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PubMed1996

The assessment of obsessive-compulsive phenomena: psychometric and normative data on the Padua Inventory from an Australian non-clinical student sample.

The Padua Inventory (PI) is a measure of obsessive-compulsive phenomena, which is used in clinical and research settings. One reason for the PI's growing acceptance is the emergence of a good deal of evidence supporting the adequacy of its reliability, convergent validity, and evidence supporting the stability of its factor structure. However, there have been some concerns about its discriminant validity. The use of the PI in Australia has been limited by the lack of local normative data and information about its psychometric properties. The cross-national validation of the PI has both theoretical and practical implications, and could add further evidence for its adequacy as a measure of obsessive-compulsive phenomena. Results from the present study found that the PI exhibited a similar but not identical factor structure compared to previous studies, consistently good reliability, adequate convergent validity, and differences in normative data compared with previous studies. Overall, while one may not necessarily assume the generalisability of normative data across different cultural contexts, there is a good deal of consistency in the psychometric properties of the PI. However, there is a need to further demonstrate the PI's discriminant validity, particularly for the "Urges and Worries" subscale.

Adolescent↗
PubMed1996

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.

The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a number of plots in PostScript format and summary statistics. These various analyses indicate both the degree of agreement of the model structures with the experimental dat, and the quality of their geometrical properties. They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results.

Amino Acid Sequence↗
PubMed2006

Introduction and validation of an invariom database for amino-acid, peptide and protein molecules.

A database of invarioms for structural refinement of amino-acid, oligopeptide and protein molecules is presented. The spherical scattering factors of the independent atom or promolecule model are replaced by ;individual' aspherical scattering factors that take into account the chemical environment of a bonded atom. All amino acids were analysed in terms of their invariom fragments. In order to generate 73 database entries that cover this class of compounds, 37 model compounds were geometry-optimized and theoretical structure factors were calculated. Multipole refinements were then performed on these theoretical structure factors to yield the invariom database. Validation of this database on an extensive number of experimental small-molecule crystal structures of varying quality and resolution shows that invariom modelling improves various figures of merit. Differences in figures of merit between invariom and promolecule models give insight into the importance of disorder for future protein-invariom refinements. The suitability of structural data for application of invarioms can be predicted by Cruickshank's diffraction-component precision index [Cruickshank (1999), Acta Cryst. D55, 583-601].

Amino Acids↗
PubMed2002

Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated assignment of the NOESY spectra. CANDID uses an iterative approach with multiple cycles of NOE cross-peak assignment and protein structure calculation using the fast DYANA torsion angle dynamics algorithm, so that the result from each CANDID cycle consists of exhaustive, possibly ambiguous NOE cross-peak assignments in all available spectra and a three-dimensional protein structure represented by a bundle of conformers. The input for the first CANDID cycle consists of the amino acid sequence, the chemical shift list from the sequence-specific resonance assignment, and listings of the cross-peak positions and volumes in one or several two, three or four-dimensional NOESY spectra. The input for the second and subsequent CANDID cycles contains the three-dimensional protein structure from the previous cycle, in addition to the complete input used for the first cycle. CANDID includes two new elements that make it robust with respect to the presence of artifacts in the input data, i.e. network-anchoring and constraint-combination, which have a key role in de novo protein structure determinations for the successful generation of the correct polypeptide fold by the first CANDID cycle. Network-anchoring makes use of the fact that any network of correct NOE cross-peak assignments forms a self-consistent set; the initial, chemical shift-based assignments for each individual NOE cross-peak are therefore weighted by the extent to which they can be embedded into the network formed by all other NOE cross-peak assignments. Constraint-combination reduces the deleterious impact of artifact NOE upper distance constraints in the input for a protein structure calculation by combining the assignments for two or several peaks into a single upper limit distance constraint, which lowers the probability that the presence of an artifact peak will influence the outcome of the structure calculation. CANDID test calculations were performed with NMR data sets of four proteins for which high-quality structures had previously been solved by interactive protocols, and they yielded comparable results to these reference structure determinations with regard to both the residual constraint violations, and the precision and accuracy of the atomic coordinates. The CANDID approach has further been validated by de novo NMR structure determinations of four additional proteins. The experience gained in these calculations shows that once nearly complete sequence-specific resonance assignments are available, the automated CANDID approach results in greatly enhanced efficiency of the NOESY spectral analysis. The fact that the correct fold is obtained in cycle 1 of a de novo structure calculation is the single most important advance achieved with CANDID, when compared with previously proposed automated NOESY assignment methods that do not use network-anchoring and constraint-combination.

Algorithms↗
PubMed2005

Sources of validity evidence for an internal medicine student evaluation system: an evaluative study of assessment methods.

BACKGROUND: Medical students' final clinical grades in internal medicine are based on the results of multiple assessments that reflect not only the students' knowledge, but also their skills and attitudes. OBJECTIVE: To examine the sources of validity evidence for internal medicine final assessment results comprising scores from 3 evaluations and 2 examinations. METHODS: The final assessment scores of 8 cohorts of Year 4 medical students in a 6-year undergraduate programme were analysed. The final assessment scores consisted of scores in ward evaluations (WEs), preceptor evaluations (PREs), outpatient clinic evaluations (OPCs), general knowledge and problem-solving multiple-choice questions (MCQs), and objective structured clinical examinations (OSCEs). Sources of validity evidence examined were content, response process, internal structure, relationship to other variables, and consequences. RESULTS: The median generalisability coefficient of the OSCEs was 0.62. The internal consistency reliability of the MCQs was 0.84. Scores for OSCEs correlated well with WE, PRE and MCQ scores with observed (disattenuated) correlation of 0.36 (0.77), 0.33 (0.71) and 0.48 (0.69), respectively. Scores for WEs and PREs correlated better with OSCE than MCQ scores. Sources of validity evidence including content, response process, internal structure and relationship to other variables were shown for most components. CONCLUSION: There is sufficient validity evidence to support the utilisation of various types of assessment scores for final clinical grades at the end of an internal medicine rotation. Validity evidence should be examined for any final student evaluation system in order to establish the meaningfulness of the student assessment scores.

Clinical Competence↗
PubMed1993

The factor structure of ADHD items in DSM-III-R: internal consistency and external validation.

Previous research employing factor-analytic procedures to study the underlying dimensions of DSM-III attention deficit disorder with hyperactivity (ADDH) symptoms have consistently supported a two-factor model. Revision of the structure of the ADHD diagnosis in DSM-III-R, as well as inclusion of new items, has raised the question of comparability of the two diagnoses. To explore the significance of these changes, teacher ratings of DSM-III ADDH items and DSM-III-R ADHD items of 85 nonreferred school children were factor-analyzed to determine their underlying factor structures. A similar two-factor solution was obtained for each diagnostic scale. The factors consisted of items believed to reflect inattention and hyperactivity-impulsivity constructs. These factors were further evaluated against results of a cognitive test battery to ascertain whether objective, external validation could be demonstrated. The hyperactivity-impulsivity factor scores were related to continuous performance test measures of response inhibition, while inattention-disorganization factor scores were related to measures of attention and visual search. Implications for assessment and diagnosis of ADHD are discussed.

Attention Deficit Disorder with Hyperactivity↗
PubMed2003

Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation.

The description of the nonbonded contact terms used in simulated annealing refinement can have a major impact on nucleic acid structures generated from NMR data. Using complete dipolar coupling cross-validation, we demonstrate that substantial improvements in coordinate accuracy of NMR structures of RNA can be obtained by making use of two conformational database potentials of mean force: a nucleic acid torsion angle database potential consisting of various multidimensional torsion angle correlations; and an RNA specific base-base positioning potential that provides a simple geometric, statistically based, description of sequential and nonsequential base-base interactions. The former is based on 416 nucleic acid crystal structures solved at a resolution of </=2 A and an R-factor </=25%; the latter is based on 131 RNA crystal structures solved at a resolution of </=3 A and an R-factor of </=25%, and includes both the large and small subunits of the ribosome. The application of these two database potentials is illustrated for the structure refinement of an RNA aptamer/theophylline complex for which extensive NOE and residual dipolar coupling data have been measured in solution.

Databases, Nucleic Acid↗
PubMed1992

Tyrosine-derived polycarbonates: backbone-modified "pseudo"-poly (amino acids) designed for biomedical applications.

Starting from L-tyrosine (Tyr) and its metabolites desaminotyrosine (Dat) and tyramine (Tym), four structurally related model dipeptides were prepared: Dat-Tym (neither N- or C-terminus present), Z-Tyr-Tym (N-terminus protected by benzyloxycarbonyl), Dat-Tyr-Hex (C-terminus protected by a hexyl ester group), and Z-Tyr-Tyr-Hex (both N- and C-termini present, protected by benzyloxycarbonyl and hexyl ester, respectively). The model dipeptides were used as monomers in the synthesis of polycarbonates. The polymerization reaction in the presence of either phosgene or triphosgene proceeded via the phenolic hydroxyl groups. Polymers with molecular weights of 105,000-400,000 da (by gel permeation chromatography, relative to polystyrene standards) were obtained. The physicomechanical properties (solubility, mechanical strength, glass transition and decomposition temperature, processibility) of the polymers were determined, and an attempt was made to correlate the polymer properties with the nature of the N- and C-terminus protecting groups. The presence of the urethane bond at the N-terminus protecting group was found to reduce solubility, ductility, and processibility, probably due to interchain hydrogen bonding. The presence of a C-terminus alkyl ester group increased solubility and processibility. Thus, the most promising candidate polymer for biomedical applications was obtained from Dat-Tyr-Hex, the monomer carrying a C-terminus protecting group only. Since very similar results had recently been obtained for a series of structurally related polyiminocarbonates, the structure property correlations seem to be generally valid.

Carbonates↗
PubMedDate not supplied

[Effect of sacral roots block in the prostatic structure of the rat].

OBJECTIVE: To validate a simplified model of neural manipulation of the lower urinary tract of the rat, by means of alcoholic blockade of sacral roots. MATERIAL AND METHODS: Twenty Sprague-Dawle rats (aged 3 months) underwent alcohol sacral root blockade under total anesthesia with previous needle placement monitoring (electrostimulation). After 28-30 days, ipsilateral ventral prostatic lobe (VL) was obtained. Macroscopic and light microscopy (LM) studies were performed (computerized image analysis). Results were compared with 20 LV from non manipulated rats. RESULTS: A slight non significant decrease of LV weight in the blockade group was notice. LM study showed a reduced epithelial height after manipulation. Gland compartment mean proportions were: control group: 28.1% (epithelial), 29.8% (stromal), y 70.2% (glandular -lumen plus epithelium-); study group: 30.5% (not significant), 37.4% y 62.3% (both p < 0.05) respectively. Epithelium area did not suffer any variation. A reduced vascular overall count was noted in the study group. Ipsilateral diffusion of blockade solution was shown in 9 rats (45%), and bilateral in 11 (55%). CONCLUSIONS: Alcoholic sacral root blockade produces an atrophy of the glandular component (due to luminal shrinkage, without epithelial change). No differences were found after the macroscopic study. This study could not reproduce the changes produced after standard surgical denervation, therefore we cannot recommend this method to be used in future models.

Animals↗
PubMed2004

Predicted 3-D structures for mouse I7 and rat I7 olfactory receptors and comparison of predicted odor recognition profiles with experiment.

The first step in the perception of an odor is the activation of one or more olfactory receptors (ORs) following binding of the odorant molecule to the OR. In order to initiate the process of determining how the molecular level receptor-odorant interactions are related to odor perception, we used the MembStruk computational method to predict the three-dimensional (3-D) structure of the I7 OR for both mouse and rat. We then used the HierDock ligand docking computational method to predict the binding site and binding energy for the library of 56 odorants to these receptors for which experiment response data are now available. We find that the predicted 3-D structures of the mouse and rat I7 OR lead to predictions of odorant binding that are in good agreement with the experimental results, thus validating the accuracy of both the 3-D structure and the predicted binding site. In particular we predict that heptanal and octanal both bind strongly to both mouse and rat I7 ORs, which conflicts with the older literature but agrees with recent experiments. To provide the basis of additional validations of our 3-D structures, we also report the odorant binding site for a new odorant (8-hydroxy-octanal) with a novel functionality designed to bind strongly to mouse I7. Such validated computational methods should be very useful in predicting the structure and function of many other ORs.

Amino Acid Sequence↗
PubMed1994

Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography.

Time-averaged structure-factor restraints have been used in two molecular dynamics refinement schemes to define ensembles of conformations for myoglobin that fit the experimentally measured Bragg scattering from P6 crystals. The geometries of the structures have been maintained to the same currently acceptable limits in all cases. Free R value analysis was used to assess the validity of the two approaches. In the first scheme, where atoms have no B values, the decrease in R value was found to be spurious as judged by a concomitant increase in the free R value. The other scheme, however, which retains individual B values, was found to yield both low R values and low free R values; thus, here the additional variables introduced by modeling the protein in terms of an evolving ensemble of states do not overfit the data. For comparison, refinements were also carried out on the system using several other techniques for isotropic and anisotropic crystallographic refinement. The time-averaged refinements with B values compare quite favorably with the standard methods, but yield additional information about substates of the system. Hence, correctly applied time-averaged refinements can yield accurate models for protein molecules; moreover, by essentially relaxing the harmonic approximation from the refinement process, these refinements allow a more detailed description of the motions of complex molecules, such as proteins, to be determined from X-ray crystallographic data.

Journal Article↗
PubMed2026

Comparative characterization of six teleost piscidins reveals distinct antimicrobial, antibiofilm and stability profiles.

Piscidins are cationic &#x3b1;-helical antimicrobial peptides (AMPs) that constitute a key component of the innate immune defense of teleost fish, yet the relationship between their genomic organization, structural properties, and functional specialization remains incompletely understood. In this study, six piscidin peptides from Epinephelus akaara, Seriola dumerili, Thunnus maccoyii, Argyrosomus regius, Dicentrarchus labrax, and Epinephelus coioides were characterized through an integrated sequence-to-function approach combining comparative genomics, structural modeling, physicochemical analysis, and in vitro validation, with the aim of identifying candidates with potential for biomedical and biotechnological applications. All genes studied exhibited the conserved four-exon, three-intron architecture characteristic of teleost piscidins. Structural modeling and circular dichroism confirmed &#x3b1;-helical conformations under membrane-mimetic conditions, despite measurable differences in hydrophobicity, charge distribution, and predicted membrane insertion parameters. Antimicrobial assays revealed distinct functional profiles: Sd_FI25 and Epinecidin_1 displayed broad antibacterial activity against Gram-positive and Gram-negative pathogens, whereas Dl_FI22 showed selective activity with reduced temporal persistence associated with lower peptide stability. Ea_FF25 exhibited comparatively weak antibacterial potency. Antibiofilm activity varied among peptides and did not uniformly parallel planktonic MIC values. Computational predictions further suggested antiviral and antitumoral potential for several sequences, extending their prospective relevance beyond classical antibacterial roles. Conserved genomic architecture and &#x3b1;-helical structure coexist with pronounced functional diversification among teleost piscidins. These findings demonstrate that integrating structural prediction with experimental validation is an effective strategy for identifying fish-derived innate immune peptides as candidates for biomedical applications.

Antimicrobial activity↗
PubMed2006

Circumplex structure and personality disorder correlates of the Interpersonal Problems model (IIP-C): construct validity and clinical implications.

This study assessed the construct validity of the circumplex model of the Inventory of Interpersonal Problems (IIP-C) in Norwegian clinical and nonclinical samples. Structure was examined by evaluating the fit of the circumplex model to data obtained by the IIP-C. Observer-rated personality disorder criteria (DSM-IV, Axis II) were used as external correlates. The reliability of the IIP-C scales was acceptable and in the same range as in the original version. A multisample analysis strategy did not support an invariant circumplex model across the 2 groups. However, the estimated structures reflected mostly the same circular pattern of a quasi-circumplex model in the 2 groups. Departures from the ideal model were of negligible practical significance. The validity results examining personality disorder correlates of the IIP-C generally conformed to predictions, providing direct evidence for agreement between self-report and expert judgments of interpersonal problems.

Expert Testimony↗
PubMed2000

Measurements used to characterize the foot and the medial longitudinal arch: reliability and validity.

BACKGROUND AND PURPOSE: Abnormality in the structure of the medial longitudinal arch of the foot is commonly thought to be a predisposing factor to injury. The purpose of this investigation was to compare the reliability and validity of several measurements used to characterize various aspects of the foot, including the medial longitudinal arch. SUBJECTS: One hundred two feet (both feet of 51 subjects) were measured to establish a reference database. From this group, a subset of 20 feet (both feet of 10 subjects) was used to determine intertester and intratester reliability. Radiographs of a further subset of 10 feet (right feet of 10 subjects) were used to determine validity. METHODS: Five foot measurements were taken in 2 stance conditions: 10% of weight bearing and 90% of weight bearing. RESULTS: Intraclass correlation coefficients (ICCs) for intertester and intratester measurements were between.480 and.995. The most reliable method of characterizing arch type in 10% of weight bearing between testers was dividing navicular height by foot length in 10% of weight bearing. However, this measure yielded highly unreliable measurements in 90% of weight bearing. The most valid measurements were navicular height divided by truncated foot length, navicular height divided by foot length in 10% of weight bearing, and navicular height divided by foot length in 90% of weight bearing. Dorsum height at 50% of foot length divided by truncated foot length showed relatively high intertester reliability (ICC=.811 in 10% of weight bearing, ICC=.848 in 90% of weight bearing) and validity (ICC=.844 in 10% of weight bearing, ICC=.851 in 90% of weight bearing). CONCLUSION AND DISCUSSION: These data suggest that, of the measures tested, the most reliable and valid method of clinically assessing arch height across 10% and 90% of weight bearing was dividing the dorsum height at 50% of foot length by truncated foot length.

Adult↗
PubMed2000

The estrogen receptor relative binding affinities of 188 natural and xenochemicals: structural diversity of ligands.

We have utilized a validated (standardized) estrogen receptor (ER) competitive-binding assay to determine the ER affinity for a large, structurally diverse group of chemicals. Uteri from ovariectomized Sprague-Dawley rats were the ER source for the competitive-binding assay. Initially, test chemicals were screened at high concentrations to determine whether a chemical competed with [3H]-estradiol for the ER. Test chemicals that exhibited affinity for the ER in the first tier were subsequently assayed using a wide range of concentrations to characterize the binding curve and to determine each chemical's IC50 and relative binding affinity (RBA) values. Overall, we assayed 188 chemicals, covering a 1 x 10(6)-fold range of RBAs from several different chemical or use categories, including steroidal estrogens, synthetic estrogens, antiestrogens, other miscellaneous steroids, alkylphenols, diphenyl derivatives, organochlorines, pesticides, alkylhydroxybenzoate preservatives (parabens), phthalates, benzophenone compounds, and a number of other miscellaneous chemicals. Of the 188 chemicals tested, 100 bound to the ER while 88 were non-binders. Included in the 100 chemicals that bound to the ER were 4-benzyloxyphenol, 2,4-dihydroxybenzophenone, and 2,2'-methylenebis(4-chlorophenol), compounds that have not been shown previously to bind the ER. It was also evident that certain structural features, such as an overall ring structure, were important for ER binding. The current study provides the most structurally diverse ER RBA data set with the widest range of RBA values published to date.

Animals↗
PubMed1996

Validity of the SCID in substance abuse patients.

Structured or semi-structured interviews, including the Structured Clinical Interview for DSM-III-R (SCID), are used widely to maximize the reliability and validity of psychiatric diagnoses. Although the reliability of such interviews appears adequate, there has been little effort to evaluate their validity. In a sample of 100 substance abuse patients, we evaluated the concurrent, discriminant and predictive validity of SCID substance use diagnoses, as well as co-morbid disorders that occur commonly among these patients. The validity of current and life-time substance use diagnoses obtained by a research technician using the SCID was good; it was moderate for antisocial personality disorder and major depression and poor for anxiety disorders. Although accurate diagnosis of substance use disorders in substance abuse patients can be accomplished by a research technician, the diagnosis of co-morbid psychiatric disorders requires either additional expertise or the use of a diagnostic instrument specially designed for that purpose.

Adult↗
PubMed1986

Charge redistribution in proteins via linear hydrogen-bond chains.

It is proposed that proteins might activate specific atomic positions within bound substrates or co-factors by means of hydrogen-bond chains. As a result of a concerted proton (tautomeric) shift in the linked residues of the hydrogen-bond chain, which includes the bound molecule, a charge separation occurs. The charge thus generated at a specific atom of the bound molecule renders it nucleophilic or electrophilic, as the case may be, and hence 'activated' towards subsequent chemical events. To test the feasibility of the theory a survey of published X-ray diffraction determined structures was performed. A search was made for hydrogen-bond chains which emanate away from bound substrates, co-factors or metal ions in order to validate the existence of such structural arrangements. Secondly, an attempt was made to incorporate the proposed proton dynamics into the proteins' mechanisms of action. Examples in which these criteria were satisfied are carboxypeptidase A, carbonic anhydrase, haemoglobin, dihydrofolate reductase, glutathione reductase and p-hydroxybenzoate hydroxylase.

Binding Sites↗
PubMed2005

[Validation of an asthma knowledge questionnaire for use in parents or guardians of children with asthma].

OBJECTIVE: Interventions to increase asthma knowledge enable children and/or their parents to acquire skills needed for the prevention and/or appropriate management of crises. Periods of illness caused by the disease can thereby be reduced. However, no validated instrument for quantifying knowledge of asthma is available in Spanish. The aim of the present study was to develop and validate an asthma knowledge questionnaire that could be self-administered by parents and/or persons charged with caring for asthmatic children. MATERIAL AND METHODS: The 17 items that make up the questionnaire were obtained on the basis of a review of the literature, focus group discussions, the professional experience of the researchers, and pilot studies. We evaluated the instrument's face, content, and concurrent validity and analyzed its factorial structure. The test-retest reliability of the questionnaire and its sensitivity to change were also assessed. RESULTS: A total of 120 pediatric patients with a mean (SD) age of 4.5 (3.7) years participated. Factor analysis demonstrated a probable structure of 3 factors that together explained 85% of the total variance in results. The opinion of an interdisciplinary group of experts on asthma confirmed the face validity of the instrument. The questionnaire's ability to distinguish between parents with high and low asthma knowledge demonstrated its concurrent validity. Test-retest reliability was demonstrated, as was sensitivity to change between 2 different testing moments. CONCLUSIONS: The asthma knowledge questionnaire developed is useful and reliable for quantifying the baseline level of asthma knowledge of parents of asthmatic children as well as to assess the efficacy of an educational intervention aiming to increase knowledge and understanding of the disease.

Adult↗