The survival, growth, foliar nutrient status, ectomycorrhiza (EM) colonization,
and associative N-fixation of ponderosa pine seedlings (Pinus ponderosa var. ponderosa
Doug!. ex Laws.) were studied under different gap sizes in forest canopy during the first growing season. Seedling performance variables were assessed relative to gap size of the forest canopy...
This dissertation describes patterns in epiphytic macrolichen community composition along a nitrogen deposition gradient in the Yosemite region of the Sierra Nevada in California. This region is part of the largest federal air quality Class 1 designated air-shed in the western United States, covering the entire crest of the Sierra...
The in vitro effects of cortisol in regulating salmonid B cell functions were
investigated. B cells at three distinct stages of differentiation were examined for
cortisol sensitivity. B lymphocyte responses were examined 1) during the early stage
of the precursor, 2) during the intermediate stage of differentiation associated with
clonal...
Letters included were sent to request increased funding for the Titles I and II of the Tribally Controlled College or University Assistance Act. Another letter to the director of Indian Health Services expresses concern over funding delays to the tribes for diabetes.
Anthropogenic nitrogen (N) deposition has had substantial impacts on forests of North America. Managers seek to monitor deposition to identify areas of concern and establish critical loads, which define the amount of deposition that can be tolerated by ecosystems without causing substantial harm. We present a new monitoring approach that...
This report shows results from the developmental evaluation of phases B-D of the Lucy Student Pipeline Accelerator and Competency Enabler (L’SPACE) Program. The STEM Research Center at Oregon State University led an external evaluation for the program. This evaluation focuses on program development and success by analyzing student outcomes and...
Many wind-power facilities in the United States have established effective monitoring programs to determine turbine-caused fatality rates of birds and bats, but estimating the number of fatalities of rare species poses special difficulties. The loss of even small numbers of individuals may adversely affect fragile populations, but typically, few (if...
Ontogenetic changes in resource use often delimit transitions between life stages. Ecological and individual factors can cause variation in the timing and consistency of these transitions, ultimately affecting community and population dynamics through changes in growth and survival. Therefore, it is important to document and understand behavioral and life history...
The objective of this study was to characterize an unknown agent associated with decline in black raspberry (Rubus occidentalis) in Oregon. A virus was found consistently associated with decline symptoms of black raspberries and was named Black raspberry decline associated virus (BRDaV). Double stranded RNA extraction from BRDaV-infected black raspberry...
Research on grief has been studied for nearly a century to understand its many facets, expressiveness, and timing. In the field of counseling, many changes in theories, models, and the lenses through which loss is responded to have been accomplished. However, one constant in the U.S. culture is that definitions...
Prostate cancer is the second most common cancer in men and the fourth most common cancer overall, causing an estimated 307,000 deaths in 2012. Prostate cancer is distinct from other cancers in that there are numerous treatment options, yet very few guarantees in relation to outcome. The most common treatments...
The western purple martin (Progne subis arboricola) is a species of conservation concern throughout the Pacific Northwest. In western Oregon, the purple martin nests in three major ecosystem types: inland open-water, coastal, and upland forest. The availability of suitable breeding habitat is a major limiting factor for western purple martin...
As XML becomes more and more popular, easy-to-use and powerful XML query languages are in great need. Xing is a visual query and restructuring language for XML documents. The objective of this project is to develop a basic version of Xing, including a user-oriented XML query interface and a simple...
In this thesis I present the choice calculus, a formal language for representing variation in software and other structured artifacts. The choice calculus is intended to support variation research in a way similar to the lambda calculus in programming language research. Specifically, it provides a simple formal basis for presenting,...
Topological results are applied to boundary value problems modeling nonlinear
beams and dry friction. A classical continuation theorem is used to prove
existence results for nonlinear beams. Unified proofs, where possible, are given for
all the physically relevant boundary conditions. Integration techniques and various
integral inequalities are used to prove...
The history of a software project plays a vital role in the software development process. Version control systems enable users of a software repository to look at the evolution of the source code, and see the changes that led to newer versions. Currently, version control systems provide commands that can...
XML is a very versatile data format that has been used to represent many different kinds of data, including web pages, books, business and accounting data, programming interfaces, vector graphics, system logs, and games. In a short span of time, it has gained wide acceptance as the document and data...
An experimental study has been made of the local natural convective
heat transfer coefficient around the circumference of a heated
horizontal cylinder oscillating vertically in water. The heat transfer
surface consisted of a 1 3/8-inch diameter cylinder with a small test
section imbedded in its surface. This enabled data to...
Software maintenance accounts for a large portion of the software development cost, particularly the process of updating programs either to adapt for requirement change or to enhance design or efficiency. Currently, program updates are generally performed manually by programmers using text editors. This is an unreliable
method because syntax and...
Functional programming is concerned with referential transparency, that is, given a certain function and its parameter, that the result will always be the same. However, it seems that this is violated in applications involving uncertainty, such as rolling a dice. This thesis defines the background of probabilistic programming and domain-specific...
Social behavior leading to the production of common goods is prone to exploitation. One such behavior in Pseudomonas aeruginosa is quorum sensing (QS), by which the bacteria produce signals to regulate extracellular common goods. Exploitation comes in the form of cheaters which have a mutation in the central quorum sensing...
As a young adult, I have been able to witness first hand just how drastically social media is changing our culture and the way that we look at things. As social media continues to become more vastly used by its members who are in many different phases of life and...
Energy expenditures, perceived family well being, and energy
conservation actions were analyzed by family composition and level of
income. Data were from a three state subsample (Arizona, Colorado,
and Oregon; N = 2,633) of a larger stratified random sample of
households in the Western United States. Data were collected in...
BoGL is a programming language created for the purpose of computer science education that is specific to the domain of board games. Although there is a language grammar and an existing implementation that is currently used by students, a complete and formal language standard does not yet exist. In the...
An interdisciplinary study into the theory of design decisions has yielded a model for tracking design changes in hardware/software systems, but it still needs to be applied to a larger system to test its efficiency at tracking important data. This thesis creates an implementation of PLEXIL, a language in development...
The opportunistic pathogen Pseudomonas aeruginosa possesses two LuxR-LuxI
type quorum-sensing systems that use diffusible acyl-homoserine lactone molecules to
autoinduce and coordinate expression of multiple virulence factors. We conducted a highthroughput
screen for mutants deficient in skim-milk proteolysis—a quorum-sensing
dependent phenotype—using a nonredundant transposon-insertion library representing
most nonessential genes in P....
Research was conducted on the Keating rangelands in north-eastern Oregon to determine the food habits of deer and cattle and
similarity of their diets, and to estimate deer and cattle months of
grazing on both a quantitative and nutritional basis. Data were
collected during the winters of 1978-1979, 1979-1980 and...
Efforts to manage stocks of salmonids in Pacific Northwest stream systems are complicated by the occurrence of several runs of a species thought to represent races rearing sympatrically as juveniles. In order to collect the population statistics needed to properly manage these stocks, managers need a method of identifying juvenile...
Sexual maturation and sex differentiation comprise facets of a
common theme: reproduction. The endocrine system regulates many
of the critical physiological processes necessary for reproduction and
offers a framework within which technologies can be developed for
controlling sexual maturation and sex differentiation. The studies
described in this thesis were undertaken...
The study of the question of why Shakespeare's Hamlet delays killing
Claudius in revenge for his father's murder is examined in light of the major
critical theories from neo-classical to modern scholarship. An expanded
treatment of the works of Fredson Bowers, Eleanor Prosser, Bertram Joseph,
and Roland Frye, is provided...
During Leg 168 of the Ocean Drilling Program, basalts were recovered by drilling and subsurface water was collected with a water sampling tool at Hole 1026B on the east flank of Juan de Fuca Ridge. Microorganisms were found in both types of samples. The microorganisms in the basalt appear to...
The majority of the Earth's shallow crust is composed of basalt that erupted on the seafloor and was subsequently altered by chemical exchange with seawater. One aspect of this alteration is the replacement of glass by secondary minerals, including clays. Petrographic thin sections from ODP Holes 504B and 896A revealed...
The purpose of this study is to investigate the role of the
source of the external trade statistics in measuring the price
responsiveness of foreign demands and relative price competitiveness
of the major exporting countries in trade of agricultural commodities
in international markets. In particular, the papers included in this...
Novel mucosal vaccines (LL-M2e, LL-HAe, SG-HAe) were constructed from live, non-pathogenic Lactococcus lactis or Streptococcus gordonii that express conserved regions of HA or M2 antigens from avian influenza virus (AIV) A. All three vaccines evoked antigen-specific serum immunoglobulin G (IgG) responses in vaccinated chickens. The addition of the adjuvant cholera...
Spreadsheets are a pervasive technology throughout personal and industrial use. Often times, the user is not the author, contributing to a lack of understanding of the purpose and functionality of a spreadsheet. Furthermore, the lack of understanding is a major reason for mistakes in the use and maintenance of spreadsheets....
Correctness and efficiency are important properties of programs. However, to support maintenance and debugging, the programs should also be understandable. Program explanations also play a vital role in educational settings, enhancing the understanding of programs among students.
Proof trees provide a sound basis for generating dynamic explanations of programs. But...
The problem of supporting more advanced selective undo operations has received a lot of attention. However, selective undo is generally missing in commonly used editors. Moreover, partial selective undo, the ability of undoing just part of some edit so that other edits may be undone, is not supported at all....
Appropriate representations of variational software simplify the analysis of their properties.This thesis proposes tailored representations of two kinds variational softwares: difference files of merge commits in Git and feature models. For the former, we use the Choice Edit Model, which is based on the choice calculus, to represent changes introduced...
The code reuse problem is a common software engineering problem in scientific computing. As a prevailing programming language in many scientific fields, Fortran does not provide support to address this problem. One particular reason is that Fortran lacks the support for generic programming. By applying program-generation techniques, we developed two...
Teaching CS is a challenging task, especially for those without prior programming experience. Even for veteran educators, having to learn CS concepts while also trying to teach those same concepts is difficult; as is the case for many K-12 CS instructors. Unfortunately, there is often no formalized order with CS...
The use of board games for teaching introductory computer science is a promising recent avenue of research. The goal is to introduce computing concepts through their use in the implementations of simple games, thereby keeping students engaged through their learning process. However, there is a gap between students' algorithmic descriptions...
In an increasingly computation-driven world, algorithms and mathematical models significantly impact decision making across various fields. To foster trust and understanding, it is crucial to provide users with clear and concise explanations of the reasoning behind the results produced by computational tools, especially when recommendations appear counterintuitive. Legal frameworks in...
Pseudomonas aeruginosa is an opportunistic human pathogen that infects immunocompromised individuals such as those suffering from burns or the genetic disorder cystic fibrosis. This organism utilizes a cell-cell communication mechanism known as quorum sensing (QS) to coordinate virulence gene expression and biofilm formation. It has three interconnected QS systems, namely...
The quorum sensing regulatory pathway has been extensively studied for its impact on the virulence of Pseudomonas aeruginosa, an opportunistic pathogen that causes acute and chronic infections in immunocompromised individuals such as those suffering from the genetic disorder cystic fibrosis. Part of the quorum sensing pathway that has not been...
Partial programming is a field of study where users specify an outline or skeleton of a program, but leave various parts undefined. The undefined parts are then completed by an external mechanism to form a complete program. Adaptation-Based Programming (ABP) is a method of partial programming that utilizes techniques from...
Pseudomonas aeruginosa is a ubiquitous environmental microbe, opportunistic pathogen, and a highly social organism. P. aeruginosa utilizes a wide array of cooperative behaviors to adapt to the environmental conditions around it. These behaviors include quorum sensing (QS), a form a cell-to-cell signaling that coordinates the expression of secreted products in...
Shape transformation is a technique for gradually changing one geometric shape to another. A recent approach presents the use of thin-plate radial basis functions as opposed to traditional "blobby sphere" implicit functions. Without the explicit evaluation of he energy function, this approach combined the two traditional steps into one by...
Pseudomonas aeruginosa is a ubiquitous gram-negative bacterium that is capable of causing infections in people who are immune compromised. The bacterium can live in a variety of environments due to the variety of virulence factors it can produce. It is well adapted to living in iron-stringent conditions because it can...
In a process called quorum sensing (QS), the bacterial pathogen Pseudomonas aeruginosa uses small diffusible signals to coordinate cooperative behaviors via secreted “public goods”. Under QS-dependent growth conditions, social cheaters arise with mutations in lasR, the gene for the primary QS signal receptor. These cheaters do not produce public goods....
Tracr is a modern browser-based user interface, designed to be used with languages that can generate customized explanations from execution traces. While Tracr is primarily designed for use with the Xtra language, Tracr defines a generalized interface that would allow it to be used with other languages as well. Explanations...
In a software development cycle, programs go through many iterations. Identifying and
understanding program changes is a tedious but necessary task for programmers, especially when
software is developed in a collaborative environment. Existing tools used by the programmers
either lack in finding the structural differences, or report the differences as...
West Coast fruit cooperatives working together in joint-venture
trading companies may well lower the prices of their fruit for export
through economies of scale. However, present and future foreign demand
for American fruit may constrain any economies of scale that are realized
in joint-venture agreements. The major objective of this...
Experimental game theory is the use of game theoretic abstractions—games, players, and strategies—in experiments and simulations. It is often used in cases where traditional, analytical game theory fails or is difficult to apply. This thesis collects three previously published papers that provide domain-specific language (DSL) support for defining and executing...
The study of variational typing originated from the problem of type inference for variational programs, which encode numerous different but related plain programs. In this dissertation, I present a sound and complete type inference algorithm for inferring types of all plain programs encoded in variational programs. The proposed algorithm runs...
Cooperative behaviors in bacteria are increasingly appreciated for their relevance to microbial ecology and utility as model systems for social evolution. One example is the secretion of siderophores, a structurally diverse group of compounds that chelate extracellular iron. Siderophore production is considered cooperative because the benefits can be shared with...
The effect of canopy orientation on fruiting performance of 'Beurre
d'Anjou' pears (Pyrus communis L.) and postharvest urea spray on ovule
longevity and fruit set of 'Doyenne du Comice' pears were studied.
Hedgerows of 'Beurre d'Anjou' pear trees planted in 1969 in two
orientations north-south (N-S) and east-west (E-W) were...
Five simulated precipitation patterns characteristic of the Columbia
Basin and Plateau region and six fertilization rates were evaluated
for their effect on percent crude protein, percent in vitro dry matter
digestibility, fiber content, and yield of wheat aftermath on a commercial
farm in north central Oregon.
The higher moisture regimes...
Cell-cell communication in bacteria is understood to facilitate the coordination of population-wide cooperative behavior in the form of concerted gene expression. The opportunistic pathogen Pseudomonas aeruginosa uses such a communication mechanism to regulate a large group of genes important to virulence strategies in this bacterium. This general mechanism of communication...
The United States is the third-largest producer of raspberries in the world. Washington
State leads the nation in red raspberry (Rubus idaeus L.) production. 'Meeker', the
most grown red raspberry cultivar in the Pacific Northwest (Washington, Oregon and
British Columbia, Canada) is highly susceptible to Raspberry crumbly fruit, a virusinduced...
Variability is an important and widely studied topic across domains such as version control, software product lines, and metaprogramming. This dissertation presents an investigation into the process of systematically adding variability to data structures and programs, leading to guidelines for variational data structures and implications for programs that create, manipulate,...
Landscape models for elk distribution developed at Starkey Experimental Forest and Range from 1993-1995 were tested on another landscape during 2003-2005 at Sled Springs Wildlife Demonstration Area. Using location data obtained from 23 wild elk captured and fitted with GPS telemetry collars, 8 spatial resource selection function models representing 8...
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...
Cell-to-cell communication by chemical signals, termed quorum sensing (QS), is a common regulatory scheme in the microbial world. Pseudomonas aeruginosa¸ an opportunistic pathogen of burn wounds and cystic fibrosis lungs, uses QS to control the expression of hundreds of genes, particularly those necessary for population level benefits such as biofilm...
Over the last several decades, there has been a marked increase in the amount of science outreach to the public with little attention paid to how scientists who conduct outreach perceive learning and how that applies to their outreach activities. This increase in outreach efforts is linked to the National...
When iron levels are low, the opportunistic pathogen Pseudomonas aeruginosa secretes the high-affinity iron-binding siderophore pyoverdine. The cognate ferripyoverdine receptor, FpvA, has gained attention as the most divergent gene in the organism’s genome, showing substantial evidence of positive selection. S-type pyocins, bacteriocins with specificity to Pseudomonads, enter cells through FpvA...
We present the evolution of a reasoning system for inferring dimension information in
spreadsheets. The three papers included in this thesis show how the initial system can be
used to check the consistency of spreadsheet formulas and thus is able to detect errors in
spreadsheets, and the evolution to a...
In June 1988 the Japanese agreed to liberalize their
beef market which had been protected by an import quota
system for twenty-four years. The purpose of this thesis is
to draw conclusions/implications concerning the effect of
the trade agreement (1988 Import Quota Removal Agreement)
upon Japanese beef imports and the...
We demonstrate an approach to transform keyword queries automatically into queries that combine keywords appropriately by boolean operations, such as and and or. Most current search engines will preprocess the queries before they really use these queries to search locally stored files or web pages. However, the search engines usually...
Spreadsheets are among the most widely used end-user programming systems. Unfortunately, there is a high incidence of errors in end-user spreadsheets, and some of these errors have high impact. In this dissertation, we describe techniques we have developed to help end users develop safer spreadsheets. As part of our research,...
Ubiquitous pathogen Pseudomonas aeruginosa coordinates population-wide activation of virulence genes through quorum sensing (QS), where individuals transition from solo to social behaviors to benefit the population. QS is complex and mechanisms vary from species to species, but the concept is common to the bacterial world and has implications in various...
Pseudomonas aeruginosa is an environmental bacterium as well as an opportunistic pathogen that primarily infects immunocompromised individuals, including those suffering from cystic fibrosis. The density-dependent regulation of gene expression via cell-to-cell communication, also termed quorum sensing (QS), is an important virulence determinant in this organism. Generally, P. aeruginosa uses three...
Two studies were conducted to determine the factors influencing distribution of cattle on northeastern Oregon mixed-conifer forested rangelands. The objective of the first study was the quantification of differences in distribution of cattle of different ages. Beginning in 1991, and continuing through 2001, radio telemetry collars were placed on a...
Research was conducted at the Starkey Experimental Forest and
Range in northeastern Oregon to determine cattle performance, diet
quality, botanical composition of forage ingested, and production
and utilization among rest-rotation, season-long, and deferred
rotation grazing systems. The grazing season lasted from June 20 to
October 10 of each year. Cows...
While the quorum-sensing (QS) diversity of the opportunistic pathogen Pseudomonas aeruginosa has been well established in cystic fibrosis (CF) lung infections and in vitro experiments, little is known about its QS-diversity in natural environments. One significant QS-deficient behavior is social cheating. Social cheaters contain mutations that prevent them from producing...
Martin Buber was an internationally known scholar,
teacher, and author whose works covered education, communication,
politics, theology, philosophy, counseling,
and related fields. The purpose of this study was to
discover the implications of Buber's philosophy of education
for the student services profession. Previous
attempts to relate Martin Buber's philosophy to...
This dissertation explores the structural dynamics of human understanding and particularly the concept of meaning and its connections to concepts of ultimate ground, necessity and contingency, language, and perception. It focuses on the history of the concept of meaning in early twentieth-century European physics and philosophy, through an analysis of...
Within the altered parts of the glass rim of pillow lavas of Hole 896A, at depths at least 432 m below seafloor (237 m below the top of volcanic basement), microbes have been identified. This is indicated by the size and shapes of alteration textures and verified by the presence...
Currently little is known about the mechanisms and locations of
lymphocyte development in teleosts. In this study several aspects of the
underlying factors which govern B lymphocyte development in trout
were investigated which included: the isolation and characterization of
immunoglobulin heavy chain (IgH) genes, the recombination activating
genes 1 and...
The central purposes of this study were to review the
historical sources of David Kolb's formulation of experiential
learning theory, and to determine the effect and
application of Kolb's theory and Learning Style Inventory
as reflected in the literature between 1971 and 1990.
It was found that Kolb based his...
The U.S. white wheat industry relies heavily on export markets.
Since the early 1960s these markets have been geographically concentrated
in a few countries in Asia. This suggests that developments
in a few Asian countries may significantly affect the prospects for
U.S. white wheat exports and thereby the economic well...
The success of the U.S. government in persuading Japan to
liberalize the beef market is viewed as a relief to the U.S.
beef industry. The economic benefit (to the U.S. beef
producers!) of the trade liberalization however is yet to be
seen. The size of this benefit is determined, among...
Ensuring correctness of real-world software applications is a challenging task. Testing can be used to find many bugs, but is typically not sufficient for proving correctness or even eliminating entire classes of bugs. However, formal proof and verification techniques tend to be very heavy weight and are simply not available...
Environmental factors such as chemical contamination can have immunomodulatory effects on the immune response of fish and may be contributing to the decline in salmonid populations by augmenting disease susceptibility. Xenobiotics can interfere with the immune system at several levels of complexity, and different immune cells and processes have variable...
Sex differentiation in fish is a labile process that allows sex inversion in several species. The inherent capacity of fish germ cells to differentiate into oocytes or spermatocytes constitutes a key factor allowing for functional sex inversion. This thesis set out to determine the mechanism involved in steroid-induced sex differentiation...