Transcription factor (TF) genes were modified endogenously to include epitope tags for identification of TF protein binding sites by Chromatin Immunoprecipitation (ChIP), followed by high throughput sequencing. We used RNA-sequencing in carbon sources of sucrose, butyrate, and oleate in far-1, far-2, and a double far-1; far-2 mutant to find transcripts...
In advanced integrated circuit (IC) processes, the metal fill inserted to meet foundry imposed density requirements degrades the performance of interconnects and passive components which ultimately affects the overall circuit performance. Accounting for this degradation through electromagnetic and equivalent circuit modeling is becoming a critical aspect of IC design. However,...
Bale Mountains National Park (BMNP) is currently considered the most important conservation area in Ethiopia. BMNP was established over forty years ago to protect Ethiopian endemic fauna and to preserve an array of habitat types including Afroalpine, Afromontane, and the second largest natural humid forest (Harenna forest) left in Ethiopia....
Existing pressure sensitive adhesives (PSAs) are mostly based on petrochemicals. In this study, a novel PSA based on a renewable material, methyl oleate, was prepared and characterized. Methyl oleate was first epoxidized to form epoxidized methyl oleate that was subsequently hydrolyzed and acidified to form epoxidized oleic acid (EOA) which...
BCL11B is a transcriptional regulatory protein that plays essential roles during mouse embryonic development. BCL11B is expressed and functions in the immune and nervous systems as well as within ectodermal organs. Multiple studies have characterized the roles of BCL11B in T cells, brain, and skin. However, very little is known...
Novel donor-type graphite intercalation compounds (GICs) containing tetra-n-alkylammonium (TAA) cations have been synthesized by using both ion-exchange and electrochemical methods. Structural and compositional data of the resulting TAA-GICs are investigated by using powder X-ray diffraction (PXRD), one-dimensional electron density calculations, thermogravimetric and elemental analyses, and capillary zone electrophoresis (CZE). A...
The rising demand on freshwater resources emphasizes the benefit of biogeochemical processes that maintain clean water by removing pollutants such as excess nitrogen. The most sensitive step in the removal of nitrogen from waterways is the oxidation of ammonia, a part of nitrification, which is carried out by ammonia oxidizing...
Carbon Nanotubes are a unique family of nanostructures that have shown remarkable promise for mechanical, electrical, and optical applications. Fundamentally similar to the earlier discovered Buckminsterfullerene (C₆₀), carbon nanotubes are hollow cylinders formed from a single sheet of carbon atoms. The research presented in this dissertation investigates several carbon nanotube...
The influence of the physical environment on organisms has long been a subject of ecological research. But, the complex drivers of environmental variation, and the multiple scales at which this can occur, make studying this topic a difficult challenge. In rocky intertidal habitats, oceanographic- and climate-scale variability influence benthic communities...
Maintaining variation in software is a difficult problem that poses serious challenges for the understanding and editing of software artifacts. Although the C preprocessor (CPP) is often the default tool used to introduce variability to software, because of its simplicity and flexibility, it is infamous for its obtrusive syntax and...
Subduction zone earthquake and tsunami hazards affect tens of millions worldwide and the recurrence of these disasters can be evaluated with paleoseismic techniques, because earthquake cycles (and their supercycles) typically span many millennia. In these three chapters, I discuss a suite of analyses I use to evaluate the sedimentary record...
Vessel disasters (e.g., vessels capsizing, sinking, grounding, burning) are the leading contributor to occupational fatalities in the U.S. commercial fishing industry. Vessel disasters are a vital area to target prevention efforts, yet it has been suggested that results produced in scientific studies are not efficiently exchanged between researchers, regulatory bodies...
Analogous to ocean surface waves, waves in the ocean interior also experience steepening, breaking, and dissipation as they approach the coastline. Much less is known about this internal beach. In this work, extensive moored Acoustic Doppler Current Profiler and temperature/salinity data together with optical remote sensing are combined to describe...
Humpback whales (Megaptera novaeangliae) are vocal baleen whales that exhibit complex social interactions that vary spatially and seasonally. Across their range, humpback whales produce a wide array of vocalizations including ‘song’, foraging vocalizations, and a range of vocalizations known as social calls -- unclassified non-song vocalizations. This study investigates the...
Short-term freeway traffic speed prediction is essential to improving mobility and safety. It has been a challenging, yet unresolved issue. Traffic speed prediction can be applied to enhance the intelligent freeway traffic management and control for applications as operational and regulation planning. For example, with more reliable traffic speed prediction,...
This thesis describes the development of a new enantioselective synthetic method employing chiral cis-2,5-diaminobicyclo[2.2.2]octane-based organometallic catalysts. The significance of this new method to organic synthesis is illustrated with preparation of enantioenriched products that are transformed to important pharmaceutical agents. Chapter 1 provides a brief historical overview of asymmetric catalysis, especially...
Stabilization of the Yaquina Bay shoreline along the northeastern edge of the Hatfield Marine Science Center (HMSC) campus became necessary to halt erosion that threatened both HMSC critical infrastructure (seawater storage tank) and public access to the HMSC Nature Trail. A Dynamic Revetment (gravel beach) was installed in November, 2011...
The genus Phytophthora contains some of the most destructive pathogens of forest trees, including the most destructive pathogen of alder in recent times, Phytophthora alni. Alder trees were reported to be suffering from canopy dieback in riparian ecosystems in western Oregon, which prompted a survey of alder health and monitoring...
There is no doubt that adhesive penetration plays an important role in wood bondline joint performance and durability; yet, to date there is no direct experimental evidence linking penetration depth with bond performance. This is, in part, because adhesive penetration is commonly assessed with various 2D microscopy techniques that are...
Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence times (compared to the main flow) increase the potential for biogeochemical reactions that can improve water quality. As STS and HTS have...
Due to the wide applications of inkjet printers in industry and our daily life, characterization of liquid droplets from inkjet printers, particularly the behaviors of the impact and diffusion of the droplets on the surface of and inside porous medium is of great interest. One conventional characterization method uses high-speed...
Academic libraries play an increasingly important role in providing research data services to faculty and students at universities around the world. One of the major challenges for libraries involves the appropriate scoping of services to meet a broad range of researcher needs. Oregon State University Libraries have developed a model...
The production of hydrogen has been one of the most heavily studied, energy related fields over the past half century, yet few methods are commercially or economically viable and none are currently sustainable. Of those aiming at the sustainable production of hydrogen using renewable resources, perhaps the most widely studied...
Academic librarianship has an intimate association with narratives and stories in their traditional role in curating, caring for, and making collections accessible. Librarians also experience the intricacies and challenges of narrative inquiry through the qualitative research they undertake, oral histories they gather, reflective teaching practices they facilitate, and oral-traditions they...
SAR11 Alphaproteobacteria are the most abundant aerobic chemoheterotrophs in ocean surface waters. Previous studies have indicated SAR11 cells play an important role in marine carbon cycling and consume up to half of some common dissolved organic compounds, such as amino acids. During sequencing of the first SAR11 genome, genes for...
A more quantitative understanding of peptide entrapment and elution from otherwise protein-repellent polyethylene oxide (PEO) brush layers will provide direction for development of new strategies for drug storage and delivery. Here we describe criteria for peptide integration and structural change within the PEO brush, and discuss the reversibility of peptide...
This research effort considers bicyclist’s left-turn behavior at roadway intersections with varying levels of traffic control; specifically, seeking to address the question where do bicyclists look to acquire information. A demographic comparison was made to determine if factors such as gender or experience influence the nature of how a bicyclist...
DNA segments in the fungus Fusarium graminearum were identified as possible genes encoding for chromodomain proteins (CDPs), and targeted for genetic manipulation. Targeted single-gene deletion strains, as wells as GFP-S tag fusion strains, were generated from wildtype F. graminearum protoplasts, and verified strains were screened for phenotypic differences, such as...
Central Oregon has attracted attention as a potential location for a biomass industry based on a locally fixed source of western juniper (Juniperus occidentalis Hook) feedstock. This study identifies a supply of juniper from private lands to determine how much of the available juniper is economically supplied at alternative prices...
The purpose of this study was to explore the issues involved with implementing and using pedagogies of engagement in community college STEM courses. The rationale for this study was based on current and emerging STEM education policy directives calling for an updated approach to teaching undergraduates, focused on student engagement,...
This dissertation focuses on the behavior of security returns around certain events that occurred in the Saudi stock market. In the first study, we measure and analyze the reaction of security returns around a major horizontal merger that occurred in the banking industry in Saudi Arabia. The objective of this...
Amorphous metal thin films (AMTFs) are of potential use for metal-insulator-metal (MIM) tunnel diode applications due to their ultra-smooth surfaces, a consequence of their amorphous microstructure. The objective of this thesis is to design a thermally-stable AMTF capable of maintaining MIM tunnel diode performance after a post-deposition anneal in excess...
In the last decade, the California Current Large Marine Ecosystem has experienced a trend of increased severity of upwelling-driven coastal hypoxia. This thesis strove to examine the potential upper trophic level impacts of moderate and severe hypoxia in the CCLME. Initially I conducted a literature review of Pacific harbor seal...
IC designers are continuously facing the challenges from reduced CMOS feature sizes and supply voltages. ADCs that deliver satisfactory resolutions/speeds while utilizing the state-of-the-art technologies to save power are in high demand. The analog circuits are more and more assisted by various digital calibration techniques to get boosted performances. This...
The potential for electric energy generation from ocean waves is substantial and much research is being conducted on the conversion process as a renewable, grid-connected, power source. Some of the same attributes that make wave energy harvesting attractive as a grid-connected source also make it attractive as a remote, or...
Easy-first, a search-based structured prediction approach, has been applied to many NLP tasks including dependency parsing and coreference resolution. This approach employs a learned greedy policy (action scoring function) to make easy decisions first, which constrains the remaining decisions and makes them easier. This thesis studies the problem of learning...
Research indicates that enduring interparental conflict before, during, and after divorce has negative effects on children. Parental conflict can be reduced utilizing alternative dispute resolution (ADR) processes such as mediation and collaborative divorce. The purpose of this dissertation was to produce two manuscripts examining the role of the child specialist...
Multiple drug resistance (MDR) Tuberculosis (TB), leads to increased use of “second-line” drugs; one of the most effective is ethionamide (ETA). ETA is a prodrug metabolized by a mycobacterial flavin-containing monooxygenase (EtaA) as well human flavin-containing monooxygenases (FMOs). Of the five functional FMOs of humans, FMOs 1, 2, and 3...
Sensors find a variety of applications in portable electronics, automotive and biomedical solutions. The demand for low power and high dynamic range makes the design of digital sensor readout circuits quite challenging. Traditionally, these circuits are realized using amplifiers with passive feedback or precision analog comparators which are power hungry...
Photobiological hydrogen production -- the use of photosynthesis to split water into hydrogen and oxygen -- presents an opportunity for efficient and large-scale solar biofuel development. One of the major challenges in this area is competition for reductant between the hydrogen-evolving hydrogenase enzyme and other metabolic pathways. In this work...
Charge transport in a semiconductor structure with heterojunction is described by a multiscale partial differential equation model. This model can be used, e.g., for the design of more efficient solar cells. Phenomena at the heterojunction must be resolved at the angstrom scale while the size of the device is that...
Macrosomia is a medical term describing a new baby born with an excessive birth weight (greater than 4000g). Fetal macrosomia may lead to both pregnancy complications, and increased risk of mother's and baby's health problems after birth. But the potential complications may be mitigated by a cesarean delivery. As such,...
Since the introduction of lean manufacturing by Toyota and publication by Womack and Jones, organizations have realized sizeable gains through lean process improvement. The spread of lean practices across organizations and industries – from manufacturing to healthcare and construction – requires adjustments of the lean process and, in the case...
Knot Theory: In Imitation of Lewis Thomas is a collection of 14, 1200-word essays written in the style of Lewis Thomas, a physician who regularly contributed to The New England Journal of Medicine. His 1200-word column, "Notes of a Biology Watcher," ran from 1971 - 1980. The resulting compilations collectively...
Synthesis and discovery lies at the core of every field in chemistry. The investigation of the structure-property relationships in compounds known or new is the fundamental purpose of solid state chemistry. Mixing related solid state compounds to form solid solutions can lead to exciting new and/or unexpected properties. Layered compounds...
Although electronic medical records systems (EMR) present promising benefits, they have not yet been widely adopted. A problem facing many EMR are that they are disruptive technologies; their complex hardware and software are not designed to account for the clinicians' characteristics and needs, thus, demanding a steep learning curve and...
The three studies that comprise this dissertation seek to answer significant
questions in paleoclimatology through unconventional applications of ice core
greenhouse gas data. These studies involve different gases and span the interval of time
between the Last Glacial Maximum and the Industrial Revolution, but are united by their
nontraditional use...