Digital Commons Network^™

Incorporating Priors For Medical Image Segmentation Using A Genetic Algorithm, Payel Ghosh, Melanie Mitchell, James A. Tanyi, Arthur Y. Hung

Computer Science Faculty Publications and Presentations

Medical image segmentation is typically performed manually by a physician to delineate gross tumor volumes for treatment planning and diagnosis. Manual segmentation is performed by medical experts using prior knowledge of organ shapes and locations but is prone to reader subjectivity and inconsistency. Automating the process is challenging due to poor tissue contrast and ill-defined organ/tissue boundaries in medical images. This paper presents a genetic algorithm for combining representations of learned information such as known shapes, regional properties and relative position of objects into a single framework to perform automated three-dimensional segmentation. The algorithm has been tested for prostate segmentation …

Slow Slip Events And Time-Dependent Variations In Locking Beneath Lower Cook Inlet Of The Alaska-Aleutian Subduction Zone, Shanshan Li, Jeffrey Freymueller, Robert Mccaffrey

Geology Faculty Publications and Presentations

We identify a series of abrupt changes in GPS site velocities in Lower Cook Inlet, Alaska, in late 2004, early 2010, and late 2011. The site motions during each time period are nearly linear. The surface deformations inferred from GPS for pre-2004 and 2010–2011 are similar to each other, as are 2004–2010 and post-2011. We estimate the slip distribution on the Alaska-Aleutian subduction plate interface accounting for upper plate block rotations and interpret this toggling between two deformation patterns as caused by transient slip. We find that by allowing negative slip deficit rates (i.e., creep rates in excess of relative …

Characterization And Comparative Analysis Of 2,4-Toluene Diisocyanate And 1,6-Hexamethylene Diisocyanate Haptenated Human Serum Albumin And Hemoglobin, Morgen Mhike, Ita Chipinda, Brandon F. Law, Toni A. Bledsoe, Angela R. Lemons, Ajay P. Nayak, Brett J. Green, Donald H. Beezhold, Reuben H. Simoyi, Paul D. Siegel

Chemistry Faculty Publications and Presentations

Diisocyanates (dNCOs) are lowmolecularweight chemical sensitizers that reactwith autologous proteins to produce neoantigens. dNCO-haptenated proteins have been used as immunogens for generation of dNCO-specific antibodies and as antigens to screen for dNCO-specific antibodies in exposed individuals. Detection of dNCOspecific antibodies in exposed individuals for diagnosis of dNCO asthma has been hampered by poor sensitivities of the assay methods in that specific IgE can only be detected in approximately 25% of the dNCO asthmatics. Apart from characterization of the conjugates used for these immunoassays, the choice of the carrier protein and the dNCO used are important parameters that can influence the …

Micrometeorological Simulations To Predict The Impacts Of Heat Mitigation Strategies On Pedestrian Thermal Comfort In A Los Angeles Neighborhood, Mohammad Taleghani, David J. Sailor, George A. Ban-Weiss

Mechanical and Materials Engineering Faculty Publications and Presentations

The urban heat island impacts the thermal comfort of pedestrians in cities. In this paper, the effects of four heat mitigation strategies on micrometeorology and the thermal comfort of pedestrians were simulated for a neighborhood in eastern Los Angeles County. The strategies investigated include solar reflective ‘cool roofs’, vegetative ‘green roofs’, solar reflective ‘cool pavements’, and increased streetlevel trees. Aseries of micrometeorological simulations for an extreme heat day were carried out assuming widespread adoption of each mitigation strategy. Comparing each simulation to the control simulation assuming current land cover for the neighborhood showed that additional street-trees and cool pavements reduced …

Exploring The Impact Of An Ld Diagnosis On The Self-Determination Of Women In Poverty, Cynthia Jakes Stadel

Dissertations and Theses

This collective case study explored the impact of a later-in-life learning disability (LD) diagnosis on women in poverty. The study focused on the perspectives of four women who were not identified with LD as children but accessed assessment services as adults receiving Oregon's Temporary Assistance for Needy Families (TANF). All four reported painful awareness of learning differences as youths; as adults they voluntarily engaged in a "labeling event," furthering a process toward personal transformation and enhanced well-being initiated by their own awareness and curiosity. The women described critical social and emotional support systems and relationships that helped them integrate understanding …

Faculty Senate Monthly Packet February 2016, Portland State University Faculty Senate

Faculty Senate Monthly Packets

The February 2016 Monthly packet includes the February agenda and appendices and the Faculty Senate minutes and attachments from the meeting held January 2016.

The Log-Exponential Smoothing Technique And Nesterov’S Accelerated Gradient Method For Generalized Sylvester Problems, N. T. An, Daniel J. Giles, Nguyen Mau Nam, R. Blake Rector

Mathematics and Statistics Faculty Publications and Presentations

The Sylvester or smallest enclosing circle problem involves finding the smallest circle enclosing a finite number of points in the plane. We consider generalized versions of the Sylvester problem in which the points are replaced by sets. Based on the log-exponential smoothing technique and Nesterov’s accelerated gradient method, we present an effective numerical algorithm for solving these problems.

Minimizing Differences Of Convex Functions With Applications To Facility Location And Clustering, Mau Nam Nguyen, R. Blake Rector, Daniel J. Giles

Mathematics and Statistics Faculty Publications and Presentations

In this paper we develop algorithms to solve generalized Fermat-Torricelli problems with both positive and negative weights and multifacility location problems involving distances generated by Minkowski gauges. We also introduce a new model of clustering based on squared distances to convex sets. Using the Nesterov smoothing technique and an algorithm for minimizing differences of convex functions called the DCA introduced by Tao and An, we develop effective algorithms for solving these problems. We demonstrate the algorithms with a variety of numerical examples.

Salem Keizer Prenatal-Grade Three Evaluation & Technical Assistance, Center For Improvement Of Child And Family Services

Early Childhood

The purpose of this document is to provide information and resources to schools, early childhood programs, and others who are seeking to improve school readiness, family engagement, and school success within a Prenatal-Grade 3 framework. While the information presented is not a comprehensive list of programs and strategies, the list reflects resources that have been identified as potentially useful within Oregon and/or strategies that have been used in Oregon to strengthen child and family outcomes. This document is one of three compilations of programs, activities, and resources. This document includes resources related to (1) Children’s Kindergarten Readiness and Transition to …

Distributed Modeling Of Ablation (1996–2011) And Climate Sensitivity On The Glaciers Of Taylor Valley, Antarctica, Matthew J. Hoffman, Andrew G. Fountain, Glen E. Liston

Geology Faculty Publications and Presentations

The McMurdo Dry Valleys of Antarctica host the coldest and driest ecosystem on Earth, which is acutely sensitive to the availability of water coming from glacial runoff. We modeled the spatial variability in ablation and assessed climate sensitivity of the glacier ablation zones using 16 years of meteorological and surface mass-balance observations collected in Taylor Valley. Sublimation was the primary form of mass loss over much of the ablation zones, except for near the termini where melt, primarily below the surface, dominated. Microclimates in ~10 m scale topographic basins generated melt rates up to ten times higher than over smooth …

The Elusive Quest For Rna Knots, Aaron S. Burton, Marco Di Stefano, Niles Lehman, Henri Orland, Cristian Micheletti

Chemistry Faculty Publications and Presentations

Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made it possible to investigate the incidence of physical knots in this type of biomolecule, too. Strikingly, no knots have been found to date in the known RNA structures. In this Point of View Article we discuss the absence of knots in currently available RNAs and consider the reasons why knots in RNA have …

In Defense Of Culturally-Specific Organizations: Understanding The Rationale And The Evidence, Ann Curry-Stevens, Jennifer Sita Muthanna

School of Social Work Faculty Publications and Presentations

Racial disparities abound in human services, with communities of color facing grave impediments to positive progress. Mainstream institutions move painstakingly slowly on reforms—movement too slow to offer this generation prospects for real hope in equity. This paper builds the rationale for expanding funding for culturally-specific organizations, detailing the ways that the literature and the tacit knowledge of culturally-specific organizations improve outcomes for clients and communities of color. The article identifies the service benefits in terms of client outcomes, accountability practices, community benefits, cultural affirmation and inclusion, building community and political capital, and lessening investments in white-centric services. We also identify …

Utilizing High Resolution Bus Gps Data To Visualize And Identify Congestion Hot-Spots In Urban Arterials, Nicholas B. Stoll

PSU Transportation Seminars

The research uses high resolution bus data to examine sources of delay on urban arterials. A set of tools were created to help visualize trends in bus behavior and movement, which allowed for larger traffic trends to be visualized along urban corridors and urban streets. By using buses as probes and examining aggregated bus behavior, contoured speed plots were used to understand the behavior of roadways outside the zone of influence of bus stops. These speed plots can be utilized to discover trends and travel patterns with only a few days’ worth of data. Congestion and speed variation can be …

Processes Controlling Carbon Cycling In Antarctic Glacier Surface Ecosystems, Elizabeth A. Bagshaw, Martyn Tranter, Jemma L. Wadham, Andrew G. Fountain, A. Dubnick, S. Fitzsimons

Geology Faculty Publications and Presentations

Glacier surface ecosystems, including cryoconite holes and cryolakes, are significant contributors to regional carbon cycles. Incubation experiments to determine the net production (NEP) of organic matter in cryoconite typically have durations of 6-24 hours, and produce a wide range of results, many of which indicate that the system is net heterotrophic. We employ longer term incubations to examine the temporal variation of NEP in cryoconite from the McMurdo Dry Valleys, Antarctica to examine the effect of sediment disturbance on system production, and to understand processes controlling production over the lifetimes of glacier surface ecosystems. The shorter-term incubations have durations of …

Efficient Bimolecular Mechanism Of Photochemical Hydrogen Production Using Halogenated Boron-Dipyrromethene (Bodipy) Dyes And A Bis(Dimethylglyoxime) Cobalt(Iii) Complex, Randy Pat Sabatini, Brian M. Lindley, Theresa M. Mccormick, Theodore Lazarides, William Brennessel, David W. Mccamant, Richard Eisenberg

Chemistry Faculty Publications and Presentations

A series of Boron-­dipyrromethene (Bodipy) dyes were used as photosensitizers for photochemical hydrogen production in conjunction with [Co^III(dmgH)2pyCl] (where dmgH = dimethylglyoximate, py = pyridine) as the catalyst and triethanolamine (TEOA) as the sacrificial electron donor. The Bodipy dyes are fully characterized by electrochemistry, x-­‐ray crystallography, quantum chemistry calculations, femtosecond transient absorption and time-­‐resolved fluorescence, as well as in long-­‐term hydrogen production assays. Consistent with other recent reports, only systems containing halogenated chromophores were active for hydrogen production, as the long-­‐lived triplet state is necessary for efficient bimolecular electron transfer. Here, it is shown that the photostability of …

The Importance Of Housing, Accessibility, And Transport Characteristic Ratings On Stated Neighborhood Preference, Kristina Marie Currans

PSU Transportation Seminars

Travel demand models commonly lack the ability to understand how changing residential preferences influence future housing, land use, and transportation policies. As communities struggle to address social challenges related to increased economic uncertainty, transportation and land use planning have become increasingly centered on assumptions concerning the market for residential environments and travel choices. In response, an added importance has been placed on the development of toolkits capable of providing robust and flexible models to aid in understanding how differing assumptions contribute to a set of planning scenarios and how future residential location decisions may be made.

In this study, we …

Keeley Probes As A Tool For Uncovering Student Ideas: How Do Teachers Use Formative Assessment Probes To Plan And Adapt Instruction?, Kalin Tobler

Dissertations and Theses

Formative assessment probes, known as Keeley probes, are one tool teachers use to reveal students' scientific misconceptions, so that they can move them closer to conceptual understanding. The purpose of this research was to document how four elementary school teachers used formative assessment probes to plan and adapt instruction to improve student learning. Specifically:

• How did teachers choose appropriate probes? What learning goals did teachers hope to address by using the probe??
• What instructional sequences did teachers envision when planning to use a probe?
• What did teachers notice when analyzing student data from a probe?
• How did teachers use the …

Slope Failure Detection Through Multi-Temporal Lidar Data And Geotechnical Soils Analysis Of The Deep-Seated Madrone Landslide, Coast Range, Oregon, Michael Scott Marshall

Dissertations and Theses

Landslide hazard assessment of densely forested, remote, and difficult to access areas can be rapidly accomplished with airborne light detection and ranging (lidar) data. An evaluation of geomorphic change by lidar-derived digital elevation models (DEMs) coupled with geotechnical soils analysis, aerial photographs, ground measurements, precipitation data, and numerical modeling can provide valuable insight to the reactivation process of unstable landslides. A landslide was selected based on previous work by Mickleson (2011) and Burns et al. (2010) that identified the Madrone Landslide with significant volumetric changes. This study expands on previous work though an evaluation of the timing and causation of …

Reactivity Measurement In Estimation Of Benzoquinone And Benzoquinone Derivatives’ Allergenicity, Wilbes Mbiya, Ita Chipinda, Reuben H. Simoyi, Paul D. Siegel

Chemistry Faculty Publications and Presentations

Benzoquinone (BQ) and benzoquinone derivatives (BQD) are used in the production of dyes and cosmetics. While BQ, an extreme skin sensitizer, is an electrophile known to covalently modify proteins via Michael Addition (MA) reaction whilst halogen substituted BQD undergo nucleophilic vinylic substitution (SNV) mechanism onto amine and thiol moieties on proteins, the allergenic effects of adding substituents on BQ have not been reported. The effects of inserting substituents on the BQ ring has not been studied in animal assays. However, mandated reduction/elimination of animals used in cosmetics testing in Europe has led to an increased need for alternatives for the …

Learning Sustainability Leadership: An Action Research Study Of A Graduate Leadership Course, Heather L. Burns

Educational Leadership and Policy Faculty Publications and Presentations

This study used action research methodology to examine the development of sustainability leadership in a graduate leadership course. The research investigated the impact of this leadership course, which was designed using transformative learning theory with attention to integrating thematic content, multiple and non-dominant perspectives, a participatory process, and a contextual place-based approach. Grounded theory was used to explore if and how students’ understanding of sustainability leadership changed, and the pedagogical strategies that were most influential to their learning. Results revealed that students came to understand sustainability leadership as: the facilitation of a shared process, a process of emergence, and a …

Worldview-Based Scenarios Highlight Stakeholder Values And Assumptions, John Rueter

Environmental Science and Management Faculty Publications and Presentations

In lake management, we have the privilege and responsibility to work with the public on highly visible resources. Everybody has an opinion based on his or her personal values and observations. While we might sometimes consider this plethora of value statements as the bane of our existence, we all realize that public engagement is crucial for the health and future of lakes. Poor lake health is often caused by many little insults that stem from a wide range of legitimate views for how the lake should be treated as a resource. We need a framework to be able to deal …

High-Resolution Ground-Penetrating Radar Profiles Of Perennial Lake Ice In The Mcmurdo Dry Valleys, Antarctica: Horizon Attributes, Unconformities, And Subbottom, Hilary A. Dugan, Steven A. Arcone, Maciej K. Obryk, Peter T. Doran

Geology Faculty Publications and Presentations

Ground-penetrating radar (GPR) is not commonly used to study lake ice, and in general, the ground-based use of radar frequencies greater than 500 MHz in cryosphere geophysics is rare, due to a general interest in deeper stratigraphy and the difficulty of extensive profiling over rough snow surfaces. Our goal was to find further information on the origin of the deposition and formation of intra-ice layers, bottom topography, and subbottom deposits using GPR with pulses centered near 850 MHz on two permanently ice-covered lakes in the Mc- Murdo Dry Valleys, Antarctica. The profiles were obtained using a one-person sled operation over …

Emerging Adaptive Architectures For Biomolecular Computation, Matthew Fleetwood

Maseeh Summer Undergraduate Research Experience

The goal of this work is to explore applications of reservoir computing in biomolecular computation. Reservoir computing is a unique model for representing a mapping from one instance in time to a specific output. A neural network of randomly connected neurons is linked with a single output neuron or multiple output neurons. The output neurons are capable of mapping inputs to desired outputs using adaptable algorithms. This framework is investigated by using the Python programming language and object oriented design and programming. Neurons are created in programs by bundling information like input data and attributes of the network, which utilize …

Theoretical Estimates Of Spherical And Chromatic Aberration In Photoemission Electron Microscopy, Joseph P. S. Fitzgerald, Robert Campbell Word, Rolf Kӧnenkamp

Physics Faculty Publications and Presentations

We present theoretical estimates of the mean coefficients of spherical and chromatic aberration for low energy photoemission electron microscopy (PEEM). Using simple analytic models, we find that the aberration coefficients depend primarily on the difference between the photon energy and the photoemission threshold, as expected. However, the shape of the photoelectron spectral distribution impacts the coefficients by up to 30%. These estimates should allow more precise correction of aberration in PEEM in experimental situations where the aberration coefficients and precise electron energy distribution cannot be readily measured.

Research & Strategic Partnerships: Quarterly Review, Volume 3, Issue 1, Portland State University. Research & Strategic Partnerships

Portland State Research Magazine

To commemorate the opening of Tilikum Crossing and the launch of this dynamic new district, this issue of the RSP Quarterly Review focuses on PSU collaborations with OHSU, OMSI, and the City of Portland.

We start by describing how OMSI, PSU, and OHSU collaborated to bring an exhibit about the human genome from the Smithsonian Institution to Portland. We then present a series of stories about projects building on the complementary health and life science talents of PSU and OHSU researchers. These include a study of ethnic inequities in health care access, a new malaria therapy, tools to improve MRI …

A Brief Review Of Speaker Recognition Technology, Clark D. Shaver, John M. Acken

Electrical and Computer Engineering Faculty Publications and Presentations

This paper reviews the development of speaker recognition systems from pre-computing days to current trends. Advances in various sciences which have allowed autonomous speaker recognition systems to become a practical means of identity authentication are also reviewed.

Greater Number Of Larger Pieces: A Strategy To Promote Prospective Teachers’ Fraction Number Sense Development, Dana Olanoff, Ziv Feldman, Rachael M. Welder, Jennifer M. Tobias, Eva Thanheiser, Amy F. Hillen

Mathematics and Statistics Faculty Publications and Presentations

Prospective teachers (PTs) need opportunities to develop fraction number sense, yet little research has explicated how this development occurs. Our research team collaboratively designed a task targeted at helping PTs develop fraction number sense through an exploration of fraction comparison strategies. This paper focuses on developing one particular strategy, which we call Greater Number of Larger Pieces (GLP). We argue that understanding this strategy has the potential to support PTs’ number sense, particularly in regards to the measure interpretation of fractions. Analysis of data from two iterations of this task (implemented by five mathematics teacher educators at five US institutions …

Measuring Fidelity Of Implementation In A Large-Scale Professional Development Efficacy Study, Kathleen Mary Melhuish, Eva Thanheiser, Brenda Rosencrans

Mathematics and Statistics Faculty Publications and Presentations

Fidelity of implementation is the essential link between professional development (PD) experiences and changes in outcomes. Yet, as a field we have few measures available to directly look at implementation. In this poster, we present our preliminary work measuring teachers’ implementation of a research-based PD.

A Verified Information-Flow Architecture, Arthur Azevedo De Amorim, Nathan Collins, André Dehon, Delphine Demange, Cătălin Hriţcu, David Pichardie, Benjamin C. Pierce, Randy Pollack, Andrew Tolmach

Computer Science Faculty Publications and Presentations

SAFE is a clean-slate design for a highly secure computer system, with pervasive mechanisms for tracking and limiting information flows. At the lowest level, the SAFE hardware supports fine-grained programmable tags, with efficient and flexible propagation and combination of tags as instructions are executed. The operating system virtualizes these generic facilities to present an information-flow abstract machine that allows user programs to label sensitive data with rich confidentiality policies. We present a formal, machine-checked model of the key hardware and software mechanisms used to dynamically control information flow in SAFE and an end-to-end proof of noninterference for this model. We …

Tridiagonal Matrices And Boundary Conditions, J. J. P. Veerman, David K. Hammond

Mathematics and Statistics Faculty Publications and Presentations

We describe the spectra of certain tridiagonal matrices arising from differential equations commonly used for modeling flocking behavior. In particular we consider systems resulting from allowing an arbitrary boundary condition for the end of a one-dimensional flock. We apply our results to demonstrate how asymptotic stability for consensus and flocking systems depends on the imposed boundary condition.