Digital Commons Network^™

Interpreting Individual Classifications Of Hierarchical Networks, Will Landecker, Michael David Thomure, Luis M.A. Bettencourt, Melanie Mitchell, Garrett T. Kenyon, Steven P. Brumby

Computer Science Faculty Publications and Presentations

Hierarchical networks are known to achieve high classification accuracy on difficult machine-learning tasks. For many applications, a clear explanation of why the data was classified a certain way is just as important as the classification itself. However, the complexity of hierarchical networks makes them ill-suited for existing explanation methods. We propose a new method, contribution propagation, that gives per-instance explanations of a trained network's classifications. We give theoretical foundations for the proposed method, and evaluate its correctness empirically. Finally, we use the resulting explanations to reveal unexpected behavior of networks that achieve high accuracy on visual object-recognition tasks using well-known …

Nonnegativity Of Exact And Numerical Solutions Of Some Chemotactic Models, Patrick De Leenheer, Jay Gopalakrishnan, Erica Zuhr

Mathematics and Statistics Faculty Publications and Presentations

We investigate nonnegativity of exact and numerical solutions to a generalized Keller–Segel model. This model includes the so-called “minimal” Keller–Segel model, but can cover more general chemistry. We use maximum principles and invariant sets to prove that all components of the solution of the generalized model are nonnegative. We then derive numerical methods, using finite element techniques, for the generalized Keller–Segel model. Adapting the ideas in our proof of nonnegativity of exact solutions to the discrete setting, we are able to show nonnegativity of discrete solutions from the numerical methods under certain standard assumptions. One of the numerical methods is …

Online Learning In A Chemical Perceptron, Peter Banda, Christof Teuscher, Matthew R. Lakin

Computer Science Faculty Publications and Presentations

Autonomous learning implemented purely by means of a synthetic chemical system has not been previously realized. Learning promotes reusability and minimizes the system design to simple input-output specification. In this article we introduce a chemical perceptron, the first full-featured implementation of a perceptron in an artificial (simulated) chemistry. A perceptron is the simplest system capable of learning, inspired by the functioning of a biological neuron. Our artificial chemistry is deterministic and discrete-time, and follows Michaelis-Menten kinetics. We present two models, the weight-loop perceptron and the weight-race perceptron, which represent two possible strategies for a chemical implementation of linear integration and …

Stability Of Large Flocks: An Example, J. J. P. Veerman, F. M. Tangerman

Mathematics and Statistics Faculty Publications and Presentations

The movement of a flock with a single leader (and a directed path from it to every agent) can be stabilized. Nonetheless for large flocks perturbations in the movement of the leader may grow to a considerable size as they propagate throughout the flock and before they die out over time. As an example we consider a string of N+1 oscillators moving in the line. Each one `observes' the relative velocity and position of only its nearest neighbors. This information is then used to determine its own acceleration. Now we fix all parameters except the number of oscillators. We then …

Wet Meadow Plant Associations, Malheur National Wildlife Refuge, Harney County, Oregon, John A. Christy

Institute for Natural Resources Publications

In July 2012, we sampled 131 plots in wet meadow habitat at the southern end of the Malheur National Wildlife Refuge. Analysis of the data identified eleven different plant associations: Alopecurus pratensis, Carex aquatilis var. aquatilis, Carex nebrascensis, Carex pellita, Carex praegracilis, Carex sheldonii, Distichlis spicata, Juncus balticus, Leymus triticoides, Phalaris arundinacea, and Sparganium eurycarpum. Plant associations spanned a wetland gradient from seasonally moist to seasonally or perennially flooded, but surface water had left most stands at time of sampling. Mean Wetland Indicator Status scores help to place the plant associations within gradients in soil moisture and alkalinity. The Alopecurus …

Model For Acid-Base Chemistry In Nanoparticle Growth (Mabnag), Taina Yli-Juuti, Kelley Barsanti, L. Hildebrandt Ruiz, Antti-Jussi Kieloaho, U. Makkonen, Tuukka Petäjä, Taina Ruuskanen, Markku Kulmala, Ilona Riipinen

Civil and Environmental Engineering Faculty Publications and Presentations

Climatic effects of newly-formed atmospheric secondary aerosol particles are to a large extent determined by their condensational growth rates. However, all the vapours condensing on atmospheric nanoparticles and growing them to climatically relevant sizes are not identified yet and the effects of particle phase processes on particle growth rates are poorly known. Besides sulfuric acid, organic compounds are known to contribute significantly to atmospheric nanoparticle growth. In this study a particle growth model MABNAG (Model for Acid-Base chemistry in NAnoparticle Growth) was developed to study the effect of salt formation on nanoparticle growth, which has been proposed as a potential …

Climate Action Progress, 2013, Campus Sustainability Office

Campus Sustainability Office Publications, Reports and Presentations

In 2010, Portland State University (PSU) adopted the University’s first Climate Action Plan (CAP) as part of the American College and University President’s Climate Commitment (ACUPCC). The CAP calls for climate neutrality by 2040 and identifies emission reduction targets in the following areas: Buildings & Energy, Materials, Travel, Commuting, Education & Research, and EcoDistrict Development. This report serves as an assessment of progress to date and provides: an updated carbon emissions profile, a snapshot of progress on individual actions, a summary of efforts contributing to CAP goals, and suggestions regarding next steps.

Pine Creek Conservation Area: 2013 Mapping And Monitoring Report, Eric M. Nielsen, Matthew D. Noone, James S. Kagan, Matthew T. Lee

Institute for Natural Resources Publications

Pine Creek Conservation Area (PCCA), just northeast of the John Day River in Wheeler County, Oregon, was acquired in 1999-2001 by the Confederate Tribes of Warm Springs with support from the Bonneville Power Administration (BPA), to mitigate for wildlife losses created by the large, hydropower Columbia River Dams, particularly the Bonneville, Dalles and John Day Dams. Many thousands of acres of grassland, shrub steppe and riparian habitats were lost due to inundation, and the objectives of the acquisition included restoration of similar habitats. As part of an interagency agreement created in 2002, the Oregon Natural Heritage Information Center established a …

Forecasting Microprocessor Technology In The Multicore Era Using Tfdea, Saranya Durairajan, Maria Ibarra Prado, Noshad Rahimi, Shabnam Razeghian Jahromi

Engineering and Technology Management Faculty Publications and Presentations

Technological advancements in the microprocessor industry are benchmarked and gauged against a set of diverse criteria, specific to the fabrication process, usage as well as achieved performance. Changing trends in the appeal factor as well as wide variety of growing application of microprocessors in different industries also have a defining impact in the advancement of the technological features in future. This study improves the previous investigation in forecasting microprocessors? technology and uses Technology Forecasting using Data Envelopment Analysis (TFDEA) methodology for an enhanced model. The study takes advantage of the recent microprocessor dataset including multi core processors, from a variety …

Forecasting Hybrid Electric Vehicles Using Tfdea, Shabnam Razeghian Jahromi, Anca-Alexandra Tudori, Timothy R. Anderson

Engineering and Technology Management Faculty Publications and Presentations

The Toyota Prius was introduced in Japan fifteen years ago and over 60 additional hybrid electric vehicles automobiles and redesigns have been brought to the market around the world since that time. There is major interest in future of the electric cars as using ?the alternative fuel? can significantly decrease the environmental and fuel dependency concerns. This work has used data envelopment analysis to forecast the future of hybrid electric cars. It is based on a previous research on the same subject with an improvement in input-output model that has enhanced the outcomes to a great extent. The former study …

A Call To Action: What Student Teachers Can Teach Us, Kathleen M. Cowin

Northwest Journal of Teacher Education

This qualitative study uses six years of survey data, collected from student teachers in a graduate level university initial teacher licensure program, to illuminate student teachers’ experiences with their cooperating teachers during their student teaching internship. The data, comments made by student teachers about their experiences with their cooperating teachers, were used to answer this research question: What are student teachers telling us about their experiences with their cooperating teachers? Using the constant comparative method of qualitative analysis (Glaser & Strauss, 1967) the survey data consisting of answers to the open form question “My cooperating teacher could have been more …

Spatial And Temporal Patterns Of Amphibian Chytrid Fungus Batrachochytrium Dendrobatidis Occupancy In Amphibian Habitats, Tara Chestnut

Environmental Science and Management Professional Master's Project Reports

Chytrid fungi are the most ancestral of the fungi and are global in distribution. There are over 1200 species of Chytridiomycota described from freshwater, marine and terrestrial systems in temperate, tropical and tundra environments. Chytridiales are characterized by a range of morphologies and share the flask- or pot-like shape of the zoosporangia, within which motile zoospores develop. Chytrids function primarily as plant saprobes and parasites, but some also parasitize animals. Chytrids are observed in conjunction with the decline of freshwater and marine algal blooms, they decompose excess pollen, and comprise the fungal flora in gut of herbivores. Some chytrids also …

Understanding The Drivers Of Forest, Residential, And Agricultural Land Values In Yamhill County Using Hedonic Models, Emily D. Dietrich

Environmental Science and Management Professional Master's Project Reports

Hedonic modeling is commonly used in land and property value estimations in an attempt to identify the impact that various attributes have on the market value of that property. The purpose of this study is to examine the factors contributing to land value of agricultural, forest, and residential properties in Yamhill County, as part of the Spatial Ecosystem Services Analysis, Modeling, and Evaluation (SESAME, http://www.pdx.edu/ecosystem-services/) project. This paper discusses the process and preliminary results of the development of hedonic models that will be utilized for predicting land value changes under future land conversion scenarios. Applying the models to future scenarios …

Yet Another Crisis Of The Book, Bennett Gilbert

University Studies Faculty Publications and Presentations

Book bindings and binding decor can reveal deep parts of our attitudes toward books and toward culture. Changes in attitudes toward the codex book during the French Revolution and the Industrial Revolution are part of continual change in book culture. The re-binding of early printed books is exemplary evidence of these changes. The new bindings express both a rejection of pre-Enlightenment culture and an attempt to stabilize traditional cultural values. This also suggests how we might view events customarily considered to be "revolutions".

Daily Temperature Fluctuations Unpredictably Influence Developmental Rate And Morphology At A Critical Early Larval Stage In A Frog, Juliana M. Arrighi, Ezra S. Lencer, Advait Jukar, Daesik Park, Patrick C. Phillips, Robert H. Kaplan

Complex Systems Faculty Publications and Presentations

Background: Environmental temperature has profound consequences for early amphibian development and many field and laboratory studies have examined this. Most laboratory studies that have characterized the influence of temperature on development in amphibians have failed to incorporate the realities of diel temperature fluctuations (DTF), which can be considerable for pond-breeding amphibians.

Results: We evaluated the effects of different ecologically relevant ranges of DTF compared with effects of constant temperatures on development of embryos and larvae of the Korean fire-bellied toad (Bombina orientalis). We constructed thermal reaction norms for developmental stage, snout- vent length, and tail length by fitting …

Meaningful Sustainability Learning: An Action Research Study Of Sustainability Pedagogy In Two University Courses, Heather Burns

Educational Leadership and Policy Faculty Publications and Presentations

Educators are increasingly aware of the importance of sustainability and the need to educate for sustainable change within higher education. This article addresses the growing need to focus on how teaching and learning can be re-oriented towards sustainability, and more specifically how educators can effectively address increasingly well-known sociocultural and ecological problems in ways that transform learners and empower them to make change based on a sense of civic responsibility and sustainability. This research study draws on the Burns Model of Sustainability Pedagogy, which integrates ecological design, systemic and interdisciplinary learning, multiple perspectives, an active and engaged learning process, and …

What Work Samples Reveal About Secondary Pre-Service Social Studies Teachers' Use Of Literacy Strategies, Susan J. Lenski, Gayle Y. Thieman

Education Faculty Publications and Presentations

The article discusses a study which aims to answer the research questions of whether secondary social studies pre-service teachers incorporate literacy strategies in their work samples during student teaching, and the extent and conditions secondary social studies pre-service teachers use higher levels of literacy strategies in their work samples. The study is framed within 3 areas of research namely activity theory, work sample methodology and disciplinary literacy.

Final Coastal Lakes Aquatic Plant Survey Report, Mary Pfauth, Mark Sytsma

Center for Lakes and Reservoirs Publications and Presentations

Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming invasive aquatic plants can result in loss of native plant biodiversity and reduction of the structural complexity of the underwater habitat.

Scientism, Philosophy And Brain-Based Learning, Gregory M. Nixon

Northwest Journal of Teacher Education

Since educators are always looking for ways to improve their practice, and since empirical science is now accepted in our worldview as the final arbiter of truth, it is no surprise they have been lured toward cognitive neuroscience in hopes that discovering how the brain learns will provide a nutshell explanation for student learning in general. I argue that identifying the person with the brain is scientism (not science), that the brain is not the person, and that it is the person who learns. In fact, the brain only responds to the learning of embodied experience within the extra-neural network …

Enhancing Ai High School Student Success: A Work In Progress, Mapuana C.K. Antonio, Mary Schilling, Sylvia Oliver, Jennifer Lebeau

Northwest Journal of Teacher Education

This paper describes the first-year activities of a five-year project funded by the U.S. Department of Education as part of the Indian Education Demonstration Grants for Indian Children program. The project brings students, families, the tribal government, and the tribal community together to improve the lives and education of students, as well as their families and community, through a comprehensive change in school culture. The project utilizes a unique, multifaceted approach to offer academic and student support; a four-year Biomedical Science program; Science, Technology, Engineering, and Math (STEM) enrichment; professional development; and community engagement. The overall goal is to assist …

Schoology-Supported Classroom Management: A Curriculum Review, Shampa Biswas

Northwest Journal of Teacher Education

Schoology is an online learning, classroom management, and social networking platform that attempts to improve learning through better communication, collaboration, and increased access to curriculum and supplemental content. In this article, the author evaluates different prospects of Schoology-supported classroom management using selected principles of students learning and literacy development from Cummin et al (2007). Innovative approaches and tools in the Schoology website facilitate both teachers, students, parents to build a collaborative community of learners to fulfill the educational goals in the 21st century. It can be expected that Schoology’s supported instruction has the strongest potentiality of connecting and collaborating school …

Interactive Ambient Visualizations For Soft Advice, Emerson Murphy-Hill, Titus Barik, Andrew P. Black

Computer Science Faculty Publications and Presentations

Some software packages offer the user soft advice: recommendations that are intended to help the user create high quality artifacts, but which may turn out to be bad advice. It is left to the user to determine whether the soft advice really will improve quality, and to decide whether or not to adopt it. Visualizations can help the user in making this decision, but we believe that conventional visualizations are less than ideal. In this paper, we describe an interactive ambient visualization to help users identify, understand and interpret soft advice.

Our visualization was developed to help programmers interpret code …

Do Cryoconite Holes Have The Potential To Be Significant Sources Of C, N, And P To Downstream Depauperate Ecosystems Of Taylor Valley, Antarctica?, Elizabeth A. Bagshaw, Martyn Tranter, Andrew G. Fountain, Kathleen A. Welch, Hassan J. Basagic, W. Berry Lyons

Geology Faculty Publications and Presentations

Nutrient recycling occurs in hydrologically isolated cryoconite holes on the glaciers of the McMurdo Dry Valleys, Antarctica. Biogeochemical processes enrich the cryoconite holes with solute and nutrients compared to the source sediment and glacier ice. The position of the glacier within the landscape affects the physical and biogeochemical character of the cryoconite holes, with those found in more biologically productive areas of the valley having higher concentrations of C, N, and P and higher pH. Comprehensive assessment of the quality and quantity of bioavailable C, N, and P shows that the cryoconite holes represent a significant store of nutrient in …

Appendix C—Deformation Models For Ucerf3, Tom Parsons, Kaj M. Johnson, Peter Bird, Jayne Bormann, Timothy E. Dawson, Edward H. Field, William C. Hammond, Thomas A. Herring, Robert Mccaffrey, Zheng-Kang Shen, Wayne R. Thatcher, Ray J. Weldon Ii, Yuehua Zeng

Geology Faculty Publications and Presentations

This document describes efforts to best characterize seismogenic deformation in and near California. The rate of hazardous earthquakes in California is expected to be proportional to deformation rates; in particular, the rates at which faults slip. Fault slip rates are determined from offsets of geologic and geomorphic features of measured age and by modeling geodetically determined surface displacement rates. Extensive use of geodesy in the form of Global Positioning System (GPS) observations is a new feature brought into the Working Group on California Earthquake Probabilities (WGCEP) forecasts for the Uniform California Earthquake Rupture Forecast, version 3 (UCERF3) model. Geodetic measurements …

Characterization Of Nano-Scale Aluminum Oxide Transport Through Porous Media, Sasha Norien Norwood

Dissertations and Theses

Land application of biosolids has become common practice in the United States as an alternative to industrial fertilizers. Although nutrient rich, biosolids have been found to contain high concentrations of emerging contaminants (e.g. pharmaceuticals, personal care products) while containing a significant fraction of inorganic nano-scale colloidal materials such as oxides of iron, titanium, and aluminum.

Given their reactivity and small size, there are many questions concerning the potential migration of these nano-sized colloidal materials through the soil column and into our surface and groundwater bodies. Transport of emerging pollutants of concern through the soil column, at minimum, is impacted by …

Analyzing Experimental Data And Model Parameters: Implications For Predictions Of Soa Using Chemical Transport Models, Kelley Barsanti, Annmarie G. Carlton, Serena H. Chung

Civil and Environmental Engineering Faculty Publications and Presentations

Despite critical importance for air quality and climate predictions, accurate representation of secondary organic aerosol (SOA) formation remains elusive. An essential addition to the ongoing discussion of improving model predictions is an acknowledgement of the linkages between experimental conditions, parameter optimization and model output, as well as the linkage between empirically-derived partitioning parameters and the physicochemical properties of SOA they represent in models. In this work, a "best available" set of SOA modeling parameters is selected by comparing predicted SOA yields and mass concentrations with observed yields and mass concentrations from a comprehensive list of published smog chamber studies. Evaluated …

Evolution Of Multispectral Aerosol Optical Properties In A Biogenically-Influenced Urban Environment During The Cares Campaign, Madhu Gyawali, W. Patrick Arnott, Rahul A. Zaveri, C. Song, Mikhail Pekour, B. Flowers, Manvendra K. Dubey, Ari Setyan, Qi Zhang, Joseph Harworth, James Gregory Radney, Dean B. Atkinson, S. China, Claudio Mazzoleni, Kyle Gorkowski, R. Subramanian, B. Tom Jobson, Hans Moosmüller

Chemistry Faculty Publications and Presentations

Ground-based aerosol measurements made in June 2010 within Sacramento urban area (site T0) and at a 40-km downwind location (site T1) in the forested Sierra Nevada foothills area are used to investigate the evolution of multispectral optical properties as the urban aerosols aged and interacted with biogenic emissions. Along with black carbon and non-refractory aerosol mass and composition observations, spectral absorption (ᵝabs), scattering (ᵝsca), and extinction (ᵝext) coefficients for wavelengths ranging from 355 to 1064nm were measured at both sites using photoacoustic (PA) instruments with integrating nephelometers and using cavity ring-down (CRD) instruments. The …

Robust Visible Light Photoswitching With Ortho-Thiol Substituted Azobenzenes, Subhas Samanta, Theresa M. Mccormick, Simone K. Schmidt, Dwight S. Seferos, G. Andrew Woolley

Chemistry Faculty Publications and Presentations

Introduction of S-ethyl groups in all four ortho positions of azobenzene prevents reduction of the azo group by intracellular glutathione, while enhancing the absorptivity to ∼10000 M⁻¹ cm⁻¹ in the blue and green regions of the visible spectrum. cis-to-trans isomerization occurs thermally on the minutes timescale. Further, this substitution pattern permits switching with red light, a color that is more penetrating through biological tissues than other parts of the visible spectrum.

Extrahepatic 25-Hydroxylation Of Vitamin D3 In An Engineered Osteoblast Precursor Cell Line Exploring The Influence On Cellular Proliferation And Matrix Maturation During Bone Development, Shelley S. Mason, Sean S. Kohles, Shelley R. Winn, Randy D. Zelick

Biology Faculty Publications and Presentations

Osteoblastic precursors experience distinct stages during differentiation and bone development, which include proliferation, extracellular matrix (ECM) maturation, and ECM mineralization. It is well known that vitamin D plays a large role in the regulation of bone mineralization and homeostasis via the endocrine system. The activation of vitamin D requires two sequential hydroxylation steps, first in the kidney and then in the liver, in order to carry out its role in calcium homeostasis. Recent research has demonstrated that human-derived mesenchymal stem cells (MSCs) and osteoblasts can metabolize the immediate vitamin D precursor 25- dihydroxyvitamin D₃(25OH₂D₃) to the active steroid 1α,25-dihydroxyvitamin D₃ …

Osmb Ais Funds Final Report: Task 1 Boat Ramp Monitoring For New Zealand Mud Snails, Valance Brenneis, Samuel Cimino, Angela L. Strecker

Center for Lakes and Reservoirs Publications and Presentations

The New Zealand mud snail (Potamopyrgus antipodarum; NZMS) is an invasive species found in a variety of ecosystems in Oregon, including brackish estuaries, heavily used recreational rivers, and highly trafficked coastal freshwater lakes. NZMS are an invasive species of concern because once established, they may out-compete native invertebrate grazers, such as native insect larvae that provide important food resources for fish, and NZMS themselves provide little nutritional value. Monitoring for the presence and population density of NZMS was performed at boat ramps located along several water bodies in 2006 – 2007. These water bodies were then re-sampled during the summer …