Digital Commons Network^™

Quasispecies-Like Behavior Observed In Catalytic Rna Populations Evolving In A Test Tube, Carolina Diaz Arenas, Niles Lehman

Chemistry Faculty Publications and Presentations

Background: During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous.

Results: Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen …

Gauge Invariance And Reciprocity In Quantum Mechanics, P.T. Leung, K. Young

Physics Faculty Publications and Presentations

Reciprocity in wave propagation usually refers to the symmetry of the Green's function under the interchange of the source and the observer coordinates, but this condition is not gauge invariant in quantum mechanics, a problem that is particularly significant in the presence of a vector potential. Several possible alternative criteria are given and analyzed with reference to different examples with nonzero magnetic fields and/or vector potentials, including the case of a multiply connected spatial domain. It is shown that the appropriate reciprocity criterion allows for specific phase factors separable into functions of the source and observer coordinates and that this …

Correction Of Dark Current In Consumer Cameras, Justin Charles Dunlap, Erik Bodegom, Ralf Widenhorn

Physics Faculty Publications and Presentations

A study of dark current in digital imagers in digital singlelens reflex (DSLR) and compact consumer-grade digital cameras is presented. Dark current is shown to vary with temperature, exposure time, and ISO setting. Further, dark current is shown to increase in successive images during a series of images. DSLR and compact consumer cameras are often designed such that they are contained within a densely packed camera body, and therefore the digital imagers within the camera frame are prone to heat generated by the sensor as well as nearby elements within the camera body. It is the scope of this work …

Automated Nanocrystal Orientation And Phase Mapping In The Transmission Electron Microscope On The Basis Of Precession Electron Diffraction, Edgar F. Rauch, Joaquin Portillo, Stavros Nicolopoulos, Daniel Bultreys, Sergei Rouvimov, Peter Moeck

Physics Faculty Publications and Presentations

An automated technique for the mapping of nanocrystal phases and orientations in a transmission electron microscope is described. It is primarily based on the projected reciprocal lattice geometry that is extracted from electron diffraction spot patterns. Precession electron diffraction patterns are especially useful for this purpose. The required hardware allows for a scanning-precession movement of the primary electron beam on the crystalline sample and can be interfaced to any older or newer mid-voltage transmission electron microscope (TEM). Experimentally obtained crystal phase and orientation maps are shown for a variety of samples. Comprehensive commercial and open-access crystallographic databases may be used …

Interview With Jacquin Dole, Riverside Farms, 2010 (Audio), Jacquin Dole

All Sustainability History Project Oral Histories

Interview of Jacquin Dole by Paul Hopper at Riverside Farm McMinnville, Oregon on February 28th, 2010.

The interview index is available for download.

Interview With Bernard Smith, Full Of Life Farms, 2010 (Audio), Bernard Smith

All Sustainability History Project Oral Histories

Interview of Bernard Smith by Kyle Dykstra on February 28th, 2010.

The interview index is available for download.

Interview With Katy Kolker, Portland Fruit Tree Project, 2010 (Audio), Katy Kolker

All Sustainability History Project Oral Histories

Interview of Katy Kolker by Dan Stillinger in Portland, Oregon on February 27th, 2010.

The interview index is available for download.

Biologically Inspired Computing: The Darpa Synapse Program & The Hierarchical Temporal Memory, Dan Hammerstrom

Systems Science Friday Noon Seminar Series

This presentation provides an update on biologically inspired computation. In particular, it focuses on two important developments in this area, the DARPA SyNAPSE program (Systems of Neuromorphic Adaptive Plastic Scalable Electronics) and the HTM (Hierarchical Temporal Memory) being developed by Numenta.

The SyNAPSE Program’s ultimate goal is to build a low-power, compact electronic chip combining novel analog circuit design and a neuroscience-inspired architecture that can address a wide range of cognitive abilities: perception, planning, decision making and motor control. According to DARPA program manager Todd Hylton, “Our research progress in this area is unprecedented, No suitable electronic synaptic device that …

Interview With Allejandro Tecum, Adelante Mujeres, 2010 (Audio), Allejandro Tecum

All Sustainability History Project Oral Histories

Interview of Allejandro Tecum by Adam Villareal at Forest Grove, Oregon on February 25th, 2010.

The interview index is available for download.

Interview With David Beller, Mercy Corp Nw, 2010 (Audio), David Beller

All Sustainability History Project Oral Histories

Interview of David Beller by Kyle Koonce at Mercy Corp Portland, Oregon on February 25th, 2010.

The interview index is available for download.

Interview With Darrell Sanders, Cully Community Garden, 2010 (Audio), Darrell Sanders

All Sustainability History Project Oral Histories

Interview of Darrell Sanders by Jeremy Cohen in Portland, Oregon on February 20th, 2010.

The interview index is available for download.

Vehicle Routing Problems In Congested Urban Areas, Miguel Figliozzi

Systems Science Friday Noon Seminar Series

This talk will discuss vehicle routing problems in congested urban areas. Modeling approaches, data collection issues, and solution algorithms to solve real-world problems will be described and analyzed.

Understanding Classification Decisions For Object Detection, Will Landecker, Michael David Thomure, Melanie Mitchell

Systems Science Friday Noon Seminar Series

Computer vision systems are traditionally tested in the object detection paradigm. In these experiments, a vision system is asked whether or not a specific object--for example an animal--occurs in a given image. A system that often answers correctly is said to be very accurate. In this talk, we will discuss some ambiguity that exists in this measure of accuracy. We will also propose a new measure of object-detection accuracy that addresses some of this ambiguity, and apply this measure to the hierarchical "standard model" of visual cortex.

Raps Sheet, February 2010, Retirement Association Of Portland State

RAPS Sheet: Monthly Newsletter

No abstract provided.

Microscopic Formulation Of The Zimm-Bragg Model For The Helix-Coil Transition, A. V. Badasyan, A. Giacometti, Y. S. Mamasakhlisov, V. F. Morozov, Albert S. Benight

Chemistry Faculty Publications and Presentations

A microscopic spin model is proposed for the phenomenological Zimm-Bragg model for the helix-coil transition in biopolymers. This model is shown to provide the same thermophysical properties of the original Zimm-Bragg model and it allows a very convenient framework to compute statistical quantities. Physical origins of this spin model are made transparent by an exact mapping into a one-dimensional Ising model with an external field. However, the dependence on temperature of the reduced external field turns out to differ from the standard one-dimensional Ising model and hence it gives rise to different thermophysical properties, despite the exact mapping connecting them. …

Emissions Of Anaerobically Produced Methane By Trees, Andrew L. Rice, Christopher Lee Butenhoff, Martha J. Shearer, Doaa Teama, Todd N. Rosenstiel, M. A. K. Khalil

Physics Faculty Publications and Presentations

Recent studies indicate that plants may be a previously overlooked but significant source of atmospheric CH₄, though there is considerable disagreement on the mechanism of production. Our work sought to verify that woody deciduous trees grown under inundated conditions had the capacity for transporting CH₄ from an anaerobic subsurface to the atmosphere and to consider if such a source could be important globally. Here, we report results from a greenhouse mesocosm study that indicate significant emissions of anaerobically produced CH₄ transmitted to the atmosphere through broadleaf riparian tree species grown under flooded conditions. Using a leaf area normalized mean emission …

Segmentation Of Thermographic Images Of Hands Using A Genetic Algorithm, Payel Ghosh, Judith Gold, Melanie Mitchell

Computer Science Faculty Publications and Presentations

This paper presents a new technique for segmenting thermographic images using a genetic algorithm (GA). The individuals of the GA also known as chromosomes consist of a sequence of parameters of a level set function. Each chromosome represents a unique segmenting contour. An initial population of segmenting contours is generated based on the learned variation of the level set parameters from training images. Each segmenting contour (an individual) is evaluated for its fitness based on the texture of the region it encloses. The fittest individuals are allowed to propagate to future generations of the GA run using selection, crossover and …

Homocystamides Promote Free-Radical And Oxidative Damage To Proteins, Martha Sibrian-Vazquez, Jorge O. Escobedo, Soojin Lim, George K. Samoei, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Elevated levels of homocysteine are associated with several major diseases. However, it is not clear whether homocysteine is a marker or a causative agent. The majority (ca. 80%) of the homocysteine present in humans is protein bound. The study of the posttranslational modification of proteins by homocysteine and its cyclic congener, homocysteine thiolactone, is emerging as an area of great current interest for unraveling the ongoing “mediator/marker controversy” [Jacobsen DW (2009) Clin Chem 55:1–2]. Interestingly, many of the pathologies associated with homocysteine are also linked to oxidative stress. In the current study, chemical evidence for a causal relationship between homocysteine-bound …

Criticisms Of Systems Science, Joshua Hughes

Systems Science Friday Noon Seminar Series

A new year often begins with a sense of optimism, but we (ever the contrarians) will begin it with a healthy dose of pessimism. This week's seminar will be a discussion about criticisms of systems science. As Winston Churchill said, "Criticism may not be agreeable, but it is necessary. It fulfills the same function as pain in the human body. It calls attention to an unhealthy state of things." Is the systems project in an unhealthy state? Since its emergence in the 1940s and 1950s, a number of people have believed that to be the case, and a few have …

A Virtual Visit To A Sustainable 2050, Robert Costanza

Institute for Sustainable Solutions Publications and Presentations

The article describes the situation in a virtual, sustainable world in 2050. Observations include stable global human population at 8 billion people, slightly decreasing material throughput of local and global economies with an average quality of life (QOL) index at 2% per year. It also notes the lower income gaps within and between countries, the return of global biodiversity and the problem with regards to the effects of climate change. It also adds the use of internal labor equivalent trading system (LETS).

Well-Prepared Middle School Teachers: Common Ground Or Subtle Divide Between Practitioners And University Faculty In The State Of Oregon, United States, Linda L. Samek, Younghee M. Kim, Jay Casbon, Micki M. Caskey, William L. Greene, Patricia Maureen Musser

Curriculum and Instruction Faculty Publications and Presentations

This qualitative study followed a survey study that investigated university faculty, classroom teachers, and principals' perceptions of well-prepared middle school teachers in the state of Oregon in the United States. A qualitative approach allowed the researchers to explore and interpret the participants' views (Denzin & Lincoln, 1998). In spite of many similarities, a number of differences in emphasis or priority were found among the groups, including views on assessment, curriculum development, and the importance of family and community connections for beginning classroom teachers. This study provides a foundation for deeper analysis and discussion among university faculty and practitioners concerning the …

Faculty Senate Monthly Packet January 2010, Portland State University Faculty Senate

Faculty Senate Monthly Packets

The January 2010 Monthly packet includes the January agenda and appendices and the Faculty Senate minutes and attachments from the meeting held December 2009

What Should Be Done With The Revenues From A Carbon Cap And Auction System?, Robert Costanza, Joshua C. Farley

Institute for Sustainable Solutions Publications and Presentations

In this article the author discusses the use of the revenues which can be generated from a carbon cap and auction system in the U.S. They believe that auction system will be politically feasible if all individuals share generated revenues equally. A significant fraction from the revenue should pay for related projects like researching and developing renewable energy in developing countries. The shareholders in this atmospheric commons should be both the current and future generations.

The Search For Real, Integrative Solutions, Robert Costanza

Institute for Sustainable Solutions Publications and Presentations

The article presents the author's views on the inaugural issue of the journal. He states that the journal is aimed at building a shared vision in the society. He believes that one of the reasons for the society's inability to make progress is because of the academia, media, law and politics cast complex problems as polar opposites, which is known as argument culture that the journal aims to resolve.

Salt Marsh Zonal Migration And Ecosystem Service Change In Response To Global Sea Level Rise: A Case Study From An Urban Region, Rusty A. Feagin, M. Luisa Martinez, Gabriela Mendoza-Gonzalez, Robert Costanza

Institute for Sustainable Solutions Publications and Presentations

Coastal wetland plants are expected to respond to global sea level rise by migrating toward higher elevations. Housing, infrastructure, and other anthropogenic modifications are expected to limit the space available for this potential migration. Here, we explore the ecological and economic effects of projected Intergovernmental Panel on Climate Change (IPCC) 2007 report sea level changes at the plant community scale using the highest horizontal (1 m) and vertical (0.01 m) resolution data available, using a 6 x 6 km area as an example. Our findings show that salt marshes do not always lose land with increasing rates of sea level …

Local Political Information On The Web: The Case Of The 2007 Philadelphia Mayoral Campaign, Lee Shaker

Communication Faculty Publications and Presentations

Scholars and pundits have widely discussed the decline of print journalism, but there has been very little empirical research focused on examining online alternatives. This article utilizes a unique sample of online local political content related to the 2007 Philadelphia mayoral campaign to address this void. A content analysis of this dataset has three objectives: to depict the range of sources of online local political information (LPI) available to Philadelphians, to compare the LPI provided by these various sources, and to determine the amount and provenance of the original LPI that is available on the web. New media sources of …

Women In Glaciology, An Historical Perspective, Christina L. Hulbe, Weili Wang, Simon Ommanney

Geology Faculty Publications and Presentations

Women's history in glaciology extends as far back in time as the discipline itself, although their contributions to the scientific discourse have for all of that history been constrained by the sociopolitical contexts of the times. The first Journal of Glaciology paper authored by a woman appeared in 1948, within a year of the founding of the Journal, but it was not until the 1980s that women produced more than a few percent of Journal and Annals of Glaciology papers. Here international perspectives on women's participation in the sciences are presented in order to establish an economic and sociopolitical context …

Grounding-Line Basal Melt Rates Determined Using Radar-Derived Internal Stratigraphy, Ginny Catania, Christina L. Hulbe, Howard Conway

Geology Faculty Publications and Presentations

We use ice-penetrating radar data across grounding lines of Siple Dome and Roosevelt Island, Antarctica, to measure the spatial pattern, magnitude and duration of sub-ice-shelf melting at these locations. Stratigraphic layers across the grounding line show, in places, a large-amplitude downwarp at, or slightly downstream of, the grounding line due to sub-ice-shelf basal melting. Localized downwarping indicates that melting is transient; melt rates, or the grounding line position, have changed within a few hundred years in order to produce the observed stratigraphy. Elsewhere, no meltrelated stratigraphic signature is preserved. In part, heterogeneity in the amount of sub-ice-shelf melt is due …

Propagation Of Long Fractures In The Ronne Ice Shelf Investigated Using A Numerical Model Of Fracture Propagation, Christina L. Hulbe, Christine Marie Ledoux, Kenneth M. Cruikshank

Geology Faculty Publications and Presentations

Long rifts near the front of the Ronne Ice Shelf, Antarctica, are observed to begin as fractures along the lateral boundaries of outlet streams feeding the shelf. These flaws eventually become the planes along which tabular icebergs calve. The fractures propagate laterally as they advect through the shelf, with orientations that can be explained by the glaciological stress field. Fracture length remains constrained over much of the advective path, and locations of crack tip arrest are observed to coincide with structural boundaries, such as suture zones between ice from adjacent outlet glaciers. Geomechanical principles and numerical models demonstrate that in …

Paleotsunami Inundation Of A Beach Ridge Plain: Cobble Ridge Overtopping And Interridge Valley Flooding In Seaside, Oregon, Usa, Curt D. Peterson, Harry M. Jol, Thomas Horning, Kenneth M. Cruikshank

Geology Faculty Publications and Presentations

The Seaside beach ridge plain was inundated by six paleotsunamis during the last ∼2500 years. Large runups (adjusted >10m in height) overtopped seawardmost cobble beach ridges (7m elevation) at ∼1.3 and ∼2.6 ka before present. Smaller paleotsunami (6−8m in height) likely entered the beach plain interior (4-5m elevation) through the paleo-Necanicum bay mouth. The AD 1700 Cascadia paleotsunami had a modest runup (6-7mheight), yet it locally inundated to 1.5 km landward distance. Bed shear stresses (100−3,300 dyne cm−2) are estimated for paleotsunami surges (0.5−2m depths) that flowed down slopes (0.002−0.017 gradient) on the landward side of the cobble beach ridges. …