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PubMed1990

A comparison of Poisson regression models fitted to multiway summary tables and Cox's survival model using data from a blood pressure screening in the city of Bergen, Norway.

Multiplicative models for the association between blood pressure and coronary heart disease mortality in 5201 men aged 40-49 years at time of examination were compared. Piecewise exponential models fitted to summary tables formed by cross-classification by three systolic and three diastolic blood pressure groups, two age groups and three time intervals gave results close to the Cox model for continuous data. The parametric integrated baseline hazard functions estimated from grouped data were close to Breslow's nonparametric estimate in the Cox model.

Adult↗

PubMedDate not supplied

The accelerated failure time model: a useful alternative to the Cox regression model in survival analysis.

For the past two decades the Cox proportional hazards model has been used extensively to examine the covariate effects on the hazard function for the failure time variable. On the other hand, the accelerated failure time model, which simply regresses the logarithm of the survival time over the covariates, has seldom been utilized in the analysis of censored survival data. In this article, we review some newly developed linear regression methods for analysing failure time observations. These procedures have sound theoretical justification and can be implemented with an efficient numerical method. The accelerated failure time model has an intuitive physical interpretation and would be a useful alternative to the Cox model in survival analysis.

Proportional Hazards Models↗

PubMed1993

Modelling lactation using an inverse polynomial in a multilevel statistical model.

A method is outlined for modelling the relationship between breast-milk production and time from delivery, suitable for data collected longitudinally. The relationship is described using inverse polynomials. In a two-level model the coefficients are specified as random variables across subjects, allowing within- and between-subject variation to be separately estimated. In a three-level model, day-to-day variation can also be separately estimated. The model is illustrated using data from the Chiang Mai Lactation Project. It allows the use of covariates that vary over time, and provides a method of analysis that is compatible with the practical constraints on the timing of data collection that are inherent in longitudinal studies.

Age Factors↗

PubMed2000

Quantitative analysis and model simplification of an epidemic model with primary and secondary infection.

Models of particular epidemiological systems can rapidly become complicated by biological detail which can obscure their essential features and behaviour. In general, we wish to retain only those components and processes that contribute to the dynamics of the system. In this paper, we apply asymptotic techniques to an SEI-type model with primary and secondary infection in order to reduce it to a much simpler form. This allows the identification of parameter groupings discriminating between regions of contrasting dynamics and leads to simple approximations for the model's transient behaviour. These can be used to follow the evolution of the developing infection process. The techniques examined in this paper will be applicable to a large number of similar models.

Chenopodiaceae↗

PubMed1997

Visualization-based analysis of multiparameter models using environment for N-dimensional model analysis.

We present a methodology, based on N-dimensional computer visualization, for analyzing multiparameter models. This approach originally consisted of three steps: behavior analysis, sensitivity analysis, identifiability analysis. We have now developed a new way of calculating sensitivity based on the statistical measure of the coefficient of variation. Furthermore, we extended the methodology through the addition of an extra step, visual regression. Visual regression allows the user to visualize the process of actual parameter identification and presents a combined, empirical view of the first three steps in a single image. Next we applied this methodology to pulmonary capillary-transport models. Finally, we implemented the model analysis process as a stand-alone program. EN-DIMAN, the resulting software, allows researchers to carry out model analysis in a graphical user interface (GUI)-based environment.

Algorithms↗

PubMed1996

Animal models of human disease. Transgenic and knockout models of autoimmunity: Building a better disease?

The development of transgenic and knockout technologies has driven an explosion in new animal models of disease. These engineered diseases are a departure from previous animal models in that pathological syndromes are created from a priori assumptions about how disease pathogenesis could develop. Such models have been useful in providing new information on the functions of effector molecules such as cytokines, and in following the behavior of lymphocytes in vivo. However, the contrived nature of the systems might generate false information, unless validated by careful reference to human disease and spontaneous disease in other animal models.

Animals↗

PubMed1996

A probabilistic model for deriving soil quality criteria based on secondary poisoning of top predators. I. Model description and uncertainty analysis.

In previous studies, the risk of toxicant accumulation in food chains was used to calculate quality criteria for surface water and soil. A simple algorithm was used to calculate maximum permissable concentrations [MPC = no-observed-effect concentration/bioconcentration factor(NOEC/BCF)]. These studies were limited to simple food chains. This study presents a method to calculate MPCs for more complex food webs of predators. The previous method is expanded. First, toxicity data (NOECs) for several compounds were corrected for differences between laboratory animals and animals in the wild. Second, for each compound, it was assumed these NOECs were a sample of a log-logistic distribution of mammalian and avian NOECs. Third, bioaccumulation factors (BAFs) for major food items of predators were collected and were assumed to derive from different log-logistic distributions of BAFs. Fourth, MPCs for each compound were calculated using Monte Carlo sampling from NOEC and BAF distributions. An uncertainty analysis for cadmium was performed to identify the most uncertain parameters of the model. Model analysis indicated that most of the prediction uncertainty of the model can be ascribed to uncertainty of species sensitivity as expressed by NOECs. A very small proportion of model uncertainty is contributed by BAFs from food webs. Correction factors for the conversion of NOECs from laboratory conditions to the field have some influence on the final value of MPC5, but the total prediction uncertainty of the MPC is quite large. It is concluded that the uncertainty in species sensitivity is quite large. To avoid unethical toxicity testing with mammalian or avian predators, it cannot be avoided to use this uncertainty in the method proposed to calculate MPC distributions. The fifth percentile of the MPC is suggested as a safe value for top predators.

Algorithms↗

PubMed2001

Modelling mammary metabolism in the dairy cow to predict milk constituent yield, with emphasis on amino acid metabolism and milk protein production: model construction.

Previous efforts to simulate mammary metabolism have focused on energy, mostly considering amino acids (AA) in aggregate. The main objective of this work was to build a model of mammary metabolism, based on data from arterio-venous difference studies, which considered AA in sufficient detail to predict yields of milk solids. The model contains 19 state variables and considers the removal of 37 metabolites from blood, including 22 AA. It is driven by blood flow and arterial concentrations, and outputs include milk protein, milk lactose, and three classes of milk fat (by chain length). The model was parameterized using a balance version of it and the mean observations from four arterio-venous difference experiments, with a limited number of assumptions, and evaluated against these experiments. In assembling the balance model, milk protein output was not predicted satisfactorily, as some essential AA were not present in quantities great enough to support the rates of milk protein synthesis observed experimentally. Tryptophan showed the greatest deficit, followed by tyrosine plus phenylalanine, methionine, and histidine. In addition, significant quantities of pyruvate were needed to synthesize serine, glycine, and alanine. The supply of alpha-ketoglutarate plus glutamate to synthesize proline and glutamine was provided in part by catabolism of arginine; the remainder was derived from catabolism of other AA and energetic substrates.

Algorithms↗

PubMed2001

A toxicokinetic model for predicting the tissue distribution and elimination of organic and inorganic mercury following exposure to methyl mercury in animals and humans. II. Application and validation of the model in humans.

The objective of this study was to develop a biologically based dynamical model describing the disposition kinetics of methyl mercury and its inorganic mercury metabolites in humans following different methyl mercury exposure scenarios. The model conceptual and functional representation was similar to that used for rats but relevant data on humans served to determine the critical parameters of the kinetic behavior. It was found that the metabolic rate of methyl mercury was on average 3 to 3.5 times slower in humans than in rats. Also, excretion rates of organic mercury from the whole body into feces and hair were 100 and 40 times smaller in humans, respectively, and urinary excretion of organic mercury in humans was found to be negligible. The human transfer rate of inorganic mercury from blood to hair was found to be 5 times lower than that of rats. On the other hand, retention of inorganic mercury in the kidney appeared more important in humans than in rats: the transfer rate of inorganic mercury from blood to kidney was 19 times higher than in rats and that from kidney to blood 19 times smaller. The excretion rate of inorganic mercury from the kidney to urine in humans was found to be twice that of rats. With these model parameters, simulations accurately predicted human kinetic data available in the published literature for different exposure scenarios. The model relates quantitatively mercury species in biological matrices (blood, hair, and urine) to the absorbed dose and tissue burden at any point in time. Thus, accessible measurements on these matrices allow inferences of past, present, and future burdens. This could prove to be a useful tool in assessing the health risks associated with various circumstances of methyl mercury exposure.

Animals↗

PubMed2005

A computer model of intracranial pressure dynamics during traumatic brain injury that explicitly models fluid flows and volumes.

A model of intracranial pressure (ICP) dynamics that uses fluid volumes as primary state variables is presented, along with clinical data for two subjects with elevated ICP. The data includes annotations to indicate the precise timing of clinical changes in cerebral spinal fluid drainage, head of bed elevation, and minute ventilation. The response to changes in the clinical parameters was used to calibrate the model to correspond to specific subjects by estimating values for key characteristics such as hematoma volume and CSF uptake resistance. The error in mean ICP predicted by the model was less than 2 mmHg when cerebral spinal fluid is drained and the head of bed elevation was increased. The error in mean ICP predicted by the model exceeded 5 mmHg during an episode when the head of bed was decreased and also during a reduction in minute ventilation. The estimated values for hematoma volume and other subject characteristics were plausible but could not be verified empirically.

Blood Pressure↗

PubMed1982

Bioorganic modelling stereoselective reactions with chiral neutral ligand complexes as model systems for enzyme catalysis.

In terms of the reporting of accomplished chemistry this review can do no more than give an indication of the rapid progress in the branch of bioorganic modelling based on the use of macrocyclic compounds that (usually) act as complexing agents. What remains to be done, however, is to point out problems that have not been satisfactorily solved and to suggest other profitable areas of investigation. From the material accumulated in this review one can draw the conclusion that especially crown (or cryptate) systems offer special advantages in bioorganic modelling because such compounds can - enzyme like - complex a potential substrate. On the basis of quite simple binding considerations, coupled with an analysis of steric interactions, accurate predictions of the stereochemistry of the complex can be made. The inclusion of catalytic groups in the crown (or cryptate) system and reactive functional groups in the substrate is then done in such a fashion that the stereoelectronic arrangement is compatible with the predicted geometry of the complex. However, the good complexing ability of the ligand is paradoxically often its greatest failing in terms of developing a system in which the functionalized ligand acts truly as a catalyst. As seen from much of the chemistry discussed in this review the ligand is incapable of the double task of complexing substrate but releasing product in an enzymic fashion, i.e. that turnover occurs. How is this problem to be solved? Induced conformational changes are an obvious approach although the design of proper systems remains a challenge for which few suggestions outside of unlimited ingenuity can be given. Much of the solution to such problems will lie also in a much better understanding than we now have of non-covalent interactions and the stereochemistry of such interactions. The assembly and disassembly of large molecular aggregates by the making and dissolution of non-covalent bonds is an art at which chemists are still relative amateurs. A better understanding of non-covalent interactions may also provide the key to achieving also the twin goals of both speed and selectivity in bioorganic modelling. As far as enantioselectivity is concerned it is clear that this can be achieved fairly effectively by the use of relatively small, but appropriately placed, groups that force the substrate to complex in an enantioselective step with the ligand. In other words, the problem of enantioselectivity can be solved at the stage of complex forming, which is kinetically rapid. The p]roblem of rate enhancement lies in the mentarity with the transition state of the reaction being catalyzed. Again the achievement of this goal lies in ingenuity of design. Potential areas of applications of chiral crown ether (or cryptate) ligand systems in bioorganic modelling lie in, for example, the formation of carbon-carbon bonds, development of oxidative processes (i.e...

Chemical Phenomena↗

PubMed1993

A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building.

A homology model building study of cytochrome P450 2D6 has been carried out based on the crystal structure of cytochrome P450 101. The primary sequences of P450 101 and P450 2D6 were aligned by making use of an automated alignment procedure. This alignment was adjusted manually by matching alpha-helices (C, D, G, I, J, K and L) and beta-sheets (beta 3/beta 4) of P450 101 that are proposed to be conserved in membrane-bound P450s (Ouzounis and Melvin [Eur. J. Biochem., 198 (1991) 307]) to the corresponding regions in the primary amino acid sequence of P450 2D6. Furthermore, alpha-helices B, B' and F were found to be conserved in P450 2D6. No significant homology between the remaining regions of P450 101 and P450 2D6 could be found and these regions were therefore deleted. A 3D model of P450 2D6 was constructed by copying the coordinates of the residues from the crystal structure of P450 101 to the corresponding residues in P450 2D6. The regions without a significant homology with P450 101 were not incorporated into the model. After energy-minimization of the resulting 3D model of P450 2D6, possible active site residues were identified by fitting the substrates debrisoquine and dextrometorphan into the proposed active site. Both substrates could be positioned into a planar pocket near the heme region formed by residues Val370, Pro371, Leu372, Trp316, and part of the oxygen binding site of P450 2D6. Furthermore, the carboxylate group of either Asp100 or Asp301 was identified as a possible candidate for the proposed interaction with basic nitrogen atom(s) of the substrates.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1975

A computer model and a mechanical model of the circulation and their use in the evaluation of indices of myocardial blood flow.

Computer and mechanical models of the circulation have been made to study isotopic techniques of determining indices of myocardial blood flow. Parameters in the program and dimensions in the mechanical model have been scaled to represent the human circulation. Single rapid injections of 131I labelled human serum albumen were given into the venous line of the mechanical model and records obtained from collimated scintillation detectors positioned over the heart, lung and brain. Similar injections and recordings were simulated in the computer model. Two indices of myocardial flow have been studied. The first, described by Mena et al. is the ratio of the half time of the downslope of the left ventricular curve to the half time of the downslope of the brain curve. This index distinguished myocardial flows of 0,5% and 10% of total cardiac output but was also affected by changes in cerebral flow. A new index is proposed in which the half time of the left ventricular curve downslope is related to the half time of the downslope of the lung curve. This index can distinguish myocardial flows of 0,5% and 10% total flow but is not affected by changes in cerebral flow.

Blood Circulation↗

PubMed1986

A dispersion model of hepatic elimination: 1. Formulation of the model and bolus considerations.

A dispersion model of hepatic elimination, based on the residence time distribution of blood elements within the liver, is presented. The general rate equations appropriate for describing the hepatic output concentration of a tracer solute are derived. Particular consideration is given to events following a bolus input dose of a tracer. The model is shown to be compatible with the known hepatic architecture and hepatic physiology. The model has been fitted to hepatic outflow data for red blood cells, albumin, and other noneliminated solutes. The experimental data suggest a high degree of dispersion of blood elements within the liver. The model has also been used to evaluate the effects of changes in enzyme activity, hepatic cell permeability, blood flow, and protein binding on the outflow concentration vs. time profiles of solutes.

Animals↗

PubMed1994

[Cell and tissue culture models in dermatology. The Frankfurt Center of Dermatology establishes models].

In the course of the Third Frankfurt Talks, for the first time a congress in dermatology was dedicated exclusively to cell and tissue culture models. The complexity of a whole organ, in this case the skin, could be reduced to single aspects without losing the holistic context. Ways of managing this were discussed on an interdisciplinary level by dermatologists, physiologists, pharmacologists and biologists. The results are also expected to be useful to the clinician. Focus points of in vitro investigations for dermatology are wound closure models and the use of in vitro skin for transplantation in the therapy of non-healing ulcers and vitiligo. As an alternative to animal experiments, cultures of human cells are gaining increasing influence in drug testing. The effect of glucocorticosteroids on normal skin fibroblasts, keratinocytes and permanent cell lines is discussed as an example, and in vitro models of diseases such as psoriasis are established. Additionally, basic events such as differentiation and ageing have been modelled in cell cultures of melanocytes and keratinocytes. Mechanical stress, UV radiation and nicotine are discussed as inductors.

Cell Differentiation↗

PubMed2001

A conceptual model for describing decision-making situations in integrated natural resource planning and modeling projects.

A conceptual model is developed herein for the purpose of stimulating discussions within groups planning and carrying out integrated natural resource projects. We first describe four basic components of integrated planning and modeling efforts: people, databases, technology, and organizational commitment. Second, we provide one view of the relationship between the size of the project's decision-making body and the timing of decisions during a project's life cycle. Finally, these two discussions are combined into a conceptual model describing the dynamic nature of decision-making within integrated projects. The abstractions and generalizations described here are not unique to private industry or governmental organizations and should provide the basis for a discussion of decision-making issues among interdisciplinary professionals embarking on large-scale or complex modeling efforts.

Computing Methodologies↗

PubMed2005

Experimental models of brainstem tumors: development of a neonatal rat model.

OBJECTIVE: Brainstem tumor models are required to advance the treatment for diffuse pontine gliomas in children. The feasibility of creating an experimental rodent model by inoculating newborn pups with tumor cells was examined. The study was performed to create an animal model for diffuse brainstem tumors. METHODS: Eighty-two Fischer rat pups aged 12-24 h were anesthetized by hypothermia. The brainstem was injected with saline to identify anatomical coordinates for subsequent tumor cell challenges. The newborn pups were then inoculated with F98 (n=30) or 9L (n=30) glioma cells. Animals were returned to their mother for nursing. Tumor growth was assessed by survival and histopathology. RESULTS: Twenty-one percent of the saline-treated animals (17 out of 82) and 5% of the tumor cell-challenged pups (3 out of 60) were eliminated by their mothers. Inoculations with 9L and F98 cells produced brainstem tumors in 83% (24 out of 29) and 93% of animals (26 out of 28) respectively that were evaluated. CONCLUSIONS: Our results demonstrate that neonatal rat models for brainstem tumors can be prepared using known injection coordinates and orthotopic cell lines. Decreasing rates of maternal removal during the course of the work suggests that the method involves a learning curve.

Animals↗

PubMed1998

Statistical model of the hippocampal CA3 region. I. The single-cell module: bursting model of the pyramidal cell.

A model with intermediate complexity is introduced to reproduce the basic firing modes of the CA3 pyramidal cell. Our model consists of a single compartment, has two variables (membrane potential and internal calcium concentration), and involves two separate stages for interspike mechanisms and firing. Interspike dynamics is governed by voltage- and calcium-dependent ionic channels but no channel kinetics are provided. This model is suitable to be included in our statistical population model (Part II, following paper). Bifurcation analysis reveals that interspike dynamics rather than sodium firing has the dominant role in the control of bursting/nonbursting behavior.

Action Potentials↗