Digital Commons Network^™

Ph-Dependent Fluorescent Probe That Can Be Tuned For Cysteine Or Homocysteine, Yongkang Yue, Fangjun Huo, Xiaoqi Li, Ying Wen, Tao Yi, James C. Salamanca, Jorge O. Escobedo, Robert Strongin, Caixia Yin

Chemistry Faculty Publications and Presentations

The very close structural similarities between cysteine and homocysteine present a great challenge to achieve their selective detection using regular fluorescent probes, limiting the biological and pathological studies of these two amino thiols. A coumarin-based fluorescent probe was designed featuring pH-promoted distinct turn-on followed by ratiometric fluorescence responses for Cys and turn-on fluorescence response for Hcy through two different reaction paths. These specific responses demonstrate the activity differences between Cys and Hcy qualitatively for the first time. The probe could also be used for Cys and Hcy imaging in living cells.

Formulation Of Colloidal Suspensions Of 3-Mercaptopropionic Acid Capped Pbs Quantum Dots As Solution Processable Qd "Inks" For Optoelectronic Applications, Chase Collier Reinhart

Dissertations and Theses

The use of colloidal quantum dots (QDs) for photovoltaic energy conversion is a nascent field that has been dominated for well over a decade by the use of 3-mercaptopropionic acid (3-MPA) capped PbS QDs. These QDs are routinely deposited via an in situ solid state ligand exchange process that displaces the native oleate ligand on the PbS QD surface. This ligand exchange procedure is wasteful of material and has been demonstrated to leave numerous impurities that limit electronic performance of the as-deposited QD devices. Until the last few years there was very little understanding in chemical literature as to many …

Algorithm For Premature Ventricular Contraction Detection From A Subcutaneous Electrocardiogram Signal, Iris Lynn Shelly

Dissertations and Theses

Cardiac arrhythmias occur when the normal pattern of electrical signals in the heart breaks down. A premature ventricular contraction (PVC) is a common type of arrhythmia that occurs when a heartbeat originates from an ectopic focus within the ventricles rather than from the sinus node in the right atrium. This and other arrhythmias are often diagnosed with the help of an electrocardiogram, or ECG, which records the electrical activity of the heart using electrodes placed on the skin. In an ECG signal, a PVC is characterized by both timing and morphological differences from a normal sinus beat.

An implantable cardiac …

Geothermometry Of Two Cascade Geothermal Systems, Donnel Alexander Malkemus

Dissertations and Theses

For this thesis I applied classical and multi-component geothermometry techniques to new water chemistry data from Breitenbush Hot Springs, Oregon and the Wind River Valley, Washington. A total of 20 well, spring, and stream samples from Breitenbush Hot Springs and 4 spring samples from the Wind River Valley were collected and analyzed for major, minor, and select trace anions and cations, as well as stable oxygen and hydrogen isotopes. I used two computer programs, GeoT and RTEst, to conduct multi-component geothermometry reservoir condition estimation on each water sample. Water chemistry data from Breitenbush Hot Springs indicates a range of thermal, …

Investigations Into The Effects Of Water Exchange And The Structure Of Lanthanide Chelates, Katherine Marie Payne

Dissertations and Theses

Lanthanide chelates are effective agents for improving contrast in MR images. Optimizing the relaxation of inner sphere water molecules is a common focus of research in this field. However, the efforts to design an optimal contrast agent have commonly over-looked the relationship of water position and water exchange kinetics. This work explores structural conformation, the impact of very fast water exchange kinetics on hydration, and differing tumbling rates for regioisomers of a number of lanthanide chelates. We have grown crystals of LnDOTMA and obtained structural data by X-ray diffraction that provide a picture of the chelate during water exchange and …

A Scalable Preconditioner For A Primal Dpg Method, Andrew T. Barker, Veselin A. Dobrev, Jay Gopalakrishnan, Tzanio Kolev

Portland Institute for Computational Science Publications

We show how a scalable preconditioner for the primal discontinuous Petrov-Galerkin (DPG) method can be developed using existing algebraic multigrid (AMG) preconditioning techniques. The stability of the DPG method gives a norm equivalence which allows us to exploit existing AMG algorithms and software. We show how these algebraic preconditioners can be applied directly to a Schur complement system arising from the DPG method. One of our intermediate results shows that a generic stable decomposition implies a stable decomposition for the Schur complement. This justifies the application of algebraic solvers directly to the interface degrees of freedom. Combining such results, we …

Introduction To Mathematical Analysis I - 2nd Edition, Beatriz Lafferriere, Gerardo Lafferriere, Mau Nam Nguyen

PDXOpen: Open Educational Resources

Video lectures explaining problem solving strategies are available

Our goal in this set of lecture notes is to provide students with a strong foundation in mathematical analysis. Such a foundation is crucial for future study of deeper topics of analysis. Students should be familiar with most of the concepts presented here after completing the calculus sequence. However, these concepts will be reinforced through rigorous proofs.

The lecture notes contain topics of real analysis usually covered in a 10-week course: the completeness axiom, sequences and convergence, continuity, and differentiation. The lecture notes also contain many well-selected exercises of various levels. Although …

Sedimentologic Changes In The Deposits Of An Evolving Lahar-Flood In 2006, Hood River Basin, Mount Hood, Oregon, Matthew Ray Poole

Dissertations and Theses

Over a span of six days from November 2-7, 2006 approximately 43 cm of precipitation fell over the Hood River Basin in Oregon. A lahar was initiated on the Eliot Branch of the Middle Fork Hood River by two or more landslides that occurred on the lateral moraines of the Eliot Glacier on the early part of November 7th, 2006. The Eliot Branch lahar was embedded within the larger regional flood that was occurring in the Hood River Basin and traveled a total of 48 km from the initiation points on the north flank of Mount Hood to the Hood …

The Distribution And Reproductive Success Of The Western Snowy Plover Along The Oregon Coast - 2016, David J. Lauten, Kathleen A. Castelein, J. Daniel Farrar, Adam A. Kotaich, Erica Krygsman, Eleanor P. Gaines

Institute for Natural Resources Publications

We monitored the distribution, abundance and productivity of the federally threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast from 5 April – 31 August 2016. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North and South Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Snowy Plover Management Area, New River HRA and adjacent lands, and Floras Lake. Our objectives in 2016 were to: 1) estimate the size of the adult Snowy Plover population, 2) locate plover nests, 3) determine nest success, 4) implement …

The Effects Of Anthropogenic Stressors On Mercury Concentrations And Community Composition Of Freshwater Zooplankton, Meredith Powers Jordan

Dissertations and Theses

Methylmercury (MeHg) bioaccumulation in freshwater aquatic systems is impacted by anthropogenic stressors, including climate change and excess nutrients. The goal of this study was to determine how warmer water temperatures and excess nutrients would impact zooplankton communities and phytoplankton concentrations, and in turn increase or decrease MeHg concentrations in freshwater zooplankton. I used a 2x2 factorial design to determine if the interaction of temperature and nutrients would impact plankton metrics and zooplankton MeHg concentrations. Mesocosms were filled with Hg-contaminated water and plankton from Cottage Grove Reservoir, Oregon, a waterbody that has experienced decades of elevated MeHg concentrations and corresponding fish …

Computational Methods For Asynchronous Basins, Ian H. Dinwoodie

Mathematics and Statistics Faculty Publications and Presentations

For a Boolean network we consider asynchronous updates and define the exclusive asynchronous basin of attraction for any steady state or cyclic attractor. An algorithm based on commutative algebra is presented to compute the exclusive basin. Finally its use for targeting desirable attractors by selective intervention on network nodes is illustrated with two examples, one cell signalling network and one sensor network measuring human mobility.

Parameterizing A Water-Balance Model For Predicting Stormwater Runoff From Green Roofs, Olyssa Starry, John Lea-Cox, Andrew Ristvey, Steven Cohan

University Honors College Faculty Publication and Presentations

Crop coefficients (kc) were calculated for three different species of common green roof succulents from March to November in 2011, to parameterize the Food and Agricultural Organization of the United Nations (FAO) Penman-Monteith equation for use in a mechanistic green roof water-balance model. Seasonally averaged kc values for each species for 2011 were used to predict plant evapotranspiration (ET) in 2012. The adjusted FAO Penman-Monteith equation predicted the total annual ET within 3–13 mm, a substantial improvement over model predictions with kc set to 1, which overpredicted ET by 100 mm or more, depending on the species. The adjusted equation …

Indoor Inhalation Intake Fractions Of Fine Particulate Matter: Review Of Influencing Factors, Natasha Hodas, Miranda Loh, Hyeong-Moo Shin, Dingsheng Li, Deborah Bennett, Thomas E. Mckone, Olivier Jolliet, Charles J. Weschler, Matti J. Jantunen, Paul Lioy, Peter Fantke

Environmental Science and Management Faculty Publications and Presentations

Exposure to fine particulate matter ( PM2.5) is a major contributor to the global human disease burden. The indoor environment is of particular importance when considering the health effects associated with PM2.5 exposures because people spend the majority of their time indoors and PM2.5 exposures per unit mass emitted indoors are two to three orders of magnitude larger than exposures to outdoor emissions. Variability in indoor PM2.5 intake fraction ( iFin,total), which is defined as the integrated cumulative intake of PM2.5 per unit of emission, is driven by a combination of building-specific, human-specific, and pollutant-specific factors. Due to a limited …

Reduced Snow Cover Alters Root-Microbe Interactions And Decreases Nitrification Rates In A Northern Hardwood Forest, Patrick O. Sorensen, Pamela H. Templer, Lynn M. Christenson, Jorge Durán, Timothy J. Fahey, Melany C. Fisk, Peter M. Groffman, Jennifer L. Morse, Adrien C. Finzi

Environmental Science and Management Faculty Publications and Presentations

Snow cover is projected to decline during the next century in many ecosystems that currently experience a seasonal snowpack. Because snow insulates soils from frigid winter air temperatures, soils are expected to become colder and experience more winter soil freeze-thaw cycles as snow cover continues to decline. Tree roots are adversely affected by snowpack reduction, but whether loss of snow will affect root-microbe interactions remains largely unknown. The objective of this study was to distinguish and attribute direct (e.g., winter snow-and/ or soil frost-mediated) vs. indirect (e.g., root-mediated) effects of winter climate change on microbial biomass, the potential activity of …

Investigation Of Jet Dynamics In Cross-Flow: Quantifying Volcanic Plume Behavior, Graham Freedland

Dissertations and Theses

Volcanic eruption columns inject high concentrations of ash into the atmosphere. Some of this ash is carried downwind forming ash clouds in the atmosphere that are hazardous for private and commercial aviation. Current models rely on inputs such as plume height, duration, eruption rate, and meteorological wind fields. Eruption rate is estimated from plume height using relations that depend on the rate of air entrainment into the plume, which is not well quantified. A wind tunnel experiment has been designed to investigate these models by injecting a vertical air jet into a cross-flow. The ratio of the cross-flow and jet …

From Drought Monitoring To Forecasting: A Combined Dynamical-Statistical Modeling Framework, Hongxiang Yan

Dissertations and Theses

Drought is the most costly hazard among all natural disasters. Despite the significant improvements in drought modeling over the last decade, accurate provisions of drought conditions in a timely manner is still one of the major research challenges. In order to improve the current drought monitoring and forecasting skills, this study presents a hybrid system with a combination of remotely sensed data assimilation based on particle filtering and a probabilistic drought forecasting model. Besides the proposed drought monitoring system through land data assimilation, another novel aspect of this dissertation is to seek the use of data assimilation to quantify land …

Secondary Analysis Of Concussion Data, Martin Zwick, Stephanie Kolakowsky-Hayner, Nancy Carney, Maya Balamane, Tracie Nettleton, D. Wright

Systems Science Faculty Publications and Presentations

Clinical studies are expensive & time-consuming. Typically in these studies specific hypotheses are subjected to confirmatory test. Yet the data may harbor evidence of unanticipated relations between variables. It is thus desirable to subject the data to secondary analyses in the hope of discovering novel & valuable associations. Exploratory analysis, however, is tentative: findings should be replicated in new data. This presentation reports some secondary analyses on concussion data. Data mining on 2 datasets will be discussed, & some unexpected findings reported. The analyses use reconstructability analysis (RA), a probabilistic graphical modeling method implemented in the Occam software package developed …

Using Transects To Understand Cyanobacterial Blooms, John Rueter

Environmental Science and Management Faculty Publications and Presentations

Presentation focuses on Toxic algae (and cyanobacteria) and on short-term mitigation:

• Monitoring
• Possible approaches

Effects Of Antibiotic Mixtures Across Marine Intertidal Trophic Levels: Examining Environmentally-Relevant Contaminant Concentrations, Jaclyn Rebecca Teixeira

Dissertations and Theses

Approximately 48% of Americans use prescription drugs within each 30-day period, and there are signs this trend is increasing. Although many studies track pharmaceuticals’ fates in contaminating waterways, only fairly recent efforts have examined the potential impacts of these drugs on non-target organisms. The antibiotics sulfamethoxazole and trimethoprim, often prescribed together to treat bacterial infections, have been detected worldwide in marine and estuarine environments at concentrations up to 700-800 ng/L each. Toxic effects of these drugs have been identified in freshwater organisms, with synergistic effects observed in short-term studies of mixtures of the two; however, little research has examined possible …

Image Stitching: Handling Parallax, Stereopsis, And Video, Fan Zhang

Dissertations and Theses

Panorama stitching increases the field of view in an image by assembling multiple views together. Traditional stitching techniques are proven to be effective only when dealing with parallax-free monocular images. Many challenges that remain unsolved in the stitching research area include how to stitch monocular images with large parallax, how to stitch stereoscopic images to maintain their stereoscopic consistency and original disparity distribution, and how to create panoramic videos with temporally coherent content. To provide more powerful stitching techniques with more universality, we first develop a parallax-tolerant image stitching technique. With the help of it, we then effectively extend the …

The Application Of Electrochemical Impedance Spectroscopy To Immediately Diagnose The Protective Quality Of Coatings On Artistic And Architectural Metalwork, Kathryn Nicole Hosbein

Dissertations and Theses

Corrosion is a spontaneous process that causes irreversible damage to nearly all metals, which has world-wide implications for architectural and artistic metalwork, such as bridges, buildings, airplanes and sculptures. Protective coatings such as wax, paint, or polymeric clear coatings are used to prolong the lifetime of metals such as steel and bronze. Unfortunately, these coatings fail over time due to oxidative damage by UV rays and by failure to exclude water that can carry salts and pollutants that cause corrosion of the underlying substrate. The current method of coating assessment is visual inspection but when coating failure is detected at …

Hydrogeochemical Evaluation Of The Uinta Formation And Green River Formation, Piceance Creek Basin, Northwestern Colorado, Usa, Megan E. Masterson

Dissertations and Theses

The Piceance Creek Basin in northwestern Colorado contains extensive oil shale deposits that produce natural gas and which could potentially yield ~1.5 trillion barrels of shale oil. However, much of the oil shale lies at depths too great for traditional mining practices and various innovative approaches for in situ conversion of kerogen to oil have been proposed. A firm understanding of the existing hydrogeochemistry is needed as resulting mineralogical changes or rock-fluid reactions may affect rock porosity and permeability. Using an existing database complied by the USGS, the water chemistry of 267 surface and groundwater samples in the Piceance Creek …

Comparing Sanitation Delivery Modalities In Urban Informal Settlement Schools: A Randomized Trial In Nairobi, Kenya, Kate Bohnert, Anna N. Chard, Alex Mwaki, Amy E., Kirby, Richard Muga, Corey L. Nagel, Evan A. Thomas, Matthew C. Freeman

Mechanical and Materials Engineering Faculty Publications and Presentations

The provision of safely managed sanitation in informal settlements is a challenge, especially in schools that require durable, clean, sex-segregated facilities for a large number of children. In informal settlements in Nairobi, school sanitation facilities demand considerable capital costs, yet are prone to breakage and often unhygienic. The private sector may be able to provide quality facilities and services to schools at lower costs as an alternative to the sanitation that is traditionally provided by the government. We conducted a randomized trial comparing private sector service delivery (PSSD) of urine-diverting dry latrines with routine waste collection and maintenance and government …

Understanding The Links Between Cyanobacteria Physiology And Hydrodynamics May Help Find Adaption Strategies For Toxic Blooms, John Rueter

Environmental Science and Management Faculty Publications and Presentations

Even though we are managing lakes to decrease algal blooms overall, harmful algal blooms seem to be showing up more and more frequently. Although the word “blooms” connotes dominance and rapid growth, dangerous accumulations of cyanobacteria can occur because of combinations of physiological advantages and particular weather and hydrodynamic conditions. I am particularly interested in specific conditions that might favor Aphanizomenon versus those that might favor Microcystis in Upper Klamath and Agency Lakes. Aphanizomenon is a nuisance and large blooms can lead to oxygen depletion and fish deaths. Microcystis can both be a nuisance and is toxic. The comparison of …

Mapped Tent Pitching Schemes For Hyperbolic Systems, Jay Gopalakrishnan, Joachim Schöberl, C. Wintersteiger

Portland Institute for Computational Science Publications

A spacetime domain can be progressively meshed by tent shaped objects. Numerical methods for solving hyperbolic systems using such tent meshes to advance in time have been proposed previously. Such schemes have the ability to advance in time by different amounts at different spatial locations. This paper explores a technique by which standard discretizations, including explicit time stepping, can be used within tent-shaped spacetime domains. The technique transforms the equations within a spacetime tent to a domain where space and time are separable. After detailing techniques based on this mapping, several examples including the acoustic wave equation and the Euler …

Ecological Investigations To Select Mitigation Options To Reduce Vehicle-Caused Mortality Of A Threatened Butterfly, Sara B. Zielin, Jalene Littlejohn, Catherine E. De Rivera, Winston P. Smith, Sandra L. Jacobson

Environmental Science and Management Faculty Publications and Presentations

Whereas roads that bisect habitat are known to decrease population size through animal-vehicle collisions or interruption of key life history events, it is not always obvious how to reduce such impacts, especially for flying organisms. We needed a quick, cost-efficient and effective way to determine how best to decrease vehicle-caused mortality while maintaining habitat connectivity for the federally listed Oregon silverspot butterfly, Speyeria zerene hippolyta. Therefore, we gathered targeted ecological information that informed selection of a mitigation option prior to implementation. We sampled butterfly behavior and environmental conditions along a highway and conducted a small-scale experiment along a decommissioned …

The Physics Of Juggling A Spinning Ping-Pong Ball., Ralf Widenhorn

Physics Faculty Publications and Presentations

Juggling a spinning ball with a ping-pong paddle represents a challenge both in terms of hand-eye coordination and physics concepts. Here, we analyze the ping-pong ball’s motion, and explore how the correct paddle angle relates to the ball’s spin and speed, as it moves vertically up and down. For students, this requires engaging with concepts like momentum, angular momentum, free-body diagrams, and friction. The activities described in this article include high-speed video motion tracking of the ping-pong ball and the investigation of the frictional characteristics of the paddle. They can be done in a physics lab or at home, requiring …

Förster Resonance Energy Transfer Between Molecules In The Vicinity Of Graphene- Coated Nanoparticles, Tingting Bian, Railing Chang, Pui T. Leung

Physics Faculty Publications and Presentations

The recent demonstration of the plasmonic enhanced Förster resonance energy transfer (FRET) between two molecules in the vicinity of planar graphene monolayers is further investigated using graphene-coated nanoparticles (GNP). Due to the flexibility of these nanostructures in terms of their geometric (size) and dielectric (e.g. core material) properties, greater tunability of the FRET enhancement can be achieved employing the localized surface plasmons. It is found that while the typical characteristic graphene plasmonic enhancements are manifested from using these GNP’s, even higher enhancements can be possible via doping and manipulating the core materials. In addition, the broadband characteristics is further expanded …

Hitting The Goalpost: Calculating The Fine Line Between Winning And Losing A Penalty Shootout, Ralf Widenhorn

Physics Faculty Publications and Presentations

The Portland Timbers won their first Major League Soccer (MLS) Cup Championship in December 2015. However, if it had not been for a kind double goalpost miss during a penalty shootout a few weeks earlier, the Timbers would never have been in the finals. On Oct. 30th, after what has been called "the greatest penalty kick shootout in MLS history," featuring a combined 22 penalties that included penalties by both goalkeepers, the Timbers won their first-round playoff against Sporting Kansas City. During the thrilling shootout, which can be watched on the MLS website, Sporting had two potentially game-winning penalties miss …

Assessing The Protective Quality Of Wax Coatings On Bronze Sculptures Using Hydrogel Patches In Impedance Measurements, Alice H. England, Kathryn N. Hosbein, Capri A. Price, Morgan K. Wylder, Kenna S. Miller, Tami Lasseter Clare

Chemistry Faculty Publications and Presentations

In this work, we used chemically cross-linked acrylamide-based hydrogel patches that have been specifically developed for use as solid electrolytes in Electrochemical Impedance Spectroscopy to measure the impedance of two waxed bronze sculptures at the Seattle Art Museum’s (SAM) Olympic Sculpture Park (OSP) and compare those results to laboratory test panels. We determined that the impedance response in the frequency range in which measurements may be taken (10 kHz to 1 MHz) is mostly capacitive and that a freshly applied wax coating should ideally be less than 1 nF·cm⁻²for optimal protective performance.