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PubMed1999

Investigating autocatalytic gene expression systems through mechanistic modeling.

A structured model of gene expression, which incorporates the stochastic behavior of cellular processes, was developed to examine the "all-or-none" phenomenon observed in autocatalytic systems (e.g. the lac operon). Autocatalytic expression systems typically have the genes encoding the inducer transport proteins controlled by internal inducer levels, so that transport of the inducer increases production of the transport protein. The model was able to predict the unique behaviors of autocatalytic expression systems that have been experimentally observed and provided valuable insight into the role of population heterogeneity in these systems. The simulations substantiate the importance of stochastic processes on induction of gene expression in autocatalytic systems. The simulation results show that the all-or-none phenomenon is governed largely by random cellular events, and that population-averaged variations in gene expression are due to changes in the frequency of full gene induction in individual cells rather than to uniform variations in gene expression across the entire population. In addition, the model shows how concentrations of inducer too low to induce expression in uninduced cells can maintain induction in pre-induced cultures. A comparison of induction behaviors from an autocatalytic system and a system having constitutive synthesis of the transport protein showed that transport protein levels must be decoupled from inducer control to achieve homogeneous expression of a gene of interest in all cells of a culture.

Biological Transport↗

PubMedDate not supplied

Adolescent dual diagnosis: a 12-step transformational model.

A structured model inpatient treatment program for multiple-diagnosed treatment-resistant adolescents is described. The chemical dependence disease model of Predisposition+Drug+Enabling System=Disease provides the fundamental theoretical approach. This model is elaborated and used similarly for psychiatric disorders, with examples presented. The role of psychiatric evaluation for pharmacological interventions is outlined. The psychotherapeutic treatment focuses on a commitment to abstinence as the goal. A "psychology of commitment" is described using a reframing of traditional psychotherapeutic approaches. This approach is used in conjunction with the first five steps of Alcoholics Anonymous as an empowering therapeutic model. The role of defenses, denial, confrontation, and cognitive distortions is described. The value of this approach as a neutral ground for discussion using concepts from traditional Freudian therapy, self-psychology, cognitive and learning therapies, and rational emotive therapy is elaborated.

Adolescent↗

PubMed2002

Analytic approaches to twin data using structural equation models.

The classical twin study is the most popular design in behavioural genetics. It has strong roots in biometrical genetic theory, which allows predictions to be made about the correlations between observed traits of identical and fraternal twins in terms of underlying genetic and environmental components. One can infer the relative importance of these 'latent' factors (model parameters) by structural equation modelling (SEM) of observed covariances of both twin types. SEM programs estimate model parameters by minimising a goodness-of-fit function between observed and predicted covariance matrices, usually by the maximum-likelihood criterion. Likelihood ratio statistics also allow the comparison of fit of different competing models. The program Mx, specifically developed to model genetically sensitive data, is now widely used in twin analyses. The flexibility of Mx allows the modelling of multivariate data to examine the genetic and environmental relations between two or more phenotypes and the modelling to categorical traits under liability-threshold models.

Chi-Square Distribution↗

PubMed2004

Estimated heterogeneity of phenotypic variance of test-day yield with a structural variance model.

First-lactation test-day milk, fat, and protein yields from New York, Wisconsin, and California herds from 1990 through 2000 were adjusted additively for age and lactation stage. A random regression model with third-order Legendre polynomials for permanent environmental and genetic effects was used. The model included a random effect with the same polynomial regressions for 2 yr of calvings within herd (herd-time effect) to provide herd-specific lactation curves that can change every 2 yr. (Co)variance components were estimated using expectation-maximization REML simultaneously with phenotypic variances that were modeled using a structural variance model. Maximum heritability for test-day milk yield was estimated to be approximately 20% around 200 to 250 d in milk; heritabilities were slightly lower for test-day fat and protein yields. Herd-time effects explained 12 to 20% of phenotypic variance and had the greatest impact at start of lactation. Variances of test-day yields increased with time, subclass size, and milking frequency. Test month had limited influence on variance. Variance increased for cows in herds with low and high milk yields and for early and late lactation stages. Repeatabilities of variances observed for a given class of herd, test-day, and milking frequency were 14 to 17% across nested variance subclasses based on lactation stage.

Age Factors↗

PubMed1988

A kinked model for the solution structure of DNA tridecamers with inserted adenosines: energy minimization and molecular dynamics.

Structural modelling techniques using energy minimization and molecular dynamics have been employed to generate kinked models for the solution structure of two DNA tridecamer sequences containing inserted adenosines: d(CGCAGAATTCGCG)2 and d(CGCAGAGCTCGCG)2. These models are consistent with NMR studies of these sequences in solution. The overall shapes of the two models are similar, consisting of three B-DNA sections: two outer segments on the same side of the central portion, with the additional adenosines acting as wedges to kink the structure. An alternative scheme for the hydrogen bond pairing at the kink site is suggested as a way for the additional adenosines to be stabilized in the duplex.

Adenosine↗

PubMed2003

A framework for power analysis using a structural equation modelling procedure.

BACKGROUND: This paper demonstrates how structural equation modelling (SEM) can be used as a tool to aid in carrying out power analyses. For many complex multivariate designs that are increasingly being employed, power analyses can be difficult to carry out, because the software available lacks sufficient flexibility. Satorra and Saris developed a method for estimating the power of the likelihood ratio test for structural equation models. Whilst the Satorra and Saris approach is familiar to researchers who use the structural equation modelling approach, it is less well known amongst other researchers. The SEM approach can be equivalent to other multivariate statistical tests, and therefore the Satorra and Saris approach to power analysis can be used. METHODS: The covariance matrix, along with a vector of means, relating to the alternative hypothesis is generated. This represents the hypothesised population effects. A model (representing the null hypothesis) is then tested in a structural equation model, using the population parameters as input. An analysis based on the chi-square of this model can provide estimates of the sample size required for different levels of power to reject the null hypothesis. CONCLUSIONS: The SEM based power analysis approach may prove useful for researchers designing research in the health and medical spheres.

Analysis of Variance↗

PubMed2004

Competitive exclusion and coexistence for a quasilinear size-structured population model.

We present a quasilinear size-structured model which describes the dynamics of a population with n competing ecotypes. We assume that the vital rates of each subpopulation depend on the total population due to competition. We provide conditions on the individual rates which guarantee competitive exclusion in the case of closed reproduction (offspring always belongs to the same ecotype as the parent). In particular, our results suggest that the ratio of the reproduction and mortality rates is a good measure to determine the winning ecotype. Meanwhile, we show that in the case of open reproduction all ecotypes coexist.

Animals↗

PubMed1992

LET, track structure and models. A review.

Swift heavy ions when penetrating through matter strip off those electrons having a smaller orbital velocity than the ion velocity. The remaining electrons screen the nuclear charge yielding an effective charge. The effective charge of the ions interacts predominantly with the target electrons causing excitation and ionizations of the target atoms. Using the Bethe Bloch formula for the energy loss combined with the Barkas formula for effective charge, the energy loss values as well as unrestricted and restricted linear transfer can be calculated within a few percent of accuracy. From the primary energy loss only a small fraction of 10% or less is transformed into excitation. The major part of the energy loss is used for the ionization of the target atoms and the emission of the corresponding electrons with a high kinetic energy. These electrons form the track around the trajectory of the primary ion in which two thirds of the primary energy is deposited by collisions of primary, secondary and later generations of electrons with the target molecules. In the electron diffusion process the energy is transported from the center of the track into the halo. The radial dose decreases with the square of the radial distance from the center. The diameter of the track is determined by the maximum range of the emitted electrons, i.e. by the maximum energy electrons. All ions having the same velocity i.e. the same specific energy produce electrons of the same energy and therefore tracks of the same diameters independent of the effective charge. But the dose inside the track increases with the square of the effective charge. Track structure models using this continuous dose distributions produce a better agreement with the experiment than models based on microdosimetry. The critical volume as used in microdosimetry is too large compared to the size of the DNA as critical structure inside the biological objects. Track structure models yield better results because the gross-structure of the track i.e. its lateral extension and the thin down toward the end of the track is included in these calculations. In a recent refinement the repair capacity of the cell has been included in a track structure model by using the complete shouldered x-ray survival curve as a template for the local damage produced by the particle tracks. This improved model yields presently the best agreement with the experiment.

Energy Transfer↗

PubMed2005

Predicting proximal femoral strength using structural engineering models.

Hip fracture related to osteoporosis and metastatic disease is a major cause of morbidity and mortality. An accurate and precise method of predicting proximal femoral strength and fracture location would be useful for research and clinical studies of hip fracture. The goals of this study were to develop a structural modeling technique that accurately predicts proximal femoral strength; to evaluate the accuracy and precision of this predicted strength on an independent data set; and to evaluate the ability of this technique to predict fracture location. Fresh human cadaveric proximal femora with and without metastatic lesions were studied using computed tomography scan-based three-dimensional structural models and mechanical testing to failure under single-limb stance-type loading. The models understated proximal femoral strength by an average of 444 N, and the precision of the predicted strength was +/- 1900 N. Therefore, the ability to predict hip strength in an individual subject is limited primarily by the level of precision, rather than accuracy. This level of precision is likely to be sufficient for many studies of hip strength. Finally, these models predict fractures involving the subcapital and cervical regions, consistent with most fractures produced experimentally under single-limb stance-type loading.

Aged↗

PubMed1994

Modelling the structure of the calcitonin gene-related peptide.

The calcitonin gene-related peptide (CGRP) is a 37 residue neuropeptide which causes vasodilatation, increases heart rate and inhibits bone resorption. These effects make it an interesting lead for drug discovery. We have combined current structural and biological information to model the structure of hCGRP-beta to be used as a basis for the rational design of novel analogues. Distinct regions of CGRP have been shown to be responsible for the activity of the whole molecule. Thus, the structure of the peptide was modelled in four parts which were finally combined. A random search of conformational space was performed for the fragments CGRP1-8 and CGRP30-37 which have been shown to be central for receptor activation and binding, respectively. Five low-energy hCGRP-beta structures were obtained from modelled fragments by molecular dynamics. The relevance of the approach was verified by comparing the models with NMR structures of CGRP and calcitonin. The models obtained for the N- and C-terminal fragments should enable the design of novel agonists and antagonists of the CGRP receptor, respectively. Models of the whole molecule may be used in the design of peptides with shortened spacers between the receptor-bound regions. The approach described is applicable to several related peptide hormones, like growth hormone-releasing hormone and secretin.

Amino Acid Sequence↗

PubMed2001

Estimation of kinetic parameters in a structured yeast model using regularisation.

In this work, a procedure for estimating kinetic parameters in biochemically structured models was developed. The approach is applicable when the structure of a kinetic model has been set up and the kinetic parameters should be estimated. The procedure consists of five steps. First, initial values were found in or calculated from literature. Hereafter using sensitivity analysis the most sensitive parameters were identified. In the third step physiological knowledge was combined with the parameter sensitivities to manually tune the most sensitive parameters. In step four, a global optimisation routine was applied for simultaneous estimation of the most sensitive parameters identified during the sensitivity analysis. Regularisation was included in the simultaneous estimation to reduce the effect of insensitive parameters. Finally, confidence intervals for the estimated parameters were calculated. This parameter estimation approach was demonstrated on a biochemically structured yeast model containing 11 reactions and 37 kinetic constants as a case study.

Algorithms↗

PubMed2005

Testing the sequential model of pain processing in irritable bowel syndrome: a structural equation modeling analysis.

Pain, the cardinal feature of irritable bowel syndrome (IBS), is a multidimensional phenomenon with sensory and affective dimensions. Price's pain processing model was used to delineate four a priori sequentially related stages (pain sensation intensity, immediate pain unpleasantness, long-term suffering, and pain-related behavior). Although prior research with both healthy individuals and somatic pain patients supports the model in general, its applicability to IBS is unclear. Our goal was to extend the scope of the sequential model and test its fundamental tenets using structural equation modeling (SEM) with data obtained from 168 Rome II diagnosed IBS patients (19% male, 81% female). A secondary goal was to assess the relationship between a set of contextual factors associated with IBS (age, gender, trait anxiety) and the four pain stages. Results were consistent with a successive order of pain processing such that the pain sensation directly impacts pain unpleasantness, which, in turn, leads to suffering and illness behaviors. However, contrary to a model with strictly successive stages, pain sensation had independent effects on illness behaviors over and above pain affect. The effect of anxiety on illness behavior was mediated by suffering, while psychopathology directly influenced pain sensation and pain unpleasantness but not later stages. Age was related to pain sensation and illness behaviors but not pain affect. Gender tended to be more strongly associated with more distal pain stages (e.g., pain affect) vis-a-vis its effects on pain sensation. These data are generally supportive of a four-stage pain processing model.

Abdominal Pain↗

PubMed2007

Sex-structured HIV/AIDS model to analyse the effects of condom use with application to Zimbabwe.

We present a sex-structured model for heterosexual transmission of HIV/AIDS in a community. The model is formulated using integro-differential equations, which are shown to be equivalent to delay differential equations with a time delay due to incubation period. The sex-structured HIV/AIDS model divides the population into a two sex-structure consisting of females and males. The threshold and equilibria for the model are determined and stabilities are examined. We extend the model to focus on the effects of condom use as a single-strategy approach in HIV prevention in the absence of any treatment. Initially we model the use of male condoms and further extend the model to incorporate the use of both female and male condoms. The model includes two primary factors in condom use to control HIV that are condom efficacy and compliance. The exposure risk of infection after each intervention is obtained. Basic reproductive numbers for these models are computed and compared to assess the effectiveness of male and female condom use in a community. The models are numerically analysed to assess the effectiveness of condom use on the transmission dynamics of HIV/AIDS using demographic and epidemiological parameters for Zimbabwe. The study demonstrates the use of sex-structured HIV/AIDS models in assessing the effectiveness of female and male condom use as a preventative strategy in a heterosexually active population.

Condoms↗

PubMed1987

Structural-equation models of current drug use: are appropriate models so simple(x)?

The simplex and common-factor models of drug use were compared using maximum-likelihood estimation of latent variable structural models in two samples: a sample of 226 high school students, using ratio-scale measures of current drug use, and a sample of 310 industrial workers and 811 college students, using ordinal-scale measures of current drug use. Latent variables of alcohol, marijuana, enhancer hard drugs, and dampener hard drugs were specified in a series of structural models. Contrary to previous findings with cumulative drug-use data, the common-factor model provided a more acceptable representation of the observed current-use data than did the simplex model in both samples. In addition, the similarity of results across both of these samples supports recent contentions by Huba and Bentler (1982) that quantitatively measured variables are not necessarily superior to qualitative, ordinal indicators in latent variable models of drug use.

Adolescent↗

PubMed2004

Appraised psychological workload, musculoskeletal symptoms, and the mediating effect of fatigue: a structural equation modeling approach.

The aim of the present study was to test two structural models of the relationship between appraised psychological workload and musculoskeletal symptoms from the neck, shoulder, and upper and lower back with different aspects of perceived fatigue as mediating variables. In this cross-sectional study a questionnaire survey was conducted among employees at three Swedish assembly plants (n= 305). The proposed models were tested for one general fatigue dimension--lack of energy--and four specific fatigue dimensions--physical discomfort, physical exertion, lack of motivation, and sleepiness--using structural equation modeling. The results indicate that the role of perceived fatigue in the relationship between appraised workload and musculoskeletal symptoms is different for different aspects of fatigue. The general fatigue dimension, lack of energy, does not mediate the relationship. As regards the specific fatigue dimensions, the relationship is partially mediated by physical discomfort and lack of motivation but not by physical exertion or sleepiness. Appraised psychological workload has a unique effect on musculoskeletal symptoms not mediated by fatigue.

Adult↗

PubMed1998

Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.

The crystal structure of the thermostable xylanase from Thermomyces lanuginosus was determined by single-crystal X-ray diffraction. The protein crystallizes in space group P21, a = 40.96(4) A, b = 52. 57(5) A, c = 50.47 (5) A, beta = 100.43(5) degrees, Z = 2. Diffraction data were collected at room temperature for a resolution range of 25-1.55 A, and the structure was solved by molecular replacement with the coordinates of xylanase II from Trichoderma reesei as a search model and refined to a crystallographic R-factor of 0.155 for all observed reflections. The enzyme belongs to the family 11 of glycosyl hydrolases [Henrissat, B., and Bairoch, A. (1993) Biochem. J. 293, 781-788]. pKa calculations were performed to assess the protonation state of residues relevant for catalysis and enzyme stability, and a heptaxylan was fitted into the active-site groove by homology modeling, using the published crystal structure of a complex between the Bacillus circulans xylanase and a xylotetraose. Molecular dynamics indicated the central three sugar rings to be tightly bound, whereas the peripheral ones can assume different orientations and conformations, suggesting that the enzyme might also accept xylan chains which are branched at these positions. The reasons for the thermostability of the T. lanuginosus xylanase were analyzed by comparing its crystal structure with known structures of mesophilic family 11 xylanases. It appears that the thermostability is due to the presence of an extra disulfide bridge, as well as to an increase in the density of charged residues throughout the protein.

Amino Acid Sequence↗

PubMed1997

Harvesting in discrete-time predator-prey systems.

Fisheries for assemblages of interacting species with seasonal recruitment occur throughout temperate and boreal regions of the world ocean. Such systems are conveniently modeled within a difference-equation framework. Here, we examine the dynamic behavior of discrete-time models for an exploited predator-prey system. We contrast the dynamic properties of an aggregate production model and an age-structured model in which recruitment and mortality are explicitly considered. The joint effects of harvesting and interspecific interactions on the stability of the system are defined and contrasted with results for single species systems. We demonstrate that harvesting is a potentially stabilizing factor in the production model and in an age-structured model in which juveniles are harvested and that the relative magnitude of the interaction between predator and prey strongly affects the exploitation levels at which stabilization occurs. In contrast, harvesting is potentially destabilizing (i.e., results in complex dynamics) in an age-structured model with harvesting of adults only; again, the magnitude of the interaction determines the stability boundaries, with stronger interactions leading to a broader range of stable parameter space. In both the aggregate production model and the age-structured model with harvesting of juvenile predator and prey, exploitation effectively reduces the intrinsic rate of increase of the populations; for prey, this effect is amplified by high predation mortality rates. Sustainable levels of exploitation for both predators and prey are lower for the case where juveniles are harvested. Predators and resource harvesters can be viewed as competitors for the prey, and sustainable harvest levels are directly affected by the magnitude of predation mortality. These considerations expand the scope of issues to be resolved in fishery management to include factors such as trade-offs between mean yield and the potential for intrinsic variability and the role of predator-prey interactions in shaping the dynamics of exploited systems.

Age Factors↗

PubMed1999

Real or virtual large-scale structure?

Modeling the development of structure in the universe on galactic and larger scales is the challenge that drives the field of computational cosmology. Here, photorealism is used as a simple, yet expert, means of assessing the degree to which virtual worlds succeed in replicating our own.

Journal Article↗