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PubMed1997

Test of the health promotion model as a causal model of construction workers' use of hearing protection.

The health promotion model (HPM) was tested as a causal model of construction workers' use of hearing protection (N = 359). Theoretical and exploratory models fit well, with the theoretical model accounting for 36.3% of variance and the exploratory model accounting for 50.6% of variance in hearing protection use. Value of use (benefits of using hearing protection), barriers to use, and self-efficacy were significant predictors in both the theoretical and exploratory models, but perceived health status was a predictor only in the theoretical model. In the exploratory model, where modifying factors were allowed direct relationships with use of hearing protection, two modifying factors--noise exposure and interpersonal influences-modeling--were significant predictors. Results of this test of the HPM are consistent with the revised HPM (Pender, 1996). There were significant direct paths from modifying factors to behaviour. Use of hearing protection was best predicted by behavior-specific predictors, such as perceived barriers to use of hearing protection. Results support the use of the HPM to predict use of hearing protection.

Adult↗

PubMed2000

Metabolic modeling of Saccharomyces cerevisiae using the optimal control of homeostasis: a cybernetic model definition.

A model is presented to describe the observed behavior of microorganisms that aim at metabolic homeostasis while growing and adapting to their environment in an optimal way. The cellular metabolism is seen as a network with a multiple controller system with both feedback and feedforward control, i.e., a model based on a dynamic optimal metabolic control. The dynamic network consists of aggregated pathways, each having a control setpoint for the metabolic states at a given growth rate. This set of strategies of the cell forms a true cybernetic model with a minimal number of assumptions. The cellular strategies and constraints were derived from metabolic flux analysis using an identified, biochemically relevant, stoichiometry matrix derived from experimental data on the cellular composition of continuous cultures of Saccharomyces cerevisiae. Based on these data a cybernetic model was developed to study its dynamic behavior. The growth rate of the cell is determined by the structural compounds and fluxes of compounds related to central metabolism. In contrast to many other cybernetic models, the minimal model does not consist of any assumed internal kinetic parameters or interactions. This necessitates the use of a stepwise integration with an optimization of the fluxes at every time interval. Some examples of the behavior of this model are given with respect to steady states and pulse responses. This model is very suitable for describing semiquantitatively dynamics of global cellular metabolism and may form a useful framework for including structured and more detailed kinetic models.

Cybernetics↗

PubMed1996

Mathematical modeling of AVM physiology using compartmental network analysis: theoretical considerations and preliminary in vivo validation using a previously developed animal model.

The development of computer modeling technique of cerebral arteriovenous malformations using circuit network analysis, validated with a previously developed animal model is presented. Such a malformation and its vascular connections are rendered into a complex system of interconnecting tubes, which is then simulated by an analogous electrical circuit using commercially available computer software. This methodology was tested using a swine model, of which a detailed computer model was constructed from anatomic and angiographic measurements of the cranial vessels. Flow conditions, before and after creation of the in vivo model, were predicted from the computer model and compared with previously reported in vivo measurements. Detailed analysis of flow within the CAVM nidus was also performed. There was a good correlation between the computer and in vivo models regarding changes in flow and pressure drop across the rete. Flow mapping within the nidus showed localized directional flow that was determined by global inputs, consistent with functional compartmentalization. This method of computer modeling appears promising for studying clinically relevant aspects of cerebral arteriovenous malformation pathophysiology. To our knowledge it is the first computer model to demonstrate functional compartmentalization.

Animals↗

PubMed1995

Population forecasting: do simple models outperform complex models?

"This paper reviews the growing literature on population forecasting to examine a curious paradox: despite continuing refinements in the specification of models used to represent population dynamics, simple exponential growth models, it is claimed, continue to outperform such more complex models in forecasting exercises. Shrinking a large complex model in order to simplify it typically involves two processes: aggregation and decomposition. Both processes are known to introduce biases into the resulting representations of population dynamics. Thus it is difficult to accept the conclusion that simple models outperform complex models. Moreover, assessments of forecasting performance are notoriously difficult to carry out, because they inevitably depend not only on the models used but also on the particular historical periods selected for examination.... This paper reviews some of the recent debate on the simple versus complex modeling issue and links it to the questions of model bias and distributional momentum impacts." (SUMMARY IN FRE)

Demography↗

PubMed2005

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli.

MOTIVATION: The modeling and simulation of genetic regulatory networks have created the need for tools for model validation. The main challenges of model validation are the achievement of a match between the precision of model predictions and experimental data, as well as the efficient and reliable comparison of the predictions and observations. RESULTS: We present an approach towards the validation of models of genetic regulatory networks addressing the above challenges. It combines a method for qualitative modeling and simulation with techniques for model checking, and is supported by a new version of the computer tool Genetic Network Analyzer (GNA). The model-validation approach has been applied to the analysis of the network controlling the nutritional stress response in Escherichia coli. AVAILABILITY: GNA and the model of the stress response network are available at http://www-helix.inrialpes.fr/gna.

Bacterial Physiological Phenomena↗

PubMed2004

Using a finite element model to evaluate human injuries application to the HUMOS model in whiplash situation.

STUDY DESIGN: In the field of numerical simulation, the finite element method provides a virtual tool to study human tolerance and postulate on potential trauma under crash situations, particularly in case of whiplash trauma. OBJECTIVES: To show how medical and biomechanical interpretations of numerical simulation can be used to postulate on human injuries during crash situations. This methodology was applied to whiplash trauma analysis. A detailed analysis of kinematics of joints, stress level in hard tissues, and strain level in soft tissues was used to postulate on chronology and patterns of injury. Data were compared with published biomechanical and clinical studies of whiplash. SUMMARY OF BACKGROUND DATA: Although many in vitro and in vivo studies have been conducted to investigate whiplash cervical injury, and despite the number of finite element models developed to simulate the biomechanical behavior of the cervical spine, to date, there are only limited finite element models reported in the literature on the biomechanical response of the whole cervical spine in these respects. METHODS: A complete finite element model of the human body (HUMOS) build in a sitting position in a car environment was created to investigate injury mechanisms and to provide data for automotive safety improvements. It includes approximately 50,000 elements, including descriptions of all bones, ligaments, tendons, skin, muscles, and internal organs. A 15-g whiplash injury was simulated with the HUMOS model. The model predicted cervical motion segment kinematics, deformations of disks and ligaments, and stresses in bone. Model output was then compared with experimental and clinical whiplash literature. RESULTS: In term of kinematics during the chronology of whiplash, two injury phases were identified: the first was hyperextension of the lower cervical spine (C6-C7 and C5-C6) and mild flexion of the upper cervical spine(C0-C4). The amount of upper cervical flexion was 15 degrees from C0 to C4. The second phase was hyperextension of the entire cervical spine. Potential patterns of ligamentous injuries were observed; the anterior longitudinal ligament experienced the most strain (30%) at the lower cervical spine at the time of lower cervical extension and the interspinous ligament experienced the most strain (60%) at the time of upper cervical flexion. Von Mises stresses in bone do not exceed 15 Mpa, which is largely under injury levels reported in the literature. CONCLUSIONS.: This study reports a methodology to describe and postulate on human injuries based on finite element model analysis. The output of the HUMOS model in the context of whiplash shows a strong correlation with clinical and experimental reported data. HUMOS shows promise for the modeling of other types of trauma as well.

Biomechanical Phenomena↗

PubMed1999

Statistical model building and model criticism for human circadian data.

Mathematical models have played an important role in the analysis of circadian systems. The models include simulation of differential equation systems to assess the dynamic properties of a circadian system and the use of statistical models, primarily harmonic regression methods, to assess the static properties of the system. The dynamical behaviors characterized by the simulation studies are the response of the circadian pacemaker to light, its rate of decay to its limit cycle, and its response to the rest-activity cycle. The static properties are phase, amplitude, and period of the intrinsic oscillator. Formal statistical methods are not routinely employed in simulation studies, and therefore the uncertainty in inferences based on the differential equation models and their sensitivity to model specification and parameter estimation error cannot be evaluated. The harmonic regression models allow formal statistical analysis of static but not dynamical features of the circadian pacemaker. The authors present a paradigm for analyzing circadian data based on the Box iterative scheme for statistical model building. The paradigm unifies the differential equation-based simulations (direct problem) and the model fitting approach using harmonic regression techniques (inverse problem) under a single schema. The framework is illustrated with the analysis of a core-temperature data series collected under a forced desynchrony protocol. The Box iterative paradigm provides a framework for systematically constructing and analyzing models of circadian data.

Adult↗

PubMed2006

Modeling Sage data with a truncated gamma-Poisson model.

BACKGROUND: Serial Analysis of Gene Expressions (SAGE) produces gene expression measurements on a discrete scale, due to the finite number of molecules in the sample. This means that part of the variance in SAGE data should be understood as the sampling error in a binomial or Poisson distribution, whereas other variance sources, in particular biological variance, should be modeled using a continuous distribution function, i.e. a prior on the intensity of the Poisson distribution. One challenge is that such a model predicts a large number of genes with zero counts, which cannot be observed. RESULTS: We present a hierarchical Poisson model with a gamma prior and three different algorithms for estimating the parameters in the model. It turns out that the rate parameter in the gamma distribution can be estimated on the basis of a single SAGE library, whereas the estimate of the shape parameter becomes unstable. This means that the number of zero counts cannot be estimated reliably. When a bivariate model is applied to two SAGE libraries, however, the number of predicted zero counts becomes more stable and in approximate agreement with the number of transcripts observed across a large number of experiments. In all the libraries we analyzed there was a small population of very highly expressed tags, typically 1% of the tags, that could not be accounted for by the model. To handle those tags we chose to augment our model with a non-parametric component. We also show some results based on a log-normal distribution instead of the gamma distribution. CONCLUSION: By modeling SAGE data with a hierarchical Poisson model it is possible to separate the sampling variance from the variance in gene expression. If expression levels are reported at the gene level rather than at the tag level, genes mapped to multiple tags must be kept separate, since their expression levels show a different statistical behavior. A log-normal prior provided a better fit to our data than the gamma prior, but except for a small subpopulation of tags with very high counts, the two priors are similar.

Algorithms↗

PubMed2005

Injection-moulded models of major and minor arteries: the variability of model wall thickness owing to casting technique.

Cardiovascular disease of major and minor arteries is a common cause of death in Western society. The wall mechanics and haemodynamics within the arteries are considered to be important factors in the disease formation process. This paper is concerned with the development of an efficient computer-integrated technique to manufacture idealized and realistic models of diseased major and minor arteries from radiological images and to address the issue of model wall thickness variability. Variations in wall thickness from the original computer models to the final castings are quantified using a CCD camera. The results found that wall thickness variation from the major and minor idealized artery models to design specification were insignificant, up to a maximum of 16 per cent. In realistic models, however, differences were up to 23 per cent in the major arterial models and 58 per cent in the minor arterial models, but the wall thickness variability remained within the limits of previously reported wall thickness results. It is concluded that the described injection moulding procedure yields idealized and realistic castings suitable for use in experimental investigations, with idealized models giving better agreement with design. Wall thickness is variable and should be assessed after the models are manufactured.

Anatomy, Cross-Sectional↗

PubMed2004

Comparison between a Weibull proportional hazards model and a linear model for predicting the genetic merit of US Jersey sires for daughter longevity.

Predicted transmitting abilities (PTA) of US Jersey sires for daughter longevity were calculated using a Weibull proportional hazards sire model and compared with predictions from a conventional linear animal model. Culling data from 268,008 Jersey cows with first calving from 1981 to 2000 were used. The proportional hazards model included time-dependent effects of herd-year-season contemporary group and parity by stage of lactation interaction, as well as time-independent effects of sire and age at first calving. Sire variances and parameters of the Weibull distribution were estimated, providing heritability estimates of 4.7% on the log scale and 18.0% on the original scale. The PTA of each sire was expressed as the expected risk of culling relative to daughters of an average sire. Risk ratios (RR) ranged from 0.7 to 1.3, indicating that the risk of culling for daughters of the best sires was 30% lower than for daughters of average sires and nearly 50% lower than than for daughters of the poorest sires. Sire PTA from the proportional hazards model were compared with PTA from a linear model similar to that used for routine national genetic evaluation of length of productive life (PL) using cross-validation in independent samples of herds. Models were compared using logistic regression of daughters' stayability to second, third, fourth, or fifth lactation on their sires' PTA values, with alternative approaches for weighting the contribution of each sire. Models were also compared using logistic regression of daughters' stayability to 36, 48, 60, 72, and 84 mo of life. The proportional hazards model generally yielded more accurate predictions according to these criteria, but differences in predictive ability between methods were smaller when using a Kullback-Leibler distance than with other approaches. Results of this study suggest that survival analysis methodology may provide more accurate predictions of genetic merit for longevity than conventional linear models.

Animals↗

PubMed2005

Calibrating E-values for hidden Markov models using reverse-sequence null models.

MOTIVATION: Hidden Markov models (HMMs) calculate the probability that a sequence was generated by a given model. Log-odds scoring provides a context for evaluating this probability, by considering it in relation to a null hypothesis. We have found that using a reverse-sequence null model effectively removes biases owing to sequence length and composition and reduces the number of false positives in a database search. Any scoring system is an arbitrary measure of the quality of database matches. Significance estimates of scores are essential, because they eliminate model- and method-dependent scaling factors, and because they quantify the importance of each match. Accurate computation of the significance of reverse-sequence null model scores presents a problem, because the scores do not fit the extreme-value (Gumbel) distribution commonly used to estimate HMM scores' significance. RESULTS: To get a better estimate of the significance of reverse-sequence null model scores, we derive a theoretical distribution based on the assumption of a Gumbel distribution for raw HMM scores and compare estimates based on this and other distribution families. We derive estimation methods for the parameters of the distributions based on maximum likelihood and on moment matching (least-squares fit for Student's t-distribution). We evaluate the modeled distributions of scores, based on how well they fit the tail of the observed distribution for data not used in the fitting and on the effects of the improved E-values on our HMM-based fold-recognition methods. The theoretical distribution provides some improvement in fitting the tail and in providing fewer false positives in the fold-recognition test. An ad hoc distribution based on assuming a stretched exponential tail does an even better job. The use of Student's t to model the distribution fits well in the middle of the distribution, but provides too heavy a tail. The moment-matching methods fit the tails better than maximum-likelihood methods. AVAILABILITY: Information on obtaining the SAM program suite (free for academic use), as well as a server interface, is available at http://www.soe.ucsc.edu/research/compbio/sam.html and the open-source random sequence generator with varying compositional biases is available at http://www.soe.ucsc.edu/research/compbio/gen_sequence

Algorithms↗

PubMed2000

Mouse prostate reconstitution model system: A series of in vivo and in vitro models for benign and malignant prostatic disease.

BACKGROUND: An elucidation of the complex, morphological and molecular changes that underlie benign and malignant prostatic disease will likely lead to improved methods of diagnosis and therapy for those disorders. To identify and understand the interrelation of the phenotypic and genetic changes inherent in these important diseases requires the development and use of in vivo and in vitro models that closely mimic specific aspects of the disease process. Once the suspected molecular underpinnings of prostatic disease are uncovered, in vivo and in vitro models will be required for further testing of the functional significance of specific genetic alterations as they are identified. In addition models of prostatic disease are necessary to evaluate novel therapeutic approaches. METHODS: The mouse prostate reconstitution (MPR) model system was developed more than a decade ago with these specific needs in mind. Over the years, specific modifications of the MPR model have demonstrated its versatility and applicability for the study of benign and malignant prostatic disease, including metastatic progression. RESULTS: We discuss various modifications of the MPR model system made for its application to specific aspects of prostatic disease; the clinically relevant information that has been gleaned thus far from the use of this model system; and advances on the horizon for the expansion of its role in prostate research. CONCLUSIONS: The MPR model system has contributed substantially to the understanding and treatment of benign and malignant prostatic diseases. Additional modifications in this series of in vivo and in vitro models will likely lead to further advances.

Animals↗

PubMed2001

Towards the development of a minimal cell model by generalization of a model of Escherichia coli: use of dimensionless rate parameters.

A model of a minimal cell would be a valuable tool in identifying the organizing principles that relate the static sequence information of the genome to the dynamic functioning of the living cell. Our approach for developing a minimal cell model is to first generalize an existing model of Escherichia coli by expressing reaction rates as ratios to a set of reference parameters. This generalized model is a prototype minimal cell model that will be developed by adding detail to explicitly include each chemical species. We tested the concept of a generalized model by testing the effect of scaling all enzyme-catalyzed reactions in the E. coli model. The scaling has little effect on cellular function for a wide range of kinetic ratios, where the kinetic ratio is defined as the rate of all enzyme-catalyzed reactions in a given model relative to those in the E. coli model.

Computer Simulation↗

PubMed1997

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.

Comparative protein modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein modeling that consists of SWISS-MODEL, a server for automated comparative protein modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated protein models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and models in the process of experiment design.

Amino Acid Sequence↗

PubMed2002

Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.

A method is presented to refine models built by homology by the use of restricted molecular dynamics (MD) techniques. The basic idea behind this method is the use of structure validation software to determine for each residue the likelihood that it is modeled correctly. This information is used to determine constraints and restraints in an MD simulation including explicit solvent molecules, which is used for model refinement. The procedure is based on the idea that residues that the validation software identifies as correctly positioned should be strongly constrained or restrained in the MD simulations, whereas residues that are likely to be positioned wrongly should move freely. Two different protocols are compared: one (applied to CASP3 target T58) using full structural constraints with separate optimization of each short fragment and the other (applied to T47) allowing some freedom using harmonic restraining potentials, with automatic optimization of the whole molecule. Structures along the MD trajectory that scored best in structural checks were selected for the construction of models that appeared to be successful in the CASP3 competition. Model refinement with MD in general leads to a model that is less like the experimental structure (Levitt et al. Nature Struct Biol 1999;6:108-111). Actually, refined T47 was slightly improved compared to the starting model; changes in model T58 led not to further enhancement. After the X-ray structure of the modeled proteins became known, the procedure was evaluated for two targets (T47 and the CASP4 target T111) by comparing a long simulation in water with the experimental target structures. It was found that structural improvements could be obtained on a nanosecond time scale by allowing appropriate freedom in the simulation. Structural checks applied to fast fluctuations do not appear to be informative for the correctness of the structure. However, both a simple hydrogen bond count and a simple compactness measure, if averaged over times of typically 300 ps, correlate well with structural correctness and we suggest that criteria based on these properties may be used in computational folding strategies.

Amino Acid Sequence↗

PubMed2002

Modeling host-parasite coevolution: a nested approach based on mechanistic models.

In this study we introduce a mechanistic framework for modeling host-parasite coevolution using a nested modeling approach. The first step in this approach is to construct a mechanistic model of the parasite population dynamics within a host. The second step is to define an epidemiological model which is used to derive the fitness functions for both the host and the parasite. The within-host model is then nested within the epidemiological model by linking the epidemiological parameters such as the transmission rate of the infection or the additional host mortality rate to the dynamics of the within-host model. Nesting the within-host model into an epidemiological model allows us to evaluate the fitness functions for each interactor which in turn allows us to determine the coevolutionary dynamics of the system. This nested approach has the advantage over other approaches in that mechanistic descriptions of the host-parasite biology are used to derive, rather than impose, life-history trade-offs. We illustrate this framework by analysing a simple host-parasite system. In this particular system we find that the coevolutionary equilibrium is always stable and that host survivorship and parasite fitness vary greatly with the cost of the immune response and parasite growth.

Animals↗

PubMed2002

Evaluation of the benchmark dose method for dichotomous data: model dependence and model selection.

The benchmark dose (BMD) method was evaluated using the USEPA BMD software. Dose-response data on cleft palate and hydronephrosis for a number of related polyhalogenated aromatic compounds were obtained from the literature. According to chi(2) test statistics, each dichotomous USEPA model failed to adequately describe only 1 of 12 cleft palate data sets. For hydronephrosis, the models were discriminated to a higher extent according to global goodness-of-fit. NOAELs for cleft palate corresponded to BMDLs (the approximate lower confidence limit on the BMD) for extra risks in the range of 5% or below. Model dependence of the BMDL estimate was more pronounced at lower levels of benchmark response (BMR). A BMR of 5% (extra risk) is recommended for cleft palate since model differences at this level were limited for all data. In addition, at BMRs of 5-10% the BMDL for all models was little affected by the specified confidence limit size (in the 90-99% range). For BMDL determination a conservative model selection approach was applied. At the suggested level of BMR (5%) this procedure resulted in use of the same model (multistage model) for the cleft palate endpoint in general. Akaike's information criterion (AIC) was considered for comparison between models. Determination of appropriateness of use of such methods in dose-response applications requires further analysis.

Abnormalities, Drug-Induced↗

PubMed1981

The z-model -- a proposal for spatial and temporal modeling of visual threshold perception.

By considering only the modulation transfer functions of stationary, uniformly moved, and time modulated sinusoidal gratings it is possible to derive a simple model, the "z-model", for the spatio-temporal frequency behaviour of one-dimensional patterns. The transmission function of this model is a band pass function of a single coordinate z, which is a quadratic form of the spatial and temporal frequencies (rotational symmetry with respect to space and time). The model is determined by only three constants. Optionally a time phase which accounts for delay and phase distortion can be added. This model can also be derived from reaction time measurements for switched on sinusoidal gratings. With this model the response of a wide variety of spaito-temporal patterns have been calculated and compared with measured threshold data. For two-dimensional patterns orientational filtering has to be added to the model leading to a further parameter. This model predicts satisfactorily the threshold modulation for a great variety of arbitrary spaito-temporal patterns. However the absolute threshold value for aperiodic transient patterns differs slightly in direction of smaller sensitivity as compared with periodic stationary patterns. This suggests that the peak detection scheme usually used in threshold detection modeling should be replaced by an integrative mechanism.

Mathematics↗