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At least 1,189 records · Page 66Linked to original sources
PubMed2006

The fear-avoidance model of chronic pain: validation and age analysis using structural equation modeling.

The cognitive-behavioral, fear-avoidance (FA) model of chronic pain (Vlaeyen JWS, Kole-Snijders AMJ, Boeren RGB, van Eek H. Fear of movement/(re)injury in chronic low back pain and its relation to behavioral performance. Pain 1995a;62:363-72) has found broad empirical support, but its multivariate, predictive relationships have not been uniformly validated. Applicability of the model across age groups of chronic pain patients has also not been tested. Goals of this study were to validate the predictive relationships of the multivariate FA model using structural equation modeling and to evaluate the factor structure of the Tampa Scale of Kinesiophobia (TSK), levels of pain-related fear, and fit of the FA model across three age groups: young (< or =40), middle-aged (41-54), and older (> or =55) adults. A heterogeneous sample of 469 chronic pain patients provided ratings of catastrophizing, pain-related fear, depression, perceived disability, and pain severity. Using a confirmatory approach, a 2-factor, 13-item structure of the TSK provided the best fit and was invariant across age groups. Older participants were found to have lower TSK fear scores than middle-aged participants for both factors (FA, Harm). A modified version of the Vlaeyen JWS, Kole-Snijders AMJ, Boeren RGB, van Eek H (Fear of movement/(re)injury in chronic low back pain and its relation to behavioral performance. Pain 1995a;62:363-72.) FA model provided a close fit to the data (chi(2)(29)=42.0, p>0.05, GFI=0.98, AGFI=0.97, CFI=0.99, RMSEA=0.031 (90% CI 0.000-0.050), p close fit=0.95). Multigroup analyses revealed significant differences in structural weights for older vs. middle-aged participants. For older chronic pain patients, a stronger mediating role for pain-related fear was supported. Results are consistent with a FA model of chronic pain, while indicating some important age group differences in this model and in levels of pain-related fear. Longitudinal testing of the multivariate model is recommended.

Adolescent↗
PubMed1983

Mutagenicity (Ames): a structure-activity model.

A statistical structure-activity model of the Salmonella typhimurium (Ames) test has been devised based on 472 chemicals for which this endpoint has been measured. The model uses substructural fragments as the independent parameters to explain the difference in mutagenicity of the different chemicals. The model is able to classify 86% of the chemicals into their correct categories; the false-positive rate is 4.7%, and the false-negative rate 5.3%. Approximately 10% of the chemicals cannot be classified by the existing equation. This structure-activity model can be used as a preliminary screen prior to other testing as well as for setting priorities for more detailed investigations.

False Negative Reactions↗
PubMed2003

Bayesian analysis of structural equation models with dichotomous variables.

Structural equation modelling has been used extensively in the behavioural and social sciences for studying interrelationships among manifest and latent variables. Recently, its uses have been well recognized in medical research. This paper introduces a Bayesian approach to analysing general structural equation models with dichotomous variables. In the posterior analysis, the observed dichotomous data are augmented with the hypothetical missing values, which involve the latent variables in the model and the unobserved continuous measurements underlying the dichotomous data. An algorithm based on the Gibbs sampler is developed for drawing the parameters values and the hypothetical missing values from the joint posterior distributions. Useful statistics, such as the Bayesian estimates and their standard error estimates, and the highest posterior density intervals, can be obtained from the simulated observations. A posterior predictive p-value is used to test the goodness-of-fit of the posited model. The methodology is applied to a study of hypertensive patient non-adherence to medication.

Algorithms↗
PubMed1985

Ultrastructure of human C4-binding protein: proposition for a new model.

The structure of human C4-binding protein (C4bp), a regulatory factor of the classical C3 convertase of complement, has been under investigation for several years, but remains poorly understood. For example, the number of subunits in the C4bp molecule has not been established. In this report, we use two different techniques (partial reduction and electron microscopy) to clarify the structure of the C4bp. Our results lead us to propose a structural model which is quite different to that suggested before, i.e. the C4bp molecule appears to be a decamer. In addition to the disulfide bonds which link each subunit to another, a second disulfide interaction leads to the association of the subunits in pairs. Each pair of subunits appears as a filament ending in a globular head at the N-terminal extremity. The pairs of subunits join to form a conical central domain (at the C-terminal extremity) linked by disulfide bonds. The proposed pentameric shape of the C4bp is consistent with the stoichiometry of the C4b-C4bp interactions. The proposed model indicates an overall structural homology between C4bp and other binding proteins.

Carrier Proteins↗
PubMed2000

Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings.

For an increasing fraction of proteins whose structures are being studied, sequence homology to known structures permits building of low resolution structural models. It is demonstrated that dipolar couplings, measured in a liquid crystalline medium, not only can validate such structural models, but also refine them. Here, experimental 1H-15N, 1Halpha-13Calpha, and 13C'-13Calpha dipolar couplings are shown to decrease the backbone rmsd between various homology models of calmodulin (CaM) and its crystal structure. Starting from a model of the Ca2+-saturated C-terminal domain of CaM, built from the structure of Ca2+-free recoverin on the basis of remote sequence homology, dipolar couplings are used to decrease the rmsd between the model and the crystal structure from 5.0 to 1.25 A. A better starting model, built from the crystal structure of Ca2+-saturated parvalbumin, decreases in rmsd from 1.25 to 0.93 A. Similarly, starting from the structure of the Ca2+-ligated CaM N-terminal domain, experimental dipolar couplings measured for the Ca2+-free form decrease the backbone rmsd relative to the refined solution structure of apo-CaM from 4.2 to 1.0 A.

Amino Acid Sequence↗
PubMed2006

Prostaglandin F2alpha formation from prostaglandin H2 by prostaglandin F synthase (PGFS): crystal structure of PGFS containing bimatoprost.

Prostaglandin H(2) (PGH(2)) formed from arachidonic acid is an unstable intermediate and is efficiently converted into more stable arachidonate metabolites by the action of enzymes. Prostaglandin F synthase (PGFS) has dual catalytic activities: formation of PGF(2)(alpha) from PGH(2) by the PGH(2) 9,11-endoperoxide reductase activity and 9alpha,11beta-PGF(2) (PGF(2)(alphabeta)) from PGD(2) by the PGD(2) 11-ketoreductase activity in the presence of NADPH. Bimatoprost (BMP), which is a highly effective ocular hypotensive agent, is a PGF(2)(alpha) analogue that inhibits both the PGD(2) 11-ketoreductase and PGH(2) 9,11-endoperoxide reductase activities of PGFS. To examine the catalytic mechanism of PGH(2) 9,11-endoperoxide reductase, a crystal structure of PGFS[NADPH + BMP] has been determined at 2.0 A resolution. BMP binds near the PGD(2) binding site, but the alpha- and omega-chains of BMP are locate on the omega- and alpha-chains of PGD(2), respectively. Consequently, the bound BMP and PGD(2) direct their opposite faces of the cyclopentane moieties toward the nicotinamide ring of the bound NADP. The alpha- and omega-chains of BMP are involved in H-bonding with protein residues, while the cyclopentane moiety is surrounded by water molecules and is not directly attached to either the protein or the bound NADPH, indicating that the cyclopentane moiety is movable in the active site. From the complex structure, two model structures of PGFS containing PGF(2)(alpha) and PGH(2) were built. On the basis of the model structures and inhibition data, a putative catalytic mechanism of PGH(2) 9,11-endoperoxide reductase of PGFS is proposed. Formation of PGF(2)(alpha) from PGH(2) most likely involves a direct hydride transfer from the bound NADPH to the endoperoxide of PGH(2) without the participation of specific amino acid residues.

Amides↗
PubMed1994

Sequencing and modeling of anti-DNA immunoglobulin Fv domains. Comparison with crystal structures.

Models for the three-dimensional structures of the combining regions of six DNA-binding antibodies have been derived from the sequence data for their Fv domains presented here. Using the amino acid sequences and the canonical structure classes described by Chothia and Lesk (Chothia, C., and Lesk, A.M. (1987) J. Mol. Biol. 196, 901), model loops were selected from immunoglobulin domains of known structure for five of the six antibody hypervariable regions. Models for the third complementarity-determining region of the heavy chain were constructed from known immunoglobulin loops of similar length and sequence. Comparison of three of the models with the respective crystal structure indicates that this procedure can generate a working model of the antibody combining region that provides useful information on the nature of the interactions between antibodies and nucleic acids. As part of our continuing investigation into the structural basis of antibody-DNA recognition, the observed and predicted models for the combining regions of nucleic acid-binding antibodies have been examined. In general, single strand-specific antibodies have deep clefts where the antigen might bind, whereas duplex-specific antibodies present a relatively flat surface. In addition, on the basis of both sequence and structure, there is little to distinguish autoimmune antibodies from those produced by immunization. Testable hypotheses for how these antibodies might interact with single- and double-stranded nucleic acids are presented.

Amino Acid Sequence↗
PubMed2003

Incorporation of experimentally-derived fiber orientation into a structural constitutive model for planar collagenous tissues.

Structural constitutive models integrate information on tissue composition and structure, avoiding ambiguities in material characterization. However, critical structural information (such as fiber orientation) must be modeled using assumed statistical distributions, with the distribution parameters estimated from fits to the mechanical test data. Thus, full realization of structural approaches continues to be limited without direct quantitative structural information for direct implementation or to validate model predictions. In the present study, fiber orientation information obtained using small angle light scattering (SALS) was directly incorporated into a structural constitutive model based on work by Lanir (J. Biomech., v. 16, pp. 1-12, 1983). Demonstration of the model was performed using existing biaxial mechanical and fiber orientation data for native bovine pericardium (Sacks and Chuong, ABME, v.26, pp. 892-902, 1998). The structural constitutive model accurately predicted the complete measured biaxial mechanical response. An important aspect of this approach is that only a single equibiaxial test to determine the effective fiber stress-strain response and the SALS-derived fiber orientation distribution were required to determine the complete planar biaxial mechanical response. Changes in collagen fiber crimp under equibiaxial strain suggest that, at the meso-scale, fiber deformations follow the global tissue strains. This result supports the assumption of affine strain to estimate the fiber strains. However, future evaluations will have to be performed for tissue subjected to a wider range of strain to more fully validate the current approach.

Animals↗
PubMed2002

Bone modeling and structural measures of complexity.

We test sensitivity and powerfulness of recently suggested Structure Measures of Complexity (SMC) with simulated test objects, represented by simple structures or modelled on the basis of a real bone image. We check how these SMC reflect the local and global disordering processes, as well as a deterioration of the bone structure. We show that applications of SMC provide additional information about any changes of the bone structure in comparison to bone mineral density (BMD), and that they can be potentially helpful in the diagnosis of osteoporosis.

Journal Article↗
PubMed1995

Objects and domains for managing medical data and knowledge.

This paper assesses the object-oriented data paradigm, and describes an algebraic approach which permits the generation of data objects from relational data, based on the knowledge captured in a formal Entity-Relationship model, the Structural Model. The advantage is that now objects can be created that satisfy a variety of particular views, as long as the hierarchies represented by the views are subsumed in the network represented by the overall structural model. The disadvantage of creating view-objects dynamically is that the additional layering has performance implications, so that the speedup expected from object-oriented databases versus relational databases, due to their hierarchical object storage, cannot be realized. However, scalability of systems is increased since large systems tend to have multiple objectives, and hence often multiple valid hierarchical views over the data. This approach has been implemented in the Penguin project, and recently some commercial successors are emerging. In truly large systems new problems arise, namely that now not only multiple views will exist, but also that the domains to be covered by the data will be autonomous and hence heterogeneous. One result is that ontologies associated with the multiple domains will differ as well. This paper proposes a knowledge-based algebra over the ontologies, so that the domain knowledge can be partitioned for maintenance. Only the articulation points, where the domains intersect, have to be agreed upon as defined by matching rules which define the shared ontologies.

Artificial Intelligence↗
PubMed1989

The political implications of psychosocial work redesign: a model of the psychosocial class structure.

The goal of this article is to further illuminate the poorly understood distribution of psychosocial well-being at the national population level (the distribution of conventional economic well-being is, of course, well understood). After reviewing psychosocial phenomena that cannot be predicted by the "conventional" class structure, the author introduces a new definition of production output value (New Value), more closely related to psychosocial well-being. A psychosocial class structure model is presented based on nine occupational subgroups in four status levels, representing both conventional and New Value-based status differences. An empirical analysis of 38 occupations in the U.S. work force (U.S. Quality of Employment Surveys 1969, 1972, 1977) uses psychosocial job dimensions of decision latitude, psychological demands, physical exertion, and social support. The author reviews job redesign strategies for three New Value "impoverished" groups with routinized, bureaucratized, and commercialized jobs, and the conditions for economic stability and political participation related to the psychosocial class structure model. Conflicts arising between conventional and New Value-based policies are discussed.

Decision Making↗
PubMedDate not supplied

Is there a gender difference in a factorial structure of the positive and negative syndrome scale? A test by structural equation modeling.

By means of the multisample structured means strategy, we examined gender differences in a five-factorial structure model of Positive and Negative Syndrome Scale (PANSS) ratings of 308 patients of both sexes with DSM-IV schizophrenia with comparable age at investigation and overall symptomatic severity across sex. The test indicated that the factors and component symptoms were common across sex, whereas the factor loadings might be different. However, the model that incorporated the difference in the factor loadings did not improve model fit indices. Therefore, it is concluded that this investigation elicited only minimal gender differences, and on the whole confirmed the PANSS five-factor structure for both sexes.

Adult↗
PubMed2006

Engineering aromatic L-amino acid transaminase for the asymmetric synthesis of constrained analogs of L-phenylalanine.

An enzymatic asymmetric synthesis was carried out for the preparation of enantiomerically pure L-diphenylalanine using the rationally engineered aromatic L-amino acid transaminase (eAroATEs) obtained from Enterobacter sp. BK2K-1. To rationally redesign the enzyme, structural model was constructed by the homology modeling. The structural model was experimentally validated by the site-directed mutagenesis of the predicted pyridoxal-5'-phosphate (PLP) binding site and the substrate-recognition region, and the cell-free protein synthesis of mutated enzymes. It was suggested that Arg281 and Arg375 were the key residues to recognize the distal carboxylate and alpha-carboxylate group of the substrates, respectively. The model also predicted that Tyr66 forms hydrogen bond with the phosphate moiety of PLP and interacts with the side chain attached to beta-carbon of the amino acid substrate. Among the various site-directed mutants, Y66L variant was able to synthesize L-diphenylalanine with 23% conversion yield for 10 h, whereas the wild-type AroATEs was inactive for the transamination between diphenylpyruvate and L-phenylalanine as amino acceptor and amino donor, respectively.

Amino Acids, Aromatic↗
PubMed1999

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

The technique of small-probe contact dot surfaces is described as a method for calculating and displaying the detailed atomic contacts inside or between molecules. It allows one both to measure and to visualize directly the goodness-of-fit of packing interactions. It requires both highly accurate structures and also the explicit inclusion of all hydrogen atoms and their van der Waals interactions. A reference dataset of 100 protein structures was chosen on the basis of resolution (1.7 A or better), crystallographic R-value, non-homology, and the absence of any unusual problems. Hydrogen atoms were added in standard geometry and, where needed, with rotational optimization of OH, SH, and NH+3 positions. Side-chain amide orientations were corrected where required by NH van der Waals clashes, as described in the accompanying paper. It was determined that, in general, methyl groups pack well in the default staggered conformation, except for the terminal methyl groups of methionine residues, which required rotational optimization. The distribution of serious clashes (i.e. non-H-bond overlap of >/=0.4 A) was studied as a function of resolution, alternate conformations, and temperature factor (B), leading to the decision that packing and other structural features would not be analyzed for residues in 'b' alternate conformations or with B-factors of 40 or above. At the level of the fine details analyzed here, structural accuracy improves quite significantly over the range from 1.7 to 1.0 A resolution. These high-resolution structures show impressively well-fitted packing interactions, with some regions thoroughly interdigitated and other regions somewhat sparser. Lower-resolution structures or model structures could undoubtedly be improved in accuracy by the incorporation of this additional information: for example, nucleic acid structures in non-canonical conformations are often very accurate for the bases and much less reliable for the backbone, whose conformation could be specified better by including explicit H atom geometry and contacts. The contact dots are an extremely sensitive method of finding problem areas, and often they can suggest how to make improvements. They can also provide explanations for structural features that have been described only as empirical regularities, which is illustrated by showing that the commonest rotamer of methionine (a left-handed spiral, with all chi values near -60 degrees) is preferred because it provides up to five good H atom van der Waals contacts. This methodology is thus applicable in two different ways: (1) for finding and correcting errors in structure models (either experimental or theoretical); and (2) for analyzing interaction patterns in the molecules themselves.

Crystallography, X-Ray↗
PubMed1994

Potassium channels: a computer prediction of structure and selectivity.

Model structures for the pore of the potassium channels Shaker and ROMK1 are predicted. The models arise from computer simulations and suggest reasons for the striking selectivity of these channels for K+ and the blocking of ROMK1 by internal Mg2+. The modelled structure of the Shaker pore is supported by mutagenesis data. The mutagenesis experiments indicate the side chains responsible for binding to blocking agents [tetraethylammonium (TEA) and charybdotoxin (CTX)] and the model has these side chains suitably oriented for binding. An aromatic K+ binding site part way down the pore is also predicted by the Shaker pore model.

Amino Acid Sequence↗