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PubMed1997

Factor structure of the Dementia Mood Assessment Scale in a cohort of community-dwelling elderly.

We examined the factor structure of the 28-item Dementia Mood Assessment Scale (DMAS), an instrument to assess depressive symptoms in older adults with cognitive impairment, in a cohort of 165 community-dwelling elderly with varying degrees of cognitive impairment. Factor analysis using principal components analysis and varimax rotation was performed to explore the presence of subscales and examine construct validity. A five-factor structure involving all 28 items accounting for 63.2% of the variance in the DMAS scores was derived. Factors were named: Depressed Affect, Environmental Interaction, Diurnal Patterns, Agitation/Suspicion, and Somatic Indicators. This factor structure reflects the often differing presentations of depressive symptoms in older adults with varying degrees of cognitive function and establishes the construct validity of the DMAS in this population. We conclude that the DMAS may be used for differentiated clinical assessment of depressive symptoms along major dimensions of depressive illness in this cohort of elderly.

Aged↗
PubMed2005

The advantages and limitations of protein crystal structures.

Crystal structure analysis using X-ray diffraction is, in many cases, the most advanced method available for obtaining high-resolution structural information about biological macromolecules. The ways in which X-ray diffraction data are collected and refined have a strong impact on the final quality of the structural models and the type and magnitude of their associated errors. It is becoming increasingly necessary for both structural and non-structural biologists to judge the reliability and accuracy of these models, which are being used in many aspects of research, including structure-based drug design, and to address detailed functional biological questions. In this article, we discuss how errors in these models arise and how they can be evaluated, and we argue for even more stringent validation checks and documentation of structures before deposition with the Protein Data Bank.

Crystallization↗
PubMed2004

Do logbooks influence recall of physical activity in validation studies?

PURPOSE: To examine whether physical activity logbooks influence estimates of validity of 7-d recall physical activity questionnaires. METHODS: A convenience sample of 551 adults aged 18-75 yr wore an MTI accelerometer for seven consecutive days and were then randomly administered two of four 7-d recall physical activity questionnaires that varied in length and format (Active Australia Survey (AAS), long and short International Physical Activity Questionnaires (IPAQ-L and IPAQ-S), and Behavioral Risk Factor Surveillance System (BRFSS)). A subsample of 75% concurrently completed a physical activity logbook. RESULTS: Correlations (rho) between self-reported and measured duration of moderate- and vigorous-intensity activity and total activity were similar among participants who received a logbook and those who did not for each of the four instruments. There was also no interaction between assessment method (survey, accelerometer) and the assignment of a logbook. For the IPAQ-L, however, variability in the difference between accelerometer data and responses to the vigorous items was smaller among those assigned a logbook (F = 4.128, df = 260, P = 0.043). Overall, there were no differences in percent agreement or kappa for participation in sufficient levels of physical activity according to receipt of a logbook for any of the surveys. CONCLUSION: The process of self-monitoring through completion of a logbook does not appear to influence estimates of validity for brief or long questionnaires with global questions. Whereas the magnitude of error in accuracy of recall of particular types of activity may be reduced by completion of a logbook that is similar in structure to the survey being validated, this does not appear to influence overall estimates of validity.

Adolescent↗
PubMed2004

Performance of the Swedish SF-36 version 2.0.

OBJECTIVES: To evaluate the performance of the first non-English (Swedish) SF-36 version 2.0 (V2) regarding scaling assumptions, reliability and validity, with special emphasis on the effects of extending the response scales of the two role functioning scales, role physical (RP) and role emotional (RE), from a dichotomous to a five-step format. METHODS: Questionnaires were mailed to a non-stratified, random national sample of 3000 18-75 year old Swedish residents in 1998-1999. Methods traditionally used in evaluating the original US SF-36 version 1.0 (V1) and other international versions were applied. RESULTS: A total of 73% of the questionnaires were returned. Scaling assumptions were satisfactorily met and generally enhanced compared with V1, particularly regarding the role functioning scales. Floor/ceiling effects were reduced and reliability estimates increased for the role scales. The factor structure was replicated and the relative validity of the role scales as measures of their components increased. Overall, the tests of the criterion-based validity using known groups comparisons produced results supporting hypotheses: scales from the physical domain distinguished best between groups expected to differ in physical health; and scales comprising the mental domain distinguished best between groups expected to differ in mental health. Furthermore, hypothesized differences in mean scale scores as a function of age and social risk factors were confirmed. CONCLUSIONS: The changes to the response formats of the role functioning scales have improved their precision, reliability and validity without jeopardizing the underlying structure of the original SF-36. These changes will likely further enhance the responsiveness of the SF-36.

Activities of Daily Living↗
PubMed1998

Subunit organization and structure in the F0 sector of Escherichia coli F1F0 ATP synthase.

In this review, we summarize recent work from our laboratory which establishes the topology and nearest neighbor organization of subunits in the F0 sector of the H+ transporting ATP synthase of Escherichia coli. The E. coli F0 sector is composed of three subunits in an a1b2c12 stoichiometric ratio. Crosslinking experiments with genetically introduced Cys establish a ring-like organization of the 12 c subunits with subunits a and b lying to the outside of the ring. The results are interpreted using an atomic resolution structural model of monomeric subunit c in a chloroform-methanol-water (4:4:1, v/v/v) solution, derived by heteronuclear NMR (M.E. Girvin, F. Abildgaard, V. Rastogi, J. Markley, R.H. Fillingame, in press). The crosslinking results validate many predictions of the structural model and confirm a front-to-back-type packing of two subunit c into a functional dimer, as was first predicted from genetic studies. Aspartyl-61, the proton translocating residue, lies at the center of the four transmembrane helices of the functional dimer, rather than at the periphery of the subunit c ring. Subunit a is shown to fold with five transmembrane helices, and a functionally important interaction of transmembrane helix-4 with transmembrane helix-2 of subunit c is established. The single transmembrane helices of the two subunit b dimerize in the membrane. The structure of the transmembrane segment of subunit b is predicted from the NMR structure of the monomeric peptide.

Dimerization↗
PubMed2005

Disulfide connectivity prediction using secondary structure information and diresidue frequencies.

MOTIVATION: We describe a stand-alone algorithm to predict disulfide bond partners in a protein given only the amino acid sequence, using a novel neural network architecture (the diresidue neural network), and given input of symmetric flanking regions of N-terminus and C-terminus half-cystines augmented with residue secondary structure (helix, coil, sheet) as well as evolutionary information. The approach is motivated by the observation of a bias in the secondary structure preferences of free cysteines and half-cystines, and by promising preliminary results we obtained using diresidue position-specific scoring matrices. RESULTS: As calibrated by receiver operating characteristic curves from 4-fold cross-validation, our conditioning on secondary structure allows our novel diresidue neural network to perform as well as, and in some cases better than, the current state-of-the-art method. A slight drop in performance is seen when secondary structure is predicted rather than being derived from three-dimensional protein structures.

Algorithms↗
PubMed2004

Stability-based validation of clustering solutions.

Data clustering describes a set of frequently employed techniques in exploratory data analysis to extract "natural" group structure in data. Such groupings need to be validated to separate the signal in the data from spurious structure. In this context, finding an appropriate number of clusters is a particularly important model selection question. We introduce a measure of cluster stability to assess the validity of a cluster model. This stability measure quantifies the reproducibility of clustering solutions on a second sample, and it can be interpreted as a classification risk with regard to class labels produced by a clustering algorithm. The preferred number of clusters is determined by minimizing this classification risk as a function of the number of clusters. Convincing results are achieved on simulated as well as gene expression data sets. Comparisons to other methods demonstrate the competitive performance of our method and its suitability as a general validation tool for clustering solutions in real-world problems.

Algorithms↗
PubMed1996

Validation of the use of intermolecular NOE constraints for obtaining docked structures of protein-ligand complexes.

The use of intermolecular NOEs for docking a small ligand molecule into its target protein has been investigated with the aim of determining the effectiveness and methodology of this type of NOE docking calculation. A high-resolution X-ray structure of a protein-ligand complex has been used to simulate loose distance constraints of varying degrees of quality, typical of those estimated from experimental NOE intensities. These simulated data were used to examine the effect of the number, distribution and representation of the experimental constraints on the precision and accuracy of the calculated structures. A standard simulated annealing protocol was used, as well as a more novel method based on rigid-body dynamics. The results showed some analogies with those from similar studies on complete protein NMR structure determinations, but it was found that more constraints per torsion angle are required to define docked structures of similar quality. The effectiveness of different NOE-constraint averaging methods was explored and the benefits of using 'R-6 averaging' rather than 'centre averaging' with small sets of NOE constraints were shown. The starting protein structure used in docking calculations was obtained from previous X-ray or NMR structure studies on a related complex. The effects on the calculated conformations of introducing structural differences into the binding site of the initial protein structure were also considered.

Binding Sites↗
PubMed2005

Factorial structure and internal consistency of the German TEMPS-A scale: validation against the NEO-FFI questionnaire.

BACKGROUND: The purpose of the study was to evaluate the psychometric properties of the German version of the TEMPS-A questionnaire. Besides the reliability of the temperament scales, validity was the focus of interest. Therefore, the relationship between the TEMPS-A and the well-established personality questionnaire NEO-FFI, whose factors show theoretical overlap with temperaments, was investigated. METHOD: A total of 227 students aged between 20 and 42 years were asked to fill in both instruments. Reliability coefficients for the five temperament scales and correlations among the scales of both questionnaires were calculated, as well as multiple linear regression analysis with the five personality factors and gender as independent, and the five temperaments as dependent variables. RESULTS: Reliability indices for the five temperament scales were satisfactory, with values ranging between 0.63 (depressive) and 0.76 (anxious). Women scored higher on depressive and anxious scales, whereas men had higher scores on hyperthymic temperament. Correlations within the temperament scales showed close relationships between depressive, anxious and cyclothymic temperaments; cyclothymic and irritable temperament were also related. The personality factors of the NEO-FFI predicted temperaments fairly well and explained between 41% and 58% of the variance; the main effects were exerted by neuroticism and extraversion, while the irritable temperament was primarily explained by low agreeableness. LIMITATION: The study sample was relatively small and selected. CONCLUSION: The TEMPS-A scale has sufficient reliability and good validity in a non-clinical sample. It opens new possibilities for clinical research at the interface of mental disorders, temperament and personality. Such research is in progress.

Adolescent↗
PubMed2003

Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures.

MOTIVATION: Multiple sequence alignments are essential tools for establishing the homology relations between proteins. Essential amino acids for the function and/or the structure are generally conserved, thus providing key arguments to help in protein characterization. However for distant proteins, it is more difficult to establish, in a reliable way, the homology relations that may exist between them. In this article, we show that secondary structure prediction is a valuable way to validate protein families at low identity rate. RESULTS: We show that the analysis of the secondary structures compatibility is a reliable way to discard non-related proteins in low identity multiple alignment. AVAILABILITY: This validation is possible through our NPS@ server (http://npsa-pbil.ibcp.fr)

Algorithms↗
PubMed2003

Detection of structural differences between the brains of schizophrenic patients and controls.

This paper investigates the validity of the null hypothesis: there are no structural differences between the brains of schizophrenic and normal control subjects that manifest themselves in MRI-T(2) data and distinguish the two populations in a statistically significant way. The data used refer to 21 schizophrenic patients and 19 normal controls, matched for age, sex and social background. The methodology used is based on three-dimensional texture analysis, which is used to quantify anisotropy in the data at scales of the order of a few millimetres. These data reject the null hypothesis. In addition, this article attempts to identify the regions of the brain that are responsible for the morphological characteristics that distinguish the two populations. For this purpose, it utilises a second texture analysis method that, in spite of being a global method, allows one to trace back to the data the origin of the features that most distinctly distinguish the two populations. This method indicates that the features that distinguish the two populations with P values smaller than 10(-6) are located in the most inferior part of the brain and in particular in the tissue that makes up the sulci. It is stressed that in order to preserve the integrity of the data for texture calculations, no registration of anatomical structures is performed, and the most inferior part of the brain is identified as referring to those slices of the scans that visually correspond to slices 1-12 of the Talairach and Tournoux brain atlas.

Adult↗
PubMed2003

Prodromal assessment with the structured interview for prodromal syndromes and the scale of prodromal symptoms: predictive validity, interrater reliability, and training to reliability.

As the number of studies related to the early identification of and intervention in the schizophrenia prodrome continues to grow, it becomes increasingly critical to develop methods to diagnose this new clinical entity with validity. Furthermore, given the low incidence of patients and the need for multisite collaboration, diagnostic and symptom severity reliability is also crucial. This article provides further data on these psychometric parameters for the prodromal assessment instruments developed by the Prevention through Risk Identification, Management, and Education (PRIME) prodromal research team at Yale University: the Structured Interview for Prodromal Syndromes and the Scale of Prodromal Symptoms. It also presents data suggesting that excellent interrater reliability can be established for diagnosis in a day-and-a-half-long training workshop.

Adolescent↗
PubMed2004

Australian data and psychometric properties of the Strengths and Difficulties Questionnaire.

OBJECTIVE: We examine the Australian psychometric properties of the Strengths and Difficulties Questionnaire (SQD), a brief screening measure of behavioural and emotional problems in children and adolescents. METHOD: Using a large community sample (n = 1359) of young Australian children (4-9 years), we assessed the internal consistency, stability, and external validity of the parent-report SDQ. Normative data and cut-offs were also produced. RESULTS: Moderate to strong internal reliability was exhibited across all SDQ subscales, and support was found for the original five-factor structure of the measure. Adequate validity was evidenced in the relationship of these scales to one another, while correlations between the SDQ subscales, teacher ratings, and diagnostic interviews demonstrated sound external validity. SDQ total difficulties scores were associated with concurrent treatment status and scores over a 12-month period were stable. CONCLUSIONS: The current study of the SDQ with Australian children presents evidence of sound psychometric properties. Being the first study to empirically support the use of the SDQ in Australia, it is recommended that the youth and teacher-report forms of the measure receive similar attention in the future.

Adolescent↗
PubMedDate not supplied

Initial validation of two opiate craving questionnaires the obsessive compulsive drug use scale and the desires for drug questionnaire.

In the present study, the factor structure, internal consistency, and the concurrent validity of two heroin craving questionnaires are examined. The Desires for Drug Questionnaire (DDQ) measures three factors: desire and intention, negative reinforcement, and control. The Obsessive Compulsive Drug Use Scale (OCDUS) also measures three factors: thoughts about heroin and interference, desire and control, and resistance to thoughts and intention. Subjects were 102 Dutch patients who were currently in treatment for drug dependency. All proposed scales have good reliability and concurrent validity. Implementation of these instruments in both clinical and research field is advocated.

Adult↗
PubMed2006

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures.

BACKGROUND: Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selection methods are limited by uncertainties in RNA secondary structure prediction. If all the predicted structures of a given mRNA within a certain energy limit could be used simultaneously, target site selection would obviously be improved in both reliability and efficiency. In this study, some key problems in ODN target selection on the basis of multiple predicted target mRNA structures are systematically discussed. RESULTS: Two methods were considered for merging topologically different RNA structures into integrated representations. Several parameters were derived to characterize local target site structures. Statistical analysis on a dataset with 448 ODNs against 28 different mRNAs revealed 9 features quantitatively associated with efficacy. Features of structural consistency seemed to be more highly correlated with efficacy than indices of the proportion of bases in single-stranded or double-stranded regions. The local structures of the target site 5' and 3' termini were also shown to be important in target selection. Neural network efficacy predictors using these features, defined on integrated structures as inputs, performed well in "minus-one-gene" cross-validation experiments. CONCLUSION: Topologically different target mRNA structures can be merged into integrated representations and then used in computer-aided ODN design. The results of this paper imply that some features characterizing multiple predicted target site structures can be used to predict ODN efficacy.

Algorithms↗