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PubMedDate not supplied

Three sides of the same coin: the analysis of paired data from dyads.

Three types of research questions are commonly asked about data from dyads: (1) What are the overall group differences between the two sets of measurements? (2) What is the association between paired data? and (3) What is the agreement between pairs? These three types of questions about the same dyad dataset lead to different analyses, and the answer to one question does not necessarily help in answering the other questions. The purpose of this article is to highlight the differences among these questions and their respective methods of data analysis. The intent is to stress the necessity for congruence between research questions and the analysis, rather than to present a review of all possible methods of analysis of paired data.

Bias↗

PubMed1991

The snRNP E protein multigene family contains five pseudogenes with common mutations.

Sequence data from three previously-uncharacterized members of the snRNP E protein multigene family suggest that each is a non-transcribed processed pseudogene, even though one clone has the potential to code for a full-length protein with greater than 90% similarity to previously-characterized E protein cDNAs. Each of the newly-analyzed family members is without introns, contains a tract of polyadenylic acid residues, and is flanked by short direct repeats. In addition, the three sequences all contain point mutations that distinguish them from the E protein coding sequence. Seven point mutations are common to the three sequences described here and to two previously-described E protein pseudogenes. Although all of these mutations are transitions, only 5 of 7 could have been generated by deamination of methylated cytosines in inactive genes. Thus, the common mutations in the pseudogenes suggest an origin other than the expressed gene that we have described. Allelic variants for two of the pseudogenes were detected and repetitive elements are located near four of the five E protein pseudogenes that have been characterized.

Amino Acid Sequence↗

PubMed2006

Common referent versus shifting referent methods when using case-control data to examine patterns of incidence across multiple exposure variables.

PURPOSE: In case-control studies, when odds ratios estimate rate ratios or risk ratios, trends in odds ratios can reflect trends in incidence in the underlying population. METHODS AND RESULTS: In this report, we use an empirical example and hypothetical data to compare two methods ("common referent" and "shifting referent") for calculating odds ratios from case-control data across multiple exposure variables. With common referent methods, a single independent variable is constructed from the joint distribution of all exposure variables. With shifting referent methods, each stratum-specific trend has its own referent. CONCLUSIONS: Using examples involving a single ordinal "trend" variable and a dichotomous "stratification" variable, we show that common referent odds ratios will reflect the pattern of incidence in the underlying population, whereas odds ratios calculated using shifting referent methods will not.

Case-Control Studies↗

PubMed2006

Bayesian variable selection for the analysis of microarray data with censored outcomes.

MOTIVATION: A common task in microarray data analysis consists of identifying genes associated with a phenotype. When the outcomes of interest are censored time-to-event data, standard approaches assess the effect of genes by fitting univariate survival models. In this paper, we propose a Bayesian variable selection approach, which allows the identification of relevant markers by jointly assessing sets of genes. We consider accelerated failure time (AFT) models with log-normal and log-t distributional assumptions. A data augmentation approach is used to impute the failure times of censored observations and mixture priors are used for the regression coefficients to identify promising subsets of variables. The proposed method provides a unified procedure for the selection of relevant genes and the prediction of survivor functions. RESULTS: We demonstrate the performance of the method on simulated examples and on several microarray datasets. For the simulation study, we consider scenarios with large number of noisy variables and different degrees of correlation between the relevant and non-relevant (noisy) variables. We are able to identify the correct covariates and obtain good prediction of the survivor functions. For the microarray applications, some of our selected genes are known to be related to the diseases under study and a few are in agreement with findings from other researchers. AVAILABILITY: The Matlab code for implementing the Bayesian variable selection method may be obtained from the corresponding author. CONTACT: mvannucci@stat.tamu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗

PubMed1983

Self-care of common illnesses in Denmark.

Survey data collected from a random sample of the Danish population in the first phase of a research investigation of self-care behavior are discussed. Self-administered postal questionnaires were used to obtain data on behavioral responses to common illness conditions. Information was obtained from 1,462 persons regarding care of 3,100 illness episodes. Log-linear analyses of multiway frequency tables were used to examine the effects of sociodemographic and attitudinal variables on the illness responses. Age, sex, perceived health status, and a reliant attitude toward physicians were the more important variables related to the illness behaviors. Interactions among these variables suggest directions for productive research into the factors shaping responses to illness. Income and social class, among respondents in relation to differences in activity levels maintained while ill suggest that some people may have limited options for caring for themselves during illness.

Adolescent↗

PubMed2004

Drug name confusion: evaluating the effectiveness of capital ("Tall Man") letters using eye movement data.

Medication errors commonly involve confusion between drug names that look or sound alike. One possible method of reducing these errors is to print sections of the names in "Tall Man" (capital) letters, in order to emphasise differences between similar products. This paper reports an eye-tracking experiment that evaluates this strategy. Participants had their eye movements monitored while they searched for a target product amongst an array of product packs. The target pack was replaced by a similar distractor in the array. Participants made fewer errors when the appearance of the names had been altered, that is, they were less likely to incorrectly identify a distractor as the target drug. This result was reflected in the eye movement data.

Adult↗

PubMed1994

Source localization using event-related desynchronization (ERD) within the alpha band.

Voluntary finger movements result in a maximal ERD in the 10-12 Hz band close to electrodes C3 and C4, overlying the sensorimotor hand areas. This ERD focus is not very pronounced with EEG data recorded against a common reference electrode (monopolar recording). After transformation of the raw data using common average, local average and weighted average reference and the Hjorth method, respectively, the ERD becomes enhanced over electrodes C3 or C4. Movement-related EEG data were studied with 17, 19, 30 and 56 electrode montages using large and small interelectrode distances. The best focused ERD was obtained with a 56 electrode montage with small interelectrode distances and local average reference data.

Alpha Rhythm↗

PubMed2004

Assessment of the functional method of hip joint center location subject to reduced range of hip motion.

Motion analysis of the lower extremities usually requires determination of the location of the hip joint center. The results of several recent studies have suggested that kinematic and kinetic variables calculated from motion analysis data are highly sensitive to errors in hip joint center location. "Functional" methods in which the location of the hip joint center is determined from the relative motion of the thigh and pelvis, rather than from the locations of bony landmarks, are promising but may be ineffective when motion is limited. The aims of the present study were to determine whether the accuracy of the functional method is compromised in young and elderly subjects when limitations on hip motion are imposed and to investigate the possibility of locating the hip joint center using data collected during commonly studied motions (walking, sit-to-stand, stair ascent, stair descent) rather than using data from an ad hoc trial in which varied hip motions are performed. The results of the study suggested that functional methods would result in worst-case hip joint center location errors of 26mm (comparable to the average errors previously reported for joint center location based on bony landmarks) when available hip motion is substantially limited. Much larger errors ( approximately 70mm worst-case), however, resulted when hip joint centers were located from data collected during commonly performed motions, perhaps because these motions are, for the most part, restricted to the sagittal plane. It appears that the functional method can be successfully implemented when range of motion is limited but still requires collection of a special motion trial in which hip motion in both the sagittal and frontal planes is recorded.

Adult↗

PubMedDate not supplied

A multiple imputation strategy for incomplete longitudinal data.

Longitudinal studies are commonly used to study processes of change. Because data are collected over time, missing data are pervasive in longitudinal studies, and complete ascertainment of all variables is rare. In this paper a new imputation strategy for completing longitudinal data sets is proposed. The proposed methodology makes use of shrinkage estimators for pooling information across geographic entities, and of model averaging for pooling predictions across different statistical models. Bayes factors are used to compute weights (probabilities) for a set of models considered to be reasonable for at least some of the units for which imputations must be produced, imputations are produced by draws from the predictive distributions of the missing data, and multiple imputations are used to better reflect selected sources of uncertainty in the imputation process. The imputation strategy is developed within the context of an application to completing incomplete longitudinal variables in the so-called Area Resource File. The proposed procedure is compared with several other imputation procedures in terms of inferences derived with the imputations, and the proposed methodology is demonstrated to provide valid estimates of model parameters when the completed data are analysed. Extensions to other missing data problems in longitudinal studies are straightforward so long as the missing data mechanism can be assumed to be ignorable.

Bayes Theorem↗

PubMedDate not supplied

Resampling techniques in the analysis of non-binormal ROC data.

The methods most commonly used for analyzing receiver operating characteristic (ROC) data incorporate "binormal" assumptions about the latent frequency distributions of test results. Although these assumptions have proved robust to a wide variety of actual frequency distributions, some data sets do not "fit" the binormal model. In such cases, resampling techniques such as the jackknife and the bootstrap provide versatile, distribution-independent, and more appropriate methods for hypothesis testing. This article describes the application of resampling techniques to ROC data for which the binormal assumptions are not appropriate, and suggests that the bootstrap may be especially helpful in determining confidence intervals from small data samples. The widespread availability of ever-faster computers has made resampling methods increasingly accessible and convenient tools for data analysis.

Bias↗

PubMed2004

Microarray data analysis: from hypotheses to conclusions using gene expression data.

We review several commonly used methods for the design and analysis of microarray data. To begin with, some experimental design issues are addressed. Several approaches for pre-processing the data (filtering and normalization) before the statistical analysis stage are then discussed. A common first step in this type of analysis is gene selection based on statistical testing. Two approaches, permutation and model-based methods are explained and we emphasize the need to correct for multiple testing. Moreover, powerful approaches based on gene sets are mentioned. Clustering of either genes or samples is frequently performed when analyzing microarray data. We summarize the basics of both supervised and unsupervised clustering (classification). The latter may be of use for creating diagnostic arrays, for example. Construction of biological networks, such as pathways, is a statistically challenging but complex task that is a relatively new development and hence mentioned only briefly. We finish with some remarks on literature and software. The emphasis in this paper is on the philosophy behind several statistical issues and on a critical interpretation of microarray related analysis methods.

Cluster Analysis↗

PubMed1994

Modeling of carbon-11-acetate kinetics by simultaneously fitting data from multiple ROIs coupled by common parameters.

UNLABELLED: One of the unique aspects of PET is its ability to noninvasively quantify metabolic processes. Metabolic rate parameters are estimated by fitting the time-activity curves from regions of interest (ROIs) placed on dynamic PET images with a kinetic model. In many cases it is possible to couple these datasets with common parameters, such as the time delay between arrival of tracer in the ROIs and the sampling site. METHODS: Data from eight ROIs placed about images of the myocardium were coupled by the parameters describing the metabolite concentration in the blood. The method was evaluated by comparing estimates of k2 made using the coupled region method and the standard process of fitting data from each region separately. In addition, comparisons were made between estimates of k2 and measured myocardial oxygen consumption. RESULTS: Very little change in mean values of k2 was obtained. The variances, however, were reduced by an average of 37%, compared to the standard method, when the common parameters were not constrained. When the values of the common metabolite parameters were constrained to values previously measured, the average variance in estimates of k2 was reduced by 30%. CONCLUSION: We have demonstrated that the use of this technique can significantly increase the precision of estimates of myocardial oxygen consumption utilizing 11C-acetate PET images. More precise estimates of such quantities can facilitate detection of small regional and/or temporal physiological changes measured with PET. Furthermore, this method can be utilized whenever it is known a priori that one or more kinetic model parameters has the same value for every set of ROI data.

Acetates↗

PubMed2004

Do pregnancy complications and CVD share common antecedents?

Considerable data link low birth weight, due to intrauterine growth restriction, to increased offspring risk of vascular disease in later adult life. This is considered to be the result, in part, of programming through fetal nutrition. These data support the hypothesis that pregnancy outcome in terms of birth weight is linked to the infant's subsequent health. In contrast, much less attention has been focused on the relationship between adverse pregnancy outcomes, such as pre-eclampsia, gestational diabetes, pre-term delivery and intrauterine growth restriction, and the mother's subsequent health. Interesting data have accumulated linking the maternal vascular, metabolic and inflammatory complications of pregnancy to an increased risk of vascular disease in later life (Table 1). This paper reviews the emerging evidence to support this fascinating concept, addresses potential mechanisms and discusses potential clinical implications.

Cardiovascular Diseases↗

PubMed2004

Distance dependence of interactions between charged centres in proteins with common structural features.

Data collected for interactions among redox centres, and interactions between redox centres and acid-base residues in a family of small multihaem cytochromes are analysed. The distance dependent attenuation of the interactions between non-surface charges, for separations that range from 8 to 23 angstroms, can be described by a simple function derived from the Debye-Huckel formalism, fit to 9.5 and 7.6 as values for the relative dielectric constant and Debye length, respectively. However, there is considerable scatter in the data despite the structural similarities among the proteins, which is discussed in the framework of using such simple models in predicting properties of novel proteins.

Amino Acids, Acidic↗

PubMed2004

Diffusion tensor magnetic resonance image regularization.

As multi-dimensional complex data become more common, new regularization schemes tailored to those data are needed. In this paper we present a scheme for regularising diffusion tensor magnetic resonance (DT-MR) data, and more generally multi-dimensional data defined by a direction map and one or several magnitude maps. The scheme is divided in two steps. First, a variational method is proposed to restore direction fields with preservation of discontinuities. Its theoretical aspects are presented, as well as its application to the direction field that defines the main orientation of the diffusion tensors. The second step makes use of an anisotropic diffusion process to regularize the magnitude maps. The main idea is that for a range of data it is possible to use the restored direction as a prior to drive the regularization process in a way that preserves discontinuities and respects the local coherence of the magnitude map. We show that anisotropic diffusion is a convenient framework to implement that idea, and define a regularization process for the magnitude maps from our DT-MR data. Both steps are illustated on synthetic and real diffusion tensor magnetic resonance data.

Algorithms↗

PubMed2003

Combined support for wholesale taxic atavism in gavialine crocodylians.

Morphological and molecular data sets favor robustly supported, contradictory interpretations of crocodylian phylogeny. A longstanding perception in the field of systematics is that such significantly conflicting data sets should be analyzed separately. Here we utilize a combined approach, simultaneous analyses of all relevant character data, to summarize common support and to reconcile discrepancies among data sets. By conjoining rather than separating incongruent classes of data, secondary phylogenetic signals emerge from both molecular and morphological character sets and provide solid evidence for a unified hypothesis of crocodylian phylogeny. Simultaneous analyses of four gene sequences and paleontological data suggest that putative adaptive convergences in the jaws of gavialines (gavials) and tomistomines (false gavials) offer character support for a grouping of these taxa, making Gavialinae an atavistic taxon. Simple new methods for measuring the influence of extinct taxa on topological support indicate that in this vertebrate order fossils generally stabilize relationships and accentuate hidden phylogenetic signals. Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed.

Adaptation, Biological↗

PubMed1997

US-based evaluation of hemodynamic parameters in the common carotid artery: a nomogram trial.

PURPOSE: To evaluate hemodynamic data of the common carotid artery (CCA) with an ultrasound (US)-based technique in an age- and sex-matched healthy population. MATERIALS AND METHODS: Measurements from a color M-mode tracing of each CCA in 205 healthy subjects (age range, 20-87 years) were performed with a time domain processing system. Lumen change of the color M-mode tracing, flow velocity, volume flow rate, and diastolic volume index (DVI) were calculated five times. Blood pressure was measured after the US examination. Fifteen subjects were excluded from the nomogram trial because of hypertension, and 12 and four subjects were excluded because of an asymptomatic carotid artery stenosis or atrial fibrillation, respectively. RESULTS: Mean volume flow rate in the CCA of the remaining 174 healthy volunteers was 415.0 mL/min +/- 87.0 (men [n = 84], 441.0 mL/min +/- 95.5; women [n = 90], 390.2 mL/min +/- 70.5). The following statistically significant associations were noted: between vessel lumen and sex and blood pressure; between peak systolic velocity and sex and age; between volume flow rate and sex, age, and systolic blood pressure; and between DVI and age, heart rate, and systolic and diastolic blood pressure. CONCLUSION: Time domain processing is an intrasessionally well-reproducible US method for measuring velocities and volume flow in the CCA.

Adult↗

PubMed2006

Patient expectations of fair complaint handling in hospitals: empirical data.

BACKGROUND: A common finding in several studies is patients' dissatisfaction with complaint handling in health care. The reasons why are for the greater part unknown. The key to an answer may be found in a better understanding of patients' expectations. We investigated patients' expectations of complaint handling in hospitals. METHODS: Subjects were patients who had lodged a complaint at the complaint committees of 74 hospitals in the Netherlands. A total of 424 patients (response 75%) completed a written questionnaire at the start of the complaint procedures. Derived from justice theory, we asked what they expected from fair procedures, fair communication and fair outcome of complaint handling. RESULTS: The predominant reason for complainants to lodge a complaint was to prevent the incident from happening again. Complainants expected fair procedures from the complaint committee, in particular an impartial position. This was most important to 87% of the complainants. They also expected to be treated respectfully. Furthermore, they expected the hospital and the professional involved to respond to their complaint. A change in hospital performances was the most wanted outcome of complaint handling, according to 79% of the complainants. They also expected disclosure from the professionals. Professionals should admit a mistake when it had occurred. More complainants (65%) considered it most important to get an explanation than an apology (41%). Only 32% of complainants expected the professional to make an effort to restore the doctor-patient relationship. A minority of complainants (7%) wanted financial compensation. CONCLUSION: Nearly all complainants want to prevent the incident from happening again, not out of pure altruism, but in order to restore their sense of justice. We conclude that complaint handling that does not allow for change is unlikely to meet patients' expectations. Secondly, complaint handling should not be left exclusively to complaint committees, the responses of hospital and professionals are indispensable.

Communication↗