Physical Sciences and Mathematics Commons^™

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.

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 …

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 …

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.

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 …

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

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 …

Glaciers In Equilibrium, Mcmurdo Dry Valleys, Antarctica, Andrew G. Fountain, Hassan J. Basagic, Spencer Niebuhr

Geology Faculty Publications and Presentations

The McMurdo Dry Valleys are a cold, dry polar desert and the alpine glaciers therein exhibit small annual and seasonal mass balances, often

Modeling The Thickness Of Perennial Ice Covers On Stratified Lakes Of The Taylor Valley, Antarctica, Maciej K. Obryk, Peter T. Doran, Jared A. Hicks, Christopher P. Mckay, John Charles Priscu

Geology Faculty Publications and Presentations

A 1-D ice cover model was developed to predict and constrain drivers of long-term ice thick-ness trends in chemically stratified lakes of Taylor Valley, Antarctica. The model is driven by surface ra-diative heat fluxes and heat fluxes from the underlying water column. The model successfully reproduced 16 a (between 1996 and 2012) of ice thickness changes for the west lobe of Lake Bonney (average ice thickness = 3.53 m) and Lake Fryxell (average ice thickness = 4.22 m). Long-term ice thick-ness trends require coupling with the thermal structure of the water column. The heat stored within the temperature maximum of …

The Associations Between Environmental Quality And Mortality In The Contiguous United States, 2000-2005, Yun Jian, Lynne C. Messer, Jyotsna S. Jagai, Kristen M. Rappazzo, Christine L. Gray, Shannon C. Grabich, Danelle T. Lobdell

OHSU-PSU School of Public Health Faculty Publications and Presentations

Background: Assessing cumulative effects of the multiple environmental factors influencing mortality remains a challenging task.

Objectives: This study aimed to examine the associations between cumulative environmental quality and all-cause and leading cause-specific (heart disease, cancer, and stroke) mortality rates.

Methods: We used the overall Environmental Quality Index (EQI) and its five domain indices (air, water, land, built and sociodemographic) to represent environmental exposure. Associations between the EQI and mortality rates (CDC WONDER) for counties in the contiguous United States (n=3109) were investigated using multiple linear regression models, and random intercept, random slope hierarchical models. Urbanicity, climate and their combination were …

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 …

Discontinuities In Hygroscopic Growth Below And Above Water Saturation For Laboratory Surrogates Of Oligomers In Organic Atmospheric Aerosols, Natasha Hodas, Andreas Zuend, Katherine Schilling, Thomas Berkemeier, Manabu Shiraiwa, Richard C. Flagan, John H. Seinfeld

Environmental Science and Management Faculty Publications and Presentations

Discontinuities in apparent hygroscopicity below and above water saturation have been observed for organic and mixed organic–inorganic aerosol particles in both laboratory studies and in the ambient atmosphere. However, uncertainty remains regarding the factors that contribute to observations of low hygroscopic growth below water saturation but enhanced cloud condensation nuclei (CCN) activity for a given aerosol population. Utilizing laboratory surrogates for oligomers in atmospheric aerosols, we explore the extent to which such discontinuities are influenced by organic component molecular mass and viscosity, non-ideal thermodynamic interactions between aerosol components, and the combination of these factors. Measurements of hygroscopic growth under subsaturated …

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.

Fast And Adaptive Indexing Of Multi-Dimensional Observational Data, Sheng Wang, David Maier, Beng Chin Ooi

Computer Science Faculty Publications and Presentations

Sensing devices generate tremendous amounts of data each day, which include large quantities of multi-dimensional measurements. These data are expected to be immediately available for real-time analytics as they are streamed into storage. Such scenarios pose challenges to state-of-the-art indexing methods, as they must not only support efficient queries but also frequent updates. We propose here a novel indexing method that ingests multi-dimensional observational data in real time. This method primarily guarantees extremely high throughput for data ingestion, while it can be continuously refined in the background to improve query efficiency. Instead of representing collections of points using Minimal Bounding …

Temporal Order Of Alzheimer's Disease-Related Cognitive Marker Changes In Blsa And Wrap Longitudinal Studies, Murat Bilgel, Rebecca L. Koscik, Yang An, Jerry L. Prince, Susan M. Resnick, Sterling C. Johnson, Bruno Jedynak

Mathematics and Statistics Faculty Publications and Presentations

Investigation of the temporal trajectories of currently used neuropsychological tests is critical to identifying earliest changing measures on the path to dementia due to Alzheimer's disease (AD). We used the Progression Score (PS) method to characterize the temporal trajectories of measures of verbal memory, executive function, attention, processing speed, language, and mental state using data spanning normal cognition, mild cognitive impairment (MCI), and AD from 1661 participants with a total of 7839 visits (age at last visit 77.6 SD 9.2) in the Baltimore Longitudinal Study of Aging and 1542 participants with a total of 4467 visits (age at last visit …

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 …

Puddle Jumping: Spontaneous Ejection Of Large Liquid Droplets From Hydrophobic Surfaces During Drop Tower Tests, Babek Attari, Mark M. Weislogel, Andrew Paul Wollman, Yongkang Chen, Trevor Snyder

Mechanical and Materials Engineering Faculty Publications and Presentations

Large droplets and puddles jump spontaneously from sufficiently hydrophobicsurfaces during routine drop tower tests. The simple low-cost passive mechanism can in turn be used as an experimental device to investigate dynamic droplet phenomena for drops up to 104 times larger than their normal terrestrial counterparts. We provide and/or confirm quick and qualitative design guides for such “drop shooters” as employed in drop tower tests including relationships to predict droplet ejection durations and velocities as functions of drop volume, surface texture, surface contour, wettability pattern, and fluid properties including contact angle. The latter is determined via profile image comparisons with numerical …

Distribution, Quantification And Toxicity Of Cinnamaldehyde In Electronic Cigarette Refill Fluids And Aerosols, Rachel Z. Behar, Wentai Luo, Sabrina C. Lin, Yuhuan Wang, Jackelyn Valle, James F. Pankow, Prue Talbot

Chemistry Faculty Publications and Presentations

Objective The aim of this study was to evaluate the distribution, concentration and toxicity of cinnamaldehyde in electronic cigarette (e-cigarette) refill fluids and aerosols.

Methods The distribution and concentration of cinnamaldehyde were determined in 39 e-cigarette refill fluids plus 6 duplicates using gas chromatography and mass spectrometry (GC/MS). A cinnamaldehyde toxicity profile was established for embryonic and adult cells using a live cell imaging assay, immunocytochemistry, the comet assay and a recovery assay.

Results Twenty of the 39 refill fluids contained cinnamaldehyde at concentrations that are cytotoxic to human embryonic and lung cells in the MTT assay. Cinnamon Ceylon aerosol …

The Economic Value Of Forest Park Ecosystem Services: Results Of Five Focus Groups Conducted In Spring 2016, Randall A. Bluffstone, Pablo Barreyro, Jenny Dempsey Stein, Cody Kent, Antonia Machado

Economics Faculty Publications and Presentations

Objective: This initial phase of research lays the foundation for a survey using contingent valuation (CV) and choice experiment (CE) methods. We asked select Portland residents what they care about most in Forest Park, their willingness to pay (WTP) for improving ecosystem services and how they generally think about the value of those goods and services. These results will help us narrow the experimental design of the forthcoming CV/CE study.

Approach: We conducted a focus group in each of Portland’s 5 “quadrants.” We chose each location - Skyline, St. John’s, Cully, Foster-Powell and Hillsdale - based on either its proximity …

Cycle Structures Of Orthomorphisms Extending Partial Orthomorphisms Of Boolean Groups, Nichole Louise Schimanski, John S. Caughman Iv

Mathematics and Statistics Faculty Publications and Presentations

A partial orthomorphism of a group GG (with additive notation) is an injection π:S→G for some S⊆G such that π(x)−x ≠ π(y) for all distinct x,y∈S. We refer to |S| as the size of π, and if S=G, then π is an orthomorphism. Despite receiving a fair amount of attention in the research literature, many basic questions remain concerning the number of orthomorphisms of a given group, and what cycle types these permutations have.

It is known that conjugation by automorphisms of G forms a group action on the set of orthomorphisms of G. In this paper, we consider the …

Transients In The Synchronization Of Asymmetrically Coupled Oscillator Arrays, Carlos E. Cantos, David K. Hammond, J.J.P. Veerman

Mathematics and Statistics Faculty Publications and Presentations

We consider the transient behavior of a large linear array of coupled linear damped harmonic oscillators following perturbation of a single element. Our work is motivated by modeling the behavior of flocks of autonomous vehicles. We first state a number of conjectures that allow us to derive an explicit characterization of the transients, within a certain parameter regime Ω. As corollaries we show that minimizing the transients requires considering non-symmetric coupling, and that within Ω the computed linear growth in N of the transients is independent of (reasonable) boundary conditions.

Reproductive Output Of Mosses Under Experimental Warming On Fildes Peninsula, King George Island, Maritime Antarctica, Angélica Casanova-Katny, G. A. Torres-Mellado, Sarah M. Eppley

Biology Faculty Publications and Presentations

Background: Mosses dominate much of the vegetation in the Antarctic, but the effect of climatic change on moss growth and sexual reproduction has scarcely been studied. In Antarctica, mosses infrequently produce sporophytes; whether this is due to physiological limitation or an adaptive response is unknown. We studied the effect of experimental warming (with Open Top Chambers, OTCs) on sporophyte production on Fildes Peninsula, King George Island for four moss species (Bartramia patens, Hennediella antarctica, Polytrichastrum alpinum, and Sanionia georgicouncinata). To determine whether reducing cold stress increases sexual reproduction as would be predicted if sex is …

Tidal-Fluvial And Estuarine Processes In The Lower Columbia River: Ii. Water Level Models, Floodplain Wetland Inundation, And System Zones, David A. Jay, Amy B. Borde, Heida Diefenderfer

Civil and Environmental Engineering Faculty Publications and Presentations

Spatially varying water-level regimes are a factor controlling estuarine and tidal-fluvial wetland vegetation patterns. As described in Part I, water levels in the Lower Columbia River and estuary (LCRE) are influenced by tides, river flow, hydropower operations, and coastal processes. In Part II, regression models based on tidal theory are used to quantify the role of these processes in determining water levels in the mainstem river and floodplain wetlands, and to provide 21-year inundation hindcasts. Analyses are conducted at 19 LCRE mainstem channel stations and 23 tidally exposed floodplain wetland stations. Sum exceedance values (SEVs) are used to compare wetland …