Statistical Analysis of Longitudinal and Multivariate Discrete Data

Correlated multivariate Poisson and binary variables occur naturally in medical, biological and epidemiological longitudinal studies. Modeling and simulating such variables is difficult because the correlations are restricted by the marginal means via Fréchet bounds in a complicated way. In this dissertation we will first discuss partially specified models and methods for estimating the regression and correlation parameters. We derive the asymptotic distributions of these parameter estimates. Using simulations based on extensions of the algorithm due to Sim (1993, Journal of Statistical Computation and Simulation, 47, pp. 1–10), we study the performance of these estimates using infeasibility, coverage probabilities of the confidence ellipsoids, and asymptotic relative efficiencies as the criteria. The second part of this dissertation is devoted to the study of fully specified models constructed using copulas, with special emphasis on the normal copula. Finding the maximum likelihood estimates and the Fisher information matrix for these models requires computation of multivariate normal probabilities. We also discuss several efficient algorithms for calculating multivariate normal integrals. For the multivariate probit and multivariate Poisson log-normal models, we implement maximum likelihood, derive the necessary equations, and illustrate it on two real life data sets. Next we study over and under dispersed models including quasi-multinomial and Lagrange families of distributions. We implement the maximum likelihood method for the quasi-multinomial model and illustrate the application of this model for market analysis of household preferences for saltine crackers

Highly scalable NewSQL database management system CockroachDB

The thesis deals with a NewSQL database called CockroachDB. The aim of the thesis is to describe key concepts used in NewSQL databases and then evaluate and compare performance of the new database CockroachDB and the well-established PostgreSQL database. NewSQL databases are built for distributed environments and integrate the properties of both SQL and NoSQL databases. NewSQL databases use the standard SQL query language for interaction with a database. They use ACID transactions that guarantee high data consistency. They enable easier horizontal scaling, replication, high availability and automatic failover. The results of simple queries showed that CockroachDB achieves on average 5 times lower throughput and 3 times higher latency compared to PostgreSQL on three node cluster. Furthermore, CockroachDB provides only basic support for join operations

Highly scalable NewSQL database management system CockroachDB

The thesis deals with a NewSQL database called CockroachDB. The aim of the thesis is to describe key concepts used in NewSQL databases and then evaluate and compare performance of the new database CockroachDB and the well-established PostgreSQL database. NewSQL databases are built for distributed environments and integrate the properties of both SQL and NoSQL databases. NewSQL databases use the standard SQL query language for interaction with a database. They use ACID transactions that guarantee high data consistency. They enable easier horizontal scaling, replication, high availability and automatic failover. The results of simple queries showed that CockroachDB achieves on average 5 times lower throughput and 3 times higher latency compared to PostgreSQL on three node cluster. Furthermore, CockroachDB provides only basic support for join operations

Knowledge, attitudes and practices towards avian influenza A (H5N1) among Cambodian women: A cross–sectional study

AbstractObjectiveTo measure highly pathogenic avian influenza (HPAI)-related knowledge, attitudes, and practices (KAPs) among Cambodian women.MethodsThis cross-sectional study selected 246 married women aged between 18–55 years who had backyard poultry and lived at least one year in the areas of the survey through multi-stage cluster sampling. An average score of correct answers was generated to evaluate respondents' knowledge (Good/Poor), attitudes (Positive/Negative), and practices (Good/Bad).ResultsWe reported that about half of the respondents had good knowledge and good practices and four-fifth of them had positive attitudes towards HPAI. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated through a logistic regression model to explore contributing factors that raise their KAP levels. Most of the sources were significant in increasing knowledge of the respondent, like television (OR=1.6, 95% CI=1.0–2.7), radio (OR=2.5, 95% CI=1.3–4.9), leaflets/booklets (OR=2.1, 95% CI=1.2–3.9), school students (OR=18.4, 95% CI=2.4–142.9), village health volunteers (OR=4.5, 95% CI=2.2–10.9) etc. Factors such as television (OR=3.7, 95% CI=2.1–6.4), leaflets/booklets (OR=2.6, 95% CI=1.4–5.1), and public health staff (OR=2.2, 95% CI=1.2–4.1) had similar influence on practices. Although, we found similar effect on raising the attitudes of the responded, it was not significant.ConclusionsWe report a satisfactory level of positive attitudes, and moderate level of knowledge and practices related to HPAI among Cambodian women. Raising KAPs through television, radio and other medias may be more efficient than using usual information, education and communication materials to prevent HPAI

The Transcription Factors Snail and Slug Activate the Transforming Growth Factor-Beta Signaling Pathway in Breast Cancer

The transcriptional repressors Snail and Slug are situated at the core of several signaling pathways proposed to mediate epithelial to mesenchymal transition or EMT, which has been implicated in tumor metastasis. EMT involves an alteration from an organized, epithelial cell structure to a mesenchymal, invasive and migratory phenotype. In order to obtain a global view of the impact of Snail and Slug expression, we performed a microarray experiment using the MCF-7 breast cancer cell line, which does not express detectable levels of Snail or Slug. MCF-7 cells were infected with Snail, Slug or control adenovirus, and RNA samples isolated at various time points were analyzed across all transcripts. Our analyses indicated that Snail and Slug regulate many genes in common, but also have distinct sets of gene targets. Gene set enrichment analyses indicated that Snail and Slug directed the transcriptome of MCF-7 cells from a luminal towards a more complex pattern that includes many features of the claudin-low breast cancer signature. Of particular interest, genes involved in the TGF-beta signaling pathway are upregulated, while genes responsible for a differentiated morphology are downregulated following Snail or Slug expression. Further we noticed increased histone acetylation at the promoter region of the transforming growth factor beta-receptor II (TGFBR2) gene following Snail or Slug expression. Inhibition of the TGF-beta signaling pathway using selective small-molecule inhibitors following Snail or Slug addition resulted in decreased cell migration with no impact on the repression of cell junction molecules by Snail and Slug. We propose that there are two regulatory modules embedded within EMT: one that involves repression of cell junction molecules, and the other involving cell migration via TGF-beta and/or other pathways

Evaluation of coagulation activation after Rhinovirus infection in patients with asthma and healthy control subjects: an observational study

Background Asthma exacerbations are frequently triggered by rhinovirus infections. Both asthma and respiratory tract infection can activate haemostasis. Therefore we hypothesized that experimental rhinovirus-16 infection and asthmatic airway inflammation act in synergy on the haemostatic balance. Methods 28 patients (14 patients with mild allergic asthma and 14 healthy non-allergic controls) were infected with low-dose rhinovirus type 16. Venous plasma and bronchoalveolar lavage fluid (BAL fluid) were obtained before and 6 days after infection to evaluate markers of coagulation activation, thrombin-antithrombin complexes, von Willebrand factor, plasmin-antiplasmin complexes, plasminogen activator inhibitor type-1, endogenous thrombin potential and tissue factor-exposing microparticles by fibrin generation test, in plasma and/or BAL fluid. Data were analysed by nonparametric tests (Wilcoxon, Mann Whitney and Spearman correlation). Results 13 patients with mild asthma (6 females, 19-29 y) and 11 healthy controls (10 females, 19-31 y) had a documented Rhinovirus-16 infection. Rhinovirus-16 challenge resulted in a shortening of the fibrin generation test in BAL fluid of asthma patients (t = -1: 706 s vs. t = 6: 498 s; p = 0.02), but not of controls (t = -1: 693 s vs. t = 6: 636 s; p = 0.65). The fold change in tissue factor-exposing microparticles in BAL fluid inversely correlated with the fold changes in eosinophil cationic protein and myeloperoxidase in BAL fluid after virus infection (r = -0.517 and -0.528 resp., both p = 0.01). Rhinovirus-16 challenge led to increased plasminogen activator inhibitor type-1 levels in plasma in patients with asthma (26.0 ng/mL vs. 11.5 ng/mL in healthy controls, p = 0.04). Rhinovirus-16 load in BAL showed a linear correlation with the fold change in endogenous thrombin potential, plasmin-antiplasmin complexes and plasminogen activator inhibitor type-1. Conclusions Experimental rhinovirus infection induces procoagulant changes in the airways of patients with asthma through increased activity of tissue factor-exposing microparticles. These microparticle-associated procoagulant changes are associated with both neutrophilic and eosinophilic inflammation. Systemic activation of haemostasis increases with Rhinoviral load