RNA-Sequencing (RNA-Seq) has rapidly become the de facto technique in transcriptome studies. However, established statistical methods for analyzing experimental and observational microarray studies need to be revised or completely re-invented to accommodate RNA-Seq data's unique characteristics. In this dissertation, we focus on statistical analyses performed at two particular stages in...
RNA-Sequencing (RNA-Seq) has been widely adopted for quantifying gene expression changes in comparative transcriptome analysis. For detecting differentially expressed genes, a variety of statistical methods based on the negative binomial (NB) distribution have been proposed. These methods differ in the ways they handle the NB nuisance parameters (i.e., the dispersion...
An intersection, due to its vehicle and pedestrian conflict movements, experiences complex traffic situations that might contribute to crashes. In the city of Corvallis, OR, historically more than 80% of the total crashes have occurred within an intersection or have been designated as intersection-related. It is important to develop a...
The objective of this thesis is to design a high speed digital FIR filter. The inputs of the
system come from a Delta-Sigma modulator. This FIR filter takes 1024 inputs,
multiplies them with their coefficients and adds the results. The main design task is to
take the input data, which...
This dissertation describes the development of a mechanistic
overlay design procedure. The mechanistic analysis represents a new
trend in both new pavement and overlay design. The greatest advantage
of the mechanistic pavement analysis is that it considers the
fundamental characteristics of materials to be used, is capable of
considering changes...
Full integration of CMOS low noise amplifiers (LNA) presents a challenge for low
cost CMOS receiver systems. A critical problem faced in the design of an RF CMOS LNA
is the inaccurate high-frequency noise model of the MOSFET implemented in circuit
simulators such as SPICE. Silicon-based monolithic inductors are another...
On June 20, 2017, members of the environmental engineering and science (EES) community convened at the Association of Environmental Engineering and Science Professors (AEESP) Biennial Conference for a workshop on antimicrobial resistance. With over 80 registered participants, discussion groups focused on the following topics: risk assessment, monitoring, wastewater treatment, agricultural...
We investigated DNA methylomes of pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large intercompartmental backbones. The deviations were exaggerated in lamina-associated...
Drosophila suzukii (Spotted Wing Drosophila) has recently become a serious invasive pest of fruit crops in the USA, Canada, and Europe, leading to substantial economic losses. D. suzukii is a direct pest, ovipositing directly into ripe or ripening fruits; in contrast, other Drosophilids utilize decaying or blemished fruits and are...