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PubMed1992

Comparison of a two-stage and three-stage interim-analysis procedure.

A statistical model for combining p values from multiple tests of significance is used to define rejection and acceptance regions for two-stage and three-stage sampling plans. Type I error rates, power, frequencies of early termination decisions, and expected sample sizes are compared. Both the two-stage and three-stage procedures provide appropriate protection against Type I errors. The two-stage sampling plan with its single interim analysis entails minimal loss in power and provides substantial reduction in expected sample size as compared with a conventional single end-of-study test of significance for which power is in the adequate range. The three-stage sampling plan with its two interim analyses introduces somewhat greater reduction in power, but it compensates with greater reduction in expected sample size. Either interim-analysis strategy is more efficient than a single end-of-study analysis in terms of power per unit of sample size.

Bias↗
PubMed1985

Maximizing the efficiency of a study on alcohol-related birth defects by means of data collection and analytic strategy dissociation.

Application of the terms "prospective" and "retrospective" to quasi/experimental research designs used in clinical investigations is often ambiguous; they often lack specification as to whether they apply to data acquisition, analytic strategy, or both. Data may be collected prospectively by preplanned protocol or retrospectively by chart review. In addition, the direction of analysis may be prospective--comparing differential outcomes for at-risk and not at-risk (exposed/not exposed) groups--or retrospective--comparing differential preceding risks for affected and nonaffected groups. Prospective data collection is advantageous in assuring the availability of crucial variables for an entire sample, but prospective analytic strategies may be inefficient, underestimating effect sizes, particularly when the outcome of interest is rare or the effect, even if large, is seen in only a small proportion of cases. In a prospective multilinear regression model of risks for lowered birthweight for gestational age, 2% of the variance was explained by alcohol variables after adjustment for confounding. In comparison, a similar multilinear regression of case-control sample, in which the frequency of the abnormal outcome is raised, showed 18% of the variance explained by alcohol variables. Data collection and analytic strategies may be dissociated. Although some statistical power may be lost because of reduced sample size, synthetic case-control analysis is efficient in examining small effects. It also has the advantage of decreasing the size of the database to be managed and the time required for analysis. Using this approach, it is feasible to perform virtually any analysis that can be done on a mainframe on medium-sized departmental computer system.

Birth Weight↗
PubMed1999

Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa.

Three-dimensional quantitative structure-activity relationship (3D QSAR) methods were applied using a training set of 72 inhibitors of the benzamidine type with respect to their binding affinities (Ki values) toward thrombin, trypsin, and factor Xa to yield statistically reliable models of good predictive power. Two methods were compared: the widely used comparative molecular field analysis (CoMFA) and the recently reported CoMSIA approach (comparative molecular similarity indices analysis). CoMSIA produced significantly better results for all correlations. Furthermore, in contrast to CoMFA, CoMSIA is not sensitive to changes in orientation of the superimposed molecules in the lattice. The correlation results obtained by CoMSIA were graphically interpreted in terms of field contribution maps allowing physicochemical properties relevant for binding to be easily mapped back onto molecular structures. The advantage of this feature is demonstrated using the maps to design new molecules. Finally, the CoMSIA method was applied to elucidate structural features among ligands which are responsible for affinity differences toward thrombin and trypsin. These selectivity-determining features were interpreted graphically in terms of spatial regions responsible for affinity discrimination. Such indicators are highly informative for the lead optimization process with respect to selectivity enhancement.

Binding Sites↗
PubMed2006

Estimating p-values in small microarray experiments.

MOTIVATION: Microarray data typically have small numbers of observations per gene, which can result in low power for statistical tests. Test statistics that borrow information from data across all of the genes can improve power, but these statistics have non-standard distributions, and their significance must be assessed using permutation analysis. When sample sizes are small, the number of distinct permutations can be severely limited, and pooling the permutation-derived test statistics across all genes has been proposed. However, the null distribution of the test statistics under permutation is not the same for equally and differentially expressed genes. This can have a negative impact on both p-value estimation and the power of information borrowing statistics. RESULTS: We investigate permutation based methods for estimating p-values. One of methods that uses pooling from a selected subset of the data are shown to have the correct type I error rate and to provide accurate estimates of the false discovery rate (FDR). We provide guidelines to select an appropriate subset. We also demonstrate that information borrowing statistics have substantially increased power compared to the t-test in small experiments.

Algorithms↗
PubMed1987

The predictive validity of lay Diagnostic Interview Schedule diagnoses in the general population. A comparison with physician examiners.

A clinical reexamination by psychiatrists is a useful comparison for exploring lay Diagnostic Interview Schedule-derived psychiatric diagnoses in general population surveys, but as a validity standard psychiatric reexamination is less than ideal. There are many potential sources of disagreement that have nothing to do with the validity of either the lay or the psychiatrist examination. Another approach to comparing lay and psychiatrist diagnoses is to examine their relative predictive power. We describe such a comparison using outcome variables derived from the one-year follow-up examination of Epidemiologic Catchment Area respondents done at the St. Louis site. We examine several outcome variables across nine diagnostic categories. Within the limits of the available data, lay and psychiatrist diagnoses appear to be essentially equal in terms of the number of outcomes better predicted and few of the differences in predictive power approach statistical significance. We discuss the implications of these findings for the analysis of lay interviewer Diagnostic Interview Schedule-derived diagnoses.

Catchment Area, Health↗
PubMed2000

Exploring local and non-local interactions for protein stability by structural motif engineering.

In order to probe the relative contribution of local and non-local interactions to the thermodynamic stability of proteins, we have devised an experimental approach based on a combination of motif engineering and sequence shuffling. Candidate chain segments in an immunoglobulin V(L) domain were identified whose conformation is proposed to be dominated by non-local interactions. Locally interacting structural motifs of a different conformation were then constructed as replacements, by introducing motif consensus sequences. We find that all nine replacements we constructed systematically reduce the folding cooperativity. By comparing this destabilising effect with the folding transitions of shuffled sequences for three of these motifs, we estimate the contribution of local, native interactions to the free energy of folding. Our results suggest that local and non-local interactions contribute to stability by an approximately equal amount, but that local interactions stabilise by increasing the resistance to denaturation while non-local interactions increase folding cooperativity. The systematic loss of stability by sequence shuffling in these host-guest experiments suggests that the designed interactions indeed are present in the native state, thus consensus sequence engineering may be a useful tool in structure design, but non-local interactions must be taken into account for global stability engineering. Statistical approaches are powerful tools for engineering protein structure and stability, but an analysis based on local sequence propensities alone does not adequately represent the balance of sequence and context in protein structures.

Amino Acid Motifs↗
PubMed1997

Multivariate cluster analysis of dynamic iodine-123 iodobenzamide SPET dopamine D2 receptor images in schizophrenia.

This paper describes the application of a multivariate statistical technique to investigate striatal dopamine D2 receptor concentrations measured by iodine-123 iodobenzamide (123I-IBZM) single-photon emission tomography (SPET). This technique enables the automatic segmentation of dynamic nuclear medicine images based on the underlying time-activity curves present in the data. Once the time-activity curves have been extracted, each pixel can be mapped back on to the underlying distribution, considerably reducing image noise. Cluster analysis has been verified using computer simulations and phantom studies. The technique has been applied to SPET images of dopamine D2 receptors in a total of 20 healthy and 20 schizophrenic volunteers (22 male, 18 female), using the ligand 123I-IBZM. Following automatic image segmentation, the concentration of striatal dopamine D2 receptors shows a significant left-sided asymmetry in male schizophrenics compared with male controls. The mean left-minus-right laterality index for controls is -1.52 (95% CI -3.72-0.66) and for patients 4.04 (95% CI 1.07-7.01). Analysis of variance shows a case-by-sex-by-side interaction, with F=10.01, P=0. 005. We can now demonstrate that the previously observed male sex-specific D2 receptor asymmetry in schizophrenia, which had failed to attain statistical significance, is valid. Cluster analysis of dynamic nuclear medicine studies provides a powerful tool for automatic segmentation and noise reduction of the images, removing much of the subjectivity inherent in region-of-interest analysis. The observed striatal D2 asymmetry could reflect long hypothesized disruptions in dopamine-rich cortico-striatal-limbic circuits in schizophrenic males.

Benzamides↗
PubMed2006

[Reliability of multicenter magnetic resonance imaging. Results of a phantom test and in vivo measurements by the German Dementia Competence Network].

BACKGROUND: Whereas a large body of evidence suggests the usefulness of volumetric measurement of cerebral atrophy for diagnosing Alzheimer's disease (AD), the clinical applicability of cerebral volumetry for early detection of AD across multiple clinical sites is not well known. In the current study, we assessed the precision of volumetric measurement of the brain based on magnetic resonance imaging (MRI) in a multicenter setting. METHODS: The reliability of MRI was assessed by a phantom test of the American College of Radiology and voxel-based morphometry applied to the images obtained from a single subject tested at 11 centers of the German Dementia Competence Network. RESULT: Nine of the 11 centers tested met the reliability criteria of the phantom test. Across all centers, a bias was found in the measurements of slice thickness and length. For voxel-based morphometry, the coefficient of variation yielded 5.02% for gray matter volume and 12.81% (SD 9.06%) for gray matter signal intensity in voxels. Power analysis showed that a sample size of 150 subjects is sufficient for statistically valid detection of reduced gray matter volume in patients with mild cognitive impairment. CONCLUSION: The reliability of measurements from multiple centers is sufficient to allow statistically valid analysis of MRI data.

Adult↗
PubMed2004

Technical variability and required sample size of helminth egg isolation procedures: revisited.

Mes [Vet Parasitol (2003) 115:311-320] recently reported a quantitative study of repeated measurements of nematode egg counts in faecal samples from dairy cattle, in order to compare the faecal egg counts resulting from two different laboratory techniques, the widely used McMaster method and a newer salt-sugar flotation (SSF) method. He concluded that the SSF technique requires much smaller sample sizes, and is also potentially simpler to carry out, making it the method of choice. Here I re-analyse these data to show that if the comparison is done on the most appropriate measurement scale (lognormal), and the large difference in multiplication factors is taken into account, then there is little to choose between the McMaster and SSF techniques as far as the required sample size is concerned. In particular, the treatment of the data as normally rather than lognormally distributed leads to incorrect statistical tests, power analyses and confidence intervals.

Analysis of Variance↗
PubMed1996

Angiogenesis in squamous cell carcinoma in situ and microinvasive carcinoma of the uterine cervix.

OBJECTIVE: To evaluate angiogenesis in squamous cell carcinoma in situ (CIS) and microinvasive squamous cell carcinoma of the uterine cervix and to investigate the relations among angiogenesis, stromal inflammation, and depth of invasion. METHODS: Three groups of women were studied: 22 controls who had undergone hysterectomy for benign conditions; 18 with squamous cell CIS of the cervix who underwent cone biopsy, hysterectomy, or both; and 14 with microinvasive squamous cell carcinoma who underwent conization of the cervix and subsequent surgical management according to depth of invasion. All specimens were stained immunohistochemically for factor VIII-related antigen. Areas below the basement membrane with the highest angiogenic density were selected. The degree of stromal inflammatory reaction was assessed. Statistical analyses included Kruskal-Wallis, analyses of variance and covariance, Scheffe and Bonferroni-Dunn post hoc procedures, and Pearson correlation analysis. P < .05 was considered statistically significant. RESULTS: Microvessel counts per high-power field (x 400) of microinvasive squamous cell carcinoma of the cervix differed significantly from those of controls and squamous cell CIS (median 34.5 per high-power field, range 9-76 versus median 17, range 7-47, and median 19, range 8-39, respectively; P < .005). Microvessel counts per high-power field in squamous cell CIS did not differ significantly from those of controls (P = .91). Among patients with microinvasive squamous cell carcinoma of the cervix, no significant correlation was found between microvessel counts per high-power field and the depth of invasion (r = 0.19, P = .51). Stromal inflammatory reaction (graded 0-3) differed significantly among controls, squamous cell CIS, and microinvasive carcinoma (mean 0.40, 0.83, and 1.64, respectively; P < .005). CONCLUSIONS: Microinvasive squamous cell carcinoma of the uterine cervix is angiogenic, but depth of invasion is not associated with increased angiogenicity. Squamous cell CIS is not angiogenic.

Adult↗
PubMed2003

Using ANOVA for gene selection from microarray studies of the nervous system.

Methods are presented for detecting differential expression using statistical hypothesis testing methods including analysis of variance (ANOVA). Practicalities of experimental design, power, and sample size are discussed. Methods for multiple testing correction and their application are described. Instructions for running typical analyses are given in the R programming environment. R code and the sample data set used to generate the examples are available at http://microarray.cpmc.columbia.edu/pavlidis/pub/aovmethods/.

Analysis of Variance↗
PubMed2002

Developmental changes in heart rate variability during exposure to prolonged hypercapnia in piglets.

The hypothesis that hypercapnia-induced differences in heart rate variability (HRV) would emerge during early maturation was tested using a developing porcine model. Piglets were randomly assigned to either exposed (10% CO2 for 1 h) or control (100% O2) conditions, and then to one of three study groups: (a) 5-8 days old, (b) 13-15 days old, (c) 26-34 days old. Experiments were performed on pairs of age-and litter-matched animals that were anesthetized, paralyzed, and artificially ventilated. HRV was evaluated using power spectral analysis, SD of differences between successive RR intervals, and cardiac interval analysis. Statistical comparisons of simultaneously studied animals were made at baseline, 15 and 55 min after onset of hypercapnia, and 2 h after offset of hypercapnia. Our analyses revealed that only HRV of 26-34-day-old animals differed significantly from values of control animals. Cardiac intervals of those animals were distributed in such a manner that hypercapnia likely elicited coactivation of sympathetic and parasympathetic systems. Comparison of the distribution of cardiac intervals for other animals showed that 5-8-day-old animals had high frequency of balanced intervals at baseline that remained so during hypercapnia. Given that such coactivation may be neuroprotective, the paucity of balanced intervals in 13-15-day-old animals could mean that the end of the second postnatal week is associated with increased vulnerability.

Age Factors↗
PubMed2004

Functional neuroimaging studies of human emotions.

Neuroimaging studies with positron emission tomography and functional magnetic resonance imaging have begun to describe the functional neuroanatomy of human emotion. Taken separately, specific studies vary in task dimensions and in type(s) of emotion studied, and are limited by statistical power and sensitivity. By examining findings across studies in a meta-analysis, we sought to determine if common or segregated patterns of activations exist in different emotions and across various emotional tasks. We surveyed over 55 positron emission tomography and functional magnetic resonance imaging activation studies, which investigated emotion in healthy subjects. This paper will review observations in several regions of interest in limbic (eg, amygdala, anterior cingulate cortex) and paralimbic (eg, medial prefrontal cortex, insula) brain regions in emotional responding.

Affect↗
PubMed1999

Heuristic-systematic information processing and risk judgment.

The heuristic-systematic information processing model (HSM) holds that individuals will use one or both of these modes of information processing when attempting to evaluate information in order to arrive at a judgment. Systematic processing is defined by effortful scrutiny and comparison of information, whereas heuristic processing is defined by the use of cues to arrive more easily at a judgment. Antecedents to the two processing modes include information sufficiency, motivation, and self-efficacy. Structural equation modeling is used to examine competing configuration of this model and to evaluate the model as appropriate for predicting risk judgment. The model also is evaluated across three groups that vary with respect to their level of concern. These analyses are executed within a case study involving an epidemiological investigation of a suspected cancer cluster. The analysis confirms the HSM's theoretically proposed structure and shows it to be a useful vehicle for evaluating risk judgment. In the overall analysis, antecedent variables generally function as specified by theory. Systematic processing is predicted by greater motivation. Heuristic processing is predicted by information sufficiency. Self-efficacy is a significant predictor of both processing modes. And heuristic processing is shown to be associated with judgment of less risk. However, when the analysis is contrasted across three groups (those concerned about cancer, not concerned and uncertain) it is shown that the model is significantly more robust for the uncertain group. This finding may have implications for the use of the HSM in risk research specifically, and in field research generally.

Analysis of Variance↗
PubMed2002

The hormone-sensitive lipase gene and body composition: the HERITAGE Family Study.

OBJECTIVE: To investigate whether the C-60G polymorphism and other markers in the hormone-sensitive lipase (LIPE) gene are associated with baseline body composition and free-fatty acid (FFA) concentrations measured at rest and during low-intensity exercise in white and black subjects participating in the HERITAGE Family Study. SUBJECTS: Adult sedentary white (245 men and 258 women) and black (91 men and 185 women) subjects. MEASUREMENTS: body mass index (BMI); fat mass (FAT); percentage body fat (%FAT); fat-free mass (FATFR); sum of eight skinfolds (SF8); subcutaneous (ASF), visceral (AVF) and total (ATF) abdominal fat areas assessed by CT scan; plasma FFA concentrations measured at rest (FFAR), at a power output of 50 W (FFA50) and at a relative power output of 60% of VO(2max) (FFA60%); and fasting insulin (INS). STATISTICAL ANALYSIS: Association between the C-60G polymorphism of the LIPE gene and each phenotype was tested separately in men and women using ANCOVA with the effects of age and race as covariates and with further adjustment for FAT for ASF, AVF, ATF, FFAR, FFA50 and FFA60%. Secondly, owing to significant gene-by-race interaction, associations were investigated separately in each of the two race groups. Linkage was tested with the C-60G polymorphism, a dinucleotide repeat polymorphism in the intron 7 of the LIPE gene and two microsatellites markers (D19S178 and D19S903) flanking the LIPE gene. RESULTS: There were no race differences in the allele frequencies of the C-60G polymorphism of the LIPE gene. No association or gene-by-race interaction was observed in men. However, in women, strong gene-by-race interactions were observed for BMI (P=0.0005), FAT (P=0.0007), %FAT (P=0.0003), SF8 (P=0.0001), ASF (P=0.03) and ATF (P=0.01). When the analysis was performed separately in each race, white women carriers of the -60G allele exhibited lower %FAT (P=0.005) and SF8 (P=0.01) than non-carriers, while in black women, the -60G allele was associated with higher BMI (P=0.004), FAT (P=0.009), %FAT (P=0.01) and SF8 (P=0.0009). These associations were no longer significant after adjusting for INS. Evidence of linkage was observed in whites with ATF, FFAR, FFA50 and FFA60%. CONCLUSION: These results suggest that the C-60G polymorphism in the LIPE gene plays a role in determining body composition and that its effect is sex-, race- and insulin-dependent.

Abdomen↗
PubMed2004

Advances in two-dimensional gel matching technology.

For many years, two-dimensional gel electrophoresis has been the method of choice for the investigation of complex mixtures of proteins. Although there are a number of emerging technologies that can be applied to proteomics, none can yet yield routinely the breadth of information available from two-dimensional gels. To be able to obtain instant information regarding molecular mass and pI, as well as to highlight quickly the expression changes or unique proteins across a gel series requires sophisticated and powerful image analysis software. The range of software products offered by Nonlinear Dynamics covers all levels of user application and throughput, from the user-guided Phoretix two-dimensional approach, when working with a small number of gels, to the automatic processing of large numbers of gels with minimal user intervention with Progenesis. Integration of the analysis software with powerful database components allows advanced gel comparisons and data mining to be performed with statistical verification of the results. Spot pick lists can be quickly created and automatically linked to a number of commercially available spot picking robots further increasing the support for proteomics research. The importance of image analysis for accurate, reliable and meaningful results will be discussed. Recent advances in development, with particular attention placed on the impact of noise contamination within gels, are illustrated and how the Progenesis product from Nonlinear Dynamics can be utilized to get the most from two-dimensional gel electrophoresis is shown.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2000

Relationship between achievement goal orientations and the perceived purposes of playing rugby union for professional and amateur players.

The recent professionalization of rugby union makes it an excellent achievement context in which to examine the relationship between achievement goal orientations and the perceived purposes of sport as a function of competitive standard. During the 1996-97 season, 73 professional and 106 amateur rugby players in England completed a series of questionnaires assessing their achievement goal orientations, beliefs about the purposes of rugby and demographic information. The results of a canonical correlation analysis revealed a conceptually coherent relationship between achievement goal orientations and purposes of rugby. Specifically, a high ego/moderate task orientation was positively related to fitness, aggression and financial remuneration as significant purposes of rugby. Professional players scored higher on those purposes of rugby related to aggression, financial remuneration and fitness, but lower on sportspersonship than amateur players. Professional players also reported higher task and ego goal orientations than amateur players. The findings are discussed in terms of the differences in lifestyle and motivation of professional and amateur rugby union players.

Achievement↗
PubMed2004

Using factor analysis to attribute health impacts to particulate pollution sources.

Laden et al. (2000) recently reported results of applying factor analysis to data taken in six cities from 1979 to 1988, identifying airborne particle sources potentially affecting daily mortality. These authors sought relationships between source groups and risk measures using source tracer elements, Se (coal combustion), Pb (light-duty motor vehicle sources), and Si (crustal--soil dispersion). Combined data analyses of this kind may overlook the complexity of source contributions, which have common tracer elements. In one of the cities, Boston, for example, the authors found coal combustion was an important source of mortality risk. For the city of Boston, the authors attribute coal combustion largely to distant upwind regional sources. The emphasis on coal combustion is confounded by the presence of major local sources of residual oil combustion, which contribute V, Se, and S (sulfur as sulfate) to the source apportionment. Evaluation of the source identification using single-element tracer analysis indicates that the detailed chemical composition or profile of major local sources needs to be taken into account in these investigations to minimize misclassification of airborne particle sources with potential adverse health effects.

Air Pollutants↗