A BAYESIAN APPROACH TO DOSE-RESPONSE ASSESSMENT AND DRUG-DRUG INTERACTION ANALYSIS: APPLICATION TO IN VITRO STUDIES

The considerable search for synergistic agents in cancer research is motivated by the therapeutic benefits achieved by combining anti-cancer agents. Synergistic agents make it possible to reduce dosage while maintaining or enhancing a desired effect. Other favorable outcomes of synergistic agents include reduction in toxicity and minimizing or delaying drug resistance. Dose-response assessment and drug-drug interaction analysis play an important part in the drug discovery process, however analysis are often poorly done. This dissertation is an effort to notably improve dose-response assessment and drug-drug interaction analysis. The most commonly used method in published analysis is the Median-Effect Principle/Combination Index method (Chou and Talalay, 1984). The Median-Effect Principle/Combination Index method leads to inefficiency by ignoring important sources of variation inherent in dose-response data and discarding data points that do not fit the Median-Effect Principle. Previous work has shown that the conventional method yields a high rate of false positives (Boik, Boik, Newman, 2008; Hennessey, Rosner, Bast, Chen, 2010) and, in some cases, low power to detect synergy. There is a great need for improving the current methodology. We developed a Bayesian framework for dose-response modeling and drug-drug interaction analysis. First, we developed a hierarchical meta-regression dose-response model that accounts for various sources of variation and uncertainty and allows one to incorporate knowledge from prior studies into the current analysis, thus offering a more efficient and reliable inference. Second, in the case that parametric dose-response models do not fit the data, we developed a practical and flexible nonparametric regression method for meta-analysis of independently repeated dose-response experiments. Third, and lastly, we developed a method, based on Loewe additivity that allows one to quantitatively assess interaction between two agents combined at a fixed dose ratio. The proposed method makes a comprehensive and honest account of uncertainty within drug interaction assessment. Extensive simulation studies show that the novel methodology improves the screening process of effective/synergistic agents and reduces the incidence of type I error. We consider an ovarian cancer cell line study that investigates the combined effect of DNA methylation inhibitors and histone deacetylation inhibitors in human ovarian cancer cell lines. The hypothesis is that the combination of DNA methylation inhibitors and histone deacetylation inhibitors will enhance antiproliferative activity in human ovarian cancer cell lines compared to treatment with each inhibitor alone. By applying the proposed Bayesian methodology, in vitro synergy was declared for DNA methylation inhibitor, 5-AZA-2'-deoxycytidine combined with one histone deacetylation inhibitor, suberoylanilide hydroxamic acid or trichostatin A in the cell lines HEY and SKOV3. This suggests potential new epigenetic therapies in cell growth inhibition of ovarian cancer cells.

Genome-wide gene-gene interaction analysis for cardiovascular disease

Numerous studies have been carried out to try to better understand the genetic predisposition for cardiovascular disease. Although it is widely believed that multifactorial diseases such as cardiovascular disease is the result from effects of many genes which working alone or interact with other genes, most genetic studies have been focused on identifying of cardiovascular disease susceptibility genes and usually ignore the effects of gene-gene interactions in the analysis. The current study applies a novel linkage disequilibrium based statistic for testing interactions between two linked loci using data from a genome-wide study of cardiovascular disease. A total of 53,394 single nucleotide polymorphisms (SNPs) are tested for pair-wise interactions, and 8,644 interactions are found to be significant with p-values less than 3.5×10-11. Results indicate that known cardiovascular disease susceptibility genes tend not to have many significantly interactions. One SNP in the CACNG1 (calcium channel, voltage-dependent, gamma subunit 1) gene and one SNP in the IL3RA (interleukin 3 receptor, alpha) gene are found to have the most significant pair-wise interactions. Findings from the current study should be replicated in other independent cohort to eliminate potential false positive results.^

The Use of Podcasts in Education

Background: The use of podcasts has emerged as an important tool for use in education. This is especially relevant in nursing schools with the shortage of nursing faculty. The use of podcasts allows the instructor to provide lectures and other course content to students. [See PDF for complete abstract]

Environmental, health and safety cost benefit analysis in the United States chemical industry

The purpose of this research project is to determine whether there is a cost/benefit to allocating financial and other company-related resources to improve environmental, health and safety performance beyond that which is required by law. The issue of whether a company benefits from spending dollars to achieve environmental, health and safety performance beyond legal compliance is an important issue to the chemical manufacturing industry in the United States because of the voluminous and complex legal requirements impacting environmental, health and safety expenditures. The cost/benefit issue has practical significance because many U.S. chemical manufacturing companies base their environmental, health and safety management strategies on just achieving and maintaining compliance with legal requirements when in reality this strategy may actually be a higher cost way of managing environmental, health and safety practices. This difference in environmental, health and safety management strategy is being investigated to determine if managing environmental, health and safety to achieve performance beyond that which is required by law results in a greater benefit to companies in the U.S. chemical manufacturing sector.

CYTOGENETIC AND DNA CONTENT ANALYSIS IN MULTIPLE MYELOMA

In this dissertation, the cytogenetic characteristics of bone marrow cells from 41 multiple myeloma patients were investigated. These cytogenetic data were correlated with the total DNA content as measured by flow cytometry. Both the cytogenetic information and DNA content were then correlated with clinical data to determine if diagnosis and prognosis of multiple myeloma could be improved.^ One hundred percent of the patients demonstrated abnormal chromosome numbers per metaphase. The average chromosome number per metaphase ranged from 42 to 49.9, with a mean of 44.99. The percent hypodiploidy ranged from 0-100% and the percent hyperdiploidy from 0-53%. Detailed cytogenetic analyses were very difficult to perform because of the paucity of mitotic figures and the poor chromosome morphology. Thus, detailed chromosome banding analysis on these patients was impossible.^ Thirty seven percent of the patients had normal total DNA content, whereas 63% had abnormal amounts of DNA (one patient with less than normal amounts and 25 patients with greater than normal amounts of DNA).^ Several clinical parameters were used in the statistical analyses: tumor burden, patient status at biopsy, patient response status, past therapy, type of treatment and percent plasma cells. Only among these clinical parameters were any statistically significant correlations found: pretreatment tumor burden versus patient response, patient biopsy status versus patient response and past therapy versus patient response.^ No correlations were found between percent hypodiploid, diploid, hyperdiploid or DNA content, and the patient response status, nor were any found between those patients with: (a) normal plasma cells, low pretreatment tumor mass burden and more than 50% of the analyzed metaphases with 46 chromosomes; (b) normal amounts of DNA, low pretreatment tumor mass burden and more than 50% of the metaphases with 46 chromosomes; (c) normal amounts of DNA and normal quantities of plasma cells; (d) abnormal amounts of DNA, abnormal amounts of plasma cells, high pretreatment tumor mass burden and less than 50% of the metaphases with 46 chromosomes.^ Technical drawbacks of both cytogenetic and DNA content analysis in these multiple myeloma patients are discussed along with the lack of correlations between DNA content and chromosome number. Refined chromosome banding analysis awaits technical improvements before we can understand which chromosome material (if any) makes up the "extra" amounts of DNA in these patients. None of the correlations tested can be used as diagnostic or prognostic aids for multiple myeloma. ^

Traditional linkage analysis in admixed families

Currently there is no general method to study the impact of population admixture within families on the assumptions of random mating and consequently, Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE) and on the inference obtained from traditional linkage analysis. ^ First, through simulation, the effect of admixture of two populations on the log of the odds (LOD) score was assessed, using Prostate Cancer as the typical disease model. Comparisons between simulated mixed and homogeneous families were performed. LOD scores under both models of admixture (within families and within a data set of homogeneous families) were closest to the homogeneous family scores of the population having the highest mixing proportion. Random sampling of families or ascertainment of families with disease affection status did not affect this observation, nor did the mode of inheritance (dominant/recessive) or sample size. ^ Second, after establishing the effect of admixture on the LOD score and inference for linkage, the presence of induced disequilibria by population admixture within families was studied and an adjustment procedure was developed. The adjustment did not force all disequilibria to disappear but because the families were adjusted for the population admixture, those replicates where the disequilibria exist are no longer affected by the disequilibria in terms of maximization for linkage. Furthermore, the adjustment was able to exclude uninformative families or families that had such a high departure from HWE and/or LE that their LOD scores were not reliable. ^ Together these observations imply that the presence of families of mixed population ancestry impacts linkage analysis in terms of the LOD score and the estimate of the recombination fraction. ^

Household health assessment and associated water sample analysis in the Miches watershed of the Dominican Republic

Background. Diarrhea and malnutrition are the leading causes of mortality for children age one to four in the Dominican Republic. Communities within the Miches watershed lack sanitation infrastructure and water purification systems, which increases the risk of exposure to water-borne pathogens. The purpose of this cross-sectional study was to analyze health information gathered through household interviews and to test water samples for the presence of diarrheagenic pathogens and antibiotic-resistant bacteria within the Miches watershed. Methods. Frequency counts and thematic analysis were used to investigate Human Health Survey responses and Fisher's exact test was used to determine correlation between water source and reported illness. Bacteria cultured from water samples were analyzed by Gram stain, real-time PCR, API® 20E biochemical identification, and for antibiotic resistance. Results. Community members reported concerns about water sources with respect to water quality, availability, and environmental contamination. Pathogenic strains of E. coli were present in the water samples. Drinking aquifer water was positively-correlated with reported stomach aches (p=0.04) while drinking from rivers or creeks was associated with the reported absence of “gripe” (cold or flu) (p=0.01). The lack of association between reported illnesses and water source for the majority of variables suggested that there were multiple vehicles of disease transmission. Antibiotic resistant bacteria were isolated from the water samples tested. Conclusions. The presence of pathogenic E. coli in water samples suggested that water is at least one route of transmission for diarrheagenic pathogens in the Miches watershed. The presence of antibiotic-resistant bacteria in the water samples may indicate the proliferation of resistance plasmids in the environment as a result of antibiotic overuse in human and animal populations and a lack of sanitation infrastructure. An intervention that targets areas of hygiene, sanitation, and water purification is recommended to limit human exposure to diarrheagenic pathogens and antibiotic-resistant organisms. ^

A new combined endpoint using U-statistic in analysis in clinical trials

Common endpoints can be divided into two categories. One is dichotomous endpoints which take only fixed values (most of the time two values). The other is continuous endpoints which can be any real number between two specified values. Choices of primary endpoints are critical in clinical trials. If we only use dichotomous endpoints, the power could be underestimated. If only continuous endpoints are chosen, we may not obtain expected sample size due to occurrence of some significant clinical events. Combined endpoints are used in clinical trials to give additional power. However, current combined endpoints or composite endpoints in cardiovascular disease clinical trials or most clinical trials are endpoints that combine either dichotomous endpoints (total mortality + total hospitalization), or continuous endpoints (risk score). Our present work applied U-statistic to combine one dichotomous endpoint and one continuous endpoint, which has three different assessments and to calculate the sample size and test the hypothesis to see if there is any treatment effect. It is especially useful when some patients cannot provide the most precise measurement due to medical contraindication or some personal reasons. Results show that this method has greater power then the analysis using continuous endpoints alone. ^

A review of economic analysis in the vaccination program; decision making and governance: Adivisory Committee on Immunization Practices (ACIP)

The Advisory Committee on Immunization Practices (ACIP) develops written recommendations for the routine administration of vaccines to children and adults in the U.S. civilian population. The ACIP is the only entity in the federal government that makes such recommendations. ACIP elaborates on selection of its members and rules out concerns regarding its integrity, but fails to provide information about the importance of economic analysis in vaccine selection. ACIP recommendations can have large health and economic consequences. Emphasis on economic evaluation in health is a likely response to severe pressures of the federal and state health budget. This study describes the economic aspects considered by the ACIP while sanctioning a vaccine, and reviews the economic evaluations (our economic data) provided for vaccine deliberations. A five year study period from 2004 to 2009 is adopted. Publicly available data from ACIP web database is used. Drummond et al. (2005) checklist serves as a guide to assess the quality of economic evaluations presented. Drummond et al.'s checklist is a comprehensive hence it is unrealistic to expect every ACIP deliberation to meet all of their criteria. For practical purposes we have selected seven criteria that we judge to be significant criteria provided by Drummond et al. Twenty-four data points were obtained in a five year period. Our results show that out of the total twenty-four data point‘s (economic evaluations) only five data points received a score of six; that is six items on the list of seven were met. None of the data points received a perfect score of seven. Seven of the twenty-four data points received a score of five. A minimum of a two score was received by only one of the economic analyses. The type of economic evaluation along with the model criteria and ICER/QALY criteria met at 0.875 (87.5%). These three criteria were met at the highest rate among the seven criteria studied. Our study findings demonstrate that the perspective criteria met at 0.583 (58.3%) followed by source and sensitivity analysis criteria both tied at 0.541 (54.1%). The discount factor was met at 0.250 (25.0%).^ Economic analysis is not a novel concept to the ACIP. It has been practiced and presented at these meetings on a regular basis for more than five years. ACIP‘s stated goal is to utilize good quality epidemiologic, clinical and economic analyses to help policy makers choose among alternatives presented and thus achieve a better informed decision. As seen in our study the economic analyses over the years are inconsistent. The large variability coupled with lack of a standardized format may compromise the utility of the economic information for decision-making. While making recommendations, the ACIP takes into account all available information about a vaccine. Thus it is vital that standardized high quality economic information is provided at the ACIP meetings. Our study may provide a call for the ACIP to further investigate deficiencies within the system and thereby to improve economic evaluation data presented. ^

Performance tiers: Implementing comparative effectiveness analysis in the health care setting through operations research and spatial methods

This dissertation develops and tests a comparative effectiveness methodology utilizing a novel approach to the application of Data Envelopment Analysis (DEA) in health studies. The concept of performance tiers (PerT) is introduced as terminology to express a relative risk class for individuals within a peer group and the PerT calculation is implemented with operations research (DEA) and spatial algorithms. The analysis results in the discrimination of the individual data observations into a relative risk classification by the DEA-PerT methodology. The performance of two distance measures, kNN (k-nearest neighbor) and Mahalanobis, was subsequently tested to classify new entrants into the appropriate tier. The methods were applied to subject data for the 14 year old cohort in the Project HeartBeat! study.^ The concepts presented herein represent a paradigm shift in the potential for public health applications to identify and respond to individual health status. The resultant classification scheme provides descriptive, and potentially prescriptive, guidance to assess and implement treatments and strategies to improve the delivery and performance of health systems. ^

The Relationship of Provincial Economic Level and Child Injury Mortality in Thailand: A Cross-Sectional Analysis in a Middle Income Country

The objective of this cross-sectional study was to examine the relationship of provincial economic development indices with incidences of child injury mortality in Thailand from 1999 - 2001. All injury deaths among children age 1-14 years were included. The independent variables included gross provincial product per capita (GPP/c), poverty and inequality indices, material and social deprivation indices, population in rural/ urban areas, and migration. Due to multicollinearity of such variables, the 76 provinces were categorized by GPP/c quartile, and means of overall injury, drowning, and transport-related mortality rates were compared among quartile groups. Spearman’s rho correlation between GPP/c and injury mortality rates was also performed. Finally, factor analysis was employed to create a set of factors to be treated as uncorrelated variables and stepwise multiple regression was carried out for the effects of the factors on injury mortality rates. A significant direct relationship was observed between GPP/c and overall injury mortality among children age 1-4 years, and 10-14 year-olds of both genders. Drowning was the main cause of this relationship among children age 1-4 years, and transport-related injury was the principle cause among children age 10-14 years. Conversely, provinces with lower GPP/c experienced higher injury mortality rates among school-age children 5-9 years old for both genders, mostly due to drowning. Factor analysis, and multiple regression results confirmed the relationships between economic development and injury mortality rates. These findings revealed that economic development had an adverse impact on injury-related mortality among children 1 to 4 and 10 to14 in Thailand.