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PubMed2005

Ecological time-series analysis through structural modelling with latent constructs: concepts, methods and applications.

Time-series analyses in ecology usually involve the use of autoregressive modelling through direct and/or delayed difference equations, which severely restricts the ability of the modeler to structure complex causal relationships within a multivariate frame. This is especially problematic in the field of population regulation, where the proximate and ultimate causes of fluctuations in population size have been hotly debated for decades. Here it is shown that this debate can benefit from the implementation of structural modelling with latent constructs (SEM) to time-series analysis in ecology. A nonparametric bootstrap scheme illustrates how this modelling approach can circumvent some problems posed by the climate-ecology interface. Stochastic Monte Carlo simulation is further used to assess the effects of increasing time-series length and different parameter estimation methods on the performance of several model fit indexes. Throughout, the advantages and limitations of the SEM method are highlighted.

Ecology↗

PubMed2005

On the concept of model structural error.

A consideration of model structural error leads to some particularly interesting tensions in the model calibration/conditioning process. In applying models we can usually only assess the total error on some output variable for which we have observations. This total error may arise due to input and boundary condition errors, model structural errors and error on the output observation itself (not only measurement error but also as a result of differences in meaning between what is modelled and what is measured). Statistical approaches to model uncertainty generally assume that the errors can be treated as an additive term on the (possibly transformed) model output. This allows for compensation of all the sources of error, as if the model predictions are correct and the total error can be treated as "measurement error." Model structural error is not easily evaluated within this framework. An alternative approach to put more emphasis on model evaluation and rejection is suggested. It is recognised that model success or failure within this framework will depend heavily on an assessment of both input data errors (the "perfect" model will not produce acceptable results if driven with poor input data) and effective observation error (including a consideration of the meaning of observed variables relative to those predicted by a model).

Environment↗

PubMed2004

Experimentally biased model structure of the Hsc70/auxilin complex: substrate transfer and interdomain structural change.

A model structure of the Hsc70/auxilin complex has been constructed to gain insight into interprotein substrate transfer and ATP hydrolysis induced conformational changes in the multidomain Hsc70 structure. The Hsc70/auxilin system, which is a member of the Hsp70/Hsp40 chaperone system family, uncoats clathrin-coated vesicles in an ATP hydrolysis-driven process. Incorporating previous results from NMR and mutant binding studies, the auxilin J-domain was docked into the Hsc70 ATPase domain lower cleft using rigid backbone/flexible side chain molecular dynamics, and the Hsc70 substrate binding domain was docked by a similar procedure. For comparison, J-domain and substrate binding domain docking sites were obtained by the rigid-body docking programs DOT and ZDOCK, filtered and ranked by the program ClusPro, and relaxed using the same rigid backbone/flexible side chain dynamics. The substrate binding domain sites were assessed in terms of conserved surface complementarity and feasibility in the context of substrate transfer, both for auxilin and another Hsp40 protein, Hsc20. This assessment favors placement of the substrate binding domain near D152 on the ATPase domain surface adjacent to the J-domain invariant HPD segment, with the Hsc70 interdomain linker in the lower cleft. Examining Hsc70 interdomain energetics, we propose that long-range electrostatic interactions, perhaps due to a difference in the pKa values of bound ATP and ADP, could play a major role in the structural change induced by ATP hydrolysis. Interdomain electrostatic interactions also appear to play a role in stimulation of ATPase activity due to J-domain binding and substrate binding by Hsc70.

Adenosine Triphosphate↗

PubMed2003

3-D structural modeling of humic acids through experimental characterization, computer assisted structure elucidation and atomistic simulations. 1. Chelsea soil humic acid.

This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D 1H and 13C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated 13C NMR spectrum of an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

Humic Substances↗

PubMed1997

Structural Modeling and Magneto-Structural Correlations for Hydroxo-Bridged Copper(II) Binuclear Complexes.

The influence of the simplifications introduced by modeling a molecular structure on the exchange coupling constant is studied for hydroxo-bridged Cu(II) binuclear complexes. This study focuses on the role of the terminal ligands and the counterions. The terminal ligands are responsible for marked changes in the exchange coupling constant, depending on their donor properties, while the counterions have an effect only when directly coordinated to the copper atoms. The study of the magneto-structural correlations for the hydroxo-bridged Cu(II) binuclear complexes has been extended by analyzing the influence of the Cu-O distance, the effect of the asymmetry at the bridging backbone, and the hinge distortion of the bridge. The increase in the Cu-O distance and the absence of the hinge distortion of the Cu(2)O(2) ring substantially enhance the antiferromagnetic interaction.

Journal Article↗

PubMed2006

Maximal reliability and power in covariance structure models.

In covariance structure modelling, the non-centrality parameter of the asymptotic chi-squared distribution is typically used as an indicator of asymptotic power for hypothesis tests. When a latent linear regression is of interest, the contribution to power by the maximal reliability coefficient, which is associated with used latent variable indicators, is examined and this relationship is further explicated in the case of congeneric measures. It is also shown that item parcelling may reduce power of tests of latent regression parameters. Recommendations on weights for parcelling to avoid power loss are provided, which are found to be those of optimal linear composites with maximal reliability.

Humans↗

PubMed2004

A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory.

Modeling the structure of natively disordered peptides has proved difficult due to the lack of structural information on these peptides. In this work, we use a novel application of the host-guest method, combining folding theory with experiments, to model the structure of natively disordered polyglutamine peptides. Initially, a minimalist molecular model (C(alpha)C(beta)) of CI2 is developed with a structurally based potential and captures many of the folding properties of CI2 determined from experiments. Next, polyglutamine "guest" inserts of increasing length are introduced into the CI2 "host" model and the polyglutamine is modeled to match the resultant change in CI2 thermodynamic stability between simulations and experiments. The polyglutamine model that best mimics the experimental changes in CI2 thermodynamic stability has 1), a beta-strand dihedral preference and 2), an attractive energy between polyglutamine atoms 0.75-times the attractive energy between the CI2 host Go-contacts. When free-energy differences in the CI2 host-guest system are correctly modeled at varying lengths of polyglutamine guest inserts, the kinetic folding rates and structural perturbation of these CI2 insert mutants are also correctly captured in simulations without any additional parameter adjustment. In agreement with experiments, the residues showing structural perturbation are located in the immediate vicinity of the loop insert. The simulated polyglutamine loop insert predominantly adopts extended random coil conformations, a structural model consistent with low resolution experimental methods. The agreement between simulation and experimental CI2 folding rates, CI2 structural perturbation, and polyglutamine insert structure show that this host-guest method can select a physically realistic model for inserted polyglutamine. If other amyloid peptides can be inserted into stable protein hosts and the stabilities of these host-guest mutants determined, this novel host-guest method may prove useful to determine structural preferences of these intractable but biologically relevant protein fragments.

Amyloid↗

PubMed2000

Quantification of age-related changes in the structure model type and trabecular thickness of human tibial cancellous bone.

Structure model type and trabecular thickness are important characteristics in describing cancellous bone architecture. It has been qualitatively observed that a radical change of trabeculae from plate-like to rod-like occurs in aging, bone remodeling, and osteoporosis. Thickness of trabeculae has traditionally been measured using model-based histomorphometric methods on two-dimensional (2-D) sections. However, no quantitative study has been published based on three-dimensional (3-D) methods on the age-related changes in structure model type and trabecular thickness for human peripheral (tibial) cancellous bone. In this study, 160 human proximal tibial cancellous bone specimens from 40 normal donors, aged 16 to 85 years, were collected. These specimens were micro-computed tomography (micro-CT) scanned, then the micro-CT images were segmented using optimal thresholds. From accurate 3-D data sets, structure model type and trabecular thickness were quantified by means of novel 3-D methods. Structure model type was assessed by calculating the structure model index (SMI). The SMI was quantified based on a differential analysis of the triangulated bone surface of a structure. This technique allows quantification of structure model type, such as plate, rod objects, or mixture of plates or rods. Trabecular thickness is calculated directly from 3-D images, which is especially important for an a priori unknown or changing structure. Furthermore, 2-D trabecular thickness was also calculated based on the plate model. Our results showed that structure model type changed towards more rod-like in the elderly, and that trabecular thickness declined significantly with age. These changes become significant after 80 years of age for human tibial cancellous bone, whereas both properties seem to remain relatively unchanged between 20 and 80 years. Although a fairly close relationship was seen between 3-D trabecular thickness and 2-D trabecular thickness, real 3-D trabecular thickness was significantly underestimated using 2-D method.

Adolescent↗

PubMed2003

Marginal structural models as a tool for standardization.

In this article, we show the general relation between standardization methods and marginal structural models. Standardization has been recognized as a method to control confounding and to estimate causal parameters of interest. Because standardization requires stratification by confounders, the sparse-data problem will occur when stratified by many confounders and one then might have an unstable estimator. A new class of causal models called marginal structural models has recently been proposed. In marginal structural models, the parameters are consistently estimated by the inverse-probability-of-treatment weighting method. Marginal structural models give a nonparametric standardization using the total group (exposed and unexposed) as the standard. In epidemiologic analysis, it is also important to know the change in the average risk of the exposed (or the unexposed) subgroup produced by exposure, which corresponds to the exposed (or the unexposed) group as the standard. We propose modifications of the weights in the marginal structural models, which give the nonparametric estimation of standardized parameters. With the proposed weights, we can use the marginal structural models as a useful tool for the nonparametric multivariate standardization.

Antineoplastic Agents, Hormonal↗

PubMed1993

Probabilistic constraint satisfaction with structural models: application to organ modeling by radial contours.

One of the key challenges within medical information sciences is the development of useful models for biological structure and its variability. Many biomedical problems involve the elucidation of structure (for example, from experimental data or from imaging studies), and structural models can often drive the process of inferring precise structure from data. Ideally, model-driven data interpretation combines knowledge about the generic features of a class of biological structures (as contained within a model) with data that provide specific information (often noisy) about a particular instance of the class. In this paper we briefly discuss model-driven determination of biological structure as an example of a structural constraint satisfaction problem. We describe a probabilistic implementation of structural constraint satisfaction, and show that our formulation of a particular organ modeling technology (Radial Contour Models) exhibits promising performance. Our results demonstrate the utility of probabilistic models for the solution of structural constraint satisfaction problems.

Computer Simulation↗

PubMed2001

[Modeling of feeling institution in pilot structural model].

Objective. To improve a structural pilot model proposed by R. A. Hess, in which element of observation feeling institution was neglected. Method. Real simulation results showed that there was a blind region for small observation signal, and pilot made no response in this region. So we knew that the basic characteristics of the observation feeling institution were observation threshold and observation noise. A Neural Network (NN) receptor model was augmented in the structural pilot model to describe the characteristics of human observation feeling institution. Furthermore, using the augmented model, the affection of the pilot model on the characteristics of the closed-loop system of pilot and controlled element was studied. Result. The affection of NN perception on the closed-loop system was that the stable gain region of the human pilot was extended. Conclusion. The proposed model was reasonable for the element of human feeling institution.

Aerospace Medicine↗

PubMed1998

Growth and product formation of Aspergillus oryzae during submerged cultivations: verification of a morphologically structured model using fluorescent probes.

A morphologically structured model is well suited for obtaining a good description of growth and product formation of filamentous fungi for use in a process model, for example. This article describes a new morphologically structured model and its application to an alpha-amylase producing strain of Aspergillus oryzae. The model is based on a division of the fungal hyphae into three different regions: an extension zone, representing the tips of the hyphae; an active region, which is responsible for growth and product formation; and an inactive hyphal region. Two metamorphosis reactions describing branching and inactivation are included in the model, and the kinetics of branching and tip extension are based on known experimentally verified models of fungal microscopic morphology. To verify the structure of the model a double-staining method, based on a combination of fluorescence microscopy and automated image analysis, has been developed for measuring the fraction of active cells. The method employs the fluorescent dye 3, 3'-dihexyloxocarbocyanin to stain organelles inside the hyphae and Calcoflour White to stain the cell wall. The ratio between the projected areas of the organelles and of the entire hyphal element is then taken to be proportional to the fraction of active cells. When applied to chemostat and fed-batch experiments, the double-staining method seemed to confirm the basic morphological structure of the model. The model is able to produce accurate simulations of steady-state and transient conditions in chemostats, of batch cultivations, and even the formation of a single hyphal element from a spore, all with the same values of the model parameters.

Aspergillus oryzae↗

PubMed1999

A curved piezo-structure model: implications on active structural acoustic control.

Current research in Active Structural Acoustic Control (ASAC) relies heavily upon accurately capturing the application physics associated with the structure being controlled. The application of ASAC to aircraft interior noise requires a greater understanding of the dynamics of the curved panels which compose the skin of an aircraft fuselage. This paper presents a model of a simply supported curved panel with attached piezoelectric transducers. The model is validated by comparison to previous work. Further, experimental results for a simply supported curved panel test structure are presented in support of the model. The curvature is shown to affect substantially the dynamics of the panel, the integration of transducers, and the bandwidth required for structural acoustic control.

Acoustics↗

PubMed2004

Protein structure modeling in the proteomics era.

Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects -- to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques.

Animals↗

PubMed1984

Structural modeling of spatial vision.

A linear structural model of mechanisms underlying spatial vision was generated from the variance-covariance matrix of contrast sensitivity data. The data had been collected on a large group of observers ranging in age from 19 to 87 yr, using gratings of 0.5-16 c/deg spatial frequency. Structural models incorporating various numbers of spatial frequency-tuned mechanisms were compared, with a three-mechanism model giving the best account of the data. The same analysis was applied to contrast sensitivity data simulated from Wilson and Bergen's (1979) model. When the stimulated data covered 0.5-16 c/deg, only three mechanisms were needed to give a satisfactory account of the data; when the simulated data covered 0.25-16 c/deg, four mechanisms were required. Peak sensitivities and bandwidths of the mechanisms extracted from the simulated data resembled those extracted from the real, population data. This reinforces the idea that at an early stage of human vision a small number of spatially-tuned mechanisms are operative. In addition, the outcome of analyses with both real and simulated data illustrate the potential value of linear structural models for vision research.

Adult↗

PubMed1994

A componential investigation of the relation between structural modelling and cognitive accounts of human judgement.

Structural modelling and cognitive process approaches have developed rather different accounts of human judgement and decision making. Two hypotheses to explain these differences were evaluated in the context of a judgement task, and formulated in terms of predictions concerning measurement of attribute importance. First, following suggestions made by Billings and Marcus (1983), it was argued that measures of judgement behaviour based on structural modelling reflect cognitive activity late in the judgement process, whereas measures derived from cognitive process approaches reflect cognitive activity early in the process. A new componential judgement task was developed which not only provided estimates of attribute importance based on structural modelling, but also two sets of cognitive process measures based on cognitive components assumed to occur early and late in the judgement process. A greater degree of convergence between approaches was predicted when the cognitive approach was based on activity in the component occurring later in the judgement process. Second, it was argued that in previous research subjects have had unlimited time to make their judgements, reducing the need for attribute importance to provide the dominant basis for determining processing strategy. The present experiment introduced a time pressure condition and, on the basis of previous research, predicted that this would increase the amount of information processing based on attribute importance, thereby increasing the convergence between estimates of attribute importance derived from the two approaches. The first, but not the second hypothesis was supported and the results were discussed in terms of their implications for understanding previous differences between the two approaches to human judgement.

Accounting↗

PubMed1991

Structural modeling of functional neural pathways mapped with 2-deoxyglucose: effects of acoustic startle habituation on the auditory system.

This paper describes the first application of structural modeling to neuroscience. Structural modeling (also known as path analysis) is a method to assess the relative impact of directional links in a system and how these interrelations may change under different conditions. The objective was to demonstrate how structural modeling can be used to determine the functional interrelationships between brain structures that form the auditory system. Using structural modeling, changes in auditory system 2-DG uptake were examined during long- and short-term habituation of the acoustic startle reflex. Models were based on the anatomical connections between central auditory system structures. Using functional 2-DG data, the correlations between these structures were calculated and numerical weights were computed for each anatomical link. The analysis revealed that the lemniscal path was dominant during short-term habituation, while during long-term habituation this influence was modified through extra-lemniscal pathways. The models are discussed in the context of previous findings to demonstrate how structural modeling can not only complement, but also extract more information from 2-DG mapping experiments.

Acoustic Stimulation↗

PubMed2004

A structural model of EmrE, a multi-drug transporter from Escherichia coli.

Using a recently reported computational method, we describe an approach to model the structure of EmrE, a proton coupled multi-drug transporter of Escherichia coli. EmrE is the smallest ion-coupled transporter known; it functions as an oligomer and each monomer comprises four transmembrane segments. Because of its size, EmrE provides a unique experimental paradigm. The computational method does not afford a unique solution for the monomer. The experimental constraints available were used to select the most likely structure and to dock two monomers together to yield a dimer. The model is further validated by modeling of Hsmr, an EmrE homolog with a remarkable amino acid composition with over 40% of Ala and Val. The Hsmr model is similar to that of EmrE, with the majority of the Ala or Val residues facing the lipid. In addition, the model of EmrE features a putative substrate-binding site very similar to that observed in BmrR, a transcription activator of multi-drug transporters, with a similar substrate profile. The two crucial residues that couple proton fluxes with substrate binding in the homo-dimer of EmrE, Glu-14, have a spatial arrangement that agrees with proposed molecular mechanisms of transport.

Alanine↗