A large-eddy simulation study was performed to characterize turbulence in sparse, row-oriented canopies. This was accomplished by simulating a set of heterogeneous row-oriented canopies with varying row vegetation density and spacing. To determine the effects of heterogeneity, results were compared to horizontally homogeneous canopies with an equivalent ‘effective’ leaf area...
The words we use to define our lives are often determined by the way we render any given moment. Every instance of writing is a moment of remembering, and a non-fiction essay gives the author free rein to unravel an instance, paint a portrait of what time has already come...
A purpose built facility was designed, built and operated at the Advanced Thermal Hydraulic Research Laboratory, which is located at Oregon State University. This facility was used to heat a plate of Alloy 304 Stainless Steel to 800 °C and then cool the plate using a fine mist of water...
Garden-based learning (GBL) with young people has long been viewed as an educational experience capable of teaching numerous types of science content including general science, technology, engineering and math (STEM), as well as discipline specific areas such as biology, horticulture, agriculture and nutrition. However, much of the GBL literature focuses...
The red tree vole (Arborimus longicaudus) is an arboreal Arvicoline rodent endemic to conifer dominated forests of western Oregon and northwestern California. While commonly associated with old forests, often inhabiting stands over 80 years old, tree voles have also been found in young forests between 20 and 80 years old....
The Line Integral Convolution (LIC) is a mainstay of flow visualization. It is, however, computationally intensive, which limits its interactivity. Also, when used to view three-dimensional (3D) vector fields, the resulting images are dense and cluttered, making it difficult to perceive the flow on the interior parts of the field....
With each generation of technology, computers become even more capable of rendering objects with an ever increasing number of polygons. As a result, the desire to add more details to a 3D model increases as well. Among the many tools provided by computer graphics software that an artist has at...
Previous reports indicate the presence of multiple CYP1A sequences in rainbow
trout, but their functional differences are unknown. This report describes the cloning and partial characterization of four trout CYP1A cDNAs, which are given the tentative
designations CYP1A1v2, v3, v4, and v5. Comparison among these four and three
previously reported...
Wildfire exclusion over the past century or more has resulted in extensive fuel accumulations throughout much of the West that combined with recent climatic patterns have increased the frequency of relatively uncommon, large, high-severity wildfires. Forest restoration treatments intended to alter landscape-level fire disturbance patterns can be difficult to implement...
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John Duff Bailey
Wildfire exclusion over the past century or more has resulted in
Parenting education is a process of providing information to parents on the
challenges of parenting, services available for families, and ideas on how to interact with
children. The federal Even Start family literacy program, designed to increase the
educational opportunities of parents and children, has a strong parenting education
component....
Forests in the western United States have changed drastically over the past 150 years given a long history of utilization (harvest and grazing) and associated fire exclusion. These actions have altered the composition and structure of these forests as well as affected ecosystem function. Current policies for federal land management...
: ______________________________________________________________
John D. Bailey
Forests in the western United States have changed drastically over the past
Severe wildfires are increasing in the western United States, impacting vegetation structure, and in turn, forest regeneration conditions. These wildfires are also raising a substantial amount of scientific and management concern regarding the resilience of forested ecosystems, or the ability of the ecosystem to return to a pre-fire condition. This...
This study introduces a layered model for rendering human teeth. Human teeth exhibit complex light interaction due to their layered structure. While the lighting responses of teeth have been studied in the dental industry for the production of realistic looking dentures, to our knowledge this is the first study of...
This thesis presents an efficient computational voxelization approach that utilizes the graphics pipeline. Our approach is hybrid in that it performs a precise gap-free computational voxelization, employs fixed-function components of the GPU, and utilizes the stages of the graphics pipeline to improve parallelism. This approach makes use of the latest...
Dedicated to the preservation and promotion of many of the nation’s most threatened and endangered species, the W.L. Finley National Wildlife Refuge is highly invested in the management of some of the last remaining upland prairies once prevalent throughout Oregon's Willamette Valley. More than a century of land fragmentation, fire...
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....
Indole-3-carbinol (I3C) inhibits chemically induced tumor
formation in rodents and rainbow trout. This study examines the
effect of I3C and its analog, indole-3-acetonitrile (I3N) on
xenobiotic-metabolizing enzyme systems. The modulation of these enzyme
systems have been shown to have significant effects on the
interaction of chemical carcinogens and cellular constituents....
Forest managers are challenged to restore resilience to forests with an elevated risk of stand-replacing fire by using mechanical thinning and prescribed fire. Implementation of these methods can be constrained by mandates to conserve sensitive wildlife species like the Pacific marten (Martes caurina). Martens avoid simplified forest stands created by...
Wildfire impacts have intensified in many ecosystems across the western United States due to the combined impact of fire exclusion, climate change, and land management practices. However, on many of these landscapes, fire is a fundamental ecological process that has shaped vegetation structural and compositional diversity, ecosystem function, landscape pattern,...
Invasive vegetation control studies traditionally aim to control existing populations as well as limit future spread of the species. However, little additional attention has been dedicated to aiding native communities to recover and reestablish. One prominent example of a studied invasive is Brachypodium sylvaticum (Huds.) P. Beauv. (false brome), a...
Dwelling on the bottom of large rivers to high alpine streams, freshwater sculpins (genus Cottus) occur in high densities across the Pacific Northwest, with 21 currently recognized species found in the Pacific Northwest. Sculpin fill many ecological roles, with some species serving as important prey sources, and others competing with...
With recent advancements in material science, industrial operations are being conducted at higher and higher temperatures. This is apparent in the nuclear industry where a division of the field is working to develop the High Temperature Gas Reactor and the Very High Temperature Gas Reactor concurrently. Both of these facilities...
: _____________________________________________________________________
Brian G. Woods
With recent advancements in material science, industrial operations are being
Research was carried out to determine the influence of increasing
the percentage base saturation of the soil on the yield of
the commercial strawberry. It was found that the effect of increasing
the bases in the soils was directly related to the original
percentage base saturation. When this original value...
We took the back-propagation algorithms of Werbos for recurrent and feed-forward neural networks and implemented them on machines with graphics processing units (GPU). The parallelism of these units gave our implementations a 10 to 100 fold increase in speed. For nets with less than 20 neurons the machine performed faster...
As the nonstop advancement of graphics hardware continues, new features are being added to the graphics pipeline on a regular basis. One of these advancements is called Pixel Synchronization, which allows a graphics programmer more power with certain types of data structures that may be accessed by multiple shader units...
The Intel Xeon Phi is a relative newcomer to the scientific computing scene. In the recent years, GPUs have been used extensively for mathematical simulations. The Xeon Phi is Intel’s response to the use of these cards. Like the GPU, it is highly parallelizable but can be programmed like a...
Extensive research has been conducted to improve the menus that allow navigation of digital world, most of it focused on the most common varieties of menu. Radial menus, a less common menu variety designed so that menu entries are aligned on a polar coordinate system, have largely been ignored. Early...
The constant increase in marine traffic requires a strategy to manage safety. The automatic identification system (AIS) was developed as a navigation safety device for ships in the 1990s. AIS is intended, primarily, to allow ships to view marine traffic in their area and to be seen by that traffic....
Oftentimes in visualization, the goal of using volume datasets is not just to visualize them but also to analyze and compare them. In order to compare the two volumes, we cannot take all the voxels into consideration. The size of a typical volume data set is quite large (maybe a...
Forests are important to Oregon for their beauty as well as economic value, and Douglas fir trees are among the most common and important in the state. Managing and monitoring Oregon’s forests is imperative to ensure they can remain healthy and productive. One tool that helps forest scientists to understand...
”Until relatively recently, mankind was not aware that there was a separable binocular depth sense. Through the ages, people like Euclid and Leonardo understood that we see different images of the world with each eye. But it was Wheatstone who in 1838 explained to the world, with his stereoscope and...
Quaking aspen (Populus tremuloides Michx.) is known to be a widely distributed, shade-intolerant and short-lived hardwood found in both seral, even-aged and stable, uneven aged stands. There have been reports of extensive aspen mortality, crown thinning, and branch dieback across North America that have been linked to the occurrence of...
This project addresses the problems of manually placing facial landmarks on a portrait and finding a fast way to warp the annotated image of a face. While there are many approaches to automatically find facial landmarks, most of them provide insufficient results in uncontrolled environments. Thus I introduce a method...
With continuing improvements in performance and capability, GPU processing has gained significant and growing interest across science and industry. With this interest, research has increasingly focused upon methods of processing algorithms with stochastic, non-uniform branching while maintaining low divergence. Central among these methods is thread-data remapping (TDR), whereby data is...
3D datasets acquire great importance in the context of medical imaging. In this thesis we survey and enhance solutions to problems inherently associated with 3D datasets-processing time,noise and visualization. Efforts include development of a tool kit to provide a multi-threaded processing platform to cut processing time, produce real time visualization...
In many traditional computer graphics applications, rendered scenes typically utilize 3D meshes to represent objects within an environment. As the demand to further improve the realism of graphics applications increases, such as for movies and games, it is becoming more important to represent the inner volumes of object meshes. In...
Mixed-severity fire occurrence is increasingly recognized in Pseudotsuga forests of the Pacific Northwest, but questions remain about how tree mortality varies, and forest structure is altered, across the disturbance gradient observed in these fires. Therefore, we sampled live and dead biological legacies at 45 one ha plots, with four 0.10...
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John Duff Bailey
Mixed-severity fire occurrence is increasingly recognized in Pseudotsuga
Computation of offset curves is an operation critical to many computer-aided design and manufacturing (CAD/CAM) applications. Though simple on the surface, differences between the straightforward mathematical definition and the demands of CAD/CAM environment in the formulation and expression of an offset curve create a problem for which only complicated, approximate...
Buses can be impractical for those who must adhere to a strict schedule or depend on them for emergencies. While variations from the official bus schedule are understandable and largely unavoidable, a lack of communication discourages adoption at a rate disproportionate with their actual likelihood. Even if a bus is...
Graphics of hair have been constantly improved since Kajiya’s famous teddy bear in 1989. By combining these concepts and real-world physics laws, I created a realistic representation of hair on a sphere-shaped head. OpenGL also provides a constantly updated display to continuously render the graphic. Using springs, the hair can...
The dream of ubiquitous virtual reality (VR) tools has been a powerful presence in pop culture since before the turn of the century. But for all of its charm, VR applications are few and far between due to the high cost of hardware setups and cumbersome form factor. This project...
The aim of this research was to provide forest managers and researchers with a better understanding of individual tree defenses and tree responses to disturbances, within a Collaborative Forest Landscape Restoration Program area. Forest restoration often aims to increase stand-level resistance to uncharacteristic changes, and stand-level resistance begins with tree-level...
Graphics hardware in mobile devices has become more powerful, allowing rendering techniques such as ray-cast volume rendering to be done at interactive rates. This increase of performance provides desktop capabilities combined with the portability of a tablet. Volumes can demand a high amount of memory in order to be loaded...
Despite software history being indispensable for developers, there is little empirical knowledge about how they examine software history. Without such knowledge, researchers and tool builders are in danger of making wrong assumptions and building inadequate tools.
In this paper we present an in-depth empirical study about the motivations developers have...
The licensing of novel nuclear reactor power plant designs requires extensive research and testing. A significant portion of this work is dedicated to the design and operation of scaled-down testing facilities that emulate various plant conditions. The data gathered from these test facilities is used to compare to predictive models....
Transport in a binary stochastic media has been an area of interest for many applications over the past three decades. Many different methods have been attempted, most based on the Levermore-Pomraning coupled transport model. However, this method has never been able to correctly solve problems where a large amount of...
Downward flow opposing mixed convection conditions have been studied using the FLUENT CFD code. This work was comprised of two primary objectives. The first was to study core channel flow reversal susceptibility in the Gas Reactor Test Section (GRTS) at low flow conditions. The second objective was the development of...
The last two decades have seen many new continuum models for
electromagnetic materials which were constructed by merely adding
terms to the classical balance laws and constitutive equations. Nonlocal
theories, such as the one developed by A. C. Eringen., however,
depart from the traditional approaches by accounting for the effects...
Traditional modeling of fluidized bed operations has focused on the development of models and correlations for specific systems or narrow areas of application. With recent advances in computing power, new methods of modeling fluidization are possible. One such approach is the Computational Fluid Dynamic Discrete Particle Method (CFD-DPM), which treats...
Human epidermal growth factor receptor 2 (HER2), a member of the receptor tyrosine kinase (RTK) family, is frequently dysregulated in a variety of cancers. Overexpression of the receptor leads to increased cell proliferation and resistance to cell death due to downstream signaling effects. Proteasomal degradation of HER2 results in the...
There is a perceived trade-off between fire risk reduction and northern spotted owl habitat protection in dry-conifer forests in southwestern Oregon. Management options for balancing this trade-off need to be sought at the landscape level. Applied landscape ecology suggests three important features to consider are (1) patch size and configuration...
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John D. Bailey Matthew G. Betts
There is a perceived trade-off between fire risk
In broiler chickens, hepatic lipid metabolism plays a significant role in whole body and muscle fatty acid (FA) incorporation. Flax seed is a rich source of α-linolenic acid and can be used to increase n-3 FA in poultry meat. Previous studies have shown that flax seed in combination with carbohydrase...
Intra- and interplant movement and dispersal of the predator mites Neoseiulus californicus (McGregor) and Neoseiulus fallacis (Garman) were studied on both lima bean (Phaseolus lunatus L.) and apple (Malus pumila Miller) branch plant systems that were seeded with excess numbers of the spider mite Tetranychus urticae Koch. Individuals of either...
The objective of this paper is to demonstrate a method for mechanically characterizing a 25 μm thick elastoviscoplastic hemodialysis membrane and for quantifying the force required to use that membrane in compression sealing. First, methods are developed for mechanically characterizing the thin elastoviscoplastic membrane. Then, a finite element model is...
Almost 600,000 people in the United States were treated for End Stage Renal Disease in 2010. A majority of those people received hemodialysis from central medical facilities. It has been reported a better treatment option for these patients would be realized if the patients had more frequent hemodialysis treatments. A...
More than 1.2 million people worldwide require regular hemodialysis therapy to treat end stage renal failure. In the United States alone, there are 300,000 patients and the National Kidney Foundation predicts that this number will double in the next 10 years. Currently most dialysis patients receive treatment at a dialysis...
Microchannel process technology (MPT) components are chemical unit operations which exploit highly-parallel arrays of microchannels to process large fluid volumes for portable and distributed applications. Microchannel heat exchangers (MCHXs) have demonstrated 3 to 5 times higher heat fluxes when compared to conventional heat exchangers resulting in proportionate reductions in size...
Transport phenomena specially the ones that occur in the various engineering disciplines such as tissue engineering and natural environment are often complex to analyze mostly due to the dynamic and geometric complexities; as such, they have been the subject of an active and intense area of research in past decades....
Characiform fishes form one of the most diverse freshwater fish clades in the world. Comprising more than 2000 species and distributed primarily in South America and Africa, characiforms vary dramatically in their ecomorphology. However, the evolutionary processes responsible for the immense ecomorphological diversity remains unknown. Recently, a study postulated that...
The immune system is a complex network of cellular processes working in harmony to guard us against pathogenic attack. Of utmost importance is the ability of the immune system to discriminate between “self” and “non-self” and diseased versus healthy. Recognition of antigens complexed to major histocompatibility complex (MHC) molecules is...
Ocean circulation is an important component in Earth's climate system. Predicting future climate and circulation changes requires an improved understanding of the past relationship between climate and ocean currents. The neodymium isotope composition (εNd) of water masses is frequently used as a quasi-conservative tracer to reconstruct ocean circulation. The current...
A novel high temperature thermal instrument is proposed, which utilizes a dual-sensing platinum resistor encased in a mono-crystalline alpha-alumina (sapphire) substrate. The instrument is comprised of four platinum trace elements, oriented with 90° rotational symmetry atop a 1120 oriented crystal lattice substrate. All four of these sensors measure temperature directly...
For ras gene mutation analysis in the rainbow trout (Oncorhynchus
mykiss) model system, a partial trout ras sequence was identified
using the polymerase chain reaction (PCR). Two synthetic
oligonucleotides based on rat K-ras gene sequence were used as
primers for the PCR procedure. A 90 base pair (bp) sequence,
referred...
Given the vital role of forest ecosystems in landscape pattern and process, it is important to quantify the effects, feedbacks, and uncertainties associated with forest disturbance dynamics. In western North America, insects and wildfires are both native disturbances that have influenced forests for millennia, and both are projected to increase...
This thesis describes an investigation of the natural products chemistry of two fungal species of the genus Tolypocladium. Natural products are small organic molecules that are considered non-essential for cell growth and reproduction, and thus part of secondary metabolism. Chemical profiling of these secondary metabolites using a combination of high-performance...
We spatially discretize the Sn transport equation using the high-order (HO) discontinuous finite element method (DFEM) on HO meshes. Previous work provided a proof-of-concept for this spatial discretization method in X-Y geometry. Included in the present work, we derive a spatial discretization for the Sn transport equation in both X-Y...
Indole-3-carbinol (I3C) and butylated hydroxyanisole (BHA), anti-carcinogens
present in the human diet, were tested for their in vivo
and in vitro effect on aflatoxin B₁. (AFB₁) metabolism, and DNA adduct
formation in the rainbow trout. Dietary BHA at either 0.3 or 0.03%
had no effect on the hepatic tumor incidence...
A digoxigenin-labeled nonradioactive detection system was used
to screen a zebrafish cDNA library for p53-like and ras-like genes.
One clone was isolated and identified as an incomplete p53-like
gene. The insert size of this clone is 1777 bp, which encodes part of
evolutionarily conserved region II and all of regions...
Forested landscapes in the Pacific Northwest have changed drastically in the last Century with large-scale wildfires, and increased extent and frequency of commercial timber harvests. Thus, landscapes once dominated by older forest cover types became a matrix of younger forests with patches of older forests dispersed throughout. These younger forests...
The Generation IV Very High Temperature Reactor (VHTR) design is being actively
studied in various countries for application due to its inherent passive safe design,
higher thermal efficiencies, and proposed capability of providing high temperature
process heat. The pebble bed core is one of two core designs used in gas...
Application Stores, such as the iTunes App Store, give developers access to their users’ complaints and requests in the form of application reviews. However, little is known about how developers are responding to application reviews. Without such knowledge developers, users, Application Stores, and researchers could make incorrect assumptions. To address...
The Department of Nuclear Engineering and Radiation Health Physics (NE/RHP) at Oregon State University (OSU) has been developing an innovative modular reactor plant concept since being initiated with a Department of Energy (DoE) grant in 1999.
This concept, the Multi-Application Small Light Water Reactor (MASLWR), is an integral pressurized water...
As a result of numerous financial scandals at the turn of the 21st century, Congress passed the Sarbanes-Oxley (SOX) Act of 2002, requiring all publicly-listed companies to comply with regulations aimed at reducing the amount of material misstatements in the financial statements, both frauds and errors. Although the costs of...
Studies of geographic variation are central to understanding ecological and evolutionary processes. Geographic variation in the shell of the black abalone (Halioth cracherodii), a marine intertidal gastropod, involves both
clinal and local variation along the eastern Pacific coast in the number and size of tremata (=respiratory pores) on the shell....
Student problem behavior continues to be a primary concern in schools and, as resources decrease and greater burden is placed upon teachers, schools are pursuing better ways to mange student behavior. Researchers have continually found that when correctly implemented, Positive Behavior Supports (PBS) is an effective system for mitigating problem...
Reported here is an investigation to determine if azinphos-methyl (AZM), an
organophosphate insecticide, adducts to hemoglobin, and if so, whether the
hemoglobin adduct could be used as a quantitative marker of occupational AZM
exposure. We hypothesized that AZM, or a metabolite of AZM, binds to hemoglobin
in erythrocytes forming an...
A study was initiated in 1961 to characterize seral plant
communities in a part of the Cedar Creek drainage in the Tillamook
Burn. Stratification of vegetation into ecological units was a necessary
first step in conifer-animal damage studies supported by the
Oregon State Game Commission.
Reconnaissance information was recorded in...
As ornamental container nurseries face diminishing water allocations, many are looking to automated irrigation solutions to increase their water application efficiency. This thesis presents the findings of a study conducted at a commercial container nursery to determine 1) whether a capacitance or load cell sensor was better suited for monitoring...
Declines in wild salmonid (Oncorhynchus spp.) populations in the Columbia River basin have resulted in managers identifying that avian predation on juvenile salmonids is an important limiting factor for salmonid recovery. Caspian Terns (Hydroprogne caspia), particularly those nesting in the Columbia River estuary, were identified as key avian predators that...
"Cotton fur" (CF) in mink (Mustela vison) is characterized
by lack of pigment in the underfur of dark mink and is part of a
syndrome including hypochromic, microcytic anemia and substandard
growth, resulting from an iron deficiency. Such symptoms
are produced by feeding rations containing raw Pacific hake
(Merluccius productus),...
The neuroendocrine system of the gut plays a significant role in regulating intestinal motor and sensory functions, as well as modulating inflammation in the intestine. The intestinal mucosa is the dominant site of serotonin (5HT) synthesis in mammals, with more than 95% of the intestinal 5HT being present in the...
Soil respiration has been identified as one of the largest natural sources of CO₂ to the global carbon cycle. Small alterations in the magnitude of soil respiration can have potentially large effects on concentrations of atmospheric CO₂ , making the rate at which respiration occurs of great scientific interest (Martin...
The inhibition of S-aden.osylmethionine: Δ²⁴-sterol methyltransferase
(EC 2.1.1.41) activity by endogenous cellular components has
been studied in vitro. The principal inhibitors were Na⁺ and K⁺; Cs⁺,
NH₄⁺ and Li⁺ were also shown to inhibit the reaction. The inhibition
by potassium cation has been studied, and we have found that energy...
With the unique conceptual and mathematical backgrounds of every introductory physics student, there is no way to design a rigid curriculum that anticipates and meets every student’s needs. We can employ machine learning to explore the correlations that exist in the voluminous data from educational settings. That is, institutional, gradebook,...
CisCis-Dichloroethylene (ciscis-DCE), 1,1,1-Trichloroethane (1,1,1-TCA), and 1,4-Dioxane (1,4-D) are chlorinated solvents used as solvents and degreasers in industrial cleaning agents that have become common groundwater contaminants. To develop an effective treatment method for these compounds, polyvinyl alcohol (PVA) and sodium alginate (SA) hydrogel beads were co-entrappcapsulated with Rhodococcus rhodochrous Strain ATCC...
Bacterial aggregation is a strategy employed by many pathogens to establish infection. Mycobacterium avium subsp. hominissuis (MAH) undergoes a phenotypic change, microaggregation, when exposed to the respiratory epithelium. This aggregation is an important step in the pathogenesis of the infection, laying the foundation for biofilm formation. We therefore compared how...
The importance of role-taking skills in the social development of
children has been well documented. Further, it has been shown that
children's development of role-taking skills is dependent upon the
quantity and quality of social interactions which require the
consideration of alternative perspectives. Given recent evidence of
the importance of...
An interactive map of important watersheds in the United States was created for use as a teaching tool in an estuarine ecology class. Figures and explanations of important factors influencing river ecology were created using data downloaded from the U.S. Geologic Survey. This interface serves as a visualization of biological,...
The rainbow trout (Oncorhynchus mykiss) model
of chemical carcinogenesis is becoming increasingly
important as a supplement to rodent studies. However,
much of the molecular biology of the carcinogenic
response is still unknown in the trout model. The ras
gene family has been implicated in the tumorigenesis of
both spontaneous and...
Dimethylbenz (a) anthracene (EMBA), a carcinogen that requires
metabolic activation to produce active metabolites capable of
binding to DNA, has been studied in the trout and other fish.
Polycyclic aromatic hydrocarbons (PAH) are of importance as they
are ubiquitous in the environment and their carcinogenic effects
in fish from contaminated...