Citations

We present an efficient feature selection algorithm for computer aided detection (CAD) computed tomographic (CT) colonography. The algorithm (1) determines an appropriate piecewise linear network (PLN) model by cross validation, (2) applies the orthonormal least square (OLS) procedure to the PLN model utilizing a Modified Schmidt procedure, and (3) uses a floating search algorithm to select features that minimize the output variance. The undesirable "nesting effect" is prevented by the floating search approach, and the piecewise linear OLS procedure makes this algorithm very computationally efficient because the Modified Schmidt procedure only requires one data pass during the whole searching process. The selected features are compared to those obtained by other methods, through cross validation with support vector machines (SVMs).

AbstractPhosphatidylcholine acyltransferase (lecithin:cholesterol acyltransferase or LCAT; EC 2.3.1.43) activity was found to be present in pig ovarian follicular fluid (POFF), in addition to pig serum (PS). The cholesterol esterification rate in both POFF and PS is linear with incubation time up to 2 hr. The mean absolute rate of POFF‐cholesterol esterification was 8.1±0.4 nmoles per ml per hr approximately one‐fourth of that in PS. However, the fractional rate (percent of labeled cholesterol esterified per hr) of POFF‐cholesterol esterification was similar to that observed in PS. There was little variation of absolute rate of cholesterol esterification in the fluid obtained from different sizes of follicles. Fatty acid or triacylglycerol did not participate in the reaction of cholesterol esterification in POFF. No appreciable change in enzymatic activity was found from storing POFF at 4 C for periods of time up to 24 hr or at −70 C up to 2 months, but activity was lost thereafter. On the other hand, PS showed a much longer period of stability (5 days at 4 C and 9 months at −70 C). A discrepancy between the fatty acid composition of cholesteryl esters formed by the LCAT reaction and the fatty acid composition at the C‐2 position of phosphatidylcholine led us to propose a two‐step mechanism for the LCAT reaction. It is concluded that the LCAT of POFF, as well as that of plasma, is specific for individual fatty acids rather than for the fatty acid composition of phosphatidylcholine. The fatty acid concentration of lysophosphatidylcholine decreased during prolonged incubation times (6 to 21 hr) suggesting that the increased lysophosphatidylcholine formed as a product of the LCAT reaction may be reused as substrate for the LCAT reaction or for hydrolysis by lysophosphatidylcholine hydrolase.

AbstractThree of six kin were identified, by high performance thin layer chromatography, capillary gas chromatography and mass spectrometry, as having phytanic acid storage disease. Phytanic acid was found in triacylglycerol and, to a lesser degree, in phosphatidylcholine and free fatty acids. An unsaturated analogue of phytanic acid was additionally identified in plasma and erythrocyte triacylglycerols. In plasma, branched chain fatty acids were primarily localized in the low density lipoprotein fraction. The concentration of plasma major fatty acids was not affected by the presence of these branched chain fatty acids. In contrast to plasma, only small amounts of phytanic acid were found in cerebrospinal fluid and biopsied sural nerve. The nerve phytanate was mainly associated with triacylglycerol in epineurial and perineurial tissues. Lack of phytanate accumulation in sural endoneurium, even in cases with severe fiber degeneration, suggests that demyelination in Refsum's disease may not be due to myelin instability resulting from the incorporation of branched chain fatty acids into peripheral nerve membrane.

ABSTRACT TaqMan hepatitis B virus (HBV) analyte-specific reagent (ASR; Roche Molecular Systems, Inc., Branchburg, NJ) is designed for the quantification of HBV DNA in serum or plasma. The performance characteristics of TaqMan HBV ASR following automated sample processing with the MagNA Pure LC instrument (MP; Roche Applied Science, Indianapolis, IN) were evaluated in this study. Analytical sensitivity and precision were assessed with commercially available HBV standards, while clinical serum specimens from HBsAg-seropositive patients and healthy blood donors were used to determine clinical sensitivity, specificity, and correlation with other commercially available assays. Analytical studies yielded a limit of detection of 2.4 IU/ml, with good linearity and correlation ( R 2 = 0.9958) with expected HBV DNA titers over a wide range (6.0 × 10 0 to 2.1 × 10 8 IU/ml). Clinical sensitivity and specificity of the assay combined with automated sample processing were both 100%. Comparison of TaqMan HBV ASR and VERSANT HBV DNA 3.0 assay (bDNA; Bayer HealthCare LLC, Tarrytown, NY) results among clinical specimens yielded good correlation ( R 2 = 0.9237), with a mean difference in titer of −0.213 log 10 IU/ml (95% confidence interval, −0.678 to 1.10 log 10 IU/ml). The overall test failure rate was 2.0% among 204 clinical serum specimens tested. Total time required for MP sample processing and automated postelution handling of 24 samples was 224 min, with 57 min of actual hands-on time. MP is a reliable, labor-saving platform suitable for use with TaqMan HBV ASR, providing sensitive and accurate quantification of HBV DNA levels over a range of 8 log 10 IU/ml.

ABSTRACT The Invader 1.0 assay (Invader HCV Genotyping Assay, version 1.0; Third Wave Technologies, Inc., Madison, WI) has been developed for the rapid differentiation of hepatitis C virus (HCV) genotypes 1 to 6 based on sequence variation within the HCV 5′ noncoding (NC) region. In the present study, we evaluated the compatibility of Invader 1.0 with the COBAS MONITOR (COBAS AMPLICOR HCV MONITOR Test, version 2.0; Roche Molecular Systems, Inc., Branchburg, NJ), COBAS AMPLICOR (COBAS AMPLICOR Hepatitis C Virus Test, version 2.0; Roche Molecular Systems, Inc.), and COBAS TaqMan (COBAS TaqMan HCV Test; Roche Molecular Systems, Inc.) assays. The minimum HCV RNA titers required for successful HCV genotyping (≥90% success rate) were 1,000 IU/ml for COBAS MONITOR, 100 IU/ml for COBAS AMPLICOR, and 10 IU/ml for COBAS TaqMan. Invader 1.0 results obtained from unpurified COBAS TaqMan amplification products of 111 retrospectively selected clinical serum specimens (genotypes 1 to 6, with virus titers ranging from 15.1 to 2.1 × 10 7 IU/ml) showed 98% concordance with results obtained from the TRUGENE HCV 5 ′ NC Genotyping Kit (Bayer HealthCare LLC, Tarrytown, NY), used in conjunction with COBAS AMPLICOR. Although the assay is sensitive, accurate, and easy to perform, additional optimization of the Invader 1.0 interpretive software (Invader Data Analysis Worksheet) may be necessary to reduce potential misidentification of HCV genotypes in low-titer specimens. In summary, Invader 1.0 is compatible with a variety of commercially available PCR-based HCV 5′ NC region amplification assays and is suitable for routine HCV genotyping in clinical laboratories.

SUMMARY Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

ABSTRACT The COBAS TaqMan HCV Test (TaqMan HCV; Roche Molecular Systems Inc., Branchburg, N.J.) for hepatitis C virus (HCV) performed on the COBAS TaqMan 48 Analyzer (Roche Molecular Systems) currently relies on a manual sample processing method. Implementation of an automated sample processing method would facilitate the clinical use of this test. In this study, we evaluated the performance characteristics of TaqMan HCV following automated sample processing by the MagNA Pure LC instrument (MP; Roche Applied Science, Indianapolis, Ind.). The analytical sensitivity of TaqMan HCV following sample processing by MP was 8.1 IU/ml (95% confidence interval, 6.1 to 15.2). The assay showed good linearity ( R 2 = 0.99) across a wide range of HCV RNA levels (25 to 5 × 10 6 IU/ml), with coefficients of variation ranging from 10% to 46%. Among 83 clinical specimens, the sensitivity and specificity of TaqMan HCV were 100% and 95%, respectively, when compared to the COBAS AMPLICOR hepatitis C virus test, version 2.0 (COBAS AMPLICOR; Roche Molecular Systems), with TaqMan HCV detecting two more HCV RNA-positive specimens than COBAS AMPLICOR. Both specimens were confirmed to be HCV RNA positive by the VERSANT HCV RNA qualitative test (Bayer HealthCare LLC, Tarrytown, N.Y.). There was also strong correlation ( R 2 = 0.95) and good agreement between the results from TaqMan HCV and the VERSANT HCV RNA 3.0 assay (bDNA) (Bayer HealthCare LLC) among a group of 93 clinical specimens. The MP is a versatile, labor-saving sample processing platform suitable for reliable performance of TaqMan HCV.

ABSTRACT The VERSANT hepatitis B virus (HBV) 3.0 Assay (branched DNA [bDNA]) (referred to herein as VERSANT 3.0) was evaluated at four external sites for analytical sensitivity, specificity, reproducibility, linearity of quantification, and limits of detection. In addition, each of the test evaluation sites provided HBV DNA-positive clinical samples that were previously analyzed by one of three commercially available HBV DNA quantitative tests: Digene Hybrid Capture II HBV DNA Test (Digene); VERSANT HBV DNA 1.0 Assay (bDNA) (VERSANT 1.0); and COBAS AMPLICOR HBV Monitor Test (COBAS AMPLICOR). These samples were reexamined using VERSANT 3.0. The results from these studies showed that VERSANT 3.0 has high specificity (99.3%), excellent reproducibility (between-run coefficient of variation [CV] = 1.6 to 9.4%; within-run CV = 6.5 to 20.7%), and a broad linear range of quantification (2.0 × 10 3 to 1.0 × 10 8 HBV DNA copies/ml) that facilitate the monitoring of HBV DNA levels at diagnosis and throughout the course of treatment. In general, correlation was very good between results obtained from clinical samples analyzed by VERSANT 3.0 and the comparative HBV DNA quantitative assays (VERSANT 1.0, R 2 = 0.900; Digene, R 2 = 0.985; COBAS AMPLICOR, R 2 = 0.771). The greatest differences in comparative quantitation occurred at HBV DNA levels approaching the limits of the dynamic ranges for the comparative assays. The performance characteristics of the new VERSANT 3.0 assay demonstrated that it provides a reliable and robust method for routinely monitoring serum HBV DNA levels in assessing disease activity and determining response to antiviral treatment.