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At least 919 records · Page 51Linked to original sources
PubMed2004

MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data.

A web application for inferring potentially stabilizing non-bonding interactions in macromolecular structures from input atomic coordinate data is described. The core software, called Monster, comprises a PERL wrapper that takes advantage of scripts developed in-house as well as established software in the public domain to validate atomic coordinate files, identify interacting residues and assign the nature of these interactions. The results are assembled and presented in an intuitive and interactive graphical format. Potential applications of Monster range from mining and validating experimentally determined structures to guiding functional analysis. Non-commercial users can perform Monster analysis free of charge at http://monster.northwestern.edu.

Internet↗
PubMed2003

A questionnaire for the assessment of biliary symptoms.

OBJECTIVES: Gallstone disease is common and causes high health care costs, but a measure of symptomatic biliary disease for outcome studies is lacking. We aimed to develop a reproducible, valid, discriminative, disease-specific measure of biliary symptoms. METHODS: We created the self-report Biliary Symptoms Questionnaire (BSQ) by combining possible biliary symptoms with validated items for gastroesophageal reflux disease (GERD), irritable bowel syndrome (IBS), and other disorders. We developed the final version through an iterative process and assessed reproducibility by the test-retest method, concurrent validity by comparing BSQ responses with symptoms obtained by structured interview, and discriminative validity by comparing BSQ-based diagnoses of biliary symptoms, GERD, and IBS with patients' final diagnoses. A shortened version (sBSQ) also underwent reproducibility testing. RESULTS: A total of 245 outpatients (mean age, 55.2 yr; 61% female) participated. Median completion times for the BSQ and sBSQ were 36 and 10 min, respectively. For the BSQ, median kappa values were 0.65 (range -0.03 to 0.95) for reproducibility and 0.61 (range 0.15-0.95) for concurrent validity. Using BSQ responses, investigators distinguished IBS and GERD 79-90% of the time. For the sBSQ, the median kappa value for reproducibility was 0.72 (range 0.32-0.86). CONCLUSIONS: The BSQ is reproducible and has good concurrent and discriminative validity for biliary symptoms. The abridged sBSQ has good reproducibility. These instruments may be useful in future outcome studies.

Adult↗
PubMed2004

Factor validation of the addiction severity index scale structure in persons with concurrent disorders.

Confirmatory factor analysis was used to test the scale structure of the Addiction Severity Index (ASI) in a sample of 1,802 substance abusers (43% alcohol dependent) with a concurrent psychiatric disorder (46% with mood disorders). The fit of the original composite score model based on the work of P. L. McGahan, J. A. Griffith, R. Parente, and A. T. McLellan (1990) was compared with the evaluation indices (EIs) developed by A. I. Alterman et al. (1998). The 5-dimensional model based on the EIs was an overall better fit to the data. Internal consistency (Cronbach's alpha) for the EIs ranged from.66 (family domain) to.75 (legal domain). The 5 EIs were moderately correlated (rs =.42-.72) with the interviewer severity ratings from the ASI. Evaluation studies involving concurrent disordered substance abusers should use the EIs as summary measures of change.

Adolescent↗
PubMed2006

Pseudo-CSA restraints for NMR refinement of nucleic acid structure.

Upon alignment of oligonucleotides in a magnetic field, the downfield TROSY component of the 13C-{1H} doublet changes its resonance frequency as a result of residual 13C-1H dipolar coupling (RDC) and residual 13C chemical shift anisotropy (RCSA), and the sum of these two second rank tensors is referred to as the pseudo-CSA. The experimentally measured difference in the resonance frequency of the 13C TROSY component in the aligned and isotropic samples is referred to as residual pseudo-CSA (RPCSA), and it can be used directly as a restraint during structure calculation. Because measurement of the RPCSA involves detection of the narrow TROSY 13C doublet component, it is applicable to systems with larger rotational correlation times than RDC measurement. The method is demonstrated for structure refinement of the helical region of a 24-nt stem-loop segment or ribosomal helix-35, uniformly enriched in 13C and 15N, with RPCSA values measured at 5 and 25 degrees C. Substantial cross-validated improvements in structural accuracy are obtained upon incorporation of RPCSA restraints.

Models, Molecular↗
PubMedDate not supplied

[Validation of a self-efficiency scale for the prevention of AIDS among adolescents].

OBJECTIVES: The objectives are obtain the internal consistency, validity and factorial structure of the Self-Efficacy for AIDS scale, which was developed in American population by Kasen, Vaughan and Walter (1992) and adapted in mexican samples for López and Padilla (1999). INSTRUMENTS: It is employed the Self-efficacy to Prevent the AIDS Scale of 27 items of López and Padilla (1999), together with closed questions Likert type, dicotomics and two opened questions on relevant aspects of the sexual conduct to validate the scale, under a format self-applied test of pencil and paper. MATERIAL AND METHODS: It is a correlacional study with a not experimental design of transverse type. It was accomplished with a simple random sample of 962 adolescents wich were taken of 60 public health centers of Monterrey. None went to consult by motives related to the AIDS. RESULTS: The scale was adjusted to a normal distribution (Zk-s(Normal) = 1.369; p = 0.047). It presents a mean of 95.14 and a standard deviation of 25.80. Its reliability, by the alpha of Cronbach, was 0.89. SEA-27 shows a structure of four independent factors that explain 58.47% of the total variance. CONCLUSIONS: Thus, it is concluded that SEA-27 is a reliable and valid scale.

Acquired Immunodeficiency Syndrome↗
PubMed1989

Patient classification in neuropsychological research.

In a number of papers we have been concerned with the type of inferences that are legitimate in "experiments of nature" where the experimenter does not and cannot control the modifications to the cognitive system that are introduced by brain damage. We have argued that in such cases very restrictive conditions must be met in order to be able to draw valid inferences about the structure of normal cognitive mechanisms. Two consequences of these conditions are (1) patient classification into syndrome types (e.g., phonological dysgraphia, agrammatism, and so forth) can play no useful role in research concerned with issues about the structure of normal cognitive functioning or its dissolution under conditions of brain damage; and (2) only single-patient studies allow valid inferences about the structure of cognitive mechanisms from the analysis of impaired performance. Zurif, Gardner, and Brownell (1989, Brain and Cognition, 10, 237-255) have taken exception to our conclusions and propose to show the limitations of our arguments. In this paper we respond to their criticisms.

Aphasia↗
PubMed2004

Diagnostic utility of reflux disease symptoms.

Symptom assessment, by structured interview or questionnaire, is central to the diagnosis of gastro-oesophageal reflux disease (GORD). However, empiric support for the diagnostic utility of reflux symptom measures is lacking. Reliable reflux symptom questionnaires have been developed with content validity. These questionnaires need to be evaluated in terms of diagnostic accuracy, support for application of specific treatment, and improved outcomes resulting from their use. The impact on clinical outcomes of GORD diagnosis by valid questionnaires or structured interview has not been studied.

Gastroesophageal Reflux↗
PubMed1993

Structured observations of hygiene behaviours in Burkina Faso: validity, variability, and utility.

The use of observation techniques has been promoted for the study of hygiene practices; however, questions still remain about the validity and repeatability of such techniques. In this article we compare data on hygiene behaviours obtained from questionnaires with data obtained using a structured observation approach and examine the repeatability of structured observations of behaviours and spot observations of environmental conditions. Poor agreement between questionnaire responses and observations was found for child defecation and stool disposal practices (kappa statistic: 0.25 and 0.28, respectively). There was evidence of over-reporting of "good" behaviours (P < 0.0001). Repeated observations of child defecation and stool disposal behaviours showed better agreement (kappa statistic: 0.76 and 0.62, respectively) based on small sample sizes. These findings suggest that our questionnaire data are less valid than data obtained by direct observation. However, different approaches to questioning may be less prone to over-reporting of "good" behaviours than our approach. Further research into the validity of different forms of question is warranted. Behaviours and conditions related to hygiene vary. Observations may be useful in determining the frequency of different behaviours/conditions in the community. However, individual practices may be too variable to assign individuals to exposed and non-exposed groups for the purpose of identifying links with health outcomes. Further studies on the variability of behaviours and the repeatability of observations are therefore needed.

Adult↗
PubMed2003

Psychometric properties of the Vanderbilt ADHD diagnostic parent rating scale in a referred population.

OBJECTIVE: s To determine the psychometric properties of the Vanderbilt Attention Deficit/Hyperactivity Disorder Parent Rating Scale (VADPRS), which utilizes information based on the Diagnostic and Statistical Manual of Mental Disorders, 4th Ed. (DSM-IV). The VADPRS was created to collect uniform patient data and minimize the time burden of lengthy interviews. METHODS: Participant data (N = 243) was used from the first 2 years of a longitudinal study on communication among physicians, teachers, and parents in diagnosing, treating, and managing children with attention deficit/hyperactivity disorder (ADHD). The reliability, factor structure, and concurrent validity of the VADPRS were evaluated and compared with ratings of children in clinical and nonclinical samples on the Vanderbilt ADHD Teacher Rating Scale and the Computerized Diagnostic Interview Schedule for Children-IV, Parent version. RESULTS: The internal consistency and factor structure of the VADPRS are acceptable and consistent with DSM-IV and other accepted measures of ADHD. CONCLUSION: The VADPRS is a reliable, cost-effective assessment for ADHD in clinical and research settings.

Attention Deficit Disorder with Hyperactivity↗
PubMed2005

Development and validation of an adolescent smoking consequences questionnaire.

Several researchers have investigated the role of outcome expectancies in the initiation and maintenance of smoking behavior. Empirical studies with adults, using a validated self-report instrument, have shown that smokers identify higher levels of positive smoking expectancies and lower levels of negative smoking expectancies compared with nonsmokers and ex-smokers. Studies examining smoking outcome expectancies among adolescents have yielded similar findings, but many of these studies did not use a self-report expectancy measure validated with teens. Therefore, the present study sought to modify a well-known adult smoking expectancy instrument, the Smoking Consequences Questionnaire (SCQ), and to validate its factor structure with a community sample of adolescent nonsmokers and current smokers (aged 11-19 years). Results of a confirmatory factor analysis provided support for a seven-latent-factor structure modeled after the SCQ-Adult. As expected, smoking behavior and the intent to smoke in the future were associated with the endorsement of positive and negative smoking outcome expectancies. The psychometric data provide early support for the validity and reliability of this modified SCQ, renamed the Adolescent Smoking Consequences Questionnaire, for the assessment of smoking expectancies among smoking inexperienced and experienced teens.

Adolescent↗
PubMed1998

Quantitative structure-activity relationships and volume fraction analysis for nonpolar narcotic chemicals to the australian cladoceran ceriodaphnia cf. dubia

The toxicity of eleven nonpolar narcotic chemicals to the cladoceran Ceriodaphnia cf. dubia was determined. C. cf. dubia was found to be approximately four times more sensitive to these narcotic chemicals than Daphnia magna tested under virtually identical conditions. The toxicity data were also used to develop and validate quantitative structure-activity relationships (QSARs) using a range of physicochemical properties of the chemicals. The three best QSARs, based on octanol-water partition coefficients and two lipid-water partition coefficients, were able to explain 98% of the variation in toxicity. The mean absolute percentage errors between the predicted and experimental EC50 values for these three QSARs were 17.3%, 20.6%, 24.6%. Neither the critical concentration (CC) nor the critical volume (CV) hypotheses validly modeled the toxicity data when octanol-water and triolein-water partition coefficients were used although the CV hypothesis was the better of the two. When a phospholipid-water partition coefficient was used the CV hypothesis was valid. The mean toxic membrane volume fraction of 0.48 x 10(-2) m3/m3 derived in this study agreed with published values for nonpolar narcotics and supports the use of this property to determine the mode of action of chemicals.

Journal Article↗
PubMed2003

Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors.

G-protein coupled receptors (GPCRs) are the largest family of cell-surface receptors involved in signal transmission. Drugs associated with GPCRs represent more than one fourth of the 100 top-selling drugs and are the targets of more than half of the current therapeutic agents on the market. Our methodology based on the internal coordinate mechanics (ICM) program can accurately identify the ligand-binding pocket in the currently available crystal structures of seven transmembrane (7TM) proteins [bacteriorhodopsin (BR) and bovine rhodopsin (bRho)]. The binding geometry of the ligand can be accurately predicted by ICM flexible docking with and without the loop regions, a useful finding for GPCR docking because the transmembrane regions are easier to model. We also demonstrate that the native ligand can be identified by flexible docking and scoring in 1.5% and 0.2% (for bRho and BR, respectively) of the best scoring compounds from two different types of compound database. The same procedure can be applied to the database of available chemicals to identify specific GPCR binders. Finally, we demonstrate that even if the sidechain positions in the bRho binding pocket are entirely wrong, their correct conformation can be fully restored with high accuracy (0.28 A) through the ICM global optimization with and without the ligand present. These binding site adjustments are critical for flexible docking of new ligands to known structures or for docking to GPCR homology models. The ICM docking method has the potential to be used to "de-orphanize" orphan GPCRs (oGPCRs) and to identify antagonists-agonists for GPCRs if an accurate model (experimentally and computationally validated) of the structure has been constructed or when future crystal structures are determined.

Animals↗
PubMed1987

Electronic absorption and EPR spectroscopy of copper alcohol dehydrogenase: pink, violet and green forms of a type 1 copper center analog.

Blue and non-blue states of the copper center in copper-substituted alcohol dehydrogenase (EC 1.1.1.1) can be attained by coenzyme binding and/or ligand binding to the copper ion. Copper alcohol dehydrogenase has been studied by electronic absorption, CD and EPR spectroscopy in the presence and absence of coenzyme. On the basis of previous work on blue (Type 1) copper proteins with a CuSS*N2 chromophore the assignment of charge transfer transitions in copper alcohol dehydrogenase is discussed. The latter contains a CuS2N(OH2) unit in the ligand-free protein and a CuS2N2 unit in the ternary complex with NAD+ and pyrazole. It is proposed that the energy of the charge transfer transitions can be used as a structural marker in combination with EPR data. A comparison is made between the spectroscopic properties of the ternary complex of copper alcohol dehydrogenase and the copper centers in stellacyanin and cytochrome-c oxidase (CuA) in order to test the validity of recent structural models of the type CuS2N2, i.e., a cupric ion coordinated to two thiolate ligands. Finally, a close resemblance between the electronic absorption spectra of copper alcohol dehydrogenase and those of other variants of Type 1 copper centers such as the 'unusual' copper center of nitrous oxide reductase is noted as an indication of similar coordination environments.

Alcohol Dehydrogenase↗
PubMed1990

Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction.

The pattern of residue substitution in divergently evolving families of globular proteins is highly variable. At each position in a fold there are constraints on the identities of amino acids from both the three-dimensional structure and the function of the protein. To characterize and quantify the structural constraints, we have made a comparative analysis of families of homologous globular proteins. Residues are classified according to amino acid type, secondary structure, accessibility of the sidechain, and existence of hydrogen bonds from sidechain to other sidechains or peptide carbonyl or amide functions. There are distinct patterns of substitution especially where residues are both solvent inaccessible and hydrogen bonded through their sidechains. The patterns of residue substitution can be used to construct templates or to identify 'key' residues if one or more structures are known. Conversely, analysis of conversation and substitution across a large family of aligned sequences in terms of substitution profiles can allow prediction of tertiary environment or indicate a functional role. Similar analyses can be used to test the validity of putative structures if several homologous sequences are available.

Amino Acid Sequence↗
PubMed2004

Reliability and validity of the Dental Satisfaction Questionnaire in a population of 23-year-olds in Norway.

OBJECTIVE: The aim of this study was to explore the internal structure, reliability, and construct validity of the Dental Satisfaction Questionnaire (DSQ) in a population of young adults in Norway. METHODS: The DSQ scale was mailed to a representative sample of 968 subjects aged 23 years in two Norwegian counties. The reliability assessment of the instrument was based on internal consistency analysis (Cronbach's alpha). A factor analysis (principal component) was used to confirm the internal structure of the scale. The construct validity of the DSQ was indicated by: (i) its correlation with the patients' beliefs regarding the way dentists deliver care, indexed by the Dental Beliefs Survey (DBS); and (ii) differences in DSQ scores between subjects who had dropped out from dental care at the age of 23 years and regular attenders. RESULTS: The response rate was 69%. The alpha (Cronbach's) coefficient for the overall construct of DSQ was 0.81 (n = 655), and 0.65 or more for the subscales pain management, quality, and access. The correlation coefficient between the sum-scores of DSQ and DBS for the entire sample was r = -0.69. Subjects in the dropout group had significantly lower satisfaction with dental care than the rest of the group (P < 0.001). CONCLUSIONS: This study generally confirms the structure of the DSQ instrument and indicates that it is a reliable and valid instrument in cultures other than the one for which it was previously tested.

Adult↗
PubMed2002

Electrospray mass spectrometry for fumonisin detection and method validation.

Fumonisins are a structurally related group of mycotoxins, characterized by a 19-20 carbon aminopolyhydroxy-alkyl chain which is diesterified with propane-1,2,3-tricarboxylic acid (tricarballylic acid). These mycotoxins are commonly found in corn and corn-based food products and have been linked to a variety of animal toxicities. The widespread prevalence of fumonisins and the toxicity associated with ingestion has resulted in a number of analytical methods for determining the amount of fumonisins present in foods. Among the most common of these methods are liquid chromatographic (LC) separation with fluorescence detection, enzyme-linked immunosorbent assay (ELISA) and LC/mass spectrometry. LC and ELISA give quantitative results while LC/MS provide quantitative analysis as well as confirmation of identity of the fumonisins.

Chromatography, High Pressure Liquid↗
PubMed2006

Initial construct validation of frequently employed ANAM measures through structural equation modeling.

ANAM measures were based on procedures used in both clinical and performance assessment. This paper reviews data from studies designed to delineate specific neurocognitive functions assessed by more commonly used ANAM measures. Data are brought together from both exploratory and confirmatory analyses. Current findings support the use of these measures for assessing aspects of attention, processing efficiency, and working memory. Recommendations for further research include the need for larger samples and the inclusion of specific marker variables.

Cognition Disorders↗
PubMedDate not supplied

[Evidence-based medicine in orthopaedics - a sensible or unnecessary addition to clinical routine? Part 2: the therapy tool].

AIM: In the second part of our project to implement evidence-based medicine into day-to-day clinical practice the module therapy is presented. METHODS: Within a teaching session in our department 20 participants guided by an extern al EBM teacher validated the results of an article according to the EBM criteria concerning the module therapy. To work with this module formal procedures are necessary, too. RESULTS: Statistical tests to evaluate the relevance and validity of the chosen article were performed. The following data were determined: relative risk reduction, absolute risk reduction, number needed to treat. CONCLUSION: In conclusion we can show, that EBM can help to solve day-to-day clinical problems, because the structured analysis concerning valid answers to concrete clinical problems is possible.

Clinical Competence↗