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PubMed2006

Use of biomarkers in epidemiologic studies: minimizing the influence of measurement error in the study design and analysis.

The inclusion of biomarkers measured on the continuous scale, such as endogenous sex hormones or antioxidant levels, has become common in epidemiologic studies, and introduces additional sources of error that are specific to biomarkers. This includes error associated with specimen collection, processing, and storage; laboratory error (both within and between batch); and variability in the biomarker levels over time within an individual. In this review, we discuss and recommend study design and analytic strategies to deal with these sources of measurement error. In particular we describe methods to prevent or minimize some sources of error through appropriate sample collection and storage, communication with the laboratory, proper batching of samples, and participant matching. We also discuss how to quantify error related to biomarkers, focusing on issues of quality control, pilot studies, and how to measure within-person stability over time. Further, we discuss analytic issues for dealing with laboratory and within-person variability. Finally we recommend that journals standardize the reporting of biomarker assays in scientific manuscripts.

Biomarkers↗
PubMed2005

Evaluation of an antimicrobial resistance monitoring program for Campylobacter in poultry by simulation.

An ideal national resistance monitoring program should deliver a precise estimate of the resistance situation for a given combination of bacteria and antimicrobial at a low cost. To achieve this, decisions need to be made on the number of samples to be collected at each of different possible sampling points. Existing methods of sample size calculation can not be used to solve this problem, because sampling decisions do not only depend on the prevalence of resistance and sensitivity and specificity of resistance testing, but also on the prevalence of the bacteria, and test characteristics of isolation of these bacteria. Our aim was to develop a stochastic simulation model that optimized a national resistance monitoring program, taking multi-stage sampling, imperfect sensitivity and specificity of diagnostic tests, and cost-effectiveness considerations into account. The process of resistance testing of Campylobacter spp. isolated from cloacal swab samples from poultry was modeled using a Markov Chain Monte Carlo model. Different sampling scenarios on the number of flocks to be tested, the number of birds from each flock, and the number of campylobacter colonies submitted to susceptibility testing were evaluated regarding the precision of the resulting prevalence estimate. Precision of the prevalence estimate was defined as the absolute difference between apparent and true prevalence of resistance. A partial budget approach was utilized to find the most cost-effective combination of samples to obtain a defined precision of the prevalence estimate. For a sampling scenario testing 100 flocks, five birds per flock, and one campylobacter colony per sample, the median error of the prevalence estimate was 2.5%, and 95% of the simulations resulted in an error of 7% or less. When the total number of samples was kept constant, maximizing the number of flocks tested, and only testing one bird per flock resulted in the most precise prevalence estimate. Submitting more than one campylobacter colony to resistance testing did not improve the prevalence estimate. Partial budget analysis indicated that the most cost-effective strategy was testing of two birds per flock, and submitting one colony per sample to resistance testing.

Animals↗
PubMed2003

Formalin fixing and paraffin embedding may lead to extra band development in PCR.

The molecular biological analysis of infectious agents requires the availability of a reliable source of microorganisms to be used to recover DNA. Clinical samples can be obtained directly from infected patients or can be propagated using in vitro or in vivo systems. However, repeated sampling from patients is not always possible as the procedure may be invasive or unpleasant, or it is not possible to catch the same agent at the time of second sampling. Moreover, the techniques used may also produce false-positive and false-negative results. We therefore studied the impact of formalin-fixing and paraffin embedding on tissue sampling, and the methodologies such as DNA isolation and PCR amplification of DNAs from archival materials in the diagnosis of Mycobacterium tuberculosis. PCR analyses were done according to standard methods with some modifications. Demonstration of mycobacteria was successful both in tissue sections of the formalin-fixed lymph nodes and in stained fresh materials from patients. However, the results showed the presence of two extra bands in the gel. We accounted for extra band development due to the harshness of the methodology used to isolate nucleic acids from formalin-fixed and paraffin embedded tissue samples or the nature of the fixation procedure, or because of the time passed during storage in which alteration in the chromosomal DNA would take place. Thus, if disease- and tissue specific morphological features, such as sample size, type of fixation, and intralesional heterogeneity are ignored, errors because of sampling and methodologies used may lead to false-positive and false-negative results.

Artifacts↗
PubMed2003

Simple procedures for blinded sample size adjustment that do not affect the type I error rate.

For normally distributed data, determination of the appropriate sample size requires a knowledge of the variance. Because of the uncertainty in the planning phase, two-stage procedures are attractive where the variance is reestimated from a subsample and the sample size is adjusted if necessary. From a regulatory viewpoint, preserving blindness and maintaining the ability to calculate or control the type I error rate are essential. Recently, a number of proposals have been made for sample size adjustment procedures in the t-test situation. Unfortunately, none of these methods satisfy both these requirements. We show through analytical computations that the type I error rate of the t-test is not affected if simple blind variance estimators are used for sample size recalculation. Furthermore, the results for the expected power of the procedures demonstrate that the methods are effective in ensuring the desired power even under initial misspecification of the variance. A method is discussed that can be applied in a more general setting and that assumes analysis with a permutation test. This procedure maintains the significance level for any design situation and arbitrary blind sample size recalculation strategy.

Anxiety Disorders↗
PubMed2005

Quality control of slope-intercept measurements of glomerular filtration rate using single-sample estimates.

OBJECTIVES: Measurement of glomerular filtration rate (GFR) using the slope-intercept technique determines the plasma clearance curve by fitting a straight line to the logarithm of sample count rate. When two samples are used there is no check on the validity of curve fitting. GFR may also be estimated from single-sample concentrations. This study describes a method of quality control for the two-sample technique using the agreement between the one-sample and two-sample estimates. METHODS: GFR measurements using Tc-DTPA were performed on 225 adults and 100 children using two samples taken between 2 h and 4 h post-injection. The two-sample values obtained using the British Nuclear Medicine Guidelines slope-intercept technique were compared to one-sample estimates obtained using a new general equation. Equations describing the variation of GFR error with GFR value were defined. These were used to determine action levels giving the limits of expected agreement between slope-intercept and single-sample values. The use of these action levels for quality control was demonstrated in a further 120 GFR measurements. RESULTS: The variation of single-sample error estimate with GFR depended both on the time of sample and body surface area. For specific sample groups, the error variation with GFR could be approximated using a truncated quadratic equation. Four studies were identified as failing quality control in the dataset used to define the error equations. Two studies failed in the test dataset. CONCLUSIONS: One-sample equations give reliable estimates of GFR, which may be used for quality control of slope-intercept GFR assessment.

Adult↗
PubMed1992

Intra-patient variation between breast cancer axillary lymph node metastases using quantifiable features.

The intra-patient variations of some clinically relevant quantifiable features, between axillary lymph node metastases were evaluated in 44 breast cancer patients. In all lymph node metastases detected (range 2-33 per patient), the mitotic figures were counted, the volume percentage epithelium was assessed and the mean nuclear area was measured. The intra-patient variation for each quantifiable feature was expressed by the coefficient of variation (CV). Since the measurement techniques used introduce a certain, well known variation themselves because of sampling and measurement errors, the CVs found had to be greater than methodological tolerance limits (established in previous studies) to be interpreted as indicating biological variation. The CVs exceeded the methodological tolerance limits in 86% of the cases for the mitotic count, in 48% of the cases for the volume percentage epithelium, and in 47% of the cases for the mean nuclear area. This indicated that in these cases, the variation found in the quantifiable features could not be explained by sampling or measurement errors and should be regarded as real biological variation. Furthermore, the variation in the quantifiable features studied showed a significant positive correlation with the number of lymph node metastases. Thus, there may be considerable intra-patient variation in quantifiable features between axillary lymph node metastases in breast cancer. This may indicate that these lymph node metastases originate independently from different clones within the primary tumour, that they are independently formed in different stages of tumour development, or that they, as an expression of intrinsic tumour heterogeneity, may develop in different directions from the start.

Axilla↗
PubMed2005

Determining PAHs and PCBs in aqueous samples: finding and evaluating sources of error.

This work describes the problems that occur during routine multi-step determinations of polyaromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), which can be present at trace levels in water, and identifies sources of analyte losses at particular steps during the analytical procedure. PAH and PCB adsorption onto the walls of the container ranged from 0 to 70%. PAH and PCB recoveries of >70% were achieved during the LLE and SPE extraction steps. During the process of enriching the dichloromethane extract with PAHs and PCBs, based on the gentle evaporation of solvent, losses were <24% and <19%, respectively. Model experiments show that neither isolation of PAHs and PCBs (performed using either LLE or SPE) nor extract enrichment reduce the reliability of PAH and PCB determination. The steps that lead to the greatest loss of analyte are the ones that involve sampling, transport and storage of the water samples.

Journal Article↗
PubMed1993

Basic theory for the diffusive sampling of radon.

From the closed-form solution of the Fickian equation describing the uptake of radon by a diffusive sampler, the following are calculated: 1) the optimal estimate of the time-weighted average radon concentration; 2) the effect of the geometry of the diffusive sampler on performance; 3) the maximum sampling time consistent with a predetermined maximum error in the estimated time-weighted average concentration of radon; and 4) the effects of temperature and pressure on the performance of the sampler. It is shown that the maximum sampling error can be greatly reduced by dividing the adsorbent bed into two layers placed in series and by using a weighted average of the uptakes on the two layers.

Air Pollutants, Radioactive↗
PubMed2004

Precision, limit of detection and range of quantitation in competitive ELISA.

This paper develops a mathematical model for describing the within-plate variation as the RSD (relative standard deviation) of absorbance measurements in a wide concentration range in competitive ELISA and proposes a method for determining the limit of detection (LOD) and range of quantitation (ROQ). The ELISA for 17 alpha-hydroxyprogesterone is taken as an example. The theoretical RSD description involves analyte concentration as an independent variable and error sources as parameters which concern the pipetting and absorbance measurement. Our model can dispense with repeated experiments of real samples, but the error parameters should be determined experimentally. The theory is in good agreement with the experiments. The most influential error sources at low and high sample concentrations are shown to be the pipetting of a viscous solution of antiserum and the absorbance inherent to the wells of a plate, respectively. The LOD and ROQ are defined as the concentration with 30% RSD and the region with <10% RSD, respectively, and are found in the theoretical plot of the RSD of concentration estimates vs concentration.

17-alpha-Hydroxyprogesterone↗
PubMed1998

Missed opportunities: teenagers and emergency contraception.

OBJECTIVE: To determine American teenagers' awareness of and knowledge about emergency contraceptive pills and their likelihood to use them. METHODS: We conducted a nationally representative telephone survey between March 28, 1996, and May 5, 1996, of 1510 teenagers (757 girls and 753 boys), aged 12 to 18 years, living in the continental United States in households with telephones. The sample overrepresented African American, Latino, and low-income teenagers. The error attributable to sampling and other random effects for the total sample is +/-3 percentage points at the 95% confidence level. RESULTS: Of the 1510 teenagers, only about one quarter (23%) were aware that "anything" could be done after unprotected sex to prevent pregnancy. Slightly more (28%) had heard of "morning-after pills" or emergency contraceptive pills. Of the 423 teenagers who had heard of emergency contraceptive pills, one third (32%) did not know that a prescription is necessary to obtain them, and three quarters (78%) underestimated how long after unprotected intercourse the emergency contraceptive pill regimen could be initiated. Only 9% knew that emergency contraceptive pills are effective as long as 72 hours after unprotected sex. After being told about the option of emergency contraceptive pills, two thirds (67%) of teenaged girls said that they would be likely to use emergency contraceptive pills. Among the 66% of teenaged girls who had not previously heard of emergency contraceptive pills, 64% said that they would be likely to use them. CONCLUSIONS: Emergency contraceptive pills have great potential as a tool for reducing unplanned pregnancies among teenaged girls in the United States. Few teenaged girls were aware that this option exists. Once informed, teenaged girls reported being very interested in taking emergency contraceptive pills if needed.

Adolescent↗
PubMed1989

An efficient procedure for manual platelet counting.

Blood samples were collected by jugular venipuncture from 15 dairy heifers and the blood platelets were counted by manual methods. The platelets were found to be uniformly distributed across the rows, columns and sides of a Neubauer haemocytometer, and it was shown that counting any 10 squares on either side of the haemocytometer and multiplying by a constant factor would accurately predict the total platelet count. This procedure would greatly reduce the time required to count large numbers of platelets per sample, and reduce errors due to the fatigue associated with counting large numbers of samples.

Animals↗
PubMed2002

[Roaming through methodology. XXXVIII. Common misconceptions involving standard deviation and standard error].

Standard deviation and standard error have a clear mutual relationship, but at the same time they differ strongly in the type of information they supply. This can lead to confusion and misunderstandings. Standard deviation describes the variability in a sample of measures of a variable, for instance the variability in ages of the members of a group. It represents the degree to which the values are scattered around their mean: the higher the standard deviation the wider the spread. The value of the standard deviation is not influenced by the number of observations in the sample. The standard error is always used for extrapolation: to estimate the intervals between which the true value of a statistic will occur, based on a sample of observations and with a certain degree of certainty. When interpreting a standard error, it is important to know which statistic (mean, percentage, relative risk, odds ratio) is to be estimated. The value of the standard error is strongly influenced by the number of observations in the sample: the bigger the sample, the smaller the standard error and the more accurate the estimation. To avoid confusion it is recommended to report no longer the standard error of the mean but instead the confidence intervals of the mean to estimate the true value of the mean.

Confidence Intervals↗
PubMed2005

The effect of intraspecific sample size on type I and type II error rates in comparative studies.

Comparative studies have increased greatly in number in recent years due to advances in statistical and phylogenetic methodologies. For these studies, a trade-off often exists between the number of species that can be included in any given study and the number of individuals examined per species. Here, we describe a simple simulation study examining the effect of intraspecific sample size on statistical error in comparative studies. We find that ignoring measurement error has no effect on type I error of nonphylogenetic analyses, but can lead to increased type I error under some circumstances when using independent contrasts. We suggest using ANOVA to evaluate the relative amounts of within- and between-species variation when considering a phylogenetic comparative study. If within-species variance is particularly large and intraspecific sample sizes small, then either larger sample sizes or comparative methods that account for measurement error are necessary.

Biological Evolution↗
PubMed2004

Distortion-free single point imaging of multi-layered composite sandwich panel structures.

The results of a magnetic resonance imaging (MRI) investigation concerning the effects of an aluminum honeycomb sandwich panel on the B1 and B0 fields and on subsequent image quality are presented. Although the sandwich panel structure, representative of an aircraft composite material, distorts B0 and attenuates B1, distortion-free imaging is possible using single point (constant time) imaging techniques. A new expression is derived for the error caused by gradient field distortion due to the heterogeneous magnetic susceptibility within a sample and this error is shown not to cause geometric distortion in the image. The origin of the B0 distortion in the sample under investigation was also examined. The graphite-epoxy 'skin' of the panel is the principal source of the B0 distortion. Successful imaging of these structures sets the stage for the development of methods for detecting moisture ingress and degradation within composite sandwich structures.

Journal Article↗
PubMed1994

Optimal data acquisition for volumetric intracoronary ultrasound.

Three-dimensional analysis using intracoronary ultrasound (ICUS) pull-back data provides the unique ability to quantitate lumen and atherosclerotic plaque volumes. Optimal data acquisition parameters for volumetric acquisition were established using simulations on computer phantoms of stenotic arteries. Eleven computer phantoms were generated using cross-sectional area data from quantitative angiography of stenotic coronary arteries. Three methods of data acquisition were simulated: conventional manual pull-back; motorized pull-back; and manual pull-back with measured displacement. Effects of pull-back velocity and cardiac gating on cross-sectional area profiles and volumes were studied. Cardiac gating eliminated errors introduced by vessel deformation within a cardiac cycle. With cardiac gating, pull-backs with mean velocities up to 1.2 mm/sec allowed reconstruction of cross-sectional area profiles within 5% RMS error. With faster pull-backs, cardiac gating resulted in sparse spatial sampling and significant errors in cross-sectional area profiles. The accuracy of both motorized and measured required equal displacements of the catheter proximal and distal ends. This assumption was validated with in vitro experiments where X-ray fluoroscopy was used to measure the displacement of the imaging tip. Excellent correlation was found between the two displacements (r = 0.99). Finally, slow pull-backs were performed by 3 operators, and pull-back velocities were measured. It was found that mean pull-back velocities as low as 0.8 mm/sec were achievable. From our simulations, we predict that accurate volumetric analysis requires cardiac gated, calibrated, slow (< 1.2 mm/sec) pull-backs.

Calibration↗
PubMed1995

The Beck Depression Inventory: testing and cross-validating a second-order factorial structure for Swedish nonclinical adolescents.

The intent of the present study was to test for the validity and equivalency of a second-order factorial structure of the Beck Depression Inventory for and across three independent samples (n1 = 661; n2 = 239; n3 = 196) of nonclinical Swedish adolescents. The model under study derived from a cross-validated study of Canadian high school adolescents. Model fitting, testing and equating were based on the analysis of covariance structures within the framework of a confirmatory factor analytic model. Of major importance was the tenability of the hypothesized model for Swedish adolescents. Only minor differences where found among samples, which involved correlated errors and one cross-loading (Sample 2). Results are expected to be of substantial interest to both researchers and clinicians whose concerns focus on depression as it bears on this population.

Adolescent↗