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Modeling population kinetics of free fatty acids in isolated rat hepatocytes using Markov Chain Monte Carlo.

The aim of this study is the characterization, by means of mathematical models, of the activity of isolated hepatic rat cells as regards the conversion of free fatty acids (FFA) to ketone bodies (KB). A new physiologically based compartmental model of FFA metabolism is used within a context of population pharmacokinetics. This analysis is based on a hierarchical model, that differs from standard model formulations, to account for the fact that some data sets belong to the same animal but have been collected under different experimental conditions. The statistical inference problem has been addressed within a Bayesian context and solved by using Markov Chain Monte Carlo (MCMC) simulation. The results obtained in this study indicate that, although hormones epinephrine and insulin are important metabolic regulatory factors in vivo, the conversion of FFA to KB by isolated hepatic rat cells is not significantly affected by epinephrine and only little influenced by insulin. So we conclude that in vivo, the interaction of these two hormones with other compounds not considered in this study plays a fundamental role in ketogenesis. From this study it appears that mathematical models of metabolic processes can be successfully employed in population kinetic studies using MCMC methods.

Animals↗

Prefrontal cortex activity in self-initiated movements is condition-specific, but not movement-related.

Activity of the prefrontal cortex (PFC) has been observed in previous block-design brain imaging studies of self-initiated movements. However, the meaning of these activations remained unclear. A functional MRI experiment was carried out, which utilized an epoch and an event-related analysis approach to the data. We hypothesized that event-related activity of the PFC would argue for a contribution to movement preparation. In contrast, epoch-, but not event-related activity pointed to tonic activations, probably reflecting enhanced attentional states or working memory processing. Twenty-one subjects were examined with 845 T2*-weighted images. During active phases, subjects were instructed to perform self-initiated movements of the right index finger with intertrial intervals of about 8 s. On single subject level, epoch- and event-related regressors were entered into a combined model, estimating the exclusive contribution of either regressor. For statistical inference on multisubject level, random effects analyses were performed. For the epoch regressor, activity within the right dorso- and ventrolateral prefrontal cortex, the bilateral insula, and the right inferior parietal lobe was observed. The event-related regressor detected activity within the right inferior parietal lobe, ventral from the activity found with the epoch regressor. The present results indicate a condition-, but not a movement-related function of the PFC in self-initiated movements. Furthermore, anatomically distinct regions within the inferior parietal cortex seem to be involved in condition-specific and movement-related processes. The observed condition-specific activations are suggested to reflect attentional or working memory processes, supervising task performance, rather than movement preparation or initiation.

Adult↗

Let the numbers speak.

Although it is often claimed that statistical techniques are ways of letting the objective data speak for themselves, in both the contrast and correlational modes of statistical inference, all the real work is done by the a priori decisions imported into the analysis--which categories are to be used to create contrasting populations, which categories are to be measured, which categories are to be held constant while others are compared, and which is cause and which is effect? The authors explore here the problem of directionality of causation and the relationship between cause and effect, on the one hand, and dependent and independent variables, on the other. In systems of any complexity there are feedbacks--negative and positive feedbacks forming loops, embedded in larger contexts and subject to influences that can impinge on the loop at any point, such that the same pair of variables may show positive correlations in some situations and negative correlations in others.

Causality↗

Biometrical implications of factorial experiments for the study of lymphocyte mitogenic response.

Lymphocyte responsiveness to mitogens is affected by a number of experimental variables; the latter may be conveniently studied several at a time, following a factorial design that allows the complete evaluation of the effects of each variable and of their interplays. Statistical inferences may be drawn through an analysis of variance, provided that the data conform to the underlying model, i.e. that the effects are additive and that the errors are normally distributed and homoscedastic. Thymidine incorporation data should first be transformed to log cpm; the effects on the metameter may then be assumed to be additive, and their errors approach normality; the error variances may be affected by the experimental variables involved, so that the homogeneity of the error must be checked before relying on the pooled estimate of the error for parametric tests of significance. The above considerations have been illustrated with factorial experiments on [3H]TdR incorporation by rabbit spleen cells stimulated with varying amounts of PHA-P or PHA-M, under a variety of culture conditions.

Analysis of Variance↗

Group imaging of task-related changes in cortical synchronisation using nonparametric permutation testing.

Synthetic aperture magnetometry (SAM) is a nonlinear beamformer technique for producing 3D images of cortical activity from magnetoencephalography data. We have previously shown how SAM images can be spatially normalised and averaged to form a group image. In this paper we show how nonparametric permutation methods can be used to make robust statistical inference about group SAM data. Data from a biological motion direction discrimination experiment were analysed using both a nonparametric analysis toolbox (SnPM) and a conventional parametric approach utilising Gaussian field theory. In data from a group of six subjects, we were able to show robust group activation at the P < 0.05 (corrected) level using the nonparametric methods, while no significant clusters were found using the conventional parametric approach. Activation was found using SnPM in several regions of right occipital-temporal cortex, including the superior temporal sulcus, V5/MT, the fusiform gyrus, and the lateral occipital complex.

Adult↗

[Popper and the problem of induction in epidemiology].

In this article we are discussing a few of the contributions by the Austro-British philosopher Karl R. Popper, one of our most influential contemporary thinkers, whose epistemological and socio-political theories have also penetrated the sphere of epidemiology. We are focusing mainly on the so-called problem of induction. We sustain, in line with Popper, that the scientific method does not use inductive reasoning, but rather hypothetical-deductive reasoning. Although the movement from the data evaluating a hypothesis to a conclusion on the latter goes from the specific to the general, that is, in an inductive direction, the induction does not exist as a reasoning process or inference. That is, there is no method that enables us to infer or to verify hypotheses or theories (we cannot explore all of the possible situations to see whether the theory stands up), or even to render them very probable. Besides, scientists look for highly informative theories, not highly probable ones. What we actually do is to propose a hypothesis as a tentative solution to a problem, to confront the prediction deduced from the hypothesis with actual experience, and evaluate whether the hypothesis is rejected or not by the facts. As theories cannot be verified, we can only accept them if they withstand an attempt to reject them. Consequently, the test of a theory consists of criticism or a serious attempt at falsification, that is, the elimination of error within a theory, in order to reject it if it is false. The objective is, thus, the search for true theories. For this purpose, the scientific method uses a systematic set of methodological (not logical) rules, that is, decisions. These methodological rules or principles can be summed up in two: [symbol: see text]be inventive and critical!, that is, propose bold hypotheses and subject them to severe tests of experience. Logic plays its role mainly by allowing us to deduce from a hypothesis the predictions to be confronted with the facts or evidence. This is applicable both to statistical inference as well as to causal inference. We argue that the criteria of causality used in epidemiology are none other than rules of the method designed for the same purpose: they are concerned with eliminating or reducing errors (chance, bias...) on testing a causal hypothesis. Consequently, the so-called ausal inference, the step from evidence to causal theory, is not a logical inductive or probabilistic process but rather a decision based on the evaluation of a causal hypothesis thanks to methodological rules such as the criteria of causality. We believe that the interest of the debate between the Popperian and the inductivist epidemiologists is not merely a matter of words, as, if we are aware that we do not operate inductively, that we cannot establish firmly hypotheses, not even affirm them probabilistically, we will presumably adopt a humbler attitude and look more for the errors in our theories than for their facile examples of confirmation.

Causality↗

A venue-based method for sampling hard-to-reach populations.

Constructing scientifically sound samples of hard-to-reach populations, also known as hidden populations, is a challenge for many research projects. Traditional sample survey methods, such as random sampling from telephone or mailing lists, can yield low numbers of eligible respondents while non-probability sampling introduces unknown biases. The authors describe a venue-based application of time-space sampling (TSS) that addresses the challenges of accessing hard-to-reach populations. The method entails identifying days and times when the target population gathers at specific venues, constructing a sampling frame of venue, day-time units (VDTs), randomly selecting and visiting VDTs (the primary sampling units), and systematically intercepting and collecting information from consenting members of the target population. This allows researchers to construct a sample with known properties, make statistical inference to the larger population of venue visitors, and theorize about the introduction of biases that may limit generalization of results to the target population. The authors describe their use of TSS in the ongoing Community Intervention Trial for Youth (CITY) project to generate a systematic sample of young men who have sex with men. The project is an ongoing community level HIV prevention intervention trial funded by the Centers for Disease Control and Prevention. The TSS method is reproducible and can be adapted to hard-to-reach populations in other situations, environments, and cultures.

Adolescent↗

Statistical modeling in case-control real-time RT-PCR assays, for identification of differentially expressed genes in schizophrenia.

Aspects of experimental design, statistical modeling, and statistical inference in case-control real-time reverse transcription-polymerase chain reaction (RT-PCR) assays are discussed. The background is mRNA expression data from an investigation of genes previously suggested to be schizophrenia related. Real-time RT-PCR allows large samples of individuals. However, with more individuals than positions per plate, incomplete designs are required. A basic multivariate (for several genes jointly) random-effects analysis of covariance model, incorporating heterogeneity both between and within individuals, is formulated. The use of reference genes to form additional regressors is found to be highly efficient. Because regressions between and within individuals are usually different, it is important first to average over the intraindividual replicates. This has consequences for the influence of plate effects. Topics also discussed are testing for a significant mean disease effect, differential coregulation, and the difficulty of identifying genes affected in only a subgroup of cases.

Analysis of Variance↗

Some scale estimators and lack-of-fit tests for the censored two-sample accelerated life model.

Some new scale estimators for the censored two-sample accelerated life model are introduced. They are zeros of some integrated weighted difference between the two cumulative hazard estimators. These estimators are asymptotically normal. The weight is chosen to result in estimators whose asymptotic variances do not involve the destiny functions and can be easily estimated. This provides a fast and simple means of statistical inference in the censored two-sample accelerated life model. Through investigating the asymptotic relative efficiency at some important censoring submodels and the finite example behaviors in various numerical studies, we obtain some estimators with very competitive performance. From the new class of scale estimators, some lack-of-fit tests for the accelerated life model are also derived. These tests are related to Gill-Schumacher type tests and require little extra computing time once the estimator is obtained. The estimators and tests are illustrated in two applications. For a vaginal cancer data set for rats, the effect of pretreatment regime was found to be well described by the two-sample accelerated life model. For a data set on progression of ovarian cancer, it was found that the effect of grade of disease could not be described either by the two-sample proportional hazards model or the two-sample accelerated life model.

9,10-Dimethyl-1,2-benzanthracene↗

Estimated Prevalence of Viral Hepatitis in the General Population of the Municipality of São Paulo, Measured by a Serologic Survey of a Stratified, Randomized and Residence-Based Population.

The present study was done to estimate the prevalence of Hepatitis A (HAV), B (HBV), C (HCV), and E (HEV) infection in the general population residing in the municipality of São Paulo, and to evaluate the level of knowledge related to the various modes of infection transmission by and protection against the different viruses. Blood samples and health questionnaires were collected from 1,059 individuals. The study design used an inductive method of predictive statistical inferences through randomized sampling stratified by Sex, age and residence region. The estimated prevalence rated found were: Hepatitis A = 66.59% (63.75%-69.44% CI); Hepatitis B = 5.94% (4.50%-7.35%); Hepatitis C = 1.42% (0,70%-2.12%); Hepatitis E = 1.68% (0.91%-2.46%). The frequency of hepatitis was similar in males and females. HAV showed an estimated prevalence of 56.16% in the population up to 17 years old, increasing to 65.30% in individuals between 18 and 29 years. The infection reached its peak of 90% in individuals 40 years of age or older. The study showed a greater tendency of dissemination of HBV among the population between 15 and 17 years. This specific age group showed an estimated prevalence of active infection of 1.04% (0.43%-1.65% CI), and also demonstrated an ascending level of acquired immunity with an estimated prevalence of 4.90% (3.60%-6.20% CI). HCV demonstrated an estimated prevalence of 1.42% (0.70%-2.12% CI). This specific infection occurred more frequently among adults 30 years of age or older, with the prevalence reaching a peak of 3.80% among the group aged 50 to 59 years. HEV showed zero prevalence among the age group between 2 and 9 years. This was followed by a slightly ascending rate starting from age 10, with an estimated prevalence of 1.05% (0.94%-3.04% CI) among those 10 to 14 years of age. This infection reached its peak of 3.00% (0.55%-6.74% CI) at the age of 60 years or older. Individuals with lower educational levels had a higher tendency of acquiring HAV and HCV, while there was no statistically significant difference for this parameter related to HBV and HEV. HBV occurred more frequently among inhabitants of the northern region of the city. All other hepatitis forms occurred at similar frequencies among the five regions of the city. Among the population, 1.90% (1.08%-2.72% CI) demonstrated an elevated hepatic enzyme with no serologic evidence indicating the cause was the viruses studied. This observation suggests the presence of other hepatic diseases, possibly including other viral diseases. It was also estimated that 75.12% of the city's population did not know the modes of transmission of hepatitis viruses and 76.70% did not know how to prevent them. This clearly suggests the need for a full-scale education program combined with public health measures regarding prevention of all forms of vial hepatitis.

Journal Article↗

The effect of collapsing multinomial data when assessing agreement.

BACKGROUND: In epidemiological studies researchers often depend on proxies to obtain information when primary subjects are unavailable. However, relatively few studies have performed formal statistical inference to assess agreement among proxy informants and primary study subjects. In this paper, we consider inference procedures for studies of interobserver agreement characterized by two raters and three or more outcome categories. Of particular interest is the consequence of dichotomizing such data on the expected confidence interval width for the kappa coefficient. The effect of dichotomization on sample size requirements for testing hypotheses concerning kappa is also evaluated. METHODS: Simulation studies were used to compare coverage levels and widths for constructing confidence intervals. Sample size requirements were compared for multinomial and dichotomous data. We illustrate our results using a published data set on drinking habits that assesses agreement among primary and proxy respondents. RESULTS: Our results show that when multinomial data are treated as dichotomous, not only do the expected confidence interval widths become greater, but the penalty in terms of larger sample size requirements for hypothesis testing can be severe. CONCLUSION: We conclude that there are clear advantages in preserving multinomial data on the original scale rather than collapsing the data into a binary trait.

Alcohol Drinking↗

Principal component analysis of the dynamic response measured by fMRI: a generalized linear systems framework.

Principal component analysis (PCA) is one of several structure-seeking multivariate statistical techniques, exploratory as well as inferential, that have been proposed recently for the characterization and detection of activation in both PET and fMRI time series data. In particular, PCA is data driven and does not assume that the neural or hemodynamic response reaches some steady state, nor does it involve correlation with any pre-defined or exogenous experimental design template. In this paper, we present a generalized linear systems framework for PCA based on the singular value decomposition (SVD) model for representation of spatio-temporal fMRI data sets. Statistical inference procedures for PCA, including point and interval estimation will be introduced without the constraint of explicit hypotheses about specific task-dependent effects. The principal eigenvectors capture both the spatial and temporal aspects of fMRI data in a progressive fashion; they are inherently matched to unique and uncorrelated features and are ranked in order of the amount of variance explained. PCA also acts as a variation reduction technique, relegating most of the random noise to the trailing components while collecting systematic structure into the leading ones. Features summarizing variability may not directly be those that are the most useful. Further analysis is facilitated through linear subspace methods involving PC rotation and strategies of projection pursuit utilizing a reduced, lower-dimensional natural basis representation that retains most of the information. These properties will be illustrated in the setting of dynamic time-series response data from fMRI experiments involving pharmacological stimulation of the dopaminergic nigro-striatal system in primates.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine↗

Latency analysis in epidemiologic studies of occupational exposures: application to the Colorado Plateau uranium miners cohort.

BACKGROUND: Latency effects are an important factor in assessing the public health implications of an occupational or environmental exposure. Usually, however, latency results as described in the literature are insufficient to answer public health related questions. Alternative approaches to the analysis of latency effects are warranted. METHODS: A general statistical framework for modeling latency effects is described. We then propose bilinear and exponential decay latency models for analyzing latency effects as they have parameters that address questions of public health interest. Methods are described for fitting these models to cohort or case-control data; statistical inference is based on standard likelihood methods. APPLICATION: A latency analysis of radon exposure and lung cancer in the Colorado Plateau uranium miners cohort was performed. We first analyzed the entire cohort and found that the relative risk associated with exposure increases for about 8.5 years and thereafter decreases until it reaches background levels after about 34 years. The hypothesis that the relative risk remains at its peak level is strongly rejected (P < 0.001). Next, we investigated the variation in the latency effects over subsets of the cohort based on attained age, level and rate of exposure, and smoking. Age was the only factor for which effect modification was demonstrated (P = 0.014). We found that the decline in effect is much steeper at older ages (60+ years) than younger. CONCLUSION: The proposed methods can provide much more information about the exposure-disease latency effects than those generally used.

Air Pollutants, Radioactive↗

Small-sample adjustments in using the sandwich variance estimator in generalized estimating equations.

The generalized estimating equation (GEE) approach is widely used in regression analyses with correlated response data. Under mild conditions, the resulting regression coefficient estimator is consistent and asymptotically normal with its variance being consistently estimated by the so-called sandwich estimator. Statistical inference is thus accomplished by using the asymptotic Wald chi-squared test. However, it has been noted in the literature that for small samples the sandwich estimator may not perform well and may lead to much inflated type I errors for the Wald chi-squared test. Here we propose using an approximate t- or F-test that takes account of the variability of the sandwich estimator. The level of type I error of the proposed t- or F-test is guaranteed to be no larger than that of the Wald chi-squared test. The satisfactory performance of the proposed new tests is confirmed in a simulation study. Our proposal also has some advantages when compared with other new approaches based on direct modifications of the sandwich estimator, including the one that corrects the downward bias of the sandwich estimator. In addition to hypothesis testing, our result has a clear implication on constructing Wald-type confidence intervals or regions.

Adult↗

Proving non-inferiority or equivalence of two treatments with dichotomous endpoints using exact methods.

Since the early work of RA Fisher, exact methods have been recognized as important tools in data analysis because they provide valid statistical inference even with small sample sizes, or with sparse or skewed data. With the recent advance of computational power and the availability of commercial software packages, exact methods have gained substantial popularity over the past two decades. However, most of these exact methods have been devoted to testing classical null hypotheses of no differences, and until recently little was known about exact methods dealing with non-inferiority or equivalence hypotheses. The presence of nuisance parameters in testing non-inferiority/equivalence hypotheses presents a special challenge for exact methods because of the intense computational requirement. In this paper, we review exact methods available for proving non-inferiority or equivalence of two treatments with a dichotomous endpoint. First, we present the general methodology for conducting exact tests for non-inferiority or equivalence; we then discuss several unconditional and conditional methods available for constructing hypothesis tests and confidence intervals based on three commonly used measures, namely, the difference, relative risk, and odds ratio of two independent proportions or rates. Finally, we illustrate with several examples the application of these exact methods in analysing and planning non-inferiority or equivalence trials.

Biomedical Research↗

Analysis of multilocus models of association.

It is increasingly recognized that multiple genetic variants, within the same or different genes, combine to affect liability for many common diseases. Indeed, the variants may interact among themselves and with environmental factors. Thus realistic genetic/statistical models can include an extremely large number of parameters, and it is by no means obvious how to find the variants contributing to liability. For models of multiple candidate genes and their interactions, we prove that statistical inference can be based on controlling the false discovery rate (FDR), which is defined as the expected number of false rejections divided by the number of rejections. Controlling the FDR automatically controls the overall error rate in the special case that all the null hypotheses are true. So do more standard methods such as Bonferroni correction. However, when some null hypotheses are false, the goals of Bonferroni and FDR differ, and FDR will have better power. Model selection procedures, such as forward stepwise regression, are often used to choose important predictors for complex models. By analysis of simulations of such models, we compare a computationally efficient form of forward stepwise regression against the FDR methods. We show that model selection includes numerous genetic variants having no impact on the trait, whereas FDR maintains a false-positive rate very close to the nominal rate. With good control over false positives and better power than Bonferroni, the FDR-based methods we introduce present a viable means of evaluating complex, multivariate genetic models. Naturally, as for any method seeking to explore complex genetic models, the power of the methods is limited by sample size and model complexity.

Chromosome Mapping↗

Quantification of transmission in one-to-one experiments.

We study the statistical inference from data on transmission obtained from one-to-one experiments, and compare two algorithms by which the reproduction ratio can be quantified. The first algorithm, the transient state (TS) algorithm, takes the time course of the epidemic into account. The second algorithm, the final size (FS) algorithm, does not take time into account but is based on the assumption that the epidemic process has ended before the experiment is stopped. The FS algorithm is a limiting case of the TS algorithm for the situation where time tends to infinity. So far quantification of transmission has relied almost exclusively on the FS algorithm, even if the TS algorithm would have been more appropriate. Its practical use, however, is limited to experiments with only a few animals. Here, we quantify the error made when the FS algorithm is applied to data of one-to-one experiments not having reached the final size. We conclude that given the chosen tests, the FS algorithm underestimates the reproduction ratio R0, is liberal when testing H0: R0 > or = 1 against H1: R0 < 1, is conservative when testing H0: R0 < or = 1 against H1: R0 > 1 and calculates the same probability as the TS algorithm when testing H0: R(0-control) = R(0-treatment) against H1: R(0-control) > R(0-treatment) We show how the power of the test depends on the duration of the experiments and on the number of replicates. The methods are illustrated by an application to porcine reproductive and respiratory syndrome virus (PRRSV).

Algorithms↗

Multiple comparison procedures updated.

1. A common statistical flaw in articles submitted to or published in biomedical research journals is to test multiple null hypotheses that originate from the results of a single experiment without correcting for the inflated risk of type 1 error (false positive statistical inference) that results from this. Multiple comparison procedures (MCP) are designed to minimize this risk. The present review focuses on pairwise contrasts, the most common sort of multiple comparisons made by biomedical investigators. 2. In an earlier review a variety of MCP were described and evaluated. It was concluded that an effective MCP should control the risk of family-wise type 1 error, so as to ensure that not more than one hypothesis within a single family is falsely rejected. One-step procedures based on the Bonferroni or Sidák inequalities do this. For continuous data and under normal distribution theory, so does the Tukey-Kramer procedure for all possible pairwise contrasts of means and the Dunnett procedure for all possible pairwise contrasts of means with a control mean. 3. There is now a new class of MCP, based on the Bonferroni or Sidák inequalities but performed in a step-wise fashion. The members of this class have certain desirable properties. They: (i) control the family-wise type 1 error rate as effectively as the one-step procedures; (ii) are more powerful than the one-step Bonferroni or Sidák procedures, especially when hypotheses are logically related; and (iii) can be applied not only to continuous data but also to ordinal or categorical data. 4. Of the new step-wise MCP, Holm's step-down procedures are commended for their combination of accuracy, power and versatility. They also have the virtue of simplicity. Given the raw P values that result from conventional tests of significance, the adjustments for multiple comparisons can be made by hand or hand-held calculator. 5. Despite the corrective abilities of the new step-wise MCP, investigators should try to design their experiments and analyses to test a single, global hypothesis rather than multiple ones.

Analysis of Variance↗