for genotyping the VKORC1 -1639G>A SNP and two SNPs (430C>T and 1075A>C) for the CYP2C9 enzyme (CYP2C9*2 and CYP2C9*3), all of which are relevant in warfarin pharmacogenentics. Copyright © 2010 Elsevier B.V. All rights reserved.

Telomere shortening reduces Alzheimer's disease amyloid pathology in mice

NARCIS (Netherlands)

Rolyan, Harshvardhan; Scheffold, Annika; Heinrich, Annette; Begus-Nahrmann, Yvonne; Langkopf, Britta Heike; Hoelter, Sabine M.; Vogt-Weisenhorn, Daniela M.; Liss, Birgit; Wurst, Wolfgang; Lie, Dieter Chichung; Thal, Dietmar Rudolf; Biber, Knut; Rudolph, Karl Lenhard

Alzheimer's disease is a neurodegenerative disorder of the elderly and advancing age is the major risk factor for Alzheimer's disease development. Telomere shortening represents one of the molecular causes of ageing that limits the proliferative capacity of cells, including neural stem cells.

Rapid real-time PCR assay for culture and tissue identification of Geomyces destructans: the etiologic agent of bat geomycosis (white nose syndrome).

Science.gov (United States)

Chaturvedi, Sudha; Rudd, Robert J; Davis, April; Victor, Tanya R; Li, Xiaojiang; Appler, Kim A; Rajkumar, Sunanda S; Chaturvedi, Vishnu

2011-10-01

Geomyces destructans is the etiologic agent of bat geomycosis, commonly referred to as white nose syndrome (WNS). This infection has caused severe morbidity and mortality in little brown bats (Myotis lucifugus) and has also spread to other bat species with significant decline in the populations. Currently, G. destructans infection is identified by culture, ITS-PCR, and histopathology. We hypothesized that a real-time PCR assay would considerably improve detection of G. destructans in bats. The 100 bp sequence of the Alpha-L-Rhamnosidase gene was validated as a target for real-time PCR. The assay sensitivity was determined from serial dilution of DNA extracted from G. destructans conidia (5 × 10(-1)-5 × 10(7)), and the specificity was tested using DNA from 30 closely and distantly related fungi and 5 common bacterial pathogens. The real-time PCR assay was highly sensitive with detection limit of two G. destructans conidia per reaction at 40 PCR cycles. The assay was also highly specific as none of the other fungal or bacterial DNA cross-reacted in the real-time PCR assay. One hundred and forty-seven bat tissue samples, suspected of infection with G. destructans, were used to compare the real-time PCR assay to other methods employed for the detection of G. destructans. Real-time PCR was highly sensitive with 80 of 147 (55%) samples testing positive for G. destructans DNA. In comparison, histopathology examination revealed 64/147 (44%) positive samples. The internal transcribed spacer (ITS)-PCR yielded positive amplicon for G. destructans from 37 tissue samples (25%). The least sensitive assay was the fungal culture with only 17 tissue samples (12%) yielding G. destructans in culture. The data suggested that the real-time PCR assay is highly promising for rapid, sensitive, and specific identification of G. destructans. Further trials and inter-laboratory comparisons of this novel assay are recommended to improve the diagnosis of bat geomycosis.

Real-time reverse transcription-polymerase chain reaction assays for identification of wild poliovirus 1 & 3.

Science.gov (United States)

Sharma, Deepa K; Nalavade, Uma P; Deshpande, Jagadish M

2015-10-01

The poliovirus serotype identification and intratypic differentiation by real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay is suitable for serotype mixtures but not for intratypic mixtures of wild and vaccine poliovirus strains. This study was undertaken to develop wild poliovirus 1 and 3 (WPV1 and WPV3) specific rRT-PCR assays for use. Specific primers and probes for rRT-PCR were designed based on VP1 sequences of WPV1 and WPV3 isolated in India since 2000. The specificity of the rRT-PCR assays was evaluated using WPV1 and WPV3 of different genetic lineages, non-polio enteroviruses (NPEVs) and mixtures of wild/wild and wild/Sabin vaccine strains. The sensitivity of the assays was determined by testing serial 10-fold dilutions of wild poliovirus 1 and 3 stock suspensions of known titre. No cross-reactivity with Sabin strains, intertypic wild poliovirus isolates or 27 types of NPEVs across all the four Enterovirus species was found for both the wild poliovirus 1 and 3 rRT-PCR assays. All WPV1 and WPV3 strains isolated since 2000 were successfully amplified. The rRT-PCR assays detected 10 4.40 CCID 50 /ml of WPV1 and 10 4.00 CCID 50 /ml of WPV3, respectively either as single isolate or mixture with Sabin vaccine strains or intertypic wild poliovirus. rRT-PCR assays for WPV1 and WPV3 have been validated to detect all the genetic variations of the WPV1 and WPV3 isolated in India for the last decade. When used in combination with the current rRT-PCR assay testing was complete for confirmation of the presence of wild poliovirus in intratypic mixtures.

[Effects of removable partial dentures on the quality of life in people with shortened dental arches].

Science.gov (United States)

Armellini, D B; Heydecke, G; Witter, D J; Creugers, N H J

2009-12-01

In order to assess the enhanced value of removable partial dentures on the quality of life, patients at 2 university clinics were screened for the presence of complete or shortened dental arches. Those selected were assigned to 1 of 5 subgroups: 1) a shortened dental arch with all frontal teeth, 2) a shortened dental arch with one or more frontal diastemas, 3) a shortened dental arch with all frontal teeth, restored by a removable partial denture, 4) a shortened dental arch and several diastemas, restored by a removable partial denture, 5) a complete dental arch. The participants completed the Oral Health Impact Profile (OHIP-49) and the Short Form Health Survey (SF-36). Clinical data recorded were: whether any teeth were missing and if so which, whether or not these had been replaced by a removable partial denture, and the number of occluding pairs of (pre)molars. The results revealed that a shortenend dental arch has a certain impact on the quality of life. However, the participants only experienced benefits from a removable partial denture if the denture also replaced frontal teeth.

A real-time PCR assay for detection and quantification of Verticillium dahliae in spinach seed.

Science.gov (United States)

Duressa, Dechassa; Rauscher, Gilda; Koike, Steven T; Mou, Beiquan; Hayes, Ryan J; Maruthachalam, Karunakaran; Subbarao, Krishna V; Klosterman, Steven J

2012-04-01

Verticillium dahliae is a soilborne fungus that causes Verticillium wilt on multiple crops in central coastal California. Although spinach crops grown in this region for fresh and processing commercial production do not display Verticillium wilt symptoms, spinach seeds produced in the United States or Europe are commonly infected with V. dahliae. Planting of the infected seed increases the soil inoculum density and may introduce exotic strains that contribute to Verticillium wilt epidemics on lettuce and other crops grown in rotation with spinach. A sensitive, rapid, and reliable method for quantification of V. dahliae in spinach seed may help identify highly infected lots, curtail their planting, and minimize the spread of exotic strains via spinach seed. In this study, a quantitative real-time polymerase chain reaction (qPCR) assay was optimized and employed for detection and quantification of V. dahliae in spinach germplasm and 15 commercial spinach seed lots. The assay used a previously reported V. dahliae-specific primer pair (VertBt-F and VertBt-R) and an analytical mill for grinding tough spinach seed for DNA extraction. The assay enabled reliable quantification of V. dahliae in spinach seed, with a sensitivity limit of ≈1 infected seed per 100 (1.3% infection in a seed lot). The quantification was highly reproducible between replicate samples of a seed lot and in different real-time PCR instruments. When tested on commercial seed lots, a pathogen DNA content corresponding to a quantification cycle value of ≥31 corresponded with a percent seed infection of ≤1.3%. The assay is useful in qualitatively assessing seed lots for V. dahliae infection levels, and the results of the assay can be helpful to guide decisions on whether to apply seed treatments.

Real-Time, Fast Neutron Coincidence Assay of Plutonium With a 4-Channel Multiplexed Analyzer and Organic Scintillators

Science.gov (United States)

Joyce, Malcolm J.; Gamage, Kelum A. A.; Aspinall, M. D.; Cave, F. D.; Lavietes, A.

2014-06-01

The design, principle of operation and the results of measurements made with a four-channel organic scintillator system are described. The system comprises four detectors and a multiplexed analyzer for the real-time parallel processing of fast neutron events. The function of the real-time, digital multiple-channel pulse-shape discrimination analyzer is described together with the results of laboratory-based measurements with 252Cf, 241Am-Li and plutonium. The analyzer is based on a single-board solution with integrated high-voltage supplies and graphical user interface. It has been developed to meet the requirements of nuclear materials assay of relevance to safeguards and security. Data are presented for the real-time coincidence assay of plutonium in terms of doubles count rate versus mass. This includes an assessment of the limiting mass uncertainty for coincidence assay based on a 100 s measurement period and samples in the range 0-50 g. Measurements of count rate versus order of multiplicity for 252Cf and 241Am-Li and combinations of both are also presented.

Carbon quantum dots-based recyclable real-time fluorescence assay for alkaline phosphatase with adenosine triphosphate as substrate.

Science.gov (United States)

Qian, Zhaosheng; Chai, Lujing; Tang, Cong; Huang, Yuanyuan; Chen, Jianrong; Feng, Hui

2015-03-03

A convenient, reliable, and highly sensitive real-time assay for alkaline phosphatase (ALP) activity in the continuous and recyclable way is established on the basis of aggregation and disaggregation of carbon quantum dots (CQDs) through the competitive assay approach. CQDs and adenosine triphosphate (ATP) were used as the fluorescent indicator and substrate for ALP activity assessment, respectively. Richness of carboxyl groups on the surface of CQDs enables their severe aggregation triggered by cerium ions, which results in effective fluorescence quenching. Under the catalytic hydrolysis of ALP, ATP can be rapidly transformed to phosphate ions. Stronger affinity of phosphate ions to cerium ions than carboxyl groups is taken advantage of to achieve fluorescence recovery induced by redispersion of CQDs in the presence of ALP and ATP. Quantitative evaluation of ALP activity in a broad range from 4.6 to 383.3 U/L with the detection limit of 1.4 U/L can be realized in this way, which endows the assay with high enough sensitivity for practical detection in human serum. The assay can be used in a recyclable way for more than three times since the generated product CePO4 as a precipitate can be easily removed from the standard assay system. This strategy broadens the sensing application of fluorescent CQDs with excellent biocompatibility and provides an example based on disaggregation in optical probe development.

Gastric wall shortening in early gastric cancer: upper gastrointestinal series and pathologic correlation

International Nuclear Information System (INIS)

Kim, In Jae; Choi, Chul Soon; Kim, Eun Ah; Kim, Kyu Sun; Yun, Ku Sub; Kim, Ho Chul; Bae, Sang Hun; Kang, Gu; Shin, Hyung Sik

1995-01-01

To investigate the causes of gastric wall shortening in early gastric cancer, upper gastrointestinal study was correlated with pathologic findings. We evaluated 41 cases (M:F = 1.7:1, average age = 49) of early gastric cancer, retrospectively. The gastric wall shortening were classified as Grade I; none, Grade II; intermediate, and Grade III; prominent. Pathologic findings such as size of lesions, depth of tumor invasion, degree of the submucosal fibrosis, degree of thickness of the submucosa and muscularis propria, and morphologic patterns of lesions including conversing mucosal folds were correlated with the degree of gastric wall shortening on upper gastrointestinal series. Submucosal fibrosis was present in 4 cases in Grade I (n = 21), 4 cases in Grade II (n = 6) and 8 cases in Grade III (n = 10). Positive conversing mucosal folds were seen in 5 cases in Grade I (n = 17), 0 case in Grade II (n = 2) and 9 cases in Grade III (n = 9). Gastric wall shortening was significantly associated with submucosal fibrosis and conversing mucosal folds of early gastric cancer. (ρ = 0.0001, and ρ = 0.02, respectively) Upper gastrointestinal finding of gastric wall protrusion in patients with early gastric cancer should not misinterprete as advanced gastric cancer since the finding could be a result of submucosal fibrosis

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....

Simultaneous detection of Zika, Chikungunya and Dengue viruses by a multiplex real-time RT-PCR assay.

Science.gov (United States)

Pabbaraju, Kanti; Wong, Sallene; Gill, Kara; Fonseca, Kevin; Tipples, Graham A; Tellier, Raymond

2016-10-01

In the recent past, arboviruses such as Chikungunya (CHIKV) and Zika (ZIKV) have increased their area of endemicity and presented as an emerging global public health threat. To design an assay for the simultaneous detection of ZIKV, CHIKV and Dengue (DENV) 1-4 from patients with symptoms of arboviral infection. This would be advantageous because of the similar clinical presentation typically encountered with these viruses and their co-circulation in endemic areas. In this study we have developed and validated a triplex real time reverse transcription PCR assay using hydrolysis probes targeting the non-structural 5 (NS5) region of ZIKV, non-structural protein 4 (nsP4) from CHIKV and 3' untranslated region (3'UTR) of DENV 1-4. The 95% LOD by the triplex assay was 15 copies/reaction for DENV-1 and less than 10 copies/reaction for all other viruses. The triplex assay was 100% specific and did not amplify any of the other viruses tested. The assay was reproducible and adaptable to testing different specimen types including serum, plasma, urine, placental tissue, brain tissue and amniotic fluid. This assay can be easily implemented for diagnostic testing of patient samples, even in a high throughput laboratory. Copyright © 2016 Elsevier B.V. All rights reserved.

Absolute nuclear material assay

Science.gov (United States)

Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

2010-07-13

A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

Real-time PCR Detection of Brucella Abortus: A Comparative Study of SYBR Green I, 5'-exonuclease, and Hybridization Probe Assays

Energy Technology Data Exchange (ETDEWEB)

Newby, Deborah Trishelle; Hadfield, Ted; Roberto, Francisco Figueroa

2003-08-01

Real-time PCR provides a means of detecting and quantifying DNA targets by monitoring PCR product accumulation during cycling as indicated by increased fluorescence. A number of different approaches can be used to generate the fluorescence signal. Three approaches—SYBR Green I (a double-stranded DNA intercalating dye), 5'-exonuclease (enzymatically released fluors), and hybridization probes (fluorescence resonance energy transfer)—were evaluated for use in a real-time PCR assay to detect Brucella abortus. The three assays utilized the same amplification primers to produce an identical amplicon. This amplicon spans a region of the B. abortus genome that includes portions of the alkB gene and the IS711 insertion element. All three assays were of comparable sensitivity, providing a linear assay over 7 orders of magnitude (from 7.5 ng down to 7.5 fg). However, the greatest specificity was achieved with the hybridization probe assay.

Factors Affecting Accuracy and Time Requirements of a Glucose Oxidase-Peroxidase Assay for Determination of Glucose

Science.gov (United States)

Accurate and rapid assays for glucose are desirable for analysis of glucose and starch in food and feedstuffs. An established colorimetric glucose oxidase-peroxidase method for glucose was modified to reduce analysis time, and evaluated for factors that affected accuracy. Time required to perform t...

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

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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

Knowledge and attitudes of dentists toward shortened dental arch ...

African Journals Online (AJOL)

Objective: The aim of this study was to assess and compare the knowledge and attitudes of dentists toward shortened dental arch (SDA) therapy in Saudi Arabia. Materials and Methods: In this cross‑sectional study, self‑designed‑structured questionnaires were distributed among specialists (SP), residents (RES), and ...

Random assay in radioimmunoassay: Feasibility and application compared with batch assay

Energy Technology Data Exchange (ETDEWEB)

Lee, Jung Min; Lee, Hwan Hee; Park, Sohyun; Kim, Tae Sung; Kim, Seok Ki [Dept. of Nuclear MedicineNational Cancer Center, Goyang (Korea, Republic of)

2016-12-15

The batch assay has been conventionally used for radioimmunoassay (RIA) because of its technical robustness and practical convenience. However, it has limitations in terms of the relative lag of report time due to the necessity of multiple assays in a small number of samples compared with the random assay technique. In this study, we aimed to verify whether the random assay technique can be applied in RIA and is feasible in daily practice. The coefficients of variation (CVs) of eight standard curves within a single kit were calculated in a CA-125 immunoradiometric assay (IRMA) for the reference of the practically ideal CV of the CA-125 kit. Ten standard curves of 10 kits from 2 prospectively collected lots (pLot) and 85 standard curves of 85 kits from 3 retrospectively collected lots (Lot) were obtained. Additionally, the raw measurement data of both 170 control references and 1123 patients' sera were collected retrospectively between December 2015 and January 2016. A standard curve of the first kit of each lot was used as a master standard curve for a random assay. The CVs of inter-kits were analyzed in each lot, respectively. All raw measurements were normalized by decay and radioactivity. The CA-125 values from control samples and patients' sera were compared using the original batch assay and random assay. In standard curve analysis, the CVs of inter-kits in pLots and Lots were comparable to those within a single kit. The CVs from the random assay with normalization were similar to those from the batch assay in the control samples (CVs % of low/high concentration; Lot1 2.71/1.91, Lot2 2.35/1.83, Lot3 2.83/2.08 vs. Lot1 2.05/1.21, Lot2 1.66/1.48, Lot3 2.41/2.14). The ICCs between the batch assay and random assay using patients' sera were satisfactory (Lot1 1.00, Lot2 0.999, Lot3 1.00). The random assay technique could be successfully applied to the conventional CA-125 IRMA kits. The random assay showed strong agreement with the batch assay. The

Real-time, high-throughput measurements of peptide-MHC-I dissociation using a scintillation proximity assay

DEFF Research Database (Denmark)

Harndahl, Mikkel; Rasmussen, Michael; Røder, Gustav Andreas

2011-01-01

and it is well suited for high-throughput screening. To exemplify this, we screened a panel of 384 high-affinity peptides binding to the MHC class I molecule, HLA-A*02:01, and observed the rates of dissociation that ranged from 0.1h to 46h depending on the peptide used.......Efficient presentation of peptide-MHC class I complexes to immune T cells depends upon stable peptide-MHC class I interactions. Theoretically, determining the rate of dissociation of a peptide-MHC class I complexes is straightforward; in practical terms, however, generating the accurate and closely...... timed data needed to determine the rate of dissociation is not simple. Ideally, one should use a homogenous assay involving an inexhaustible and label-free assay principle. Here, we present a homogenous, high-throughput peptide-MHC class I dissociation assay, which by and large fulfill these ideal...

A Multiplexed Assay That Monitors Effects of Multiple Compound Treatment Times Reveals Candidate Immune-Enhancing Compounds.

Science.gov (United States)

Zhao, Ziyan; Henowitz, Liza; Zweifach, Adam

2018-05-01

We previously developed a flow cytometry assay that monitored lytic granule exocytosis in cytotoxic T lymphocytes stimulated by contacting beads coated with activating anti-CD3 antibodies. That assay was multiplexed in that responses of cells that did or did not receive the activating stimulus were distinguished via changes in light scatter accompanying binding of cells to beads, allowing us to discriminate compounds that activate responses on their own from compounds that enhance responses in cells that received the activating stimulus, all within a single sample. Here we add a second dimension of multiplexing by developing means to assess in a single sample the effects of treating cells with test compounds for different times. Bar-coding cells before adding them to test wells lets us determine compound treatment time while also monitoring activation status and response amplitude at the point of interrogation. This multiplexed assay is suitable for screening 96-well plates. We used it to screen compounds from the National Cancer Institute, identifying several compounds that enhance anti-LAMP1 responses. Multiple-treatment-time (MTT) screening enabled by bar-coding and read via high-throughput flow cytometry may be a generally useful method for facilitating the discovery of compounds of interest.

Measurement of clavicular length and shortening after a midshaft clavicular fracture: Spatial digitization versus planar roentgen photogrammetry.

Science.gov (United States)

Stegeman, Sylvia A; de Witte, Pieter Bas; Boonstra, Sjoerd; de Groot, Jurriaan H; Nagels, Jochem; Krijnen, Pieta; Schipper, Inger B

2016-08-01

Clavicular shortening after fracture is deemed prognostic for clinical outcome and is therefore generally assessed on radiographs. It is used for clinical decision making regarding operative or non-operative treatment in the first 2weeks after trauma, although the reliability and accuracy of the measurements are unclear. This study aimed to assess the reliability of roentgen photogrammetry (2D) of clavicular length and shortening, and to compare these with 3D-spatial digitization measurements, obtained with an electromagnetic recording system (Flock of Birds). Thirty-two participants with a consolidated non-operatively treated two or multi-fragmented dislocated midshaft clavicular fracture were analysed. Two observers measured clavicular lengths and absolute and proportional clavicular shortening on radiographs taken before and after fracture consolidation. The clavicular lengths were also measured with spatial digitization. Inter-observer agreement on the radiographic measurements was assessed using the Intraclass Correlation Coefficient (ICC). Agreement between the radiographic and spatial digitization measurements was assessed using a Bland-Altman plot. The inter-observer agreement on clavicular length, and absolute and proportional shortening on trauma radiographs was almost perfect (ICC>0.90), but moderate for absolute shortening after consolidation (ICC=0.45). The Bland-Altman plot compared measurements of length on AP panorama radiographs with spatial digitization and showed that planar roentgen photogrammetry resulted in up to 37mm longer and 34mm shorter measurements than spatial digitization. Measurements of clavicular length on radiographs are highly reliable between observers, but may not reflect the actual length and shortening of the clavicle when compared to length measurements with spatial digitization. We recommend to use proportional shortening when measuring clavicular length or shortening on radiographs for clinical decision making. Copyright �

Early telomere shortening and genomic instability in tubo-ovarian preneoplastic lesions.

Science.gov (United States)

Chene, Gautier; Tchirkov, Andrei; Pierre-Eymard, Eleonore; Dauplat, Jacques; Raoelfils, Ines; Cayre, Anne; Watkin, Emmanuel; Vago, Philippe; Penault-Llorca, Frederique

2013-06-01

Genetic instability plays an important role in ovarian carcinogenesis. We investigated the level of telomere shortening and genomic instability in early and preinvasive stages of ovarian cancer, serous tubal intraepithelial carcinoma (STIC), and tubo-ovarian dysplasia (TOD). Fifty-one TOD from prophylactic salpingo-oophorectomies with BRCA1 or 2 mutation, 12 STICs, 53 tubo-ovarian high-grade serous carcinoma, and 36 noncancerous controls were laser capture microdissected from formalin-fixed, paraffin-embedded sections, analyzed by comparative genomic hybridization (array CGH) and for telomere length (using quantitative real-time PCR based on the Cawthon's method). TOD and STICs were defined by morphologic scores and immunohistochemical expressions of p53, Ki67, and γH2AX. TOD showed marked telomere shortening compared with noncancerous controls (P STICs had even shorter telomeres than TOD (P = 0.0008). Ovarian carcinoma had shorter telomeres than controls but longer than STICs and dysplasia. In TOD, telomeres were significantly shorter in those with BRCA1 mutation than in those with BRCA2 mutation (P = 0.005). In addition, γH2AX expression in TOD and STIC groups with short telomeres was significantly increased (P STICs. The total number of genetic alterations was the highest in ovarian cancers. These findings suggest that genetic instability occurs in early stages of ovarian tumorigenesis. STICs and noninvasive dysplasia are likely an important step in early serous ovarian neoplasia. ©2013 AACR

Optimized Pan-species and speciation duplex real-time PCR assays for Plasmodium parasites detection in malaria vectors.

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Maurice Marcel Sandeu

Full Text Available BACKGROUND: An accurate method for detecting malaria parasites in the mosquito's vector remains an essential component in the vector control. The Enzyme linked immunosorbent assay specific for circumsporozoite protein (ELISA-CSP is the gold standard method for the detection of malaria parasites in the vector even if it presents some limitations. Here, we optimized multiplex real-time PCR assays to accurately detect minor populations in mixed infection with multiple Plasmodium species in the African malaria vectors Anopheles gambiae and Anopheles funestus. METHODS: Complementary TaqMan-based real-time PCR assays that detect Plasmodium species using specific primers and probes were first evaluated on artificial mixtures of different targets inserted in plasmid constructs. The assays were further validated in comparison with the ELISA-CSP on 200 field caught Anopheles gambiae and Anopheles funestus mosquitoes collected in two localities in southern Benin. RESULTS: The validation of the duplex real-time PCR assays on the plasmid mixtures demonstrated robust specificity and sensitivity for detecting distinct targets. Using a panel of mosquito specimen, the real-time PCR showed a relatively high sensitivity (88.6% and specificity (98%, compared to ELISA-CSP as the referent standard. The agreement between both methods was "excellent" (κ=0.8, P<0.05. The relative quantification of Plasmodium DNA between the two Anopheles species analyzed showed no significant difference (P=0, 2. All infected mosquito samples contained Plasmodium falciparum DNA and mixed infections with P. malariae and/or P. ovale were observed in 18.6% and 13.6% of An. gambiae and An. funestus respectively. Plasmodium vivax was found in none of the mosquito samples analyzed. CONCLUSION: This study presents an optimized method for detecting the four Plasmodium species in the African malaria vectors. The study highlights substantial discordance with traditional ELISA-CSP pointing out the

BurkDiff: a real-time PCR allelic discrimination assay for Burkholderia pseudomallei and B. mallei.

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Jolene R Bowers

2010-11-01

Full Text Available A real-time PCR assay, BurkDiff, was designed to target a unique conserved region in the B. pseudomallei and B. mallei genomes containing a SNP that differentiates the two species. Sensitivity and specificity were assessed by screening BurkDiff across 469 isolates of B. pseudomallei, 49 isolates of B. mallei, and 390 isolates of clinically relevant non-target species. Concordance of results with traditional speciation methods and no cross-reactivity to non-target species show BurkDiff is a robust, highly validated assay for the detection and differentiation of B. pseudomallei and B. mallei.

A real-time PCR assay for the detection of atypical strains of Chlamydiaceae from pigeons.

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Aleksandar Zocevic

Full Text Available Recent evidence of the occurrence of atypical Chlamydiaceae strains in pigeons, different from the established Chlamydiaceae, requires the development of a specific and rapid detection tool to investigate their prevalence and significance. Here is described a new real-time PCR assay that allows specific detection of atypical Chlamydiaceae from pigeons. The assay has been used to assess the dissemination of these strains in field samples collected from Parisian pigeon populations in 2009. The results suggest a limited dissemination compared to the usually higher prevalence of Chlamydia psittaci that is the main species associated with avian chlamydiosis.

Real-time polymerase chain reaction assay for the rapid detection and characterization of chloroquine-resistant Plasmodium falciparum malaria in returned travelers.

Science.gov (United States)

Farcas, Gabriella A; Soeller, Rainer; Zhong, Kathleen; Zahirieh, Alireza; Kain, Kevin C

2006-03-01

Imported drug-resistant malaria is a growing problem in industrialized countries. Rapid and accurate diagnosis is essential to prevent malaria-associated mortality in returned travelers. However, outside of a limited number of specialized centers, the microscopic diagnosis of malaria is slow, unreliable, and provides little information about drug resistance. Molecular diagnostics have the potential to overcome these limitations. We developed and evaluated a rapid, real-time polymerase chain reaction (PCR) assay to detect Plasmodium falciparum malaria and chloroquine (CQ)-resistance determinants in returned travelers who are febrile. A real-time PCR assay based on detection of the K76T mutation in PfCRT (K76T) of P. falciparum was developed on a LightCycler platform (Roche). The performance characteristics of the real-time assay were compared with those of the nested PCR-restriction fragment-length polymorphism (RFLP) and the sequence analyses of samples obtained from 200 febrile returned travelers, who included 125 infected with P. falciparum (48 of whom were infected CQ-susceptible [K76] and 77 of whom were CQ-resistant [T76] P. falciparum), 22 infected with Plasmodium vivax, 10 infected with Plasmodium ovale, 3 infected with Plasmodium malariae malaria, and 40 infected with other febrile syndromes. All patient samples were coded, and all analyses were performed blindly. The real-time PCR assay detected multiple pfcrt haplotypes associated with CQ resistance in geographically diverse malaria isolates acquired by travelers. Compared with nested-PCR RFLP (the reference standard), the real-time assay was 100% sensitive and 96.2% specific for detection of the P. falciparum K76T mutation. This assay is rapid, sensitive, and specific for the detection and characterization of CQ-resistant P. falciparum malaria in returned travelers. This assay is automated, standardized, and suitable for routine use in clinical diagnostic laboratories.

Limiting values for the RBE of fission neutrons at low doses for life shortening in mice

International Nuclear Information System (INIS)

Storer, J.B.; Mitchell, T.J.

1984-01-01

The authors have analyzed recently published data on the effects of low doses of fission neutrons on the mean survival times of mice. The analysis for single-dose exposures was confined to doses of 20 rad or less, while for fractionated exposures only total doses of 80 rad or less were considered. They fitted the data to the frequently used power function model: life shortening = βD/sup γ/, where D is the radiation dose. They show that, at low doses per fraction, either the effects are not additive or the dose-effect curve for single exposures cannot show a greater negative curvature than about the 0.9 power of dose. Analysis of the data for γ rays showed that an exponent of 1.0 gave an acceptable fit. They conclude that at neutron doses of 20 rad or less the RBE for life shortening is constant and ranges from 13 to 22 depending on mouse strain and sex

Applying a Real-Time PCR Assay for Histoplasma capsulatum to Clinically Relevant Formalin-Fixed Paraffin-Embedded Human Tissue

Science.gov (United States)

Koepsell, Scott A.; Hinrichs, Steven H.

2012-01-01

A real-time PCR assay to detect Histoplasma capsulatum in formalin-fixed, paraffin-embedded (FFPE) tissue is described. The assay had an analytical sensitivity of 6 pg/μl of fungal DNA, analytical specificity of 100%, and clinical sensitivity of 88.9%. This proof-of-concept study may aid in the diagnosis of histoplasmosis from FFPE tissue. PMID:22855519

Device and method for shortening reactor process tubes

Science.gov (United States)

Frantz, Charles E.; Alexander, William K.; Lander, Walter E. B.

1980-01-01

This disclosure describes a device and method for in situ shortening of nuclear reactor zirconium alloy process tubes which have grown as a result of radiation exposure. An upsetting technique is utilized which involves inductively heating a short band of a process tube with simultaneous application of an axial load sufficient to cause upsetting with an attendant decrease in length of the process tube.

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

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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.

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.

Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV.

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Sanchita Bhadra

Full Text Available The Middle East respiratory syndrome coronavirus (MERS-CoV, an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU (5 to 50 PFU/ml of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens.

Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen.

Science.gov (United States)

Denman, Stuart E; McSweeney, Christopher S

2006-12-01

Traditional methods for enumerating and identifying microbial populations within the rumen can be time consuming and cumbersome. Methods that involve culturing and microscopy can also be inconclusive, particularly when studying anaerobic rumen fungi. A real-time PCR SYBR Green assay, using PCR primers to target total rumen fungi and the cellulolytic bacteria Ruminococcus flavefaciens and Fibrobacter succinogenes, is described, including design and validation. The DNA and crude protein contents with respect to the fungal biomass of both polycentric and monocentric fungal isolates were investigated across the fungal growth stages to aid in standard curve generation. The primer sets used were found to be target specific with no detectable cross-reactivity. Subsequently, the real-time PCR assay was employed in a study to detect these populations within cattle rumen. The anaerobic fungal target was observed to increase 3.6-fold from 0 to 12 h after feeding. The results also indicated a 5.4-fold increase in F. succinogenes target between 0 and 12 h after feeding, whereas R. flavefaciens was observed to maintain more or less consistent levels. This is the first report of a real-time PCR assay to estimate the rumen anaerobic fungal population.

Comparison of real-time and quantitative polymerase chain reaction assays in detection of cytomegalovirus DNA in clinical specimens

International Nuclear Information System (INIS)

Gokahmetoglu, S.; Deniz, E.

2007-01-01

To compare the real-time (RT) and qualitative (Q) polymerase chain reaction (PCR) assays for detection of Cytomegalovirus (CMV) DNA. The study took place in the Department of Microbiology, Erciyes University, Kayseri and in Iontek Laboratory, Istanbul, Turkey, from August to December 2006. One hundred and seven clinical specimens from 67 patients were included in the study. Cytomegalovirus DNA was investigated using RT-PCR kit (Fluorion Iontek, Turkey) and Q-PCR kit (Fluorion Iontek, Turkey). Deoxyribonucleic acid sequencing was applied to the samples that yielded discrepant results in both assays. Mac Nema's Chi Square test was used for statistical analysis. Of the specimens, 27 were found positive with both assays: 9 with only RT-PCR, and 11 with only Q-PCR assay. Both assays were found negative in 60 of the specimens. There was a good agreement between the 2 assays in 87(81.3%) of the specimens. There was no statistical significant difference between the assays (p>0.05). Two of the 11 samples that RT-PCR negative Q-PCR positive, and 3 of 9 samples that RT-PCR positive Q-PCR negative were found to be CMV DNA positive by DNA sequencing. A good level of concordance between RT-PCR and Q-PCR assays for CMV DNA detection has been found. (author)

A deadenylase assay by size-exclusion chromatography.

Science.gov (United States)

He, Guang-Jun; Yan, Yong-Bin

2012-01-01

The shortening of the 3'-end poly(A) tail, also called deadenylation, is crucial to the regulation of mRNA processing, transportation, translation and degradation. The deadenylation process is achieved by deadenylases, which specifically catalyze the removal of the poly(A) tail at the 3'-end of eukaryotic mRNAs and release 5'-AMP as the product. To achieve their physiological functions, all deadenylases have numerous binding partners that may regulate their catalytic properties or recruit them into various protein complexes. To study the effects of various partners, it is important to develop new deadenylase assay that can be applied either in vivo or in vitro. In this research, we developed the deadenylase assay by the size-exclusion chromatography (SEC) method. The SEC analysis indicated that the poly(A) or oligo(A) substrate and the product AMP could be successfully separated and quantified. The enzymatic parameters of deadenylase could be obtained by quantifying the AMP generation. When using the commercial poly(A) as the substrate, a biphasic catalytic process was observed, which might correlate to the two distinct states of poly(A) in the commercial samples. Different lots of commercial poly(A) had dissimilar size distributions and were dissimilar in response to the degradation of deadenylase. The deadenylation pattern, processive or distributive, could also be investigated using the SEC assay by monitoring the status of the substrate and the generation kinetics of AMP and A2. The SEC assay was applicable to both simple samples using the purified enzyme and complex enzyme reaction conditions such as using protein mixtures or crude cell extracts as samples. The influence of solutes with absorption at 254 nm could be successfully eliminated by constructing the different SEC profiles.

The Shortened Raven Standard Progressive Matrices: Item Response Theory-Based Psychometric Analyses and Normative Data

Science.gov (United States)

Van der Elst, Wim; Ouwehand, Carolijn; van Rijn, Peter; Lee, Nikki; Van Boxtel, Martin; Jolles, Jelle

2013-01-01

The purpose of the present study was to evaluate the psychometric properties of a shortened version of the Raven Standard Progressive Matrices (SPM) under an item response theory framework (the one- and two-parameter logistic models). The shortened Raven SPM was administered to N = 453 cognitively healthy adults aged between 24 and 83 years. The…

Influence of sex on performance fatigability of the plantar flexors following repeated maximal dynamic shortening contractions.

Science.gov (United States)

Lanning, Amelia C; Power, Geoffrey A; Christie, Anita D; Dalton, Brian H

2017-10-01

The purpose was to determine sex differences in fatigability during maximal, unconstrained velocity, shortening plantar flexions. The role of time-dependent measures (i.e., rate of torque development, rate of velocity development, and rate of neuromuscular activation) in such sex-related differences was also examined. By task termination, females exhibited smaller reductions in power and similar changes in rate of neuromuscular activation than males, indicating females were less fatigable than males.

A Comparative Field Monitoring of Column Shortenings in Tall Buildings Using Wireless and Wired Sensor Network Systems

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Sungho Lee

2016-01-01

Full Text Available A comparative field measurement for column shortening of tall buildings is presented in this study, with a focus on the reliability and stability of a wireless sensor network. A wireless sensor network was used for monitoring the column shortenings of a 58-story building under construction. The wireless sensor network, which was composed of sensor and master nodes, employed the ultra-high-frequency band and CDMA communication methods. To evaluate the reliability and stability of the wireless sensor network system, the column shortenings were also measured using a conventional wired monitoring system. Two vibration wire gauges were installed in each of the selected 7 columns and 3 walls. Measurements for selected columns and walls were collected for 270 days after casting of the concrete. The results measured by the wireless sensor network were compared with the results of the conventional method. The strains and column shortenings measured using both methods showed good agreement for all members. It was verified that the column shortenings of tall buildings could be monitored using the wireless sensor network system with its reliability and stability.

Evaluation and validation of a real-time PCR assay for detection and quantitation of human adenovirus 14 from clinical samples.

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David Metzgar

Full Text Available In 2007, the Centers for Disease Control and Prevention (CDC reported that Human adenovirus type 14 (HAdV-14 infected 106 military personnel and was responsible for the death of one U.S. soldier at Lackland Air Force Base in Texas. Identification of the responsible adenovirus, which had not previously been seen in North America and for which rapid diagnostic tools were unavailable, required retrospective analysis at reference laboratories. Initial quarantine measures were also reliant on relatively slow traditional PCR analysis at other locations. To address this problem, we developed a real-time PCR assay that detects a 225 base pair sequence in the HAdV-14a hexon gene. Fifty-one oropharyngeal swab specimens from the Naval Health Research Center, San Diego, CA and Advanced Diagnostic Laboratory, Lackland AFB, TX were used to validate the new assay. The described assay detected eight of eight and 19 of 19 confirmed HAdV-14a clinical isolates in two separate cohorts from respiratory disease outbreaks. The real-time PCR assay had a wide dynamic range, detecting from 10(2 to 10(7 copies of genomic DNA per reaction. The assay did not cross-react with other adenoviruses, influenza, respiratory syncytial virus, or common respiratory tract bacteria. The described assay is easy to use, sensitive and specific for HAdV-14a in clinical throat swab specimens, and very rapid since turnaround time is less than four hours to obtain an answer.

Damage sensing ability of polymer nanocomposites filled with long, shortened and damaged carbon nanotubes

OpenAIRE

Inam, Fawad; Okolo, Chichi; Vo, Thuc

2016-01-01

Carbon nanotubes (CNTs) were aggressively tip-ultrasonicated to produce shortened and damaged carbon nanotubes. High-resolution scanning electron microscopic analysis was performed to measure the dimensions of CNTs. Thermo-gravimetric analysis (TGA) was used to evaluate the damage in the sonicated CNTs. Shortened CNTs, in their pristine form (undamaged), were used for comparison with damaged CNTs. Nanocomposite bars, containing CNTs, were indented using Vickers hardness testing machine to pro...

Protein degradation and post-deboning tenderization in broiler breast meat with different degrees of muscle shortening

Science.gov (United States)

Deboning broiler breast fillets prior to rigor mortis negatively influences tenderness due to sarcomere shortening. The effects of sarcomere shortening on muscle protein degradation and breast meat tenderization during post-deboning aging are not well understood. The objective of this study was to m...

Relative sensitivity of conventional and real-time PCR assays for detection of SFG Rickettsia in blood and tissue samples from laboratory animals.

Science.gov (United States)

Zemtsova, Galina E; Montgomery, Merrill; Levin, Michael L

2015-01-01

Studies on the natural transmission cycles of zoonotic pathogens and the reservoir competence of vertebrate hosts require methods for reliable diagnosis of infection in wild and laboratory animals. Several PCR-based applications have been developed for detection of infections caused by Spotted Fever group Rickettsia spp. in a variety of animal tissues. These assays are being widely used by researchers, but they differ in their sensitivity and reliability. We compared the sensitivity of five previously published conventional PCR assays and one SYBR green-based real-time PCR assay for the detection of rickettsial DNA in blood and tissue samples from Rickettsia- infected laboratory animals (n = 87). The real-time PCR, which detected rickettsial DNA in 37.9% of samples, was the most sensitive. The next best were the semi-nested ompA assay and rpoB conventional PCR, which detected as positive 18.4% and 14.9% samples respectively. Conventional assays targeting ompB, gltA and hrtA genes have been the least sensitive. Therefore, we recommend the SYBR green-based real-time PCR as a tool for the detection of rickettsial DNA in animal samples due to its higher sensitivity when compared to more traditional assays.

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...

Clinical evaluation of the Abbott RealTime MTB Assay for direct detection of Mycobacterium tuberculosis-complex from respiratory and non-respiratory samples.

Science.gov (United States)

Hinić, Vladimira; Feuz, Kinga; Turan, Selda; Berini, Andrea; Frei, Reno; Pfeifer, Karin; Goldenberger, Daniel

2017-05-01

Rapid and reliable diagnosis is crucial for correct management of tuberculosis. The Abbott RealTime MTB Assay represents a novel qualitative real-time PCR assay for direct detection of M. tuberculosis-complex (MTB) DNA from respiratory samples. The test targets two highly conserved sequences, the multi-copy insertion element IS6110 and the protein antigen B (PAB) gene of MTB, allowing even the detection of IS6610-deficient strains. We evaluated this commercial diagnostic test by analyzing 200 respiratory and, for the first time, 87 non-respiratory clinical specimens from our tertiary care institution and compared its results to our IS6110-based in-house real-time PCR for MTB as well as MTB culture. Overall sensitivity for Abbott RealTime MTB was 100% (19/19) in smear positive and 87.5% (7/8) in smear negative specimens, while the specificity of the assay was 100% (260/260). For both non-respiratory smear positive and smear negative specimens Abbott RealTime MTB tests showed 100% (8/8) sensitivity and 100% (8/8) specificity. Cycle threshold (Ct) value analysis of 16 MTB positive samples showed a slightly higher Ct value of the Abbott RealTime MTB test compared to our in-house MTB assay (mean delta Ct = 2.55). In conclusion, the performance of the new Abbott RealTime MTB Assay was highly similar to culture and in-house MTB PCR. We document successful analysis of 87 non-respiratory samples with the highly automated Abbott RealTime MTB test with no inhibition observed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multiplex real-time PCR assay for the detection of extended-spectrum β-lactamase and carbapenemase genes using melting curve analysis.

Science.gov (United States)

Singh, Prashant; Pfeifer, Yvonne; Mustapha, Azlin

2016-05-01

Real-time PCR melt curve assays for the detection of β-lactamase, extended-spectrum β-lactamase and carbapenemase genes in Gram-negative bacteria were developed. Two multiplex real-time PCR melt curve assays were developed for the detection of ten common β-lactamase genes: blaKPC-like, blaOXA-48-like, blaNDM-like, blaVIM-like, blaIMP-like, blaCTX-M-1+2-group, blaCMY-like, blaACC-like, blaSHV-like and blaTEM-like. The assays were evaluated using 25 bacterial strains and 31 DNA samples (total n=56) comprising different Enterobacteriaceae genera and Pseudomonas spp. These strains were previously characterized at five research institutes. Each resistance gene targeted in this study generated a non-overlapping and distinct melt curve peak. The assay worked effectively and detected the presence of additional resistance genes in 23 samples. The assays developed in this study offer a simple, low cost method for the detection of prevalent β-lactamase, ESBL and carbapenemase genes among Gram-negative pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

The psychometric properties of a shortened corporate entrepreneurship assessment instrument

Directory of Open Access Journals (Sweden)

Renier Steyn

2017-08-01

Aim: The aim of this research was to evaluate the psychometric properties of a measure of entrepreneurial climate. Entrepreneurial climate was measured using a shortened version of the Hornsby, Kuratko and Zahra (2002 instrument, called the Corporate Entrepreneurship Assessment Instrument (CEAI. Making information on the psychometric properties of the instrument available directly relates to its utility. Setting: The setting was medium to large South African companies. A random sample of employees was drawn from 53 selected companies across South Africa, with 60 respondents per company (N = 3 180. Methods: A cross-sectional survey design was used. Several instruments were administered, including the shortened version of the CEAI. Cronbach’s alpha was used to test for reliability and several methods were used to test for validity. Correlation analysis was used to test for concurrent validity, convergent validity and divergent validity. Principle component factor analysis was used to test for factorial validity and a t-test to test for known-group validity. Results: The results showed that the reliability for the total score of the shortened version of the CEAI was acceptable at 0.758. The results also showed some evidence of concurrent validity, as well as homogeneity among the items. With regard to factorial validity, all items loaded in accordance with the subscales of the instrument. The measure was able to distinguish, as expected, between government organisations and private business entities, suggesting known-group validity. Convergent validity and divergent validity were also assessed. Interesting to note was that entrepreneurship climate correlates more with general employee attitude (e.g. employee engagement; R= 0.420, p < 0.001 and organisational commitment, R = 0.331, p < 0.001 than with self-reported innovation (R = 0.277, p < 0.001 and R = 0.267, p < 0.001. Contribution: This paper not only provided information on the reliability

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.

High spatial and temporal resolution retrospective cine cardiovascular magnetic resonance from shortened free breathing real-time acquisitions.

Science.gov (United States)

Xue, Hui; Kellman, Peter; Larocca, Gina; Arai, Andrew E; Hansen, Michael S

2013-11-14

Cine cardiovascular magnetic resonance (CMR) is challenging in patients who cannot perform repeated breath holds. Real-time, free-breathing acquisition is an alternative, but image quality is typically inferior. There is a clinical need for techniques that achieve similar image quality to the segmented cine using a free breathing acquisition. Previously, high quality retrospectively gated cine images have been reconstructed from real-time acquisitions using parallel imaging and motion correction. These methods had limited clinical applicability due to lengthy acquisitions and volumetric measurements obtained with such methods have not previously been evaluated systematically. This study introduces a new retrospective reconstruction scheme for real-time cine imaging which aims to shorten the required acquisition. A real-time acquisition of 16-20s per acquired slice was inputted into a retrospective cine reconstruction algorithm, which employed non-rigid registration to remove respiratory motion and SPIRiT non-linear reconstruction with temporal regularization to fill in missing data. The algorithm was used to reconstruct cine loops with high spatial (1.3-1.8 × 1.8-2.1 mm²) and temporal resolution (retrospectively gated, 30 cardiac phases, temporal resolution 34.3 ± 9.1 ms). Validation was performed in 15 healthy volunteers using two different acquisition resolutions (256 × 144/192 × 128 matrix sizes). For each subject, 9 to 12 short axis and 3 long axis slices were imaged with both segmented and real-time acquisitions. The retrospectively reconstructed real-time cine images were compared to a traditional segmented breath-held acquisition in terms of image quality scores. Image quality scoring was performed by two experts using a scale between 1 and 5 (poor to good). For every subject, LAX and three SAX slices were selected and reviewed in the random order. The reviewers were blinded to the reconstruction approach and acquisition protocols and

One-stage lengthening using a locked nailing technique for distal femoral shaft nonunions associated with shortening.

Science.gov (United States)

Wu, Chi-Chuan; Lee, Zhon-Liau

2004-02-01

To assess the effectiveness of a one-stage lengthening using a locked nail technique for the treatment of distal femoral shaft nonunions associated with shortening. Retrospective. University hospital. During a 6-year period, 36 distal femoral shaft nonunions associated with shortening (>1.5 cm) were treated by the one-stage lengthening technique. Indications for this technique were distal femoral shaft aseptic or quiescent infected nonunions, 1.5-5 cm shortening, and a fracture level suitable for the insertion of two distal locked screws. The surgical technique involved skeletal traction using the femoral condyle, local débridement, lengthening by lengthening was 2.5 cm (range 1.5-3.5 cm). One-stage lengthening using the locked nailing technique to treat distal femoral shaft nonunions associated with shortening can achieve a high success rate and low complication rate. The key to successful treatment is the patient's complete cooperation with strictly protected weight bearing until the fracture has healed.

Methods for Shortening and Extending the Carbon Chain in Carbohydrates

DEFF Research Database (Denmark)

Monrad, Rune Nygaard

2008-01-01

in this thesis focuses on the development and application of transition metal mediated methods for shortening and extending the carbon chain in carbohydrates thereby providing access to lower and higher sugars.A new catalytic procedure for shortening unprotected sugars by one carbon atom has been developed....... The procedure has been employed as the key step in a short five-step synthesis of the unnatural sugar L-threose in 74% overall yield from D-glucose. A zinc-mediated one-pot fragmentation-allylation reaction has been used to elongate D-glucose and D-ribose by three carbon atoms thereby producing carbohydrate......-derived α,ω-dienes, which have been converted into the natural products calystegine A3 and gabosine A. The glycosidase inhibitor calystegine A3 was produced by two similar routes from commercially available methyl α-D-glucopyranoside in 13 and 14 steps with 8.3 and 5.3% overall yield, respectively...

A FIFO based neutron arrival time collection technique for assay of plutonium

International Nuclear Information System (INIS)

Parthasarathy, R.; Saisubalakshmi, D.; Venkatasubramani, C.R.

2004-01-01

The system assays plutonium by counting the time correlated neutrons emitted by the spontaneous fissions of the even-even Pu isotopes in the presence of random neutron background, originating principally from (a,n) reactions in the material. The correlation technique discussed in this paper utilizes twofold neutron coincidence counting but the system is proposed to be enhanced for neutron multiplicity counting. A microcontroller based data acquisition system has been developed using a couple of fast FIFO 2kX9 bit memory ICs and a 16 bit counter for identifying time-correlated neutrons. Since the neutron pulses are arriving at a rapid rate, the incoming pulses are buffered in the FIFO and then transferred to PC by the microcontroller through the parallel port. The correlation analysis based on this time arrival information is done in the PC off-line. (author)

Long-axis fractional shortening and mitral annulus motion in dogs

Directory of Open Access Journals (Sweden)

Marlos Gonçalves Sousa

2016-10-01

Full Text Available Ventricular systolic dynamics involves the contraction of transverse and longitudinal myocardial fibers. Unfortunately, only the activity of the transverse myocardial fibers is foreseen by the standard systolic echocardiographic parameters. Although strain and strain rate have been used to assess the radial, circumferential and longitudinal planes of cardiac contraction, such analysis requires advanced equipment which is not always available in veterinary medicine. On the contrary, some unusual parameters may be recorded via standard methodology, allowing for the specific evaluation of left ventricular longitudinal contractility. In this study, the longitudinal contractile activity was evaluated using the long-axis fractional shortening and the mitral annulus motion, which were compared with several standard echocardiographic parameters in 14 beagles, including seven with asymptomatic mitral valve disease. The long-axis fractional shortening was positively correlated with both the mitral annulus motion and the end-diastolic left-ventricular diameter. Also, a significant correlation was found to exist between the mitral annulus motion and the left-ventricular end-diastolic diameter, which is likely supportive of its preload dependency. Even though no difference was documented in either mitral annulus motion or long-axis fractional shortening between healthy dogs and dogs with mitral valve disease, the latter only included animals with minimal cardiac remodeling, with no overt compromise of systolic function. Since it is possible to obtain these two parameters with any echocardiographic equipment, their inclusion in the routine exam would probably add information regarding the activity of the longitudinal myocardial fibers, whose functional deterioration supposedly occurs prior to the impairment of transverse fibers.

Development and validation of a real-time PCR assay for specific and sensitive detection of canid herpesvirus 1.

Science.gov (United States)

Decaro, Nicola; Amorisco, Francesca; Desario, Costantina; Lorusso, Eleonora; Camero, Michele; Bellacicco, Anna Lucia; Sciarretta, Rossana; Lucente, Maria Stella; Martella, Vito; Buonavoglia, Canio

2010-10-01

A TaqMan-based real-time PCR assay targeting the glycoprotein B-encoding gene was developed for diagnosis of canid herpesvirus 1 (CHV-1) infection. The established assay was highly specific, since no cross-reactions were observed with other canine DNA viruses, including canine parvovirus type 2, canine minute virus, or canine adenovirus types 1 and 2. The detection limit was 10(1) and 1.20 x 10(1) DNA copies per 10 microl(-1) of template for standard DNA and a CHV-1-positive kidney sample, respectively: about 1-log higher than a gel-based PCR assay targeting the thymidine kinase gene. The assay was also reproducible, as shown by satisfactory low intra-assay and inter-assay coefficients of variation. CHV-1 isolates of different geographical origins were recognised by the TaqMan assay. Tissues and clinical samples collected from three pups which died of CHV-1 neonatal infection were also tested, displaying a wide distribution of CHV-l DNA in their organs. Unlike other CHV-1-specific diagnostic methods, this quantitative assay permits simultaneous detection and quantitation of CHV-1 DNA in a wide range of canine tissues and body fluids, thus providing a useful tool for confirmation of a clinical diagnosis, for the study of viral pathogenesis and for evaluation of the efficacy of vaccines and antiviral drugs. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Telomere shortening in the colonic mucosa of patients with ulcerative colitis.

Science.gov (United States)

Kinouchi, Y; Hiwatashi, N; Chida, M; Nagashima, F; Takagi, S; Maekawa, H; Toyota, T

1998-06-01

Telomere length in human somatic cells gradually decreases with the number of cell divisions and is regarded as a marker of somatic cell turnover. Mucosal cells of the affected colon show rapid turnover in individuals with active ulcerative colitis (UC). Telomere length was determined by Southern blot analysis of terminal restriction fragments (TRFs) from the colonic mucosa of 17 patients with UC in remission, two of whom showed dysplasia, and 17 control subjects without colitis. For each individual, mean TRF length was compared between rectal mucosa and unaffected cecal mucosa. The mean TRF length of the rectal mucosa was significantly less than that of cecal mucosa in UC patients (7.87 +/- 0.36kb versus 8.77 +/- 0.21 kb; P = 0.0015, Wilcoxon signed rank test), whereas no significant difference was detected in the control subjects. The extent of telomere shortening was 10.6 +/- 3.35% in UC patients, compared with 0.8 +/- 0.64% in noncolitis controls (P = 0.0024, Mann-Whitney U-test). Four UC patients, two of whom had dysplasia, showed telomere shortening of more than 20% in the rectal mucosa. These observations suggest that telomere shortening in the colonic mucosa of individuals with UC may represent the history of mucosal inflammation during disease of long duration, and that it may contribute to aneuploidy in UC.

Broad-range (pan) Salmonella and Salmonella serotype typhi-specific real-time PCR assays: potential tools for the clinical microbiologist.

Science.gov (United States)

Farrell, John J; Doyle, Laura J; Addison, Rachel M; Reller, L Barth; Hall, Geraldine S; Procop, Gary W

2005-03-01

We describe broad-range salmonellae (ie, Salmonella) and Salmonella serotype Typhi-specific LightCycler (Roche Diagnostics, Indianapolis, IN) real-time polymerase chain reaction assays. We validated these with a battery of 280 bacteria, 108 of which were salmonellae representing 20 serotypes. In addition, 298 isolates from 170 clinical specimens that were suspected to possibly represent Salmonella were tested with the pan- Salmonella assay. Finally, the pan-Salmonella assay also was used to test DNA extracts from 101 archived, frozen stool specimens, 55 of which were culture-positive for salmonellae. Both assays were 100% sensitive and specific when cultured isolates of the battery were tested. The pan- Salmonella assay also characterized correctly all salmonellae on the primary isolation agar and was 96% sensitive (53/55) and 96% specific (49/51) when nucleic acid extracts from direct stool specimens were tested. These assays represent potential tools the clinical microbiologist could use to screen suspect isolates or stool specimens for Salmonella.

Development of a real-time RT-PCR and Reverse Line probe Hybridisation assay for the routine detection and genotyping of Noroviruses in Ireland.

LENUS (Irish Health Repository)

Menton, John F

2007-01-01

BACKGROUND: Noroviruses are the most common cause of non-bacterial gastroenteritis. Improved detection methods have seen a large increase in the number of human NoV genotypes in the last ten years. The objective of this study was to develop a fast method to detect, quantify and genotype positive NoV samples from Irish hospitals. RESULTS: A real-time RT-PCR assay and a Reverse Line Blot Hybridisation assay were developed based on the ORF1-ORF2 region. The sensitivity and reactivity of the two assays used was validated using a reference stool panel containing 14 NoV genotypes. The assays were then used to investigate two outbreaks of gastroenteritis in two Irish hospitals. 56 samples were screened for NoV using a real-time RT-PCR assay and 26 samples were found to be positive. Genotyping of these positive samples found that all positives belonged to the GII\\/4 variant of NoV. CONCLUSION: The combination of the Real-time assay and the reverse line blot hybridisation assay provided a fast and accurate method to investigate a NoV associated outbreak. It was concluded that the predominant genotype circulating in these Irish hospitals was GII\\/4 which has been associated with the majority of NoV outbreaks worldwide. The assays developed in this study are useful tools for investigating NoV infection.

Evaluation of two real time PCR assays for the detection of bacterial DNA in amniotic fluid.

Science.gov (United States)

Girón de Velasco-Sada, Patricia; Falces-Romero, Iker; Quiles-Melero, Inmaculada; García-Perea, Adela; Mingorance, Jesús

2018-01-01

The aim of this study was to evaluate two non-commercial Real-Time PCR assays for the detection of microorganisms in amniotic fluid followed by identification by pyrosequencing. We collected 126 amniotic fluids from 2010 to 2015 for the evaluation of two Real-Time PCR assays for detection of bacterial DNA in amniotic fluid (16S Universal PCR and Ureaplasma spp. specific PCR). The method was developed in the Department of Microbiology of the University Hospital La Paz. Thirty-seven samples (29.3%) were positive by PCR/pyrosequencing and/or culture, 4 of them were mixed cultures with Ureaplasma urealyticum. The Universal 16S Real-Time PCR was compared with the standard culture (81.8% sensitivity, 97.4% specificity, 75% positive predictive value, 98% negative predictive value). The Ureaplasma spp. specific Real-Time PCR was compared with the Ureaplasma/Mycoplasma specific culture (92.3% sensitivity, 89.4% specificity, 50% positive predictive value, 99% negative predictive value) with statistically significant difference (p=0.005). Ureaplasma spp. PCR shows a rapid response time (5h from DNA extraction until pyrosequencing) when comparing with culture (48h). So, the response time of bacteriological diagnosis in suspected chorioamnionitis is reduced. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid, actionable diagnosis of urban epidemic leptospirosis using a pathogenic Leptospira lipL32-based real-time PCR assay.

Science.gov (United States)

Riediger, Irina N; Stoddard, Robyn A; Ribeiro, Guilherme S; Nakatani, Sueli M; Moreira, Suzana D R; Skraba, Irene; Biondo, Alexander W; Reis, Mitermayer G; Hoffmaster, Alex R; Vinetz, Joseph M; Ko, Albert I; Wunder, Elsio A

2017-09-01

With a conservatively estimated 1 million cases of leptospirosis worldwide and a 5-10% fatality rate, the rapid diagnosis of leptospirosis leading to effective clinical and public health decision making is of high importance, and yet remains a challenge. Based on parallel, population-based studies in two leptospirosis-endemic regions in Brazil, a real-time PCR assay which detects lipL32, a gene specifically present in pathogenic Leptospira, was assessed for the diagnostic effectiveness and accuracy. Patients identified by active hospital-based surveillance in Salvador and Curitiba during large urban leptospirosis epidemics were tested. Real-time PCR reactions were performed with DNA-extracted samples obtained from 127 confirmed and 23 unconfirmed cases suspected of leptospirosis, 122 patients with an acute febrile illness other than leptospirosis, and 60 healthy blood donors. The PCR assay had a limit of detection of 280 Leptospira genomic equivalents/mL. Sensitivity for confirmed cases was 61% for whole blood and 29% for serum samples. Sensitivity was higher (86%) for samples collected within the first 6 days after onset of illness compared to those collected after 7 days (34%). The real-time PCR assay was able to detect leptospiral DNA in blood from 56% of serological non-confirmed cases. The overall specificity of the assay was 99%. These findings indicate that real-time PCR may be a reliable tool for early diagnosis of leptospirosis, which is decisive for clinical management of severe and life-threatening cases and for public health decision making.

Relative sensitivity of conventional and real-time PCR assays for detection of SFG Rickettsia in blood and tissue samples from laboratory animals.

Directory of Open Access Journals (Sweden)

Galina E Zemtsova

Full Text Available Studies on the natural transmission cycles of zoonotic pathogens and the reservoir competence of vertebrate hosts require methods for reliable diagnosis of infection in wild and laboratory animals. Several PCR-based applications have been developed for detection of infections caused by Spotted Fever group Rickettsia spp. in a variety of animal tissues. These assays are being widely used by researchers, but they differ in their sensitivity and reliability. We compared the sensitivity of five previously published conventional PCR assays and one SYBR green-based real-time PCR assay for the detection of rickettsial DNA in blood and tissue samples from Rickettsia- infected laboratory animals (n = 87. The real-time PCR, which detected rickettsial DNA in 37.9% of samples, was the most sensitive. The next best were the semi-nested ompA assay and rpoB conventional PCR, which detected as positive 18.4% and 14.9% samples respectively. Conventional assays targeting ompB, gltA and hrtA genes have been the least sensitive. Therefore, we recommend the SYBR green-based real-time PCR as a tool for the detection of rickettsial DNA in animal samples due to its higher sensitivity when compared to more traditional assays.

Telomere shortening in hematopoietic stem cell transplantation: a potential mechanism for late graft failure?

Science.gov (United States)

Awaya, Norihiro; Baerlocher, Gabriela M; Manley, Thomas J; Sanders, Jean E; Mielcarek, Marco; Torok-Storb, Beverly; Lansdorp, Peter M

2002-01-01

Telomeres serve to maintain the structural integrity of chromosomes, yet each somatic cell division is associated with a decrease in telomere length. The cumulative decrease in telomere length can impose an upper limit for the number of cell divisions that can occur before a cell senesces. When studied in vitro with fibroblasts, this limit is referred to as the Hayflick limit and usually occurs after 40 to 80 cell doublings. In theory, a similar replicative potential in a hematopoietic stem cell could support hematopoiesis in a person for more than 100 years. However, stem cells differentiate, and the telomere length differs among chromosomes within a single cell, among cell types, and among age-matched individuals. This variation in telomere length raises the possibility that long-term hematopoiesis by transplanted stem cells could, depending on the telomere length of the engrafted stem cell and the proliferative demand to which it is subjected, reach a Hayflick limit during the life span of the patient. Although significant shortening of telomeres is reported to occur within the first year posttransplantation, as yet no evidence has indicated that this shortening is associated with marrow function. In this review, we summarize reports on telomere shortening in stem cell transplantation recipients and report 2 cases in which graft failure is associated with significant telomere shortening.

A FRET-based real-time PCR assay to identify the main causal agents of New World tegumentary leishmaniasis.

Directory of Open Access Journals (Sweden)

Pablo Tsukayama

Full Text Available In South America, various species of Leishmania are endemic and cause New World tegumentary leishmaniasis (NWTL. The correct identification of these species is critical for adequate clinical management and surveillance activities. We developed a real-time polymerase chain reaction (PCR assay and evaluated its diagnostic performance using 64 archived parasite isolates and 192 prospectively identified samples collected from individuals with suspected leishmaniasis enrolled at two reference clinics in Lima, Peru. The real-time PCR assay was able to detect a single parasite and provided unambiguous melting peaks for five Leishmania species of the Viannia subgenus that are highly prevalent in South America: L. (V. braziliensis, L. (V. panamensis, L. (V. guyanensis, L. (V. peruviana and L. (V. lainsoni. Using kinetoplastid DNA-based PCR as a gold standard, the real-time PCR had sensitivity and specificity values of 92% and 77%, respectively, which were significantly higher than those of conventional tests such as microscopy, culture and the leishmanin skin test (LST. In addition, the real-time PCR identified 147 different clinical samples at the species level, providing an overall agreement of 100% when compared to multilocus sequence typing (MLST data performed on a subset of these samples. Furthermore, the real-time PCR was three times faster and five times less expensive when compared to PCR - MLST for species identification from clinical specimens. In summary, this new assay represents a cost-effective and reliable alternative for the identification of the main species causing NWTL in South America.

Development of field-based real-time reverse transcription-polymerase chain reaction assays for detection of Chikungunya and O'nyong-nyong viruses in mosquitoes.

Science.gov (United States)

Smith, Darci R; Lee, John S; Jahrling, Jordan; Kulesh, David A; Turell, Michael J; Groebner, Jennifer L; O'Guinn, Monica L

2009-10-01

Chikungunya (CHIK) and O'nyong-nyong (ONN) are important emerging arthropod-borne diseases. Molecular diagnosis of these two viruses in mosquitoes has not been evaluated, and the effects of extraneous mosquito tissue on assay performance have not been tested. Additionally, no real-time reverse transcription-polymerase chain reaction (RT-PCR) assay exists for detecting ONN virus (ONNV) RNA. We describe the development of sensitive and specific real-time RT-PCR assays for detecting CHIK and ONN viral RNA in mosquitoes, which have application for field use. In addition, we compared three methods for primer/probe design for assay development by evaluating their sensitivity and specificity. This comparison resulted in development of virus-specific assays that could detect less than one plaque-forming unit equivalent of each of the viruses in mosquitoes. The use of these assays will aid in arthropod-borne disease surveillance and in the control of the associated diseases.

A triplex quantitative real-time PCR assay for differential detection of human adenovirus serotypes 2, 3 and 7.

Science.gov (United States)

Qiu, Fang-Zhou; Shen, Xin-Xin; Zhao, Meng-Chuan; Zhao, Li; Duan, Su-Xia; Chen, Chen; Qi, Ju-Ju; Li, Gui-Xia; Wang, Le; Feng, Zhi-Shan; Ma, Xue-Jun

2018-05-02

Human adenovirus (HAdV) serotypes 2, 3 and 7 are more prevalent than other serotypes and have been associated with severe pneumonia in pediatric children. Molecular typing of HAdV is not routinely performed in clinical diagnostic laboratories as it is time-consuming and labor-intensive. In the present study, we developed a triplex quantitative real-time PCR assay (tq-PCR) in a single closed tube for differential detection and quantitative analysis of HAdV serotypes 2, 3 and 7. The sensitivity, specificity, reproducibility and clinical performance of tq-PCR were evaluated. The analytical sensitivity of the tq-PCR was 100 copies/reaction for each of HAdV serotypes 2, 3 and 7, and no cross-reaction with other common respiratory viruses or HAdV serotypes 1,4,5,6,31,55 and 57 was observed. The coefficients of variation (CV) of intra-assay and inter-assay were between 0.6% to 3.6%. Of 138 previously-defined HAdV-positive nasopharyngeal aspirates samples tested, the detection agreement between tq-PCR and nested PCR was 96.38% (133/138). The proposed tq-PCR assay is a sensitive, specific and reproducible method and has the potential for clinical use in the rapid and differential detection and quantitation of HAdV serotypes 2, 3 and 7.

Reversibility of Defective Hematopoiesis Caused by Telomere Shortening in Telomerase Knockout Mice.

Directory of Open Access Journals (Sweden)

Aparna Raval

Full Text Available Telomere shortening is common in bone marrow failure syndromes such as dyskeratosis congenita (DC, aplastic anemia (AA and myelodysplastic syndromes (MDS. However, improved knowledge of the lineage-specific consequences of telomere erosion and restoration of telomere length in hematopoietic progenitors is required to advance therapeutic approaches. We have employed a reversible murine model of telomerase deficiency to compare the dependence of erythroid and myeloid lineage differentiation on telomerase activity. Fifth generation Tert-/- (G5 Tert-/- mice with shortened telomeres have significant anemia, decreased erythroblasts and reduced hematopoietic stem cell (HSC populations associated with neutrophilia and increased myelopoiesis. Intracellular multiparameter analysis by mass cytometry showed significantly reduced cell proliferation and increased sensitivity to activation of DNA damage checkpoints in erythroid progenitors and in erythroid-biased CD150hi HSC, but not in myeloid progenitors. Strikingly, Cre-inducible reactivation of telomerase activity restored hematopoietic stem and progenitor cell (HSPC proliferation, normalized the DNA damage response, and improved red cell production and hemoglobin levels. These data establish a direct link between the loss of TERT activity, telomere shortening and defective erythropoiesis and suggest that novel strategies to restore telomerase function may have an important role in the treatment of the resulting anemia.

Assay optimization for molecular detection of Zika virus

NARCIS (Netherlands)

Corman, Victor M.; Rasche, Andrea; Baronti, Cecile; Aldabbagh, Souhaib; Cadar, Daniel; Reusken, Chantal Bem; Pas, Suzan D.; Goorhuis, Abraham; Schinkel, Janke; Molenkamp, Richard; Kümmerer, Beate M.; Bleicker, Tobias; Brünink, Sebastian; Eschbach-Bludau, Monika; Eis-Hübinger, Anna M.; Koopmans, Marion P.; Schmidt-Chanasit, Jonas; Grobusch, Martin P.; de Lamballerie, Xavier; Drosten, Christian; Drexler, Jan Felix

2016-01-01

To examine the diagnostic performance of real-time reverse transcription (RT)-polymerase chain reaction (PCR) assays for Zika virus detection. We compared seven published real-time RT-PCR assays and two new assays that we have developed. To determine the analytical sensitivity of each assay, we

Repopulation in the SCCVII squamous cell carcinoma assessed by an in vivo-in vitro excision assay

International Nuclear Information System (INIS)

Hansen, Olfred; Grau, Cai; Bentzen, Soeren M.; Overgaard, Jens

1996-01-01

An in vivo-in vitro excision assay was used to study repopulation after a single dose of clamped irradiation (40 Gy) in the SCCVII tumour implanted in the foot of C3H/Km mice. The growth pattern of clonogenic cells was analysed by two different mathematical models: the logistic model and the Gompertz model. The logistic model described the data better than the Gompertz model. Accelerated repopulation was found when the regrowth rate after irradiation was compared to the growth rate at the time of treatment, and when it was compared to the growth rate in untreated tumours with a number of cells equivalent to the number that was found after irradiation. The clonogenic doubling time (cDT) was estimated at 15.1 h (95% c.i.: 14.2; 16.0) after irradiation, and 27.8 h (95% c.i.: 16.7; 43.5) in untreated controls of matching size. However, the estimate relies on the mathematical model chosen and on extrapolation below actually measured data. A small cDT points to shortening of the cell cycle time and recruitment of non-cycling clonogenic tumour cells to be the main mechanism behind the accelerated repopulation

Clinical evaluation of a Mucorales-specific real-time PCR assay in tissue and serum samples.

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Springer, Jan; Lackner, Michaela; Ensinger, Christian; Risslegger, Brigitte; Morton, Charles Oliver; Nachbaur, David; Lass-Flörl, Cornelia; Einsele, Hermann; Heinz, Werner J; Loeffler, Juergen

2016-12-01

Molecular diagnostic assays can accelerate the diagnosis of fungal infections and subsequently improve patient outcomes. In particular, the detection of infections due to Mucorales is still challenging for laboratories and physicians. The aim of this study was to evaluate a probe-based Mucorales-specific real-time PCR assay (Muc18S) using tissue and serum samples from patients suffering from invasive mucormycosis (IMM). This assay can detect a broad range of clinically relevant Mucorales species and can be used to complement existing diagnostic tests or to screen high-risk patients. An advantage of the Muc18S assay is that it exclusively detects Mucorales species allowing the diagnosis of Mucorales DNA without sequencing within a few hours. In paraffin-embedded tissue samples this PCR-based method allowed rapid identification of Mucorales in comparison with standard methods and showed 91 % sensitivity in the IMM tissue samples. We also evaluated serum samples, an easily accessible material, from patients at risk from IMM. Mucorales DNA was detected in all patients with probable/proven IMM (100 %) and in 29 % of the possible cases. Detection of IMM in serum could enable an earlier diagnosis (up to 21 days) than current methods including tissue samples, which were gained mainly post-mortem. A screening strategy for high-risk patients, which would enable targeted treatment to improve patient outcomes, is therefore possible.

Application of europium(III) chelates-bonded silica nanoparticle in time-resolved immunofluorometric detection assay for human thyroid stimulating hormone

International Nuclear Information System (INIS)

Zhou Yulin; Xia Xiaohu; Xu Ye; Ke Wei; Yang Wei; Li Qingge

2012-01-01

Highlights: ► A rapid and ultrasensitive TSH immunoassay was developed using fluorescent silica nanoparticles-based TrIFA. ► The assay is of high sensitivity with short period time request. ► method can be potentially used at hospitals for daily clinical practice in hTSH screening. - Abstract: Eu(III) chelate-bonded silica nanoparticle was used as a fluorescent label to develop a highly sensitive time-resolved immunofluorometric assay (TrIFA) for human thyroid stimulating hormone (hTSH). The limit of detection of the assay calculated according to the 2SD method was 0.0007 mIU L −1 and became 0.003 mIU L −1 when serum-based matrix was used for calibrators, indicating that this TrIFA is comparable with the most sensitive assays. The linear range was from 0.005 to 100 mIU L −1 of hTSH with coefficient of variation between 1.9% and 8.3%. The correlation study using 204 blood spot samples from newborns showed that the results from this new method were coincident with that of the commercial dissociation-enhanced lanthanide fluorescence immunoassay (DELFIA) system, with a correlation coefficient of 0.938. The fluorescent nanoparticle label allows directly reading the fluorescent signal, omitting the signal development step required for the DELFIA system, and the whole procedure of this assay is fulfilled within 2 h. Thus, we developed a novel, sensitive, quantitative and simple nanoparticle label-based TrIFA assay, suitable for routine application in hTSH screening of neonatal hypothyroidism.

Application of europium(III) chelates-bonded silica nanoparticle in time-resolved immunofluorometric detection assay for human thyroid stimulating hormone

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Zhou Yulin [Xiamen Branch of Fujian Newborn Screening Centre and Xiamen Prenatal Diagnosis Centre, Xiamen Maternal and Children' s Health Care Hospital, Xiamen, Fujian 361003 (China); Xia Xiaohu; Xu Ye; Ke Wei [Engineering Research Centre of Molecular Diagnostics Laboratory, MOE, Department of Biomedical Sciences and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005 (China); Yang Wei, E-mail: weiyang@xmu.edu.cn [Engineering Research Centre of Molecular Diagnostics Laboratory, MOE, Department of Biomedical Sciences and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005 (China); Li Qingge, E-mail: qgli@xmu.edu.cn [Engineering Research Centre of Molecular Diagnostics Laboratory, MOE, Department of Biomedical Sciences and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005 (China)

2012-04-13

Highlights: Black-Right-Pointing-Pointer A rapid and ultrasensitive TSH immunoassay was developed using fluorescent silica nanoparticles-based TrIFA. Black-Right-Pointing-Pointer The assay is of high sensitivity with short period time request. Black-Right-Pointing-Pointer method can be potentially used at hospitals for daily clinical practice in hTSH screening. - Abstract: Eu(III) chelate-bonded silica nanoparticle was used as a fluorescent label to develop a highly sensitive time-resolved immunofluorometric assay (TrIFA) for human thyroid stimulating hormone (hTSH). The limit of detection of the assay calculated according to the 2SD method was 0.0007 mIU L{sup -1} and became 0.003 mIU L{sup -1} when serum-based matrix was used for calibrators, indicating that this TrIFA is comparable with the most sensitive assays. The linear range was from 0.005 to 100 mIU L{sup -1} of hTSH with coefficient of variation between 1.9% and 8.3%. The correlation study using 204 blood spot samples from newborns showed that the results from this new method were coincident with that of the commercial dissociation-enhanced lanthanide fluorescence immunoassay (DELFIA) system, with a correlation coefficient of 0.938. The fluorescent nanoparticle label allows directly reading the fluorescent signal, omitting the signal development step required for the DELFIA system, and the whole procedure of this assay is fulfilled within 2 h. Thus, we developed a novel, sensitive, quantitative and simple nanoparticle label-based TrIFA assay, suitable for routine application in hTSH screening of neonatal hypothyroidism.

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

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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.

Real-time Quaking-induced Conversion Assay for Detection of CWD Prions in Fecal Material.

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Cheng, Yo Ching; Hannaoui, Samia; John, Theodore Ralph; Dudas, Sandor; Czub, Stefanie; Gilch, Sabine

2017-09-29

The RT-QuIC technique is a sensitive in vitro cell-free prion amplification assay based mainly on the seeded misfolding and aggregation of recombinant prion protein (PrP) substrate using prion seeds as a template for the conversion. RT-QuIC is a novel high-throughput technique which is analogous to real-time polymerase chain reaction (PCR). Detection of amyloid fibril growth is based on the dye Thioflavin T, which fluoresces upon specific interaction with ᵦ-sheet rich proteins. Thus, amyloid formation can be detected in real time. We attempted to develop a reliable non-invasive screening test to detect chronic wasting disease (CWD) prions in fecal extract. Here, we have specifically adapted the RT-QuIC technique to reveal PrP Sc seeding activity in feces of CWD infected cervids. Initially, the seeding activity of the fecal extracts we prepared was relatively low in RT-QuIC, possibly due to potential assay inhibitors in the fecal material. To improve seeding activity of feces extracts and remove potential assay inhibitors, we homogenized the fecal samples in a buffer containing detergents and protease inhibitors. We also submitted the samples to different methodologies to concentrate PrP Sc on the basis of protein precipitation using sodium phosphotungstic acid, and centrifugal force. Finally, the feces extracts were tested by optimized RT-QuIC which included substrate replacement in the protocol to improve the sensitivity of detection. Thus, we established a protocol for sensitive detection of CWD prion seeding activity in feces of pre-clinical and clinical cervids by RT-QuIC, which can be a practical tool for non-invasive CWD diagnosis.

Time Series Modeling of Nano-Gold Immunochromatographic Assay via Expectation Maximization Algorithm.

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Zeng, Nianyin; Wang, Zidong; Li, Yurong; Du, Min; Cao, Jie; Liu, Xiaohui

2013-12-01

In this paper, the expectation maximization (EM) algorithm is applied to the modeling of the nano-gold immunochromatographic assay (nano-GICA) via available time series of the measured signal intensities of the test and control lines. The model for the nano-GICA is developed as the stochastic dynamic model that consists of a first-order autoregressive stochastic dynamic process and a noisy measurement. By using the EM algorithm, the model parameters, the actual signal intensities of the test and control lines, as well as the noise intensity can be identified simultaneously. Three different time series data sets concerning the target concentrations are employed to demonstrate the effectiveness of the introduced algorithm. Several indices are also proposed to evaluate the inferred models. It is shown that the model fits the data very well.

Comparison of the analytical and clinical performances of Abbott RealTime High Risk HPV, Hybrid Capture 2, and DNA Chip assays in gynecology patients.

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Park, Seungman; Kang, Youjin; Kim, Dong Geun; Kim, Eui-Chong; Park, Sung Sup; Seong, Moon-Woo

2013-08-01

The detection of high-risk (HR) HPV in cervical cancer screening is important for early diagnosis of cervical cancer or pre-cancerous lesions. We evaluated the analytical and clinical performances of 3 HR HPV assays in Gynecology patients. A total of 991 specimens were included in this study: 787 specimens for use with a Hybrid Capture 2 (HC2) and 204 specimens for a HPV DNA microarray (DNA Chip). All specimens were tested using an Abbott RealTime High Risk HPV assay (Real-time HR), PGMY PCR, and sequence analysis. Clinical sensitivities for severe abnormal cytology (severe than high-grade squamous intraepithelial lesion) were 81.8% for Real-time HR, 77.3% for HC2, and 66.7% for DNA Chip, and clinical sensitivities for severe abnormal histology (cervical intraepithelial neoplasia grade 2+) were 91.7% for HC2, 87.5% for Real-time HR, and 73.3% for DNA Chip. As compared to results of the sequence analysis, HC2, Real-time HR, and DNA Chip showed concordance rates of 94.3% (115/122), 90.0% (117/130), and 61.5% (16/26), respectively. The HC2 assay and Real-time HR assay showed comparable results to each other in both clinical and analytical performances, while the DNA Chip assay showed poor clinical and analytical performances. The Real-time HR assay can be a good alternative option for HR HPV testing with advantages of allowing full automation and simultaneous genotyping of HR types 16 and 18. Copyright © 2013 Elsevier Inc. All rights reserved.

Rapid, actionable diagnosis of urban epidemic leptospirosis using a pathogenic Leptospira lipL32-based real-time PCR assay.

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Irina N Riediger

2017-09-01

Full Text Available With a conservatively estimated 1 million cases of leptospirosis worldwide and a 5-10% fatality rate, the rapid diagnosis of leptospirosis leading to effective clinical and public health decision making is of high importance, and yet remains a challenge.Based on parallel, population-based studies in two leptospirosis-endemic regions in Brazil, a real-time PCR assay which detects lipL32, a gene specifically present in pathogenic Leptospira, was assessed for the diagnostic effectiveness and accuracy. Patients identified by active hospital-based surveillance in Salvador and Curitiba during large urban leptospirosis epidemics were tested. Real-time PCR reactions were performed with DNA-extracted samples obtained from 127 confirmed and 23 unconfirmed cases suspected of leptospirosis, 122 patients with an acute febrile illness other than leptospirosis, and 60 healthy blood donors.The PCR assay had a limit of detection of 280 Leptospira genomic equivalents/mL. Sensitivity for confirmed cases was 61% for whole blood and 29% for serum samples. Sensitivity was higher (86% for samples collected within the first 6 days after onset of illness compared to those collected after 7 days (34%. The real-time PCR assay was able to detect leptospiral DNA in blood from 56% of serological non-confirmed cases. The overall specificity of the assay was 99%.These findings indicate that real-time PCR may be a reliable tool for early diagnosis of leptospirosis, which is decisive for clinical management of severe and life-threatening cases and for public health decision making.

Performance of a Multiplex Serological Helicobacter pylori Assay on a Novel Microfluidic Assay Platform

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Angela Filomena

2017-10-01

Full Text Available Infection with Helicobacter pylori (H. pylori occurs in 50% of the world population, and is associated with the development of ulcer and gastric cancer. Serological diagnostic tests indicate an H. pylori infection by detecting antibodies directed against H. pylori proteins. In addition to line blots, multiplex assay platforms provide smart solutions for the simultaneous analysis of antibody responses towards several H. pylori proteins. We used seven H. pylori proteins (FliD, gGT, GroEL, HpaA, CagA, VacA, and HP0231 and an H. pylori lysate for the development of a multiplex serological assay on a novel microfluidic platform. The reaction limited binding regime in the microfluidic channels allows for a short incubation time of 35 min. The developed assay showed very high sensitivity (99% and specificity (100%. Besides sensitivity and specificity, the technical validation (intra-assay CV = 3.7 ± 1.2% and inter-assay CV = 5.5 ± 1.2% demonstrates that our assay is also a robust tool for the analysis of the H. pylori-specific antibody response. The integration of the virulence factors CagA and VacA allow for the assessment of the risk for gastric cancer development. The short assay time and the performance of the platform shows the potential for implementation of such assays in a clinical setting.

Real-time PCR assays for detection of Brucella spp. and the identification of genotype ST27 in bottlenose dolphins (Tursiops truncatus).

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Wu, Qingzhong; McFee, Wayne E; Goldstein, Tracey; Tiller, Rebekah V; Schwacke, Lori

2014-05-01

Rapid detection of Brucella spp. in marine mammals is challenging. Microbiologic culture is used for definitive diagnosis of brucellosis, but is time consuming, has low sensitivity and can be hazardous to laboratory personnel. Serological methods can aid in diagnosis, but may not differentiate prior exposure versus current active infection and may cross-react with unrelated Gram-negative bacteria. This study reports a real-time PCR assay for the detection of Brucella spp. and application to screen clinical samples from bottlenose dolphins stranded along the coast of South Carolina, USA. The assay was found to be 100% sensitive for the Brucella strains tested, and the limit of detection was 0.27fg of genomic DNA from Brucella ceti B1/94 per PCR volume. No amplification was detected for the non-Brucella pathogens tested. Brucella DNA was detected in 31% (55/178) of clinical samples tested. These studies indicate that the real-time PCR assay is highly sensitive and specific for the detection of Brucella spp. in bottlenose dolphins. We also developed a second real-time PCR assay for rapid identification of Brucella ST27, a genotype that is associated with human zoonotic infection. Positive results were obtained for Brucella strains which had been identified as ST27 by multilocus sequence typing. No amplification was found for other Brucella strains included in this study. ST27 was identified in 33% (18/54) of Brucella spp. DNA-positive clinical samples. To our knowledge, this is the first report on the use of a real-time PCR assay for identification of Brucella genotype ST27 in marine mammals. Copyright © 2014 Elsevier B.V. All rights reserved.

Performance of a real-time PCR assay in routine bovine mastitis diagnostics compared with in-depth conventional culture.

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Hiitiö, Heidi; Riva, Rauna; Autio, Tiina; Pohjanvirta, Tarja; Holopainen, Jani; Pyörälä, Satu; Pelkonen, Sinikka

2015-05-01

Reliable identification of the aetiological agent is crucial in mastitis diagnostics. Real-time PCR is a fast, automated tool for detecting the most common udder pathogens directly from milk. In this study aseptically taken quarter milk samples were analysed with a real-time PCR assay (Thermo Scientific PathoProof Mastitis Complete-12 Kit, Thermo Fisher Scientific Ltd.) and by semi-quantitative, in-depth bacteriological culture (BC). The aim of the study was to evaluate the diagnostic performance of the real-time PCR assay in routine use. A total of 294 quarter milk samples from routine mastitis cases were cultured in the national reference laboratory of Finland and examined with real-time PCR. With BC, 251 out of 294 (85.7%) of the milk samples had at least one colony on the plate and 38 samples were considered contaminated. In the PCR mastitis assay, DNA of target species was amplified in 244 samples out of 294 (83.0%). The most common bacterial species detected in the samples, irrespective of the diagnostic method, was the coagulase negative staphylococci (CNS) group (later referred as Staphylococcus spp.) followed by Staphylococcus aureus. Sensitivity (Se) and specificity (Sp) for the PCR assay to provide a positive Staph. aureus result was 97.0 and 95.8% compared with BC. For Staphylococcus spp., the corresponding figures were 86.7 and 75.4%. Our results imply that PCR performed well as a diagnostic tool to detect Staph. aureus but may be too nonspecific for Staphylococcus spp. in routine use with the current cut-off Ct value (37.0). Using PCR as the only microbiological method for mastitis diagnostics, clinical relevance of the results should be carefully considered before further decisions, for instance antimicrobial treatment, especially when minor pathogens with low amount of DNA have been detected. Introducing the concept of contaminated samples should also be considered.

Quantification of Xylella fastidiosa from Citrus Trees by Real-Time Polymerase Chain Reaction Assay.

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Oliveira, Antonio C; Vallim, Marcelo A; Semighini, Camile P; Araújo, Welington L; Goldman, Gustavo H; Machado, Marcos A

2002-10-01

ABSTRACT Xylella fastidiosa is the causal agent of citrus variegated chlorosis (CVC), a destructive disease of sweet orange cultivars in Brazil. Polymerase chain reaction (PCR)-based assays constitute the principal diagnostic method for detection of these bacteria. In this work, we established a real-time quantitative PCR (QPCR) assay to quantify X. fastidiosa in naturally and artificially infected citrus. The X. fastidiosa cell number detected in the leaves increased according to the age of the leaf, and bacteria were not detected in the upper midrib section in young leaves, indicating temporal and spatial distribution patterns of bacteria, respectively. In addition, the X. fastidiosa cell number quantified in leaves of 'Pera' orange and 'Murcott' tangor reflected the susceptible and resistant status of these citrus cultivars. None of the 12 endophytic citrus bacteria or the four strains of X. fastidiosa nonpathogenic to citrus that were tested showed an increase in the fluorescence signal during QPCR. In contrast, all 10 CVC-causing strains exhibited an increase in fluorescence signal, thus indicating the specificity of this QPCR assay. Our QPCR provides a powerful tool for studies of different aspects of the Xylella-citrus interactions, and can be incorporated into breeding programs in order to select CVC-resistant plants more quickly.

Real-time monitoring of enzyme-free strand displacement cascades by colorimetric assays

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Duan, Ruixue; Wang, Boya; Hong, Fan; Zhang, Tianchi; Jia, Yongmei; Huang, Jiayu; Hakeem, Abdul; Liu, Nannan; Lou, Xiaoding; Xia, Fan

2015-03-01

The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications.The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications. Electronic supplementary information (ESI) available: Experimental procedures and analytical data are provided. See DOI: 10.1039/c5nr00697j

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

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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.

Novel Molecular Beacon Probe-Based Real-Time RT-PCR Assay for Diagnosis of Crimean-Congo Hemorrhagic Fever Encountered in India

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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.

Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli.

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Hasanpour, Mojtaba; Najafi, Akram

2017-06-01

Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (T m ) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of post mortem temperature on rigor tension, shortening and ...

African Journals Online (AJOL)

Fully developed rigor mortis in muscle is characterised by maximum loss of extensibility. The course of post mortem changes in ostrich muscle was studied by following isometric tension, shortening and change in pH during the first 24 h post mortem within muscle strips from the muscularis gastrocnemius, pars interna at ...

Mini-open spinal column shortening for the treatment of adult tethered cord syndrome.

Science.gov (United States)

Safaee, Michael M; Winkler, Ethan A; Chou, Dean

2017-10-01

Tethered cord syndrome (TCS) is a challenging entity characterized by adhesions at the caudal spinal cord that prevent upward movement during growth and result in stretching of the cord with a concomitant constellation of neurologic symptoms. Although growth in height stops in adulthood, some patients still develop progressive symptoms; many underwent detethering as a child or adolescent, resulting in significant scar tissue and re-tethering. Recent strategies have focused on spinal column shortening to reduce tension on the spinal cord without exposing the previous de-tethering site. Mini-open and minimally invasive approaches avoid the large dissection and exposure associated with traditional approaches and are associated with reduced blood loss, shorter hospital stay, and similar outcomes when compared to conventional open approaches. We describe a technique for mini-open spinal column shortening. Using intraoperative navigation pedicle screws were placed at T10, T11, L1, and L2. A mini-open 3-column "egg shell" decancellation osteotomy of T12 was performed through a transpedicular approach with preservation of the superior and inferior endplates. This procedure was performed on a 28year old male with recurrent TCS and neurogenic bladder. Postoperative imaging showed a reduction in spinal column length of 1.5cm and evidence of decreased tension on the spinal cord. At last follow-up he was recovering well with improved urinary function. Spinal column shortening for adult TCS can be safely achieved through a mini-open approach. Future studies should compare the efficacy of this technique to both traditional de-tethering and open spinal column shortening. Copyright © 2017 Elsevier Ltd. All rights reserved.

Operative shortening of the sling as a second-line treatment after TVT failure

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Matuszewski, Marcin; Michajłowski, Jerzy; Krajka, Kazimierz

2011-01-01

Introduction Stress urinary incontinence (SUI) is defined as an involuntary loss of urine during physical exertion, sneezing, coughing, laughing, or other activities that put pressure on the bladder. In some cases, recurrent or persistent SUI after sling operations may be caused by too loose placement of the sling. In the current study, we describe our method of shortening of the sling as a second-line treatment of tension-free vaginal tape (TVT) failure. Materials and methods Four women, aged 46-61, after initial TVT operation were treated for persistent SUI. The severity of SUI was estimated by: physical examinations, cough tests, 24-h pad tests, and King's Health Questionnaire. The shortening procedure, based on excising the fragment of tape and suturing it back, was performed in all patients. Results All cases achieved a good result, which was defined as restoration of full continence. No complications occurred. The 12-month follow-up showed no side-effects. The postoperative control tests: the cough and 24-h pad tests were negative in all women. The general health perceptions increased after the shortening procedure by a mean value 44.25%. The incontinence impact decreased by a mean value 44.6%. In all patients, role and physical limitations significantly decreased (by 88.5% and 80.5%, respectively). The negative emotions connected with SUI significantly decreased after the second procedure. Conclusions The operative shortening of the implanted sling is a simple, cheap, and effective method of second-line treatment in cases of TVT failure and may be offered to the majority of patients with insufficient urethral support after the first procedure. PMID:24578885

Decayed/missing/filled teeth and shortened dental arches in Tanzanian adults.

NARCIS (Netherlands)

Sarita, P.T.N.; Witter, D.J.; Kreulen, C.M.; Matee, M.I.N.; Hof, M.A. van 't; Creugers, N.H.J.

2004-01-01

PURPOSE: This study assessed decayed/missing/filled teeth (DMFT), presence of occlusal units, and prevalence of shortened dental arches in a Tanzanian adult population. MATERIALS AND METHODS: The dental state of samples of the Tanzanian population was studied. Oral examinations were conducted on

Mid-term clinical outcome of radial shortening for kienbock disease

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Mohammad H Ebrahimzadeh

2015-01-01

Full Text Available Background: To evaluate the intermediate-term outcomes of radius shortening as a treatment for Kienbock′s disease. Materials and Methods: In a historical cohort, 16 skeletally mature patients (9 men and 7 women with Kienbock disease, who were treated with radial shortening osteotomy between 2002 and 2012, were reviewed in our study. The mean age of our patients was 30 (range 18-43 years old. According to Litchman staging, there were 7 wrists at stage II and 9 wrists at stage III (6 at stage IIIA and 3 at stage IIIB. The data of grip strength, pain (visual analog scale (VAS score, wrist range of motion (ROM, ulnar variance (according to Palmer method, and the Lichtman stage were gathered before and after surgery. We evaluated overall wrist function using the Mayo Wrist score and disabilities of the arm shoulder and hand (DASH score before surgery and at the last follow-up. Results: The average of follow-up was 7 years (range from 5 to 9 years. Preoperative ulnar variance was -1.3 mm (range from 2.5 to 1 preoperatively. The mean postoperative ulnar variance was 1 mm positive (range from 0.5 to 1.5. The VAS pain score, the mean arc of wrist flexion and extension, and grip strength improved significantly preoperatively compared to after recovery from surgery. The Lichtman stage was unchanged in nine patients, one grade worse in six patients, and one grade better in one patient. The mean DASH and Mayo scores improved significantly postoperatively compare with preoperation. Comparing preoperative positive, neuter, and negative ulnar variance, there was no significant difference in terms of VAS, DASH, and Mayo scores as well as ROM and grip strength. Conclusion: Our study shows that radius shortening surgery improves pain and disability regardless of ulnar variance.

Development and assessment of a shortened Quality of Life in Childhood Epilepsy Questionnaire (QOLCE-55).

Science.gov (United States)

Goodwin, Shane W; Lambrinos, Anastasia I; Ferro, Mark A; Sabaz, Mark; Speechley, Kathy N

2015-06-01

To develop and validate a shortened version of the Quality of Life in Childhood Epilepsy Questionnaire (QOLCE). A secondary aim was to compare baseline risk factors predicting health-related quality of life (HRQoL) in children newly diagnosed with epilepsy, as identified using the original and shortened version. Data came from the Health-Related Quality of Life in Children with Epilepsy Study (HERQULES, N = 373), a multicenter prospective cohort study. Principal component analysis reduced the number of items from the original QOLCE, and factor analysis was used to assess the factor structure of the shortened version. Convergent and divergent validity was assessed by correlating the Child Health Questionnaire (CHQ) with the shortened QOLCE. Multiple regression identified risk factors at diagnosis for HRQoL at 24 months. A four-factor, higher-order, 55-item solution was obtained. A total of 21 items were removed. The final model represents functioning in four dimensions of HRQoL: Cognitive, Emotional, Social, and Physical. The shortened QOLCE demonstrated acceptable fit: Bentler's Comparative Fit Index = 0.944; Tucker-Lewis Index = 0.942; root mean square approximation = 0.058 (90% CI: 0.056-0.061); weighted root mean square residuals (WRMR) = 1.582, and excellent internal consistency (α = 0.96, subscales α > 0.80). Factor loadings were good (first-order: λ = 0.66-0.93; higher-order λ = 0.66-0.85; p QOLCE scores correlated strongly with similar subscales of the Child Health Questionnaire (ρ = 0.38-0.70) while correlating weakly with dissimilar subscales (ρ = 0.30-0.31). While controlling for HRQoL at diagnosis, predictors for better HRQoL at 24 months were the following: no cognitive problems reported (p = 0.001), better family functioning (p = 0.014), fewer family demands (p = 0.008), with an interaction between baseline HRQoL and cognitive problems (p = 0.011). Results offer initial evidence regarding reliability and validity of the proposed 55-item shortened

Evaluation of a duplex reverse-transcription real-time PCR assay for the detection of encephalomyocarditis virus.

Science.gov (United States)

Qin, Shaomin; Underwood, Darren; Driver, Luke; Kistler, Carol; Diallo, Ibrahim; Kirkland, Peter D

2018-06-01

We evaluated a fluorogenic probe-based assay for the detection of encephalomyocarditis virus (EMCV) by comparing a set of published primers and probe to a new set of primers and probe. The published reagents failed to amplify a range of Australian isolates and an Italian reference strain of EMCV. In contrast, an assay based on 2 new sets of primers and probes that were run in a duplex reverse-transcription real-time PCR (RT-rtPCR) worked well, with high amplification efficiency. The analytical sensitivity was ~100-fold higher than virus isolation in cell culture. The intra-assay variation was 0.21-4.90%. No cross-reactivity was observed with a range of other porcine viruses. One hundred and twenty-two clinical specimens were tested simultaneously by RT-rtPCR and virus isolation in cell culture; 72 specimens gave positive results by RT-rtPCR, and 63 of these were also positive by virus isolation. Of 245 archived cell culture isolates of EMCV that were tested in the RT-rtPCR, 242 samples were positive. The new duplex RT-rtPCR assay is a reliable tool for the detection of EMCV in clinical specimens and for use in epidemiologic investigations.

Time-gated luminescence assay using nonmetal probes for determination of protein kinase activity-based disease markers.

Science.gov (United States)

Kasari, Marje; Padrik, Peeter; Vaasa, Angela; Saar, Kristi; Leppik, Krista; Soplepmann, Jaan; Uri, Asko

2012-03-15

A novel nonmetal optical probe ARC-1063 whose long-lifetime luminescence is induced by association with the target protein kinase is used for the measurement of the concentration of catalytic subunit of protein kinase A (PKAc) in complicated biological solutions. High affinity (K(D) = 10 pM toward PKAc) and unique optical properties of the probe enable its application for the measurement of picomolar concentrations of PKAc in the presence of high concentrations of other proteins. The described assay is applicable in the high-throughput format with the instrument setups designed for lanthanide-based time-gated (time-resolved) luminescence methods. The assay is used for demonstration that extracellular PKAc (ECPKA) is present in plasma samples of all healthy persons and cancer patients but great care must be taken for procedures of treatment of blood samples to avoid disruption, damage, or activation of platelets in the course of plasma (or serum) preparation and conservation. Copyright © 2012 Elsevier Inc. All rights reserved.

Development of a real-time PCR assay for detection of planktonic red king crab (Paralithodes camtschaticus (Tilesius 1815)) larvae

Science.gov (United States)

Jensen, Pamela C.; Purcell, Maureen K.; Morado, J. Frank; Eckert, Ginny L.

2012-01-01

The Alaskan red king crab (Paralithodes camtschaticus) fishery was once one of the most economically important single-species fisheries in the world, but is currently depressed. This fishery would benefit from improved stock assessment capabilities. Larval crab distribution is patchy temporally and spatially, requiring extensive sampling efforts to locate and track larval dispersal. Large-scale plankton surveys are generally cost prohibitive because of the effort required for collection and the time and taxonomic expertise required to sort samples to identify plankton individually via light microscopy. Here, we report the development of primers and a dual-labeled probe for use in a DNA-based real-time polymerase chain reaction assay targeting the red king crab, mitochondrial gene cytochrome oxidase I for the detection of red king crab larvae DNA in plankton samples. The assay allows identification of plankton samples containing crab larvae DNA and provides an estimate of DNA copy number present in a sample without sorting the plankton sample visually. The assay was tested on DNA extracted from whole red king crab larvae and plankton samples seeded with whole larvae, and it detected DNA copies equivalent to 1/10,000th of a larva and 1 crab larva/5mL sieved plankton, respectively. The real-time polymerase chain reaction assay can be used to screen plankton samples for larvae in a fraction of the time required for traditional microscopial methods, which offers advantages for stock assessment methodologies for red king crab as well as a rapid and reliable method to assess abundance of red king crab larvae as needed to improve the understanding of life history and population processes, including larval population dynamics.

Microbead agglutination based assays

KAUST Repository

Kodzius, Rimantas

2013-01-21

We report a simple and rapid room temperature assay for point-of-care (POC) testing that is based on specific agglutination. Agglutination tests are based on aggregation of microbeads in the presence of a specific analyte thus enabling the macroscopic observation. Such tests are most often used to explore antibody-antigen reactions. Agglutination has been used for protein assays using a biotin/streptavidin system as well as a hybridization based assay. The agglutination systems are prone to selftermination of the linking analyte, prone to active site saturation and loss of agglomeration at high analyte concentrations. We investigated the molecular target/ligand interaction, explaining the common agglutination problems related to analyte self-termination, linkage of the analyte to the same bead instead of different microbeads. We classified the agglutination process into three kinds of assays: a two- component assay, a three-component assay and a stepped three- component assay. Although we compared these three kinds of assays for recognizing DNA and protein molecules, the assay can be used for virtually any molecule, including ions and metabolites. In total, the optimized assay permits detecting analytes with high sensitivity in a short time, 5 min, at room temperature. Such a system is appropriate for POC testing.

Response of slow and fast muscle to hypothyroidism: maximal shortening velocity and myosin isoforms

Science.gov (United States)

Caiozzo, V. J.; Herrick, R. E.; Baldwin, K. M.

1992-01-01

This study examined both the shortening velocity and myosin isoform distribution of slow- (soleus) and fast-twitch (plantaris) skeletal muscles under hypothyroid conditions. Adult female Sprague-Dawley rats were randomly assigned to one of two groups: control (n = 7) or hypothyroid (n = 7). In both muscles, the relative contents of native slow myosin (SM) and type I myosin heavy chain (MHC) increased in response to the hypothyroid treatment. The effects were such that the hypothyroid soleus muscle expressed only the native SM and type I MHC isoforms while repressing native intermediate myosin and type IIA MHC. In the plantaris, the relative content of native SM and type I MHC isoforms increased from 5 to 13% and from 4 to 10% of the total myosin pool, respectively. Maximal shortening velocity of the soleus and plantaris as measured by the slack test decreased by 32 and 19%, respectively, in response to hypothyroidism. In contrast, maximal shortening velocity as estimated by force-velocity data decreased only in the soleus (-19%). No significant change was observed for the plantaris.

Intramedullary stabilization and over-nail lengthening as two-stage treatment of femoral nonunion with shortening. Case study.

Science.gov (United States)

Kącki, Wojciech; Jasiewicz, Barbara; Radło, Paweł

2014-01-01

Nonunion is one of the most serious complications of long bone fractures. It may be accompanied by a shortening of the segment. The authors describe the case of a 21-year-old woman with a post-traumatic nonunion with shortening of the femur. Treatment was divided into two stages: first, a previously placed nail was removed and new intramedullary stabilization was carried out while bone defects were filled with a bone graft substitute and platelet rich plasma was administered. After the nonunion had healed, the femur was lengthened over an external fixator and an intramedullary nail, resulting in equality of limb length. After eight years of follow-up, the lower limbs remain equal with a properly aligned long axis of the lower limb operated on and a full range of motion in the joints. The treatment strategy described in our article may be an alternative to one-stage surgery if the patient does not consent to it or in the presence of contraindications, but it is associated with a longer treatment time and necessity of additional surgeries.

Differential Telomere Shortening in Blood versus Arteries in an Animal Model of Type 2 Diabetes

Directory of Open Access Journals (Sweden)

Samira Tajbakhsh

2015-01-01

Full Text Available Vascular dysfunction is an early feature of diabetic vascular disease, due to increased oxidative stress and reduced nitric oxide (NO bioavailability. This can lead to endothelial cell senescence and clinical complications such as stroke. Cells can become senescent by shortened telomeres and oxidative stress is known to accelerate telomere attrition. Sirtuin 1 (SIRT1 has been linked to vascular health by upregulating endothelial nitric oxide synthase (eNOS, suppressing oxidative stress, and attenuating telomere shortening. Accelerated leukocyte telomere attrition appears to be a feature of clinical type 2 diabetes (T2D and therefore the telomere system may be a potential therapeutic target in preventing vascular complications of T2D. However the effect of T2D on vascular telomere length is currently unknown. We hypothesized that T2D gives rise to shortened leukocyte and vascular telomeres alongside reduced vascular SIRT1 expression and increased oxidative stress. Accelerated telomere attrition was observed in circulating leukocytes, but not arteries, in T2D compared to control rats. T2D rats had blunted arterial SIRT1 and eNOS protein expression levels which were associated with reduced antioxidant defense capacity. Our findings suggest that hyperglycemia and a deficit in vascular SIRT1 per se are not sufficient to prematurely shorten vascular telomeres.

End-systolic stress-velocity relation and circumferential fiber velocity shortening for analysing left ventricular function in mice

Energy Technology Data Exchange (ETDEWEB)

Fayssoil, A. [Cardiologie, Hopital europeen Georges Pompidou, 20, rue le blanc, Paris (France)], E-mail: fayssoil2000@yahoo.fr; Renault, G. [CNRS UMR 8104, Inserm, U567, Institut Cochin, Universite Paris Descartes, Paris (France); Fougerousse, F. [Genethon, RD, Evry (France)

2009-08-15

Traditionally, analysing left ventricular (LV) performance relies on echocardiography by evaluating shortening fraction (SF) in mice. SF is influenced by load conditions. End-systolic stress-velocity (ESSV) relation and circumferential fiber velocity (VcF) shortening are more relevant parameters for evaluating systolic function regardless load conditions particularly in mice's models of heart failure.

Cholinesterase assay by an efficient fixed time endpoint method

Directory of Open Access Journals (Sweden)

Mónica Benabent

2014-01-01

The method may be adapted to the user needs by modifying the enzyme concentration and applied for simultaneously testing many samples in parallel; i.e. for complex experiments of kinetics assays with organophosphate inhibitors in different tissues.

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.

Science.gov (United States)

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

Validation of an in vitro contractility assay using canine ventricular myocytes

Energy Technology Data Exchange (ETDEWEB)

Harmer, A.R., E-mail: alex.harmer@astrazeneca.com; Abi-Gerges, N.; Morton, M.J.; Pullen, G.F.; Valentin, J.P.; Pollard, C.E.

2012-04-15

Measurement of cardiac contractility is a logical part of pre-clinical safety assessment in a drug discovery project, particularly if a risk has been identified or is suspected based on the primary- or non-target pharmacology. However, there are limited validated assays available that can be used to screen several compounds in order to identify and eliminate inotropic liability from a chemical series. We have therefore sought to develop an in vitro model with sufficient throughput for this purpose. Dog ventricular myocytes were isolated using a collagenase perfusion technique and placed in a perfused recording chamber on the stage of a microscope at ∼ 36 °C. Myocytes were stimulated to contract at a pacing frequency of 1 Hz and a digital, cell geometry measurement system (IonOptix™) was used to measure sarcomere shortening in single myocytes. After perfusion with vehicle (0.1% DMSO), concentration–effect curves were constructed for each compound in 4–30 myocytes taken from 1 or 2 dog hearts. The validation test-set was 22 negative and 8 positive inotropes, and 21 inactive compounds, as defined by their effect in dog, cynolomolgous monkey or humans. By comparing the outcome of the assay to the known in vivo contractility effects, the assay sensitivity was 81%, specificity was 75%, and accuracy was 78%. With a throughput of 6–8 compounds/week from 1 cell isolation, this assay may be of value to drug discovery projects to screen for direct contractility effects and, if a hazard is identified, help identify inactive compounds. -- Highlights: ► Cardiac contractility is an important physiological function of the heart. ► Assessment of contractility is a logical part of pre-clinical drug safety testing. ► There are limited validated assays that predict effects of compounds on contractility. ► Using dog myocytes, we have developed an in vitro cardiac contractility assay. ► The assay predicted the in vivo contractility with a good level of accuracy.

Soil Baiting, Rapid PCR Assay and Quantitative Real Time PCR to Diagnose Late Blight of Potato in Quarantine Programs

Directory of Open Access Journals (Sweden)

Touseef Hussain

2018-05-01

Full Text Available Phytophthora infestans (mont de Bary is a pathogen of great concern across the globe, and accurate detection is an important component in responding to the outbreaks of potential disease. Although the molecular diagnostic protocol used in regulatory programs has been evaluated but till date methods implying direct comparison has rarely used. In this study, a known area soil samples from potato fields where light blight appear every year (both A1 and A2 mating type was assayed by soil bait method, PCR assay detection and quantification of the inoculums. Suspected disease symptoms appeared on bait tubers were further confirmed by rapid PCR, inoculums were quantified through Real Time PCR, which confirms presence of P. infestans. These diagnostic methods can be highly correlated with one another. Potato tuber baiting increased the sensitivity of the assay compared with direct extraction of DNA from tuber and soil samples. Our study determines diagnostic sensitivity and specificity of the assays to determine the performance of each method. Overall, molecular techniques based on different types of PCR amplification and Real-time PCR can lead to high throughput, faster and more accurate detection method which can be used in quarantine programmes in potato industry and diagnostic laboratory.

The slack test does not assess maximal shortening velocity of muscle fascicle in human.

Science.gov (United States)

Hager, Robin; Dorel, Sylvain; Nordez, Antoine; Rabita, Giuseppe; Couturier, Antoine; Hauraix, Hugo; Duchateau, Jacques; Guilhem, Gaël

2018-06-14

The application of a series of extremely high accelerative motor-driven quick releases while muscles contract isometrically (i.e. slack test) has been proposed to assess unloaded velocity in human muscle. This study aimed to measure gastrocnemius medialis fascicle (V F ) and tendinous tissues shortening velocity during motor-driven quick releases performed at various activation levels to assess the applicability of the slack test method in human. Maximal fascicle shortening velocity and joint velocity recorded during quick releases and during fast contraction without external load (ballistic condition) were compared. Gastrocnemius medialis fascicle behaviour was investigated from 25 participants using high-frame rate ultrasound during quick releases performed at various activation levels (from 0% to 60% of maximal voluntary isometric torque) and ballistic contractions. Unloaded joint velocity calculated using the slack test method increased whereas V F decreased with muscle activation level (P≤0.03). Passive and low-level quick releases elicited higher V F values (≥ 41.4±9.7 cm.s -1 ) compared to ballistic condition (36.3±8.7 cm.s -1 ), while quick releases applied at 60% of maximal voluntary isometric torque produced the lowest V F These findings suggest that initial fascicle length, complex fascicle-tendon interactions, unloading reflex and motor-driven movement pattern strongly influence and limit the shortening velocity achieved during the slack test. Furthermore, V F elicited by quick releases is likely to reflect substantial contributions of passive processes. Therefore, the slack test is not appropriate to assess maximal muscle shortening velocity in vivo. © 2018. Published by The Company of Biologists Ltd.

Novel 3′-Processing Integrase Activity Assay by Real-Time PCR for Screening and Identification of HIV-1 Integrase Inhibitors

Directory of Open Access Journals (Sweden)

Supachai Sakkhachornphop

2015-01-01

Full Text Available The 3′-end processing (3′P of each viral long terminal repeat (LTR during human immunodeficiency virus type-1 (HIV-1 integration is a vital step in the HIV life cycle. Blocking the 3′P using 3′P inhibitor has recently become an attractive strategy for HIV-1 therapeutic intervention. Recently, we have developed a novel real-time PCR based assay for the detection of 3′P activity in vitro. The methodology usually involves biotinylated HIV-1 LTR, HIV-1 integrase (IN, and specific primers and probe. In this novel assay, we designed the HIV-1 LTR substrate based on a sequence with a homology to HIV-1 LTR labeled at its 3′ end with biotin on the sense strand. Two nucleotides at the 3′ end were subsequently removed by IN activity. Only two nucleotides labeled biotin were captured on an avidin-coated tube; therefore, inhibiting the binding of primers and probe results in late signals in the real-time PCR. This novel assay has successfully detected both the 3′P activity of HIV-1 IN and the anti-IN activity by Raltegravir and sodium azide agent. This real-time PCR assay has been shown to be effective and inexpensive for a high-throughput screening of novel IN inhibitors.

Interlayer material transport during layer-normal shortening. Part I. The model

NARCIS (Netherlands)

Molen, I. van der

1985-01-01

To analyse mass-transfer during deformation, the case is considered of a multilayer experiencing a layer-normal shortening that is volume constant on the scale of many layers. Strain rate is homogeneously distributed on the layer-scale if diffusion is absent; when transport of matter between the

Multiple congenital brachymetatarsia. A one-stage combined shortening and lengthening procedure without iliac bone graft.

Science.gov (United States)

Kim, J S; Baek, G H; Chung, M S; Yoon, P W

2004-09-01

We performed nine metatarsal and three proximal phalangeal lengthenings in five patients with congenital brachymetatarsia of the first and one or two other metatarsal bones, by a one-stage combined shortening and lengthening procedure using intercalcary autogenous bone grafts from adjacent shortened metatarsal bones. Instead of the isolated lengthening of the first and the other metatarsal bones, we shortened the adjacent normal metatarsal and used the excised bone to lengthen the short toes, except for the great toe, to restore the normal parabola. One skin incision was used. All the operations were performed bilaterally and the patients were followed up for a mean period of 69.5 months (29 to 107). They all regained a nearly normal parabola and were satisfied with the cosmetic results. Our technique is straightforward and produces good cosmetic results. Satisfactory, bony union is achieved, morbidity is low, and no additional surgery is required for the removal of metal implants.

Quantum gravity removes classical singularities and shortens the life of black holes

International Nuclear Information System (INIS)

Frolov, V.P.; Vilkovisky, G.A.

1979-07-01

The problem of the gravitational collapse is considered in the framework of the quantum gravity effective action. It is shown that quantum gravity removes classical singularity and possibly shortens the lifetime of the black hole. (author)

Radioactive wastes assay technique and equipment

International Nuclear Information System (INIS)

Lee, K. M.; Hong, D. S; Kim, T. K.; Bae, S. M.; Shon, J. S.; Hong, K. P.

2004-12-01

The waste inventory records such as the activities and radio- nuclides contained in the waste packages are to be submitted with the radioactive wastes packages for the final disposal. The nearly around 10,000 drums of waste stocked in KAERI now should be assayed for the preparation of the waste inventory records too. For the successive execution of the waste assay, the investigation into the present waste assay techniques and equipment are to be taken first. Also the installation of the waste assay equipment through the comprehensive design, manufacturing and procurement should be proceeded timely. As the characteristics of the KAERI-stocked wastes are very different from that of the nuclear power plant and those have no regular waste streams, the application of the in-direct waste assay method using the scaling factors are not effective for the KAERI-generated wastes. Considering for the versal conveniency including the accuracy over the wide range of waste forms and the combination of assay time and sensitivity, the TGS(Tomographic Gamma Scanner) is appropriate as for the KAERI -generated radioactive waste assay equipment

Paradoxical results of two automated real-time PCR assays in the diagnosis of pleural tuberculosis

Directory of Open Access Journals (Sweden)

Soraya E. Morales-López

2017-01-01

Full Text Available Tuberculosis (TB is a major cause of worldwide mortality. We report the case of a non-HIV-infected woman with clinical suspicion of pleural tuberculosis and contradictory results between Xpert® MTB/RIF and Abbott RealTime MTB assays from pleural fluid specimen. Liquid and solid cultures for tuberculosis were performed with negative results. The patient received treatment, and clinical improvement was observed. Both techniques detect Mycobacterium tuberculosis complex, but they have different targets and limits of detection. Abbott RealTime MTB results correlated well with the clinical findings of the patient.

Development and validation of a real-time quantitative PCR assay to detect Xanthomonas axonopodis pv. allii from onion seed.

Science.gov (United States)

Robène, Isabelle; Perret, Marion; Jouen, Emmanuel; Escalon, Aline; Maillot, Marie-Véronique; Chabirand, Aude; Moreau, Aurélie; Laurent, Annie; Chiroleu, Frédéric; Pruvost, Olivier

2015-07-01

Bacterial blight of onion is an emerging disease threatening world onion production. The causal agent Xanthomonas axonopodis pv. allii is seed transmitted and a reliable and sensitive tool is needed to monitor seed exchanges. A triplex quantitative real-time PCR assay was developed targeting two X. axonopodis pv. allii-specific markers and an internal control chosen in 5.8S rRNA gene from Alliaceae. Amplification of at least one marker indicates the presence of the bacterium in seed extracts. This real-time PCR assay detected all the 79 X. axonopodis pv. allii strains tested and excluded 85.2% of the 135 non-target strains and particularly all 39 saprophytic and pathogenic bacteria associated with onion. Cross-reactions were mainly obtained for strains assigned to nine phylogenetically related X. axonopodis pathovars. The cycle cut-off was estimated statistically at 36.3 considering a risk of false positive of 1%. The limit of detection obtained in at least 95% of the time (LOD 95%) was 5×10(3) CFU/g (colony forming unit/g). The sensitivity threshold was found to be 1 infected seed in 32,790 seeds. This real-time PCR assay should be useful for preventing the long-distance spread of X. axonopodis pv. allii via contaminated seed lots and determining the epidemiology of the bacterium. Copyright © 2015 Elsevier B.V. All rights reserved.

Increased Risk Proneness or Social Withdrawal? The Effects of Shortened Life Expectancy on the Expression of Rescue Behavior in Workers of the ant Formica cinerea (Hymenoptera: Formicidae).

Science.gov (United States)

Miler, Krzysztof; Symonowicz, Beata; Godzińska, Ewa J

2017-01-01

In social insects behavioral consequences of shortened life expectancy include, among others, increased risk proneness and social withdrawal. We investigated the impact of experimental shortening of life expectancy of foragers of the ant Formica cinerea achieved by their exposure to carbon dioxide on the expression of rescue behavior, risky pro-social behavior, tested by means of two bioassays during which a single worker (rescuer) was confronted with a nestmate (victim) attacked by a predator (antlion larva capture bioassay) or immobilized by an artificial snare (entrapment bioassay). Efficacy of carbon dioxide poisoning in shortening life expectancy was confirmed by the analysis of ant mortality. Rescue behavior observed during behavioral tests involved digging around the victim, transport of the sand covering the victim, pulling the limbs/antennae/mandibles of the victim, direct attack on the antlion (in antlion larva capture tests), and snare biting (in entrapment tests). The rate of occurrence of rescue behavior was lower in ants with shortened life expectancy, but that effect was significant only in the case of the entrapment bioassay. Similarly, only in the case of the entrapment bioassay ants with shortened life expectancy displayed rescue behavior after a longer latency and devoted less time to that behavior than ants from the control groups. Our results demonstrated that in ant workers shortened life expectancy may lead to reduced propensity for rescue behavior, most probably as an element of the social withdrawal syndrome that had already been described in several studies on behavior of moribund ants and honeybees.

A multiplex calibrated real-time PCR assay for quantitation of DNA of EBV-1 and 2.

Science.gov (United States)

Gatto, Francesca; Cassina, Giulia; Broccolo, Francesco; Morreale, Giuseppe; Lanino, Edoardo; Di Marco, Eddi; Vardas, Efthiya; Bernasconi, Daniela; Buttò, Stefano; Principi, Nicola; Esposito, Susanna; Scarlatti, Gabriella; Lusso, Paolo; Malnati, Mauro S

2011-12-01

Accurate and highly sensitive tests for the diagnosis of active Epstein-Barr virus (EBV) infection are essential for the clinical management of individuals infected with EBV. A calibrated quantitative real-time PCR assay for the measurement of EBV DNA of both EBV-1 and 2 subtypes was developed, combining the detection of the EBV DNA and a synthetic DNA calibrator in a multiplex PCR format. The assay displays a wide dynamic range and a high degree of accuracy even in the presence of 1μg of human genomic DNA. This assay measures with the same efficiency EBV DNA from strains prevalent in different geographic areas. The clinical sensitivity and specificity of the system were evaluated by testing 181 peripheral blood mononuclear cell (PBMCs) and plasma specimens obtained from 21 patients subjected to bone marrow transplantation, 70 HIV-seropositive subjects and 23 healthy controls. Patients affected by EBV-associated post-transplant lymphoprolipherative disorders had the highest frequency of EBV detection and the highest viral load. Persons infected with HIV had higher levels of EBV DNA load in PBMCs and a higher frequency of EBV plasma viremia compared to healthy controls. In conclusion, this new assay provides a reliable high-throughput method for the quantitation of EBV DNA in clinical samples. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

Solution assay instrument operations manual

International Nuclear Information System (INIS)

Li, T.K.; Marks, T.; Parker, J.L.

1983-09-01

An at-line solution assay instrument (SAI) has been developed and installed in a plutonium purification and americium recovery process area in the Los Alamos Plutonium Processing Facility. The instrument was designed for accurate, timely, and simultaneous nondestructive analysis of plutonium and americium in process solutions that have a wide range of concentrations and americium/plutonium ratios and for routine operation by process technicians who lack instrumentation background. The SAI, based on transmission-corrected, high-resolution gamma-ray spectroscopy, has two measurement stations attached to a single multichannel analyzer/computer system. To ensure the quality of assay results, the SAI has an internal measurement control program, which requires daily and weekly check runs and monitors key aspects of all assay runs. For a 25-ml sample, the assay precision is 5 g/l within a 2000-s count time

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.

High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants

OpenAIRE

Otti, Gerald; Bouvaine, Sophie; Kimata, Bernadetha; Mkamillo, Geoffrey; Kumar, Lava; Tomlins, Keith; Maruthi, M.N.

2016-01-01

Aims: To develop a multiplex TaqMan-based real-time PCR assay (qPCR) for the simultaneous detection and quantification of both RNA and DNA viruses affecting cassava (Manihot esculenta) in eastern Africa.\\ud \\ud Methods and Results: The diagnostic assay was developed for two RNA viruses; Cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV) and two predominant DNA viruses; African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV), which cause t...

A TaqMan-based real time PCR assay for specific detection and quantification of Xylella fastidiosa strains causing bacterial leaf scorch in oleander.

Science.gov (United States)

Guan, Wei; Shao, Jonathan; Singh, Raghuwinder; Davis, Robert E; Zhao, Tingchang; Huang, Qi

2013-02-15

A TaqMan-based real-time PCR assay was developed for specific detection of strains of X. fastidiosa causing oleander leaf scorch. The assay uses primers WG-OLS-F1 and WG-OLS-R1 and the fluorescent probe WG-OLS-P1, designed based on unique sequences found only in the genome of oleander strain Ann1. The assay is specific, allowing detection of only oleander-infecting strains, not other strains of X. fastidiosa nor other plant-associated bacteria tested. The assay is also sensitive, with a detection limit of 10.4fg DNA of X. fastidiosa per reaction in vitro and in planta. The assay can also be applied to detect low numbers of X. fastidiosa in insect samples, or further developed into a multiplex real-time PCR assay to simultaneously detect and distinguish diverse strains of X. fastidiosa that may occupy the same hosts or insect vectors. Specific and sensitive detection and quantification of oleander strains of X. fastidiosa should be useful for disease diagnosis, epidemiological studies, management of oleander leaf scorch disease, and resistance screening for oleander shrubs. Published by Elsevier B.V.

Minimal residual HIV viremia: verification of the Abbott Real-Time HIV-1 assay sensitivity

Directory of Open Access Journals (Sweden)

Alessandra Amendola

2010-06-01

Full Text Available Introduction: In the HIV-1 infection, the increase in number of CD4 T lymphocytes and the viral load decline are the main indicators of the effectiveness of antiretroviral therapy. On average, 85% of patients receiving effective treatment has a persistent suppression of plasma viral load below the detection limit (<50 copies/mL of clinically used viral load assays, regardless of treatment regimen in use. It is known, however, that, even when viremia is reduced below the sensitivity limit of current diagnostic assays, the virus persists in “reservoirs” and traces of free virions can be detected in plasma.There is a considerable interest to investigate the clinical significance of residual viremia. Advances in molecular diagnostics allows nowadays to couple a wide dynamic range to a high sensitivity.The Abbott Real-time HIV-1 test is linear from 40 to 107 copies/mL and provides, below 40 copies/mL, additional information such as “<40cp/mL, target detected” or “target not detected”. The HIV-1 detection is verified by the max-Ratio algorithm software.We assessed the test sensitivity when the qualitative response is considered as well. Methods: A ‘probit’ analysis was performed using dilutions of the HIV-1 RNA Working Reagent 1 for NAT assays (NIBSC code: 99/634, defined in IU/mL and different from that used by the manufacturer (VQA,Virology Quality Assurance Laboratory of the AIDS Clinical Trial Group for standardization and definition of performances.The sample input volume (0.6 mL was the same used in clinical routine. A total of 196 replicates at concentrations decreasing from 120 to 5 copies/mL, in three different sessions, have been tested.The ‘probit’ analysis (binomial dose-response model, 95% “hit-rate” has been carried out on the SAS 9.1.3 software package. Results: The sensitivity of the “<40cp/mL, target detected” response was equal to 28,76 copies/mL, with 95% confidence limits between 22,19 and 52,27 copies

Evaluation of total PSA assay on vitros ECi and correlation with Kryptor-PSA assay.

Science.gov (United States)

Cassinat, B; Wacquet, M; Toubert, M E; Rain, J D; Schlageter, M H

2001-01-01

An increasing number of multiparametric immuno-analysers for PSA assays are available. As different immuno-assays may vary in their analytical quality and their accuracy for the follow-up of patients, expertise is necessary for each new assay. The PSA assay on the Vitros-ECi analyser has been evaluated and compared with the PSA assay from the Kryptor analyser. Variation coefficients were 0.91 to 1.98% for within-run assays, and 4.2% to 5.4% for interassay (PSA levels = 0.8 microgram/L to 33.6 micrograms/L). Dilution tests showed 93 to 136% recovery until 70 micrograms/L PSA. Functional sensitivity was estimated at 0.03 microgram/L. Equimolarity of the test was confirmed. Correlation of PSA levels measured with Vitros-ECi and Kryptor analysers displayed a correlation coefficient r2 of 0.9716. The half-lives and doubling times of PSA were similar using both methods. Vitros-ECi PSA assay meets the major criteria for the management of prostate cancer patients.

Dyslipidemia and chronic inflammation markers are correlated with telomere length shortening in Cushing's syndrome.

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Anna Aulinas

Full Text Available Cushing's syndrome (CS increases cardiovascular risk (CVR and adipocytokine imbalance, associated with an increased inflammatory state. Telomere length (TL shortening is a novel CVR marker, associated with inflammation biomarkers. We hypothesized that inflammatory state and higher CVR in CS might be related to TL shortening, as observed in premature aging.To evaluate relationships between TL, CVR and inflammation markers in CS.In a cross-sectional study, 77 patients with CS (14 males, 59 pituitary-, 17 adrenal- and 1 ectopic-origin; 21 active disease and 77 age-, gender-, smoking-matched controls were included. Total white blood cell TL was measured by TRF-Southern technique. Clinical data and blood samples were collected (lipids, adrenal function, glucose. Adiponectin, interleukin-6 (IL6 and C-reactive protein (CRP were available in a subgroup of patients (n=32. Correlations between TL and clinical features were examined and multiple linear regression analysis was performed to investigate potential predictors of TL.Dyslipidemic CS had shorter TL than non-dyslipidemic subjects (7328±1274 vs 7957±1137 bp, p<0.05. After adjustment for age and body mass index, cured and active CS dyslipidemic patients had shorter TL than non-dyslipidemic CS (cured: 7187±1309 vs 7868±1104; active: 7203±1262 vs 8615±1056, respectively, p<0.05. Total cholesterol and triglycerides negatively correlated with TL (r-0.279 and -0.259, respectively, p<0.05, as well as CRP and IL6 (r-0.412 and -0.441, respectively, p<0.05. No difference in TL according the presence of other individual CVR factors (hypertension, diabetes mellitus, obesity were observed in CS or in the control group. Additional TL shortening was observed in dyslipidemic obese patients who were also hypertensive, compared to those with two or less CVR factors (6956±1280 vs 7860±1180, respectively, p<0.001. Age and dyslipidemia were independent negative predictors of TL.TL is shortened in dyslipidemic CS

Femtosecond pulse self-shortening in Kerr media: role of modulational instability in the spectrum formation

Science.gov (United States)

Grudtsyn, Ya. V.; Koribut, A. V.; Mikheev, L. D.; Trofimov, V. A.

2018-04-01

The mechanism of femtosecond pulse self-shortening in thin optical materials with Kerr nonlinearity is investigated. The experimentally observed spectral-angular distribution of the radiation intensity on the exit surface of a 1-mm-thick fused silica sample is compared with the results of numerical simulation based on solving the nonlinear Schrödinger equation for an electromagnetic wave with a transverse perturbation on the axis. Qualitative agreement between the calculated and experimental results confirms the hypothesis about the transient regime of multiple filamentation as a mechanism of femtosecond pulse self-shortening.

Psychometric properties of a shortened version of the Physical Self-Concept Questionnaire (PSQ-S).

Science.gov (United States)

Rodríguez-Fernández, Arantzazu; Axpe, Inge; Goñi, Alfredo

2015-01-01

The four-dimensional model of physical self-concept which differentiates the physical self-perceptions of ability, condition, attractiveness and strength is widely accepted. In the last two decades much research has been done on the physical self-concept and its relations with the psychological well-being/distress, anxiety disorders or Eating Behavior Disorders (EBD). To validate a shortened version of the Physical Self-Concept Questionnaire (PSQ-S) and verify its ability to discriminate between people with different levels of EBD. Responses of 1478 subjects between 13 and 21 years old to the shortened version of the PSQ were analyzed in order to check indexes of reliability and validity. Furthermore, the scores of 96 women aged 14 to 23 years old diagnosed of EBD were compared to 96 others without clinical diagnosis. The results indicate a reliability of 0.93 and confirm the tetrafactorial structure of the physical selfconcept. The highest physical self-concept is that of those without a clinical diagnosis of EBD. The Shortened-PSQ is a simple, reliable and suitable screening tool both for educational and clinical settings. It also provides a sufficient measure of physical self-concept for research purposes.

A 16-channel real-time digital processor for pulse-shape discrimination in multiplicity assay

International Nuclear Information System (INIS)

Joyce, Malcolm J.; Aspinall, M.D.; Cave, F.D.; Lavietes, A.

2013-06-01

In recent years, real-time neutron/γ-ray pulse-shape discrimination has become feasible for use with scintillator-based detectors that respond extremely quickly, on the order of 25 ns in terms of pulse width, and their application to a variety of nuclear material assays has been reported. For the in-situ analysis of nuclear materials, measurements are often based on the multiplicity assessment of spontaneous fission events. An example of this is the 240 Pu eff assessment stemming from long-established techniques developed for 3 He-based neutron coincidence counters when 3 He was abundant and cheap. However, such measurements when using scintillator detectors can be plagued by low detection efficiencies and low orders of coincidence (often limited to triples) if the number of detectors in use is similarly limited to 3-4 detectors. Conversely, an array of >10 detector modules arranged to optimize efficiency and multiplicity sensitivity, shifts the emphasis in terms of performance requirement to the real-time digital analyzer and, critically, to the scope remaining in the temporal processing window of these systems. In this paper we report on the design, development and commissioning of a bespoke, 16-channel real-time pulse-shape discrimination analyzer specified for the materials assay challenge summarized above. The analyzer incorporates 16 dedicated and independent high-voltage supplies along with 16 independent digital processing channels offering pulse-shape discrimination at a rate of 3 x 10 6 events per second. These functions are configured from a dedicated graphical user interface, and all settings can be adjusted on-the-fly with the analyzer effectively configured one-time-only (where desired) for subsequent plug-and-play connection, for example to a fuel bundle organic scintillation detector array. (authors)

Development and validation of a duplex real-time PCR assay for the diagnosis of equine piroplasmosis.

Science.gov (United States)

Lobanov, Vladislav A; Peckle, Maristela; Massard, Carlos L; Brad Scandrett, W; Gajadhar, Alvin A

2018-03-02

Equine piroplasmosis (EP) is an economically significant infection of horses and other equine species caused by the tick-borne protozoa Theileria equi and Babesia caballi. The long-term carrier state in infected animals makes importation of such subclinical cases a major risk factor for the introduction of EP into non-enzootic areas. Regulatory testing for EP relies on screening of equines by serological methods. The definitive diagnosis of EP infection in individual animals will benefit from the availability of sensitive direct detection methods, for example, when used as confirmatory assays for non-negative serological test results. The objectives of this study were to develop a real-time quantitative polymerase chain reaction (qPCR) assay for simultaneous detection of both agents of EP, perform comprehensive evaluation of its performance and assess the assay's utility for regulatory testing. We developed a duplex qPCR targeting the ema-1 gene of T. equi and the 18S rRNA gene of B. caballi and demonstrated that the assay has high analytical sensitivities for both piroplasm species. Validation of the duplex qPCR on samples from 362 competitive enzyme-linked immunosorbent assay (cELISA)-negative horses from Canada and the United States yielded no false-positive reactions. The assay's performance was further evaluated using samples collected from 430 horses of unknown EP status from a highly endemic area in Brazil. This set of samples was also tested by a single-target 18S rRNA qPCR for T. equi developed at the OIE reference laboratory for EP in Japan, and a previously published single-target 18S rRNA qPCR for B. caballi whose oligonucleotides we adopted for use in the duplex qPCR. Matching serum samples were tested for antibodies to these parasites using cELISA. By the duplex qPCR, T. equi-specific 18S rRNA qPCR and cELISA, infections with T. equi were detected in 87.9% (95% confidence interval, CI: 84.5-90.7%), 90.5% (95% CI: 87.3-92.3%) and 87.4% (95% CI: 84

Effect of kinesiotaping in shortening rehabilitation deadlines in sportsmen operated of anterior cruciate ligament : Randomized clinical trial, double blinded and multicentre

OpenAIRE

Franco Vargas, Daniel

2015-01-01

Background: There is not much scientific evidence available about this application of kinesiotaping (KNT) due to it being a new and recent technique of application in physiotherapy world. This study is pioneer in demonstrating the effectiveness of KNT in shortening deadlines of recuperation time after a cruciate ligament (ACL) surgery. Objectives: To demonstrate the capacity of KNT to recover the correct muscular tone in hamstrings and this make a reduction in recovery times after an ACL surg...

Development and validation of duplex, triplex, and pentaplex real-time PCR screening assays for the detection of genetically modified organisms in food and feed.

Science.gov (United States)

Huber, Ingrid; Block, Annette; Sebah, Daniela; Debode, Frédéric; Morisset, Dany; Grohmann, Lutz; Berben, Gilbert; Stebih, Dejan; Milavec, Mojca; Zel, Jana; Busch, Ulrich

2013-10-30

Worldwide, qualitative methods based on PCR are most commonly used as screening tools for genetically modified material in food and feed. However, the increasing number and diversity of genetically modified organisms (GMO) require effective methods for simultaneously detecting several genetic elements marking the presence of transgenic events. Herein we describe the development and validation of a pentaplex, as well as complementary triplex and duplex real-time PCR assays, for the detection of the most common screening elements found in commercialized GMOs: P-35S, T-nos, ctp2-cp4-epsps, bar, and pat. The use of these screening assays allows the coverage of many GMO events globally approved for commercialization. Each multiplex real-time PCR assay shows high specificity and sensitivity with an absolute limit of detection below 20 copies for the targeted sequences. We demonstrate by intra- and interlaboratory tests that the assays are robust as well as cost- and time-effective for GMO screening if applied in routine GMO analysis.

Strategies for shortening the output pulse of silicon photomultipliers

OpenAIRE

Antoranz Canales, Pedro; Miranda Pantoja, José Miguel; Yebras Rivera, José Manuel

2012-01-01

In this work, three strategies for shortening the output pulse of a silicon photomultiplier (SiPM) are reported. The first strategy is passive filtering, where band-pass filtering removes the lowest frequency components in the signal, getting a noticeable reduction in pulse width (a compression ratio of 10: 1 was obtained). In the second place, a reflectometric scheme is proposed where the amplified signal coming from the SiPM is injected into a signal splitter with one of its stubs connected...

3'UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells.

Directory of Open Access Journals (Sweden)

Yonit Hoffman

2016-02-01

Full Text Available Most mammalian genes often feature alternative polyadenylation (APA sites and hence diverse 3'UTR lengths. Proliferating cells were reported to favor APA sites that result in shorter 3'UTRs. One consequence of such shortening is escape of mRNAs from targeting by microRNAs (miRNAs whose binding sites are eliminated. Such a mechanism might provide proliferation-related genes with an expression gain during normal or cancerous proliferation. Notably, miRNA sites tend to be more active when located near both ends of the 3'UTR compared to those located more centrally. Accordingly, miRNA sites located near the center of the full 3'UTR might become more active upon 3'UTR shortening. To address this conjecture we performed 3' sequencing to determine the 3' ends of all human UTRs in several cell lines. Remarkably, we found that conserved miRNA binding sites are preferentially enriched immediately upstream to APA sites, and this enrichment is more prominent in pro-differentiation/anti-proliferative genes. Binding sites of the miR17-92 cluster, upregulated in rapidly proliferating cells, are particularly enriched just upstream to APA sites, presumably conferring stronger inhibitory activity upon shortening. Thus 3'UTR shortening appears not only to enable escape from inhibition of growth promoting genes but also to potentiate repression of anti-proliferative genes.

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.

Spinal column shortening for tethered cord syndrome associated with myelomeningocele, lumbosacral lipoma, and lipomyelomeningocele in children and young adults.

Science.gov (United States)

Aldave, Guillermo; Hansen, Daniel; Hwang, Steven W; Moreno, Amee; Briceño, Valentina; Jea, Andrew

2017-06-01

OBJECTIVE Tethered cord syndrome is the clinical manifestation of an abnormal stretch on the spinal cord, presumably causing mechanical injury, a compromised blood supply, and altered spinal cord metabolism. Tethered cord release is the standard treatment for tethered cord syndrome. However, direct untethering of the spinal cord carries potential risks, such as new neurological deficits from spinal cord injury, a CSF leak from opening the dura, and retethering of the spinal cord from normal scar formation after surgery. To avoid these risks, the authors applied spinal column shortening to children and transitional adults with primary and secondary tethered cord syndrome and report treatment outcomes. The authors' aim with this study was to determine the safety and efficacy of spinal column shortening for tethered cord syndrome by analyzing their experience with this surgical technique. METHODS The authors retrospectively reviewed the demographic and procedural data of children and young adults who had undergone spinal column shortening for primary or secondary tethered cord syndrome. RESULTS Seven patients with tethered cord syndrome caused by myelomeningocele, lipomyelomeningocele, and transitional spinal lipoma were treated with spinal column shortening. One patient with less than 24 months of follow-up was excluded from further analysis. There were 3 males and 4 females; the average age at the time was surgery was 16 years (range 8-30 years). Clinical presentations for our patients included pain (in 5 patients), weakness (in 4 patients), and bowel/bladder dysfunction (in 4 patients). Spinal column osteotomy was most commonly performed at the L-1 level, with fusion between T-12 and L-2 using a pedicle screw-rod construct. Pedicle subtraction osteotomy was performed in 6 patients, and vertebral column resection was performed in 1 patient. The average follow-up period was 31 months (range 26-37 months). Computed tomography-based radiographic outcomes showed solid

Study of the Efficacy of Real Time-PCR Method for Amikacin Determination Using Microbial Assay

Directory of Open Access Journals (Sweden)

Farzaneh Lotfipour

2015-06-01

Full Text Available Purpose: Microbial assay is used to determine the potency of antibiotics and vitamins. In spite of its advantages like simplicity and easiness, and to reveal the slight changes in the molecules, the microbial assay suffers from significant limitations; these methods are of lower specificity, accuracy and sensitivity. The objective of the present study is to evaluate the efficacy of real time-PCR technique in comparison with turbidimetric method for microbial assay of amikacin. Methods: Microbial determination of amikacin by turbidimetric method was performed according to USP. Also amikacin concentrations were determined by microbial assay using taq-man quantitative PCR method. Standard curves in different concentration for both methods were plotted and method validation parameters of linearity, precision and accuracy were calculated using statistical procedures. Results: The RT-PCR method was linear in the wider concentration range (5.12 – 38.08 for RT-PCR versus 8.00 – 30.47 for turbidimetric method with a better correlation coefficient (0.976 for RT-PCR versus 0.958 for turbidimetric method. RT-PCR method with LOQ of 5.12 ng/ml was more sensitive than turbidimetric method with LOQ of 8.00 ng/ml and the former could detect and quantify low concentrations of amikacin. The results of accuracy and precision evaluation showed that the RT-PCR method was accurate and precise in all of the tested concentration. Conclusion: The RT-PCR method described here provided an accurate and precise technique for measurement of amikacin potency and it can be a candidate for microbial determination of the antibiotics with the same test organism.

Comparison of Real-Time Multiplex Human Papillomavirus (HPV) PCR Assays with INNO-LiPA HPV Genotyping Extra Assay▿

OpenAIRE

Else, Elizabeth A.; Swoyer, Ryan; Zhang, Yuhua; Taddeo, Frank J.; Bryan, Janine T.; Lawson, John; Van Hyfte, Inez; Roberts, Christine C.

2011-01-01

Real-time type-specific multiplex human papillomavirus (HPV) PCR assays were developed to detect HPV DNA in samples collected for the efficacy determination of the quadrivalent HPV (type 6, 11, 16, and 18) L1 virus-like particle (VLP) vaccine (Gardasil). Additional multiplex (L1, E6, and E7 open reading frame [ORF]) or duplex (E6 and E7 ORF) HPV PCR assays were developed to detect high-risk HPV types, including HPV type 31 (HPV31), HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV56, HPV58, and H...

Effects of Estrogen Fluctuation during the Menstrual Cycle on the Response to Stretch-Shortening Exercise in Females

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Saulė Sipavičienė

2013-01-01

Full Text Available The aim of this study was to investigate whether variation in estrogen levels during the menstrual cycle influences susceptibility to exercise-induced muscle damage after stretch-shortening cycle exercise. Physically active women (n=18; age = 20.2 ± 1.7 yr participated in this research. The subjects performed one session of 100 maximal drop jumps on day 1 or 2 of the follicular phase and another identical session on day 1 or 2 of the ovulatory phase; the order of the sessions was randomized. Quadriceps femoris muscle peak torque evoked by electrical stimulation and maximal voluntary contraction, muscle pain, and CK activity were measured before and at various times up to 72 h after exercise. It was found that the high estrogen level during the ovulatory phase might be related to an earlier return to baseline muscle strength after strenuous stretch-shortening cycle exercise in that phase compared with the follicular phase. The estrogen effect appears to be highly specific to the damaged site because the differences in most EIMD markers (CK, soreness, and low-frequency fatigue between the two menstrual cycle phases were small.

Increasing flux rate to shorten leaching period and ramp-up production

Science.gov (United States)

Ngantung, Billy; Agustin, Riska; Ravi'i

2017-01-01

J Resources Bolaang Mongondow (JBRM) has operated a dynamic heap leach in its Bakan Gold Mine since late 2013. After successfully surpassing its name plate capacity of 2.6 MT/annum in 2014, the clayey and transition ore become the next operational challenge. The presence of transition and clayey ore requires longer leaching period, hence reducing the leach pad capacity which then caused reduced production. Maintaining or even increasing production with such longer leaching ore types can be done by expanding the leach pad area which means an additional capital investment, and/or shortening the leaching cycle which compromise a portion of gold extraction. JBRM has been successfully increasing the leach pad production from 2.6 MT/annum to 3.8 MT/annum, whilst improving the gold extraction from around 70% to around 80%. This was achieved by managing the operation of the leach pad which is shortening the leach cycle by identifying and combining the optimal flux rate application versus the tonne processed in each cell, at no capital investment for expanding the cell capacity.

Chordee and Penile Shortening Rather Than Voiding Function Are Associated With Patient Dissatisfaction After Urethroplasty.

Science.gov (United States)

Maciejewski, Conrad C; Haines, Trevor; Rourke, Keith F

2017-05-01

To identify factors that predict patient satisfaction after urethroplasty by prospectively examining patient-reported quality of life scores using 3 validated instruments. A 3-part prospective survey consisting of the International Prostate Symptom Score (IPSS), the International Index of Erectile Function (IIEF) score, and a urethroplasty quality of life survey was completed by patients who underwent urethroplasty preoperatively and at 6 months postoperatively. The quality of life score included questions on genitourinary pain, urinary tract infection (UTI), postvoid dribbling, chordee, shortening, overall satisfaction, and overall health. Data were analyzed using descriptive statistics, paired t test, univariate and multivariate logistic regression analyses, and Wilcoxon signed-rank analysis. Patients were enrolled in the study from February 2011 to December 2014, and a total of 94 patients who underwent a total of 102 urethroplasties completed the study. Patients reported statistically significant improvements in IPSS (P Wilcoxon signed-rank analysis revealed significant improvements in pain scores (P = .02), UTI (P 4 cm and the absence of UTI, pain, shortening, and chordee as predictors of patient satisfaction. Multivariate analysis of quality of life domain scores identified absence of shortening and absence of chordee as independent predictors of patient satisfaction following urethroplasty (P < .01). Patient voiding function and quality of life improve significantly following urethroplasty, but improvement in voiding function is not associated with patient satisfaction. Chordee status and perceived penile shortening impact patient satisfaction, and should be included in patient-reported outcome measures. Copyright © 2017 Elsevier Inc. All rights reserved.

Development of a highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus 71 in hand, foot, and mouth disease.

Science.gov (United States)

Niu, Peihua; Qi, Shunxiang; Yu, Benzhang; Zhang, Chen; Wang, Ji; Li, Qi; Ma, Xuejun

2016-11-01

Enterovirus 71 (EV71) is one of the major causative agents of outbreaks of hand, foot, and mouth disease (HFMD). A commercial TaqMan probe-based real-time PCR assay has been widely used for the differential detection of EV71 despite its relatively high cost and failure to detect samples with a low viral load (Ct value > 35). In this study, a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of EV71 in HFMD was developed. The sensitivity and specificity of this assay were evaluated using a reference EV71 stock and a panel of controls consisting of coxsackievirus A16 (CVA16) and common respiratory viruses, respectively. The clinical performance of this assay was evaluated and compared with those of a commercial TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional two-step nested RT-PCR assay. The limit of detection for the RTN RT-PCR assay was 0.01 TCID50/ml, with a Ct value of 38.3, which was the same as that of the traditional two-step nested RT-PCR assay and approximately tenfold lower than that of the qRT-PCR assay. When testing the reference strain EV71, this assay showed favorable detection reproducibility and no obvious cross-reactivity. The testing results of 100 clinical throat swabs from HFMD-suspected patients revealed that 41 samples were positive for EV71 by both RTN RT-PCR and traditional two-step nested RT-PCR assays, whereas only 29 were EV71 positive by qRT-PCR assay.

Clinical utility of an optimised multiplex real-time PCR assay for the identification of pathogens causing sepsis in Vietnamese patients.

Science.gov (United States)

Tat Trung, Ngo; Van Tong, Hoang; Lien, Tran Thi; Van Son, Trinh; Thanh Huyen, Tran Thi; Quyen, Dao Thanh; Hoan, Phan Quoc; Meyer, Christian G; Song, Le Huu

2018-02-01

For the identification of bacterial pathogens, blood culture is still the gold standard diagnostic method. However, several disadvantages apply to blood cultures, such as time and rather large volumes of blood sample required. We have previously established an optimised multiplex real-time PCR method in order to diagnose bloodstream infections. In the present study, we evaluated the diagnostic performance of this optimised multiplex RT-PCR in blood samples collected from 110 septicaemia patients enrolled at the 108 Military Central Hospital, Hanoi, Vietnam. Positive results were obtained by blood culture, the Light Cylcler-based SeptiFast ® assay and our multiplex RT-PCR in 35 (32%), 31 (28%), and 31 (28%) samples, respectively. Combined use of the three methods confirmed 50 (45.5%) positive cases of bloodstream infection, a rate significantly higher compared to the exclusive use of one of the three methods (P=0.052, 0.012 and 0.012, respectively). The sensitivity, specificity and area under the curve (AUC) of our assay were higher compared to that of the SeptiFast ® assay (77.4%, 86.1% and 0.8 vs. 67.7%, 82.3% and 0.73, respectively). Combined use of blood culture and multiplex RT-PCR assay showed a superior diagnostic performance, as the sensitivity, specificity, and AUC reached 83.3%, 100%, and 0.95, respectively. The concordance between blood culture and the multiplex RT-PCR assay was highest for Klebsiella pneumonia (100%), followed by Streptococcus spp. (77.8%), Escherichia coli (66.7%), Staphylococcus spp. (50%) and Salmonella spp. (50%). In addition, the use of the newly established multiplex RT-PCR assay increased the spectrum of identifiable agents (Acintobacter baumannii, 1/32; Proteus mirabilis, 1/32). The combination of culture and the multiplex RT-PCR assay provided an excellent diagnostic accomplishment and significantly supported the identification of causative pathogens in clinical samples obtained from septic patients. Copyright © 2017 The

Inter-laboratory and inter-assay comparison on two real-time PCR techniques for quantification of PCV2 nucleic acid extracted from field samples

DEFF Research Database (Denmark)

Hjulsager, Charlotte Kristiane; Grau-Roma, L.; Sibila, M.

2009-01-01

Several real-time PCR assays for quantification of PCV2 DNA (qPCR) have been described in the literature. and different in-house assays are being used by laboratories around the world. A general threshold of it copies of PCV2 per millilitre serum for postweaning multisystemic wasting syndrome (PMWS......) diagnosis has been suggested. However, neither inter-laboratory nor inter-assay comparisons have been published so far. In the present study two different qPCR probe assays Used routinely in two laboratories were compared on DNA extracted From serum, nasal and rectal swabs. Results showed a significant...

SYBR green-based one step quantitative real-time polymerase chain reaction assay for the detection of Zika virus in field-caught mosquitoes.

Science.gov (United States)

Tien, Wei-Ping; Lim, Gareth; Yeo, Gladys; Chiang, Suzanna Nicole; Chong, Chee-Seng; Ng, Lee-Ching; Hapuarachchi, Hapuarachchige Chanditha

2017-09-19

The monitoring of vectors is one of the key surveillance measures to assess the risk of arbovirus transmission and the success of control strategies in endemic regions. The recent re-emergence of Zika virus (ZIKV) in the tropics, including Singapore, emphasizes the need to develop cost-effective, rapid and accurate assays to monitor the virus spread by mosquitoes. As ZIKV infections largely remain asymptomatic, early detection of ZIKV in the field-caught mosquitoes enables timely implementation of appropriate mosquito control measures. We developed a rapid, sensitive and specific real-time reverse transcription polymerase chain reaction (rRT-PCR) assay for the detection of ZIKV in field-caught mosquitoes. The primers and PCR cycling conditions were optimized to minimize non-specific amplification due to cross-reactivity with the genomic material of Aedes aegypti, Aedes albopictus, Culex quinquefasciatus, Culex tritaeniorhynchus, Culex sitiens and Anopheles sinensis, as well as accompanying microbiota. The performance of the assay was further evaluated with a panel of flaviviruses and alphaviruses as well as in field-caught Ae. aegypti mosquitoes confirmed to be positive for ZIKV. As compared to a probe-based assay, the newly developed assay demonstrated 100% specificity and comparable detection sensitivity for ZIKV in mosquitoes. Being a SYBR Green-based method, the newly-developed assay is cost-effective and easy to adapt, thus is applicable to large-scale vector surveillance activities in endemic countries, including those with limited resources and expertise. The amplicon size (119 bp) also allows sequencing to confirm the virus type. The primers flank relatively conserved regions of ZIKV genome, so that, the assay is able to detect genetically diverse ZIKV strains. Our findings, therefore, testify the potential use of the newly-developed assay in vector surveillance programmes for ZIKV in endemic regions.

Single-label kinase and phosphatase assays for tyrosine phosphorylation using nanosecond time-resolved fluorescence detection.

Science.gov (United States)

Sahoo, Harekrushna; Hennig, Andreas; Florea, Mara; Roth, Doris; Enderle, Thilo; Nau, Werner M

2007-12-26

The collision-induced fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) by hydrogen atom abstraction from the tyrosine residue in peptide substrates was introduced as a single-labeling strategy to assay the activity of tyrosine kinases and phosphatases. The assays were tested for 12 different combinations of Dbo-labeled substrates and with the enzymes p60c-Src Src kinase, EGFR kinase, YOP protein tyrosine phosphatase, as well as acid and alkaline phosphatases, thereby demonstrating a broad application potential. The steady-state fluorescence changed by a factor of up to 7 in the course of the enzymatic reaction, which allowed for a sufficient sensitivity of continuous monitoring in steady-state experiments. The fluorescence lifetimes (and intensities) were found to be rather constant for the phosphotyrosine peptides (ca. 300 ns in aerated water), while those of the unphosphorylated peptides were as short as 40 ns (at pH 7) and 7 ns (at pH 13) as a result of intramolecular quenching. Owing to the exceptionally long fluorescence lifetime of Dbo, the assays were alternatively performed by using nanosecond time-resolved fluorescence (Nano-TRF) detection, which leads to an improved discrimination of background fluorescence and an increased sensitivity. The potential for inhibitor screening was demonstrated through the inhibition of acid and alkaline phosphatases by molybdate.

HybProbes-based real-time PCR assay for specific identification of Streptomyces scabies and Streptomyces europaeiscabiei, the potato common scab pathogens.

Science.gov (United States)

Xu, R; Falardeau, J; Avis, T J; Tambong, J T

2016-02-01

The aim of this study was to develop and validate a HybProbes-based real-time PCR assay targeting the trpB gene for specific identification of Streptomyces scabies and Streptomyces europaeiscabiei. Four primer pairs and a fluorescent probe were designed and evaluated for specificity in identifying S. scabies and Streptomyces europaeiscabiei, the potato common scab pathogens. The specificity of the HybProbes-based real-time PCR assay was evaluated using 46 bacterial strains, 23 Streptomyces strains and 23 non-Streptomyces bacterial species. Specific and strong fluorescence signals were detected from all nine strains of S. scabies and Streptomyces europaeiscabiei. No fluorescence signal was detected from 14 strains of other Streptomyces species and all non-Streptomyces strains. The identification was corroborated by the melting curve analysis that was performed immediately after the amplification step. Eight of the nine S. scabies and S. europaeiscabiei strains exhibited a unique melting peak, at Tm of 69·1°C while one strain, Warba-6, had a melt peak at Tm of 65·4°C. This difference in Tm peaks could be attributed to a guanine to cytosine mutation in strain Warba-6 at the region spanning the donor HybProbe. The reported HybProbes assay provides a more specific tool for accurate identification of S. scabies and S. europaeiscabiei strains. This study reports a novel assay based on HybProbes chemistry for rapid and accurate identification of the potato common scab pathogens. Since the HybProbes chemistry requires two probes for positive identification, the assay is considered to be more specific than conventional PCR or TaqMan real-time PCR. The developed assay would be a useful tool with great potential in early diagnosis and detection of common scab pathogens of potatoes in infected plants or for surveillance of potatoes grown in soil environment. © 2015 Her Majesty the Queen in Right of Canada © 2015 The Society for Applied Microbiology.

Qualification of a select one-stage activated partial thromboplastin time-based clotting assay and two chromogenic assays for the post-administration monitoring of nonacog beta pegol.

Science.gov (United States)

Tiefenbacher, S; Bohra, R; Amiral, J; Bowyer, A; Kitchen, S; Lochu, A; Rosén, S; Ezban, M

2017-10-01

Essentials Nonacog beta pegol (N9-GP) is an extended half-life, recombinant human factor IX (FIX). One-stage clotting (OSC) and chromogenic FIX activity assays were assessed for N9-GP recovery. OSC STA ® -Cephascreen ® , ROX FIX and BIOPHEN FIX chromogenic assays were qualified for N9-GP. Other extended half-life factor products should be assessed in a similar way prior to approval. Background Nonacog beta pegol (N9-GP) is an extended half-life, glycoPEGylated recombinant human factor IX that is under development for the prophylaxis and treatment of bleeding episodes in hemophilia B patients. Considerable reagent-dependent variability has been observed when one-stage clotting assays are used to measure the recovery of recombinant FIX products, including N9-GP. Objective To qualify select one-stage clotting and chromogenic FIX activity assays for measuring N9-GP recovery. Methods The accuracy and precision of the one-stage clotting assay (with the STA-Cephascreen activated partial thromboplastin [APTT] reagent) and the ROX Factor IX and BIOPHEN Factor IX chromogenic assays for measuring N9-GP recovery were assessed in N9-GP-spiked hemophilia B plasma samples in a systematic manner at three independent sites, with manufacturer-recommended protocols and/or site-specific assay setups, including different instruments. Results For each of the three FIX activity assays qualified on five different reagent-instrument systems, acceptable intra-assay and interassay accuracy and precision, dilution integrity, reagent robustness and freeze-thaw and short-term sample stabilities were demonstrated. The STA-Cephascreen assay showed a limited reportable range at one of the three qualification sites, and the BIOPHEN Factor IX assay showed suspect low-end sensitivity at one of the three qualification sites. An individual laboratory would account for these limitations by adjusting the assay's reportable range; thus, these findings are not considered to impact the respective

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

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

Hypocretin measurement: shelf age of radioimmunoassay kit, but not freezer time, influences assay variability.

Science.gov (United States)

Keating, Glenda; Bliwise, Donald L; Saini, Prabhjyot; Rye, David B; Trotti, Lynn Marie

2017-09-01

The hypothalamic peptide hypocretin 1 (orexin A) may be assayed in cerebrospinal fluid to diagnose narcolepsy type 1. This testing is not commercially available, and factors contributing to assay variability have not previously been comprehensively explored. In the present study, cerebrospinal fluid hypocretin concentrations were determined in duplicate in 155 patient samples, across a range of sleep disorders. Intra-assay variability of these measures was analyzed. Inter-assay correlation between samples tested at Emory and at Stanford was high (r = 0.79, p hypocretin values, such that kits closer to expiration exhibit significantly more variability.

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.

Variable exhumation rates and variable displacement rates: Documenting recent slowing of Himalayan shortening in western Bhutan

Science.gov (United States)

McQuarrie, Nadine; Tobgay, Tobgay; Long, Sean P.; Reiners, Peter W.; Cosca, Michael A.

2014-01-01

We link exhumational variability in space and time to the evolving geometry of the Himalayan fold–thrust belt in western Bhutan. By combining new and published geochronologic and thermochronologic data we document the burial age, peak temperatures and complete cooling history from 20 Ma to the present over an across-strike distance of ∼125 km. These integrated cooling curves highlight windows of fast exhumation that vary spatially and temporally. We propose that pulses of fast exhumation are a result of structures that facilitate the vertical motion of material, illustrated in sequentially-restored cross sections. Due to a range of permissible geometries at depth, we explore and evaluate the impact of geometry on kinematics and rates of deformation. The linked cooling history and cross sections provide estimates of both magnitude and timing of thrust sheet displacement and highlight temporal variability in potential shortening rates. Structural and chronologic data illustrate a general north to south progression of Himalayan deformation, with emplacement of the Main Central thrust (MCT), Paro thrust and Shumar thrust by 12 to no later than 9 Ma. Two different geometries and kinematic scenarios for the Lesser Himalayan duplex are proposed. A north to south propagating duplex system requires that the southern portion of that system, south of the MCT, deformed and cooled by 9 Ma, leaving only the southernmost thrust sheets, including the Main Boundary and Main Frontal thrusts, to deform between 9 and 0 Ma. This limited post 9 Ma shortening would necessitate a marked slowdown in convergence accommodated on the Main Himalayan thrust. A two-tiered duplex system, which allows for the Paro window duplex and the southern Baxa duplex to form simultaneously, permits duplex formation and accompanying exhumation until 6 Ma. Limited cooling from ∼200 °C to the surface post 6 Ma suggests either a decrease in shortening rates from 6 to 0 Ma or that duplex formation and

Paradoxical results of two automated real-time PCR assays in the diagnosis of pleural tuberculosis.

Science.gov (United States)

Morales-López, Soraya E; Yepes, Jayr A; Anzola, Irina; Aponte, Hernán; Llerena-Polo, Claudia R

2017-01-01

Tuberculosis (TB) is a major cause of worldwide mortality. We report the case of a non-HIV-infected woman with clinical suspicion of pleural tuberculosis and contradictory results between Xpert ® MTB/RIF and Abbott RealTime MTB assays from pleural fluid specimen. Liquid and solid cultures for tuberculosis were performed with negative results. The patient received treatment, and clinical improvement was observed. Both techniques detect Mycobacterium tuberculosis complex, but they have different targets and limits of detection. Abbott RealTime MTB results correlated well with the clinical findings of the patient. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Variation in Bluetongue virus real-time reverse transcription polymerase chain reaction assay results in blood samples of sheep, cattle, and alpaca.

Science.gov (United States)

Brito, Barbara P; Gardner, Ian A; Hietala, Sharon K; Crossley, Beate M

2011-07-01

Bluetongue is a vector-borne viral disease that affects domestic and wild ruminants. The epidemiology of this disease has recently changed, with occurrence in new geographic areas. Various real-time quantitative reverse transcription polymerase chain reaction (real-time qRT-PCR) assays are used to detect Bluetongue virus (BTV); however, the impact of biologic differences between New World camelids and domestic ruminant samples on PCR efficiency, for which the BTV real-time qRT-PCR was initially validated are unknown. New world camelids are known to have important biologic differences in whole blood composition, including hemoglobin concentration, which can alter PCR performance. In the present study, sheep, cattle, and alpaca blood were spiked with BTV serotypes 10, 11, 13, and 17 and analyzed in 10-fold dilutions by real-time qRT-PCR to determine if species affected nucleic acid recovery and assay performance. A separate experiment was performed using spiked alpaca blood subsequently diluted in 10-fold series in sheep blood to assess the influence of alpaca blood on performance efficiency of the BTV real-time qRT-PCR assay. Results showed that BTV-specific nucleic acid detection from alpaca blood was consistently 1-2 logs lower than from sheep and cattle blood, and results were similar for each of the 4 BTV serotypes analyzed.

Muscle damage induced by stretch-shortening cycle exercise.

Science.gov (United States)

Kyröläinen, H; Takala, T E; Komi, P V

1998-03-01

Strenuous stretch-shortening cycle exercise was used as a model to study the leakage of proteins from skeletal muscle. The analysis included serum levels of creatine kinase (S-CK), myoglobin (S-Mb), and carbonic anhydrase (S-CA III). Blood samples from power- (N=11) and endurance-trained (N=10) athletes were collected before, 0, and 2 h after the exercise, which consisted of a total of 400 jumps. The levels of all determined myocellular proteins increased immediately after the exercise (P exercise, and the ratio of S-CA III and S-Mb decreased (P recruitment order of motor units, and/or differences in training background.

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.

Comparison of multiplex RT-PCR and real-time HybProbe assay for serotyping of dengue virus using reference strains and clinical samples from India

Directory of Open Access Journals (Sweden)

Anita Chakravarti

2016-01-01

Full Text Available Background: Dengue virus serotyping is crucial from clinical management and epidemiological point of view. Aims: To compare efficacy of two molecular detection and typing methods, namely, multiplex reverse transcription polymerase chain reaction (RT-PCR and real-time Hybprobe assay using a panel of known dilution of four reference Dengue virus strains and a panel of sera collected from clinically suspected dengue patients. Settings: This study was conducted at a tertiary-care teaching hospital in Delhi, India. Materials and Methods: Dengue serotype specific virus strains were used as prototypes for serotyping assays. Viral load was quantified by quantitative real time reverse transcription polymerase chain reaction (qRT-PCR. Acute phase serum samples were collected from 79 patients with clinically suspected Dengue fever on their first day of presentation during September-October 2012. Viral RNA from serum and cell culture supernatant was extracted. Reverse transcription was carried out. Quantitative detection of DENV RNA from reference strain culture supernatants and each of the 79 patient samples by real-time PCR was performed using light cycler Taqman master mix kit. Serotyping was done by multiplex RT-PCR assay and Hybprobe assay. Results: The multiplex RT-PCR assay, though found to be 100% specific, couldn't serotype either patient or reference strains with viral load less than 1000 RNA copies/ml. The Hybprobe assay was found to have 100% specificity and had a lower limit of serotype detection of merely 3.54 RNA copies/ml. Conclusions: HybProbe assay has an important role especially in situations where serotyping is to be performed in clinical samples with low viral load.

Real-time PCR assay using fine-needle aspirates and tissue biopsy specimens for rapid diagnosis of mycobacterial lymphadenitis in children

NARCIS (Netherlands)

Bruijnesteijn van Coppenraet, E. S.; Lindeboom, J. A.; Prins, J. M.; Peeters, M. F.; Claas, E. C. J.; Kuijper, E. J.

2004-01-01

A real-time PCR assay was developed to diagnose and identify the causative agents of suspected mycobacterial lymphadenitis. Primers and probes for the real-time PCR were designed on the basis of the internal transcribed spacer sequence, enabling the recognition of the genus Mycobacterium and the

Bit Error Rate Minimizing Channel Shortening Equalizers for Single Carrier Cyclic Prefixed Systems

National Research Council Canada - National Science Library

Martin, Richard K; Vanbleu, Koen; Ysebaert, Geert

2007-01-01

.... Previous work on channel shortening has largely been in the context of digital subscriber lines, a wireline system that allows bit allocation, thus it has focused on maximizing the bit rate for a given bit error rate (BER...

Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples.

LENUS (Irish Health Repository)

Meyler, Kenneth L

2012-12-01

Since the introduction of the Haemophilus influenzae serotype b vaccine, invasive H. influenzae disease has become dominated by nontypeable (NT) strains. Several widely used molecular diagnostic methods have been shown to lack sensitivity or specificity in the detection of some of these strains. Novel real-time assays targeting the fucK, licA, and ompP2 genes were developed and evaluated. The fucK assay detected all strains of H. influenzae tested (n = 116) and had an analytical sensitivity of 10 genome copies\\/polymerase chain reaction (PCR). This assay detected both serotype b and NT H. influenzae in 12 previously positive specimens (culture and\\/or bexA PCR) and also detected H. influenzae in a further 5 of 883 culture-negative blood and cerebrospinal fluid (CSF) samples. The fucK assay has excellent potential as a diagnostic test for detection of typeable and nontypeable strains of invasive H. influenzae in clinical samples of blood and CSF.

Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples.

Science.gov (United States)

Meyler, Kenneth L; Meehan, Mary; Bennett, Desiree; Cunney, Robert; Cafferkey, Mary

2012-12-01

Since the introduction of the Haemophilus influenzae serotype b vaccine, invasive H. influenzae disease has become dominated by nontypeable (NT) strains. Several widely used molecular diagnostic methods have been shown to lack sensitivity or specificity in the detection of some of these strains. Novel real-time assays targeting the fucK, licA, and ompP2 genes were developed and evaluated. The fucK assay detected all strains of H. influenzae tested (n = 116) and had an analytical sensitivity of 10 genome copies/polymerase chain reaction (PCR). This assay detected both serotype b and NT H. influenzae in 12 previously positive specimens (culture and/or bexA PCR) and also detected H. influenzae in a further 5 of 883 culture-negative blood and cerebrospinal fluid (CSF) samples. The fucK assay has excellent potential as a diagnostic test for detection of typeable and nontypeable strains of invasive H. influenzae in clinical samples of blood and CSF. Copyright © 2012 Elsevier Inc. All rights reserved.

Validation of a Pan-Orthopox Real-Time PCR Assay for the Detection and Quantification of Viral Genomes from Nonhuman Primate Blood

Science.gov (United States)

2017-06-19

Validation of a pan-orthopox real-time PCR assay for the detection and quantification of viral genomes from nonhuman primate blood. Eric...medical countermeasures by the U.S. FDA, the assay was designed to quantitate poxvirus genomic DNA in a nonhuman primate (cynomolgus macaque) blood...monkeypox virus into nonhuman primate blood, we chose to use the HA standard after considering the potential biological safety and logistical issues with

A Possible Differentially Shortened Strike-slip Plate Boundary: the Okhotsk Plate Example.

Science.gov (United States)

Hindle, D.; Egorov, V.; Mackey, K. G.; Fujita, K.

2004-12-01

The Okhotsk plate has been postulated based on a combination of GPS geodetic inversions (REVEL1), seimsicity, geologic and lineament data. Lying between the North American and Eurasian plates, its northwestern corner would appear to be undergoing compression in a scissors motion between the two bounding plates. Extrusion tectonics along multiple, large strike-slip faults within the Okhotsk plate itself have been suggested to allow the escape of material away from the apex of Eurasia-North America. The plate boundary between Okhotsk and North America has been suggested to be diffuse, based on widely scattered minor seismicity. However, the large, left lateral, Ulakhan fault has also been suggested as a candidate plate boundary. We present field geological and geomorphological evidence of the partitioning of deformation between the Ulakhan fault, and several parallel and oblique, linked faults. The Ulakhan fault strand appears to have a maximum displacement of 24 km based on river valley offsets and closing large pull apart basins. Some of the displacement from the Ulakhan fault appears relayed into the plate margin along oblique trending, thrust/oblique slip faults. Estimated shortening over these faults is equivalent to the amount of shortening relayed into the plate margin from the plate boundary. There may be several thrust/oblique slip faults along the Ulakhan fault, which leads to the interesting situation of a segmented, strike-slip plate boundary being actively shortened in a margin parallel direction. This may be the result of postulated extrusion of the Okhotsk plate due to North America/Eurasia convergence. Such a situation would have important consequences for the interpretation of GPS data in a plate tectonic context.

Real-time polymerase chain reaction assay for endogenous reference gene for specific detection and quantification of common wheat-derived DNA (Triticum aestivum L.).

Science.gov (United States)

Vautrin, Sonia; Zhang, David

2007-01-01

A species-specific endogenous reference gene system was developed for polymerase chain reaction (PCR)-based analysis in common wheat (Triticum aestivum L.) by targeting the ALMT1 gene, an aluminium-activated malate transporter. The primers and probe were elaborated for real-time PCR-based qualitative and quantitative assay. The size of amplified product is 95 base pairs. The specificity was assessed on 17 monocot and dicot plant species. The established real-time PCR assay amplified only T. aestivum-derived DNA; no amplification occurred on other phylogenetically related species, including durum wheat (T. durum). The robustness of the system was tested on the DNA of 15 common wheat cultivars using 20 000 genomic copies per PCR the mean cycle threshold (Ct) values of 24.02 +/- 0.251 were obtained. The absolute limits of detection and quantification of the real-time PCR assay were estimated to 2 and 20 haploid genome copies of common wheat, respectively. The linearity was experimentally validated on 2-fold serial dilutions of DNA from 650 to 20 000 haploid genome copies. All these results show that the real-time PCR assay developed on the ALMT1 gene is suitable to be used as an endogenous reference gene for PCR-based specific detection and quantification of T. aestivum-derived DNA in various applications, in particular for the detection and quantification of genetically modified materials in common wheat.

Evaluation of three 5' exonuclease-based real-time polymerase chain reaction assays for detection of pathogenic Leptospira species in canine urine.

Science.gov (United States)

Fink, Jamie M; Moore, George E; Landau, Ruth; Vemulapalli, Ramesh

2015-03-01

Leptospirosis is caused by several pathogenic Leptospira species, and is an important infectious disease of dogs. Early detection of infection is crucial for an effective antibiotic treatment of the disease. Though different polymerase chain reaction (PCR) assays have been developed for detection of pathogenic Leptospira spp., thorough evaluation of the performance of these assays using dog urine samples has not been carried out. In the current study, the performance of 3 real-time PCR (qPCR) assays was assessed, 1 targeting the 16S ribosomal RNA (rRNA) gene and the other 2 targeting the lipL32 gene, a gene for the LipL32 outer membrane protein. With DNA extracted from laboratory-cultured pathogenic Leptospira spp., all 3 qPCR assays showed 100% specificity and had identical lower limits of detection. Compared to a conventional, gel-based PCR assay, all 3 qPCR assays were 100-fold more sensitive. There was a 100% agreement in the results of the 3 assays when tested on urine samples collected aseptically from 30 dogs suspected for leptospirosis. However, when tested on 30 urine samples that were collected by the free-catch method, the 16S rRNA-based assay falsely detected 13.3% of the samples as positive for pathogenic Leptospira spp. Nucleotide sequence analysis of the amplified DNA fragments showed that the assay resulted in false positives because of unrelated bacteria. All urine samples collected from 100 apparently healthy dogs at a local animal shelter tested negative for pathogenic Leptospira spp. These results highlight the importance of sample-specific validation of PCR-based diagnostic assays and the application of appropriately validated assays for more reliable pathogen detection. © 2015 The Author(s).

The T2-Shortening Effect of Gadolinium and the Optimal Conditions for Maximizing the CNR for Evaluating the Biliary System: a Phantom Study

International Nuclear Information System (INIS)

Lee, Mi Jung; Kim, Myung Joon; Yoon, Choon Sik; Song, Si Young; Park, Kyung Soo; Kim, Woo Sun

2011-01-01

Clear depiction of the common bile duct is important when evaluating neonatal cholestasis in order to differentiate biliary atresia from other diseases. During MR cholangiopancreatography, the T2-shortening effect of gadolinium can increase the contrast-to-noise ratio (CNR) of the bile duct and enhance its depiction. The purpose of this study was to confirm, by performing a phantom study, the T2-shortening effect of gadolinium, to evaluate the effect of different gadolinium chelates with different gadolinium concentrations and different magnetic field strengths for investigating the optimal combination of these conditions, and for identifying the maximum CNR for the evaluation of the biliary system. MR imaging using a T2-weighted single-shot fast spin echo sequence and T2 relaxometry was performed with a sponge phantom in a syringe tube. Two kinds of contrast agents (Gd-DTPA and Gd-EOB-DTPA) with different gadolinium concentrations were evaluated with 1.5T and 3T scanners. The signal intensities, the CNRs and the T2 relaxation time were analyzed. The signal intensities significantly decreased as the gadolinium concentrations increased (p < 0.001) with both contrast agents. These signal intensities were higher on a 3T (p < 0.001) scanner. The CNRs were higher on a 1.5T (p < 0.001) scanner and they showed no significant change with different gadolinium concentrations. The T2 relaxation time also showed a negative correlation with the gadolinium concentrations (p < 0.001) and the CNRs showed decrease more with Gd-EOB-DTPA (versus Gd-DTPA; p < 0.001) on a 3T scanner (versus 1.5T; p < 0.001). A T2-shortening effect of gadolinium exhibits a negative correlation with the gadolinium concentration for both the signal intensities and the T2 relaxation time. A higher CNR can be obtained with Gd-DTPA on a 1.5T MRI scanner.

Validation of a newly developed hexaplex real-time PCR assay for screening for presence of GMOs in food, feed and seed.

Science.gov (United States)

Bahrdt, C; Krech, A B; Wurz, A; Wulff, D

2010-03-01

For years, an increasing number and diversity of genetically modified plants has been grown on a commercial scale. The need for detection and identification of these genetically modified organisms (GMOs) calls for broad and at the same time flexible high throughput testing methods. Here we describe the development and validation of a hexaplex real-time polymerase chain reaction (PCR) screening assay covering more than 100 approved GMOs containing at least one of the GMO targets of the assay. The assay comprises detection systems for Cauliflower Mosaic Virus 35S promoter, Agrobacterium tumefaciens NOS terminator, Figwort Mosaic Virus 34S promoter and two construct-specific sequences present in novel genetically modified soybean and maize that lack common screening elements. Additionally a detection system for an internal positive control (IPC) indicating the presence or absence of PCR inhibiting substances was included. The six real-time PCR systems were allocated to five detection channels showing no significant crosstalk between the detection channels. As part of an extensive validation, a limit of detection (LOD(abs)) GMOs in processed and unprocessed food, feed and seed samples with high efficiency.

Development of a real-time RT-PCR assay based on primer-probe energy transfer for the detection of all serotypes of bluetongue virus

DEFF Research Database (Denmark)

Leblanc, N; Rasmussen, Thomas Bruun; Fernandez, J

2010-01-01

A real-time RT-PCR assay based on the primer–probe energy transfer (PriProET) was developed to detect all 24 serotypes of bluetongue virus (BTV). BTV causes serious disease, primarily in sheep, but in other ruminants as well. A distinguishing characteristic of the assay is its tolerance toward...

Pooled Open Blocks Shorten Wait Times for Nonelective Surgical Cases.

Science.gov (United States)

Zenteno, Ana C; Carnes, Tim; Levi, Retsef; Daily, Bethany J; Price, Devon; Moss, Susan C; Dunn, Peter F

2015-07-01

Assess the impact of the implementation of a data-driven scheduling strategy that aimed to improve the access to care of nonelective surgical patients at Massachusetts General Hospital (MGH). Between July 2009 and June 2010, MGH experienced increasing throughput challenges in its perioperative environment: approximately 30% of the nonelective patients were waiting more than the prescribed amount of time to get to surgery, hampering access to care and aggravating the lack of inpatient beds. This work describes the design and implementation of an "open block" strategy: operating room (OR) blocks were reserved for nonelective patients during regular working hours (prime time) and their management centralized. Discrete event simulation showed that 5 rooms would decrease the percentage of delayed patients from 30% to 2%, assuming that OR availability was the only reason for preoperative delay. Implementation began in January 2012. We compare metrics for June through December of 2012 against the same months of 2011. The average preoperative wait time of all nonelective surgical patients decreased by 25.5% (P reason for delay. Rigorous metrics were developed to evaluate its performance. Strong managerial leadership was crucial to enact the new practices and turn them into organizational change.

Clinical Application of a Multiplex Real-Time PCR Assay for Simultaneous Detection of Legionella Species, Legionella pneumophila, and Legionella pneumophila Serogroup 1

OpenAIRE

Benitez, Alvaro J.; Winchell, Jonas M.

2014-01-01

We developed a single-tube multiplex real-time PCR assay capable of simultaneously detecting and discriminating Legionella spp., Legionella pneumophila, and Legionella pneumophila serogroup 1 in primary specimens. Evaluation of 21 clinical specimens and 115 clinical isolates demonstrated this assay to be a rapid, high-throughput diagnostic test with 100% specificity that may aid during legionellosis outbreaks and epidemiologic investigations.

3’UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells

Science.gov (United States)

Hoffman, Yonit; Bublik, Debora Rosa; P. Ugalde, Alejandro; Elkon, Ran; Biniashvili, Tammy; Agami, Reuven; Oren, Moshe; Pilpel, Yitzhak

2016-01-01

Most mammalian genes often feature alternative polyadenylation (APA) sites and hence diverse 3’UTR lengths. Proliferating cells were reported to favor APA sites that result in shorter 3’UTRs. One consequence of such shortening is escape of mRNAs from targeting by microRNAs (miRNAs) whose binding sites are eliminated. Such a mechanism might provide proliferation-related genes with an expression gain during normal or cancerous proliferation. Notably, miRNA sites tend to be more active when located near both ends of the 3’UTR compared to those located more centrally. Accordingly, miRNA sites located near the center of the full 3’UTR might become more active upon 3'UTR shortening. To address this conjecture we performed 3' sequencing to determine the 3' ends of all human UTRs in several cell lines. Remarkably, we found that conserved miRNA binding sites are preferentially enriched immediately upstream to APA sites, and this enrichment is more prominent in pro-differentiation/anti-proliferative genes. Binding sites of the miR17-92 cluster, upregulated in rapidly proliferating cells, are particularly enriched just upstream to APA sites, presumably conferring stronger inhibitory activity upon shortening. Thus 3’UTR shortening appears not only to enable escape from inhibition of growth promoting genes but also to potentiate repression of anti-proliferative genes. PMID:26908102

A novel and highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus.

Science.gov (United States)

Shen, Xin-Xin; Qiu, Fang-Zhou; Zhao, Huai-Long; Yang, Meng-Jie; Hong, Liu; Xu, Song-Tao; Zhou, Shuai-Feng; Li, Gui-Xia; Feng, Zhi-Shan; Ma, Xue-Jun

2018-03-01

The sensitivity of qRT-PCR assay is not adequate for the detection of the samples with lower viral load, particularly in the cerebrospinal fluid (CSF) of patients. Here, we present the development of a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of human enterovirus (HEV). The clinical performance of both RTN RT-PCR and qRT-PCR was also tested and compared using 140 CSF and fecal specimens. The sensitivities of RTN RT-PCR assay for EV71, Coxsackievirus A (CVA)16, CVA6 and CVA10 achieved 10 -8 dilution with a corresponding Ct value of 38.20, 36.45, 36.75, and 36.45, respectively, which is equal to traditional two-step nested RT-PCR assay and approximately 2-10-fold lower than that of qRT-PCR assay. The specificity of RTN RT-PCR assay was extensively analyzed insilico and subsequently verified using the reference isolates and clinical samples. Sixteen qRT-PCR-negative samples were detected by RTN RT-PCR and a variety of enterovirus serotypes was identified by sequencing of inner PCR products. We conclude RTN RT-PCR is more sensitive than qRT-PCR for the detection of HEV in clinical samples. Copyright © 2017 Elsevier Inc. All rights reserved.

Assay strategies and methods for phospholipases

International Nuclear Information System (INIS)

Reynolds, L.J.; Washburn, W.N.; Deems, R.A.; Dennis, E.A.

1991-01-01

Of the general considerations discussed, the two issues which are most important in choosing an assay are (1) what sensitivity is required to assay a particular enzyme and (2) whether the assay must be continuous. One can narrow the options further by considering substrate availability, enzyme specificity, assay convenience, or the presence of incompatible side reactions. In addition, the specific preference of a particular phospholipase for polar head group, micellar versus vesicular substrates, and anionic versus nonionic detergents may further restrict the options. Of the many assays described in this chapter, several have limited applicability or serious drawbacks and are not commonly employed. The most commonly used phospholipase assays are the radioactive TLC assay and the pH-stat assay. The TLC assay is probably the most accurate, sensitive assay available. These aspects often outweigh the disadvantages of being discontinuous, tedious, and expensive. The radioactive E. coli assay has become popular recently as an alternative to the TLC assay for the purification of the mammalian nonpancreatic phospholipases. The assay is less time consuming and less expensive than the TLC assay, but it is not appropriate when careful kinetics are required. Where less sensitivity is needed, or when a continuous assay is necessary, the pH-stat assay is often employed. With purified enzymes, when free thiol groups are not present, a spectrophotometric thiol assay can be used. This assay is ∼ as sensitive as the pH-stat assay but is more convenient and more reproducible, although the substrate is not available commercially. Despite the many assay choices available, the search continues for a convenient, generally applicable assay that is both sensitive and continuous

Measurement of nucleotide exchange rate constants in single rabbit soleus myofibrils during shortening and lengthening using a fluorescent ATP analog.

Science.gov (United States)

Shirakawa, I; Chaen, S; Bagshaw, C R; Sugi, H

2000-02-01

The kinetics of displacement of a fluorescent nucleotide, 2'(3')-O-[N[2-[[Cy3]amido]ethyl]carbamoyl]-adenosine 5'-triphosphate (Cy3-EDA-ATP), bound to rabbit soleus muscle myofibrils were studied using flash photolysis of caged ATP. Use of myofibrils from this slow twitch muscle allowed better resolution of the kinetics of nucleotide exchange than previous studies with psoas muscle myofibrils (, Biophys. J. 73:2033-2042). Soleus myofibrils in the presence of Cy3-EDA-nucleotides (Cy3-EDA-ATP or Cy3-EDA-ADP) showed selective fluorescence staining of the A-band. The K(m) for Cy3-EDA-ATP and the K(d) for Cy3-EDA-ADP binding to the myofibril A-band were 1.9 microM and 3.8 microM, respectively, indicating stronger binding of nucleotide to soleus cross-bridges compared to psoas cross-bridges (2.6 microM and 50 microM, respectively). After flash photolysis of caged ATP, the A-band fluorescence of the myofibril in the Cy3-EDA-ATP solution under isometric conditions decayed exponentially with a rate constant of 0.045 +/- 0.007 s(-1) (n = 32) at 10 degrees C, which was about seven times slower than that for psoas myofibrils. When a myofibril was allowed to shorten with a constant velocity, the nucleotide displacement rate constant increased from 0.066 s(-1) (isometric) to 0.14 s(-1) at 20 degrees C with increasing shortening velocity up to 0.1 myofibril length/s (V(max), the shortening velocity under no load was approximately 0. 2 myofibril lengths/s). The rate constant was not significantly affected by an isovelocity stretch of up to 0.1 myofibril lengths/s. These results suggest that the cross-bridge kinetics are not significantly affected at higher strain during lengthening but depend on the lower strain during shortening. These data also indicate that the interaction distance between a cross-bridge and the actin filament is at least 16 nm for a single cycle of the ATPase.

Automation of the dicentric chromosome assay and related assays

International Nuclear Information System (INIS)

Balajee, Adayabalam S.; Dainiak, Nicholas

2016-01-01

Dicentric Chromosome Assay (DCA) is considered to be the 'gold standard' for personalized dose assessment in humans after accidental or incidental radiation exposure. Although this technique is superior to other cytogenetic assays in terms of specificity and sensitivity, its potential application to radiation mass casualty scenarios is highly restricted because DCA is time consuming and labor intensive when performed manually. Therefore, it is imperative to develop high throughput automation techniques to make DCA suitable for radiological triage scenarios. At the Cytogenetic Biodosimetry Laboratory in Oak Ridge, efforts are underway to develop high throughput automation of DCA. Current status on development of various automated cytogenetic techniques in meeting the biodosimetry needs of radiological/nuclear incident(s) will be discussed

Moderate reagent mixing on an orbital shaker reduces the incubation time of enzyme-linked immunosorbent assay.

Science.gov (United States)

Kumar, Saroj; Ahirwar, Rajesh; Rehman, Ishita; Nahar, Pradip

2017-07-01

Rapid diagnostic tests can be developed using ELISA for detection of diseases in emergency conditions. Conventional ELISA takes 1-2 days, making it unsuitable for rapid diagnostics. Here, we report the effect of reagents mixing via shaking or vortexing on the assay timing of ELISA. A 48-min protocol of ELISA involving 12-min incubations with reagent mixing at 750 rpm for every step was optimized. Contrary to this, time-optimized control ELISA performed without mixing produced similar results in 8 h, leaving a time gain of 7 h using the developed protocol. Collectively, the findings suggest the development of ELISA-based rapid diagnostics. Copyright © 2017 Elsevier Inc. All rights reserved.

Multiplex real-time PCR assay for detection of Escherichia coli O157:H7 and screening for non-O157 Shiga toxin-producing E. coli.

Science.gov (United States)

Li, Baoguang; Liu, Huanli; Wang, Weimin

2017-11-09

Shiga toxin-producing Escherichia coli (STEC), including E. coli O157:H7, are responsible for numerous foodborne outbreaks annually worldwide. E. coli O157:H7, as well as pathogenic non-O157:H7 STECs, can cause life-threating complications, such as bloody diarrhea (hemolytic colitis) and hemolytic-uremic syndrome (HUS). Previously, we developed a real-time PCR assay to detect E. coli O157:H7 in foods by targeting a unique putative fimbriae protein Z3276. To extend the detection spectrum of the assay, we report a multiplex real-time PCR assay to specifically detect E. coli O157:H7 and screen for non-O157 STEC by targeting Z3276 and Shiga toxin genes (stx1 and stx2). Also, an internal amplification control (IAC) was incorporated into the assay to monitor the amplification efficiency. The multiplex real-time PCR assay was developed using the Life Technology ABI 7500 System platform and the standard chemistry. The optimal amplification mixture of the assay contains 12.5 μl of 2 × Universal Master Mix (Life Technology), 200 nM forward and reverse primers, appropriate concentrations of four probes [(Z3276 (80 nM), stx1 (80 nM), stx2 (20 nM), and IAC (40 nM)], 2 μl of template DNA, and water (to make up to 25 μl in total volume). The amplification conditions of the assay were set as follows: activation of TaqMan at 95 °C for 10 min, then 40 cycles of denaturation at 95 °C for 10 s and annealing/extension at 60 °C for 60 s. The multiplex assay was optimized for amplification conditions. The limit of detection (LOD) for the multiplex assay was determined to be 200 fg of bacterial DNA, which is equivalent to 40 CFU per reaction which is similar to the LOD generated in single targeted PCRs. Inclusivity and exclusivity determinants were performed with 196 bacterial strains. All E. coli O157:H7 (n = 135) were detected as positive and all STEC strains (n = 33) were positive for stx1, or stx2, or stx1 and stx2 (Table 1). No cross reactivity was detected with Salmonella

Performance of the Abbott RealTime MTB RIF/INH resistance assay when used to test Mycobacterium tuberculosis specimens from Bangladesh

Directory of Open Access Journals (Sweden)

Kostera J

2018-05-01

Full Text Available Joshua Kostera, Gregor Leckie, Klara Abravaya, Hong Wang Abbott Molecular, Abbott Laboratories, Des Plaines, IL, USA Introduction: The Abbott RealTime MTB RIF/INH Resistance Assay (RT MTB RIF/INH is an assay for the detection of rifampicin (RIF- and/or isoniazid (INH-resistant Mycobacterium tuberculosis (MTB. The assay can be used to test sputum, bronchial alveolar lavage, and N-Acetyl-L-Cysteine (NALC/NaOH pellets prepared from these samples. The assay can be used in direct testing mode, or in reflex mode following a MTB positive result produced by its companion assay, Abbott RT MTB. Methods: In this study, the direct testing mode was used to test paired sputum and NALC/NaOH pellets prepared from sputum collected from Bangladesh TB patients. One hundred and thirty two paired samples were tested. Results: The RT MTB RIF/INH inhibition rate was 0%. One hundred and twenty-two paired samples had results above the assay limit of detection and were analyzed by comparing with results from phenotypic drug sensitivity testing, GeneXpert MTB/RIF (Xpert, and MTBDR plus (Hain. RT MTB RIF/INH results were in good agreement with those of GeneXpert and Hain. Conclusion: The ability of this assay to detect RIF and INH resistance may contribute to the global control of multidrug resistant tuberculosis. Keywords: tuberculosis, rifampicin, isoniazid, resistance

Loop mediated isothermal amplification assay using hydroxy naphthol blue, conventional polymerase chain reaction and real-time PCR in the diagnosis of intraocular tuberculosis

Directory of Open Access Journals (Sweden)

P K Balne

2015-01-01

Full Text Available This study is a comparative evaluation (Chi-square test of a closed tube loop mediated isothermal amplification assay using hydroxy naphthol blue dye (HNB-LAMP, real-time polymerase chain reaction (PCR and conventional PCR in the diagnosis of intraocular tuberculosis. Considering clinical presentation as the gold standard in 33 patients, the sensitivity of HNB-LAMP assay (75.8% was higher (not significant, P value 0.2 than conventional PCR (57.6% and lower than real-time PCR (90.9%. Specificity was 100% by all three methods. No amplification was observed in negative controls (n = 20 by all three methods. The cost of the HNB-LAMP assay was Rs. 500.00 and it does not require thermocycler, therefore, it can be used as an alternative to conventional PCR in resource-poor settings.

Shortened carbon nanotubes and their influence on the electrical properties of polymer nanocomposites

NARCIS (Netherlands)

Inam, F.; Reece, M.J.; Peijs, A.A.J.M.

2012-01-01

Multi-wall carbon nanotubes of medium length (mCNTs) were aggressively tip-ultrasonicated to produce shortened and damaged carbon nanotubes (xCNTs). High-resolution electron microscopic analysis was performed to measure the dimensions of carbon nanotubes (CNTs). Thermo-gravimetric analysis and Raman

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...

A multiplex, internally controlled real-time PCR assay for detection of toxigenic Clostridium difficile and identification of hypervirulent strain 027/ST-1

DEFF Research Database (Denmark)

Hoegh, A M; Nielsen, J B; Lester, A

2012-01-01

The purpose of this study was to validate a multiplex real-time PCR assay capable of detecting toxigenic Clostridium difficile and simultaneously identifying C. difficile ribotype 027/ST-1 by targeting the toxin genes tcdA, tcdB and cdtA in one reaction and in a separate reaction identifying the Δ...... to confirm the correct identification of the Δ117 deletion in tcdC and C. difficile ribotype 027/ST-1, respectively. The PCR assay displayed a sensitivity, specificity, PPV and NPV of 99.0%, 97.4%, 87.4% and 99.8%, respectively, compared to toxigenic culture on 665 samples evaluable both by PCR and culture....... Sequencing of tcdC, ribotyping and MLST of cultured isolates validated the genotyping assay and confirmed the ability of the assay to correctly identify C. difficile ribotype 027/ST-1 in our current epidemiological setting. We describe the use of a combination of two separate PCR assays for sensitive...

Femoral neck shortening in adult patients under the age of 55 years is associated with worse functional outcomes: Analysis of the prospective multi-center study of hip fracture outcomes in China (SHOC).

Science.gov (United States)

Slobogean, Gerard P; Stockton, David J; Zeng, Bing-Fang; Wang, Dong; Ma, Baotong; Pollak, Andrew N

2017-08-01

Young femoral neck fracture patients require surgical fixation to preserve the native hip joint and accommodate increased functional demands. Recent reports have identified a high incidence of fracture shortening and this may have negative functional consequences. We sought to determine if fracture shortening is associated with poor functional outcome in young femoral neck fracture patients. One hundred and forty-two patients with femoral neck fractures age 18-55 were recruited in this prospective cohort study across three Level 1 trauma hospitals in Mainland China. Patient-reported and objective functional outcomes were measured with the Harris Hip Score (HHS), Timed Up and Go (TUG), and SF-36 Physical Component Summary (SF-36 PCS) at 12 months. Radiographic fracture shortening was measured along the long axis of the femoral neck and corrected for magnification. Severe shortening was defined as ≥10mm. The primary analysis measured associations between severe radiographic shortening and HHS at one-year post-fixation. One hundred and two patients had complete radiographic and functional outcomes available for analysis at one year. The mean age of participants was 43.7±10.8years and 53% were male. Fifty-five percent of fractures were displaced and 37% were vertically orientated (Pauwels Type 3). The mean functional outcome scores were: HHS 90.0±10.8, TUG 12.0±5.1s, and PCS 48.5±8.6. Severe shortening occurred in 13% of patients and was associated with worse functional outcome scores: HHS mean difference 9.9 (p=0.025), TUG mean difference 3.2s (p=0.082), and PCS mean difference 5.4 (p=0.055). Severe shortening is associated with clinically important decreases in functional outcome as measured by HHS following fixation of young femoral neck fractures, occurring in 13% of patients in this population. The principle of fracture site compression utilized by modern constructs may promote healing; however, excessive shortening is associated with worse patient

The microculture-kinetic (MiCK) assay: the role of a drug-induced apoptosis assay in drug development and clinical care.

Science.gov (United States)

Bosserman, Linda; Prendergast, Franklyn; Herbst, Roy; Fleisher, Martin; Salom, Emery; Strickland, Steven; Raptis, Anastasios; Hallquist, Allan; Perree, Mathieu; Rajurkar, Swapnil; Karimi, Misagh; Rogers, Karl; Davidson, Dirk; Willis, Carl; Penalver, Manuel; Homesley, Howard; Burrell, Matthew; Garrett, Audrey; Rutledge, James; Chernick, Michael; Presant, Cary A

2012-08-15

A drug-induced apoptosis assay, termed the microculture-kinetic (MiCK) assay, has been developed. Blinded clinical trials have shown higher response rates and longer survival in groups of patients with acute myelocytic leukemia and epithelial ovarian cancer who have been treated with drugs that show high apoptosis in the MiCK assay. Unblinded clinical trials in multiple tumor types have shown that the assay will be used frequently by clinicians to determine treatment, and when used, results in higher response rates, longer times to relapse, and longer survivals. Model economic analyses suggest possible cost savings in clinical use based on increased generic drug use and single-agent substitution for combination therapies. Two initial studies with drugs in development are promising. The assay may help reduce costs and speed time to drug approval. Correlative studies with molecular biomarkers are planned. This assay may have a role both in personalized clinical therapy and in more efficient drug development. ©2012 AACR.

A real-time loop-mediated isothermal amplification assay for rapid detection of Shigella species.

Science.gov (United States)

Liew, P S; Teh, C S J; Lau, Y L; Thong, K L

2014-12-01

Shigellosis is a foodborne illness caused by the genus Shigella and is an important global health issue. The development of effective techniques for rapid detection of this pathogen is essential for breaking the chain of transmission. Therefore, we have developed a novel loop-mediated isothermal amplification (LAMP) assay targeting the invasion plasmid antigen H (ipaH) gene to rapidly detect Shigella species. This assay could be performed in 90 min at an optimal temperature of 64ºC, with endpoint results visualized directly. Notably, the method was found to be more sensitive than conventional PCR. Indeed, the detection limit for the LAMP assay on pure bacterial cultures was 5.9 x 10(5) CFU/ml, while PCR displayed a limit of 5.9 x 10(7) CFU/ml. In spiked lettuce samples, the sensitivity of the LAMP assay was 3.6 x 10(4) CFU/g, whereas PCR was 3.6 x 10(5) CFU/g. Overall, the assay accurately identified 32 Shigella spp. with one enteroinvasive Escherichia coli displaying positive reaction while the remaining 32 non-Shigella strains tested were negative.

Comparison of hydrogenated vegetable shortening and nutritionally complete high fat diet on limited access-binge behavior in rats

OpenAIRE

Davis, Jon F.; Melhorn, Susan J.; Heiman, Justin U.; Tschöp, Matthias H.; Clegg, Deborah J.; Benoit, Stephen C.

2007-01-01

Previous studies have suggested that intermittent exposure to hydrogenated vegetable shortening yields a binge/compensate pattern of feeding in rats. The present study was designed to assess whether rats would exhibit similar patterns of intake when given intermittent access to a nutritionally complete high-fat diet. Four groups of rats received varying exposure to either hydrogenated vegetable shortening or high-fat diet for 8 consecutive weeks. Animals were given daily and intermittent acce...

Cost and cost-effectiveness of tuberculosis treatment shortening: a model-based analysis.

Science.gov (United States)

Gomez, G B; Dowdy, D W; Bastos, M L; Zwerling, A; Sweeney, S; Foster, N; Trajman, A; Islam, M A; Kapiga, S; Sinanovic, E; Knight, G M; White, R G; Wells, W A; Cobelens, F G; Vassall, A

2016-12-01

Despite improvements in treatment success rates for tuberculosis (TB), current six-month regimen duration remains a challenge for many National TB Programmes, health systems, and patients. There is increasing investment in the development of shortened regimens with a number of candidates in phase 3 trials. We developed an individual-based decision analytic model to assess the cost-effectiveness of a hypothetical four-month regimen for first-line treatment of TB, assuming non-inferiority to current regimens of six-month duration. The model was populated using extensive, empirically-collected data to estimate the economic impact on both health systems and patients of regimen shortening for first-line TB treatment in South Africa, Brazil, Bangladesh, and Tanzania. We explicitly considered 'real world' constraints such as sub-optimal guideline adherence. From a societal perspective, a shortened regimen, priced at USD1 per day, could be a cost-saving option in South Africa, Brazil, and Tanzania, but would not be cost-effective in Bangladesh when compared to one gross domestic product (GDP) per capita. Incorporating 'real world' constraints reduces cost-effectiveness. Patient-incurred costs could be reduced in all settings. From a health service perspective, increased drug costs need to be balanced against decreased delivery costs. The new regimen would remain a cost-effective option, when compared to each countries' GDP per capita, even if new drugs cost up to USD7.5 and USD53.8 per day in South Africa and Brazil; this threshold was above USD1 in Tanzania and under USD1 in Bangladesh. Reducing the duration of first-line TB treatment has the potential for substantial economic gains from a patient perspective. The potential economic gains for health services may also be important, but will be context-specific and dependent on the appropriate pricing of any new regimen.

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.

Placental telomere shortening in stillbirth: a sign of premature senescence?

Science.gov (United States)

Ferrari, Francesca; Facchinetti, Fabio; Saade, George; Menon, Ramkumar

2016-01-01

The objective of this study is to investigate placental telomere shortening in unexplained stillbirths (SBs) as an indication of premature senescence. Placentas were collected from 42 unexplained SB (>22 weeks), 43 term and 15 preterm live births, at the Policlinico Hospital of Modena (Italy). DNA extracted from placentae was studied for telomere length by real time PCR. Standard curves were generated for telomere lengths from single copy gene amplifications using a reference DNA. The telomere length for each sample was derived based on the ratio of telomere length between the sample and single copy gene standard (T/S ratio). The mean ratio of placental telomere in term live births was 5.181 ± 3.841. A twofold decrease in telomere length was seen in SBs (over all 2.455 ± 1.239; p PTBs) (6.382 ± 5.525; p < 0.01), whereas SBs telomere length were similar to those of preterm premature rupture of membranes (pPROM) (3.296 ± 3.599; p = ns). Substantial reduction in telomere length in SBs is indicative of placental senescence. These data provide mechanistic insights that premature aging may lead to placental dysfunction as an initiator of fetal demise in unexplained SBs.

Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

Science.gov (United States)

Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

2018-05-01

The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

Time matters--realism in resuscitation training.

Science.gov (United States)

Krogh, Kristian B; Høyer, Christian B; Ostergaard, Doris; Eika, Berit

2014-08-01

The advanced life support guidelines recommend 2min of cardiopulmonary resuscitation (CPR) and minimal hands-off time to ensure sufficient cardiac and cerebral perfusion. We have observed doctors who shorten the CPR intervals during resuscitation attempts. During simulation-based resuscitation training, the recommended 2-min CPR cycles are often deliberately decreased in order to increase the number of scenarios. The aim of this study was to test if keeping 2-min CPR cycles during resuscitation training ensures better adherence to time during resuscitation in a simulated setting. This study was designed as a randomised control trial. Fifty-four 4th-year medical students with no prior advanced resuscitation training participated in an extra-curricular one-day advanced life support course. Participants were either randomised to simulation-based training using real-time (120s) or shortened CPR cycles (30-45s instead of 120s) in the scenarios. Adherence to time was measured using the European Resuscitation Council's Cardiac Arrest Simulation Test (CASTest) in retention tests conducted one and 12 weeks after the course. The real-time group adhered significantly better to the recommended 2-min CPR cycles (time-120s) (mean 13; standard derivation (SD) 8) than the shortened CPR cycle group (mean 45; SD 19) when tested (ptraining to optimise outcome. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Development and comparison of a real-time PCR assay for detection of Dichelobacter nodosus with culturing and conventional PCR: harmonisation between three laboratories

DEFF Research Database (Denmark)

Frosth, Sara; Slettemeås, Jannice S.; Jørgensen, Hannah J.

2012-01-01

BACKGROUND: Ovine footrot is a contagious disease with worldwide occurrence in sheep. The main causative agent is the fastidious bacterium Dichelobacter nodosus. In Scandinavia, footrot was first diagnosed in Sweden in 2004 and later also in Norway and Denmark. Clinical examination of sheep feet...... was tested using 55 bacterial and two fungal strains. To evaluate the sensitivity and harmonisation of results between different laboratories, aliquots of a single DNA preparation were analysed at three Scandinavian laboratories. The developed real-time PCR assay was compared to culturing by analysing 126...... laboratories and corresponds to approximately three copies of the D. nodosus genome per reaction. The assay showed 100% inclusivity and 100% exclusivity for the strains tested. The real-time PCR assay found 54.8% more positive samples than by culturing and 8% more than conventional PCR. CONCLUSIONS...

Options for shortening nuclear power plant refueling outages

International Nuclear Information System (INIS)

Kastl, H.

2001-01-01

Deregulation of the European electricity market on 01.01.1999 forced a large number of electric utilities- especially nuclear power plant operators - to find ways of drastically cutting down their costs in order to be able to compete successfully within the new market environment. Nuclear power plants currently in operation mainly have three potential ways of reducing their power generating costs: by increasing plant availability, reducing fuel costs and cutting down operating costs. The optimization of plant refueling outages offers considerable potential for enhancing plant availability, but also helps bring down operating costs by reducing expenditure on maintenance. In order to optimize an outage in terms of its duration and costs, a variety of approaches are possible - all of which, however, involve certain key factors such as good organization, planning, logistics and control, improvement of equipment and tools, as well as motivation of personnel. Another aspect is the introduction of innovative technologies. In the last few years, such technologies have frequently enabled maintenance effort to be reduced, thus saving considerable time, and have also resulted in a need for fewer personnel to carry out the work, thus reducing radiation exposure. In many instances they have also improved the quality of work and outage performance as a whole. The paper uses recent examples to show how innovative technologies can contribute to-wards reducing nuclear plant maintenance costs and shorten the duration of refueling out-ages. (author)

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.

Development and validation of sensitive real-time RT-PCR assay for broad detection of rabies virus.

Science.gov (United States)

Faye, Martin; Dacheux, Laurent; Weidmann, Manfred; Diop, Sylvie Audrey; Loucoubar, Cheikh; Bourhy, Hervé; Sall, Amadou Alpha; Faye, Ousmane

2017-05-01

Rabies virus (RABV) remains one of the most important global zoonotic pathogens. RABV causes rabies, an acute encephalomyelitis associated with a high rate of mortality in humans and animals and affecting different parts of the world, particularly in Asia and Africa. Confirmation of rabies diagnosis relies on laboratory diagnosis, in which molecular techniques such as detection of viral RNA by reverse transcription polymerase chain reaction (RT-PCR) are increasingly being used. In this study, two real-time quantitative RT-PCR assays were developed for large-spectrum detection of RABV, with a focus on African isolates. The primer and probe sets were targeted highly conserved regions of the nucleoprotein (N) and polymerase (L) genes. The results indicated the absence of non-specific amplification and cross-reaction with a range of other viruses belonging to the same taxonomic family, i.e. Rhabdoviridae, as well as negative brain tissues from various host species. Analytical sensitivity ranged between 100 to 10 standard RNA copies detected per reaction for N-gene and L-gene assays, respectively. Effective detection and high sensitivity of these assays on African isolates showed that they can be successfully applied in general research and used in diagnostic process and epizootic surveillance in Africa using a double-check strategy. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a real-time PCR melt curve assay for simultaneous detection of virulent and antibiotic resistant Salmonella.

Science.gov (United States)

Singh, Prashant; Mustapha, Azlin

2014-12-01

Multiple drug resistance in Salmonella is an emerging problem in the area of food safety. Depending on the virulence and antibiotic resistance characteristics of the Salmonella strain, infections of varying severity could result. In this study, a multiplex melt curve real-time PCR assay for the detection of virulent and antibiotic resistance strains of Salmonella was developed with two primer sets. The first set targets the virulence gene, invasin (invA), and tetracycline (tetG), streptomycin (aadA2) and sulphonamide (sulI) antibiotic resistance genes, and the second set amplifies ampicillin (blaPSE,blaTEM) and chloramphenicol (floR) resistance genes. The multiplex assay was evaluated using 41 Salmonella strains and was further tested on eight different artificially inoculated food samples. The fluorescent DNA intercalating dye, SYTO9, generated high resolution melt curve peaks and, hence, was used for the development of the assay. This multiplex assay worked efficiently over a DNA concentration range of 20 ng-200 fg and showed a sensitivity of 290 CFU/mL with serially diluted broth cultures. The detection limit for un-enriched artificially inoculated food samples was 10(4) CFU/g, but an enrichment period of 6 h allowed for detection of 10 CFU/g of cells in the samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

LDLCHOLESTEROLEXAMINATION (LDL-C USINGHOMOGENEOUS ASSAY

Directory of Open Access Journals (Sweden)

Made DwiAmbara Putra

2013-07-01

Full Text Available Homogeneous method describe as a method that does not require separation of free and bound label. This method has the ability tofully automate the determination of LDL-C directly small sample volume sand short examination time. In addition this method use automated pipette and control of time and temperature more accurate. There are 5 methods i.e. Solubilization homogeneous LDL-C assay (SOL from KyowaMedex, Surfactant LDL-C assay (SUR from Daiichi Pure Chemicals, Protecting LDL-assay reagent (PRO from Wako Chemicals, LDL-C assaycatalase (CAT Denka Seiken and Calixarene of LDL-C assay (CAL from International Reagents Corporation. All method is to use a variety of detergents and other chemicals that cause blocking or dissolution of specific lipoprotein classes to achieve specificity for LDL. Normal 0 false false false EN-US X-NONE X-NONE /* 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:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; 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;}

Comparison of the performance in detection of HPV infections between the high-risk HPV genotyping real time PCR and the PCR-reverse dot blot assays.

Science.gov (United States)

Zhang, Lahong; Dai, Yibei; Chen, Jiahuan; Hong, Liquan; Liu, Yuhua; Ke, Qiang; Chen, Yiwen; Cai, Chengsong; Liu, Xia; Chen, Zhaojun

2018-01-01

A new multiplex real-time PCR assay, the high-risk HPV genotyping real time PCR assay (HR HPV RT-PCR), has been developed to detect 15 high-risk HPV types with respective viral loads. In this report, a total of 684 cervical specimens from women diagnosed with vaginitis were assessed by the HR HPV RT-PCR and the PCR reaction and reverse dot blot (PCR-RDB) assays, using a PCR-sequencing method as a reference standard. A total coincidence of 97.7% between the HR HPV RT PCR and the PCR-RDB assays was determined with a Kappa value of 0.953. The HR HPV RT PCR assay had sensitivity, specificity, and concordance rates (accuracy) of 99.7%, 99.7%, and 99.7%, respectively, as confirmed by PCR-sequencing, while the PCR-RDB assay had respective rates of 98.8%, 97.1%, and 98.0%. The overall rate of HPV infection, determined by PCR-sequencing, in women diagnosed with vaginitis was 49.85%, including 36.26% of single infection and 13.6% of multiple infections. The most common infections among the 15 high-risk HPV types in women diagnosed with vaginitis were HPV-52, HPV-16, and HPV-58, with a total detection rate of 10.23%, 7.75%, and 5.85%, respectively. We conclude that the HR HPV RT PCR assay exhibits better clinical performance than the PCR-RDB assay, and is an ideal alternative method for HPV genotyping. In addition, the HR HPV RT PCR assay provides HPV DNA viral loads, and could serve as a quantitative marker in the diagnosis and treatment of single and multiple HPV infections. © 2017 Wiley Periodicals, Inc.

A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus

Directory of Open Access Journals (Sweden)

Qin E-de

2010-06-01

Full Text Available Abstract A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009 influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02 TCID50 (50% tissue culture infective dose for H5N1 and 0.2 TCID50 for the pandemic H1N1, which was the same as that of each single-target RT-PCR for pandemic H1N1 and even more sensitive for H5N1 with the same primers and probes. No cross reactivity of detecting other subtype influenza viruses or respiratory tract viruses was observed. Two hundred and thirty-six clinical specimens were tested by comparing with single real-time RT-PCR and result from the duplex assay was 100% consistent with the results of single real-time RT-PCR and sequence analysis.

Validation of a norovirus multiplex real-time RT-PCR assay for the detection of norovirus GI and GII from faeces samples.

LENUS (Irish Health Repository)

Jones, S

2011-01-01

Norovirus is a leading cause of infectious non-bacterial gastroenteritis. The virus is highly contagious and has multiple modes of transmission, presenting a growing challenge to hospital-based healthcare. In this study, a total of 120 stool samples are tested for the presence of norovirus GI and GII by the Roche two-step Lightcycler 2.0 assay incorporating primers and probes produced by TIB Molbiol, and the results are compared with results from the National Virus Reference Laboratory. The Roche\\/TIB Molbiol assay produced 51 positive results and 69 negative results. Discrepancy analysis was performed for six conflicting results using a second real-time polymerase chain reaction (PCR) assay (Roche\\/TIB Molbiol) and this confirmed that four of the five discrepant positive results were true positives. A single discrepant negative result generated by the Roche assay remained negative using the second assay. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated to be 98%, 98.6%, 98.0% and 98.6%, respectively. Melting curve analysis was used to differentiate genogroups I and II and this showed that 92% of strains belonged to genogroup II.

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.

Charcot arthropathy of the lumbar spine treated using one-staged posterior three-column shortening and fusion.

Science.gov (United States)

David, Kenny Samuel; Agarwala, Amit Omprakash; Rampersaud, Yoga Raja

2010-06-15

Case report. We present a case of lumbar Charcot arthropathy successfully treated surgically using posterior 3-column resection, spinal shortening, and fusion. The operative treatment of Charcot arthropathy of the spine has conventionally been a combination of anterior and posterior surgery. The morbidity associated with these surgical procedures can be considerable. A posterior-only approach to the problem would avoid the additional morbidity associated with an anterior approach. We present a case of lumbar Charcot arthropathy with deformity treated successfully using such a procedure. Discussion of the patient's clinical and radiologic history, the technical merits of the operative intervention and a review of the relevant background literature are presented. A multilevel, single-stage, posterior 3-column resection with primary shortening and instrumented fusion augmented with rhBMP2 in a multiply operated patient with deformity provided a optimal biologic and mechanical environment for healing of the Charcot arthropathy and improved the sagittal and coronal profile of the spine. A single-stage, multilevel, posterior 3-column resection and primary shortening can be a useful surgical strategy in symptomatic patients with Charcot arthropathy of the spine.

Analytical and clinical performance characteristics of the Abbott RealTime MTB RIF/INH Resistance, an assay for the detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis in pulmonary specimens.

Science.gov (United States)

Kostera, Joshua; Leckie, Gregor; Tang, Ning; Lampinen, John; Szostak, Magdalena; Abravaya, Klara; Wang, Hong

2016-12-01

Clinical management of drug-resistant tuberculosis patients continues to present significant challenges to global health. To tackle these challenges, the Abbott RealTime MTB RIF/INH Resistance assay was developed to accelerate the diagnosis of rifampicin and/or isoniazid resistant tuberculosis to within a day. This article summarizes the performance of the Abbott RealTime MTB RIF/INH Resistance assay; including reliability, analytical sensitivity, and clinical sensitivity/specificity as compared to Cepheid GeneXpert MTB/RIF version 1.0 and Hain MTBDRplus version 2.0. The limit of detection (LOD) of the Abbott RealTime MTB RIF/INH Resistance assay was determined to be 32 colony forming units/milliliter (cfu/mL) using the Mycobacterium tuberculosis (MTB) strain H37Rv cell line. For rifampicin resistance detection, the Abbott RealTime MTB RIF/INH Resistance assay demonstrated statistically equivalent clinical sensitivity and specificity as compared to Cepheid GeneXpert MTB/RIF. For isoniazid resistance detection, the assay demonstrated statistically equivalent clinical sensitivity and specificity as compared to Hain MTBDRplus. The performance data presented herein demonstrate that the Abbott RealTime MTB RIF/INH Resistance assay is a sensitive, robust, and reliable test for realtime simultaneous detection of first line anti-tuberculosis antibiotics rifampicin and isoniazid in patient specimens. Copyright © 2016 The Author. Published by Elsevier Ltd.. All rights reserved.

High-throughput multiplex real-time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants.

Science.gov (United States)

Otti, G; Bouvaine, S; Kimata, B; Mkamillo, G; Kumar, P L; Tomlins, K; Maruthi, M N

2016-05-01

To develop a multiplex TaqMan-based real-time PCR assay (qPCR) for the simultaneous detection and quantification of both RNA and DNA viruses affecting cassava (Manihot esculenta) in eastern Africa. The diagnostic assay was developed for two RNA viruses; Cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV) and two predominant DNA viruses; African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV), which cause the economically important cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) respectively. Our method, developed by analysing PCR products of viruses, was highly sensitive to detect target viruses from very low quantities of 4-10 femtograms. Multiplexing did not diminish sensitivity or accuracy compared to uniplex alternatives. The assay reliably detected and quantified four cassava viruses in field samples where CBSV and UCBSV synergy was observed in majority of mixed-infected varieties. We have developed a high-throughput qPCR diagnostic assay capable of specific and sensitive quantification of predominant DNA and RNA viruses of cassava in eastern Africa. The qPCR methods are a great improvement on the existing methods and can be used for monitoring virus spread as well as for accurate evaluation of the cassava varieties for virus resistance. © 2016 The Society for Applied Microbiology.

The Comet Assay: Tails of the (Unexpected. Use of the comet assay in pharmaceutical development.

Directory of Open Access Journals (Sweden)

Bas-jan Van Der Leede

2015-08-01

Full Text Available In genotoxicity testing of pharmaceuticals the rodent alkaline comet assay is being increasingly used as a second in vivo assay in addition to the in vivo micronucleus assay to mitigate in vitro positive results as recommended by regulatory guidance. In this presentation we want to give insight into the circumstances in vivo comet assay is deployed in a Genetic Toxicology Department of a pharmaceutical company. As the in vivo comet assay is a salvage assay, it means that some events have occurred in an in vitro assay and that the compound (or metabolite responsible for this signal is potentially deselected for further development. More than often the decision to perform an in vivo comet assay is at a very early stage in development and the first time that the compound will be tested in vivo at high/toxic dose levels. As almost no toxicokinetic data and tissue distribution data are available a careful design with maximizes the chances for successful mitigation is necessary. Decisions on acute or repeated dosing need to be made and arrangements for combining the in vivo comet assay with the in vivo micronucleus assay are to be considered. Often synthesis methods need to be scaled up fast to provide the required amount of compound and information on suitable formulations needs to be in place. As exposure data is crucial for interpretation of results, analytical methods need to be brought in place rapidly. An experienced multi skilled and communicative team needs to be available to deploy successfully this kind of assays at an early stage of development. We will present a few scenarios on study conduct and demonstrate how this assay can make a difference for the further development of a new drug.

The effect of varying plyometric volume on stretch-shortening cycle capability in collegiate male rugby players.

Science.gov (United States)

Jeffreys, Mark; De Ste Croix, Mark; Lloyd, Rhodri S; Oliver, Jon L; Hughes, Jonathan

2017-03-25

The purpose of this study was to identify the effectiveness of low and high volume plyometric loads on developing stretch shortening cycle capability in collegiate rugby players. A between- group repeated measures design was used. Thirty six subjects (age 20.3 ±1.6 yrs, mass 91.63 ±10.36kg, stature 182.03 ±5.24cm) were randomly assigned to one of three groups, a control group (CG), a low volume plyometric group (LPG) or a high volume plyometric group (HPG). Data were collected from a force plate, and measures of reactive strength index (RSI) and leg stiffness were calculated from jump height, contact time and flight time. A significant between group × time (F = 4.01, P plyometric program. The low volume program elicited the same performance improvement in RSI as a high volume program whilst undertaking a lower dose. This suggests that strength and conditioning coaches may be able to benefit from the ability to develop more time efficient and effective plyometric programs.

Vastus lateralis surface and single motor unit EMG following submaximal shortening and lengthening contractions

NARCIS (Netherlands)

Altenburg, T.M.; de Ruiter, C.J.; Verdijk, P.W.L.; van Mechelen, W.; de Haan, A.

2008-01-01

A single shortening contraction reduces the force capacity of muscle fibers, whereas force capacity is enhanced following lengthening. However, how motor unit recruitment and discharge rate (muscle activation) are adapted to such changes in force capacity during submaximal contractions remains

Effect of Pre-gelatinized Wheat Starch on Physical and Rheological Properties of Shortened Cake Batter and Cake Texture

Directory of Open Access Journals (Sweden)

F. Ebrahimi

2016-10-01

Full Text Available The focus of this study was the effect of 1.5%, 3% and 4.5% pre-gelatinized wheat starch (based on the total weight of cake batter on improving the qualitative properties of shortened cake batter. Specific volume and viscosity of the shortened cake batter were measured for controls, 1.5%, 3% and 4.5% gelatinized starch; some important properties such as texture and sensory evaluation were examined. By increasing pre-gelatinized wheat starch used in the batter, a significant difference was observed in the rheological properties of the batter. Cake batter properties were found improved compared to the control samples. The sample with 3% pre-gelatinized starch had a lower viscosity than other treatments. The treatment with 4.5% pre-gelatinized starch had the lowest specific volume compared to other treatments. The overall results showed that the shortened cake with 3% pre-gelatinized starch was the best treatment in terms of texture and sensory evaluation factors.

Development of Candida-Specific Real-Time PCR Assays for the Detection and Identification of Eight Medically Important Candida Species.

Science.gov (United States)

Zhang, Jing; Hung, Guo-Chiuan; Nagamine, Kenjiro; Li, Bingjie; Tsai, Shien; Lo, Shyh-Ching

2016-01-01

Culture-based identification methods have been the gold standard for the diagnosis of fungal infection. Currently, molecular technologies such as real-time PCR assays with short turnaround time can provide desirable alternatives for the rapid detection of Candida microbes. However, most of the published PCR primer sets are not Candida specific and likely to amplify DNA from common environmental contaminants, such as Aspergillus microbes. In this study, we designed pan-Candida primer sets based on the ribosomal DNA-coding regions conserved within Candida but distinct from those of Aspergillus and Penicillium. We demonstrate that the final two selected pan-Candida primer sets would not amplify Aspergillus DNA and could be used to differentiate eight medically important Candida pathogens in real-time PCR assays based on their melting profiles, with a sensitivity of detection as low as 10 fg of Candida genomic DNA. Moreover, we further evaluated and selected species-specific primer sets covering Candida albicans, Candida glabrata, Candida tropicalis, and Candida dubliniensis and show that they had high sensitivity and specificity. These real-time PCR primer sets could potentially be assembled into a single PCR array for the rapid detection of Candida species in various clinical settings, such as corneal transplantation.

Development of a Rapid Real-Time PCR Assay for Quantitation of Pneumocystis carinii f. sp. Carinii

DEFF Research Database (Denmark)

Larsen, Hans Henrik; Kovacs, Joseph A; Stock, Frida

2002-01-01

) PCR assay for detecting P. carinii f. sp. carinii, the subspecies of P. carinii commonly used in research models of PCP. The assay was based on the single-copy dihydrofolate reductase gene and was able to detect r = 0.99) over...... 6 log values for standards containing > or =5 copies/tube. Application of the assay to a series of 10-fold dilutions of P. carinii organisms isolated from rat lung demonstrated that it was reproducibly quantitative over 5 log values (r = 0.99). The assay was applied to a recently reported in vitro....... In conclusion, a rapid, sensitive, and reproducible quantitative PCR assay for P. carinii f. sp. carinii has been developed and is applicable to in vivo as well as in vitro systems. The assay should prove useful for conducting studies in which quantification of organism burden or growth assessment is critical...

Trans Fatty Acid content in Danish margarines and shortenings

DEFF Research Database (Denmark)

Leth, Torben; Bysted, Anette; Hansen, Kirsten

2003-01-01

with similar investigations in 1992 and 1995. A gradual decline of TFA in Danish margarines was observed. From 1992 to 1995, a reduction of TFA from 10.4 to 3.6% took place in margarines with 20-40% linoleic acid. In 1999, TFA was practically absent in all the margarines, but it remained unchanged...... in shortenings, averaging about 6-7%. Long-chain TFA from hydrogenated,fish oil, although present in 13 brands in 1995, were not found at all in the 1999 samples. Trans-linoleic acids or CLA were not found. The reduction in TFA content in margarines has not resulted in a systematic change over the years...

Urine assay for tenofovir to monitor adherence in real time to tenofovir disoproxil fumarate/emtricitabine as pre-exposure prophylaxis.

Science.gov (United States)

Koenig, H C; Mounzer, K; Daughtridge, G W; Sloan, C E; Lalley-Chareczko, L; Moorthy, G S; Conyngham, S C; Zuppa, A F; Montaner, L J; Tebas, P

2017-07-01

Tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) is approved for pre-exposure prophylaxis (PrEP) against HIV infection. Adherence is critical for the success of PrEP, but current adherence measurements are inadequate for real-time adherence monitoring. We developed and validated a urine assay to measure tenofovir (TFV) to objectively monitor adherence to PrEP. We developed a urine assay using high-performance liquid chromatography coupled to tandem mass spectrometry with high sensitivity/specificity for TFV that allowed us to determine TFV concentrations in log 10 categories between 0 and 10 000 ng/mL. We validated the assay in three cohorts: (1) HIV-positive subjects with undetectable viral loads on a TDF/FTC-based regimen, (2) healthy HIV-negative subjects who received a single dose of TDF/FTC, and (3) HIV-negative subjects receiving daily TDF/FTC as PrEP for 24 weeks. The urine assay detected TFV with greater sensitivity than plasma-based measures and with a window of measurements within 7 days of the last TDF/FTC dose. Based on the urine log-linear clearance after the last dose and its concordance with all detectable plasma levels, a urine TFV concentration > 1000 ng/mL was identified as highly predictive of the presence of TFV in plasma at > 10 ng/mL. The urine assay was able to distinguish high and low adherence patterns within the last 48 h (> 1000 ng/mL versus 10-1000 ng/mL), as well as nonadherence (< 10 ng/mL) extended over at least 1 week prior to measurement. We provide proof of concept that a semiquantitative urine assay measuring levels of TFV could be further developed into a point-of-care test and be a useful tool to monitor adherence to PrEP. © 2017 British HIV Association.

An ultrafiltration assay for lysyl oxidase

International Nuclear Information System (INIS)

Shackleton, D.R.; Hulmes, D.J.

1990-01-01

A modification of the original microdistillation assay for lysyl oxidase is described in which Amicon C-10 microconcentrators are used to separate, by ultrafiltration, the 3H-labeled products released from a [4,5-3H]-lysine-labeled elastin substrate. Enzyme activity is determined by scintillation counting of the ultrafiltrate, after subtraction of radioactivity released in the presence of beta-aminopropionitrile, a specific inhibitor of the enzyme. Conditions are described which optimize both the sensitivity and the efficient use of substrate. The assay shows linear inhibition of activity in up to 1 M urea; hence, as the enzyme is normally diluted in the assay, samples in 6 M urea can be assayed directly, without prior dialysis, and corrected for partial inhibition. Comparable results are obtained when enzyme activity is assayed by ultrafiltration or microdistillation. The assay is simple and convenient and, by using disposable containers throughout, it eliminates the need for time-consuming decontamination of radioactive glassware

Effect of N-acetylcysteine on the accuracy of the prothrombin time assay of plasma coagulation factor II plus VII plus X activity in subjects infused with the drug. Influence of time and temperature

DEFF Research Database (Denmark)

Thorsen, S.; Teisner, A.; Jensen, S.A.

2009-01-01

Objectives: The prothrombin time (PT) assay of factor II+VII+X activity is an important predictor of liver damage in paracetamol poisoned patients. It complicates interpretation of results that the antidote, acetylcysteine (NAC) depresses this activity. The aim was to investigate if NAC influences...... added to plasma in vitro decreased factor II+VII+X activity at 37 degrees C in a time-dependent manner. This effect was quenched at temperatures 24 degrees C. Activity lost at 37 degrees C could partly be recovered by subsequent incubation at 5 or 20 degrees C. Incubation at 37 degrees C prior to assay...... led to a significant additional depression of factor II+VII+X activity in plasma from subjects infused with NAC during the first 3h of infusion indicating that it contained reactive NAC. The risk that this NAC interfered with the accuracy of the PT assay was considered minimal with samples stored...

A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus

OpenAIRE

Kang, Xiao-ping; Jiang, Tao; Li, Yong-qiang; Lin, Fang; Liu, Hong; Chang, Guo-hui; Zhu, Qing-yu; Qin, E-de; Qin, Cheng-feng; Yang, Yin-hui

2010-01-01

Abstract A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02 TCID50 (50% tissue culture infective dose) for H5N1 and 0.2 TCID50 for the pandemic H1N1, which was the same a...

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.

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.

Effect of N-acetylcysteine on the accuracy of the prothrombin time assay of plasma coagulation factor II+VII+X activity in subjects infused with the drug. Influence of time and temperature.

Science.gov (United States)

Thorsen, Sixtus; Teisner, Ane; Jensen, Søren Astrup; Philips, Malou; Dalhoff, Kim; Bendtsen, Flemming

2009-01-01

The prothrombin time (PT) assay of factor II+VII+X activity is an important predictor of liver damage in paracetamol poisoned patients. It complicates interpretation of results that the antidote, acetylcysteine (NAC) depresses this activity. The aim was to investigate if NAC influences the accuracy of the plasma PT assay. The accuracy of Nycotest PT was studied using plasma added NAC in vitro and plasma from subjects infused with NAC. The latter results were compared with those obtained by analysis of PT by CoaguChek S. Therapeutic NAC concentrations added to plasma in vitro decreased factor II+VII+X activity at 37 degrees C in a time-dependent manner. This effect was quenched at temperatures depression of factor II+VII+X activity in plasma from subjects infused with NAC during the first 3h of infusion indicating that it contained reactive NAC. The risk that this NAC interfered with the accuracy of the PT assay was considered minimal with samples stored below 24 degrees C. This was supported by similarity of results obtained by analysis of appropriately stored plasma and simultaneously drawn blood by CoaguChek S. Residual reactive NAC does not interfere with the accuracy of the PT assay of plasma stored below 24 degrees C, but NAC-induced loss in activity at 37 degrees C may be partly recovered during subsequent storage below 24 degrees C.

Real time monitoring and quantification of reactive oxygen species in breast cancer cell line MCF-7 by 2',7'-dichlorofluorescin diacetate (DCFDA) assay.

Science.gov (United States)

Figueroa, Daniela; Asaduzzaman, Mohammad; Young, Fiona

2018-04-07

The detection of reactive oxygen species (ROS) using 2',7'-dichlorofluorescin diacetate (DCFDA) is commonly performed by a single measurement of fluorescence but this fails to capture a profile of ROS generation over time. This study aimed to develop a real-time monitoring method to increase the utility of the assay, to incorporate cytotoxicity screening and to describe the combined effects of DCFDA and the ROS generator, Ter-butyl hydrogen peroxide (TBHP). Breast cancer MCF-7 cells were loaded with DCFDA (0-50 μM) for 45 min, and then exposed to TBHP (0-50 μM). Fluorescence was recorded according to three different schedules: every hour for 6 h, or once after 6 h or 24 h. Viability was assessed in a crystal violet assay and cell morphology was examined by microscopy. TBHP caused a time and dose-dependent increase in ROS and the magnitude of the fluorescent signal was affected by the loading concentration of DCFDA. Reading the fluorescence every hour for 6 h did not diminish the emission signal. The most sensitive and reliable combination for this ROS assay was 10 μM DCFDA with 25 μM TBHP; since higher concentrations of DCFDA compromised cell viability. In conclusion we adapted a single point ROS assay to enable production of a profile of ROS generation over an extended 6 h period, and related this to cell viability and morphology. Published by Elsevier Inc.

Dose-effect relationships for fife shortening, tumorigenesis, and systemic injuries in mice irradiated with fission neutron or 60Co gamma radiation

International Nuclear Information System (INIS)

Ainsworth, E.J.; Fry, R.J.M.; Williamson, F.S.; Brennan, P.C.; Stearner, S.P.; Yang, V.V.; Crouse, D.A.; Rust, J.H.; Borak, T.B.

1977-01-01

The objective of this research is to provide additional data on life shortening, neoplastic and non-neoplastic diseases, and other systematic injuries necessary for the determination of dose-response relationships. The data are used to test existing predictive models and formulate new models which may assist with radiation risk assessment. Late somatic effects of fission neutrons from the JANUS reactor or from cobalt-60 gamma radiation are evaluated in young adult B6CF 1 mice that receive either a range of single doses or protracted doses at low dose rates; the protracted irradiation is administered over a 6-month period. After single doses of gamma radiation the relationship between radiation dose and percent life shortening appears linear whereas after single doses of fission spectrum neutrons a non-linear dose response is observed. These results suggest that estimates of radiation risk for fission spectrum neutrons should take into account the following: the curvilinearity of the neutron dose-response curve for life shortening, and the increased life shortening produced by neutron dose fractionation

HCV-RNA quantification in liver bioptic samples and extrahepatic compartments, using the abbott RealTime HCV assay.

Science.gov (United States)

Antonucci, FrancescoPaolo; Cento, Valeria; Sorbo, Maria Chiara; Manuelli, Matteo Ciancio; Lenci, Ilaria; Sforza, Daniele; Di Carlo, Domenico; Milana, Martina; Manzia, Tommaso Maria; Angelico, Mario; Tisone, Giuseppe; Perno, Carlo Federico; Ceccherini-Silberstein, Francesca

2017-08-01

We evaluated the performance of a rapid method to quantify HCV-RNA in the hepatic and extrahepatic compartments, by using for the first time the Abbott RealTime HCV-assay. Non-tumoral (NT), tumoral (TT) liver samples, lymph nodes and ascitic fluid from patients undergoing orthotopic-liver-transplantation (N=18) or liver resection (N=4) were used for the HCV-RNA quantification; 5/22 patients were tested after or during direct acting antivirals (DAA) treatment. Total RNA and DNA quantification from tissue-biopsies allowed normalization of HCV-RNA concentrations in IU/μg of total RNA and IU/10 6 liver-cells, respectively. HCV-RNA was successfully quantified with high reliability in liver biopsies, lymph nodes and ascitic fluid samples. Among the 17 untreated patients, a positive and significant HCV-RNA correlation between serum and NT liver-samples was observed (Pearson: rho=0.544, p=0.024). Three DAA-treated patients were HCV-RNA "undetectable" in serum, but still "detectable" in all tested liver-tissues. Differently, only one DAA-treated patient, tested after sustained-virological-response, showed HCV-RNA "undetectability" in liver-tissue. HCV-RNA was successfully quantified with high reliability in liver bioptic samples and extrahepatic compartments, even when HCV-RNA was "undetectable" in serum. Abbott RealTime HCV-assay is a good diagnostic tool for HCV quantification in intra- and extra-hepatic compartments, whenever a bioptic sample is available. Copyright © 2017 Elsevier B.V. All rights reserved.

Spying on real-time computers to improve performance

International Nuclear Information System (INIS)

Taff, L.M.

1975-01-01

The sampled program-counter histogram, an established technique for shortening the execution times of programs, is described for a real-time computer. The use of a real-time clock allows particularly easy implementation. (Auth.)

Absolute nuclear material assay using count distribution (LAMBDA) space

Science.gov (United States)

Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

2012-06-05

A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

Performance evaluation of the QIAGEN EZ1 DSP Virus Kit with Abbott RealTime HIV-1, HBV and HCV assays.

Science.gov (United States)

Schneider, George J; Kuper, Kevin G; Abravaya, Klara; Mullen, Carolyn R; Schmidt, Marion; Bunse-Grassmann, Astrid; Sprenger-Haussels, Markus

2009-04-01

Automated sample preparation systems must meet the demands of routine diagnostics laboratories with regard to performance characteristics and compatibility with downstream assays. In this study, the performance of QIAGEN EZ1 DSP Virus Kit on the BioRobot EZ1 DSP was evaluated in combination with the Abbott RealTime HIV-1, HCV, and HBV assays, followed by thermalcycling and detection on the Abbott m2000rt platform. The following performance characteristics were evaluated: linear range and precision, sensitivity, cross-contamination, effects of interfering substances and correlation. Linearity was observed within the tested ranges (for HIV-1: 2.0-6.0 log copies/ml, HCV: 1.3-6.9 log IU/ml, HBV: 1.6-7.6 log copies/ml). Excellent precision was obtained (inter-assay standard deviation for HIV-1: 0.06-0.17 log copies/ml (>2.17 log copies/ml), HCV: 0.05-0.11 log IU/ml (>2.09 log IU/ml), HBV: 0.03-0.07 log copies/ml (>2.55 log copies/ml)), with good sensitivity (95% hit rates for HIV-1: 50 copies/ml, HCV: 12.5 IU/ml, HBV: 10 IU/ml). No cross-contamination was observed, as well as no negative impact of elevated levels of various interfering substances. In addition, HCV and HBV viral load measurements after BioRobot EZ1 DSP extraction correlated well with those obtained after Abbott m2000sp extraction. This evaluation demonstrates that the QIAGEN EZ1 DSP Virus Kit provides an attractive solution for fully automated, low throughput sample preparation for use with the Abbott RealTime HIV-1, HCV, and HBV assays.

The Spiritual Well-Being Scale : Psychometric Evaluation of the Shortened Version in Czech Adolescents

NARCIS (Netherlands)

Malinakova, Klara; Kopcakova, Jaroslava; Kolarcik, Peter; Geckova, Andrea Madarasova; Polackova Solcova, Iva; Husek, Vit; Kracmarova, Lucie Kluzova; Dubovska, Eva; Kalman, Michal; Puzova, Zuzana; van Dijk, Jitse P.; Tavel, Peter

The aim of this study was to psychometrically evaluate the shortened version of the Spiritual Well-Being Scale (SWBS) in Czech adolescents. A nationally representative sample of 4217 adolescents participated in the 2014 Health Behaviour in School-aged Children survey. The internal consistency of the

Attitudes toward Seeking Professional Psychological Help: A Shortened Form and Considerations for Research.

Science.gov (United States)

Fischer, Edward H.; Farina, Amerigo

1995-01-01

Tested a new, shortened scale for measuring willingness to seek help from mental health professionals. Scores correlated with the 29-item scale developed by Fischer and Turner (1970); the new scale's brevity (10 items) should make it easier and less obtrusive for use in research. Discusses the need for further studies on attitudes toward…

Multiplex Real-Time PCR Assay Targeting Eight Parasites Customized to the Korean Population: Potential Use for Detection in Diarrheal Stool Samples from Gastroenteritis Patients.

Directory of Open Access Journals (Sweden)

Eun Jeong Won

Full Text Available Intestinal parasitic diseases occur worldwide and can cause diarrhea or gastroenteritis; however, their diagnosis is quite difficult, especially in low-endemism countries. We developed a multiplex real-time PCR assay for detection of eight intestinal parasites and prospectively evaluated it for patients with gastroenteritis. The assay targeted Cryptosporidium parvum, Giardia lamblia, Entamoeba histolytica, Blastocystis hominis, Dientamoeba fragilis, Clonorchis sinensis, Metagonimus yokogawai, and Gymnophalloides seoi. Performance characteristics were evaluated based on recovery after DNA extraction, analytical sensitivity, specificity, reproducibility, cross-reactivity, and interference characteristics. Clinical performance was validated against microscopy on 123 diarrheal samples. The assay demonstrated strong correlations between DNA concentrations and Ct values (R2, 0.9924-0.9998, and had a high PCR efficiency (83.3%-109.5%. Polymerase chain reactions detected as few as 10-30 copies of genomic DNA, and coefficient of variance was 0-7%. There was no cross-reactivity to the other 54 microorganisms tested. Interference occurred only in presence of high concentrations of erythrocytes or leukocytes. This assay had a higher correct identification rate (100.0% vs. 90.2% and lower incorrect ID rate (0.0% vs. 9.8% when compared to microscopy. Overall, this assay showed a higher sensitivity (100.0%; 95% confidence interval [CI] of 80.5-100.0 than microscopy (29.4%; 95% CI 10.31-55.96, and the specificity levels were comparable for both methods (100.0%; 95% CI 96.58-100.0. This newly developed multiplex real-time PCR assay offers a potential use for detecting intestinal parasitic pathogens customized to the Korean population.

Two-stage revision of infected hip arthroplasty using a shortened post-operative course of antibiotics.

LENUS (Irish Health Repository)

McKenna, Paul B

2009-04-01

We present a series of 30 consecutive patients with 31 infected total hip arthroplasties treated by a single surgeon over a 4-year period in whom a shortened post-operative course of antimicrobial chemotherapy was used.

Effect of N-acetylcysteine on the accuracy of the prothrombin time assay of plasma coagulation factor II+VII+X activity in subjects infused with the drug. Influence of time and temperature

DEFF Research Database (Denmark)

Thorsen, Sixtus; Teisner, Ane; Jensen, Søren Astrup

2009-01-01

OBJECTIVES: The prothrombin time (PT) assay of factor II+VII+X activity is an important predictor of liver damage in paracetamol poisoned patients. It complicates interpretation of results that the antidote, acetylcysteine (NAC) depresses this activity. The aim was to investigate if NAC influences...... to plasma in vitro decreased factor II+VII+X activity at 37 degrees C in a time-dependent manner. This effect was quenched at temperatures ... to a significant additional depression of factor II+VII+X activity in plasma from subjects infused with NAC during the first 3h of infusion indicating that it contained reactive NAC. The risk that this NAC interfered with the accuracy of the PT assay was considered minimal with samples stored below 24 degrees C...

Detection of Different Genotypes of Clostridium perfringens in Feces of Healthy Dairy Cattle from China using Real-Time Duplex PCR Assay

Directory of Open Access Journals (Sweden)

Guanghua Wang, Jizhang Zhou, Fuying Zheng, Guozhen Lin, Xiaoan Cao, Xiaowei Gong and Changqing Qiu*

2011-04-01

Full Text Available Dual-labeled fluorescence hybridization probe-based multiplex quantitative real-time polymerase chain reaction (qPCR assay was used for the detection of Clostridium perfringens toxin genes alpha (cpa, beta (cpb, iota (ia, epsilon (etx, beta2 (cpb2 and enterotoxin (cpe directly from the feces of cattle. Fecal samples from 261 lactating cattle, belonging to three dairy herds in Ningxia (China, were examined using the developed assays. The duplex qPCR assay revealed that cpa, etx, cpb2 and cpe toxin genes were detected in 176 (100%, 15 (8.5%, 142 (80.7% and 4 (2.3% of 176 PCR positive samples, respectively. The findings of this study revealed that C. perfringens beta2-toxin-producing strains were widely prevalent in lactating cows in Ningxia, possibly playing an important role in C. perfringens-associated diarrheal disease.

Principles of validation of diagnostic assays for infectious diseases

International Nuclear Information System (INIS)

Jacobson, R.H.

1998-01-01

Assay validation requires a series of inter-related processes. Assay validation is an experimental process: reagents and protocols are optimized by experimentation to detect the analyte with accuracy and precision. Assay validation is a relative process: its diagnostic sensitivity and diagnostic specificity are calculated relative to test results obtained from reference animal populations of known infection/exposure status. Assay validation is a conditional process: classification of animals in the target population as infected or uninfected is conditional upon how well the reference animal population used to validate the assay represents the target population; accurate predictions of the infection status of animals from test results (PV+ and PV-) are conditional upon the estimated prevalence of disease/infection in the target population. Assay validation is an incremental process: confidence in the validity of an assay increases over time when use confirms that it is robust as demonstrated by accurate and precise results; the assay may also achieve increasing levels of validity as it is upgraded and extended by adding reference populations of known infection status. Assay validation is a continuous process: the assay remains valid only insofar as it continues to provide accurate and precise results as proven through statistical verification. Therefore, the work required for validation of diagnostic assays for infectious diseases does not end with a time-limited series of experiments based on a few reference samples rather, to assure valid test results from an assay requires constant vigilance and maintenance of the assay, along with reassessment of its performance characteristics for each unique population of animals to which it is applied. (author)

Magnitude of crustal shortening and structural framework of the easternmost Himalayan orogen, northern Indo-Burma Ranges of northeastern India

Science.gov (United States)

Haproff, P. J.; Yin, A.

2016-12-01

Along-strike variation in crustal shortening throughout the Himalayan orogen has been attributed to (1) diachronous, eastward-increasing convergence, or (2) localized controls including pre-collisional stratigraphic configuration and climate. In this study, we present new geologic maps and balanced cross-sections across the easternmost segment of the Himalayan orogen, the N-S-trending N. Indo-Burma Ranges of northeastern India. First order structures are NE-dipping, km-wide ductile thrust shear zones with mylonitic fabrics indicating top-to-the SW motion. Major structures include the Mayodia klippe and Hunli window, generated during folding of the SW-directed Tidding thrust and duplexing of Lesser Himalayan rocks (LHS) at depth. Reconstruction of two balanced cross-sections yields minimum shortening estimates of 70% (48 km) and 71% (133 km), respectively. The widths of the orogen for each transect are 21 km and 54 km, respectively. Our percent strain values are comparable to that of western Arunachal Himalaya, reflecting eastward-increasing strain due to counterclockwise rotation of India during convergence or along-strike variation in India's subduction angle. However, shortening magnitudes much less than that of the Sikkim (641 km), Bhutan (414-615 km), and western Arunachal Himalaya (515-775 km) could signal eastward increasing shortening of a unique Himalayan stratigraphic framework, evidenced by few GHC rocks, absence of Tethyan strata, and an extensive subduction mélange and forearc complex.

A Novel Duplex Real-Time Reverse-Transcription PCR Assay for the Detection of Influenza A and the Novel Influenza A(H1N1 Strain

Directory of Open Access Journals (Sweden)

Theo P. Sloots

2009-12-01

Full Text Available Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1 strain. In this study we developed a duplex real-time PCR (RT-PCR (dFLU-TM assay for the simultaneous detection of a broad range of influenza A subtypes and specific detection of the novel H1N1 2009 pandemic strain. The assay was compared to the combined results of two previously described monoplex RT-PCR assays using 183 clinical samples and 10 seasonal influenza A isolates. Overall, the results showed that the dFLU-TM RT-PCR method is suitable for detection of influenza A, including the novel H1N1 pandemic strain, in clinical samples.

Diagnosis of Barmah Forest Virus Infection by a Nested Real-Time SYBR Green RT-PCR Assay

OpenAIRE

Hueston, Linda; Toi, Cheryl S.; Jeoffreys, Neisha; Sorrell, Tania; Gilbert, Gwendolyn

2013-01-01

Barmah Forest virus (BFV) is a mosquito borne (+) ssRNA alphavirus found only in Australia. It causes rash, myalgia and arthralgia in humans and is usually diagnosed serologically. We developed a real-time PCR assay to detect BFV in an effort to improve diagnosis early in the course of infection. The limit of detection was 16 genome equivalents with a specificity of 100%. Fifty five serum samples from BFV-infected patients were tested by the PCR. 52 of 53 antibody-positive samples were PCR ne...