Nonrandom Errors Research Articles

Population substructure in Finland and Sweden revealed by the use of spatial coordinates and a small number of unlinked autosomal SNPs

BackgroundDespite several thousands of years of close contacts, there are genetic differences between the neighbouring countries of Finland and Sweden. Within Finland, signs of an east-west duality have been observed, whereas the population structure within Sweden has been suggested to be more subtle. With a fine-scale substructure like this, inferring the cluster membership of individuals requires a large number of markers. However, some studies have suggested that this number could be reduced if the individual spatial coordinates are taken into account in the analysis.ResultsWe genotyped 34 unlinked autosomal single nucleotide polymorphisms (SNPs), originally designed for zygosity testing, from 2044 samples from Sweden and 657 samples from Finland, and 30 short tandem repeats (STRs) from 465 Finnish samples. We saw significant population structure within Finland but not between the countries or within Sweden, and isolation by distance within Finland and between the countries. In Sweden, we found a deficit of heterozygotes that we could explain by simulation studies to be due to both a small non-random genotyping error and hidden substructure caused by immigration. Geneland, a model-based Bayesian clustering algorithm, clustered the individuals into groups that corresponded to Sweden and Eastern and Western Finland when spatial coordinates were used, whereas in the absence of spatial information, only one cluster was inferred.ConclusionWe show that the power to cluster individuals based on their genetic similarity is increased when including information about the spatial coordinates. We also demonstrate the importance of estimating the size and effect of genotyping error in population genetics in order to strengthen the validity of the results.

Quantification of the function of the left ventricle using 2-dimensional echocardiography

Left ventricular volumes and the ejection fraction can be determined by two-dimensional echocardiography. Because of methodological problems, cineventriculographic normal values can not be transferred to two-dimensional echocardiography. Therefore, normal values for two-dimensional echocardiographically determined left ventricular volumes and the ejection fraction were established in 55 normal controls. Basing on these volumes, the sensitivity and specificity of two-dimensional echocardiography for detection of impaired left ventricular function was analysed and compared with results from cineventriculography. Sensitivity for detection of a reduced ejection fraction was 84%, specificity 89% and predictive accuracy 98%. Thus, two-dimensional echocardiography can be used as a screening method for analysing left ventricular function. Analysis of beat-to-beat variation revealed that for two-dimensional echocardiography 3 consecutive beats should be analysed because evaluation of 5 instead of 3 beats increased reliability only by less than 1%. It was necessary to analyse the day-to-day variations. To separate a random error from a non-random error for an individual change, an absolute change of volumes of more than 10-12% and of ejection fraction of more than 10% had to be observed. Group changes can of course be smaller and yet significant. Intraobserver variation was not significant and below 5%. However, interobserver variability must be considered. This depends on observer experience. For a 4-chamber view no significant variability was observed, but for the RAO-equivalent view the observer variation was significant for end-diastolic and end-systolic volume. For the ejection fraction no significant difference was found. Two-dimensional echocardiography can be used for pharmacodynamic studies if percentage changes instead of absolute changes are listed.

The effect of reporting errors on the cross-country relationship between inequality and crime

This paper analyzes reporting errors in crime data to see how they impact econometric estimates, particularly of the key relationship between inequality and crime. Criminal victimization surveys of 140,000 respondents in 37 industrial, transition and developing countries are used. Comparing the crimes experienced by these respondents with those reported to the police, non-random and mean-reverting errors are apparent. Time-varying factors affect the propensity of victims to report crimes to the police, undermining the use of country-specific fixed effects as a means of dealing with measurement error in official crime data. These errors substantially attenuate both cross-sectional and panel estimates of the partial correlation between inequality and crime.

A note on non-random error structure in trawl survey abundance indices

Abstract Cordue, P. L. 2007. A note on non-random error structure in trawl survey abundance indices. – ICES Journal of Marine Science, 64: 1333–1337. Trawl survey time-series are routinely used in stock assessments to provide indices of relative abundance. There is the general assumption, for each year y, that the expected value of the trawl survey index (Xy) is related to the biomass (By) by a single proportionality constant q: E(Xy) = qBy. In reality, the constant q varies due to many factors. An important factor, which is almost always ignored, is the role that non-trawlable ground can play in the variation of q. A general formula is derived for the q of a stratified random trawl survey. When the survey area contains non-trawlable ground, strata-specific data on the proportion of non-trawlable ground and on the preference of the species for trawlable/non-trawlable ground is required to weight stratum estimates correctly. In the absence of the correct stratum weights, a shift in the spatial distribution of the stock can combine with differing proportions of non-trawlable ground to introduce non-random error and possibly spurious trends into biomass indices. Each survey and species/stock should be considered on a case-by-case basis. A stratum-specific assessment of the proportion of non-trawlable ground is a pre-requisite for the production of trawl survey biomass indices.

A Psychometric Toolbox for Testing Validity and Reliability

To review the concepts of reliability and validity, provide examples of how the concepts have been used in nursing research, provide guidance for improving the psychometric soundness of instruments, and report suggestions from editors of nursing journals for incorporating psychometric data into manuscripts. CINAHL, MEDLINE, and PsycINFO databases were searched using key words: validity, reliability, and psychometrics. Nursing research articles were eligible for inclusion if they were published in the last 5 years, quantitative methods were used, and statistical evidence of psychometric properties were reported. Reports of strong psychometric properties of instruments were identified as well as those with little supporting evidence of psychometric soundness. Reports frequently indicated content validity but sometimes the studies had fewer than five experts for review. Criterion validity was rarely reported and errors in the measurement of the criterion were identified. Construct validity remains underreported. Most reports indicated internal consistency reliability (alpha) but few reports included reliability testing for stability. When retest reliability was asserted, time intervals and correlations were frequently not included. Planning for psychometric testing through design and reducing nonrandom error in measurement will add to the reliability and validity of instruments and increase the strength of study findings. Underreporting of validity might occur because of small sample size, poor design, or lack of resources. Lack of information on psychometric properties and misapplication of psychometric testing is common in the literature.

Measurement Error in Recall Surveys and the Relationship between Household Size and Food Demand

Variation in household survey design and implementation is used to obtain evidence of nonrandom measurement error in recall surveys of household expenditure. These surveys, which are used especially in developing countries, appear to have measurement errors in food expenditures and in food budget shares that are correlated with household size. These correlated errors may be part of the explanation for a puzzling pattern of falling food demand with rising household size in poorer countries.

Measuring Exposure to Political Advertising in Surveys

Research on the influence of negative political advertising in America is characterized by fundamentally conflicting findings. In recent years, however, survey research using estimates of exposure based on a combination of self-reported television viewing habits and Campaign Media Analysis Group data (a database of all advertisements broadcast on national and cable television in the top 75 media markets) has argued that exposure to negative political advertising boosts interest in the campaign and turnout. This paper examines the measurement properties of self-reports of television viewing. I argue that the errors from common survey formats may both be nonrandom and larger than previously acknowledged. The nonrandom error is due to the tendency of politically knowledgeable individuals to be more sensitive to question format. Thus the inferences drawn about the relationship between political knowledge, exposure to negative ads, and political behavior are also sensitive to the measures used to estimate exposure. I demonstrate, however, that one commonly used measure of exposure—the log of estimated exposure—is not only more theoretically defensible but also alleviates some of the more serious problems due to measurement error.

GEL: a novel genotype calling algorithm using empirical likelihood

Preliminary results on the data produced using the Affymetrix large-scale genotyping platforms show that it is necessary to construct improved genotype calling algorithms. There is evidence that some of the existing algorithms lead to an increased error rate in heterozygous genotypes, and a disproportionately large rate of heterozygotes with missing genotypes. Non-random errors and missing data can lead to an increase in the number of false discoveries in genetic association studies. Therefore, the factors that need to be evaluated in assessing the performance of an algorithm are the missing data (call) and error rates, but also the heterozygous proportions in missing data and errors. We introduce a novel genotype calling algorithm (GEL) for the Affymetrix GeneChip arrays. The algorithm uses likelihood calculations that are based on distributions inferred from the observed data. A key ingredient in accurate genotype calling is weighting the information that comes from each probe quartet according to the quality/reliability of the data in the quartet, and prior information on the performance of the quartet. The GEL software is implemented in R and is available by request from the corresponding author at nicolae@galton.uchicago.edu.

Hardy–Weinberg disequilibrium identified genotyping error of the serotonin transporter (SLC6A4) promoter polymorphism

We analyzed the putative functional promoter polymorphism of the serotonin transporter (5-HTTLPR) in two large autism spectrum disorder samples and a control sample. A Hardy-Weinberg disequilibrium was detected for 5-HTTLPR in the unaffected founders of both autism spectrum disorder samples and control samples. When we lowered the total magnesium concentration in the polymerase chain reaction below levels reported in previously published studies, we observed a shift in relative allele frequencies and restoration of the Hardy-Weinberg equilibrium. Our data suggest that higher magnesium concentrations caused allele-dependent, non-random genotyping errors. Genotyping data obtained from the 2 mM magnesium protocol increased the significance of linkage and gave suggestive (P=0.06) association with autism spectrum disorder, whereas the corrected genotypes of 5-HTTLPR provide no linkage information beyond the results we have previously published and no evidence of association with autism spectrum disorder. We present details regarding appropriate polymerase chain reaction conditions for the accurate genotyping of this polymorphism.

Digital venous photoplethysmography in the seated position is a reproducible noninvasive measure of lower limb venous function in patients with isolated superficial venous reflux

The value of photoplethysmography (PPG) has been questioned because of a lack of reproducibility. We performed this study to determine whether new digital technology has improved the reproducibility of PPG in the noninvasive assessment of lower limb venous function in patients with isolated superficial venous reflux. This was a prospective study of 140 legs in 110 patients (65% female; median age [interquartile range], 45 years [36-59.25 years]; CEAP clinical grade C2/3, n = 114; C4-6, n = 26) who underwent repeated digital PPG measurements of refilling time (RT) in both the sitting and standing position after standard exercise regimens by a single observer. RT was measured in all patients 2 to 5 minutes apart and in a randomly selected subgroup of 30 patients (38 limbs) 1 to 2 weeks apart. RT variability was assessed by using Bland and Altman's coefficient of repeatability (CR-RT), where the CR-RT was 1.96 times the standard deviation of the mean difference in RT between two tests. Venous duplex scanning of both the deep and superficial veins was also performed, and a reverse flow of greater than 0.5 seconds was considered abnormal. Only patients with isolated superficial venous reflux were included in the study. The CR-RT of the tests on 140 limbs performed 2 to 5 minutes apart was 10 seconds overall, 3 seconds for RT up to 10 seconds, and 16 seconds for RT between 20 and 40 seconds. The CR-RT of the 38 tests performed 1 to 2 weeks apart was also 10 seconds. No systematic variation due to a nonrandom error was found between the measurements performed either 2 to 5 minutes or 1 to 2 weeks apart. Digital PPG performed in the seated position in patients with isolated superficial venous reflux provides a reproducible method for the noninvasive assessment of lower limb venous function for both clinical and research purposes. However, the variation in precision of RT with the magnitude of the measurement must be taken into account when results are interpreted in individual patients.

A sensitivity analysis of a randomized controlled trial of zinc in treatment of falciparum malaria in children

Background The randomized trial has long been recognized as a means to assess the efficacy of new interventions, because the investigator can reduce or eliminate many sources of error. As such, clinical trials often do not include quantitative assessments of the extent that systematic error could affect their results. We examined the impact of different sources of bias on a randomized controlled trial of the efficacy of zinc as an adjuvant to malaria therapy in reducing time to total parasite clearance. Methods Using data from a previously published study, we identified two sources of bias and used the sensitivity analysis technique developed by Lash and Fink to assess the impact of each source of bias on the outcome. Results After correcting for each source of bias and reincorporating random error into our results, the point estimate of effect comparing those who received placebo to those who received zinc changed slightly (SMR changed from 0.92 to 0.90) but the 95% interval increased 22% (changing from 0.73–1.16 in the conventional analysis to 0.65–1.26 in the sensitivity analysis). Conclusions The findings of this sensitivity analysis serve as a reminder that the frequentist confidence interval underestimates the total error, even in a randomized controlled trial. Authors of randomized controlled trial investigations ought to conduct a complete assessment of the impact of potential sources of bias in their studies. CONSORT guidelines for reporting trial results should be updated to encourage authors to assess the impact of non-random errors on their studies.

Random and Non-Random Uncertainties in Precision GPR Measurements: Identifying and Compensating for Instrument Drift

The precision of ground penetrating radar (GPR) data is of increasing interest, as the technology finds ever increasing applications to near surface geophysical studies. Our group has undertaken a series of studies to identify the precision and accuracy with which GPR traveltimes, velocities and interval properties can be estimated under controlled conditions, recently reporting that random errors in two-way traveltime and velocity are on the order of ±0.7 ns and ±0.001 m/ns, respectively, at the 95% confidence level. The high degree of precision in that dataset makes it possible to observe non-random patterns in the independent estimates of the same parameter, suggesting possible systematic biases in the data. One source of systematic error that workers often encounter is the effect of back-scattering from above ground features. Another that we documented in our previous study is that the material properties of the subsurface may change from one survey to the next. A third possibility is non-random instrumentation error, one source of which, and the focus of the present report, is a variation in the time base. We address ways to identify its presence, to assess its influence on estimating GPR parameters, and how and when to compensate for its effects. Using a static transmitter (Tx) and receiver (Rx) offset to record a series of GPR traces over a nominal period of one hour, we find that time base drift can be significant for up to 25 min after turning on the instrument. Fortunately, the type of drift that we have found to be most apparent—time zero drift—can be readily identified and compensated for, if one employs the air phase at a number of Tx–Rx offsets. An invariant condition in a GPR survey is that the true velocity of the direct air phase should be the velocity of an electromagnetic pulse in free space. Thus, upon carefully determining the observed velocity of the air phase, and using the ratio between it and the true value of 0.29979 m/ns, one can correct the entire time base of a radargram. Guidelines for when to apply the air phase compensation technique are based on whether the observed velocity of the air phase falls outside the limits of an acceptable precision under the most ideal circumstances. We illustrate the compensation procedure using two CMPs collected on different days at the same survey position. Analyzing the uncompensated data unsurprisingly yields two different subsurface velocities, however the depth estimates of the same subsurface reflector differ by 0.5 m, which for this site is physically unlikely. The difference between the observed and the true air phase velocities for both data sets exceeded the minimum expected error according to our guidelines, thus after applying our time base correction, the difference between the depth estimates improves to 0.05~m.

Sources of Non-Random Error in the Self-Report of Physical Activity

Sources of Non-Random Error in the Self-Report of Physical Activity

Sources of Non-Random Error in the Self-Report of Physical Activity

Sources of Non-Random Error in the Self-Report of Physical Activity

The assessment of subjective well-being (issues raised by the Oxford Happiness Questionnaire)

This commentary raises conceptual issues related to recent efforts to develop measures of subjective well-being (SWB). Specifically, Hills’ and Argyle's (2002) article on the development of the 29-item Oxford Happiness Questionnaire (OHQ), and its predecessor, the 20-item Oxford Happiness Inventory (Argyle, Martin & Crossland, 1989). Instead of assessing the structure of subjective well-being (SWB), items of the OHQ tap into self-esteem, sense of purpose, social interest and kindness, sense of humor, and aesthetic appreciation. The item content of the OHQ fails to differentiate the assessment of SWB from the predictors, correlates, and consequences of SWB. In contrast to published SWB findings with other measures, data are presented suggesting that the OHQ has artificially inflated correlations with those constructs tapped by the OHQ: self-esteem, sense of purpose, and social interest/extraversion. The operationalization of SWB by the OHQ is not based on relevant definition and theory and appears to invite nonrandom error into the study of SWB. The article concludes with an appeal for the use of more stringent conceptual and analytic approaches.

Learning from Their Mistakes: Glimpses of symbolic functioning in two-and-a-half to three-year-old children

In this cross-sectional study done in the United States, 19 female and 17 male children ( N =36) ranging in age from 30- to 36-months ( M =33 months, 8 days) were presented with two different search and retrieval type problems to solve. Examination of the data revealed clear age-related differences between children who fluidly and efficiently problem solve using symbolically mediated knowledge and those who do not. Younger children tended to rely on a trial and error, motor-based strategy for solving the problems presented, whereas older children consistently used symbolic strategies. This conclusion supports findings from other similar studies. Further analyses of the data, however, revealed an interesting phenomenon in the form of a patterned, non-random error. This error pattern, a perseverative-type error, and the other problem-solving strategies used by the two-year-olds and young threes in this study offer insight into how young children become efficient users of symbols. Facilitating the development of symbolic problem solving in young children is discussed.

Identification of Special Patterns of Numerical Typographic Errors Increases the Likelihood of Finding a Misplaced Patient File

When a typographic error of a patient identification number occurs on a patient document such as an envelope for radiology films or the cover of a patient record, it will result in misplacement of the document. Once misplaced, such documents are often extremely difficult to recover. After analyzing 290 numerical typos, we found that errors do not occur randomly. Instead, many of the typos share certain specific patterns. Six major types of non-random numeral typographic error patterns have been identified and their frequency characterized. Knowing these patterns and their odds increases the likelihood of finding a misplaced file. In addition, awareness of these patterns during transcribing or writing a patient ID may decrease the chance of typographic errors.

On the role of non-random errors in inverse problems in radiative transfer and other applications

The inverse solution of the radiative transfer equation—which here serves as an example for the more general case of multi-dimensional inverse problems—is affected by measurement noise and by uncertain model parameters. We propose to transform the model parameter uncertainties into the measurement domain and include related signal uncertainties in the measurement covariance matrix. The solution of the inverse problem where the Jacobian is weighted by this extended covariance matrix rather than by the pure measurement covariance matrix is shown to be equivalent to an optimal estimation solution where the uncertain parameter is treated as an additional unknown parameter. The advantage of the proposed approach is that, contrary to the optimal estimation approach, the number of fit variables does not increase with the number of uncertain model parameters.

Nonrandom quantization errors in timebases

Timebase distortion causes nonlinear distortion of waveforms measured by sampling instruments. When such instruments are used to measure the RMS amplitude of the sampled waveforms, such distortions result in errors in the measured RMS values. This paper looks at the nature of the errors that result from nonrandom quantization errors in an instrument timebase circuit. Simulations and measurements on a sampling voltmeter show that the errors in measured RMS amplitude have a nonnormal probability distribution, such that the probability of large errors is much greater than would be expected from the usual quantization noise model. A novel timebase compensation method is proposed which makes the measured RMS errors normally distributed and reduces their standard deviation by a factor of 25. This compensation method was applied to a sampling voltmeter and the improved accuracy was realized.

To Balance or not to Balance: Confirmatory Factor Analysis of the Affect-Balance Scale

This study examined the psychometric quality of the Affect-Balance Scale (ABS) (Bradburn, 1969) using data collected from 292 middle-aged and older adults, living independently. The dimensionality of the scale was examined, the quality of individual items was tested, and the validity of the ABS was studied. Using a tetrachoric correlation matrix with the robust weighted least squares (WLSMV) estimation method of the Mplus program, we found that two moderately correlated (r = -0.37) constructs are needed to adequately account for the pattern of item scores in the ABS. Two of the 10 ABS items were found to be problematic. When raw sum scores were used in analysis, the correlation between the positive-affect and the negative-affect subscales was lower (r = -0.17), indicating that random and nonrandom measurement error masked the relationship between the two. While affect-balance correlated substantially with five criterion well-being measures, the negative-affect subscale (which constitutes half of the ABS) had a similar pattern of correlations, with only slightly lower magnitude. The theoretical construct of nobreak 'balance' is also questioned. The 'balance' scoring method (subtracting the negative-affect subscale score from the positive-affect subscale score) nets exactly the same score as does summing scores from both subscales together. Accordingly, the summed scores have the very same correlations with other variables as do the balance scores.