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PubMed1991

Building structural models of peptides: a semi-automatic software.

We present a software package that allows the construction and display of structural models of proteins starting from the amino acid sequence written in the one-letter code of standard data bank format. The software includes a very fast and efficient algorithm aimed at finding the global energy minimum of the potential function describing the molecular interactions. The whole package is conceived to have maximum flexibility. Completely automatic procedures are envisaged for standard problems. For non-standard problems, the construction procedure can be interactively adopted to meet with different options.

Algorithms↗
PubMed1992

A structural model examining the relationship between physical child abuse, sexual victimization, and marijuana/hashish use in delinquent youth: a longitudinal study.

A structural model of the relationships among physical abuse and sexual victimization experiences, marijuana/hashish use (measured by self-report and urine test data) and self-reported delinquent behavior (theft crimes, index offenses, crimes against persons, drug sales and total delinquency) over time was tested in a longitudinal study of juvenile detainees. The hypothesized model was supported by the data. Theoretical, research and policy implications of the results are drawn.

Adolescent↗
PubMed1989

A covariance structure model test of antecedents of adolescent alcohol misuse and a prevention effort.

As part of an alcohol misuse prevention evaluation, questionnaires were administered to 4,157 junior high school students to determine levels of alcohol misuse, exposure to peer use and misuse of alcohol, susceptibility to peer pressure, internal health locus of control, and self-esteem. A conceptual model of the antecedents of adolescent alcohol misuse and the effectiveness of a prevention effort was tested using covariance structure modeling techniques. The factor loadings for the model were all moderate to high, indicating that the observed variables served well as measurement instruments for the latent variables. The hypothesized structural relationships among the latent variables of alcohol misuse, exposure to peer use and misuse of alcohol, susceptibility to peer pressure, internal health locus of control, and self-esteem were supported by the data. The full model explained 45 percent of the variance in alcohol misuse in the analysis based on the total sample. The direct effect of the intervention on alcohol misuse was small but significant in the hypothesized direction. The direct effects of the intervention on susceptibility to peer pressure and internal health locus of control were not significant. The model was tested separately for groups of students who had high versus low scores on susceptibility to peer pressure in order to test the interaction between susceptibility to peer pressure and exposure to peer use and misuse of alcohol. The percentage of variance accounted for in alcohol misuse did not increase upon testing the model separately for students who had high versus low scores on susceptibility to peer pressure. Observed differences in the significance of the parameter estimates between the high and low susceptibility to peer pressure groups suggest that different approaches to the design and evaluation of substance abuse prevention programs may be necessary for different subgroups of students.

Alcoholism↗
PubMed1992

Structured modeling of fish physiology.

The use of models in simulation and state estimation has proved useful in diverse applications, especially in industrial process control. The project presented here looked into the modeling of fish physiology for applications in fish physiology research and aquaculture. The models deal with gastric evacuation, metabolism, kidneys, gills, the cardiovascular system, and feeding behavior and are based on data from the literature. Model responses are mostly in accord with real responses in principle, but, as with most models of complex biological systems, the numerical accuracy is low in several cases. However, these structured models enable researchers to test hypotheses by altering the submodels and parameters.

Animals↗
PubMed1991

Structural modeling of mixed longitudinal and cross-sectional data.

In this paper we describe some mathematical and statistical models for dealing with changes over age. We concentrate specifically on the use of a structural equation modeling (SEM) approach (using computer programs like LISREL) to deal with issues of: (1) group differences in regression parameters, (2) differences in longitudinal and cross-sectional results, (3) differences due to longitudinal attrition, and (4) mixtures of these problems. To illustrate these ideas we use data from a previous study of hypertension and intellectual abilities (from Schultz, Elias, Robbins, Streeten, and Blakeman, 1986).

Adult↗
PubMed1990

Comparative fit indexes in structural models.

Normed and nonnormed fit indexes are frequently used as adjuncts to chi-square statistics for evaluating the fit of a structural model. A drawback of existing indexes is that they estimate no known population parameters. A new coefficient is proposed to summarize the relative reduction in the noncentrality parameters of two nested models. Two estimators of the coefficient yield new normed (CFI) and nonnormed (FI) fit indexes. CFI avoids the underestimation of fit often noted in small samples for Bentler and Bonett's (1980) normed fit index (NFI). FI is a linear function of Bentler and Bonett's non-normed fit index (NNFI) that avoids the extreme underestimation and overestimation often found in NNFI. Asymptotically, CFI, FI, NFI, and a new index developed by Bollen are equivalent measures of comparative fit, whereas NNFI measures relative fit by comparing noncentrality per degree of freedom. All of the indexes are generalized to permit use of Wald and Lagrange multiplier statistics. An example illustrates the behavior of these indexes under conditions of correct specification and misspecification. The new fit indexes perform very well at all sample sizes.

Humans↗
PubMedDate not supplied

A structural model of stress, psychosocial resources, and symptomatic experience in chronic physical illness.

The purpose of this investigation was to test a theory-based structural model describing the relationships among psychosocial resources (strength of psychosocial attributes and basic need satisfaction), perceived stress, disease severity, and symptomatic experience in people with chronic obstructive pulmonary disease (COPD). One hundred nine subjects (58 males and 51 females) participated in the cross-sectional mail survey. Psychosocial attribute strength was a significant predictor of basic need satisfaction; basic need satisfaction was a significant predictor of perceived stress; and basic need satisfaction, perceived stress, and disease severity were significant predictors of symptomatic experience. The psychosocial attributes variable was a significant predictor of basic need satisfaction for both sexes. For males, basic need satisfaction and stress were significant predictors of symptomatic experience, while psychosocial attributes were not. For females, the psychosocial attributes variable was a significant predictor of symptomatic experience, while basic need satisfaction and stress were not. The findings suggest that psychosocial resources and perceived stress may be important factors in the symptomatic experience of adults with COPD. Males and females seem to differ in the role psychosocial attributes and basic need satisfaction play in the dynamics of the proposed model.

Adult↗
PubMed1989

A detailed structural model of cytotactin: protein homologies, alternative RNA splicing, and binding regions.

A combination of cDNA sequencing of the complete coding region, protein comparisons, binding site mapping, and electron microscopic imaging has permitted the formulation of a structural model of cytotactin. Cytotactin is a large extracellular matrix glycoprotein that displays a restricted tissue distribution during development. Although there appears to be a single cytotactin gene, multiple cytotactin polypeptides and mRNAs are detected in a variety of tissues. We report here the sequences and relationships of cDNAs that encode the complete amino acid sequences of two cytotactin polypeptides in chicken brain. The translated cDNA sequences agree with those obtained by direct analysis of cytotactin and fragments of the molecule. All regions of the polypeptides appear to be identical except for a 273 amino acid segment found in the larger but not in the smaller. At their amino termini, both polypeptides contain a cysteine-rich segment that probably includes those residues that link monomers into hexamers. This segment is followed by 13 epidermal growth factor-like (EGFL) repeats and then 8 consecutive segments that each resemble the type III repeats found in fibronectin. At their carboxyl termini, the polypeptides are similar to the beta and gamma chains of fibrinogen, including a calcium-binding segment. The additional sequence in the large polypeptide is inserted after the fifth type III repeat and includes three additional type III repeats. On RNA transfer blot analyses, cytotactin cDNA probes detected a 6.4-kilobase (kb) component in both brain and gizzard and larger mRNAs in both tissues, but those in gizzard were larger by about 1 kb than those in brain. A probe specific to the insert did not hybridize to the 6.4-kb mRNA in either tissue but detected the larger mRNAs in both tissues. At least a portion of the insert is thus present in both tissues, but there may be additional inserts in the gizzard mRNAs. The proposed model of cytotactin specifies the orientation of the polypeptides, the localization of interchain disulfide bonds, the structural elements constituting the thin and thick segments (EGFL repeats and type III repeats, respectively), the terminal fibrinogen-like nodular region, and the relative location of the cell-binding region.

Amino Acid Sequence↗
PubMed1992

Bayesian analysis of stochastic constraints in structural equation models.

Structural equation models are analysed in the presence of stochastic constraints. Based on a Bayesian perspective, a prior distribution on nuisance parameters in the unknown covariance matrix of error measurements with stochastic constraints is considered. An iterative procedure is implemented to produce the various Bayesian estimates with stochastic constraints. A simulation study is conducted to illustrate the accuracy and behaviour of this Bayesian approach. A real-life example is provided to illustrate the theory.

Bayes Theorem↗
PubMed1987

Structural models of the redox centres in cytochrome oxidase.

Evolutionary conservation, predicted membrane topography of the subunits, and known chemical and physical properties of the catalytic metals in cytochrome oxidase provided the basis for plausible structural models of the enzyme's redox centres. Subunit II probably binds one of the copper ions (CuA) whilst subunit I is likely to bind the two haems (a and a3) and the other redox-active copper (CuB). Two cysteine and two histidine residues of subunit II are the likely ligands of CuA, forming a centre that may be structurally similar to that in azurin. The two haems may be sandwiched between two transmembranous segments of subunit I, one of which also provides a histidine ligand to CuB. A third segment may provide two more histidine ligands to the latter. The model was constructed with a 4 A Fe-Cu distance in the binuclear haem a3-CuB centre, and a 14 A distance between the haem irons. The subunit I model involves only three transmembranous helices which bind three catalytic metal groups. The fit of this model to several known physicochemical properties of the redox centres is analysed.

Animals↗
PubMed1990

Structural model of factors V and Va based on scanning transmission electron microscope images and mass analysis.

Coagulation factor V (fV) is a single-chain glycoprotein (Mr 330,000; domain structure A1-A2-B-A3-C1-C2) that is activated to factor Va (fVa; Mr 174,000) by thrombin, which cleaves away the B domain leaving a heterodimeric structure composed of a heavy chain (A1-A2; Mr 94,000) and a light chain (A3-C1-C2; Mr 74,000). We analyzed the ultrastructure of scanning transmission electron microscope images of bovine and human fV, bovine fVa, and its constituent light chains and heavy chains. Factor V molecules had irregularly globular (10-12 nm) to oblong (8-14 nm) core structures which commonly displayed a peripheral satellite appendage of variable morphology attached to the core by a narrow stalk. Scanning transmission electron microscope mass analyses indicated that monomolecular bovine fV molecules had a mass of 322 +/- 45 kDa and human fV, 315 +/- 31 kDa. Factor Va molecules were irregular, globular (8-12 nm) structures that resembled the fV core structure, lacked the satellite appendage representing B domainal structures, and had a mass of 180 +/- 22 kDa. Our findings permit us to propose a structural model of fV suggesting the relative orientation of its closely associated light chain and heavy chain core components and indicating that these constituents remain associated in the transition from fV to fVa.

Animals↗
PubMed1990

Structural model of ATP-binding proteins associated with cystic fibrosis, multidrug resistance and bacterial transport.

The ATP-binding cassette (ABC) superfamily of transport systems now includes over thirty proteins that share extensive sequence similarity and domain organization. This superfamily includes the well characterized periplasmic binding protein-dependent uptake systems of prokaryotes, bacterial exporters, and eukaryotic proteins including the P-glycoprotein associated with multidrug resistance in tumours (MDR), the STE6 gene product that mediates export of yeast a-factor mating pheromone, pfMDR that is implicated in chloroquine resistance of the malarial parasite, and the product of the cystic fibrosis gene (CFTR). Here we present a tertiary structure model of the ATP-binding cassettes characteristic of this class of transport system, based on similarities between the predicted secondary structures of members of this family and the previously determined structure of adenylate kinase. This model has implications for both the molecular basis of transport and cystic fibrosis and provides a framework for further experimentation.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1976

A data structure model for a health information system.

The Ministry of Health and Environmental Control of Berlin is developing a Health Information System (HIS) on the basis of a multi-satellite network system, comprising a central, regional, local and functional unit level. The main part of this paper describes the conceptual structure of the Common Data Base (CDB) of HIS with special regard to the patient-oriented medical information originating from the various institutions of the health care system. This structure comprises the following five levels: 1. PATIENT 2. PROBLEM 3. CASE 4. EVENT 5. ACT Each of the levels represents a node in the structure model. A node is an entity with a set of "local properties" being specified for each level, referring to selected data on inferior levels. The structures of these five levels are described in detail. In the last part, so-called "data-manipulation procedures" are treated. These are descriptions covering any data manipulation and represent the basis of data integrity through system controlled transaction with the data base.

Berlin↗
PubMed1990

Phylogenetic and biochemical evidence for a secondary structure model of a small cytoplasmic RNA from Bacilli.

Small cytoplasmic RNA (scRNA; 271 nucleotides) is an abundant, stable RNA identified in the Gram-positive eubacterium Bacillus subtilis. Several findings suggest an important role of scRNA in protein biosynthesis: it shares structural and biochemical features with the Escherichia coli 4.5S RNA (114 nucleotides), a molecule known to be involved in this process, and it can complement the essential function of 4.5S RNA in vivo. The common apical hairpin motif of scRNA and 4.5S RNA also exists in eukaryotic 7SL RNA, the RNA component of the signal recognition particle. To elucidate the higher-order structure of scRNA, we have combined a phylogenetic approach with a biochemical one. The sequence of scRNA from a thermophilic relative of B. subtilis, Bacillus stearothermophilus, was determined and compared with the B. subtilis scRNA. In addition, the solution structure of B. stearothermophilus scRNA was probed with single- and double-strand-specific nucleases. Both types of analysis support a secondary structure model for scRNA that strongly resembles 4.5S RNA and respective parts of 7SL RNA. The results provide further evidence for the suggestion of a functional relationship between these RNAs.

Bacillus subtilis↗
PubMedDate not supplied

A chronomorphological structural model of rat thyroid gland.

Circadian rhythmicity of the structural morphometric model of thyroid has been studied in 36 Wistar rats kept in LD 12:12. The parameters evaluated are: a. the volume fraction occupied by: 1. follicle epithelium, 2. colloid, 3. interstitium at 6 time points in 24h; b. the follicle size distribution; c. the number of follicles per unit tissue volume. The circadian rhythms of mean follicular diameter and of follicular cavity mean diameter have been demonstrated (p less than 0.03 and p less than 0.01 respectively) and show overlapping acrophases of -120 degrees (-64 degrees/-176 degrees) and -108 degrees (-99 degrees/-116 degrees). The synchronization between rhythms, shown for mean follicular diameter and for follicular cavity mean diameter, suggests a rhythmical pulsation of the whole follicle, while the thickness of the follicular epithelium does not undergo a statistically significant periodic variation.

Animals↗
PubMed1978

A structural model of cholinergic synaptic vesicles from the electric organ of Torpedo marmorata deduced from density measurements at different osmotic pressures.

Density measurements made on cholinergic synaptic vesicles from the electric organs of Torpedo marmorata at different osmotic pressures are consistent with the following structural model of the vesicle. The particle behaves like a sphere 80-100 nm in diameter bounded by a semi-permeable membrane. The bulk of its soluble constituents are in true solution at physiological osmolalities. The limiting membrane is approximately 4-5 nm thick, suggesting that it contains large areas of phospholipid bilayer exposed to its bathing medium. The limiting membrane takes up about 26% (v/v) of the particle, a further 34% (v/v) of which is osmotically active water and 31% (v/v) hydrated core material at 800 mosmol/1. The buoyant density of the membrane is 1.132 g . cm-3. The density of the hydrated core material is approximately 1.05 g . cm-3. The membrane is selectively permeable to small molecules when subjected to hypo-osmotic stress. It is proposed that this occurs by the formation of small transient pores in the lipid bilayer of the membrane, which are induced by stretching caused by the osmotic pressure change.

Acetylcholine↗
PubMedDate not supplied

A proposed structural model of endothelin.

We have assessed the hydropathic nature, secondary structure, and flexibility of endothelin and report a testable model for the structure of this 21-amino acid vasoconstrictor peptide. The proposed model consists of a rigid (disulfide bonded), hydrophilic amino-terminal half of the molecule with two turns, and an extended hydrophobic sheet structure comprising the C-terminal half of the molecule. The extended structure may be stabilized by intermolecular hydrogen bonding, leading to dimers or higher order aggregates, and is hydrophobic enough to partition into an organic solvent such as ether, as long as the molecule can keep its hydrophilic amino terminus in an aqueous phase. To test this model, partitioning measurements were made on bioactive synthetic endothelin. It was found to partition at the interface of an ether/water system in a concentration- and surface area-dependent manner. A further indication as to the amphipathic nature of the molecule is that microcrystals of synthetic endothelin tend to grow at an organic-aqueous interface in a two-phase system.

Amino Acid Sequence↗
PubMed1991

A tree-structure model for analyzing laboratory test costs.

A method of costing clinical laboratory tests is described in which total laboratory costs are apportioned into 3 components: an 'organizational overhead cost' to describe the cost of running an organization; a 'cost per episode' to describe the costs incurred per request; and a 'cost per test' to describe the actual analytical costs of tests performed. A tree-like structural model is described which allows for distribution of this 'cost per test' component to the contributing tests and the calculation of the true 'cost per test'. The implementation of this model on a computer spreadsheet has been achieved. When combined with the other cost components, the true total costs of laboratory testing can be determined for any particular test. The model also allows calculation of the incremental and marginal costs of a test and permits optimization of laboratory test frequencies and work-load to minimize laboratory analytical costs.

Algorithms↗