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PubMed1995

A genetic algorithm to search for optimal and suboptimal RNA secondary structures.

Genetic algorithms are a search method used in solving problems by selection, recombination and mutation of tentative solutions, until the better ones are achieved. They are very efficient when the 'building block' hypothesis is effective for the solutions, which means that a better solution can be obtained by assembling short 'motifs' or 'schemata' that can be retrieved in some other worse solutions. The additive nature of the secondary structure free energy rules suggests the validity of this hypothesis, and therefore the likely power of a genetic algorithm approach to search for RNA secondary structures. We describe in detail an original genetic algorithm specific for this problem. The sharing function used to obtain differentiated solutions is also described. It results in a greater effectiveness of the algorithm in retrieving a large number of suboptimal RNA foldings besides the optimal one. RNA sequences of different length are used to test the method. The PSTV viroid sequence has been studied.

Algorithms↗
PubMed2006

eHiTS: a new fast, exhaustive flexible ligand docking system.

The flexible ligand docking problem is divided into two subproblems: pose/conformation search and scoring function. For successful virtual screening the search algorithm must be fast and able to find the optimal binding pose and conformation of the ligand. Statistical analysis of experimental data of bound ligand conformations is presented with conclusions about the sampling requirements for docking algorithms. eHiTS is an exhaustive flexible-docking method that systematically covers the part of the conformational and positional search space that avoids severe steric clashes, producing highly accurate docking poses at a speed practical for virtual high-throughput screening. The customizable scoring function of eHiTS combines novel terms (based on local surface point contact evaluation) with traditional empirical and statistical approaches. Validation results of eHiTS are presented and compared to three other docking software on a set of 91 PDB structures that are common to the validation sets published for the other programs.

Algorithms↗
PubMed2004

Development and evaluation of a generic evolutionary method for protein-ligand docking.

We have developed a generic evolutionary method with an empirical scoring function for the protein-ligand docking, which is a problem of paramount importance in structure-based drug design. This approach, referred to as the GEMDOCK (Generic Evolutionary Method for molecular DOCKing), combines both continuous and discrete search mechanisms. We tested our approach on seven protein-ligand complexes, and the docked lowest energy structures have root-mean-square derivations ranging from 0.32 to 0.99 A with respect to the corresponding crystal ligand structures. In addition, we evaluated GEMDOCK on crossdocking experiments, in which some complexes with an identical protein used for docking all crystallized ligands of these complexes. GEMDOCK yielded 98% docked structures with RMSD below 2.0 A when the ligands were docked into foreign protein structures. We have reported the validation and analysis of our approach on various search spaces and scoring functions. Experimental results show that our approach is robust, and the empirical scoring function is simple and fast to recognize compounds. We found that if GEMDOCK used the RMSD scoring function, then the prediction accuracy was 100% and the docked structures had RMSD below 0.1 A for each test system. These results suggest that GEMDOCK is a useful tool, and may systematically improve the forms and parameters of a scoring function, which is one of major bottlenecks for molecular recognition.

Drug Design↗
PubMed2006

Psychometric adequacy and comparability of the short and full forms of the Personality Assessment Inventory.

The 160-item short form of the Personality Assessment Inventory (PAI) was developed for situations in which respondents complete only the 1st half of the test. The present study evaluates the adequacy and comparability of the full and short forms of the PAI in terms of a wide range of psychometric characteristics. In all, 421 participants completed the full form as part of a neuropsychological evaluation. Results indicated slightly lower internal consistency reliability of the short compared with the full form. Group-level agreement of short and full form scales ranged from adequate to excellent. However, within-subject agreement was somewhat more variable. Low levels of within-subject agreement were strongly associated with elevated validity scale scores. The factor structures of the full and short forms showed high congruence for a 3-factor solution. These findings suggest that many scales of the short form have adequate comparability with their respective full form scales. However, low levels of reliability across less impaired ranges of the latent trait, diminished content coverage, and altered validity detection may limit the utility of some of the short form scales.

Adolescent↗
PubMed2006

Oligosaccharide structures studied by hydrogen-deuterium exchange and MALDI-TOF mass spectrometry.

Hydrogen-deuterium exchange matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (HX-MALDI-TOF MS) is reported for the determination of exchangeable protons in diverse oligosaccharide and glycoconjugate structures. The method has broad application for determining carbohydrate structure and conformation and to the study of carbohydrate-ligand interactions. The proton exchange process has been optimized to maximize the forward deuterium exchange and to suppress the well-known problem of back-exchange and is suitable for the analysis of all exchangeable proton types in carbohydrates. This has been validated for several diverse carbohydrate structures, including series of malto- and xylopyranose oligosaccharides; alpha- and beta-cyclodextrins; a nonreducing tetrasaccharide, stachyose; an N-acetylamide-containing oligosaccharide, chitotetraose; and a tertiary hydroxyl-containing antibiotic glycoconjugate, erythromycin.

Deuterium↗
PubMed1997

VATAM: developing consensus in validation of health telematics applications.

VATAM (Validation of Telematics Applications in Medicine) is an EU supported project in the Health care sector of the Telematics Application Programme. Its objective is to assist other health telematics projects by providing a platform for discussion on validation, eventually resulting in 'guidelines for validation of telematics applications in medicine'. The VATAM work can be subdivided into three phases: the inventory phase (1996) in which information is collected on validation approaches in the Telematics Application Programme, previous efforts and expertise. The dissemination phase (1997) will be used to extend and adapt the framework developed in the inventory phase, through cooperation with other projects The experiences phase (1998) in which the projects are actually applying validation, will be used by VATAM to validate the VATAM methodology. VATAM has finished the inventory phase successfully and is now working on the dissemination phase by--among others--establishing contacts with other projects, and providing information on the inventory through the World Wide Web (URL: http:(/)/www-vatam.unimaas.nl). This paper discusses the approach adopted and the proposed VATAM framework to structure the large variety of validation approaches.

Computer Communication Networks↗
PubMed1997

[Dimensional structure of the German version of the Brief Psychiatric Rating Scale (BPRS)].

Since the early 1960s the Brief Psychiatric Rating Scale (BPRS) has been one of the most frequently used standardized methods in international psychiatric research. The BPRS is used mainly for the rating of psychopathological symptoms of schizophrenic subjects. According to the results of factorial analyses, the original version of the BPRS is divided into five subscales, which have been preserved in the German translation. The validity of this original scale structure for the German BPRS version has not been investigated, however. A principal-components analysis of the 18 BPRS items carried out on the data of 301 schizophrenics yielded four factors that are comparable with four of the original subscales: Thought disturbance, Hostility/suspiciousness, Anxiety/depression, and Anergia. These results are compared with earlier findings and similarities and differences are discussed.

Adolescent↗
PubMed1990

Measuring locus of control in elderly persons.

Confirmatory factor analysis was used to examine the appropriateness of using with elderly persons Levenson's multidimensional locus of control (LoC) scale that measures beliefs in Internal Control (I), Control by Powerful Others (P), and Chance (C). Data were obtained from elderly individuals in Florida and Texas and reformulated to allow cross-validation at each step in a series of model evaluations. Results indicated that Levenson's three-factor specification of control was not a valid representation of the samples' responses. A model that specified the elimination of eleven unreliable items and the formation of a new external control factor that was based on the remaining C and P items provided an adequate fit to the data for both samples. The failure to confirm Levenson's three-factor structure poses a construct-validity and measurement-equivalence problem when making age-based comparisons of LoC scores.

Aged↗
PubMed1993

Lipid phase transitions and a possible lipid-protein lattice structure as an activity regulator in maturing spermatozoa.

This study was performed, in order to define the sperm-egg interaction as a membrane-membrane interaction, to validate the hypothesis that the physical structure of the biomembranes can dictate their overall fusion behavior and that the sperm membranes undergo 'fusion-favoring' modifications during epididymal maturation. Informations from the lipophilic domains, aqueous compartments and the protein components were gathered. The lipophilic domains were found to undergo profound alterations in their local viscosity, polarity, molecular ordering and lateral diffusion patterns. The rotational mobility of proteins appeared to be restricted, and the aqueous compartments transformed to a more viscous state at the late phase of maturation. Correlative evidence suggests a possible relation between the specific protein activation/inactivation reported earlier and the physical changes reported herein.

Animals↗
PubMed1983

Polymorphism and stability of histone gene clusters in Drosophila melanogaster cultured cells.

In a previous communication (Saigo, K., Millstein, L. and Thomas, C.A., Jr. (1981) Cold Spring Harbor Symp. Quant. Biol. 45, 815-827), the overall structure of histone genes of Schneider line 2 cells was shown to extensively differ from that of Oregon-R embryo from which the cell line was established, and it was speculated that the histone genes might be reshuffled extensively during either the periods of the establishment, or maintenance of cell lines, or both. To establish the validity of this notion the structure of histone genes was examined in Drosophila melanogaster cultured cells. The overall organization of histone gene clusters was found to be stably maintained in both the periods for the establishment and maintenance of cultured cells, indicating that the previous assumption is inadequate. Instead of an extensive rearrangement, minor structural changes were found to occasionally occur probably by simple base substitutions and/or, deletion or insertion of very short DNA pieces. It was also shown that the extensive variation in structures of histone genes in cultured cells such as Schneider line 2 are attributable to polymorphism on the level of individual flies.

Animals↗
PubMed2005

Computational approach to the rational design of molecularly imprinted polymers for voltammetric sensing of homovanillic acid.

A methodology based on density functional theory calculations for the design of molecularly imprinted polymers (MIPs) is described. The method allows the rational choice of the most suitable monomer and polymerization solvent among a set of chemicals traditionally used in MIP formulations for the molecular imprinting of a given template. It is based on the comparison of the stabilization energies of the prepolymerization adducts between the template and different functional monomers. The effect of the polymerization solvent is included using the polarizable continuum model. A voltammetric sensor for homovanillic acid was constructed using different MIPs as recognition element, confirming that the solvent (toluene) and functional monomer (methacrylic acid) selected according to the theoretical predictions lead to the most efficient molecular recognition sensing phase. With the voltammetric sensor prepared using the MIP designed according to the theoretical predictions, a linear response for concentrations of homovanillic acid between 5 x 10(-8) and 1 x 10(-5) M can be obtained. The limit of detection is 7 x 10(-9) M. The selectivity obtained for homovanillic acid over other structurally related compounds buttresses the validity of this strategy of design.

Computer Simulation↗
PubMed2003

Modeling the 3D structure of GPCRs: advances and application to drug discovery.

G protein-coupled receptors (GPCRs) are membrane-embedded proteins responsible for signal transduction; these receptors are, therefore, among the most important pharmaceutical drug targets. In the absence of X-ray structures, there have been numerous attempts to model the three-dimensional (3D) structure of GPCRs. In this review, the current status of GPCR modeling is evaluated, highlighting recent progress made in rhodopsin-based homology modeling and de novo modeling technology. Assessment of recent rhodopsin-based homology modeling studies indicates that, despite significant progress, these models do not yield hit rates that are sufficiently high for in silico screening (10 to 40% when screening for known binders). In contrast, the PREDICT modeling algorithm, which is independent of the rhodopsin structure, has now been fully validated in the context of drug discovery. PREDICT models are successfully used for drug discovery, yielding excellent hit rates (85 to 100% when screening for known binders), leading to the discovery of nanomolar-range new chemical entities for a variety of GPCR targets. Thus, 3D models of GPCRs should now allow the use of productive structure-based approaches for drug discovery.

Animals↗
PubMed1987

Factorial dimensions of the Revised Behavior Problem Checklist: replication and validation within a kindergarten sample.

The factor structure of the Revised Behavior Problem Checklist (RBPC) was examined in a large sample of suburban kindergarten children. Teacher-rated dimensions of Conduct Disorder, Attention Problems-Immaturity, Anxiety-Withdrawal, and Psychotic Behavior were closely replicated, and a new factor labeled Unmotivated-Isolated was also revealed. These principal components were consistent across gender and across subsamples of children differing as to risk status for learning failure. Evidence was found for the divergent validity of the externalizing dimensions of Conduct Disorder and Attention Problems-Immaturity with respect to criterion measures of alternative behavior ratings, cognitive functioning, and academic achievement. Parent-rated components of Conduct Disorder, Attention Problems-Immaturity, Hyperactive-Impatient, Tense-Withdrawn, Anxiety, and Passive-Conforming were less clearly validated, and parent-teacher agreement was modest. It was concluded that the RBPC shows promise for the assessment of preschool-aged children and that narrow-band externalizing dimensions of inattentive versus conduct-disordered behavior are reasonably distinct at this age.

Anxiety Disorders↗
PubMed2004

The measure of processes of care (MPOC): validation of the Dutch translation.

AIM: The objective was to validate the Dutch translation of the Canadian measure of processes of care (MPOC) questionnaire for use in children's rehabilitation centres in the Netherlands. MPOC consists of 56 items (assessing five domains) and was designed to find out what parents of children with chronic health problems think of the services they and their child receive and to measure the extent to which these services are family-centred. METHODS: The Canadian validation procedures were followed, consisting of construct and concurrent validation and reliability analyses. Participants were parents of 427 children aged 1-18 years recruited through nine children's rehabilitation centres in the Netherlands. RESULTS: The construct validity of the Dutch version of MPOC (MPOC-NL) was examined with confirmative analyses of the scale structure. These analyses all supported the construct validity of MPOC-NL. MPOC-NL showed adequate internal consistency, with Cronbach's alpha ranging from 0.80 to 0.95. The intraclass correlation coefficients (ICCs) ranged from 0.79 to 0.94, which demonstrated good stability of MPOC-NL. The Spearman correlations between MPOC-NL scores and satisfaction questions ranged from 0.39 to 0.73, and thus supported the construct validity of MPOC-NL. Correlations between MPOC-NL scores and a question about parents' stress in relation to services received were moderately negative (r(s) = -0.28 to -0.39). CONCLUSION: The construct and concurrent validity of MPOC-NL was shown by confirmative analyses of the original Canadian scale structure, and by modest Spearman correlations between MPOC-NL scores and satisfaction and stress variables. MPOC-NL is internally consistent and reliable.

Adolescent↗
PubMed2005

Development of the Hebrew-Multidimensional Inventory of Dissociation (H-MID): a valid and reliable measure of pathological dissociation.

The Multidimensional Inventory of Dissociation (MID; Dell, 2004b) has 168 dissociation items and 50 validity items. The MID assesses 14 major facets of dissociation, 23 symptoms of dissociation, and has 5 validity scales. The MID operationalizes (a) the subjective/ phenomenological domain of dissociation, and (b) 23 hypothesized symptoms of dissociative identity disorder (DID). This article describes the development of a Hebrew version of the MID (H-MID). In a sample of clinical and nonclinical research participants, the H-MID had strong internal consistency, temporal stability, and strong structural, convergent, discriminant, and construct validity. In addition, mean H-MID scores demonstrated incremental validity over the Hebrew Dissociative Experiences Scale (H-DES) by predicting an additional 17% of the variance in weighted trauma scores on the Traumatic Experiences Questionnaire (TEQ). Factor analysis of the H-MID extracted a single factor: dissociation. Both the MID and the subjective/phenomenological concept of pathological dissociation appear to have applicability not only in North America, but also in a heterogeneous Middle Eastern culture.

Adult↗
PubMed2006

Theoretical performance of Bragg gratings based on long-range surface plasmon-polariton waveguides.

A plasmon-polariton Bragg grating (PPBG) concept, based on the propagation of the long-range ss0b mode in structures comprising a thin metal film of finite width embedded in a homogeneous background dielectric, is discussed theoretically. The PPBGs are operated in an end-fire arrangement with access plasmon-polariton waveguides or optical fibers being directly butt-coupled to their input and output ports. A model for the PPBGs, which was recently proposed and validated experimentally for third order structures, is used to generate theoretical results describing their expected performance for various architectures. First order uniform periodic, interleaved, and apodized grating structures are considered and compared. Third order uniform periodic designs are also considered. The gratings investigated are based on a 20 nm thick Au film embedded in SiO2 and have a Bragg wavelength near 1550 nm. First order uniform periodic gratings provide the strongest reflection, with a maximum reflectance of about 97% being achievable over a length of a few millimeters and over a full width at half-maximum bandwidth of about 0.8 nm. The off-resonance insertion loss of the gratings can be as low as a few decibels. Specific Bragg wavelengths can easily be attained using interleaving without requiring extraordinary resolution from the fabrication process. Apodized designs providing low sidelobe levels are also investigated.

Journal Article↗
PubMed2004

An experimental and theoretical study of the Cp2VO2CO: use of 13CO3(2-) for structure investigation of d1-metallocene complexes.

EPR study has shown that the anticancer agent vanadocene dichloride (Cp2VCl2) interacts with carbonate contained in physiological solutions. Chelate complex Cp2VO2CO (|A(iso)(51V)| = 175.1 MHz, g(iso) = 1.9861) is the only paramagnetic species formed in the range about the physiological pH (5.5-11.0). The super-hyperfine coupling (|a(iso)(13C)| = 24.1 MHz) was evidenced at measurements using 13C labelled carbonate. The structure of carbonate complex was validated by comparison of observed and theoretical calculated HFC tensors (at the density functional level of theory).

Carbon Isotopes↗
PubMed2001

The structured interview for anorexic and bulimic disorders for DSM-IV and ICD-10 (SIAB-EX): reliability and validity.

OBJECTIVE: For reliable and valid assessment and diagnostic categorization of eating disorders, self-report measures have considerable limitations. A semi-structured interview - the SIAB-EX - was developed for a more reliable and valid assessment of eating disorders. METHODS: One study (videotapes of 31 inpatients, seven raters) was made to establish inter-rater reliability; in another study with 80 patients the SIAB-EX was compared to another semi-structured interview designed for comparable purposes (EDE). In a third study data was obtained on 377 eating disorder patients seeking treatment to explore discriminant and convergent (construct) validity using the following self-rating scales: EDI, TFEQ, SCL-90, BDI, and the PERI Demoralization Scale. RESULTS: Inter-rater reliability of dichotomous ratings was good with mean kappa values of.81 (current) and.85 (past). Comparison of the SIAB-EX with the EDE generally showed quite similar results and higher intercorrelation of the total scale (.77). There are, however, a number of differences between the two scales, which are discussed in detail. Construct validity of the SIAB-EX was established. CONCLUSION: Inter-rater reliability was good. Convergent and discriminant (construct) validity of the SIAB-EX was demonstrated. The constructs assessed by the SIAB and its subscales and items are discussed in the context of their correlations with other well-known scales.

Adaptation, Psychological↗