Digital Commons Network^™

Interdisciplinary: Feminist Teaching, Research And Activism, Jamie P. Ross

Women, Gender, and Sexuality Studies Faculty Publications and Presentations

Feminists' interdisciplinary work is a critical response to claims that disciplinary expertise provides real knowledge. Interdisciplinary teaching, research, and activism emerge in opposition to claims that only certain kinds of ideas are valuable. This paper will briefly delineate those concepts that have created an intellectual tradition that does not recognize the political and strategic elements entailed by all knowledge formation. Feminist activism is a reaction to the narrowly defined boundaries of what counts as a good idea. The distinction between passive and active knowledge acquisition allows us to view feminist teaching, research, and activism as active, ongoing engagements that emerge …

Accelerated Erosion Of Saltmarshes Infested By The Non-Native Burrowing Crustacean Sphaeroma Quoianum, Timothy Mathias Davidson, Catherine E. De Rivera

Environmental Science and Management Faculty Publications and Presentations

Lateral erosion of saltmarshes is affected by many abiotic and biotic factors. While abiotic factors are typically regarded as primary drivers of erosion, biotic influences such as burrowing or bioturbating taxa can also extensively modify the physical structure of this marine habitat. Many estuaries on the Pacific coast of North America have been invaded by populations of the burrowing non-native isopod Sphaeroma quoianum, which are thought to exacerbate the erosion of saltmarshes. We conducted a mensurative experiment to examine the relationship between populations of S. quoianum and lateral erosion rate of saltmarshes in Coos Bay, Oregon, USA. After 1 …

Bandwidth Tuning Triggers Interplay Of Charge Order And Superconductivity In Two-Dimensional Organic Materials, S. Kaiser, M. Dressel, Y. Sun, A. Greco, J. A. Schlueter, Gary L. Gard, N. Drichko

Chemistry Faculty Publications and Presentations

We observe charge-order fluctuations in the quasi-two-dimensional organic superconductor β″-(BEDT-TTF)₂SF₅CH₂CF₂SO₃, both by means of vibrational spectroscopy, locally probing the fluctuating charge order, and by investigating the in-plane dynamical response by infrared reflectance spectroscopy. The decrease of the effective electronic interaction in an isostructural metal suppresses both charge-order fluctuations and superconductivity, pointing to their interplay. We compare the results of our experiments with calculations on the extended Hubbard model.

Neural Coding And Decoding, Alexander Dimitrov

Systems Science Friday Noon Seminar Series

Methods based on Rate Distortion theory have been successfully used to cluster stimuli and neural responses in order to study neural codes at a level of detail supported by the amount of available data. They approximate the joint stimulus-response distribution by quantizing paired stimulus-response observations into smaller reproductions of the stimulus and response spaces. An optimal quantization is found by maximizing an information-theoretic cost function subject to both equality and inequality constraints, in hundreds to thousands of dimensions. This analytical approach has several advantages over other current approaches:

• it yields the most informative approximation of the encoding scheme given the …

Understanding, Modeling And Valuing Ecosystem Services, Robert Costanza

Systems Science Friday Noon Seminar Series

Ecosystem services (ES) are the direct and indirect contributions of ecosystems (in combination with other inputs) to human well-being. An ES-based approach can assess the trade-offs inherent in managing humans embedded in ecological systems. Evaluating trade-offs requires both an understanding of the biophysical magnitudes of ES changes that result from human actions, as well as an understanding of their impact on human well-being, broadly conceived. This talk discusses the state of the art of ES assessment, valuation, and modeling, including the potential of integrated ecological economic modeling. Valuation is about assessing trade-offs – not necessarily about trades (exchanges) in markets …

Accurate Description Of The Optical Response Of A Multilayered Spherical System In The Long Wavelength Approximation, H. Y. Chung, G. Y. Guo, Hai-Pang Chiang, D. P. Tsai, P.T. Leung

Physics Faculty Publications and Presentations

The optical response of a multilayered spherical system of unlimited number of layers (a “matryoshka”) in the long wavelength limit can be accounted for from the knowledge of the static multipole polarizability of the system to first-order accuracy. However, for systems of ultrasmall dimensions or systems with sizes not-too-small compared to the wavelength, this ordinary quasistatic long wavelength approximation (LWA) becomes inaccurate. Here we introduce two significant modifications of the LWA for such a nanomatryoshka in each of the two limits: the nonlocal optical response for ultrasmall systems (<10 >nm), and the “finite-wavelength corrections” for systems ∼100 nm. This is …

Scoring Function To Predict Solubility Mutagenesis, Ye Tian, Christopher Deutsch, Bala Krishnamoorthy

Chemistry Faculty Publications and Presentations

Background: Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results: We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to …

Portland State Library Newsletter; Fall 2010, Portland State University Library

Library Newsletters

In this issue: Meet the Interim University Librarian; Access to The Chronicle of Higher Education; Distance Learning Students; Posters for Check-Out; Paperless Library Notices; Fall Term Event & Exhibit; Films on Demand and Donor Honor Roll

Heard On The Net: One Byte, Two Bytes, Three Bytes For Dollars. All For E-Books, Stand Up And Holler!, Jill Emery

Library Faculty and Staff Publications and Presentations

This column explores two e-book purchasing models, Evidence-Based Selection (EBS) and patron-driven (demanddriven) model. Both hold promise as new ways to purchase e-books in libraries and provoke interesting questions about the future of e-book purchasing.

A Class Of Discontinuous Petrov–Galerkin Methods. Part Iv: The Optimal Test Norm And Time-Harmonic Wave Propagation In 1d., Jeffrey Zitelli, Leszek Demkowicz, Jay Gopalakrishnan, D. Pardo, V. M. Calo

Mathematics and Statistics Faculty Publications and Presentations

The phase error, or the pollution effect in the finite element solution of wave propagation problems, is a well known phenomenon that must be confronted when solving problems in the high-frequency range. This paper presents a new method with no phase errors for one-dimensional (1D) time-harmonic wave propagation problems using new ideas that hold promise for the multidimensional case. The method is constructed within the framework of the discontinuous Petrov–Galerkin (DPG) method with optimal test functions. We have previously shown that such methods select solutions that are the best possible approximations in an energy norm dual to any selected test …

Structure Of The Cholera Toxin Secretion Channel In Its Closed State, Steve Reichow, Konstantin V. Korotkov, Wim Gj Hol, Tamir Gonen

Chemistry Faculty Publications and Presentations

The type II secretion system (T2SS) is a macromolecular complex spanning the inner and outer membranes of Gram-negative bacteria. Remarkably, the T2SS secretes folded proteins including multimeric assemblies like cholera toxin and heat-labile enterotoxin from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. The major outer membrane T2SS protein is the “secretin” GspD. Electron cryomicroscopy reconstruction of the V. cholerae secretin at 19 Å resolution reveals a dodecameric structure reminiscent of a barrel with a large channel at its center that appears to contain a closed periplasmic gate. The GspD periplasmic domain forms a vestibule with a conserved constriction, and binds …

Tabor To The River: An Evaluation Of Outreach Efforts And Opportunities For Engaging Residents In Stormwater Management, Vivek Shandas, Anne Nelson, Carine Arendes, Cathy Cibor

Institute for Sustainable Solutions Publications and Presentations

This report summarizes the key findings from a neighborhood survey that focused on household perceptions of sustainable stormwater systems. The survey was conducted in collaboration with the City of Portland?s Bureau of Environmental Services (BES) and Portland State University?s Center for Urban Studies.

Extensive Aerosol Optical Properties And Aerosol Mass Related Measurements During Tramp/Texaqs 2006 – Implications For Pm Compliance And Planning, Monica Elizabeth Wright, Dean B. Atkinson, Luke Ziemba, Robert Griffin, Naruki Hiranuma, Sarah D. Brooks, James Flynn, Ryan Perna, Bernhard Rappenglück, Winston Luke, Paul Kelley

Chemistry Faculty Publications and Presentations

Extensive aerosol optical properties, particle size distributions, and Aerodyne quadrupole aerosol mass spectrometer measurements collected during TRAMP/TexAQS 2006 were examined in light of collocated meteorological and chemical measurements. Much of the evident variability in the observed aerosol-related air quality is due to changing synoptic meteorological situations that direct emissions from various sources to the TRAMP site near the center of the Houston-Galveston-Brazoria (HGB) metropolitan area. In this study, five distinct long-term periods have been identified. During each of these periods, observed aerosol properties have implications that are of interest to environmental quality management agencies. During three of the periods, long …

Cooperative Interaction Of Transcription Termination Factors With The Rna Polymerase Ii C-Terminal Domain, Bradley M. Lunde, Steve Reichow, Minkyu Kim, Hyunsuk Suh, Thomas C. Leeper, Fan Yang, Hannes Mutschler, Stephen Buratowski, Anton Meinhart, Gabriele Varani

Chemistry Faculty Publications and Presentations

Phosphorylation of the C-terminal domain of RNA polymerase II controls the co-transcriptional assembly of RNA processing and transcription factors. Recruitment relies on conserved CTDinteracting domains that recognize different CTD phosphoisoforms during the transcription cycle, but the molecular basis for their specificity remains unclear. We show that the CTD-interacting domains of two transcription termination factors, Rtt103 and Pcf11, achieve high affinity and specificity both by specifically recognizing the phosphorylated CTD and by cooperatively binding to neighboring CTD repeats. Single amino acid mutations at the protein-protein interface abolish cooperativity and affect recruitment at the 3′-end processing site in vivo. We suggest that …

Facile Pyrolytic Synthesis Of Silicon Nanowires, Joo C. Chan, Hoang Tran, James W. Pattison, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

One-dimensional nanostructures such as silicon nanowires (SiNW) are attractive candidates for low power density electronic and optoelectronic devices including sensors. A new simple method for SiNW bulk synthesis[1, 2] is demonstrated in this work, which is inexpensive and uses low toxicity materials, thereby offering a safe, energy efficient and green approach. The method uses low flammability liquid phenylsilanes, offering a safer avenue for SiNW growth compared with using silane gas. A novel, duo-chamber glass vessel is used to create a low-pressure environment where SiNWs are grown through vapor-liquid-solid mechanism using gold nanoparticles as a catalyst. The catalyst decomposes silicon precursor …

Biological Computation, Melanie Mitchell

Computer Science Faculty Publications and Presentations

In this article, the term biological computation refers to the proposal that living organisms themselves perform computations, and, more specifically, that the abstract ideas of information and computation may be key to understanding biology in a more unified manner. It is important to point out that the study of biological computation is typically not the focus of the field of computational biology, which applies computing tools to the solution of specific biological problems. Likewise, biological computation is distinct from the field of biologically-inspired computing, which borrows ideas from biological systems such as the brain, insect colonies, and the immune system …

Systems For Assessing And Enhancing The Performance Of Scanning Electron Microscopes By Quantifying And Enforcing Symmetries And Periodicities In Two Dimensions, Peter Moeck

Physics Faculty Publications and Presentations

Scanning probe microscope (SPM) images are enhanced by enforcing one or more symmetries that can be selected based on suitable Fourier coefficient amplitude or phase angle residuals, and/ or geometric Akaike information criteria, and/ or cross correlation techniques. Alternatively, this selection can be based on prior knowledge of specimen characteristics. In addition, a scanning microscope point spread function is obtained based on the evaluation of a calibration image by enforcing at least one symmetry and can be applied to other image acquisitions.

The Effectiveness Of Vertebrate Passage And Prevention Structures: A Study Of Boeckman Road In Wilsonville, Catherine E. De Rivera, Leslie L. Bliss-Ketchum

Environmental Science and Management Faculty Publications and Presentations

One of the most obvious impacts roads have on the natural world is direct mortality to individual animals that attempt to cross roads. A less obvious but likely more important impact of roads on many species is habitat fragmentation. The ability for individuals to travel between subpopulations is the key to genetic diversity as well as ultimately the survival of the species. Considering these impacts and management goals to increase habitat connectivity, increased attention has been given to creating road design that reduces wildlife collisions. Most studies, however, have been in other countries or regions and most focus on connectivity …

Multiple Trophic Levels Fueled By Recirculation In The Columbia River Plume, Raphael M. Kudela, Alexander R. Horner-Devine, Neil S. Banas, Barbara M. Hickey, Tawnya D. Peterson, Ryan M. Mccabe, Evelyn J. Lessard, Elizabeth R. Frame, Kenneth W. Bruland, David A. Jay, Jay O. Peterson, William T. Peterson, P. Michael Kosro, Sherry L. Palacios, Maeve C. Lohan, Edward P. Dever

Civil and Environmental Engineering Faculty Publications and Presentations

Large rivers represent gateways for the transport of terrigenous and anthropogenic material to the coastal ocean. Here we document a ?700 km2 recirculation or bulge associated with the Columbia River plume that retains recently discharged river water sufficiently to create a regional bioreactor. Fueled by a fluvial nitrate source, this feature stimulated growth across three trophic levels and may buffer this gateway system during periods of increased warming and stratification that lead to decreased ocean productivity, potentially enhancing production at multiple trophic levels and enriching surfacewaters far from the river mouth.

The Effect Of Tidal Asymmetry And Temporal Settling Lag On Sediment Trapping In Tidal Estuaries, Alexander S. Chernetsky, Henk M. Schuttelaars, Stefan A. Talke

Civil and Environmental Engineering Faculty Publications and Presentations

Over decades and centuries, the mean depth of estuaries changes due to sea-level rise, land subsidence, infilling, and dredging projects. These processes produce changes in relative roughness (friction) and mixing, resulting in fundamental changes in the characteristics of the horizontal (velocity) and vertical tides (sea surface elevation) and the dynamics of sediment trapping. To investigate such changes, a 2DV model is developed. The model equations consist of the width-averaged shallow water equations and a sediment balance equation. Together with the condition of morphodynamic equilibrium, these equations are solved analytically by making a regular expansion of the various physical variables in …

Characteristics Of Transitions In Freeway Traffic, Robert L. Bertini, Soyoung Ahn

Civil and Environmental Engineering Faculty Publications and Presentations

This research seeks to understand the characteristics of transitions as freeway traffic changes from one state to another. This study addresses the features of two types of transitions; transitions near a merge and transitions along shock waves during the onsets and dissipations of queues at several freeway sites.

Individual vehicle trajectory data were analyzed for studying the transitions near a merge. The length of a transition zone was measured by analyzing the spatial changes in flow, density and speed along kinematic waves near a merge. It was found that the length of transition in terms of flow, density and speed …

Center For Academic Excellence: Annual Report 2009-2010, Patrice Hudson, Leslie G. Mcbride, Kevin Kecskes, Amy Spring, Janelle De Carrico Voegele, Michael Chamberlain, Vincent Schreck

Community Health Faculty Publications and Presentations

Admittedly, a certain amount of tedium is involved in assembling an annual report. Retrieving, verifying, and summarizing all the data generated from CAE’s programs and services during the year feels a lot like double-checking references in a manuscript before sending it off for review. It’s a necessary part of the larger project; sometimes we are surprised.

Somewhere in the midst of the process, we may suddenly see a project from an entirely diff erent perspective, identify a theme that ties together threads or themes we hadn’t realized previously were connected, or more clearly see why faculty members may (or may …

The Perfect Spill: Solutions For Averting The Next Deepwater Horizon, Robert Costanza, David Batker, John W. Day, Rusty A. Feagin, M. Luisa Martinez, Joe Roman

Institute for Sustainable Solutions Publications and Presentations

In this article the authors comment on the oil spill incident from the Deepwater Horizon, particularly on its economic and ecological damages. The authors highlighted the disaster as an event wherein much is needed to be learned so that future oil spills can be avoided. One lesson refers to the valuability of natural capital assets and other public entities that are at risks due to private interests and that better regulations and incentives are needed to protect these assets against risks.

Technology And Communications Coursework: Facilitating The Progression Of Students With Learning Disabilities Through High School Science And Math Coursework, Dara Shifrer, Rebecca Callahan

Sociology Faculty Publications and Presentations

Students identified with learning disabilities experience markedly lower levels of science and mathematics achievement than students who are not identified with a learning disability. Seemingly compounding their disadvantage, students with learning disabilities also complete more credits in non-core coursework—traditionally considered nonacademic coursework—than students who are not identified with a learning disability. The Education Longitudinal Study of 2002, a large national dataset with both regular and special education high school students, is utilized to determine whether credit accumulation in certain types of non-core coursework, such as technology and communications courses, is associated with improved science and math course taking outcomes for …

Places For Races: The White Supremacist Movement Imagines U.S. Geography, Barbara Perry, Randy Blazak

Sociology Faculty Publications and Presentations

Increasingly, scholars are acknowledging that racial and other forms of animus assume a spatial dimension. Not only does intercultural hostility take different forms depending on location, but so, too, does the concomitant bias-motivated violence imply “places for races.” The very intent and motive of hate crimes are grounded in the perceived need of perpetrators to defend carefully crafted boundaries. While these boundaries are largely cultural, they may also take on a real, physical form, at least from the perpetrator’s perspective. Nowhere is this more evident than in the geographical imagination of the White Supremacist movement. This paper will trace the …

Mixing Layer Dynamics In Separated Flow Over An Estuarine Sill With Variable Stratification, Stefan A. Talke, Alexander R. Horner-Devine, C. Chris Chickadel

Civil and Environmental Engineering Faculty Publications and Presentations

We investigate the generation of a mixing layer in the separated flow behind an estuarine sill (height H ∼ 4 m) in the Snohomish River, Washington as part of a larger investigation of coherent structures using remote and in situ sensing. During increasing ebb flows the depth d and stratification decrease and a region of sheared flow characterized by elevated production of turbulent kinetic energy develops. Profiles of velocity and acoustic backscatter exhibit coherent fluctuations of order 0.1 Hz and are used to define the boundaries of the mixing layer. Variations in the mixing layer width and its embedded coherent …

Empirical Observation Of The Impact Of Traffic Oscillations On Freeway Safety, Christopher M. Monsere, Soyoung Ahn

TREC Final Reports

Traffic oscillations are typical features of congested traffic flow that are characterized by recurring decelerations followed by accelerations (stop-and-go driving). The negative environmental impacts of these oscillations are widely accepted, but their impact on traffic safety has been debated. This report describes the impact of freeway traffic oscillations on traffic safety. This study employs a matched case-control design using high resolution traffic and crash data from a freeway segment. Traffic conditions prior to each crash were taken as cases, while traffic conditions during the same periods on days without crashes were taken as controls. These were also matched by presence …

Modeling Acoustic Scattering From The Seabed Using Transport Theory, Jorge Quijano, Lisa M. Zurk

Electrical and Computer Engineering Faculty Publications and Presentations

Radiative Transfer (RT) theory has established itself as an important tool for electromagnetic remote sensing in parallel plane geometries with random distributions of scatterers, and most recently it has also been proposed as a model for the propagation of elastic waves in layered ocean sediments. In this work the capabilities of this model are illustrated, as the RT method is used to predict backscattering strength from laboratory models of random media. The RT model is characterized by its flexibility on accommodating scatterers in a broad variety of sizes, shapes, and acoustic contrast relative to the background media. Additionally, this formulation …

Virus Silicification Under Simulated Hot Spring Conditions, James R. Laidler, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Silicification of organisms in silica-depositing environments can impact both their ecology and their presence in the fossil record. Although microbes have been silicified under laboratory and environmental conditions, viruses have not. Bacteriophage T4 was successfully silicified under laboratory conditions that closely simulated those found in silica-depositing hot springs. Virus morphology was maintained, and a clear elemental signature of phosphorus was detected by energy-dispersive X-ray spectrophotometry (EDS).

Interview With Crystal Benson, Green Building Services, 2010 (Audio), Crystal Benson

All Sustainability History Project Oral Histories

Interview of Crystal M. Benson by Alex Woolery at Green Building Services Portland, Oregon on August 12th, 2010.

The interview index is available for download.