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PubMedDate not supplied

Enumeration of total aerobic microorganisms in foods by SimPlate Total Plate Count-Color Indicator methods and conventional culture methods: collaborative study.

The relative efficacy of the SimPlate Total Plate Count-Color Indicator (TPC-CI) method (SimPlate 35 degrees C) was compared with the AOAC Official Method 966.23 (AOAC 35 degrees C) for enumeration of total aerobic microorganisms in foods. The SimPlate TPC-CI method, incubated at 30 degrees C (SimPlate 30 degrees C), was also compared with the International Organization for Standardization (ISO) 4833 method (ISO 30 degrees C). Six food types were analyzed: ground black pepper, flour, nut meats, frozen hamburger patties, frozen fruits, and fresh vegetables. All foods tested were naturally contaminated. Nineteen laboratories throughout North America and Europe participated in the study. Three method comparisons were conducted. In general, there was <0.3 mean log count difference in recovery among the SimPlate methods and their corresponding reference methods. Mean log counts between the 2 reference methods were also very similar. Repeatability (Sr) and reproducibility (SR) standard deviations were similar among the 3 method comparisons. The SimPlate method (35 degrees C) and the AOAC method were comparable for enumerating total aerobic microorganisms in foods. Similarly, the SimPlate method (30 degrees C) was comparable to the ISO method when samples were prepared and incubated according to the ISO method.

Bacteria, Aerobic↗
PubMed1997

Methods for comparison of cost data.

BACKGROUND: Researchers are increasingly interested in examining costs of care, and large administrative and clinical databases have made relevant data readily available. Because a few patients incur high costs relative to most patients, the distribution of cost data is often skewed. How robust are the usual methods of cost analysis against the skewed distribution of cost data? OBJECTIVE: To determine the methods commonly used for comparing cost data, describe their limitations, and provide an alternate method of analysis. DESIGN: Review of statistical methods used in studies of medical costs published in medical journals between January 1991 and January 1996. Description of a Z-score method appropriate for testing the equality of mean costs between two log-normal samples; and reanalysis of published two-sample comparison results done by using the Z-score method. RESULTS: For two-sample comparisons, three methods were commonly used: the Student t-test on untransformed costs, the Wilcoxon test on untransformed costs, and the Student t-test on log-transformed costs. The t-test on untransformed costs ignores the skewness in cost data, the Wilcoxon test ignores unequal variances, and the t-test on log-transformed costs tests the wrong null hypothesis unless variances in the log-scale are equal. Eleven articles included two-sample tests and had enough information to allow reanalysis of the data using the Z-score method. These articles described a total of 23 Wilcoxon tests and 24 t-tests on untransformed costs. Most results did not change on reanalysis, but six results changed enough to alter conclusions. Specifically, reanalysis of data for which one Wilcoxon test had shown statistically significant results showed nonsignificant results; reanalysis of data for which two Wilcoxon tests had shown nonsignificant results showed statistically significant results. In articles that used t-tests on untransformed costs, two statistically significant results became nonsignificant on reanalysis and one nonsignificant result became statistically significant on reanalysis. CONCLUSIONS: The methods commonly used to compare costs of two groups have limitations. Some limitations may change some conclusions, and the direction of the change cannot be predicted. The Z-score method is designed to adjust for skewness in cost data and is appropriate for comparing means of log-normally distributed cost data.

Costs and Cost Analysis↗
PubMed2002

Comparison of methods for characterization of reversed-phase liquid chromatographic selectivity.

The goal of the present work is to obtain a better understanding of the chemical factors affecting liquid chromatographic retention. One of the most commonly used formats for liquid chromatographic separations is based on a nonpolar stationary phase, typically an octadecyl-derivatized silica material. A wide variety of these reversed-phase columns are commercially available that differ significantly in their chromatographic retention and selectivity. We seek to quantitatively characterize these differences. Retention data for a range of compounds with many diverse characteristics have been measured on several different octadecyl silica columns (J. Chromatogr. A, submitted for publication). Principal components analysis is used to characterize the different properties of these stationary phases and predict retention factors. The key set factor analysis method and the typical solute method are used in conjunction with the principal components analysis to identify small subsets of solutes that can be used to quantitatively describe the retention of a broad range of compounds. In addition, a quantitative comparison to alternative data analysis methods is made, including linear solvation energy relationships and an iterative subtraction method based on linear regression techniques. Although many earlier studies have reported the application of these methods, this study is the first to make a quantitative comparison of these methods using a highly precise and structurally variable set of test compounds.

Chromatography, Liquid↗
PubMed2002

The hydraulic conductance of the angiosperm leaf lamina: a comparison of three measurement methods.

A comparison was made of three methods for measuring the leaf lamina hydraulic conductance (K(lamina)) for detached mature leaves of six woody temperate angiosperm species. The high-pressure method, the evaporative flux method and the vacuum pump method involve, respectively, pushing, evaporating and pulling water out of the lamina while determining the flow rate into the petiole and the water potential drop across the leaf. Tests were made of whether the high-pressure method and vacuum pump method measurements of K(lamina) on single leaves were affected by irradiance. In Quercus rubra, the high pressure method was sensitive to irradiance; K(lamina) measured under high irradiance (>1200 micro mol m(-2) s(-1 )photosynthetically active radiation) was 4.6-8.8 times larger than under ambient laboratory lighting (approximately 6 micro mol m(-2) s(-1 )photosynthetically active radiation). By constrast, the vacuum pump method was theoretically expected to be insensitive to irradiance, and this expectation was confirmed in experiments on Hedera helix. When used in the ways recommended here, the three methods produced measurements that agreed typically within 10%. There were significant differences in species' K(lamina); values ranged from 1.24x10(-4) kg s(-1) m(-2) MPa(-1) for Acer saccharum to 2.89x10(-4) kg s(-1) m(-2) MPa(-1) for Vitis labrusca. Accurate, rapid determination of K(lamina) will allow testing of the links between K(lamina), water-use, drought tolerance, and the enormous diversity of leaf form, structure and composition.

Acer↗
PubMed1990

Accuracy and precision of methods for theophylline measurement in physicians' offices.

We tested the accuracy and precision of five theophylline methods intended for use in physicians' offices. The Syntex AccuLevel, Ames Seralyzer, and 3M Diagnostics TheoFAST methods were less reproducible (CVs 6.3% to 9.2%) than the Abbott Vision and Kodak DT-60 (CVs 2.2% to 3.3%). Caffeine interfered with the Vision, Seralyzer, and AccuLevel methods, and theobromine interfered with the Vision, Seralyzer, and TheoFAST methods. Only the DT-60 method was free from interference from any of the 24 compounds tested. Results by all methods correlated well with those by the HPLC comparison method (Clin Chem 1981;27:1931-3) and by the Abbott TDx method for assay of 100 serum (or, when appropriate, paired whole-blood) samples. The frequency of sample results differing from the comparison method by greater than 2.0 mg/L was as follows: TDx, 11%; Vision (serum), 12%; Vision (whole blood), 18%; DT-60, 14%; AccuLevel, 18%; Seralyzer, 25%; and TheoFAST, 31%. The Kodak DT-60 method was the most nearly accurate and precise among these physician's office methods. Some physician's office methods for theophylline analysis are not adequate to guide dosage adjustments.

Humans↗
PubMed2004

Estimating admixture proportions with microsatellites: comparison of methods based on simulated data.

Several methods have been developed to estimate the parental contributions in the genetic pool of an admixed population. Some pair-comparisons have been performed on real data but, to date, no systematic comparison of a large number of methods has been attempted. In this study, we performed a simulated data-based comparison of six of the most cited methods in the literature of the last 20 years. Five of these methods use allele frequencies and differ in the statistical treatment of the data. The last one also considers the degree of molecular divergence by estimating the coalescence times. Comparisons are based on the frequency at which the method can be applied, the bias and the mean square error of the estimation, and the frequency at which the true value is within the confidence interval. Eventually, each method was applied to a real data set of variously introgressed honeybee populations. In optimal conditions (highly differentiated parental populations, recent hybridization event), all methods perform equally well. When conditions are not optimal, the methods perform differently, but no method is always better or worse than all others. Some guidelines are given for the choice of the method.

Animals↗
PubMed1985

A BASIC computer program for evaluating the effect of sample distribution on the least-squares regression slope estimate.

Least-squares regression analysis is widely used in analytical method comparison studies even though model assumptions are typically violated. The advantages favoring the use of the least-squares technique, when applicable, are that its theoretical characteristics are thoroughly developed and the calculations are straightforward and universally known. In order to aid an investigator in determining whether or not the least-squares technique can be acceptably applied in a given method comparison situation, a BASIC computer program is developed that evaluates the bias of the least-squares slope estimate as a function of the precision characteristics of the analytical methods and the proposed sampling distribution for the method comparison experiment.

Clinical Laboratory Techniques↗
PubMed2002

On calculating the power of a TDT study--comparison of methods.

We show that the methods for calculating the power of the TDT of Risch & Merikangas (1996), McGinnis (1998, 2000), Tu & Whittemore (1999) and Knapp (1999) consist of three distinct approaches. The differences between the methods arise either by treating parental transmissions independently or not, and either conditioning on parental heterozygosity or not. Transmissions are only truly independent when the mode of inheritance of the disease is multiplicative, making this assumption invalid and the methods that assume them (Risch & Merikangas, 1996; McGinnis, 1998, 2000) inappropriate. We demonstrate a basic model that allows analytical comparisons of the methods, and suggest a new method that calculates power at least as accurately as any of the three previously published.

Genetic Diseases, Inborn↗
PubMed2004

Comparison of methods for evaluation of a medical terminological system.

The importance of terminological systems (TS) to support standardized and structured documentation of medical data is commonly recognized. The usability of TS in real practice strongly depends on the completeness and the correctness of the content of the TS. We here present four different methods that can be applied to evaluate a TS' content. All four methods were applied in a case study. We make a comparison of 1) the results of two methods that focus on the completeness of the content and that differ in the application of the TS that they focus on and 2) the results of an automated and a manual evaluation of the correctness of the content. Finally we summarize the results of all four methods and analyze whether they overlap or complement each other.

Critical Care↗
PubMed2000

Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL.

MOTIVATION: For large-scale structural assignment to sequences, as in computational structural genomics, a fast yet sensitive sequence search procedure is essential. A new approach using intermediate sequences was tested as a shortcut to iterative multiple sequence search methods such as PSI-BLAST. RESULTS: A library containing potential intermediate sequences for proteins of known structure (PDB-ISL) was constructed. The sequences in the library were collected from a large sequence database using the sequences of the domains of proteins of known structure as the query sequences and the program PSI-BLAST. Sequences of proteins of unknown structure can be matched to distantly related proteins of known structure by using pairwise sequence comparison methods to find homologues in PDB-ISL. Searches of PDB-ISL were calibrated, and the number of correct matches found at a given error rate was the same as that found by PSI-BLAST. The advantage of this library is that it uses pairwise sequence comparison methods, such as FASTA or BLAST2, and can, therefore, be searched easily and, in many cases, much more quickly than an iterative multiple sequence comparison method. The procedure is roughly 20 times faster than PSI-BLAST for small genomes and several hundred times for large genomes. AVAILABILITY: Sequences can be submitted to the PDB-ISL servers at http://stash.mrc-lmb.cam.ac.uk/PDB_ISL/ or http://cyrah.ebi.ac.uk:1111/Serv/PDB_ISL/ and can be downloaded from ftp://ftp.ebi.ac.uk/pub/contrib/jong/PDB_+ ++ISL/ CONTACT: sat@mrc-lmb.cam.ac.uk and jong@ebi.ac.uk

Peptide Library↗
PubMed2001

Recalibration of the point-of-care test for CARDIAC T Quantitative with Elecsys Troponin T 3rd generation.

The rapid troponin T assay CARDIAC T Quantitative was recalibrated using Elecsys Troponin T 3rd Generation as a new reference method. This paper presents the method comparisons at six centres using the new reference method. Method comparison between CARDIAC T Quantitative versus Elecsys Troponin T 3rd Generation were performed using 319 samples from patients with acute coronary syndromes. The quality of the CARDIAC T Quantitative was controlled by a daily single determination of CARDIAC Control Troponin T, and for the Elecsys Troponin T 3rd Generation, the Elecsys controls were included in each run. The results for the control materials for the CARDIAC T Quantitative were between 93% and 107% of the target values. The CV ranged from 7% to 16%. From the regression analysis, according to Bablok and Passing (y=1.07x) and the Bland and Altman plot, the bias between CARDIAC T Quantitative and Elecsys Troponin T 3rd Generation is from +6% to +7%. The correlation coefficient is 0.93, and a 3x3 comparison of the clinical efficiency yielded 92% clinical concordance between CARDIAC T Quantitative and Elecsys Troponin T 3rd Generation. In conclusion, CARDIAC T Quantitative was in good agreement with the reference and calibration method Elecsys Troponin T 3rd Generation.

Calibration↗
PubMed1996

An evaluation of the Ektachem serum lithium method and comparison with flame emission spectrometry.

We evaluated the performance of a new colorimetric method in dry chemistry for serum lithium (Li) assay using an Ektachem E500 analyser. Imprecision results were acceptable and the linearity was verified for concentrations within the range of 0.2-3.9 mmol l-1, i.e. y(measured) = 1.02x(calculated) + 0.07, r = 0.99. The Ektachem Li assay was unaffected by potassium (K), calcium (Ca) and magnesium (Mg) at all concentrations tested. Significant interference was caused by sodium (Na) and haemoglobin. Statistically and clinically significant interference was caused by high concentrations of Na (213 mmol l-1) with a bias of 0.20 mmol l-1 (p = 0.02) and by high levels of haemoglobin (280 mumol l-1) with a bias of 0.20 mmol l-1 (p = 0.01). Comparison of serum Li results from 80 patient samples assayed using the Ektachem method with those obtained using the IL943, a flame atomic emission spectrometry (FAES)-based method, gave a regression line equation: Ektachem = 0.95xFAES + 0.13, r = 0.96. The data revealed a mean difference of 0.10 mmol l-1 between the Ektachem and FAES results that was statistically significant (p = 0.01), but clinically negligible. We conclude that the Kodak method provides reliable Li serum results and represents a valid alternative to the FAES method.

Colorimetry↗
PubMed2005

Not so different after all: a comparison of methods for detecting amino acid sites under selection.

We consider three approaches for estimating the rates of nonsynonymous and synonymous changes at each site in a sequence alignment in order to identify sites under positive or negative selection: (1) a suite of fast likelihood-based "counting methods" that employ either a single most likely ancestral reconstruction, weighting across all possible ancestral reconstructions, or sampling from ancestral reconstructions; (2) a random effects likelihood (REL) approach, which models variation in nonsynonymous and synonymous rates across sites according to a predefined distribution, with the selection pressure at an individual site inferred using an empirical Bayes approach; and (3) a fixed effects likelihood (FEL) method that directly estimates nonsynonymous and synonymous substitution rates at each site. All three methods incorporate flexible models of nucleotide substitution bias and variation in both nonsynonymous and synonymous substitution rates across sites, facilitating the comparison between the methods. We demonstrate that the results obtained using these approaches show broad agreement in levels of Type I and Type II error and in estimates of substitution rates. Counting methods are well suited for large alignments, for which there is high power to detect positive and negative selection, but appear to underestimate the substitution rate. A REL approach, which is more computationally intensive than counting methods, has higher power than counting methods to detect selection in data sets of intermediate size but may suffer from higher rates of false positives for small data sets. A FEL approach appears to capture the pattern of rate variation better than counting methods or random effects models, does not suffer from as many false positives as random effects models for data sets comprising few sequences, and can be efficiently parallelized. Our results suggest that previously reported differences between results obtained by counting methods and random effects models arise due to a combination of the conservative nature of counting-based methods, the failure of current random effects models to allow for variation in synonymous substitution rates, and the naive application of random effects models to extremely sparse data sets. We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments.

Amino Acids↗
PubMed2000

On statistical methods for comparison of intrasample morphometric variability: Zalavár revisited.

In studies of morphology, methods for comparing amounts of variability are often important. Three different ways of utilizing determinants of covariance matrices for testing for surplus variability in a hypothesis sample compared to a reference sample are presented: an F-test based on standardized generalized variances, a parametric bootstrap based on draws on Wishart matrices, and a nonparametric bootstrap. The F-test based on standardized generalized variances and the Wishart-based bootstrap are applicable when multivariate normality can be assumed. These methods can be applied with only summary data available. However, the nonparametric bootstrap can be applied with multivariate nonnormally distributed data as well as multivariate normally distributed data, and small sample sizes. Therefore, this method is preferable when raw data are available. Three craniometric samples are used to present the methods. A Hungarian Zalavár sample and an Austrian Berg sample are compared to a Norwegian Oslo sample, the latter employed as reference sample. In agreement with a previous study, it is shown that the Zalavár sample does not represent surplus variability, whereas the Berg sample does represent such a surplus variability.

Multivariate Analysis↗
PubMed1985

Comparison of methods of metallothionein quantification: cadmium radioassay, mercury radioassay, and radioimmunoassay.

A comparison of the Hg radioassay (i.e. "Piotrowski" assay), the Cd radioassay (i.e. "cadmium-hemolysate" assay), and the radioimmunoassay (RIA) for metallothionein (MT) was performed for livers from control, Cd-, and Zn-pretreated rats. Results indicate that the Cd and Hg radioassays gave similar results in all cases. The RIA values compared very favorably to those obtained by the metal saturation assays for livers from control rats. The values obtained for livers from Cd- or Zn-treated animals were generally lower in the RIA than in the Hg or Cd radioassay, ranging from 36 to 75% of the metal saturation assays. The source of this discrepancy cannot be discerned from the present data. However, the various assay systems employed did yield MT concentrations that followed similar intraassay patterns, being lowest in control, elevated to an intermediate level with Cd treatment, and highest following Zn treatment.

Animals↗
PubMed2000

The measurement of plasma catecholamine and lactate thresholds: a comparison of methods.

Plasma lactate and catecholamine thresholds were calculated using three different variations of linear regression, an algorithmic linear regression method, a log-log transformation method and a semi-log method. A group of 18 male sports science students undertook an incremental test to exhaustion on a cycle ergometer. A 5-ml blood sample was drawn at rest, after 4 min of exercise and every 2 min thereafter until the cessation of the test. Lactate, adrenaline and noradrenaline concentrations were measured. Lactate threshold (Th1a), adrenaline threshold (ThA) and noradrenaline threshold (ThNA) were calculated using each of the three methods. The best fits of the methods were examined by comparing their standard error of estimates (SEEs). The algorithmic method demonstrated a higher SEE than the other two methods, but only for Th1a and ThNA. The power output for which each method calculated the thresholds demonstrated a main effect for method. Tukey post hoc tests showed that the algorithmic method produced significantly higher outputs than the other two methods, which did not differ significantly from one another. Comparison of these power outputs showed that Th1a and ThA differed significantly, regardless of method, there were no other significant differences. Plasma concentrations of lactate, adrenaline and noradrenaline showed that the values of Th1a and ThNA calculated by the algorithmic method were significantly higher than those calculated using the other two methods, which did not differ significantly from one another. The only significant difference for ThA was between the algorithmic and semi-log methods. Correlations between the power outputs at which each method calculated the thresholds varied greatly between methods, and were at best only moderate (r = 0.63). It was concluded that the algorithmic method was less powerful than the other two methods, and that Th1a, ThA and ThNA are not highly correlated.

Adult↗
PubMed1975

Comparison of methods for calculating serum osmolality form chemical concentrations, and the prognostic value of such calculations.

Sodium, potassium, glucose, blood urea nitrogen, and osmolality were determined for 715 hospital-patient sera. The chemical concentrations were used to calculate osmolalities according to 13 different methods taken from the literature. The goodness of the comparison between calculated and measured osmolality was quite similar for several of the better methods. The aggreement was unimproved when molal chemical concentrations were used instead of molar values. The difference between measured and calculated osmolality was unrelated to whether a patient was discharged from the hospital after a short or long period or ultimately died. The equation we found to yield the most accurately calculated osmolalities is Osmolality = 1.86 Na + (Glu/18) + - (BUN/2.8) + 9.

Autoanalysis↗