Differential expression (DE) analysis is a key task in gene expression study, because it uncovers the association between expression levels of a gene and the covariates of interest. This dissertation pertains to two particular aspects of DE analysis—identifying stably expressed genes for count normalization and accounting for correlation between DE...
Differential expression (DE) analysis allows us to identify genes that respond differently under varying experimental conditions, therefore granting us an understanding of the molecular basis of phenotypic variation. Following the identification of significantly differentially expressed genes, it is often of the researcher's interest to elucidate hidden patterns or groups in...
In some cases a canopy height model (CHM) is the only available source of forest height information. For these cases it is important to understand the predictive power of CHM data for forest attributes. In this study we examined the use of lidar-derived CHM metrics to predict forest structure classes...
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...
For the first time we report the results of a survey to determine the presence, seasonal phenology and biological control status of indigenous parasitoid populations utilizing Drosophila suzukii (Matsumura) and Drosophila melanogaster Meigen (Diptera Drosophilidae) as hosts in Trento Province, Northern Italy, and the Willamette Valley, Oregon, USA. Larval and...
Thermal decomposition of several di-p-toluenesulfonylhydrazones
was studied. It was found that the carbene decomposition
of tetramethyl-1,3-cyclobutanedione, di-p-toluenesulfonylhydrazone
gave two products resulting from
rearrangement. One was identified as 2,5-dimethyl-1,3,4-hexatriene. A tentative structure for the second was
proposed. During the course of the study, a more convenient
procedure for thermal decompositions was...
Human operator performance was evaluated using two
types of displays in a simulated ocean surveillance task.
The two types of displays studied included a display in
which position uncertainty information was given (polygon
display) and a display in which uncertainty was not
explicitly shown (line display). The experimental task
was...
In order to synthesize polyethylene by the microreactor with a catalyst, this thesis prepares the chemical coating layers for the reactor channel. There are two layers in the channel: the Phillips catalysts and an antimony-doped tin oxide layer on glass substrate. The Phillips catalyst help to synthesize polyethylene in the...
Green sea turtles, Chelonia mydas, have endangered and threatened populations globally, but several populations show signs of population recovery. In Hawaii, nesting female green turtles have increased 5.7% year⁻¹ since 1973, but wide fluctuations in census counts of nesting females make recovery diagnosis difficult. For effective management planning, it is...
Understanding sandbar dynamics and variability is integral to developing a predictive
capacity for nearshore flows, sediment transport, morphological change, and
ultimately for determining coastline exposure to damaging storm waves. Along the
high-energy U.S. Pacific Northwest (PNW) coast, sandbars typically dominate the
bathymetry of the active zone. Here we report on...
The Red Dog Mine transports concentrated zinc and lead ore in northwestern Alaska through Cape Krusenstern National monument along a haul road. High metal levels in the moss Hylocomium splendens along the haul road have been attributed to ore dust released during transport. The mine has implemented several pollution abatement...
Easter Island and Sala y Gomez are part of the Sala y Gomez
Ridge, a broad band of high topography and scattered seamounts
extending ESE from the East Pacific Rise. It has been proposed that
the Sala y Gomez Ridge results from the movement of the Nazca Plate
over a...
Projects have a life cycle, and termination of a project by a firm from the market is considered to be a part of the project life cycle. Project needs to be terminated when the project has failed or at the point when the company is expecting the project to fail....
Coastal sand dunes and beaches offer a variety of ecosystem services such as coastal protection, sand stabilization, species conservation, and recreation. However, the management and balance of ecosystem services offered by dunes and beaches is challenging when ecosystem services interact across the landscape. Management focusing only on one ecosystem service...
The commercial groundfish fishing industry and groundfish research have a long concurrent history of activity on the Oregon continental margin. Within the non-whiting groundfish fishery, the target species are primarily flatfishes, sablefish, lingcod, and rockfishes, though landings of each have fluctuated over time. Recent work shows that over the past...
This research focused on population dynamics of two gelatinous zooplankters (Aequorea & Pyrosoma atlanticum) in the northern California Current to assess their relationship to environmental conditions and role in the pelagic ecosystem. Data collected since 1999 showed seasonal and interannual fluctuations in the abundance and distribution of Aequorea in the...
As the effect of ocean acidification (OA) on marine calcifiers is better understood, a range of potential mitigative strategies have been proposed, many of which are plagued by concerns of scale and feasibility. One oft-cited option is to increase the biomass of photosynthetic organisms to remove CO₂ from the water...
Small-scale fisheries around the world are increasingly facing pressures from a range of environmental, economic, and social sources. In order to sustain the societal benefits of small-scale fisheries, it is imperative to understand how fishing communities adapt to disturbances. Fishermen often catch multiple different species as an adaptation technique because...
Biological invasions and climate change represent two preeminent threats to ecological communities and biodiversity, altering the distribution and abundance of species, disrupting existing species interactions and forming unprecedented ones, and creating novel ecological communities. Many of the most successful invasive species are also ecosystem engineers, species that physically modify the...
The absorption, translocation and metabolism of a new
herbicide, n-propyl-C¹⁴ N, N-di-n-propyl-thiolcarbamate (PDPC), were
studied in both peanut and soybean plants. These studies were
carried out on plants of different ages and treated at two rates of
application. The residue content of the plants was also determined
from germination to...
The metabolism of ¹⁴C-labeled ethyl -N, N-di-n- propylthiolcarbamate
(EPTC- ¹⁴C) was studied in adult female rats. Single
oral doses of EPTC-¹⁴C ranging from 0. 6 to 100. 6 mg were given
and the elimination pattern of ¹⁴C was determined.
Results of 18 experiments showed that increasing the doses
of EPTC-...
A line of four garments was designed and developed using the various stages of the design process, based on the idea of translating music into fashion, the intangible into the tangible. The line was inspired by Tchaikovsky’s Symphony No. 4 in F Minor, guided by the composer’s music and symphonic...
This publication is an extended revision of the previous edition. It describes how to grow tomatoes and tomatillos in the home garden. Topics include site and soil preparation, cultivar selection, propagation, planting and plant care, techniques for extending the growing season, pruning and training systems, and harvest and storage.
The development of hybrids with enhanced expression of heterosis depends on the genetic background of the source population and the effectiveness of a breeding scheme used to identify and use divergent inbred lines with good combining ability. The present study was conducted to examine the potential of improved tropical reciprocal...
Is it possible to determine whether a signal violates a formula in Signal Temporal Logic (STL), if the monitor only has access to a low-resolution version of the signal? We answer this question affirmatively by demonstrating that temporal logic has a multiresolution structure, which parallels the multiresolution structure of signals....
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...
This thesis is the combination of two research publications working toward a unified strategy in which the design of complex engineered systems can be completed using a multiagent coordination approach. Current engineered system modeling techniques segment large complex models into multiple groups to be simulated independently. These methods restrict the...
In this report, three studies are presented that utilize computations to predict transformations, identities, and properties of environmental organic molecules. Each study shows how computations can lead to models of chemical behavior. The importance of this research is rooted in the need for understanding how human behavior and health intersect...
Understanding sandbar dynamics and variability is integral to developing a predictive capacity for nearshore flows, sediment transport, morphological change, and ultimately for determining coastline exposure to damaging storm waves. Here we report on a nearshore bathymetric data set from the U.S. Pacific Northwest (PNW) that stretches from Point Grenville, Washington...
Vitamin K₅, 4-amino-2-methyl-1-naphthol hydrochloride, a
water soluble analog of vitamin K has been shown to possess an antimicrobial
activity toward many bacteria, molds, and yeast. Much
of the work reported in the literature is on its use as a food preservative,
and it was the purpose of this study to...
Vibrio marinus, strain MP-1, was shown to grow from pH 6.7
to 8.5, with an optimum at 7.3. Growth was inhibited below salinity
10%₀ and above 60%₀ . The upper temperature limit of
growth was 20 C, and growth was very rapid with aeration at 15 C.
Heating of the...
Compounds belonging to the vitamin K family possess anti-hemorrhagic
property, and are used in treating patients suffering
from hypoprothrombinemia and obstructive jaundice. Some of
these compounds also exhibit marked antimicrobial activity toward
various microorganisms. Vitamin K₅, 4-amino-2-methyl-
1-naphthol hydrochloride, a water-soluble analog of vitamin K
has been shown to possess...
This work presents a new energy saving technique for modern digital designs. We propose Time Interleaved Multi-Rail (TIMR) - a method for providing two dynamic supply rails to a circuit. This technique uses the first supply rail to mask the transition delay while changing the voltage of the second rail....
Many different strains of yeast have been isolated from the natural
microflora on fruits. It has been known for some time that these
strains of yeast have distinct fermentation characteristics and, when
used in the production of wine, impart these characteristics to the
wine. These characteristics may be evidenced in...
As modern systems continue to increase in size and complexity, they pose significant safety and risk management challenges. System engineers and much of the government research efforts are focused on understanding the attributes and characteristics that emerge from the interactions of components and subsystems. As a result, the objective of...
While many organizations claim to "put safety first," safety is rarely considered early in the design process when system-level architectural decisions are made. Instead, system design follows an abstraction-to-detail process to first meet functional and then performance requirements. Following this process, safety assurance occurs in the later stages of design...
It has long been recognized that fermented food products possess a characteristic but pleasant flavor. The use of such foods, however, has been limited by the presence of ethanol. Thus the objective of this research was to investigate the possibility of producing non-alcoholic fermented juice concentrates. Three varieties of juices,...
Cell populations of the marine bacterium ANT-300, from
either batch culture or continuous culture with dilution
rates ranging from D = 0.170 h⁻¹ (fast) to D = 0.015 h⁻¹ (slow) were monitored for 98 days under starvation.
Viability (CFU), acridine orange direct counts (AODC), and
optical density were measured. DNA,...
Since the 1960s, Vietnamese scholars have written autobiographical literature catered to the American public though they have not gotten as much recognition as soldier accounts and anti-war literature. These Vietnamese literatures shifted in scope and form with the succeeding waves of refugee resulted from the war in Việt Nam. As...
Complex engineered systems design is a collaborative activity. To design a system, experts from the relevant disciplines must work together to create the best overall system from their individual components. This situation is analogous to a multiagent system in which agents solve individual parts of a larger problem. Current multiagent...
The effects of various physical parameters on the binding, uptake,
and catabolism of glucose in the marine psychrophilic bacterium,
Vibrio marinus, were studied. It was shown that shortly after
the cell was exposed to labeled glucose, the radioactive label became
rapidly associated with the cell fraction. It was also shown...
A gap exists in the methods used in industry and available in academia that prevents customers and engineers from having a voice when considering engineering risk appetite in the dynamic shaping of early-phase conceptual design trade study outcomes. Current methods used in Collaborative Design Centers either collect risk information after...
The metabolic fate of cholesterol delivered to rat hepatocytes by rat plasma lipoproteins was determined. Binding and degradation of rat low and high density lipoproteins (LDL and HDL) in rat hepatocytes were studied. ¹²⁵I-labelled LDL and HDL were incubated with cells in the presence of varying concentrations of unlabelled lipoproteins...
In cases where complex systems routinely experience extreme operating conditions, preventative maintenance is often employed to guard against system failure. Yet, with accessible real-time data and the standard practice becoming prohibitively expensive, the test stand can serve as a vital contributor to the development of system health and reliability estimations....
My work has focused on investigating synthetic organic reactions using applied computational methods. Non-covalent interactions are critical to catalysis, mechanism, and stereoselectivity, with the most prominent interaction for isothioureas being the S···O contact between the catalyst sulfur atom and the oxygen of the acyl group. A comprehensive joint experimental and...
Complex organic transformations, such as the addition of pyrrole to ketene using planar chiral organocatalyst (*PPY), the four-component anhydride- Manniach reactions, and the site-selective desymmetrization of meso-1,2-diol, are remarkable synthetic reactions that provide high yield and high selectivity. However, the exact mechanism and origins of stereocontrol for theses synthetic organic...