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PubMed1983

Standard sera in solid-phase immunoassays.

Solid-phase immunoassay-derived antibody titers are often converted to weight unit concentrations with the aid of standard sera containing known antibody concentrations. Systematic studies justifying this procedure have not yet been published. We therefore investigated the magnitude of errors associated with this conversion. Antibody concentrations of thirteen sera or ascites fluids were determined by quantitative precipitation or equilibrium dialysis, and one was then used as a "standard antibody" for the others in solid-phase radioimmunoassay (SP-RIA) or enzyme-linked immunosorbent (ELISA) assays. Antibody concentrations determined by the conventional solid-phase assay (the "standard serum" has the same specificity as the "sample") had up to fourfold errors. These errors could be reduced by basing the conversion on the combination of two standard sera instead of one. The possibility was studied of whether the conversion to weight units could be done with the aid of a standard serum directed to a different antigen than the sample antibody. Errors associated with the use of such a heterologous standard were not significantly greater than those found using the conventional conversion. A combination of two reference sera again reduced the errors. The use of such heterologous standard(s), however, requires checking the binding capacity of the antigen coats.

Animals↗
PubMed1987

Parallel forms of the Knowledge of Behavioral Principles as Applied to Children questionnaire: an independent, multi-centred, British replication.

The psychometric properties of the test entitled Knowledge of Behavioral Principles as Applied to Children and two shortened forms of this test were investigated in two samples of British subjects. The first consisted of 162 psychiatric nurses, psychiatrists, occupational therapists, physiotherapists and clinical psychologists attending behaviour modification courses. The second consisted of 49 teachers and nurses, all working with the mentally retarded, who completed the test by post. The whole test and the two sets of parallel forms all showed good internal consistency and sensitivity to change. Some shrinkage during replication was found. The 25-item forms showed evidence of the properties of parallel forms (equal means, standard deviations and standard errors) in both samples. The 10-item forms were also parallel in sample 1. However the 10-item forms did not remain parallel in sample 2 and so cannot always be recommended.

Behavior Therapy↗
PubMed2002

Influence of delayed isotopic equilibration in urine on the accuracy of the (2)H(2)(18)O method in the elderly.

Isotopic determination of total energy expenditure (TEE) by the doubly labeled water (DLW) method may be affected by urine retention in the elderly. The isotopic enrichments in urine and plasma sampled simultaneously 4 h post-DLW dose were compared in a subset of 281 subjects [139 women, 142 men, 75 +/- 3 (SD) yr] of the 3,075 participants in the Health, Aging, and Body Composition study. Based on analytic precisions, a +/- 2% urine-plasma difference was set as the cut-off value. Ten percent of the population presented a difference lower than -2%, suggesting a delay in urine isotopic equilibration. This -13 +/- 10% urine-plasma difference was not linked to analytic errors, illnesses, the sampling time, or the time and quantity of water intake, suggesting that urine retention may be the main factor. The consequences are an 18 +/- 13 and 21 +/- 16% overestimation of the total body water and the TEE, respectively. Unexpectedly, 21% of the population presented a urine-plasma difference higher than +/- 2% that resulted, however, in a nonsignificant TEE underestimation of -3 +/- 5%. In conclusion, the delayed isotopic equilibration observed in urine reduces the accuracy of the DLW method in the elderly. It is recommended, when blood sampling is impossible, to adopt the intercept method with urine sampling 24 h postdose.

Aged↗
PubMed2004

Sample size for detecting differentially expressed genes in microarray experiments.

BACKGROUND: Microarray experiments are often performed with a small number of biological replicates, resulting in low statistical power for detecting differentially expressed genes and concomitant high false positive rates. While increasing sample size can increase statistical power and decrease error rates, with too many samples, valuable resources are not used efficiently. The issue of how many replicates are required in a typical experimental system needs to be addressed. Of particular interest is the difference in required sample sizes for similar experiments in inbred vs. outbred populations (e.g. mouse and rat vs. human). RESULTS: We hypothesize that if all other factors (assay protocol, microarray platform, data pre-processing) were equal, fewer individuals would be needed for the same statistical power using inbred animals as opposed to unrelated human subjects, as genetic effects on gene expression will be removed in the inbred populations. We apply the same normalization algorithm and estimate the variance of gene expression for a variety of cDNA data sets (humans, inbred mice and rats) comparing two conditions. Using one sample, paired sample or two independent sample t-tests, we calculate the sample sizes required to detect a 1.5-, 2-, and 4-fold changes in expression level as a function of false positive rate, power and percentage of genes that have a standard deviation below a given percentile. CONCLUSIONS: Factors that affect power and sample size calculations include variability of the population, the desired detectable differences, the power to detect the differences, and an acceptable error rate. In addition, experimental design, technical variability and data pre-processing play a role in the power of the statistical tests in microarrays. We show that the number of samples required for detecting a 2-fold change with 90% probability and a p-value of 0.01 in humans is much larger than the number of samples commonly used in present day studies, and that far fewer individuals are needed for the same statistical power when using inbred animals rather than unrelated human subjects.

Animals↗
PubMed2005

Phase retrieval errors in standard Fourier fringe analysis of digitally sampled model interferograms.

We investigate the reliability of phase retrieval by use of the fringe Fourier analysis method for measuring the displacements of facets during the growth of equilibriumlike-shaped crystals. The mean phase change between two successive interferometric images contains an inherent error that emerges from the noninteger number of fringes in the image field. The magnitude of the retrieved phase error of the ideal fringe pattern is investigated as a function of spatial carrier frequency, of the initial phase setting, and of the deviation of the number of fringes from the nearest integer value. The suggested modified algorithm suppresses the error more than threefold.

Journal Article↗
PubMed2002

Human factors in aviation crashes involving older pilots.

BACKGROUND: Pilot errors are recognized as a contributing factor in as many as 80% of aviation crashes. Experimental studies using flight simulators indicate that due to decreased working memory capacity, older pilots are outperformed by their younger counterparts in communication tasks and flight summary scores. OBJECTIVE: This study examines age-related differences in crash circumstances and pilot errors in a sample of pilots who flew commuter aircraft or air taxis and who were involved in airplane or helicopter crashes. METHODS: A historical cohort of 3306 pilots who in 1987 flew commuter aircraft or air taxis and were 45-54 yr of age was constructed using the Federal Aviation Administration's airmen information system. Crash records of the study subjects for the years 1983-1997 were obtained from the National Transportation Safety Board (NTSB) by matching name and date of birth. NTSB's investigation reports were reviewed to identify pilot errors and other contributing factors. Comparisons of crash circumstances and human factors were made between pilots aged 40-49 yr and pilots aged 50-63 yr. RESULTS: A total of 165 crash records were studied, with 52% of these crashes involving pilots aged 50-63 yr. Crash circumstances, such as time and location of crash, type and phase of flight, and weather conditions, were similar between the two age groups. Pilot error was a contributing factor in 73% of the crashes involving younger pilots and in 69% of the crashes involving older pilots (p = 0.50). Age-related differences in the pattern of pilot errors were statistically insignificant. Overall, 23% of pilot errors were attributable to inattentiveness, 20% to flawed decisions, 18% to mishandled aircraft kinetics, and 18% to mishandled wind/runway conditions. CONCLUSIONS: Neither crash circumstances nor the prevalence and patterns of pilot errors appear to change significantly as age increases from the 40s to the 50s and early 60s.

Accidents, Aviation↗
PubMed1993

Species identification and determination of high-level aminoglycoside resistance among enterococci. Comparison study of sterile body fluid isolates, 1985-1991.

Enterococcus spp. have become the third most common cause of nosocomial infections. High-level aminoglycoside resistance (HLR), an important clinical concern, has been associated with some species of the enterococci. We evaluated the Vitek and API 20S systems for species identification and the Vitek for the detection of HLR. Enterococci from nosocomial infections (208 strains) at the University of Iowa Hospital (1985-1991) were tested by Vitek, API 20S, and reference methods. The error rate for species identification was 6.7% for the API 20S and 5.8% for the Vitek Gram-positive identification (GPI) cards. Both systems tended to incorrectly identify other enterococcal species as Enterococcus faecium. HLR was found in Enterococcus faecalis and E. faecium isolates only. The highest rates of HLR to streptomycin alone (17.9%) and with gentamicin (13.5%) was observed among E. faecalis strains, and to gentamicin alone (7.3%) was found among E. faecium isolates. No apparent differences in HLR rates were found from year-to-year over the 7-year enterococcus sample interval. Susceptibility errors for Vitek were among the streptomycin tests only. Our results demonstrated acceptable performance by the Vitek cards for enterococcal species identification and the detection of HLR. API 20S also provided an acceptable ability to speciate the enterococci within its data base, however, both systems must be improved by adding other clinical important Enterococcus species.

Aminoglycosides↗
PubMed1988

The determination of extracellular fluid volume in whole dental plaque using potassium- or chloride-selective micro-electrodes.

This paper describes a procedure for the determination of the volume of water available for diffusion in whole plaque samples collected from single sites. In this procedure, known micro volumes of H2O were added to single-site plaque samples with calibrated nanoliter pipettes and the potassium or chloride concentration at each dilution measured with ion-selective micro-electrodes. By plotting the inverse of the concentration versus the volume of H2O added, one can determine the original volume of plaque fluid available for diffusion. Volumes determined in simultaneous measurements performed with chloride and potassium micro-electrodes were statistically indistinguishable. From the observed constancy in the initial potassium concentration in rat and human plaque fluid, a simplified macro method is suggested which allows for estimation of the extracellular fluid volume within 20% error in plaque samples.

Animals↗
PubMed1997

Analysis of donor splice sites in different eukaryotic organisms.

We present here a new algorithm for functional site analysis. It is based on four main assumptions: each variation of nucleotide composition makes a different contribution to the overall binding free energy of interaction between a functional site and another molecule; nonfunctioning site-like regions (pseudosites) are absent or rare in genomes; there may be errors in the sample of sites; and nucleotides of different site positions are considered to be mutually dependent. In this algorithm, the site set is divided into subsets, each described by a certain consensus. Donor splice sites of the human protein-coding genes were analyzed. Comparing the results with other methods of donor splice site prediction has demonstrated a more accurate prediction of consensus sequences AG/GU(A,G), G/GUnAG, /GU(A,G)AG, /GU(A,G)nGU, and G/GUA than is achieved by weight matrix and consensus (A,C)AG/GU(A,G)AGU with mismatches. The probability of the first type error, E1, for the obtained consensus set was about 0.05, and the probability of the second type error, E2, was 0.15. The analysis demonstrated that accuracy of the functional site prediction could be improved if one takes into account correlations between the site positions. The accuracy of prediction by using human consensus sequences was tested on sequences from different organisms. Some differences in consensus sequences for the plant Arabidopsis sp., the invertebrate Caenorhabditis sp., and the fungus Aspergillus sp. were revealed. For the yeast Saccharomyces sp. only one conservative consensus, /GUA(U,A,C)G(U,A,C), was revealed (E1 = 0.03, E2 = 0.03). Yeast is a very interesting model to use for analysis of molecular mechanisms of splicing.

Algorithms↗
PubMed1998

Agglutination behavior of mesophilic starter cultures as a function of proteolysis.

Seven mesophilic starter cultures were grown separately in sterilized skim milk for 8 h at 25 degrees C. At the end of the incubation period, samples were analyzed for agglutination behavior by using microscopic examination. Samples were also assayed for proteolytic activity by the spectrophotometric o-phthaldialdehyde (OPA) and trinitrobenzenesulfonic acid (TNBS) methods. This experiment was replicated three times in a randomized block design. Microscopic examination showed that some cultures existed as single cells, diplococci, or short chains; other cultures tended to form long chains. Short-chain-forming cultures had high proteolytic activities, whereas long-chain-forming cultures had low proteolytic activities as measured by the TNBS and OPA methods. Proteolysis measured by both methods ranked starter cultures in the same order (R2 = 0.82). Low detectability values (obtained by dividing the standard error of the sample estimate for each method by its slope ratio) for OPA and TNBS methods indicated that the two assays do not differ significantly (P > 0.05).

Agglutination↗
PubMed2001

Uncertainties of Monod kinetic parameters nonlinearly estimated from batch experiments.

Monod kinetic parameters (Ks, micromax, and Y) that are estimated from batch experimental data can have large uncertainties due to linear correlations between them. The degree of correlation and the resulting uncertainties of the Monod parameters are functions of the initial experimental conditions, the values of the parameters, the type and magnitude of measurement errors, and the sampling number. Careful manipulation of experimental conditions can reduce the correlations between Monod parameters allowing for the estimation of Monod kinetic parameters with the lowest degree of uncertainty. By dimensionless analysis, the correlation and relative standard deviations of Monod parameters were found to be functions of a few dimensionless variables involving the initial substrate (S0) and cell (X0) concentrations. Quantitative relationships were analyzed between the dimensionless variables and the correlation and the uncertainties of the Monod parameters. This analysis allowed for identification of the optimal experimental conditions for estimating Monod parameters under both no growth and growth conditions coupled with two kinds of measurement errors: those with constant absolute standard deviation and those with constant relative standard deviation. Examples involving the microbial reduction of iron(III) as an electron acceptor are used to illustrate the application of the developed technique.

Cell Division↗
PubMed1996

Technetium-99m L,L-ethylenedicysteine clearance and correlation with iodine-125 orthoiodohippurate for the determination of effective renal plasma flow.

Technetium-99m L,L-ethylenedicysteine (99mTc-L,L-EC) is a new renal tubular tracer that allows the determination of the effective renal plasma flow (ERPF). The aim of this study was to derive simplified methods for the estimation of 99mTc-L,L-EC clearance using one or two plasma samples after bolus injection. Fifty-nine multiple plasma dual-tracer samples (nine samples from 5 to 120 min after injection) were obtained after injection of kit-formulated 99mTc-L,L-EC and iodine-125 orthoiodohippurate (OIH). The studies were performed in 25 stable and 24 unstable transplant recipients, in five patients with renal insufficiency (four on chronic haemodialysis) and in five normal volunteers. This allowed a wide range of renal function values to be covered, with ERPF (estimated by OIH clearance) ranging from 25.4 to 604.0 ml/min. The reference 99mTc-L,L-EC clearance, as calculated from the multisample model, could be estimated from two samples at 15 and 90 min with an error of 11.3 ml/min and from one sample at 90 min with an error of 17.8 ml/min. Using appropriate linear regression analysis, ERPF could be estimated by the two- and one-sample 99mTc-L,L-EC clearance with an error of 24.2 and 22.8 ml/min, respectively. In conclusion, 99mTc-L,L-EC clearance can be accurately estimated by simplified one- or two-sample methods. Moreover, these methods can be used to estimate ERPF with an error that remains acceptable for clinical purposes.

Cysteine↗
PubMed2006

Fruit and vegetable intake and the risk of stomach and oesophagus adenocarcinoma in the European Prospective Investigation into Cancer and Nutrition (EPIC-EURGAST).

It is considered that fruit and vegetable (F&V) protect against oesophagus and gastric cancer (GC). However, 2 recent meta-analyses suggest that the strength of association on GC seems to be weaker for vegetables than for fruit and weaker in cohort than in case-control studies. No evidence exists from cohort studies about adenocarcinoma of oesophagus (ACO). In 521,457 men and women participating in the EPIC cohort in 10 European countries, information of diet and lifestyle was collected at baseline. After an average of 6.5 years of follow-up, a total of 330 GC and 65 ACO, confirmed and classified by a panel of pathologists, was used for the analysis. We examined the relation between F&V intake and GC and ACO. A calibration study in a sub-sample was used to control diet measurement errors. In a sub-sample of cases and a random sample of controls, antibodies against Helicobacter pylori (Hp) were measured and interactions with F&V were examined in a nested case-control study. We observed no association with total vegetable intake or specific groups of vegetables and GC risk, except for the intestinal type, where a negative association is possible regarding total vegetable (calibrated HR 0.66; 95% CI 0.35-1.22 per 100 g increase) and onion and garlic intake (calibrated HR 0.70; 95% CI 0.38-1.29 per 10 g increase). No evidence of association between fresh fruit intake and GC risk was observed. We found a negative but non significant association between citrus fruit intake and the cardia site (calibrated HR 0.77; 95% CI 0.47-1.22 per 100 g increase) while no association was observed with the non-cardia site. Regarding ACO, we found a non significant negative association for vegetable intake and for citrus intake (calibrated HRs 0.72; 95% CI 0.32-1.64 and 0.77; 95% CI 0.46-1.28 per 100 and 50 g increase, respectively). It seems that Hp infection does not modify the effect of F&V intake. Our study supports a possible protective role of vegetable intake in the intestinal type of GC and the ACO. Citrus fruit consumption may have a role in the protection against cardia GC and ACO.

Adenocarcinoma↗
PubMed1997

Systematic and random errors in compression testing of trabecular bone.

We sought to quantify the systematic and random errors associated with end-artifacts in the platens compression test for trabecular bone. Our hypothesis was that while errors may depend on anatomic site, they do not depend on apparent density and therefore have substantial random components. Trabecular bone specimens were first tested nondestructively using newly developed accurate protocols and then were tested again using the platens compression test. Percentage differences in modulus between the techniques (bovine proximal tibia [n = 18] and humerus [n = 17] and human lumbar spine, [n = 9]) were in the range of 4-86%. These differences did not depend on anatomic site (p = 0.21) and were only weakly dependent on apparent density and specimen aspect ratio (r2 < 0.10). The mean percentage difference in modulus was 32.6%, representing the systematic component of the end-artifact error. Neglecting the minor variations explained by density and specimen size (approximately 10%), an upper bound on the random error from end-artifacts in this experiment was taken as the SD of the modulus difference (+/-18.2%). Based on a synthesis of data taken from this study and from the literature, we concluded that the systematic underestimation error in the platens compression test can be only approximated and is in the range of 20-40%; the substantial random error (+/-12.5%) confounds correction, particularly when the sample size is small. These errors should be considered when interpreting results from the platens test, and more accurate testing techniques should be used when such errors are not acceptable.

Animals↗
PubMed2005

Off-resonance rotating-frame amide proton spin relaxation experiments measuring microsecond chemical exchange in proteins.

NMR spin relaxation in the rotating frame (R(1rho)) is a unique method for atomic-resolution characterization of conformational (chemical) exchange processes occurring on the microsecond time scale. Here, we use amide 1H off-resonance R(1rho) relaxation experiments to determine exchange parameters for processes that are significantly faster than those that can be probed using 15N or 13C relaxation. The new pulse sequence is validated using the E140Q mutant of the C-terminal domain of calmodulin, which exhibits significant conformational exchange contributions to the transverse relaxation rates. The 1H off-resonance R(1rho) data sample the entire relaxation dispersion profiles for the large majority of residues in this protein, which exchanges between conformations with a time constant of approximately 20 micros. This is in contrast to the case for 15N, where additional laboratory-frame relaxation data are required to determine the exchange parameters reliably. Experiments were performed on uniformly 15N-enriched samples that were either highly enriched in 2H or fully protonated. In the latter case, dipolar cross-relaxation with aliphatic protons were effectively decoupled to first order using a selective inversion pulse. Deuterated and protonated samples gave the same results, within experimental errors. The use of deuterated samples increases the sensitivity towards exchange contributions to the 1H transverse relaxation rates, since dipolar relaxation is greatly reduced. The exchange correlation times determined from the present 1H off-resonance R(1rho) experiments are in excellent agreement with those determined previously using a combination of 15N laboratory-frame and off-resonance R(1rho) relaxation data, with average values of [see text] and 21 +/- 3 micros , respectively.

Ammonium Chloride↗
PubMed1988

Estimation of extracellular fluid volume from plasma clearance on technetium-99m DTPA by a single-injection, two-sample method.

A simple method is presented for estimating extracellular fluid volume from the plasma clearance of [99mTc])DTPA or [169Yb]DTPA. Two plasma samples are required, at 1 and 3 hr, following a single intravenous injection. (The same plasma samples can be used for measurement of glomerular filtration rate.) Using the complete plasma clearance curve as a reference (eight samples at 10 to 240 min), the error of the two-sample method in 40 patients was 1.5 I for [99mTc]DTPA, 2.1 I for [169Yb]DTPA (residual standard deviation).

Extracellular Space↗
PubMed1997

Asthma in Greenwich, UK: impact of the disease and current management practices.

A great deal of the care of patients with asthma takes place in general practices. The aim of the present study was to describe the impact of asthma in the community and to identify current asthma self-management practices. A two-part questionnaire survey was conducted in a random sample (23%; n=24,398) of persons aged 16-50 yrs, registered with one of the 41 general practices in Greenwich, London, UK. The two parts were: a screening questionnaire identifying persons with current asthma (defined as waking with shortness of breath in the last 12 months, attack of asthma in the last 12 months, or currently taking treatment for asthma); and an asthma questionnaire (completed by those with asthma) assessing quality of life, frequency of asthma symptoms, possession and use of self-management tools, and action in the event of an exacerbation of asthma. The crude response rate was 51%, but this may be an underestimate due to errors in the sampling frame. The prevalences of wheeze and asthma in the past 12 months were 26% and 14%, respectively. Among asthma patients: 43% reported symptoms occurring three or more times per week, and 20% were woken by asthma symptoms on three or more nights per week; most had asthma with a mild impact on quality of life; 26% used inhaled steroids on most days in the preceding month; 16% had a peak flow meter at home; and 7% had oral steroids available. Of the 44% of subjects with asthma, who could identify an exacerbation of asthma in the preceding 6 months: 19% had used a peak flow meter during the episode; 19% had changed their treatment without first being told to do so by a doctor; and 50% had sought urgent medical help. Smokers used less appropriate asthma management and subjects whose asthma had a severe impact on quality of life used more treatment and peak flow monitoring. In conclusion, the prevalence of asthma among adults in Greenwich, UK, has increased since a similar survey in 1986. Many people have fairly mild asthma and a smaller number have severe disease. Much remains to be done to promote appropriate strategies for self-management of asthma exacerbations.

Adolescent↗
PubMed2004

Age estimation from aspartic acid racemization of root dentin by internal standard method.

In this study, we investigated the application of the internal standard method to determine age from aspartic acid (Asp) racemization. D-Methionine (D-Met) and D-norleucine (D-Nleu) were tested as internal standards for the purpose of validating the derivatization and gas chromatographic measurements. Using a set of standard amino acids plus the internal standards in constant volume, calibration plots with reasonable linearity (R > 0.98) were constructed. Based on the analysis of sample chromatograms, D-Met appeared to meet the criteria for internal standards, hence it was selected for use in D- and L-Asp quantification. The correlation between dentin age and D-/L-Asp ratios from the peak areas as well as from the absolute concentrations was investigated. Correlation coefficients were calculated as 0.98 and 0.90, respectively. The slight decrease in accuracy was attributed to the conversion of D-Asp/D-Met ratios to concentrations employing the calibration curves figured from pure Asp. Because the application of the internal standard method produced reproducible and precise measurements, the employment of internal standards in age estimation based on Asp racemization appears to provide quality assurance by avoiding possible errors arising from sample preparation.

Adolescent↗