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Results for “Models, Structural”

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PubMedDate not supplied

Psychometric properties of the healthful eating belief scales for persons at risk of diabetes.

OBJECTIVE: To examine the validity and reliability of Theory of Planned Behavior (TPB) scales for healthful eating for persons at risk for diabetes. DESIGN: Cross-sectional, using a self-administered questionnaire. SETTING: Community in the Midwest. PARTICIPANTS: 106 adults who self-identified based on one or more American Diabetes Association diabetes risks. VARIABLES MEASURED: Behavioral, normative, and control beliefs; and attitude, subjective norm, perceived behavioral control, and intention to eat a healthful diet. ANALYSIS: Construct validity was assessed with factor analyses and measurement and structural models using structural equation modeling. Reliability of the scales was assessed with Cronbach alpha and a 2-month test-retest. RESULTS: Factor analysis loadings were greater than .37. Cronbach alphas for the behavioral, normative, and control belief scales were .80, .91, and .84, respectively. The measurement model revealed that the measures were significant estimates for the TPB constructs, and they fit well as indirect measures of attitude, subjective norm, and perceived behavioral control in predicting intention to eat a healthful diet. Test-retest revealed 2-month stability of the scales. CONCLUSIONS AND IMPLICATIONS: Scales for measuring TPB behavioral, normative, and control beliefs were valid and reliable for use with adults at risk for diabetes. Further examination with minority persons is warranted.

Adult↗

PubMed1992

Model modifications in covariance structure analysis: the problem of capitalization on chance.

In applications of covariance structure modeling in which an initial model does not fit sample data well, it has become common practice to modify that model to improve its fit. Because this process is data driven, it is inherently susceptible to capitalization on chance characteristics of the data, thus raising the question of whether model modifications generalize to other samples or to the population. This issue is discussed in detail and is explored empirically through sampling studies using 2 large sets of data. Results demonstrate that over repeated samples, model modifications may be very inconsistent and cross-validation results may behave erratically. These findings lead to skepticism about generalizability of models resulting from data-driven modifications of an initial model. The use of alternative a priori models is recommended as a preferred strategy.

Adolescent↗

PubMed1996

Equilibrium studies of kinesin-nucleotide intermediates.

We have examined the energetics of the interactions of two kinesin constructs with nucleotide and microtubules to develop a structural model of kinesin-dependent motility. Dimerization of the constructs was found to reduce the maximum rate of the microtubule-activated kinesin ATPase 5-fold. Beryllium fluoride and aluminum fluoride also reduce this rate, and they increase the affinity of kinesin for microtubules. By contrast, inorganic phosphate reduces the affinity of a dimeric kinesin construct for microtubules. These findings are consistent with a model in which the kinesin head can assume one of two conformations, "strong" or "weak" binding, determined by the nature of the nucleotide that occupies the active site. Data for dimeric kinesin are consistent with a model in which kinesin.ATP binds to the microtubule in a strong state with positive cooperativity; hydrolysis of ATP to ADP+P(i) leads to dissociation of one of the attached heads and converts the second, attached head to a weak state; and dissociation of phosphate allows the second head to reattach. These results also argue that a large free energy change is associated with formation of kinesin.ADP.P(i) and that this step is the major pathway for dissociation of kinesin from the microtubule.

Adenosine Diphosphate↗

PubMed1980

An experimentally-derived model for the secondary structure of the 16S ribosomal RNA from Escherichia coli.

Ribonucleoprotein fragments are isolated by mild ribonuclease digestion of E. coli 30S ribosomal subunits, and are deproteinized and subjected to a second partial digestion. Base-pairing between the resulting small RNA fragments is investigated using the two-dimensional gel electrophoresis procedure already reported (see Ref. 1). The interactions thus found are incorporated into a secondary structure model covering approximately 80% of the 16S RNA.

Base Sequence↗

PubMed2005

A structured-population model of Proteus mirabilis swarm-colony development.

In this paper we present continuous age- and space-structured models and numerical computations of Proteus mirabilis swarm-colony development. We base the mathematical representation of the cell-cycle dynamics of Proteus mirabilis on those developed by Esipov and Shapiro, which are the best understood aspects of the system, and we make minimum assumptions about less-understood mechanisms, such as precise forms of the spatial diffusion. The models in this paper have explicit age-structure and, when solved numerically, display both the temporal and spatial regularity seen in experiments, whereas the Esipov and Shapiro model, when solved accurately, shows only the temporal regularity. The composite hyperbolic-parabolic partial differential equations used to model Proteus mirabilis swarm-colony development are relevant to other biological systems where the spatial dynamics depend on local physiological structure. We use computational methods designed for such systems, with known convergence properties, to obtain the numerical results presented in this paper.

Agar↗

PubMedDate not supplied

The structural identifiability and parameter estimation of a multispecies model for the transmission of mastitis in dairy cows with postmilking teat disinfection.

A mathematical model for the transmission of two interacting classes of mastitis causing bacterial pathogens in a herd of dairy cows is presented and applied to a specific data set. The data were derived from a field trial of a specific measure used in the control of these pathogens, where half the individuals were subjected to the control and in the others the treatment was discontinued. The resultant mathematical model (eight non-linear simultaneous ordinary differential equations) therefore incorporates heterogeneity in the host as well as the infectious agent and consequently the effects of control are intrinsic in the model structure. A structural identifiability analysis of the model is presented demonstrating that the scope of the novel method used allows application to high order non-linear systems. The results of a simultaneous estimation of six unknown system parameters are presented. Previous work has only estimated a subset of these either simultaneously or individually. Therefore not only are new estimates provided for the parameters relating to the transmission and control of the classes of pathogens under study, but also information about the relationships between them. We exploit the close link between mathematical modelling, structural identifiability analysis, and parameter estimation to obtain biological insights into the system modelled.

Animals↗

PubMedDate not supplied

Studies in the assessment of folding quality for protein modeling and structure prediction.

A diagnostic for assessing the quality of a fold has been developed to which further criteria can be progressively added. The goal is to create a measure that can follow the status of a protein structure in a simulation or modeling process, when the answer (the experimental structure) is not known in advance, rather than simply reject deliberate misfolds. This places greater emphasis on the need to study, and calibrate against, marginal cases, i.e., unusual native structures, incomplete structures, partially erroneous X-ray structures, good models, poor models, and the effect of cofactors. The first three terms introduced in the diagnostic are appropriate core-forming properties or noncore properties of residues in relation to tertiary structure, appropriate neighboring structure density for each residue in relation to tertiary structure, and secondary structure consistency. While the method emerges as a useful simulation analysis tool, we find a need for further fine-tuning to diminish sensitivity to minor conformational changes that retain essential features of the fold, balanced against the need to obtain a more sensitive response when a conformational change involves less physically meaningful interatomic interactions. This dual utility is difficult to obtain: the investigation highlights some of the issues. Initial attempts to obtain it have led to terms in the diagnostic that are admittedly complex: simplifications must also be explored.

Animals↗

PubMed1993

Modeling protein structures: construction and their applications.

Although no general solution to the protein folding problem exists, the three-dimensional structures of proteins are being successfully predicted when experimentally derived constraints are used in conjunction with heuristic methods. In the case of interleukin-4, mutagenesis data and CD spectroscopy were instrumental in the accurate assignment of secondary structure. In addition, the tertiary structure was highly constrained by six cysteines separated by many residues that formed three disulfide bridges. Although the correct structure was a member of a short list of plausible structures, the "best" structure was the topological enantiomer of the experimentally determined conformation. For many proteases, other experimentally derived structures can be used as templates to identify the secondary structure elements. In a procedure called modeling by homology, the structure of a known protein is used as a scaffold to predict the structure of another related protein. This method has been used to model a serine and a cysteine protease that are important in the schistosome and malarial life cycles, respectively. The model structures were then used to identify putative small molecule enzyme inhibitors computationally. Experiments confirm that some of these nonpeptidic compounds are active at concentrations of less than 10 microM.

Amino Acid Sequence↗

PubMed2003

A structured clinical model for predicting the probability of pulmonary embolism.

PURPOSE: To develop a structured model to predict the clinical probability of pulmonary embolism. METHODS: We studied 1,100 consecutive patients with suspected pulmonary embolism in whom a definite diagnosis had been established. We used logistic regression analysis to estimate the probability of pulmonary embolism based on patients' clinical characteristics; the probability was categorized as low (< or = 10%), intermediate (>10%, < or = 50%), moderately high (>50%, < or = 90%), or high (>90%). RESULTS: The overall prevalence of pulmonary embolism was 40% (n = 440). Ten characteristics were associated with an increased risk of pulmonary embolism (male sex, older age, history of thrombophlebitis, sudden-onset dyspnea, chest pain, hemoptysis, electrocardiographic signs of acute right ventricular overload, radiographic signs of oligemia, amputation of the hilar artery, and pulmonary consolidation suggestive of infarction), and five were associated with a decreased risk (prior cardiovascular or pulmonary disease, high fever, pulmonary consolidation other than infarction, and pulmonary edema on the chest radiograph). With this model, 432 patients (39%) were rated a low probability, of whom 19 (4%) had pulmonary embolism; 283 (26%) were rated an intermediate probability, of whom 62 (22%) had pulmonary embolism; 72 (7%) were rated a moderately high probability, of whom 53 (74%) had pulmonary embolism; and 313 (28%) were rated a high probability, of whom 306 (98%) had pulmonary embolism. CONCLUSION: This prediction model may be useful for estimating the probability of pulmonary embolism before obtaining definitive test results.

Adolescent↗

PubMed1990

Appropriateness of composites in structural equation models.

The appropriateness of using composites instead of multiple indicators in a structural model of physical health was evaluated. Liang's (1986) specification of self-reported physical health is a relatively complex multiple indicators model which may not be practical in actual application. To simplify this formulation, a two-stage strategy was used. First, reliability was estimated for each composite to fix the measurement error variance and the regression of the composite on the latent variable. Second, the model was reestimated by constraining these parameters. Regression analyses were undertaken to assess the impact of using composites instead of multiple indicators. Parameter estimates for causal linkages and residual error variances based on multiple indicators approach were closely reproduced by using composites, thus providing justification for the proposed strategy.

Activities of Daily Living↗

PubMed1985

[A model of structural transition based on the molecular-type population structure theorem].

The author presents a model of structural transition based on a theorem of molecular-type population structure. "Household or family has been sometimes called [a] demographic molecule, when compared with the unit of ordinary population, i.e., a person, which in turn [is called a] demographic atom. Molecular population structure is defined by the author as the age structure of the population composed of people included in certain [sorts] of molecules. The molecular age structure is basically represented by matrices whose elements...are the numbers of people aged i whose other member person in the same molecule, for example mother, is aged j." (summary in ENG)

Age Distribution↗

PubMed2025

The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.

The computational modeling of chromatin structure is highly complex due to the hierarchical organization of chromatin, which reflects its diverse biophysical principles, as well as inherent dynamism, which underlies its complexity. Chromatin structure modeling can be based on diverse approaches and assumptions, making it essential to determine how different methods influence the modeling outcomes. We conducted a project at the NIH-funded 4D Nucleome Hackathon on March 18-21, 2024, at The University of Washington in Seattle, USA. The hackathon provided an amazing opportunity to gather an international, multi-institutional and unbiased group of experts to discuss, understand and undertake the challenges of chromatin model comparison and validation. Here we give an overview of the current state of the 3D chromatin field and discuss our efforts to run and validate the models. We used distance matrices to represent chromatin models and we calculated Spearman correlation coefficients to estimate differences between models, as well as between models and experimental data. In addition, we discuss challenges in chromatin structure modeling that include: 1) different aspects of chromatin biophysics and scales complicate model comparisons, 2) large diversity of experimental data (e.g., population-based, single-cell, protein-specific) that differ in mathematical properties, heatmap smoothness, noise and resolutions complicates model validation, 3) expertise in biology, bioinformatics, and physics is necessary to conduct comprehensive research on chromatin structure, 4) bioinformatic software, which is often developed in academic settings, is characterized by insufficient support and documentation. We also emphasize the importance of establishing guidelines for software development and standardization.

Chromatin↗

PubMed2006

Electronic origins of structural distortions in post-transition metal oxides: experimental and theoretical evidence for a revision of the lone pair model.

Structural distortions in post-transition metal oxides are often explained in terms of the influence of sp hybrid "lone pairs." Evidence is presented here showing that this model must be revised. The electronic structures of prototypically distorted alpha-PbO and alpha-Bi2O3 have been measured by high-resolution x-ray photoemission and soft x-ray emission spectroscopies. In contrast with the expectations of the lone pair model, a high density of metal 6s states is observed at the bottom of the valence band. The measurements are consistent with the results of density functional theory calculations.

Journal Article↗

PubMed1997

Predicting RNA structures: the model of the RNA element binding Rev meets the NMR structure.

BACKGROUND: How accurate are the predictions of RNA three-dimensional structures? Assessing this accuracy requires the detailed comparison of the prediction with the experimentally determined structure. Previously, sequence variation in RNA aptamers that bind the Rev protein was used to infer a three-dimensional model of the Rev-binding element (RBE) RNA. Although much of this model has been substantiated by subsequent experimental data, its validity remains to be determined by confronting it with the structure determined by NMR spectroscopy. RESULTS: A series of different criteria such as geometric parameters (root mean square deviation, interproton distances, torsions and puckering), helicoidal parameters (base pairing and base stacking) and stability considerations (conformational energies) have been evaluated to identify common and distinguishing structural characteristics of the model and the NMR structure. CONCLUSIONS: The detailed comparison of the two structures reveals striking structural similarities at both the global and local level that validate the RNA modeling approach that we have used. Analysis of the structural differences and the precision of the model suggest that the limitations of the method are related to the amount of structural information available for modeling.

Binding Sites↗

PubMed2005

Associations among overeating, overweight, and attention deficit/hyperactivity disorder: a structural equation modelling approach.

BACKGROUND: Some recent studies have reported strong links between obesity and ADHD in adults; however, to date, little work has focussed on possible behavioural mechanisms that could account for this association. METHOD: This study used structural equation modelling (SEM) in a sample of healthy adult women to test the predictions that ADHD symptoms predict aspects of overeating, including binge eating and emotionally-induced eating, which in turn are positively correlated with Body Mass Index. RESULTS: The SEM produced a non-significant chi-square and both the measurement model and the structural model fit the data very well. CONCLUSIONS: Plausible mechanisms are discussed to help explain how the symptomatology of ADHD could foster different forms of overeating.

Adult↗

PubMed2003

Platelet-derived growth factor (PDGF)-C, a PDGF family member with a vascular endothelial growth factor-like structure.

Platelet-derived growth factor (PDGF)-C is a novel member of the PDGF family that binds to PDGF alphaalpha and alphabeta receptors. The growth factor domain of PDGF-C (GFD-PDGF-C) was expressed in high yields in Escherichia coli and was purified and refolded from inclusion bodies obtaining a biologically active growth factor with dimeric structure. The GFD-PDGF-C contains 12 cysteine residues, and Ellman assay analysis indicates that it contains three intramonomeric disulfide bonds, which is in accordance with GFD-PDGF-C being a member of the cystine knot superfamily of growth factors. The recombinant GFD-PDGF-C was characterized by CD, fluorescence, NMR, and infrared spectroscopy. Together, our data indicate that GFD-PDGF-C is a highly thermostable protein that contains mostly beta-sheet secondary structure and some (6%) alpha-helix structure. The structural model of PDGF-C, obtained by homology-based molecular modeling using the structural representatives of this family of growth factors, shows that GFD-PDGF-C has a higher structural homology to the vascular endothelial growth factor than to PDGF-B. The modeled structure can give further insights into the function and specificity of this molecule.

Amino Acid Sequence↗

PubMed2004

Protein modeling and structure prediction with a reduced representation.

Protein modeling could be done on various levels of structural details, from simplified lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular mechanics. Here I describe a new high resolution reduced model, its force field and applications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sampling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic protein-like conformational biases, statistical potentials for the short-range conformational propensities, a model of the main chain hydrogen bonds and context-dependent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.

Amino Acid Sequence↗

PubMed2006

A structured erythropoiesis model with nonlinear cell maturation velocity and hormone decay rate.

We develop a quasilinear structured model that describes the regulation of erythropoiesis, the process in which red blood cells are developed. In our model, the maturation velocity of precursor cells is assumed to be a function of the erythropoietin hormone, and the decay rate of this hormone is assumed to be a function of the number of precursor cells, unlike other models which assume these parameters to be constants. Existence-uniqueness results are established and convergence of a finite difference approximation to the unique solution of the model is obtained. The finite difference scheme is then used to investigate the effects of these nonlinear parameters on the model dynamics. Our results show that a velocity of precursor cells maturation rate which is an increasing function of the hormone level and a decay rate of the hormone which is an increasing function of the number of precursor cells have a stabilizing effect on the dynamics of the model. While assuming that one parameter is a function and letting the other be a constant stabilizes the oscillations in the mature cells level, the effect is more significant when both parameters are taken to be functions. A study of robustness with respect to the forms of these functions and parameter sensitivity is also carried out.

Cell Differentiation↗