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At least 109 records · Page 6Linked to original sources
PubMed2001

DNA isolation protocols affect the detection limit of PCR approaches of bacteria in samples from the human gastrointestinal tract.

A major concern in molecular ecological studies is the lysis efficiency of different bacteria in a complex ecosystem. We used a PCR-based 16S rDNA approach to determine the effect of two DNA isolation protocols (i.e. the bead beating and Triton-X100 method) on the detection limit of seven feces-associated bacterial species of different genera. Glycogen was used in these protocols to improve the precipitation of small concentrations of DNA in ethanol without affecting the sequential procedures. The PCR detection limit of 16S rDNA amplicons on agarose gel from the seven strains tested varied between 8.0 (+/- 1.3) x 10(4) and 4.3 (+/- 1.6) x 10(6) cells for the bead beating method, and between 8.0 (+/- 1.3) x 10(4) and 5.4 (+/- 0.7) x 10(8) cells for the Triton X-100 method. These large differences are most like due to the difference in cell lysis efficiency, since a competitive PCR experiment did not indicate any preference for gram negative, low G+C gram positive or high G+C gram positive bacteria. Denaturing gradient gel electrophoresis (DGGE) analysis was performed to investigate the effect of both DNA isolation protocols on the lysis efficiency of bacteria in fecal samples. A higher diversity in fecal samples was observed with the bead beating method than with the Triton-X100 method. Bands in the bead beating method-derived DGGE profiles corresponding to bands of cloned sequences of the Clostridium coccoides-Eubacterium rectale group and uncultured Fusobacterium prausnitzii were absent or had low intensity in the Triton X-100 method-derived profiles. The applicability of the bead beating method was further investigated by analyzing biopsy samples from the human colon which contain approximately 10(6) cells.

Biopsy↗
PubMed2001

Correlating two viral load assays with known detection limits.

A timely objective common to many HIV studies involves assessing the correlation between two different measures of viral load obtained from each of a sample of patients. This correlation has scientific utility in a number of contexts, including those aimed at a comparison of competing assays for quantifying virus and those aimed at determining the level of association between viral loads in two different reservoirs using the same assay. A complication for the analyst seeking valid point and interval estimates of such a correlation is the fact that both variables may be subject to left censoring due to values below assay detection limits. We address this problem using a bivariate normal likelihood that accounts for left censoring of two variables that may have different detection limits. We provide simulation results to evaluate sampling properties of the resulting correlation estimator and compare it with ad hoc estimators in the presence of nondetects. In an effort to obtain improved confidence interval properties relative to the Wald approach, we evaluate and compare profile likelihood-based intervals. We apply the methods to HIV viral load data on women and infants from a trial in Bangkok, Thailand, and we discuss an extension of the original model to accommodate interval censoring arising due to the study design.

Biometry↗
PubMed2004

Spectroelectrochemical sensing based on multimode selectivity simultaneously achievable in a single device. 17. Improvement in detection limits using ultrathin perfluorosulfonated ionomer films in conjunction with continuous sample flow.

We report herein an attenuated total reflectance (ATR) absorbance-based spectroelectrochemical sensor for tris(2,2'-bipyridyl)ruthenium(II) ion [Ru(bpy)(3)(2+)] that employs ultrathin (24-50 nm) Nafion films as the charge-selective layer. This film serves to sequester and preconcentrate the analyte at the optically transparent electrode surface such that it can be efficiently detected optically via electrochemical modulation. Our studies indicate that use of ultrathin films in tandem with continuous flow of sample solution through the cell compartment leads to a 100-500-fold enhancement in detection limit (10 nM) compared to earlier absorbance-based spectroelectrochemical sensors ( approximately 1-5 microM); markedly shorter analysis times also result. We report the dependence of the measured absorbance on sample flow rate and Nafion film thickness, and also provide calibration curves that illustrate the linear range and detection limits of the sensor using a 24 nm film at a constant sample flow rate of 0.07 mL/min.

Journal Article↗
PubMed2004

In vivo detection limits of magnetically labeled embryonic stem cells in the rat brain using high-field (17.6 T) magnetic resonance imaging.

Stem cell transplantation is a promising therapeutic approach for several neurological disorders. However, it has yet to fulfill its high expectations, partially due to the lack of a reliable noninvasive method for monitoring the biodistribution of the grafted stem cells in vivo. We have used high-resolution magnetic resonance imaging (MRI) at 17.6 T, combined with efficient magnetic labeling of the stem cells with iron oxide nanoparticles, in order to assess the in vivo detection limit in small animal models. Injection of different concentrations of magnetically labeled stem cells in gel phantoms led to significant reductions in image intensity from small cellular clusters of less than 10 cells. To determine the detection limit in vivo, various numbers of both labeled and unlabeled cells were injected stereotactically into the striatum of rats. Significant hypointense signal changes were observed for 100 labeled cells. After injection of approximately 20 labeled cells, signal reduction at the injection site was observed but could not be assigned unambiguously to the cells. Our results show that high-field MRI allows tracking of a minimal number of cells in vivo, well below the number used in previous studies, opening the possibility of gaining new insights into cell migration and differentiation.

Animals↗
PubMed2004

Salivary cortisol and administration of concentrated oral glucose in newborn infants: improved detection limit and smaller sample volumes without glucose interference.

Newborn infants are subject to repetitive painful and stressful events during neonatal intensive care. When the baby attempts to cope with a stressful situation the hypothalamus-pituitary-adrenal axis is activated, releasing cortisol. The free cortisol response is optimally measured in saliva and saliva samples can be taken easily and without pain. However, saliva is very scarce in infants and saliva stimulants can interfere with analytical methods. Nowadays, sweet solutions are frequently administered to neonates prior to a disturbing procedure in order to reduce pain. The possible interference of sweet solutions with the measurement of salivary cortisol has not yet been documented. The aims of the present study were to further improve the detection limit of the radioimmunoassay used for cortisol analysis and to determine the degree of interference of high concentrations of glucose with the analytical method. By decreasing incubation temperature and prolonging the incubation time it was possible to improve the detection limit of the radio immunoassay (RIA) to 0.5 nmol/L at the same time as the sample volume was decreased to 10 microL saliva. Saliva was collected from full-term and preterm babies and was sufficient for analysis in 113 out of 116 (97%) samples. Glucose in the concentrations and amounts commonly used for pain relief did not interfere with the RIA method. In conclusion, it is feasible to collect microlitre volumes of saliva and analyse even very low concentrations of cortisol in newborns. It is also possible to offer the baby oral glucose prior to a painful procedure and still reliably measure salivary cortisol.

Administration, Oral↗
PubMed2004

Electrospray sample deposition for matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI mass spectrometry with attomole detection limits.

Electrospray sample deposition was explored for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). In this method, nanoliter volumes of matrix/analyte mixture were electrosprayed from a high voltage biased (1-2 kV) fused-silica capillary onto a grounded MALDI plate mounted 100-500 microm from the capillary outlet. Electrospray deposition with these conditions produced sample spots 200-300 microm in diameter thus matching the laser spot size. Varying spray voltage and distance resulted in different crystal sizes and volatilization rates for alpha-cyano-4-hydroxycinnamic acid matrix. Best results were obtained when the sample was deposited as wet droplets as opposed to deposition as dried solid. Under 'wet-spray' conditions, 2-4 microm diameter crystals were formed and detection limits for several neuropeptides were 0.7-25 amol. Samples could be pre-concentrated on the plate by spraying continuously and allowing sample to evaporate in a small spot. Sample volumes as large as 580 nL were deposited yielding a detection limit of 35 pM for neurotensin 1-11. Electrospray sample deposition yielded similar results when using atmospheric pressure-MALDI coupled with a quadrupole ion trap mass spectrometer, except that the sensitivity was approximately seven-fold worse.

Atmospheric Pressure↗
PubMed2000

Assay of D-lactate in urine of infants and children with reference values taking into account data below detection limit.

Accumulation of D-lactic acid produced by intestinal bacteria such as streptococci and lactobacilli has been extensively studied in ruminants [1-4]. In humans an increased production of D-lactate by intestinal bacteria under pathological conditions such as the short bowel syndrome can cause metabolic acidosis [5-8]. Since the lactate assays routinely used only measure L-lactate we developed a sensitive method of D-lactate quantification and established reference values in spot urines of infants and children (0 to 4 years of age). The enzymatic method with fluorimetric quantification of NADH is linear up to 2 mmol/l. It has a detection limit of 3.4 micromol/l. Among structurally related organic acids an interference was found only for L-lactate and DL-2-hydroxybutyrate at concentrations which are way beyond their physiological excretion. One hundred and sixty five spot urines of healthy Swiss (S), Austrian (A), German (G) and Chilean (CHI) infants aged from 0 to 4 years were analyzed. The distribution of the data is close to a lognormal one. Values below the detection limit were simulated and age groups were formed. In all populations D-lactate excretion was found highest during the first year of life; it declines with age during infancy and remains stable from 2.5 to 4 years of age. We show that D-lactate is excreted physiologically by healthy infants and children below 4 years of age and present reference values for D-lactate excretion which show some differences between the populations tested.

Aging↗
PubMed1987

Reliability and practicability of the fluorometric-fluoroenzymatic histamine determination in pathogenetic studies on peptic ulcer: detection limits and problems with specificity.

Histamine, among various "biologic-physiologic" abnormalities, is considered as a pathogenetic factor in chronic duodenal ulcer disease. The 10-30 per cent difference between its concentration in gastric and duodenal mucosa of patients compared to healthy controls, however, has to be demonstrated to be specific for the disease. It has to be shown to be neither a methodological artefact nor a common effect, concomitant factor or consequence. This study, after a series of pathogenetic trials examines systematic errors (biases) in the fluorometric-fluoroenzymatic histamine assay under the conditions of field studies including tests on specificity over a time period of 10 years. It concentrates on sensitivity (detection limits) and specificity of a standard technique described herein. A modified Shore procedure for large scale assays in human biopsies was developed including reference luminescence values for all reagents, cleaning material and glassware, reduction of OPD concentration to 0.05%, purification of n-heptan, omission of centrifugation steps in the extraction procedure and use of 2 ml 1 M HClO4 in the homogenization step to prevent losses of histamine due to adherence to the mechanical homogenizer. This assay was sensitive enough to measure histamine without difficulty in any biopsy taken. The detection limit was 3 ng/biopsy, but the smallest quantities of the amine ever obtained were 10.6 and 18.3 ng/biopsy (depending on both histamine content and biopsy weight). A series of problems had to be solved both in achieving and demonstrating specificity. It had to be defined not only for the assay in general, but also for assessing the difference in histamine content between ulcer patients and healthy controls. Exogenous more than endogenous fluorescing material interfering with the determination had to be excluded. A series of pitfalls were detected which had to be overcome in demonstrating the specificity of the assay by physicochemical and enzymatic tests. The specificity of the identification tests was more often impaired than the histamine assay itself. Fluorescing material interfering with the assay occurred in the homogenization, extraction and condensation steps, was found in water, OPD, the organic solvents, the cleaning material and in all kinds of plastic vessels. Plasticizers were shown by physicochemical characteristics including fluorescence spectra to be most likely responsible for this interfering material. Rules were developed to exclude such hazards in specificity in longterm pathobiochemical studies. Enzymatic identification test were applied to exclude endogenous fluorecing substances interfering with the standard technique. Simil

Biopsy↗
PubMed2005

Increased levels of HIV RNA detected in samples with viral loads close to the detection limit collected in Plasma Preparation Tubes (PPT).

BACKGROUND: The accurate and reliable quantification of HIV RNA is an essential part of the management of HIV infected individuals, and elucidation of factors that may affect HIV RNA measurements, such as the use of Vacutainer Plasma Preparation Tubes (PPT), is crucial. OBJECTIVES: The objective of this study was to determine if plasma samples with viral loads close to the lower limit of the dynamic range of the assay collected in PPT tubes had increased levels of HIV RNA as compared to samples collected in standard EDTA tubes. STUDY DESIGN: HIV RNA levels were compared in 112 paired plasma samples collected in PPT and standard EDTA tubes. All samples had been frozen prior to testing. RESULTS: Discrepancies between PPT and EDTA tubes did not occur for samples with high viral loads. However, in samples with viral loads close to the lower limit of the dynamic range, levels of HIV RNA detected were higher in a large proportion of PPT as compared to the corresponding EDTA plasma samples. Forty percent of plasma pairs had no detectable HIV RNA in the EDTA aliquot, but had low levels of HIV RNA in the corresponding PPT aliquot. CONCLUSIONS: This prospective study underlines the need for cautious interpretation of small transient viral load changes in samples with values close to the detection limit.

Acquired Immunodeficiency Syndrome↗
PubMed2005

Detection limits for nanoscale biosensors.

We examine through analytical calculations and finite element simulations how the detection efficiency of disk and wire-like biosensors in unmixed fluids varies with size from the micrometer to nanometer scales. Specifically, we determine the total flux of DNA-like analyte molecules on a sensor as a function of time and flow rate for a sensor incorporated into a microfluidic system. In all cases, sensor size and shape profoundly affect the total analyte flux. The calculations reveal that reported femtomolar detection limits for biomolecular assays are very likely an analyte transport limitation, not a signal transduction limitation. We conclude that without directed transport of biomolecules, individual nanoscale sensors will be limited to picomolar-order sensitivity for practical time scales.

Biosensing Techniques↗
PubMed1999

RT-PCR and its detection limit for cell culture grown bluetongue virus 1 using NS1 gene group specific primers.

RT-PCR was standardised for the detection of bluetongue viral RNA using highly expressed non structural protein 1 gene as the target gene with specific primers targeted to 274 bp of 5' end of NS1 gene. PCR product was consistently obtained in 30 PCR cycles. Further, detection limit of RT-PCR was estimated using serial 10 fold dilutions of BHK 21 cells grown BTV 1. The study suggested that RT-PCR can be used for detection of BTV in Indian conditions with the sensitivity limit of 10 infectious particles of the virus. The study suggested that this technique may be used as a tool for sensitive detection of BTV in carrier/reservoir animals, insect vectors and certification of animals and their germ- plasm for export and import purposes.

Animals↗
PubMed2005

[Estimation of detection limit from slope of B/B0 in competitive ELISA].

A method has been proposed for determining the detection limit (L(D)) from the slope of a semilogarithmic plot of a B/B(0) curve in competitive enzyme linked immunosorbent assay (ELISA). As an application, this paper describes a graphic determination of L(D) from analogue data in the literature. The L(D) obtained corresponds to the concentration at which the relative standard deviation of concentration estimates is 30%.

Calibration↗
PubMed2003

Determination of lanthanides in synthetic standards by reversed-phase high-performance liquid chromatography with the aid of a weighted least-squares regression model estimation of method sensitivities and detection limits.

A reversed-phase liquid chromatography method was used for determining lanthanides in synthetic standards. The separation of lanthanide group was achieved in less than 15 min using a linear gradient program of alpha-hydroxyisobutyricacid eluent from 0.05 to 0.5 M (pH 3.8) with a UV-Vis detection system at 658 nm. A post-column reagent of Arsenazo III was employed for improving the sensitivity and selectivity of the method as well as for lowering the limits of detection (LODs). Linear calibration curves for all lanthanides were constructed using an ordinary least-squares (OLS) regression as well as a weighted least-squares (WLS) regression model for taking into account the heteroscedastic errors. The WLS model was successfully used for a better estimation of the sensitivities and the LODs of the RP-HPLC method than the conventional OLS model. The lanthanide sensitivity obtained from the slope of each calibration curve seems to be better for a lanthanide with an odd-atomic number compared to its neighboring element with an even-atomic number, as if nature is helping us to quantify the concentrations of the less abundant lanthanides. This observation was also confirmed when the LODs computed for all lanthanides were examined. The LODs observed for all lanthanides depicted a clear systematic "zigzag" pattern. This is actually the first time that the lanthanide detection limits determined by a HPLC method are shown to mimic the zigzag patterns for the concentration data in geological and cosmological materials. Such a "zigzag" pattern should be used as a standard criterion for evaluating the quality of detection limit data.

Chromatography, High Pressure Liquid↗
PubMed2002

Evaluation of uncertainties in 90Sr-body-burdens obtained by whole-body count: application of Bayes' rule to derive detection limits by analysis of a posteriori data.

A whole body counter (WBC) designed to measure bremsstrahlung from 90Y, the short-lived daughter of 90Sr, has been used since 1974 to measure 90Sr-body burdens in residents along the Techa River, which was contaminated by releases from the Mayak Production Association. Bayes' rule has been applied to the a posteriori WBC data in order to derive the uncertainties associated with the data: The lower limit of reliable detection is 2.0 kBq and the uncertainty of routine measurements is 1.6 kBq.

Bayes Theorem↗
PubMed2006

Expiratory flow limitation detected by forced oscillation and negative expiratory pressure.

The within-breath change in reactance (Delta(rs)) measured by forced oscillation technique (FOT) at 5 Hz reliably detects expiratory flow limitation in chronic obstructive pulmonary disease (COPD). The present study compared this approach to the standard negative expiratory pressure (NEP) method. In total, 21 COPD patients were studied by applying both techniques to the same breath and in 15 patients the measurements were repeated after bronchodilator. For each patient and condition five NEP tests were performed and independently scored by three operators unaware of the FOT results. In 180 tests, FOT classified 53.3% as flow limited. On average, the operators scored 27.6% of tests flow limited and 47.6% non-flow limited, but could not score 24.8%. The methods disagreed in 7.9% of cases; in 78% of these the NEP scores differed between operators. Bronchodilation reduced NEP and DeltaX(rs) scores, with only the latter achieving significance. Averaging the operators' NEP scores, a threshold between 24.6-30.8% of tidal volume being flow limited by NEP produced 94% agreement between methods. In conclusion, when negative expiratory pressure and forced oscillation technique were both available they showed good agreement. As forced oscillation technique is automatic and can measure multiple breaths over long periods, it is suitable for monitoring expiratory flow limitation continuously and identifying patients' breathing close to the onset of expiratory flow limitation, where intermittent sampling may be unrepresentative.

Forced Expiratory Flow Rates↗
PubMed2006

Evaluation of statistical methods for left-censored environmental data with nonuniform detection limits.

Monte Carlo simulations were used to evaluate statistical methods for estimating 95% upper confidence limits of mean constituent concentrations for left-censored data with nonuniform detection limits. Two primary scenarios were evaluated: data sets with 15 to 50% nondetected samples and data sets with 51 to 80% nondetected samples. Sample size and the percentage of nondetected samples were allowed to vary randomly to generate a variety of left-censored data sets. All statistical methods were evaluated for efficacy by comparing the 95% upper confidence limits for the left-censored data with the 95% upper confidence limits for the noncensored data and by determining percent coverage of the true mean (micro). For data sets with 15 to 50% nondetected samples, the trimmed mean, Winsorization, Aitchison's, and log-probit regression methods were evaluated. The log-probit regression was the only method that yielded sufficient coverage (99-100%) of micro, as well as a high correlation coefficient (r2 = 0.99) and small average percent residuals (-0.1%) between upper confidence limits for censored versus noncensored data sets. For data sets with 51 to 80% nondetected samples, a bounding method was effective (r2 = 0.96 - 0.99, average residual = -5% to -7%, 95-98% coverage of micro), except when applied to distributions with low coefficients of variation (standard deviation/micro < 0.5). Thus, the following recommendations are supported by this research: data sets with 15 to 50% nondetected samples--log-probit regression method and use of Chebyshev theorem to estimate 95% upper confidence limits; data sets with 51 to 80% nondetected samples-bounding method and use of Chebyshev theorem to estimate 95% upper confidence limits.

Computer Simulation↗
PubMed1997

Noise-limited detection in young and old observers.

11 young (M age = 24.3 yr.) and 11 old (M age = 67.4 yr.) observers attempted to detect signals of limited bandwidth in visual noise. The older observers did not perform as well as the young ones. We considered whether, as suggested by a current hypothesis, these differences could be attributed to higher internal additive noise in the elderly observers. The results suggested that internal noise did not differ across the two age groups and that the lower performance of the older observers stemmed instead from reduced processing efficiency.

Adult↗