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Extending the simple linear regression model to account for correlated responses: an introduction to generalized estimating equations and multi-level mixed modelling.

Much of the research in epidemiology and clinical science is based upon longitudinal designs which involve repeated measurements of a variable of interest in each of a series of individuals. Such designs can be very powerful, both statistically and scientifically, because they enable one to study changes within individual subjects over time or under varied conditions. However, this power arises because the repeated measurements tend to be correlated with one another, and this must be taken into proper account at the time of analysis or misleading conclusions may result. Recent advances in statistical theory and in software development mean that studies based upon such designs can now be analysed more easily, in a valid yet flexible manner, using a variety of approaches which include the use of generalized estimating equations, and mixed models which incorporate random effects. This paper provides a particularly simple illustration of the use of these two approaches, taking as a practical example the analysis of a study which examined the response of portable peak expiratory flow meters to changes in true peak expiratory flow in 12 children with asthma. The paper takes the reader through the relevant practicalities of model fitting, interpretation and criticism and demonstrates that, in a simple case such as this, analyses based upon these model-based approaches produce reassuringly similar inferences to standard analyses based upon more conventional methods.

Adolescent↗

Visit-driven endpoints in randomized HIV/AIDS clinical trials: impact of missing data on treatment difference measured on summary statistics.

In randomized HIV/AIDS clinical trials, CD4 lymphocyte counts and plasma HIV-1 RNA measurements are often used as endpoints. The comparison between treatment groups is mainly based on a summary measure of outcome, so-called summary statistic. Such analyses are often complicated by missing data occurring as drop-outs. For the most currently used summary statistics in these trials, we examined the impact of missing data occurring as drop-outs on test size, in order to help choosing between these statistics. A simulation of missing-data patterns was performed, using HIV-1 plasma RNA measurements as the main endpoint, to compare the effect of three plausible informative patterns, depending on treatment group, and on baseline or current plasma viral load, on eight different summary statistics. Missing data resulted in test sizes over the nominal value for the area under the curve minus baseline, the least-squares slope, the slope estimated with use of a mixed effects linear model, assuming a linear trend over the entire study, the difference between baseline and nadir, and the difference between baseline and week 24. The difference between baseline and week 8 was an acceptable summary with respect to the test size, but did not reflect accurately the durability of the effect of treatment. Two criteria appeared as the best summary statistics: the slope estimated by a mixed effects model, with a change of slope after two weeks of treatment, and to a lesser degree, the area under the curve after carrying forward the last observation.

Acquired Immunodeficiency Syndrome↗

Weight correction of MoM values: which method?

BACKGROUND: Adjusting maternal serum markers for maternal weight is considered to be a standard practice when screening for pregnancies associated with Down's syndrome. The choice of model for taking maternal weight into account is, however, rarely explicitly evaluated. METHOD: The relationship between the maternal serum markers alphafetoprotein (AFP), human chorionic gonadotropin (HCG) and unconjugated oestriol (uE3), determined with the Beckman Coulter access reagents and maternal weight was investigated in a cohort of 752 Belgian women being screened for pregnancy associated with Down's syndrome. Two different models (the log-linear equation and the linear-reciprocal equation) were used to determine the relationship between the serum markers and maternal weight. RESULTS: A significant relationship between log(10) multiples of median (MoM) values and weight (kg) was obtained for all markers, and the log-linear model had higher coefficients of determination (r(2)) when compared with the linear-reciprocal model. Weight correction with either method achieved the optimum effect that the correction factor for a woman with a population median weight of 65.5 kg was not significantly different from 1. Simulated weight-corrected MoM values with the two approaches were compared and variation was estimated. The mean difference between the weight-corrected MoM values calculated by the two methods was 7.8% (SD 4.3%) for AFP, 14.0% (4.4%) for HCG and 5.9% (3.2%) for uE3. This resulted in a difference in risk estimate of 1.66-5.34% for Down's syndrome owing to weight correction algorithm differences in women of median weight. CONCLUSION: The log-linear weight correction approach was shown to be marginally more effective by a goodness-of-fit analysis. Differences in weight-corrected MoM values estimated with the two approaches are highly significant (p<0.0001, Wilcoxon's paired sample test), but the effect on risk calculation was not significant. It was observed that the changes in risk became significant the more the MoM correction factors deviated from 1.

Biomarkers↗

An asymptotic maximum principle for essentially linear evolution models.

Recent work on mutation-selection models has revealed that, under specific assumptions on the fitness function and the mutation rates, asymptotic estimates for the leading eigenvalue of the mutation-reproduction matrix may be obtained through a low-dimensional maximum principle in the limit N-->infinity (where N, or N(d) with d> or =1, is proportional to the number of types). In order to extend this variational principle to a larger class of models, we consider here a family of reversible matrices of asymptotic dimension N(d) and identify conditions under which the high-dimensional Rayleigh-Ritz variational problem may be reduced to a low-dimensional one that yields the leading eigenvalue up to an error term of order 1/N. For a large class of mutation-selection models, this implies estimates for the mean fitness, as well as a concentration result for the ancestral distribution of types.

Animals↗

The viscoelastic responses of the human cervical spine in torsion: experimental limitations of quasi-linear theory, and a method for reducing these effects.

The dynamic torsional viscoelastic responses of the human cadaver cervical spine were measured in vitro. The quasi-linear formulation of time dependent behavior was used to describe and predict the resultant torque as a function of applied angular deflection and time. The performance of the quasi-linear model was good, reaching correlation at the 99% confidence level; however, it tended to underestimate hysteresis energy (mean relative deviation = -19.1%) and observed stiffness. This was in part due to difficulties in establishing the physical constants of the quasi-linear model from finite rate relaxation testing. An extrapolation deconvolution technique to enhance the experimentally derived constants was developed, to reduce the detrimental effects of finite rate testing. The quasi-linear model based on this enhanced derivation showed improved predictive ability and hysteresis energy determination.

Biomechanical Phenomena↗

The use of fractional polynomials to model continuous risk variables in epidemiology.

BACKGROUND: The traditional method of analysing continuous or ordinal risk factors by categorization or linear models may be improved. METHODS: We propose an approach based on transformation and fractional polynomials which yields simple regression models with interpretable curves. We suggest a way of presenting the results from such models which involves tabulating the risks estimated from the model at convenient values of the risk factor. We discuss how to incorporate several continuous risk and confounding variables within a single model. The approach is exemplified with data from the Whitehall I study of British Civil Servants. We discuss the approach in relation to categorization and non-parametric regression models. RESULTS: We show that non-linear risk models fit the data better than linear models. We discuss the difficulties introduced by categorization and the advantages of the new approach. CONCLUSIONS: Our approach based on fractional polynomials should be considered as an important alternative to the traditional approaches for the analysis of continuous variables in epidemiological studies.

Coronary Disease↗

A branching non-linear autoregressive model for the transmission of the fragile X dynamic repeat mutation.

A non-linear time series version of a model for the transmission of fragile X previously described in Ashley & Sherman (1995) is developed. The model retains the biological features of the Ashley/Sherman model but is easier to generalize and in particular allows the inclusion of covariates such as haplotype to model different paths and random effects to model family effects. The model is fitted to data from Murray et al. (1997) and its properties are illustrated in a simulation study.

Female↗

The concept of gene transfer-misrepair mechanism of radiation carcinogenesis may challenge the linear extrapolation model of risk estimation for low radiation doses.

The recent demonstration that transformation of cultured cells can be induced by exposure to DNA fragments prepared from normal mouse tissues provides experimental support to the gene transfer-misrepair hypothesis of radiation carcinogenesis. Employing various assumptions with regard to the generation of oncogenic DNA fragments and of cells which are susceptible to incorporate these fragments into their genome, it is predicted that the proposed mechanism implies a non-linear extrapolation model for the calculation of cancer risks caused by very low doses of ionizing radiation of low LET. It also follows from this hypothesis that X- and gamma-radiation delivered at an extremely low dose rate will be less carcinogenic than at high dose rate, in particular where low total doses are concerned. Several aspects of the hypothesis can be verified experimentally by the use of in vitro cultured cell systems.

Cell Transformation, Neoplastic↗

137Cs in freshwater fish in Finland since 1986--a statistical analysis with multivariate linear regression models.

The accident at the Chernobyl nuclear power plant in 1986 significantly elevated the 137Cs levels of fish in Finnish lakes. About 6200 fish samples from 390 lakes comprising 20 species have been analysed for 137Cs since 1986. The sizes of the lakes varied from a few hectares to about 1000 km2. Activity concentrations of 137Cs in fish still varied widely in 2003, from 16 to 6400 Bq/kg fresh weight. This paper presents the results of statistical analyses with multivariate linear regression models carried out on the empirical data collected since 1986. The statistical analysis resulted in separate models for two time periods describing temporal changes of 137Cs in fish. The explanatory variables were fish species with various feeding habits, the size class of the lake, municipal division, drainage area, time since the deposition and deposition level of the municipality. The calculated values for 137Cs in fish did not differ statistically significantly from the observed values in the validation data. The explanatory variables explained 58% (the first time period) and 72% (the second time period) of the total variability of 137Cs in fish.

Animal Feed↗

[The selection of Tikhonov regularization parameter in dynamic electrical impedance imaging].

Dynamic electrical impedance imaging is a non-linear inverse problem which is always discretized by finite element method and solved by linear model. Since the coefficient matrix of the linear model is ill-conditioned, the regularization method is used to get stable solution. However Tikhonov regularization is easy to realize, the selection of the regularization parameter is bothering. In this paper, according to the results of a great number of experiments, a new method for determining the regularization parameter is presented which uses the characteristic of the product of the norm of the error and the regularization solution. The reconstructed image using the regularization parameter selected by the proposed method has good spatial resolution.

Algorithms↗

Determination of drug-plasma protein binding using human serum albumin chromatographic column and multiple linear regression model.

Reversible attachment to serum proteins plays a significant role in pharmacokinetics and pharmacodynamics, and a clear understanding of this process is fundamental in the development of the rational use of many therapeutics agents. Over the last few years, it has been demonstrated that immobilized human serum albumin (HSA) could be used to estimate plasma protein binding. A series of 40 structurally unrelated pharmaceutical compounds were chromatographed on an immobilized HSA column in order to construct a protein binding 'calibration curve' and multiple linear regression system. When studying the relationship between the chromatographic retention and the percentage of binding determined in vitro, a good correlation can be observed (r(2) = 0.799) using a wide variety of compounds with different binding affinities (from 0 to 99% binding). Using a quantitative structure-retention relationships (QSRR) approach to analysing chromatographic data, the correlation was improved compared to the traditional approach (r(2) = 0.824).

Chromatography, Liquid↗

Quantitative risk assessment and the limitations of the linearized multistage model.

1. Quantifying carcinogenic risk is an important objective for assisting in the assessment and management of risks from chemical exposure. The most widely used of the many mathematical models proposed for extrapolation of carcinogenicity data from animal studies to low dose human exposures is the linearized multistage (LMS) model. This has, in effect, become the default approach for much of Quantitative Risk Assessment (QRA). The practical properties of this model have been investigated. 2. Analysis of stimulated data using the LMS model showed (i) that the Maximum Likelihood Estimate (MLE) of the low dose slope, q1, was unstable and extremely sensitive to small changes in the data; (ii) the 95% Upper Confidence Limit (UCL) estimate, q1*, preferred by the US Environmental Protection Agency (EPA) was insensitive with only small changes in values being obtained for large changes in the data; (iii) data sets where there was no statistical significance could give risk estimates similar to those obtained from data sets with clear dose-related effects; (iv) the size of the values of the Virtually Safe Dose (VSD) obtained did not necessarily relate to the biological interpretation of the data sets; (v) the value of q1* obtained was closely related to the top dose used in the study. 3. Limitations of the LMS model were illustrated by examples of its use in assessing the carcinogenicity of 2, 3, 7, 8-TCDD leading to the conclusion that the existing models are not suitable for routine use in the estimation of the risk from chemical carcinogens. The use of the LMS model has been justified in part by its original derivation from a mathematical model based upon a multistage model of carcinogenesis. However, estimates of the parameters of the model used to provide estimates of low dose risk to humans have no direct relationship to specific biological event in carcinogenesis. Further developments in mathematical models and increased understanding of the biological events underlying the carcinogenesis will lead to more biologically plausible QRA methods which would then justify serious consideration of QRA by regulatory authorities throughout the world.

Animals↗

Equivalent total doses for different fractionation schemes, based on the linear quadratic model.

A majority of patients receiving radical radiation therapy are treated with 1.8-2.0-Gy fractions, a dose that has evolved from clinical experience. However, other fractionation schemes can be advantageous. When fractionation is altered, the total dose prescribed should lead to equivalent or higher tumor control with the same or less tissue toxicity. To facilitate the use of different fractionation schemes, the authors compiled tables for equivalent biologic doses for late toxicity in normal tissues and tumoricidal doses for epithelial tumors, for various fraction sizes. The linear quadratic model according to Fowler was used. It is shown how these tables should be modified for proliferation of tumors during the course of radiation therapy. The tables make the use of different fractionation schemes easy. They also allow adjustment of total dose if fractionation needs to be changed during the course of treatment.

Cell Survival↗

Use of generalized linear mixed models in analyzing mutant frequency data from the transgenic mouse assay.

The transgenic mouse assay is now widely used for the study of mutagenesis in diverse rodent tissues and to test chemicals for genotoxic potential. This kind of assay generally involves nested observations at several levels of sampling, e.g., animals, packaging reactions, and plates. Due to the common origin, the mutant frequency (MF) in tissues from the same animal are likely to be positively correlated, inducing extra variation relative to the common binomial variation. In this article, a generalized linear mixed model is used to analyze the overdispersed binomial data on mutant frequency from the transgenic mouse assay, with a random effect for each level of the sampling hierarchy. This is a comprehensive framework within which different sources of variation in the data can be evaluated in nested factorial experiments and treatment effects can be assessed simultaneously. It avoids the current practice of repeated testing for excess binomial variability at each level of the sampling hierarchy and aggregating data up the levels, but fits the data with one single model. Parameters associated with the fixed effects, particularly dose, and the variance components for the random effects (e.g., animals, packages, and plates) can be estimated and tested for significance. Data previously reported in the literature involving the lacl gene from the Big Blue mouse are used to illustrate the proposed method.

Animals↗

Respiratory mechanics in rabbits ventilated with different tidal volumes.

Respiratory mechanics was studied in 11 rabbits at tidal volumes (VT) of 6.7, 10, and 20 ml/kg. Flow interruptions were performed during the full respiratory cycle. The viscoelastic pressure (Pve) was measured as the dynamic elastic pressure (Pel(dyn)) after flow cessation minus the static elastic pressure (Pel(st)). Static elastic and viscoelastic parameters were determined with numerical technique. Static hysteresis was minimal even at large VT. The Pel(st)-V curve was linear at small VT and in 6 animals at moderate VT. In 5 animals at moderate VT and in all animals at large VT, a linear segment with constant compliance was followed by a segment with decreasing compliance. The Pve-V curve could be described with a linear model only at small VT. A non-linear model was needed at increased VT. Compliance increased with VT. Both static and viscoelastic behaviours were linear up to larger volume ranges at large VT compared to moderate VT.

Animals↗

Analysis of covariance and standardization as instances of prediction.

In this paper, prediction provides the basis for unifying the procedures of covariances adjustment and standardization. Analysis of covariance is a method of forming predictions from a linear model; it is used when qualitative effects are to be studied and the effects of continuous variables are to be adjusted for. An essential feature is the division into effects of interest and effects for which adjustment is required. Covariates may also be qualitative: as such, they are used implicitly in experimental designs with blocks, where treatment effects are adjusted for the effect of blocks. The technique of standardization is well-known in epidemiology and demography as a method of adjusting explicitly for qualitative effects. The same division of effects applies when an analysis that uses generalized linear models is summarized. Two distinct types of prediction, which give identical results in classical linear models, are available: prediction may be conditional on a fixed value of a covariate, or marginal on a distribution of values such as the distribution in the set of data being analysed. Prediction methods are illustrated by the analysis of a table of proportions by use of a logit model.

Adult↗

Suramin: development of a population pharmacokinetic model and its use with intermittent short infusions to control plasma drug concentration in patients with prostate cancer.

PURPOSE: This study aimed to (1) develop a population pharmacokinetic model for suramin; (2) use Bayesian methods to assess suramin pharmacokinetics in individual patients; (3) use individual patients' pharmacokinetic parameter estimates to individualize suramin dose and schedule and maintain plasma suramin concentrations within predetermined target ranges; and (4) assess the feasibility of outpatient administration of suramin by intermittent, short infusions. METHODS: Plasma suramin concentrations were measured by high-performance liquid chromatography (HPLC), and compartmental pharmacokinetic models were fit using a Bayesian algorithm. Population pharmacokinetic models were developed using an iterative two-stage approach. Estimates of each patient's central-compartment volume were used to calculate suramin dosage. Simulation of that patient's suramin clearance was used to predict the time of his next dose. Using this approach, plasma suramin concentration was maintained at between 200 and 300, 175 and 275, 150 and 250, or 100 and 200 microgram/mL in four sequential patient cohorts. The ability of two- and three-compartment, open, linear models to fit the pharmacokinetic data was compared. Population pharmacokinetic parameters were estimated, using both two- and three-compartment structural models in 69 hormone-refractory prostate cancer patients. RESULTS: Target plasma suramin concentrations in individual patients were rapidly achieved. Concentrations were maintained within desired ranges for > or = 85% of treatment duration in all cohorts. A three-compartment, open, linear model described suramin pharmacokinetics better than did a two-compartment, open, linear model. Population pharmacokinetic estimates generated for two- and three-compartment pharmacokinetic models demonstrated modest interpatient pharmacokinetic variability and the long terminal half-life of suramin. CONCLUSION: Suramin can be administered by intermittent short infusion. Adaptive-control-with-feedback dosing facilitated precise control of plasma suramin concentrations and allowed a number of different concentration ranges to be studied. This approach is expensive and labor-intensive. Although we have demonstrated the ability to control drug exposure, simpler dosing schedules require critical evaluation. Population pharmacokinetic parameters generated in men with hormone-refractory prostate cancer will facilitate rational design of such schedules.

Adult↗

Stochastic models of a parasitic infection, exhibiting three basic reproduction ratios.

Two closely related stochastic models of parasitic infection are investigated: a non-linear model, where density dependent constraints are included, and a linear model appropriate to the initial behaviour of an epidemic. Host-mortality is included in both models. These models are appropriate to transmission between homogeneously mixing hosts, where the amount of infection which is transferred from one host to another at a single contact depends on the number of parasites in the infecting host. In both models, the basic reproduction ratio R0 can be defined to be the lifetime expected number of offspring of an adult parasite under ideal conditions, but it does not necessarily contain the information needed to separate growth from extinction of infection. In fact we find three regions for a certain parameter where different combinations of parameters determine the behavior of the models. The proofs involve martingale and coupling methods.

Animals↗