Digital Commons Network^™

Genetically Encoded Phase Contrast Agents For Digital Holographic Microscopy, Arash Farhadi, Manuel Bedrossian, Justin Lee, Gabrielle H. Ho, Mikhail G. Shapiro, Jay Nadeau

Physics Faculty Publications and Presentations

Quantitative phase imaging and digital holographic microscopy have shown great promise for visualizing the motion, structure and physiology of microorganisms and mammalian cells in three dimensions. However, these imaging techniques currently lack molecular contrast agents analogous to the fluorescent dyes and proteins that have revolutionized fluorescence microscopy. Here we introduce the first genetically encodable phase contrast agents based on gas vesicles. The relatively low index of refraction of the air-filled core of gas vesicles results in optical phase advancement relative to aqueous media, making them a “positive” phase contrast agent easily distinguished from organelles, dyes, or microminerals. We demonstrate this …

Trail Impact Monitoring In Forest Park, James Mitchell

Environmental Science and Management Professional Master's Project Reports

Forest Park is an appropriately named 5,200 acre natural area located in northwest Portland, Oregon. A recent study estimated park usage near half a million annual visits and found "trails" to be the park’s most highly valued feature. Unfortunately, many trails were not designed for such traffic as evidenced by slipping hazards, erosion and other ecological impacts. In response to these observations, I partnered with Portland Parks & Recreation to conduct an objective trail impact assessment prescribed by the Forest Park Natural Resource Management Plan. I modified methods from past studies to expand on a recently completed trail condition class …

Why Is Dishonesty Difficult To Mitigate? The Interaction Between Descriptive Norm And Monetary Incentive, Arnab Mitra, Quazi Shahriar

Economics Faculty Publications and Presentations

We examine whether changes in perceived norm of dishonesty can offset the effects of changes in benefit from the dishonest action. We find partial support for the hypothesis in laboratory experiments on lying behavior in a cheap-talk sender-receiver game, conducted in two countries. In the experiments, we vary benefit from lying and shift senders’ norm perception by providing them information on lying from prior sessions. The findings suggest that senders adjust their perceived norm as expected, but they respond to norm in a somewhat self-serving manner. Specifically, when benefit from lying is lowered but senders are induced to believe in …

Disrupting The Deficit Gaze: Equity Work With University Supervisors, Maika J. Yeigh

Education Faculty Publications and Presentations

Teacher candidates commonly experience tensions within their clinical field placement classroom. Recently, candidates have brought forward tensions around the use of a deficit gaze (Dudley-Marling, 2007) on students and their families by their mentor teachers. Where candidates of the past would ignore negative framing, current candidates want to disrupt the status quo. This conceptual article describes one EPPs attempt to support teacher candidates “disruption” of instances where a mentor teacher used a deficit-lens toward students and/or their families. Clinical supervisors were offered professional development to support teacher candidates and guide them to disrupt in ways that maintained the professional relationship …

Interests And Priorities In Sockeye Salmon Management: How Are Policies Enacted And Interpreted On Three Alaskan Rivers?, Jake P. Palazzi

University Honors Theses

The large export abundance of Alaskan salmon is well documented, and many studies have been performed to assess the economic and environmental viability of the industry and its management. Less research has been done to characterize how state intentions regarding fisheries allocation are conceived of by management or perceived by vulnerable groups in the user pool. This study seeks to qualitatively characterize the disconnect between state and Native Alaskan perceptions of management effectiveness, public interest, and Native Alaskan involvement using interviews. Results showed that Native Alaskan and state manager respondents had very different perceptions of management effectiveness and equity. When …

Do Fungal Symbionts Of Salt Marsh Plants Affect Interspecies Competition?, Vanessa Robertson-Rojas

Dissertations and Theses

The effects of arbuscular mycorrhizal fungi (AMF) as salt marsh plant symbionts may have significant effects on landscape scale distribution patterns and plant-related ecosystem functions that are important to estuarine habitats. This work investigates the effects AMF have on Phalaris arundinacea, Deschampsia cespitosa, and Juncus balticus when grown in a common garden experiment. Plants were grown with and without AMF inoculation in both polyculture and monoculture communities and examined for a variety of response variables that represent different competition strategies. Factorial ANOVA analysis revealed a significant three-way interaction among fungal treatment type, community type, and species for …

Approximate Pattern Matching Using Hierarchical Graph Construction And Sparse Distributed Representation, Aakanksha Mathuria

Dissertations and Theses

With recent developments in deep networks, there have been significant advances in visual object detection and recognition. However, some of these networks are still easily fooled/hacked and have shown "bag of features" kinds of failures. Some of this is due to the fact that even deep networks make only marginal use of the complex structure that exists in real-world images. Primate visual systems appear to capture the structure in images, but how?

In the research presented here, we are studying approaches for robust pattern matching using static, 2D Blocks World images based on graphical representations of the various components of …

Indoor Air Quality Impacts Of A Woodstove Exchange Program In Washington County, Oregon, Matthew Forrest Survilo

Dissertations and Theses

More than six million people in the United States use wood stoves as their primary heat source. Wood stoves emit air pollutants that may impact health, e.g., wood combustion products are associated with premature death and aggravation of pulmonary and cardiovascular conditions. There are few studies investigating the efficacy of wood stove exchange programs (WSEPs) as a method to improve indoor air quality (IAQ). In partnership with Washington County Department of Health and Human Services we conducted an air quality study to measure the impact of a WSEP on indoor and neighborhood levels of wood combustion products. Twenty households engaged …

Waste Management In The Global South: An Inquiry On The Patterns Of Plastic And Waste Material Flows In Colombo, Sri Lanka, Katie Ann Conlon

Dissertations and Theses

Global plastic production continues to increase at an exponential pace, and global waste projections show waste generation rising by 70% by 2050. Plastic waste connects to all social processes, especially within the context of urbanization and development; urban planning and land management; GHG emissions; labor; social equity; public health; rural-to-urban migration; increasing population; increasing consumption; climate change; etc. The focus of this dissertation is an analysis of waste management practices in Sri Lanka using a grounded theory based methodology, with a goal to better understand the social and ecological impacts of plastic waste in Sri Lanka. This research fills a …

Forest Density Intensifies The Importance Of Snowpack To Growth In Water-Limited Pine Forests, Kelly E. Gleason, John B. Bradford, Anthony W. D'Amato, Shawn Fraver, Brian J. Palik, Michael A. Battaglia

Environmental Science and Management Faculty Publications and Presentations

Warming climate and resulting declines in seasonal snowpack have been associated with drought stress and tree mortality in seasonally snow‐covered watersheds worldwide. Meanwhile, increasing forest density has further exacerbated drought stress due to intensified tree–tree competition. Using a uniquely detailed data set of population‐level forest growth (n = 2,495 sampled trees), we examined how inter‐annual variability in growth relates to snow volume across a range of forest densities (e.g., competitive environments) in sites spanning a broad aridity gradient across the United States. Forest growth was positively related to snowpack in water‐limited forests located at low latitude, and this relationship was …

Investigation Of Magnetism In Transition Metal Chalcogenide Thin Films, Michael Adventure Hopkins

Dissertations and Theses

Layered two dimensional films have been a topic of interest in the materials science community driven by the intriguing properties demonstrated in graphene. Tunable layer dependent electrical and magnetic properties have been shown in these materials and the ability to grow in the hexagonal phase provides opportunities to grow isostructural stacked heterostructures. In this investigation, cobalt selenide (CoSe) and nickel selenide (NiSe) were grown in the hexagonal phase, which consist of central metal atoms that are natively ferromagnetic in bulk, hence providing the potential for interesting magnetic phases in thin film arrangements as well. These structures may play a role …

A Seasonal Study Of Ecoroof Metal And Nutrient Dynamics And Associated Drivers In An Ecoroof On A Commercial Building In North Portland Oregon, Alex Vijay Bans

Dissertations and Theses

Green stormwater infrastructure (GSI), specifically ecoroofs, is increasingly seen as an effective stormwater management tool in urban planning strategies. However, the literature suggests that ecoroofs can be sources of certain metals and nutrients. The goal of our study was to address two research questions: 1) How does ecoroof runoff compare to conventional roof runoff chemically: do ecoroofs retain certain chemicals and leach others? and 2) what are the roof characteristics and environmental variables that affect runoff quality? For 10 months, runoff events from an ecoroof were compared to those of a conventional roof; water samples were collected with autosamplers, and …

Analog Statistical Design For Manufacturability, Yu-Shan Wang

Dissertations and Theses

The manufacturing yield, overkill, and defect level limit the feasibility of analog circuits in SoCs. The conventional method of handling process and environmental variation is to assign a design margin such that the design meets specifications at several processes and environmental corners. However, checking only extreme corners limits performance in comparison to the more rigorous statistical approach of the computing manufacturing and quality figure of merit. The statistical approach requires transistor-level simulation of hundreds or even thousands of samples, not just a few corners, and thus is very time consuming.

This research offers a method for reducing the time required …

Reducing A Class Of Two-Dimensional Integrals To One-Dimension With An Application To Gaussian Transforms, Jack C. Straton

Physics Faculty Publications and Presentations

Quantum theory is awash in multidimensional integrals that contain exponentials in the integration variables, their inverses, and inverse polynomials of those variables. The present paper introduces a means to reduce pairs of such integrals to one dimension when the integrand contains powers multiplied by an arbitrary function of xy/ (x + y) multiplying various combinations of exponentials. In some cases these exponentials arise directly from transition-amplitudes involving products of plane waves, hydrogenic wave functions, and Yukawa and/or Coulomb potentials. In other cases these exponentials arise from Gaussian transforms of such functions.

Late-Holocene Shoreline Responses To Competing Shelf, Bay, And Beach Accommodation Spaces Under Conditions Of Relative Sea Level Change, And The Potential For Future Catastrophic Beach Retreat In The Columbia River Littoral Cell, Washington And Oregon, Usa, Curt D. Peterson, Tamara C. Linde, Sandy Vanderburgh

Geology Faculty Publications and Presentations

The Columbia River Littoral Cell (CRLC) (160 km in length) provides opportunities to compare competing accommodation space relations under different conditions of relative sea level change. The CRLC system includes abundant littoral sand supply from the large Columbia River, late-Holocene prograded beach plains and barrier spits (0.5–5 km in width), two large marine-dominated estuaries (Willapa Bay and Grays Harbor), and a high-wave-energy inner-shelf. Littoral sand accumulation rates in prograded beach plains and barrier deposits are based on paleo-shoreline positions that are dated by great-earthquake catastrophic beach retreat scarps (n = 10) from 0.3 to 5.0 ka. The retreat scarp timelines …

Electromagnetic Reciprocity In The Presence Of Topological Insulators, Huai-Yi Xie, P. T. Leung

Physics Faculty Publications and Presentations

Electromagnetic reciprocity is studied in the presence of topological insulators (TI) with application of axion electrodynamics for harmonic electromagnetic fields. The corresponding generalized Lorentz and Feld-Tai type lemmas are derived in terms of the axion coupling parameter, and their correlation to the conditional symmetry in source-observer coordinates for the various Green dyadics is established subjected to different types of boundary conditions. Possible application of the results to the probing of the topological magneto-electric effects from TI is discussed.

Rainfall Triggers More Deep-Seated Landslides Than Cascadia Earthquakes In The Oregon Coast Range, Usa, Sean R. Lahusen, Alison R. Duvall, Adam M. Booth, A. Grant, Ben A. Mishkin, David R. Montgomery, Will Struble, Joshua J. Roering, J. Wartman

Geology Faculty Publications and Presentations

The coastal Pacific Northwest USA hosts thousands of deep-seated landslides. Historic landslides have primarily been triggered by rainfall, but the region is also prone to large earthquakes on the 1100-km-long Cascadia Subduction Zone megathrust. Little is known about the number of landslides triggered by these earthquakes because the last magnitude 9 rupture occurred in 1700 CE. Here, we map 9938 deep-seated bedrock landslides in the Oregon Coast Range and use surface roughness dating to estimate that past earthquakes triggered fewer than half of the landslides in the past 1000 years. We find landslide frequency increases with mean annual precipitation but …

From Theory To Practice: Gathering Evidence For The Validity Of Data Collected With The Interdisciplinary Science Rubric (Idsr)., Brie Tripp, Erin E. Shortlidge

Biology Faculty Publications and Presentations

In a world of burgeoning societal issues, future scientists must be equipped to work inter-disciplinarily to address real-world problems. To train undergraduate students toward this end, practitioners must also have quality assessment tools to measure students' ability to think within an interdisciplinary system. There is, however, a dearth of instruments that accurately measure this competency. Using a theoretically and empirically based model, we developed an instrument, the Interdisciplinary Science Rubric (IDSR), to measure undergraduate students' interdisciplinary science thinking. An essay assignment was administered to 102 students across five courses at three different institutions. Students' work was scored with the newly …

Designing A More Effective Mri Contrast Agent: Investigation Into Various Functionalization Strategies For Targeted Imaging, Lauren Nicole Rust

Dissertations and Theses

Magnetic resonance imaging (MRI) is a medical imaging technique that provides high-resolution images used for diagnostic medicine while maintaining a superior safety profile compared to other radiative techniques. The administration of gadolinium-based contrast agents (GBCAs) improves the diagnostic power of MRI and have been used clinically for over three decades. Although GBCAs are effective at improving the contrast in the image, their detection limits are high and require a large dose to generate an observable effect. This high dose is the consequence of the current available designs of clinical GBCAs; their structures are not tuned to generate optimal efficacy. Efficacy …

Distribution, Geochronology, And Petrogenesis Of The Picture Gorge Basalt With Special Focus On Petrological Relationships To The Main Columbia River Basalt Group, Emily Bogdan Cahoon

Dissertations and Theses

The Columbia River Basalt Group (CRBG) is the youngest and volumetrically smallest continental flood basalt exposed across the Pacific Northwest, USA. Similar to other large igneous provinces, the majority of material erupted during the initial 1 million years of activity, these lavas are subdivided into four main-phase units. The Picture Gorge Basalt (PGB) is the only main-phase unit of the CRBG whose age is not precisely known and understanding of PGB petrogenesis is largely based on a limited number of samples when compared with other main-phase units. It is suggested that a time gap of over 0.5 myr existed between …

Relativity Lite: A Pictorial Translation Of Einstein’S Theories Of Motion And Gravity, Jack C. Straton

PDXOpen: Open Educational Resources

Relativity Lite is designed for the General Astronomy sequence (PH 361-2U, SCI 315-6U) whose primary book glosses over Special Relativity and General Relativity while trying to explain the Cosmology that is based on those subjects. Relativity Lite translates the mathematical equations conventional relativity texts rely upon into pictures that are readily understood and contain within them the mathematical essentials. This book provides the comprehensive coverage needed to understand, in sufficient depth, these three linked areas of our reality.

Readers seeking this knowledge on their own, and those in other courses for nonscientists, may also find it helpful.

Adopt/Adapt
If you …

Numerical Model Of A Radio Frequency Ion Source For Fusion Plasma Using Particle-In-Cell And Finite Difference Time Domain, Augustin L. Griswold

University Honors Theses

Radio frequency (RF) plasma sources are common tool for application and study, and of particular interest for inertial electrostatic (IEC) fusion. Computational analysis is often carried out using particle in cell (PIC) methods or finite difference time domain (FDTD). However, a more holistic analysis is necessary as the particle distribution is highly dependant on the fields created by the plasma source. Herein, an analysis of a particular planar RF electrode with deuterium gas is provided which covers the fields and the particle behaviour using first FDTD then PIC. Further applications are discussed as well as further directions for this study.

Multicourse Comparative Study Of The Core Aspects For Flipped Learning: Investigating In-Class Structure And Student Use Of Video Resources, Nicole Naibert, Emryse Geye, Michael M. Phillips, Jack Barbera

Chemistry Faculty Publications and Presentations

Since 2013, the number of publications on flipped learning within chemistry have steadily increased. However, most of these studies focus on flipped course reforms within individual institutions, while the outcomes of any learning environment are dependent on how the environment is structured and the degree to which students interact with its elements. In this study, we apply a coordinated set of assessment practices to investigate similarities among flipped chemistry courses at five institutions in the United States. All courses in the study followed the two basic tenets of flipped learning: (1) foundational information was delivered through preclass materials (PCMs), and …

Ronald E. Mcnair Scholars Program Profiles And Abstracts 2020, Mcnair Scholars Program

McNair Symposium

This is the complete event program and provides presentation abstracts and biographies of McNair scholars and their mentors.

Novel View Synthesis - A Neural Network Approach, Hoang Le

Dissertations and Theses

Novel view synthesis is an important research problem in computer vision and computational photography. It enables a wide range of applications including re-cinematography, video enhancement, virtual reality, etc. These algorithms leverage a pre-acquired set of images taken from a set of viewpoints to synthesize another image at a novel viewpoint as if it was captured by a real camera. To synthesize a high-quality novel view, these algorithms often assume a static scene, or the images were captured synchronously. However, the scenes in practice are often dynamic, and taking a dense set of images of these scenes at the same moment …

Image Object Extraction Based On Semantic Segmentation And Label Loss, Xiaoru Wang, Peirong Xu, Zhihong Yu, Fu Li

Electrical and Computer Engineering Faculty Publications and Presentations

Object extraction refers to the operation of obtaining an object area from an image based on a small amount of mark information given by users, which is a key step in image processing. In order to obtain a complete object profile, current methods usually require a large number of manual annotations, especially for objects with irregular contours. Since traditional algorithms rely on low-level pixel features without semantic information, and are based on obvious mathematical assumptions (ie, strong inductive bias), it is difficult to completely identify objects. At present, in order to improve the integrity of object extraction, semantic segmentation-based methods …

Synthesis And Assessment Of Radiotherapy-Enhancing Nanoparticles, Hayden Winter

Dissertations and Theses

Radiation Therapy (RT) is a common treatment for cancerous lesions that acts by ionizing matter in the affected tissue, causing cell death. The disadvantage of RT is that it is most often delivered via an external beam of radiation which must pass through healthy tissues to reach the target site, ionizing matter within healthy tissues as well. To address this drawback, techniques are being developed for increasing RT-induced cell death in a target tissue while minimizing cell death in surrounding tissues. This effect is known as radiation dose enhancement or RT enhancement.

The approach to RT enhancement studied in this …

Urban Air Quality Modeling: Evaluating Impacts Of Ecoroofs On Urban Air Quality In Portland, Oregon, Danlyn L. Brennan, Selina Teng

altREU Projects

In this work, the authors present a mathematical model simulating the impact of ecoroof vegetation on air quality in an urban microclimate. An ecoroof is a layer of vegetation established on rooftops to reduce stormwater runoff, mitigate heat, and enhance air quality. Certain plant species in ecoroofs may however have a detrimental effect on air quality, due to their emission of biogenic volatile organic compounds (BVOCs), which include potentially reactive species such as isoprene. These chemical species can interact with urban air pollution, particularly NOx produced by car traffic, to create other harmful pollutants such as ozone and particulate matter …

Exploring Food Deserts And Environmental Impacts On Health In Chicago And Oregon, Sivasomasundari Arunarasu, Paulina Grzybowicz

altREU Projects

Food deserts are defined as, “an impoverished area where residents lack access to healthy foods”. This lack of access can be due to a combination of socioeconomic, geographic, and food-related variables, and has been proven to impact the health of residents in the area. In this project, several statistical and machine learning techniques are used to model the impact of food desserts and various other factors on health outcomes, including diabetes and obesity rates, in both the different neighborhoods in the City of Chicago and the various counties in the state of Oregon. The models are then used to determine …

Combating Covid On College Campuses: The Impact Of Structural Changes On Viral Transmissions, Jared Knofczynski, Aria Killebrew Bruehl, Ben Warner, Ryne Shelton

altREU Projects

One of the most significant issues in the COVID-19 pandemic is the reopening of schools while minimizing the transmission of coronavirus. Opportunities for evaluating the effectiveness of policies that might be utilized at such institutions are limited, as the necessary empirical data has not been gathered yet. Agent-based modeling, where various entities within an environment are simulated as agents, offers an opportunity to examine the effectiveness of various policies in a way that drastically minimizes the health and economic risks involved. Agent-based modeling is common within biology, ecology and other fields; and has seen some use within the coronavirus literature. …