Digital Commons Network^™

Tension Directly Stabilizes Reconstituted Kinetochore-Microtubule Attachments, Bungo Akiyoshi, Krishna K. Sarangapani, Andrew F. Powers, Christian R. Nelson, Steve Reichow, Hugo Arellano-Santoyo, Tamir Gonen, Jeffrey A. Ranish, Charles L. Asbury, Sue Biggins

Chemistry Faculty Publications and Presentations

Kinetochores are macromolecular machines that couple chromosomes to dynamic microtubule tips during cell division, thereby generating force to segregate the chromosomes. Accurate segregation depends on selective stabilization of correct ‘bi-oriented’ kinetochore-microtubule attachments, which come under tension due to opposing forces exerted by microtubules. Tension is thought to stabilize these bi-oriented attachments indirectly, by suppressing the destabilizing activity of a kinase, Aurora B. However, a complete mechanistic understanding of the role of tension requires reconstitution of kinetochore-microtubule attachments for biochemical and biophysical analyses in vitro. Here we show that native kinetochore particles retaining the majority of kinetochore proteins can be …

Embedding Parallel Computation In A Stochastic Mesh Network: A Morphogenetic Approach, Max Orhai

Anthós

Many basic techniques in computer science have been founded on the assumption that physical computing resources are scarce but orderly, and that the cost of effective direct communication between physically distant parts of a computer system is affordable. In ubiquitous computing systems such as sensor networks, or in the design of nano-scale systems, these familiar assumptions may not hold.

What if we suppose instead that computing capacity is plentiful, but that only local communication is possible, and the exact structure of the communication network is not known in advance? This is the domain of spatial programming.

How can we program …

Landslide Susceptibility In Tryon State Park, Oregon, Tracy E. Handrich

Anthós

LIDAR and topographic data were used to identify areas of high landslide susceptibility. An arctangent equation was used to calculate slope angle, design criteria of susceptibility and designate zones of high, moderate, and low risk.

Mapping Conservation Opportunity Areas For The Intertwine's Regional Conservation Strategy, Theresa Burcsu, James S. Kagan

Institute for Natural Resources Publications

As part of efforts to develop the Regional Conservation Strategy (RCS) for the greater Portland-Vancouver region, Oregon State University’s Institute for Natural Resources (INR) was asked to use spatial modeling to identify conservation opportunity areas (COAs). To complete the project, INR analysts proposed a strategy that would map high value areas using a landscape approach that is focused on relatively high spatial resolution data sets available for the whole metropolitan region. The approach creates 2 main metrics: one focused on terrestrial organisms and the other focused on aquatic and riparian organisms. These are combined to create a map of highly …

Resizable, Scalable, Concurrent Hash Tables Via Relativistic Programming, Josh Triplett, Paul E. Mckenney, Jonathan Walpole

Computer Science Faculty Publications and Presentations

Presentation focusing on software synchronization, thread locking, transactional memory, and relativistic programming. Hash table algorithms are presented with examples of relativistic list insertion and removal, and related data structures. Existing approaches are compared to new methodologies and future work with relativistic data structures.

Resizable, Scalable, Concurrent Hash Tables, Josh Triplett, Paul E. Mckenney, Jonathan Walpole

Computer Science Faculty Publications and Presentations

We present algorithms for shrinking and expanding a hash table while allowing concurrent, wait-free, linearly scalable lookups. These resize algorithms allow the hash table to maintain constant-time performance as the number of entries grows, and reclaim memory as the number of entries decreases, without delaying or disrupting readers.

We implemented our algorithms in the Linux kernel, to test their performance and scalability. Benchmarks show lookup scalability improved 125x over readerwriter locking, and 56% over the current state-of-the-art for Linux, with no performance degradation for lookups during a resize.

To achieve this performance, this hash table implementation uses a new concurrent …

Interview With Franklin Jones, B-Line, 2011 (Audio), Franklin Jones

All Sustainability History Project Oral Histories

Interview of Franklin Jones by Grant Russ at Portland, Oregon on May 31st, 2011.

The interview index is available for download.

Systems Ideas For The Scientific And Societal Imperatives Of The Coastal Ocean: Case Of The Bp Oil Gusher In The Gulf Of Mexico, Spring & Summer 2010, Christopher Mooers

Systems Science Friday Noon Seminar Series

In recent decades, great progress has been made in advancing the scientific understanding of the coastal ocean (i.e., the 200 nautical mile Exclusive Economic Zone (EEZ)) across a broad set of disciplines. Simultaneously, the societal use of the coastal ocean has skyrocketed through, for example, increased shipping & boating, sports & commercial fishing, and exploitation of non-living resources, such as, oil & gas extraction and sand & gravel mining. International law and national policy assign coastal nations the responsibility for stewardship (i.e., wise management) of their respective EEZs. The scope of the stewardship and applications can be summarized as (1) …

Spatial And Temporal Patterns In The Influence Of Land Use On Water Quality In Five Portland Area Creeks Representing Differing Levels Of Urbanization, Heejun Chang, Madeline Steele, Zoe Bonak

Geography Faculty Publications and Presentations

While the negative effects of urban development on freshwater systems are well documented, impacts of human disturbance on water quality vary depending on land cover, local climate, and temporal and spatial scales of analysis. To better understand this variation, we analyzed water quality data for a total of 15 sites from six Portland, Oregon area creeks at multiple spatial and temporal scales. The creeks are characterized by differing levels of urban development, from relatively pristine to highly developed. More than ten years of monthly data gathered by the Portland Bureau of Environmental Services were used to analyze temporal trends, and …

Assessment Of The Hydrologic Response To Climate Change In The Upper Deschutes River Basin, Central Oregon, Heejun Chang, M. Scott Waibel, Marshall W. Gannett, Christina L. Hulbe

Geography Faculty Publications and Presentations

Effects of climate change in the Cascade Range will likely include more rain, less snow, and earlier snowmelt in the Cascade Range as compared to present conditions. These changes, in turn, will affect the timing of runoff, groundwater recharge, and groundwater discharge to spring-fed streams. This hydrologic response needs to be examined and understood due to implications for water management. In this study, a water- and energy-balance model was used to explore 21st century changes in the water budget in the upper Deschutes Basin, and a groundwater model was used to evaluate the response of the groundwater system to those …

Climate Change Impact On Drought Risk And Uncertainty In The Willamette River Basin, Heejun Chang, Il-Won Jung

Geography Faculty Publications and Presentations

Climate change due to global warming could induce more frequent droughts in the Willamette River Basin because less snowfall in winter and earlier snowmelt due to temperature increase may lead to decreases in spring and summer streamflow. This study examines possible changes in drought risk using two drought indices, Standardized Precipitation Index (SPI) and Standardized Runoff Index (SRI). SPI represents a climatological drought index that considers only precipitation change, while SRI is a hydrological drought index that considers water balance change. In rainfall-dominated regions in the Willamette Valley, SPI is a useful drought index. In snow-dominated regions in the High …

Effects Of Climate Change On Water Quality In The Yaquina Estuary, Oregon, Cheryl A. Brown, Darrin Sharp, Heejun Chang, Madeline Steele

Geography Faculty Publications and Presentations

As part of a larger study to examine the effect of climate change (CC) on estuarine resources, we simulated the effect of rising sea level, alterations in river discharge, and increasing atmospheric temperatures on water quality in the Yaquina Estuary. Due to uncertainty in the effects of climate change, initial model simulations were performed for different steady river discharge rates that span the historical range in inflow, and for a range of increases in sea level and atmospheric temperature. Model simulations suggest that in the central portion of the estuary (19 km from mouth), a 60-cm increase in sea level …

Climate Change And Shifts In Water Related Ecosystem Services In The Tualatin And Yamhill River Basins, Heejun Chang, Terrance Anthony, Driss Ennaanay, Manu Sharma

Geography Faculty Publications and Presentations

Water related ecosystem services (WES), such as flow regulation, drinking water supply, temperature regulation, and water recreational activities, are affected by anthropogenic climate change. Forecasting potential shifts in such WES is critical to identifying the form and magnitude of likely impacts. We quantified the levels and values of WES under multiple climate change scenarios in the two watersheds located in the Portland metropolitan area, Oregon, USA using the combination of a hydrologic model Better Assessment Science Integrating point and Non-point Sources - Soil and Water Assessment Tool (BASINS-SWAT) and an ecosystem evaluation model ? Integrated Valuation of Ecosystem Services and …

Climate Change And Climate Variability: Personal Motivation For Adaptation And Mitigation, Jan C. Semenza, George B. Ploubidis, Linda Acha George

Environmental Science and Management Faculty Publications and Presentations

Background: Global climate change impacts on human and natural systems are predicted to be severe, far reaching, and to affect the most physically and economically vulnerable disproportionately. Society can respond to these threats through two strategies: mitigation and adaptation. Industry, commerce, and government play indispensable roles in these actions but so do individuals, if they are receptive to behavior change. We explored whether the health frame can be used as a context to motivate behavioral reductions of greenhouse gas emissions and adaptation measures. Methods: In 2008, we conducted a cross-sectional survey in the United States using random digit dialing. Personal …

Hardware Acceleration Of Inference Computing: The Numenta Htm Algorithm, Dan Hammerstrom

Systems Science Friday Noon Seminar Series

In this presentation I will describe the latest version of the Numenta HTM Cortical Learning Algorithm and why it is interesting for doing research into radical new computer architectures. Then I will discuss the hardware acceleration research we are doing, and briefly look at some preliminary applications development.

Interview With Michelle Markesteyn-Ratcliffe, Oda, 2011, Michelle Markesteyn-Ratcliffe

All Sustainability History Project Oral Histories

Interview of Michelle Markesteyn-Ratcliffe by Megan Rice in Portland, Oregon on May 10th, 2011.

The interview index is available for download.

Can Nuclear Power Be Part Of The Solution?, Robert Costanza, Cutler Cleveland, Bruce Cooperstein, Ida Kubiszewski

Institute for Sustainable Solutions Publications and Presentations

The author discusses the importance of incorporating the full costs of operating a nuclear power plant in the U.S., such as climate impact, risk of accidents, and safe disposal of radioactive waste. He argues on the need for changes in the country's evaluation of nuclear power which include the elimination of subsidies, and the requirement to buy full-coverage insurance for accidents. The author further highlights the cost of greenhouse gas emissions from nuclear power plants.

The Need For Authentic Assessments, Gayle Y. Thieman

Education Faculty Publications and Presentations

As state and local policymakers develop valid assessments, as proposed by Secretary Duncan, I suggest they incorporate criteria of “authentic assessment.” Unlike traditional tests of factual recall, authentic assessments are designed to examine students’ performance on real-world tasks. Authentic assessments require active learning and involvement on the part of students who construct their own understanding and apply what they have learned. Students may use digital tools to interpret and evaluate complex information while considering multiple perspectives and alternative solutions. Students use ideas and methods of inquiry that are central to the discipline, e.g., doing the work of policy makers, historians, …

Statistical Comparisons Of Watershed-Scale Response To Climate Change In Selected Basins Across The United States, John Risley, Hamid Moradkhani, Lauren Hay, Steve Markstrom

Civil and Environmental Engineering Faculty Publications and Presentations

In an earlier global climate-change study, air temperature and precipitation data for the entire twenty-first century simulated from five general circulation models were used as input to precalibrated watershed models for 14 selected basins across the United States. Simulated daily streamflow and energy output from the watershed models were used to compute a range of statistics. With a side-by-side comparison of the statistical analyses for the 14 basins, regional climatic and hydrologic trends over the twenty-first century could be qualitatively identified. Low-flow statistics (95% exceedance, 7-day mean annual minimum, and summer mean monthly streamflow) decreased for almost all basins. Annual …

How Defining Planetary Boundaries Can Transform Our Approach To Growth, W. L. Steffen, Johan Rockström, Robert Costanza

Institute for Sustainable Solutions Publications and Presentations

The article focuses on the importance to identify safe boundaries based on the fundamental characteristics of our planet to address the growing threats of climate change. It highlights the rapid transition of the planet from the stable Holocene state to an unknown future state of significantly different conditions. In addition, climate change, biodiversity loss and phosphorus production were already transgressed by humanity and require innovative frameworks and effective solutions.

Policy Analysis For Optimizing Native Fisheries On The Mckenzie River, Mary Ray

Environmental Science and Management Professional Master's Project Reports

The impact of hatchery fish on native populations has been extensively studied, especially as environmental management has generally moved toward a conservation focus. In Oregon, the McKenzie River native rainbow trout population has been the focus of recent interest groups attempting to induce a change in management practices to support native fisheries. The McKenzie River Chapter of Trout Unlimited is interested in learning more about the impacts that hatchery stocked rainbow trout have on native river populations. It is the group's intent to seek a rule change to management by the Oregon Department of Fish and Wildlife. A review of …

Multiple And Long-Term Effects Of An Introduced Predatory Crab, Catherine E. De Rivera, Edwin D. Grosholz, Gregory M. Ruiz

Environmental Science and Management Faculty Publications and Presentations

Despite the importance of invasions, few studies have explored their long-term consequences in marine systems or examined multiple types of population-level effects. Initial effects, however, may not persist over longer time frames; effects have been shown to wane in freshwater systems. We combined 14 yr of field surveys (1993 to 2006) with manipulative experiments to examine the potential for multiple effects of a nonindigenous crab Carcinus maenas on the native shore crab Hemigrapsus oregonensis over time in central California. H. oregonensis abundance was negatively correlated with C. maenas abundance. However, H. oregonensis abundance rebounded to pre-invasion levels once C. maenas …

A Relativistic Enhancement To Software Transactional Memory, Philip William Howard, Jonathan Walpole

Computer Science Faculty Publications and Presentations

Relativistic Programming is a technique that allows low overhead, linearly-scalable concurrent reads. It also allows joint access parallelism between readers and a writer. Unfortunately, it has so far been limited to a single writer so it does not scale on the write side. Software Transactional Memory (STM) is a technique that allows programs to take advantage of disjoint access parallelism on both the read-side and write-side. Unfortunately, STM systems have a higher overhead than many other synchronization mechanisms so although STM scales, STM starts from a lower baseline. We propose combining relativistic programming and software transactional memory in a way …

Biokinetic Mechanisms Linked With Musculoskeletal Health Disparities: Stochastic Models Applying Tikhonov's Theorem To Biomolecule Homeostasis., Asit K. Saha, Yu Liang, Sean S. Kohles

Mechanical and Materials Engineering Faculty Publications and Presentations

Multiscale technology and advanced mathematical models have been developed to control and characterize physicochemical interactions, respectively, enhancing cellular and molecular engineering progress. Ongoing tissue engineering development studies have provided experimental input for biokinetic models examining the influence of static or dynamic mechanical stimuli (Saha, A. K., and Kohles, S. S., 2010, “A Distinct Catabolic to Anabolic Threshold Due to Single-Cell Nanomechanical Stimulation in a Cartilage Biokinetics Model,” J. Nanotechnol. Eng. Med., 1(3) p. 031005; 2010, “Periodic Nanomechanical Stimulation in a Biokinetics Model Identifying Anabolic and Catabolic Pathways Associated With Cartilage Matrix Homeostasis,” J. Nanotechnol. Eng. Med., 1(4), p. 041001). In …

Integer Optimization And Computational Algebraic Topology, Bala Krishnamoorthy

Systems Science Friday Noon Seminar Series

We present recently discovered connections between integer optimization, or integer programming (IP), and homology. Under reasonable assumptions, these results lead to efficient solutions of several otherwise hard-to-solve problems from computational topology and geometric analysis. The main result equates the total unimodularity of the boundary matrix of a simplicial complex to an algebraic topological condition on the complex (absence of relative torsion), which is often satisfied in real-life applications . When the boundary matrix is totally unimodular, the problem of finding the shortest chain homologous under Z (ring of integers) to a given chain, which is inherently an integer program, can …

The Aquarium Trade As An Invasion Pathway In The Pacific Northwest, Angela L. Strecker, Philip M. Campbell, Julian D. Olden

Environmental Science and Management Faculty Publications and Presentations

The aquarium trade moves thousands of species around the globe, and unwanted organisms may be released into freshwaters, with adverse ecological and economic effects. We report on the first investigation of the ornamental pet trade as an invasion pathway in the Pacific Northwest region of the United States, where a moderate climate and a large human population present ample opportunities for the introduction and establishment of aquarium trade species. Results from a regional survey of pet stores found that the number of fish (n=400) and plant (n=124) species currently in the aquarium trade is vast. Pet stores import thousands of …

Systems Views Of The Economics Of Sustainable Development, Joshua Hughes

Systems Science Friday Noon Seminar Series

The mainstream economics of the 20th century (and now 21st century) has often failed to predict what will happen--or explain what has happened--in the real world, even with (or because of?) an ever-increasing reliance on quantitative and computational methods. Since the mid-20th century a number of people part of, or closely associated with, the systems community--economists among them--have provided insights about what is wrong with "traditional" economics. Systems science offers a number of alternative methods for understanding economic systems that take heed of these criticisms, especially in the context of sustainable development. Yet, while promising, few of these alternatives …

Portland's Goose Hollow, Tracy J. Prince

Curriculum and Instruction Faculty Publications and Presentations

One of Portland’s oldest neighborhoods, Goose Hollow is steps from downtown and beloved for its quirky character, historic homes, spectacular views, and walkability. Over a century ago, the actual “hollow” was dramatically altered when the meandering Tanner Creek, in a deep gulch with several trestle bridge crossings, was diverted underground and infilled. The creek’s presence is still felt in the ravine carved through the Tualatin Mountains (spanned by the Vista Bridge) and in the neighborhood’s identity. This book provides definitive answers to how Goose Hollow got its name and how Tanner Creek Gulch was filled. Stories are also told of …

Higher-Level Application Of Adaptive Dynamic Programming/Reinforcement Learning – A Next Phase For Controls And System Identification?, George G. Lendaris

Systems Science Friday Noon Seminar Series

Humans have the ability to make use of experience while performing system identification and selecting control actions for changing situations. In contrast to current technological implementations that slow down as more knowledge is stored, as more experience is gained, human processing speeds up and has enhanced effectiveness. An emerging experience-based (“higher level”) approach promises to endow our technology with enhanced efficiency and effectiveness.

The notions of context and context discernment are important to understanding this human ability. These are defined as appropriate to controls and system-identification. Some general background on controls, Dynamic Programming, and Adaptive Critic leading to Adaptive Dynamic …

Faculty Senate Monthly Packet April 2011, Portland State University Faculty Senate

Faculty Senate Monthly Packets

The April 2011 Monthly packet includes the April agenda and appendices and the Faculty Senate minutes and attachments from the meeting held March 2011