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PubMed1994

Structural equation modeling with longitudinal data: strategies for examining group differences and reciprocal relationships.

This article describes the use of structural equation modeling with latent variables to examine group differences and test competing models about cause-effect relationships in passive longitudinal designs. This approach is compared with several other statistical methods including analysis of cross-lagged panel correlations, regression analysis, and path analysis. The mechanics and advantages of structural equation modeling are illustrated using an example based on a 3-wave longitudinal study of adolescents' alcohol use. Within this example, the generalizability of the measurement model and structural model are assessed across gender and time, and competing models about the causes and consequences of adolescents' alcohol use are tested. The article concludes with a discussion of some of the strengths and limitations of using structural equation modeling with longitudinal data.

Adolescent↗

PubMed1995

Accuracy of a structural homology model for a class II histocompatibility protein, HLA-DR1: comparison to the crystal structure.

Structural homology modeling is used to test the accuracy by which a Class I major histocompatibility complex (MHC) could be used to model a Class II MHC. The crystal structure of HLA-aw68 served as a reference molecule to model HLA-DR1. The resulting model was compared to the recently released crystal structure by Brown et al. (Nature, Vol. 364, p. 33-39 (1993)). The overall tertiary structure motif (two alpha-helices and a beta-sheet forming a peptide binding cleft) was maintained. However, significant deviations in the secondary structure elements were found between the model and the DR1 crystal structure. These deviations were consistent with the differences between Class I and Class II crystal structures. In regions where the model and DR1 crystals structures are most similar, side chain orientations are also similar. Specific peptide-MHC interactions are discussed and compared with the crystal structure results.

Amino Acid Sequence↗

PubMed1984

A universal model for the secondary structure of 5.8S ribosomal RNA molecules, their contact sites with 28S ribosomal RNAs, and their prokaryotic equivalent.

The phylogenetic approach (ref. 1) has been utilized in construction of a universal 5.8S rRNA secondary structure model, in which about 65% of the residues exist in paired structures. Conserved nucleotides primarily occupy unpaired regions. Multiple compensating base changes are demonstrated to be present in each of the five postulated helices, thereby forming a major basis for their proof. The results of chemical and enzymatic probing of 5.8S rRNAs (ref. 13, 32) are fully consistent with, and support, our model. This model differs in several ways from recently proposed 5.8S rRNA models (ref. 3, 4), which are discussed. Each of the helices in our model has been extended to the corresponding bacterial, chloroplast and mitochondrial sequences, which are demonstrated to be positionally conserved by alignment with their eukaryotic counterparts. This extension is also made for the base paired 5.8S/28S contact points, and their prokaryotic and organelle counterparts. The demonstrated identity of secondary structure in these diverse molecules strongly suggests that they perform equivalent functions in prokaryotic and eukaryotic ribosomes.

Animals↗

PubMed2004

Model column structure for the analysis of the flow and band-broadening characteristics of silica monoliths.

We report on the use of commercial computational fluid dynamics software to study the band broadening in a perfectly ordered three-dimensional model structure, the so-called tetrahedral skeleton column (TSC), selected for its close geometrical resemblance to the specific pore network topology of silica monoliths. Van Deemter plots are presented for the case of a species flow through a non-porous skeleton and for the case of a retained component (k' = 1) in a porous skeleton (mesopore porosity epsilon = 0.6 in both cases). Using the flow domain as the characteristic scaling dimension, the TSC model yields reduced plate heights as small as h(min) = 0.8 and separation impedances as small as Emin = 120 for a retained component with k' = 1. The very small reduced plate heights for the TSC model can without any doubt largely be attributed to the perfect homogeneity of the considered model structure: the B and C terms are similar to those obtained in real silica monoliths with similar external porosity, whereas the A term is significantly (about a factor of 10) smaller. The present study hence suggests that further experimental work to obtain more homogeneous silica networks could yield large gains in reduced plate height and separation impedance. Comparing the three-dimensional TSC model with a 2D array of cylinders, it was found that the use of the domain size as the characteristic dimension in the reduced plate height expression is much more appropriate than the use of the skeleton size, hence validating earlier approaches adopted in the literature.

Pressure↗

PubMed2006

A structural equation model relating impaired sensorimotor function, fear of falling and gait patterns in older people.

Many falls in older people occur while walking, however the mechanisms responsible for gait instability are poorly understood. Therefore, the aim of this study was to develop a plausible model describing the relationships between impaired sensorimotor function, fear of falling and gait patterns in older people. Temporo-spatial gait parameters and acceleration patterns of the head and pelvis were obtained from 100 community-dwelling older people aged between 75 and 93 years while walking on an irregular walkway. A theoretical model was developed to explain the relationships between these variables, assuming that head stability is a primary output of the postural control system when walking. This model was then tested using structural equation modeling, a statistical technique which enables the testing of a set of regression equations simultaneously. The structural equation model indicated that: (i) reduced step length has a significant direct and indirect association with reduced head stability; (ii) impaired sensorimotor function is significantly associated with reduced head stability, but this effect is largely indirect, mediated by reduced step length, and; (iii) fear of falling is significantly associated with reduced step length, but has little direct influence on head stability. These findings provide useful insights into the possible mechanisms underlying gait characteristics and risk of falling in older people. Particularly important is the indication that fear-related step length shortening may be maladaptive.

Accidental Falls↗

PubMed2006

Effects of amiodarone on electrical and structural remodeling induced in a canine rapid pacing-induced persistent atrial fibrillation model.

Structural in addition to electrical remodeling may be induced by persistent atrial fibrillation per se and make atrial fibrillation refractory to antiarrhythmic drug therapy. Matrix metalloproteinases (MMPs) contribute to structural remodeling in the interstitial space. Amiodarone is effective in treating persistent atrial fibrillation compared with other antiarrhythmic drugs. In mongrel dogs, right atrial pacing at 540 beats/min (bpm) was performed along with ventricular pacing at 100 bpm for 6 weeks after atrioventricular node ablation. Right atrial pacing at 400 bpm was continued for 4 weeks with (n=5) or without (n=5) oral amiodarone (30 mg/kg/day). In sham dogs, only ventricular pacing was done with (n=4) or without (n=6) amiodarone. In atrial pacing without amiodarone group, electrical remodeling characterized by monophasic action potential duration shortening, loss of action potential duration-rate adaptation and depressed conduction velocity and structural remodeling characterized by slightly but significantly increased interstitial fibrosis and enhanced MMP-2 activity compared with sham group were observed, and sustained atrial fibrillation was easily induced. In atrial pacing with amiodarone group, both electrical and structural remodeling were reversed and sustained atrial fibrillation was not induced. In sham group with amiodarone, action potential duration prolongation and depressed conduction velocity compared with sham without amiodarone were observed, but either increased fibrosis or enhanced MMP-2 activity was not observed. Not only electrical but structural remodeling were induced in a canine persistent atrial fibrillation model. Amiodarone reversed both of them, which may be related to its high efficacy in preventing recurrence of persistent atrial fibrillation.

Action Potentials↗

PubMed1996

Testing the simplex assumption underlying the Sport Motivation Scale: a structural equation modeling analysis.

Self-determination theory (Deci & Ryan, 1985) suggests that motivational orientation or regulatory styles with respect to various behaviors can be conceptualized along a continuum ranging from low (a motivation) to high (intrinsic motivation) levels of self-determination. This pattern is manifested in the rank order of correlations among these regulatory styles (i.e., adjacent correlations are expected to be higher than those more distant) and is known as a simplex structure. Using responses from the Sport Motivation Scale (Pelletier et al., 1995) obtained from a sample of 857 college students (442 men, 415 women), the present study tested the simplex structure underlying SMS subscales via structural equation modeling. Results confirmed the simplex model structure, indicating that the various motivational constructs are empirically organized from low to high self-determination. The simplex pattern was further found to be invariant across gender. Findings from this study support the construct validity of the SMS and have important implications for studies focusing on the influence of motivational orientation in sport.

Adult↗

PubMed1983

A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire 'dihydrouridine' loop and stem.

The mammalian mitochondrial tRNA(AGY)Ser is unique in lacking the entire dihydrouridine arm. This reduces its secondary structure to a 'truncated cloverleaf'. Experimental evidence on the tertiary structure has been obtained by chemically probing the conformation of both the bovine and human species in their native conformation and at various stages of denaturation. A structural model of the bovine tRNA is presented based on the results of this chemical probing, on a comparison between nine homologous 'truncated cloverleaf' secondary structures and on analogies with the crystal structure of yeast phenylalanine tRNA. The proposed structure is very similar in shape to that of yeast tRNA(Phe) but is slightly smaller in size. It is defined by a unique set of tertiary interactions. Structural considerations suggest that other mammalian mitochondrial tRNAs have smaller dimensions as well.

Animals↗

PubMedDate not supplied

Carcinogenesis: a predictive structure-activity model.

A statistical structure-activity equation has been developed for the estimation of carcinogenic potential for chemicals that have not been subjected to carcinogenesis assays. This discriminant equation is based on substructural fragments and molecular weight obtained for 343 compounds. The data base used for the design of the equation was obtained from the monographs of the International Agency for Research on Cancer. The accuracy of classification for the carcinogens in the model is between 87 and 91%, and for noncarcinogens between 78 and 80% in the presence of between 5.5 and 10.2% of the compounds not being classifiable. The false negative rate ranges between 4 and 5%; the false positive rate is near 11%.

Carcinogens↗

PubMed2006

Reactivity-based analysis of domain structures in native replication protein A.

Replication protein A (RPA) is an essential heterotrimeric ssDNA binding protein that participates in DNA repair, replication, and recombination. Though X-ray and NMR experiments have been used to determine three-dimensional structure models of the protein's domain fragments, a complete RPA structural model has not been reported. To test whether the fragment structures faithfully represent the same portions in the native solution-state protein, we have examined the structure of RPA under biologically relevant conditions. We have probed the location of multiple amino acids within the native RPA three-dimensional structure using reactivity of these amino acids toward proteolytic and chemical modification reagents. In turn, we evaluated different structural models by comparing the observed native RPA reactivities with anticipated reactivities based on candidate structural models. Our results show that our reactivity analysis approach is capable of critically assessing structure models and can be a basis for selecting the most relevant from among alternate models of a protein structure. Using this analytical approach, we verified the relevance of RPA fragment models to the native protein structure. Our results further indicate several important features of native RPA's structure in solution, such as flexibility at specific locations in RPA, particularly in the C-terminal region of RPA70. Our findings are consistent with reported DNA-free structural models and support the role of conformational change in the ssDNA binding mechanism of RPA.

Amino Acid Sequence↗

PubMed1991

Modeling study of the structure of the macromolecular antitumor antibiotic neocarzinostatin. Origin of the stabilization of the chromophore.

A three-dimensional structure of the apoprotein of neocarzinostatin (NCS) was built by using the actinoxanthin (AXN) crystal structure as template, and the subsequent favored-site search for the binding of the fragments of the chromophore of NCS at the binding cleft led to a reasonable complex structure of apo-NCS and the chromophore, after refinement of the molecular mechanics program AMBER. The refined three-dimensional structure model of NCS shows the "Y"-shaped cleft of the binding site in which the bicyclic epoxy dienediyne part 4 and its substituents, the naphthoate 3, the amino sugar 2, and cyclic carbonate 1 moieties are nicely fitted. Contacts of the chromophore with the specific amino acid residues in the cleft indicate their contribution to the specific and high affinity binding through ionic interaction, hydrogen bonding, aromatic stacking, and van der Waals contact. Stabilization of the labile chromophore is likely due to the steric hindrance toward the reactive sites such as the C12 position as well as the epoxide, and, more interestingly, the stabilization interaction between the disulfide group (Cys37 and Cys47) and the acetylenic bond is also suggested.

Amino Acid Sequence↗

PubMed2001

On the need for another type of predictive model in structured foods.

Most of the models discussed up till now in predictive microbiology do not take into account the variability of microbial growth with respect to space. In structured (solid) foods, microbial growth can strongly depend on the position in the food and the assumption of homogeneity can thus not be accepted: space must be considered as an independent variable. Indeed, experimental evidence exists of bacteria competition on agar not showing the same behavior as the competition in a well-mixed liquid culture system. It is conjectured that this is due to the spatially structured habitat. Therefore, in the current paper, a prototype two species competition model proposed in previous work by the authors is extended to take space into account. The extended model describes two phenomena: (i) local evolution of biomass and (ii) transfer of biomass through the medium. The structure of the food product is taken into account by limiting the diffusion through the medium. The smaller mobility of the micro-organisms in solid foods allows spatial segregation which causes pattern formation. Evidence is given for the fact that taking space into account indeed has an influence on the behavior (coexistence/extinction) of the populations. Although the reported simulations are by no means to be interpreted as accurate predictions, the proposed model structure allows one to highlight (i) important characteristics of microbial growth in structured foods and (ii) future research trends in predictive microbiology.

Bacteria↗

PubMed2006

Beyond logistic regression: structural equations modelling for binary variables and its application to investigating unobserved confounders.

BACKGROUND: Structural equation modelling (SEM) has been increasingly used in medical statistics for solving a system of related regression equations. However, a great obstacle for its wider use has been its difficulty in handling categorical variables within the framework of generalised linear models. METHODS: A large data set with a known structure among two related outcomes and three independent variables was generated to investigate the use of Yule's transformation of odds ratio (OR) into Q-metric by (OR-1)/(OR+1) to approximate Pearson's correlation coefficients between binary variables whose covariance structure can be further analysed by SEM. Percent of correctly classified events and non-events was compared with the classification obtained by logistic regression. The performance of SEM based on Q-metric was also checked on a small (N = 100) random sample of the data generated and on a real data set. RESULTS: SEM successfully recovered the generated model structure. SEM of real data suggested a significant influence of a latent confounding variable which would have not been detectable by standard logistic regression. SEM classification performance was broadly similar to that of the logistic regression. CONCLUSION: The analysis of binary data can be greatly enhanced by Yule's transformation of odds ratios into estimated correlation matrix that can be further analysed by SEM. The interpretation of results is aided by expressing them as odds ratios which are the most frequently used measure of effect in medical statistics.

Cesarean Section↗

PubMed1988

Method of modeling protein structure by the two-dimensional nuclear magnetic resonance spectroscopy data; application to the proteinase inhibitor BUSI IIA from bull seminal plasma.

A new approach is suggested to model the spatial structure of protein molecules in solution based on combined use of the methods of theoretical conformational analysis and NMR spectroscopy data. At the first stage, special means are used to convert d connectivity information into the most probable values of dihedral angles. This allows search for possible spatial structures in the limited regions of the conformational space at further stages using the methods of the theoretical conformational analysis. The suggested approach was verified in reconstructing the spatial backbone structure of the fragment 17-57 of the proteinase inhibitor BUSI IIA from the bull seminal plasma. The structural model parameters are compared with the corresponding characteristics obtained from the X-ray analysis data for the homologic proteinase inhibitor from the Japanese quail ovomucoid. The suggested approach is shown to correctly reproduce both the general molecule topology and the conformations of individual amino acid residues.

Amino Acid Sequence↗

PubMed2002

Modelling the structure of the fusion protein from human respiratory syncytial virus.

The fusion protein of respiratory syncytial virus (RSV-F) is responsible for fusion of virion with host cells and infection of neighbouring cells through the formation of syncytia. A three-dimensional model structure of RSV-F was derived by homology modelling from the structure of the equivalent protein in Newcastle disease virus (NDV). Despite very low sequence homology between the two structures, most features of the model appear to have high credibility, although a few small regions in RSV-F whose secondary structure is predicted to be different to that in NDV are likely to be poorly modelled. The organization of individual residues identified in escape mutants against monoclonal antibodies correlates well with known antigenic sites. The location of residues involved in point mutations in several drug-resistant variants is also examined.

Amino Acid Sequence↗

PubMed2006

ALAMEDA, a structural-functional model for faba bean crops: morphological parameterization and verification.

BACKGROUND: Plant structural (i.e. architectural) models explicitly describe plant morphology by providing detailed descriptions of the display of leaf and stem surfaces within heterogeneous canopies and thus provide the opportunity for modelling the functioning of plant organs in their microenvironments. The outcome is a class of structural-functional crop models that combines advantages of current structural and process approaches to crop modelling. ALAMEDA is such a model. METHODS: The formalism of Lindenmayer systems (L-systems) was chosen for the development of a structural model of the faba bean canopy, providing both numerical and dynamic graphical outputs. It was parameterized according to the results obtained through detailed morphological and phenological descriptions that capture the detailed geometry and topology of the crop. The analysis distinguishes between relationships of general application for all sowing dates and stem ranks and others valid only for all stems of a single crop cycle. RESULTS AND CONCLUSIONS: The results reveal that in faba bean, structural parameterization valid for the entire plant may be drawn from a single stem. ALAMEDA was formed by linking the structural model to the growth model 'Simulation d'Allongement des Feuilles' (SAF) with the ability to simulate approx. 3500 crop organs and components of a group of nine plants. Model performance was verified for organ length, plant height and leaf area. The L-system formalism was able to capture the complex architecture of canopy leaf area of this indeterminate crop and, with the growth relationships, generate a 3D dynamic crop simulation. Future development and improvement of the model are discussed.

Computer Simulation↗

PubMed2003

Testing mediational models with longitudinal data: questions and tips in the use of structural equation modeling.

R. M. Baron and D. A. Kenny (1986; see record 1987-13085-001) provided clarion conceptual and methodological guidelines for testing mediational models with cross-sectional data. Graduating from cross-sectional to longitudinal designs enables researchers to make more rigorous inferences about the causal relations implied by such models. In this transition, misconceptions and erroneous assumptions are the norm. First, we describe some of the questions that arise (and misconceptions that sometimes emerge) in longitudinal tests of mediational models. We also provide a collection of tips for structural equation modeling (SEM) of mediational processes. Finally, we suggest a series of 5 steps when using SEM to test mediational processes in longitudinal designs: testing the measurement model, testing for added components, testing for omitted paths, testing the stationarity assumption, and estimating the mediational effects.

Cross-Sectional Studies↗

PubMed1992

Three-dimensional structure for the beta 2 adrenergic receptor protein based on computer modeling studies.

Computer-aided model building techniques have been used to construct three-dimensional model structures for hamster beta 2 adrenergic receptor. Experimental data were used as constraints to guide the model building procedure, and a number of rather strict criteria were applied to assess the physical plausibility of model structures. We present details of our best model structure to date, which is consistent with a large body of experimental data. We also discuss in detail our model building procedures and evaluation criteria, which we believe may be of general utility in modeling projects.

Amino Acid Sequence↗