An ordinal logistic regression model with misclassification of the outcome variable and categorical covariate

Ordinal outcomes are frequently employed in diagnosis and clinical trials. Clinical trials of Alzheimer's disease (AD) treatments are a case in point using the status of mild, moderate or severe disease as outcome measures. As in many other outcome oriented studies, the disease status may be misclassified. This study estimates the extent of misclassification in an ordinal outcome such as disease status. Also, this study estimates the extent of misclassification of a predictor variable such as genotype status. An ordinal logistic regression model is commonly used to model the relationship between disease status, the effect of treatment, and other predictive factors. A simulation study was done. First, data based on a set of hypothetical parameters and hypothetical rates of misclassification was created. Next, the maximum likelihood method was employed to generate likelihood equations accounting for misclassification. The Nelder-Mead Simplex method was used to solve for the misclassification and model parameters. Finally, this method was applied to an AD dataset to detect the amount of misclassification present. The estimates of the ordinal regression model parameters were close to the hypothetical parameters. β1 was hypothesized at 0.50 and the mean estimate was 0.488, β2 was hypothesized at 0.04 and the mean of the estimates was 0.04. Although the estimates for the rates of misclassification of X1 were not as close as β1 and β2, they validate this method. X 1 0-1 misclassification was hypothesized as 2.98% and the mean of the simulated estimates was 1.54% and, in the best case, the misclassification of k from high to medium was hypothesized at 4.87% and had a sample mean of 3.62%. In the AD dataset, the estimate for the odds ratio of X 1 of having both copies of the APOE 4 allele changed from an estimate of 1.377 to an estimate 1.418, demonstrating that the estimates of the odds ratio changed when the analysis includes adjustment for misclassification. ^

An Emerging Technology: To Model Patient Education for the Dental Hygiene Student

Introduction: Could Livestream Video, an emerging audiovisual media, be used more effectively than the traditional demonstration method of teaching or modeling dental hygiene students on how to provide chairside patient education? [See PDF for complete abstract]

Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.

In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations.

Antitumor activity of an Ets protein, PEA3, in breast cancer cell lines MDA-MB-361DYT2 and BT474M1

Polyomavirus enhancer activator 3 (PEA3) is a member of the Ets family of transcription factors. We demonstrated in a previous study that, through down-regulating the HER-2/neu oncogene at the transcriptional level, PEA3 can inhibit the growth and tumor development of HER-2/neu-overexpressing ovarian cancer cells. Here, we established stable clones of the human breast cancer cell line MDA-MB-361DYT2 that express PEA3 under the control of a tetracycline-inducible promoter. The expression of PEA3 in this cell line inhibited cell growth and resulted in cell cycle delay in the G1 phase independently of the HER-2/neu down-regulation. In an orthotopic breast cancer model, we showed that expression of PEA3 inhibited tumor growth and prolonged the survival of tumor-bearing mice. In a parallel experiment in another breast cancer cell line, BT474M1, we were unable to obtain stable PEA3-inducible transfectants, which suggests that PEA3 possessed a strong growth inhibitory effect in this cell line. Indeed, PEA3 coupled with the liposome SN2 demonstrated therapeutic effects in mice bearing tumors induced by BT474M1. These results provide evidence that the PEA3 gene could function as an antitumor and gene therapy agent for human breast cancers. ^

Chimpanzee: A predictive model for the human cytochrome P450 3A subfamily

The human cytochrome P450 3A (CYP3A) subfamily is responsible for most of the metabolism of therapeutic drugs; however, an adequate in vivo model has yet to be discovered. This study begins with an investigation of a controversial topic surrounding the human CYP3As--estrogen regulation. A novel approach to this topic was used by defining expression in the estrogen-responsive endometrium. This study shows that estrogen down-regulates CYP3A4 expression in the endometrium. On the other hand, analogous studies showed an increase in CYP3A expression as age increases in liver tissue. Following the discussion of estrogen regulation, is an investigation of the cross-species relationships among all of the CYP3As was completed. The study compares isoforms from piscines, avians, rodents, canines, ovines, bovines, and primates. Using the traditional phylogenetic analyses and employing a novel approach using exon and intron lengths, the results show that only another primate could be the best animal model for analysis of the regulation of the expression of the human CYP3As. This analysis also demonstrated that the chimpanzee seems to be the best available human model. Moreover, the study showed the presence and similarities of one additional isoform in the chimpanzee genome that is absent in humans. Based on these results, initial characterization of the chimpanzee CYP3A subfamily was begun. While the human genome contains four isoforms--CYP3A4, CYP3A5, CYP3A7, and CYP3A43--the chimpanzee genome has five, the four previously mentioned and CYP3A67. Both species express CYP3A4, CYP3A5, and CYP3A43, but humans express CYP3A7 while chimpanzees express CYP3A67. In humans, CYP3A4 is expressed at higher levels than the other isoforms, but some chimpanzee individuals express CYP3A67 at higher levels than CYP3A4. Such a difference is expected to alter significantly the total CYP3A metabolism. On the other hand, any study considering individual isoforms would still constitute a valid method of study for the human CYP3A4, CYP3A5, and CYP3A43 isoforms. ^

Effect of a lifestyle physical activity intervention on transtheoretical model variables

Purpose. To determine the effect a stage-based, lifestyle physical activity intervention has on Transtheoretical Model variables in a population of breast cancer survivors. ^ Methods. Sedentary breast cancer survivors (N=60) were randomized to either a standard care study condition or to a 6-month, 21-session intervention. The Transtheoretical Model variables stage of change, self-efficacy, decisional balance (pros and cons to exercise), and processes of change were measured at baseline, 3 months, and 6 months. ^ Results. Women in the lifestyle group had significantly higher self-efficacy than women in the standard care group (F=9.55, p=0.003). Although there was not a significant difference between the two groups for perceived pros of exercise, there was a significant difference between the groups for perceived cons of exercise. Women in the lifestyle group perceived significantly fewer cons of exercise at both 3 and 6 months compared with women in the standard care condition (F=5.416, p=0.025). Between baseline and the 6 month assessment, the intervention also had an effect on three of the processes of change, while seven of the processes were not significantly affected by the intervention. ^ Conclusions. Data from the pilot study suggest that a stage-based, lifestyle physical activity intervention has an effect on Transtheoretical Model variables, which have been shown to facilitate exercise adoption, and should be tested in a larger trial. ^