A Diagnostic Test for the Mixing Distribution in a Generalised Linear Mixed Model

We introduce a diagnostic test for the mixing distribution in a generalised linear mixed model. The test is based on the difference between the marginal maximum likelihood and conditional maximum likelihood estimates of a subset of the fixed effects in the model. We derive the asymptotic variance of this difference, and propose a test statistic that has a limiting chi-square distribution under the null hypothesis that the mixing distribution is correctly specified. For the important special case of the logistic regression model with random intercepts, we evaluate via simulation the power of the test in finite samples under several alternative distributional forms for the mixing distribution. We illustrate the method by applying it to data from a clinical trial investigating the effects of hormonal contraceptives in women.

MODIFIED TEST STATISTICS BY INTER-VOXEL VARIANCE SHRINKAGE WITH AN APPLICATION TO fMRI

Functional Magnetic Resonance Imaging (fMRI) is a non-invasive technique which is commonly used to quantify changes in blood oxygenation and flow coupled to neuronal activation. One of the primary goals of fMRI studies is to identify localized brain regions where neuronal activation levels vary between groups. Single voxel t-tests have been commonly used to determine whether activation related to the protocol differs across groups. Due to the generally limited number of subjects within each study, accurate estimation of variance at each voxel is difficult. Thus, combining information across voxels in the statistical analysis of fMRI data is desirable in order to improve efficiency. Here we construct a hierarchical model and apply an Empirical Bayes framework on the analysis of group fMRI data, employing techniques used in high throughput genomic studies. The key idea is to shrink residual variances by combining information across voxels, and subsequently to construct an improved test statistic in lieu of the classical t-statistic. This hierarchical model results in a shrinkage of voxel-wise residual sample variances towards a common value. The shrunken estimator for voxelspecific variance components on the group analyses outperforms the classical residual error estimator in terms of mean squared error. Moreover, the shrunken test-statistic decreases false positive rate when testing differences in brain contrast maps across a wide range of simulation studies. This methodology was also applied to experimental data regarding a cognitive activation task.

Content comparison of health-related quality of life instruments for COPD

BACKGROUND: Due to the increasing importance of quality of life assessments in chronic obstructive pulmonary disease (COPD) patients, and the increased use of the International Classification of Functioning, Disability and Health (ICF) for comparative purposes it is essential to understand the relationship between health-related quality of life (HRQL) instruments and the ICF. OBJECTIVE: The objective of this study was to compare the content of recommended COPD-specific HRQL instruments using the ICF as reference. COPD-specific instruments mentioned in widely accepted guidelines were linked to the ICF using standardized linking rules. The degree of agreement between various health professionals was assessed by calculating the kappa statistic. RESULTS: Eleven instruments were included. They varied strongly in the number of concepts contained and the number of ICF categories used to map these concepts. A total of 548 concepts were identified and linked to 60 different ICF categories. Only the single category 'dyspnea' was covered by all instruments, whilst 21 categories were unique to specific instruments. The relationships of the measures with the ICF were identified. CONCLUSIONS: This study may aid researchers and clinicians to choose the most appropriate instrument for a specific purpose as well as help compare studies that have used different instruments for HRQL assessment.

Effect of therapeutic exercise for hip osteoarthritis pain: results of a meta-analysis

OBJECTIVE: Recommendations for lower extremity osteoarthritis (OA) and exercise have been primarily based on knee studies. To provide more targeted recommendations for the hip, we gathered evidence for the efficacy of exercise for hip OA from randomized controlled trials. METHODS: A bibliographic search identified trials that were randomized, controlled, completed by >or=60% of subjects, and involved an exercise group (strengthening and/or aerobic) versus a non exercise control group for pain relief in hip OA. Two reviewers independently performed the data extraction and contacted the authors when necessary. Effect sizes (ES) of treatment versus control and the I(2) statistic to assess heterogeneity across trials were calculated. Trial data were combined using a random-effects meta-analysis. RESULTS: Nine trials met the inclusion criteria (1,234 subjects), 7 of which combined hip and knee OA; therefore, we contacted the authors who provided the data on hip OA patients. In comparing exercise treatment versus control, we found a beneficial effect of exercise with an ES of -0.38 (95% confidence interval [95% CI] -0.68, -0.08; P = 0.01), but with high heterogeneity (I(2) = 75%) among trials. Heterogeneity was caused by 1 trial consisting of an exercise intervention that was not administered in person. Removing this study left 8 trials (n = 493) with similar exercise strategy (specialized hands-on exercise training, all of which included at least some element of muscle strengthening), and demonstrated exercise benefit with an ES of -0.46 (95% CI -0.64, -0.28; P < 0.0001). CONCLUSION: Therapeutic exercise, especially with an element of strengthening, is an efficacious treatment for hip OA.

Berry-Esseen bounds for nonlinear statistics, and asymptotic relative efficiency between correlation statistics

Four papers, written in collaboration with the author’s graduate school advisor, are presented. In the first paper, uniform and non-uniform Berry-Esseen (BE) bounds on the convergence to normality of a general class of nonlinear statistics are provided; novel applications to specific statistics, including the non-central Student’s, Pearson’s, and the non-central Hotelling’s, are also stated. In the second paper, a BE bound on the rate of convergence of the F-statistic used in testing hypotheses from a general linear model is given. The third paper considers the asymptotic relative efficiency (ARE) between the Pearson, Spearman, and Kendall correlation statistics; conditions sufficient to ensure that the Spearman and Kendall statistics are equally (asymptotically) efficient are provided, and several models are considered which illustrate the use of such conditions. Lastly, the fourth paper proves that, in the bivariate normal model, the ARE between any of these correlation statistics possesses certain monotonicity properties; quadratic lower and upper bounds on the ARE are stated as direct applications of such monotonicity patterns.

Content comparison of health-related quality of life instruments for obstructive sleep apnea

BACKGROUND AND PURPOSE: Due to the increasing importance of quality of life assessments in obstructive sleep apnea (OSA) patients and due to an increased use of the International Classification of Functioning, Disability and Health (ICF), for comparative purposes it is essential to understand the relationship between health-related quality of life (HRQOL) instruments and the ICF. The purpose of this study was to compare the content covered by OSA-specific instruments using the ICF. PATIENTS AND METHODS: OSA-specific instruments were identified, including the Calgary Sleep Apnea Quality of Life Index, the Functional Outcomes of Sleep Questionnaire, the Obstructive Sleep Apnea Patient-Oriented Severity Index, and the Quebec Sleep Questionnaire, and linked to the ICF by six health professionals according to standardized guidelines. The degree of agreement between health professionals was calculated by means of the kappa statistic. RESULTS: A total of 308 concepts were identified and linked to 78 different ICF categories; 35 categories of the component body function, one category of the component body structure, 38 categories of the component activities and participation, and four categories of the component environmental factors. Only contents within the chapters mental functions, mobility and social life were addressed by all instruments. Forty-seven categories were covered by only one instrument. CONCLUSION: The ICF proved highly useful for the comparison of HRQOL instruments. This analysis may help researchers and clinicians to choose the most appropriate HRQOL instrument for a specific purpose as well as help to compare study outcomes of studies using different instruments for HRQOL assessment.

A systematic review assessing soft tissue augmentation techniques

AIM: The aim of the present review was to systematically assess the dental literature in terms of soft tissue grafting techniques. The focused question was: is one method superior over others for augmentation and stability of the augmented soft tissue in terms of increasing the width of keratinized tissue (part 1) and gain in soft tissue volume (part 2). METHODS: A Medline search was performed for human studies focusing on augmentation of keratinized tissue and/or soft tissue volume, and complemented by additional hand searching. Relevant studies were identified and statistical results were reported for meta-analyses including the test minus control weighted mean differences with 95% confidence intervals, the I-squared statistic for tests of heterogeneity, and the number of significant studies. RESULTS: Twenty-five (part 1) and three (part 2) studies met the inclusion criteria; 14 studies (part 1) were eligible for comparison using meta-analyses. An apically positioned flap/vestibuloplasty (APF/V) procedure resulted in a statistically significantly greater gain in keratinized tissue than untreated controls. APF/V plus autogenous tissue revealed statistically significantly more attached gingiva compared with untreated controls and a borderline statistical significance compared with APF/V plus allogenic tissue. Statistically significantly more shrinkage was observed for the APF/V plus allogenic graft compared with the APF/V plus autogenous tissue. Patient-centered outcomes did not reveal any of the treatment methods to be superior regarding postoperative complications. The three studies reporting on soft tissue volume augmentation could not be compared due to lack of homogeneity. The use of subepithelial connective tissue grafts (SCTGs) resulted in statistically significantly more soft tissue volume gain compared with free gingival grafts (FGGs). CONCLUSIONS: APF/V is a successful treatment concept to increase the width of keratinized tissue or attached gingiva around teeth. The addition of autogenous tissue statistically significantly increases the width of attached gingiva. For soft tissue volume augmentation, only limited data are available favoring SCTGs over FGG.

Leg ischemia: assessment with MR angiography and spectroscopy

PURPOSE: To prospectively determine reproducibility of magnetic resonance (MR) angiography and MR spectroscopy of deoxymyoglobin in assessment of collateral vessels and tissue perfusion in patients with critical limb ischemia (CLI) and to follow changes in patients undergoing intramuscular vascular endothelial growth factor (pVEGF)-C gene therapy, percutaneous transluminal angioplasty, supervised exercise training, or no therapy. MATERIALS AND METHODS: Study and gene therapy protocols were approved, and all patients gave written informed consent. To determine repeatability and reproducibility, seven patients underwent MR angiography and five underwent MR spectroscopy. The techniques were used to judge disease progress in 12 other patients with or without therapy: MR angiography to help determine change in visualization of collateral vessels and MR spectroscopy to help assess change in perfusion at proximal and distal calf levels. MR angiographic results were subjectively analyzed by three blinded readers. Intraobserver variability was expressed as 95% confidence interval (CI) (n=7); interobserver variability, as kappa statistic (n=15). Reexamination variability of MR spectroscopy was given as 95% CI for subsequent recovery times, and correlation with disease extent was calculated with Kendall taub rank correlation. Fisher-Yates test was used to correlate changes with pressure measurements and clinical course. RESULTS: Intraobserver and interobserver concordance was sensitive for detection of collateral vessels. Intraobserver agreement was 85.7% (95% CI: 42.1%, 99.6%). Interobserver agreement was high for small collateral vessels (kappa=0.74, P <.001) and fair for large collateral vessels (kappa=0.36, P=.002). MR spectroscopy was reproducible (95% CI: +/-26 seconds for proximal, +/-21 seconds for distal) and showed a correlation with disease extent (proximal calf, taub=0.84, P <.001; distal calf, taub=0.68, P=.04). Small collateral vessels increased over time (P=.04) but did not correlate with pressure measurements and clinical course. Recovery time correlated with clinical course (proximal calf, P=.03; distal calf, P=.005). CONCLUSION: MR angiography and MR spectroscopy of deoxymyoglobin can help document changes in visualization of collateral vessels and tissue perfusion in patients with CLI.

Comparative Analysis of Evolving Software Systems Using the Gini Coefficient

Software metrics offer us the promise of distilling useful information from vast amounts of software in order to track development progress, to gain insights into the nature of the software, and to identify potential problems. Unfortunately, however, many software metrics exhibit highly skewed, non-Gaussian distributions. As a consequence, usual ways of interpreting these metrics --- for example, in terms of "average" values --- can be highly misleading. Many metrics, it turns out, are distributed like wealth --- with high concentrations of values in selected locations. We propose to analyze software metrics using the Gini coefficient, a higher-order statistic widely used in economics to study the distribution of wealth. Our approach allows us not only to observe changes in software systems efficiently, but also to assess project risks and monitor the development process itself. We apply the Gini coefficient to numerous metrics over a range of software projects, and we show that many metrics not only display remarkably high Gini values, but that these values are remarkably consistent as a project evolves over time.

A connection between two nonparametric tests for perfect ranking in balanced ranked set sampling

In this note, we show that an extension of a test for perfect ranking in a balanced ranked set sample given by Li and Balakrishnan (2008) to the multi-cycle case turns out to be equivalent to the test statistic proposed by Frey et al. (2007). This provides an alternative interpretation and motivation for their test statistic.

Prediction of 1-year mortality in patients with acute coronary syndromes undergoing percutaneous coronary intervention: validation of the logistic clinical SYNTAX (Synergy Between Percutaneous Coronary Interventions With Taxus and Cardiac Surgery) score

OBJECTIVES This study sought to validate the Logistic Clinical SYNTAX (Synergy Between Percutaneous Coronary Intervention With Taxus and Cardiac Surgery) score in patients with non-ST-segment elevation acute coronary syndromes (ACS), in order to further legitimize its clinical application. BACKGROUND The Logistic Clinical SYNTAX score allows for an individualized prediction of 1-year mortality in patients undergoing contemporary percutaneous coronary intervention. It is composed of a "Core" Model (anatomical SYNTAX score, age, creatinine clearance, and left ventricular ejection fraction), and "Extended" Model (composed of an additional 6 clinical variables), and has previously been cross validated in 7 contemporary stent trials (>6,000 patients). METHODS One-year all-cause death was analyzed in 2,627 patients undergoing percutaneous coronary intervention from the ACUITY (Acute Catheterization and Urgent Intervention Triage Strategy) trial. Mortality predictions from the Core and Extended Models were studied with respect to discrimination, that is, separation of those with and without 1-year all-cause death (assessed by the concordance [C] statistic), and calibration, that is, agreement between observed and predicted outcomes (assessed with validation plots). Decision curve analyses, which weight the harms (false positives) against benefits (true positives) of using a risk score to make mortality predictions, were undertaken to assess clinical usefulness. RESULTS In the ACUITY trial, the median SYNTAX score was 9.0 (interquartile range 5.0 to 16.0); approximately 40% of patients had 3-vessel disease, 29% diabetes, and 85% underwent drug-eluting stent implantation. Validation plots confirmed agreement between observed and predicted mortality. The Core and Extended Models demonstrated substantial improvements in the discriminative ability for 1-year all-cause death compared with the anatomical SYNTAX score in isolation (C-statistics: SYNTAX score: 0.64, 95% confidence interval [CI]: 0.56 to 0.71; Core Model: 0.74, 95% CI: 0.66 to 0.79; Extended Model: 0.77, 95% CI: 0.70 to 0.83). Decision curve analyses confirmed the increasing ability to correctly identify patients who would die at 1 year with the Extended Model versus the Core Model versus the anatomical SYNTAX score, over a wide range of thresholds for mortality risk predictions. CONCLUSIONS Compared to the anatomical SYNTAX score alone, the Core and Extended Models of the Logistic Clinical SYNTAX score more accurately predicted individual 1-year mortality in patients presenting with non-ST-segment elevation acute coronary syndromes undergoing percutaneous coronary intervention. These findings support the clinical application of the Logistic Clinical SYNTAX score.

Development and validation of GT3X accelerometer cut-off points in 5- to 9-year-old children based on indirect calorimetry measurements

The ActiGraph accelerometer is commonly used to measure physical activity in children. Count cut-off points are needed when using accelerometer data to determine the time a person spent in moderate or vigorous physical activity. For the GT3X accelerometer no cut-off points for young children have been published yet. The aim of the current study was thus to develop and validate count cut-off points for young children. Thirty-two children aged 5 to 9 years performed four locomotor and four play activities. Activity classification into the light-, moderate- or vigorous-intensity category was based on energy expenditure measurements with indirect calorimetry. Vertical axis as well as vector magnitude cut-off points were determined through receiver operating characteristic curve analyses with the data of two thirds of the study group and validated with the data of the remaining third. The vertical axis cut-off points were 133 counts per 5 sec for moderate to vigorous physical activity (MVPA), 193 counts for vigorous activity (VPA) corresponding to a metabolic threshold of 5 MET and 233 for VPA corresponding to 6 MET. The vector magnitude cut-off points were 246 counts per 5 sec for MVPA, 316 counts for VPA - 5 MET and 381 counts for VPA - 6 MET. When validated, the current cut-off points generally showed high recognition rates for each category, high sensitivity and specificity values and moderate agreement in terms of the Kappa statistic. These results were similar for vertical axis and vector magnitude cut-off points. The current cut-off points adequately reflect MVPA and VPA in young children. Cut-off points based on vector magnitude counts did not appear to reflect the intensity categories better than cut-off points based on vertical axis counts alone.

Genome-wide analysis reveals selection for important traits in domestic horse breeds.

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.