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Corvallis, OR, United States

Oregon State University is a coeducational, public research university in Corvallis, Oregon, United States. The university offers more than 200 undergraduate, graduate, and doctoral degree programs and has the largest total enrollment in Oregon. More than 160,000 people have attended OSU since its founding. The Carnegie Foundation classifies the Oregon State University as a research university with very high research activity. In addition, it is designated by Carnigie Foundation with 'Community Engagement' classification.OSU is one of 73 land-grant universities in the United States. The school is also a sea-grant, space-grant, and sun-grant institution, making it one of only two US institutions to obtain all four designations and the only public university to do so . OSU received almost $285 million in research grants and contracts for the 2014 fiscal year, which is more research funding than all other public universities in Oregon combined. Wikipedia.


Bean S.J.,Oregon State University
Vaccine | Year: 2011

Context: Anti-vaccination websites appeal to persons searching the Internet for vaccine information that reinforces their predilection to avoid vaccination for themselves or their children. Few published studies have systematically examined these sites. Objectives: The aim of this study was to employ content analysis as a useful tool for examining and comparing anti-vaccination websites for recurring and changing emphases in content, design, and credibility themes since earlier anti-vaccination website content analyses were conducted. Methods: Between February and May 2010, using a commonly available search engine followed by a deep web search, 25 websites that contained anti-vaccination content were reviewed and analyzed for 24 content, 14 design, and 13 credibility attributes. Results: Although several content claims remained similar to earlier analyses, two new themes emerged: (1) the 2009 H1N1 epidemic threat was " manufactured," and (2) the increasing presence of so-called " expert" testimony in opposing vaccination. Conclusion: Anti-vaccination websites are constantly changing in response to the trends in public health and the success of vaccination. Monitoring the changes can permit public health workers to mount programs more quickly to counter the opposition arguments. Additionally, opposition claims commonly appeal to emotions whereas the supporting claims appeal to reason. Effective vaccine support may be better served by including more emotionally compelling content. © 2011 Elsevier Ltd.


Ripple W.J.,Oregon State University | Van Valkenburgh B.,University of California at Los Angeles
BioScience | Year: 2010

Humans, in conjunction with natural top-down processes and through a sequence of cascading trophic interactions, may have contributed to the Pleistocene megafaunal extinctions. The arrival of the first humans, as hunters and scavengers, through top-down forcing, could have triggered a population collapse of large herbivores and their predators. We present evidence that the large mammalian herbivores of the North American Pleistocene were primarily predator limited and at low densities, and therefore highly susceptible to extinction when humans were added to the predator guild. Our empirical evidence comes from data on carnivore dental attrition, proboscidean age structure, life history, tusk growth rates, and stable isotopes from the fossil record. We suggest a research agenda for further testing of this hypothesis that will provide a more detailed comprehension of late Pleistocene megafaunal ecology, and thereby allow us to better understand and manage remaining megafauna. © 2010 by American Institute of Biological Sciences. All rights reserved.


Fu R.,Oregon Health And Science University | Selph S.,Oregon Health And Science University | McDonagh M.,Oregon Health And Science University | Peterson K.,Oregon Health And Science University | And 3 more authors.
Annals of Internal Medicine | Year: 2013

Background: Recombinant human bone morphogenetic protein-2 (rhBMP-2) is used as a bone graft substitute in spinal fusion, which unites (fuses) bones in the spine. The accuracy and completeness of journal publications of industry-sponsored trials on the effectiveness and harms of rhBMP-2 has been called into question. Purpose: To independently assess the effectiveness and harms of rhBMP-2 in spinal fusion and reporting bias in industry-sponsored journal publications. Data Sources: Individual-patient data (IPD) from 17 industry-sponsored studies; related internal documents; and searches of MEDLINE (1996 to August 2012), other databases, and reference lists. Study Selection: Randomized, controlled trials (RCTs) and cohort studies of rhBMP-2 versus any control and uncontrolled studies of harms. Data Extraction: Effectiveness outcomes in IPD were recalculated using consistent definitions. Study characteristics and results were abstracted by 1 investigator and confirmed by another. Two investigators independently assessed quality using predefined criteria. Data Synthesis: Thirteen RCTs and 31 cohort studies were included. For lumbar spine fusion, rhBMP-2 and iliac crest bone graft were similar in overall success, fusion, and other effectiveness measures and in risk for any adverse event, although rates were high across interventions (77% to 93% at 24 months from surgery). For anterior lumbar interbody fusion, rhBMP-2 was associated with nonsignificantly increased risk for retrograde ejaculation and urogenital problems. For anterior cervical spine fusion, rhBMP-2 was associated with increased risk for wound complications and dysphagia. At 24 months, the cancer risk was increased with rhBMP-2 (risk ratio, 3.45 [95% CI, 1.98 to 6.00]), but event rates were low and cancer was heterogeneous. Early journal publications misrepresented the effectiveness and harms through selective reporting, duplicate publication, and underreporting. Limitations: Outcome assessment was not blinded, and ascertainment of harms in trials was poor. No trials were truly independent of industry sponsorship. Conclusion: In spinal fusion, rhBMP-2 has no proven clinical advantage over bone graft and may be associated with important harms, making it difficult to identify clear indications for rhBMP-2. Earlier disclosure of all relevant data would have better informed clinicians and the public than the initial published trial reports did. © 2013 American College of Physicians.


Ebert T.A.,San Diego State University | Ebert T.A.,Oregon State University
Marine Ecology Progress Series | Year: 2010

The abundant center model of geographic distribution has been tested for the purple sea urchin by others who found highest densities and reproduction towards the southern end rather than in the center of the range and so rejected the model. A question is whether size, growth, and survival data would yield other or contrary results. Intertidal densities and size structures were measured for purple sea urchins along the Pacific coast of North America during 1985-1987 from 29.93 to 50.47°N, covering about 65% of the reported geographic range; these historical data were used to explore latitudinal patterns. Recruitment was based on the fractions of individuals in the smallest mode of the size distributions. Growth was determined by tagging with tetracycline and survival was estimated using size distributions and growth. Density of purple sea urchins was highest between 35 and 37°N and the samples with the highest numbers of recruits occurred between 34 and 38° N. Maximum diameter was largest at 43 to 44°N and smallest at about 34° N. There was no latitudinal pattern to growth or survival. Patterns of population traits did not fit simple models or previously published results. The interplay of coastal topography and currents are suggested as the primary determinants of density and recruitment. No general models for describing geographic distributions predict the observed patterns. The southern range limit is best explained by thermal tolerance and the northern limit by development times of larvae at low temperatures. © Inter-Research 2010.


Wilson J.B.,Oregon State University
Wood and Fiber Science | Year: 2010

Life-cycle inventory (LCI) data are needed to scientifically document the environmental performance of materials for applications as governed by the many new green building standards, purchasing guidelines, and energy and climate change policy issues. This study develops the LCI data for particleboard, a composite wood panel product comprised of wood particles, urea-formaldehyde resin, wax, and other additives. Data are given for both gate-to-gate (particleboard manufacture) and cradle-to-gate (from the product upstream to in-ground resources) that, in addition to gate-to-gate impacts, include those to produce and deliver input fuels, electricity, water, wood residue, resin, wax, catalyst, and scavenger. LCI output data are given per 1.0 m3 of particleboard in terms of raw materials use and emissions to air, water, and land. Data are also presented on embodied energy, carbon flux, store, and footprint. Particleboard has favorable characteristics in terms of energy use and carbon store. Of significance for the LCI of particleboard is the large component of embodied energy because of the use of wood fuel, a renewable resource, and its small carbon footprint, which lessens its impact on climate change. © 2010 by the Society of Wood Science and Technology.


Life-cycle inventory (LCI) data are needed to scientifically document the environmental performance of formaldehyde-based resins used in the manufacture of wood composite products. The resin data are needed by others to conduct LCI studies of wood composites when providing performance data for applications as governed by the many green building standards, purchasing guidelines, and energy and climate change-related polices. This study develops LCI data for urea-formaldehyde, melamine- urea-formaldehyde, phenol-formaldehyde, and phenol-resorcinol-formaldehyde resins as produced in the US for 2005. Data are given for both on-site (resin manufacture) and cradle-to-gate (from the resin upstream to in-ground resources), which include those resources to produce and deliver input chemicals, fuels, water, and electricity. The LCI data are given per 1.0 kg of neat (liquid) resin at their industry use solids content in terms of raw materials use and emissions to air, water, and land; data are also presented on embodied energy, carbon flow, store, and footprint. © 2010 by the Society of Wood Science and Technology.


Nonogaki H.,Oregon State University
Plant and Cell Physiology | Year: 2010

MicroRNAs (miRNAs) regulate various developmental programs of plants. This review focuses on miRNA involvement in early events of plant development, such as seed germination, seedling development and the juvenile to adult phase transition. miR159 and miR160 are involved in the regulation of seed germination through their effects on the sensitivity of seeds to ABA. miR156 and miR172 play critical roles in the emergence of vegetative leaves at post-germinative stages, which is important for the transition to autotrophic growth. The phase transition from the juvenile to adult stage in both monocots and dicots is also regulated by miR156 and miR172. In these early developmental processes, there are miRNA gene regulation cascades where the miR156 pathway acts upstream of the miR172 pathway. Moreover, targets of miR156 and miR172 exert positive feedback on the expression of MIR genes that suppress themselves. The early events of plant development appear to be controlled by complex mechanisms involving sequential expression of different miRNA pathways and feedback loops among miRNAs and their target genes. © 2010 The Author.


Antle J.M.,Oregon State University
American Journal of Agricultural Economics | Year: 2010

Partial-moment functions are proposed as a flexible way to characterize and estimate asymmetric effects of inputs on output distributions. Methods for econometric estimation of partial-moment functions, and tests for input symmetry and location-scale distributions, are presented. A Monte Carlo study demonstrates properties of proposed tests. A study of Ecuadorian potato production illustrates the methods. Hypotheses of input symmetry and location scale are rejected. A risk-value model based on partial moments implies that fertilizer is risk increasing and fungicides and labor are risk reducing in potato production, whereas an expected utility model based on full moments has the opposite implications. © The Author (2010).


Hansen E.N.,Oregon State University
Journal of Forestry | Year: 2010

The US forest products industry has lost several hundred thousand jobs over recent years. It is argued that low-cost, foreign competition is largely responsible for this loss. Given this situation, enhancing innovation is increasingly seen as a path to competitive advantage and improved financial performance. Strategies have been and are being developed at the state and national level in the United States as well as the national level in many other countries. Although there is general recognition that innovation can positively impact competitiveness in the industry, there is little research verifying this relationship. This article discusses current innovation research focusing on the forest products industry. It also provides a brief example of a competitor nation's (Finland) efforts to enhance innovation in its forest products industry. With this background, the potential roles in enhancing innovation in the US forest products industry of company executives, policymakers, and researchers/educators are outlined. For example, it is recommended that companies concentrate on creating more innovation-centric cultures and policymakers are encouraged to support the future forest products industry workforce. Finally, it is suggested that the research and education community can be more effective in supporting industry through industry-focused research and developing skills of current and future employees. Copyright © 2010 by the Society of American Foresters.


Coral reefs are threatened with worldwide decline from multiple factors, chief among them climate change (Hughes et al. 2003; Hoegh-Guldberg et al. 2007). The foundation of coral reefs is an endosymbiosis between coral hosts and their resident photosynthetic dinoflagellates (genus Symbiodinium) and this partnership (or holobiont) is exquisitely sensitive to temperature stress. The primary response to hyperthermic stress is coral bleaching, which is the loss of symbionts from coral tissues - the collapse of the symbiosis (Weis 2008). Bleaching can result in increased coral mortality which can ultimately lead to severely compromised reef health (Hoegh-Guldberg et al. 2007). Despite this grim picture of coral bleaching and reef degradation, coral susceptibility to stress and bleaching is highly variable (Coles & Brown 2003). There is enormous interest in discovering the factors that determine susceptibility in order to help us predict if and how corals will survive a period of rapid global warming. In this issue, Barshis et al. (2010) examine the ecophysiological and genetic basis for differential responses to stress in Porites lobata in American Samoa. They combine a reciprocal transplant experimental design between two neighbouring, but very different reef environments with state-of-the-art physiological biomarkers and molecular genetic markers for both partners to tease apart the contribution of environmental and fixed influences on stress susceptibility. Their results suggest the presence of a fixed, rather than environmental effect on expression of ubiquitin conjugates, one key marker for physiological stress response. In addition, the authors show genetic differentiation in host populations between the two sites suggesting strong selection for physiological adaptation to differing environments across small geographic distances. These conclusions point the study of coral resilience and susceptibility in a new direction. © 2010 Blackwell Publishing Ltd.


Animals must manage interactions with beneficial as well as detrimental microbes. Immunity therefore includes strategies for both resistance to and tolerance of microbial invaders. Transforming growth factor beta (TGFβ) cytokines have many functions in animals including a tolerance-promoting (tolerogenic) role in immunity in vertebrates. TGFβ pathways are present in basal metazoans such as cnidarians but their potential role in immunity has never been explored. This study takes a two-part approach to examining an immune function for TGFβ in cnidarians. First bioinformatic analyses of the model anemone Aiptasia pallida were used to identify TGFβ pathway components and explore the hypothesis that an immune function for TGFβs existed prior to the evolution of vertebrates. A TGFβ ligand from A. pallida was identified as one that groups closely with vertebrate TGFβs that have an immune function. Second, cellular analyses of A. pallida were used to examine a role for a TGFβ pathway in the regulation of cnidarian-dinoflagellate mutualisms. These interactions are stable under ambient conditions but collapse under elevated temperature, a phenomenon called cnidarian bleaching. Addition of exogenous human TGFβ suppressed an immune response measured as LPS-induced nitric oxide (NO) production by the host. Addition of anti-TGFβ to block a putative TGFβ pathway resulted in immune stimulation and a failure of the symbionts to successfully colonize the host. Finally, addition of exogenous TGFβ suppressed immune stimulation in heat-stressed animals and partially abolished a bleaching response. These findings suggest that the dinoflagellate symbionts somehow promote host tolerance through activation of tolerogenic host immune pathways, a strategy employed by some intracellular protozoan parasites during their invasion of vertebrates. Insight into the ancient, conserved nature of host-microbe interactions gained from this cnidarian-dinoflagellate model is valuable to understanding the evolution of immunity and its role in the regulation of both beneficial and detrimental associations. Copyright © 2012 Elsevier Ltd. All rights reserved.


Garzoli S.L.,National Oceanic and Atmospheric Administration | Matano R.,Oregon State University
Deep-Sea Research Part II: Topical Studies in Oceanography | Year: 2011

This article discusses the contribution of the South Atlantic circulation to the variability of the Meridional Overturning Circulation (MOC). The South Atlantic connects the North Atlantic to the Indian and Pacific oceans, being the conduit through which the southward outflow of North Atlantic Deep Water (NADW) is compensated by northward inflows of upper and intermediate waters. This circulation pattern, in which cold waters flow poleward and warm waters equatorward, generates a distinct heat flux that is directed from the poles towards the equator. Observations and models indicate that the South Atlantic is not just a passive conduit but that its circulation influences significantly the water mass structure of the Atlantic Meridional Overturning Circulation (AMOC). These transformations occur across the whole basin but are most intensified in regions of high mesoscale variability. Models and observations also show that the South Atlantic plays a significant role in the establishment of oceanic teleconnections. Anomalies generated in the Southern Ocean, for example, are transmitted through inter-ocean exchanges to the northern basins. These results highlight the need for sustained observations in the South Atlantic and Southern Ocean, which, in conjunction with modeling efforts, would improve the understanding of the processes necessary to formulate long-term climate predictions. © 2011.


Magnusson K.R.,Oregon State University
Future Neurology | Year: 2012

Our elderly population is growing and declines in cognitive abilities, such as memory, can be costly, because it can interfere with a persons ability to live independently. The NMDA receptor is very important for many different forms of memory and this receptor is negatively affected by aging. This review examines the progress that has been made recently in characterizing selective vulnerabilities of different subunits and splice variants of the NMDA receptor to normal aging in C57BL/6 mice. Evidence is also presented for changes in the relationships of NMDA receptors to plasticity across aging. Recent interventions show that enhancing NMDA receptors in aged individuals is associated with improvements in memory, but mouse models of neurodegenerative diseases suggest that finding the right balance between too little and too much NMDA receptor activity will be the key to enhancing memory without inducing pathology. © 2012 Future Medicine Ltd.


Stolpe M.,Saarland University | Kruzic J.J.,Oregon State University | Busch R.,Saarland University
Acta Materialia | Year: 2014

Two-dimensional cold rolling was performed on a bulk metallic glass (BMG) with composition Zr58.5Cu15.6Ni12.8Al 10.3Nb2.8. The average shear band density continuously increased with plastic strain. By comparing with published data, a common relation is proposed whereby the average shear band density scales with the square root of the induced true plastic strain, independent of changes in BMG composition or loading mode. Also, the measured exothermal heat release preceding the glass transition, and thus also the free volume, was found to increase linearly with shear band density. Based on an analysis of the measured shear band densities and enthalpy changes, it is concluded that the free volume of both the matrix and the shear bands must evolve continuously during deformation. Finally, the measured hardness during cold rolling was found to decrease initially within the low deformation regime and then increase at higher deformations with a minimum at a strain of ∼0.073. By recognizing the commonality in the shear band formation among different loading modes, the contributions of shear band generation and residual stresses to the hardness changes were separated. The initial decrease in hardness was attributed to free volume generation and a softening of the material, while the subsequent increase in hardness was related to the evolution of compressive residual stresses during cold rolling. It is suggested that these competing mechanisms affecting hardness may help to explain the different observations in the literature concerning the influence of pre-deformation. © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


In this technical note, a steady-state analytical solution of concentrations of a parent solute reacting to a daughter solute, both of which are undergoing transport and multirate mass transfer, is presented. Although the governing equations are complicated, the resulting solution can be expressed in simple terms. A function of the ratio of concentrations, In (daughter/parent + P), can be used as a metric of mass transfer and reaction if the reactions are mostly confined to the immobile domain, where P is the ratio of production of daughter to decay of parent. This metric is applied with the resazurin-resorufin (Raz-Rru) tracer system in a stream to obtain an integrated measure of respiration that occurs on or in a stream bed. The slope of the graph of In (Rru/Raz + P) versus advective travel time is a function of the strength of surface-bed interaction and respiration. This graph can be used for rapid comparison of different experiments and streams. © 2013. American Geophysical Union. All Rights Reserved.


Peterson R.B.,Oregon State University
Energy | Year: 2011

A concept is introduced here for storing utility-scale electrical energy in the form of latent heat. The storage process utilizes a boiling refrigerant at sub-ambient temperatures to freeze a latent heat storage material using electrically driven compressors. Recovery of the latent heat for electrical generation then uses vapor expansion and condensation which essentially reverses the storage process. Sensible heat storage is incorporated into the cycle to efficiently implement the concept. Both energy storage and generation are carried out under steady flow closed-loop conditions where the T-s diagram is similar to a Rankine cycle. From a thermodynamic perspective, work is supplied to the system while heat is transferred to the surroundings from the latent heat store. The reverse process generates work while using heat supplied by the surroundings. An analysis with expander/compressor isentropic efficiencies and small temperature differentials for the heat transfer processes can give projected round trip efficiencies in the 50-60% range using a common refrigerant. One of the attractive features of this approach is the ability to use different ambient temperatures for storage and generation. Exploiting diurnal temperature differences or sources of low grade heat (50-90 °C) significantly increases the apparent round trip storage efficiency. © 2011 Elsevier Ltd.


Mccallum M.L.,University of Missouri - Kansas City | Bury G.W.,Oregon State University
Biodiversity and Conservation | Year: 2013

Public interest in most aspects of the environment is sharply declining relative to other subjects, as measured by internet searches performed on Google. Changes in the search behavior by the public are closely tied to their interests, and those interests are critical to driving public policy. Google Insights for Search (GIFS) was a tool that provided access to search data but is now combined with another tool, Google Trends. We used GIFS to obtain data for 19 environment-related terms from 2001 to 2009. The only environment-related term with large positive slope was climate change. All other terms that we queried had strong negative slopes indicating that searches for these topics dropped over the last decade. Our results suggest that the public is growing less interested in the environment. © 2013 Springer Science+Business Media Dordrecht.


Briggs J.C.,Oregon State University | Bowen B.W.,Hawaii Institute of Marine Biology
Journal of Biogeography | Year: 2013

We synthesize the evolutionary implications of recent advances in the fields of phylogeography, biogeography and palaeogeography for shallow-water marine species, focusing on marine speciation and the relationships among the biogeographic regions and provinces of the world. A recent revision of biogeographic provinces has resulted in the recognition of several new provinces and a re-evaluation of provincial relationships. These changes, and the information that led to them, make possible a clarification of distributional dynamics and evolutionary consequences. Most of the new conclusions pertain to biodiversity hotspots in the tropical Atlantic, tropical Indo-West Pacific, cold-temperate North Pacific, and the cold Southern Ocean. The emphasis is on the fish fauna, although comparative information on invertebrates is utilized when possible. Although marine biogeographic provinces are characterized by endemism and thus demonstrate evolutionary innovation, dominant species appear to arise within smaller centres of high species diversity and maximum interspecies competition. Species continually disperse from such centres of origin and are readily accommodated in less diverse areas. Thus, the diversity centres increase or maintain species diversity within their areas of influence, and are part of a global system responsible for the maintenance of biodiversity over much of the marine world. © 2013 Blackwell Publishing Ltd.


Graybosch R.A.,University of Nebraska - Lincoln | Peterson C.J.,Oregon State University
Crop Science | Year: 2010

Data from USDA-coordinated winter wheat (Triticum aestivum L.) regional performance nurseries collected over the time period 1959 to 2008 were used to estimate genetic gain (loss) in grain yield, grain volume weight, days to heading, and plant height in winter wheats adapted to the Great Plains of North America. In both the Southern Regional (SRPN) and Northern Regional Performance Nurseries (NRPN), linear regression revealed significant positive relationships between relative grain yields of advanced breeding lines and calendar year of the nursery trial. The estimated genetic gain in grain yield potential since 1959 was approximately 1.1% (of the control cultivar Kharkof) yr-1 for all entries in the SRPN, and 1.3% yr-1 if only the most productive entry was considered. For the NRPN, the estimates of genetic gain in grain yield were 0.79% yr-1 for all entries, and also 0.79% yr-1 for the most productive entry. Linear regressions of relative grain yields vs. year over the time period 1984 to 2008, however, showed no statistically significant trend in the SRPN. For the same time period in the NRPN, a statistically significant positive slope of 0.83 was observed, though the coefficient of determination (R2) was only 0.28. Relative grain yields of Great Plains hard winter wheats may have peaked in the early to mid- 1990s, and further improvement in the genetic potential for grain yield awaits some new technological or biological advance. © Crop Science Society of America.


Thomas T.D.,Oregon State University
Journal of Electron Spectroscopy and Related Phenomena | Year: 2013

Three features of small-molecule photoelectron spectroscopy are considered (1) the atom from which a photoelectron is emitted must have a recoil momentum equal to that of the emitted electron. This is shared among the various modes of motion of the ion, leading to rotational and vibrational excitation. Furthermore, any initial velocity of the atom (due to either translational, rotational, or vibrational motion) will lead to Doppler broadening. These effects are observable and can, in general, be accounted for by simple models. In some cases, however, the simple models fail and a deeper insight is necessary. (2) Inner-shell photoionization is essentially an atomic process, and it is expected that the intensity for emission of a photoelectron from the core of an atom in a molecule will be independent of its chemical environment. Recent measurements on the carbon 1s photoelectron spectra of three chloroethanes show that this is not the case. At energies not far above the ionization threshold there are strong oscillations of the intensity ratio (CCl/CH) with increasing photon energy. These are similar to those seen in EXAFS and can be accounted for by considering backscattering of the photoelectrons from the chlorine atoms. Moreover, even at high energies the cross section for ionization has been found to depend on the chemical environment of the atom. These results have important consequences for the use of inner-shell electron spectroscopy for quantitative analysis. (3) Single-core-hole ionization energies have long been used as a tool for investigating chemical phenomena. Double-core-hole ionization energies provide additional chemical information. By combining the single-hole and double-hole ionization energies it is possible to determine the effects of the initial-state charge distribution and final-state charge rearrangement on the chemical shifts and on other chemical properties. Until recently double-core-hole ionization energies have not been experimentally accessible for first-row elements. New experimental techniques have, however, made it possible to measure these not only for single sites in a molecule, but also for two different sites in the same molecule. The chemical information that can be obtained from such measurements is discussed. © 2013 Elsevier Ltd. All rights reserved.


Patro P.K.,National Geophysical Research Institute | Egbert G.D.,Oregon State University
Physics of the Earth and Planetary Interiors | Year: 2011

Using synthetic data Siripunvaraporn et al. (2005b) demonstrated possible advantages of interpreting single-profile MT data with a three-dimensional (3D) inversion program. Here we explore this idea further using real MT data from two profiles on the Indian subcontinent. The first profile (330 km long) cuts across the Deccan Volcanic Province of Peninsular India. The second (130 km long) is in the Narmada Son Lineament zone, approximately 100. km further north. Using the data-space Occam inversion code of Siripunvaraporn et al. (2005a) 3D inversion is carried out on each of these profiles independently, and results are compared with previously-published two-dimensional (2D) interpretations. In addition to inversion of the full impedance tensor, we consider 3D inversion of only the off-diagonal components. We also experiment with variants on the model covariance, in particular allowing for longer smoothing length scales along the geoelectric strike. Not surprisingly, the 3D inversion finds models that fit the data better than had been possible with the 2D programs. Many of the features inferred from these previous 2D interpretations are also present in the 3D inverse solutions, but the positions and amplitudes of individual conductive features are in some cases changed. The 3D models suggest substantial non-uniqueness in the single profile data. Even without explicit or special treatment, we find that the (relatively modest) near surface distortion effects in these datasets were well fit by the 3D inversion, by inserting small scale conductive and resistive features in surface layers, mostly off-profile. © 2011 Elsevier B.V.


Ripple W.J.,Oregon State University
Science (New York, N.Y.) | Year: 2014

Large carnivores face serious threats and are experiencing massive declines in their populations and geographic ranges around the world. We highlight how these threats have affected the conservation status and ecological functioning of the 31 largest mammalian carnivores on Earth. Consistent with theory, empirical studies increasingly show that large carnivores have substantial effects on the structure and function of diverse ecosystems. Significant cascading trophic interactions, mediated by their prey or sympatric mesopredators, arise when some of these carnivores are extirpated from or repatriated to ecosystems. Unexpected effects of trophic cascades on various taxa and processes include changes to bird, mammal, invertebrate, and herpetofauna abundance or richness; subsidies to scavengers; altered disease dynamics; carbon sequestration; modified stream morphology; and crop damage. Promoting tolerance and coexistence with large carnivores is a crucial societal challenge that will ultimately determine the fate of Earth's largest carnivores and all that depends upon them, including humans.


Steffl J.L.,Oregon State University
Journal of clinical pharmacology | Year: 2012

Chronic kidney disease is a worldwide problem. Accurate assessment of kidney function is important for defining stages of kidney disease and assisting with drug dosing. Glomerular filtration rate (GFR) is a good index of the health of the kidney. Although measured GFR using an exogenous substance is the most accurate, it is difficult to obtain due to cost and resources. Equations calculating creatinine clearance and estimated GFR as a measure of kidney function have been developed using serum creatinine as a marker of kidney function. The Cockcroft-Gault, Modification of Diet in Renal Disease, and Chronic Kidney Disease Epidemiology Collaboration equations have been shown to have statistically significant differences in estimating GFR in various populations. Drug-dosing adjustments based on the various equations may differ. However, without clinical outcome data, it is yet to be determined whether these differences are clinically significant.


Shaman J.,Oregon State University | Tziperman E.,Harvard University
Journal of Climate | Year: 2011

Numerous studies have demonstrated statistical associations between the El Niño-Southern Oscillation (ENSO) and precipitation in the Mediterranean basin. The dynamical bases for these teleconnections have yet to be fully identified. Here, observational analyses and model simulations are used to show how ENSO variability affects rainfall over southwestern Europe (Iberia, Southern France, and Italy). A precipitation index for the region, named southwestern European Precipitation (SWEP), is used. The observational analyses show that ENSO modulates SWEP during the September-December wet season. These precipitation anomalies are associated with changes in large-scale atmospheric fields to the west of Iberia that alter low-level westerly winds and onshore moisture advection from the Atlantic. The vorticity anomalies associated with SWEP variability are linked to ENSO through a stationary barotropic Rossby wave train that emanates from the eastern equatorial Pacific and propagates eastward to the Atlantic and Mediterranean. Solutions of the linearized barotropic vorticity equation produce such eastward-propagating Rossby waves with trajectories that traverse the region of observed ENSO-related anomalies. In addition, these linearized barotropic vorticity equation solutions produce a dipole of positive and negative vorticity anomalies to the west of Iberia that matches observations and is consistent with the onshore ad-vection of moisture. Thus, interannual variability of fall and early winter precipitation over southwestern Europe is linked to ENSO variability in the eastern Pacific via an eastward-propagating atmospheric stationary barotropic Rossby wave train. © 2011 American Meteorological Society.


Vano J.A.,Oregon State University | Vano J.A.,University of Washington | Lettenmaier D.P.,University of Washington
Climatic Change | Year: 2014

Projections of a drier, warmer climate in the U.S. Southwest would complicate management of the Colorado River system-yet these projections, often based on coarse resolution global climate models, are quite uncertain. We present an approach to understanding future Colorado River discharge based on land surface characterizations that map the Colorado River basin's hydrologic sensitivities (e.g., changes in streamflow magnitude) to annual and seasonal temperature and precipitation changes. The approach uses a process-based macroscale land surface model (LSM; in this case, the Variable Infiltration Capacity hydrologic model, although methods are applicable to any LSM) to develop sensitivity maps (equivalent to a simple empirical model), and uses these maps to evaluate long-term annual streamflow responses to future precipitation and temperature change. We show that global climate model projections combined with estimates of hydrologic sensitivities, estimated for different seasons and at different change increments, can provide a basis for approximating cumulative distribution functions of streamflow changes similar to more common, computationally intensive full-simulation approaches that force the hydrologic model with downscaled future climate scenarios. For purposes of assessing risk, we argue that the sensitivity-based approach produces viable first-order estimates that can be easily applied to newly released climate information to assess underlying drivers of change and bound, at least approximately, the range of future streamflow uncertainties for water resource planners. © 2013 Springer Science+Business Media Dordrecht.


Stuedlein A.W.,Oregon State University | Holtz R.D.,University of Washington
Journal of Geotechnical and Geoenvironmental Engineering | Year: 2014

Aggregate piers, also known as stone columns, are commonly used to improve ground for the support of structure foundations. Despite the number of existing analytical and semiempirical methods available to predict the displacement of shallow foundations resting on aggregate pier reinforced clay, the accuracy of these models remains uncertain. After a brief review of existing load-displacement estimation methods, the accuracy of those models valid for isolated spread footings was investigated using a database of high-quality footing load test data. The methods were compared using the bias (i.e., the ratio of measured bearing capacity to that calculated) and were shown to exhibit a high degree of variability in the prediction of load and displacement. Then, the database was used to develop a multiple linear regression model for the prediction of footing displacements for aggregate pier reinforced clay under a wide range of pier configurations and soil conditions. The proposed statistical model is shown to produce unbiased displacement estimates with low prediction variability that is appropriate for planning and designing ground-improvement projects. © 2014 American Society of Civil Engineers.


Arason P.,The Icelandic Meteorological Office | Levi S.,Oregon State University
Geophysical Journal International | Year: 2010

We have developed a new robust maximum likelihood method for estimating the unbiased mean inclination from inclination-only data. In paleomagnetic analysis, the arithmetic mean of inclination-only data is known to introduce a shallowing bias. Several methods have been introduced to estimate the unbiased mean inclination of inclination-only data together with measures of the dispersion. Some inclination-only methods were designed to maximize the likelihood function of the marginal Fisher distribution. However, the exact analytical form of the maximum likelihood function is fairly complicated, and all the methods require various assumptions and approximations that are often inappropriate. For some steep and dispersed data sets, these methods provide estimates that are significantly displaced from the peak of the likelihood function to systematically shallower inclination. The problem locating the maximum of the likelihood function is partly due to difficulties in accurately evaluating the function for all values of interest, because some elements of the likelihood function increase exponentially as precision parameters increase, leading to numerical instabilities. In this study, we succeeded in analytically cancelling exponential elements from the log-likelihood function, and we are now able to calculate its value anywhere in the parameter space and for any inclination-only data set. Furthermore, we can now calculate the partial derivatives of the log-likelihood function with desired accuracy, and locate the maximum likelihood without the assumptions required by previous methods. To assess the reliability and accuracy of our method, we generated large numbers of random Fisher-distributed data sets, for which we calculated mean inclinations and precision parameters. The comparisons show that our new robust Arason-Levi maximum likelihood method is the most reliable, and the mean inclination estimates are the least biased towards shallow values. © 2010 The Authors Journal compilation © 2010 RAS.


The recent irruption of Pacific red lionfish (Pterois volitans) on Caribbean and Atlantic coral reefs could prove to be one of the most damaging marine invasions to date. Invasive lionfish are reaching densities much higher than those reported from their native range, and they have a strong negative effect on the recruitment and abundance of a broad diversity of native coral-reef fishes. Otherwise, little is known about how lionfish affect native coral-reef communities, especially compared to ecologically similar native predators. A controlled field experiment conducted on small patch-reefs in the Bahamas over an 8-week-period demonstrated that (1) lionfish caused a reduction in the abundance of small native coral-reef fishes that was 2. 5 ± 0. 5 times (mean ± SEM) greater than that caused by a similarly sized native piscivore, the coney grouper Cephalopholis fulva (93. 7 vs. 36. 3 % reduction); (2) lionfish caused a reduction in the species richness of small coral-reef fishes (loss of 4. 6 ± 1. 6 species), whereas the native piscivore did not have a significant effect on prey richness; (3) the greatest effects on the reef-fish community, in terms of both abundance and richness, occurred when both native and invasive predators were present; and (4) lionfish grew significantly faster (>6 times) than the native predator under the same field conditions. These results suggest that invasive lionfish have stronger ecological effects than similarly sized native piscivores, and may pose a substantial threat to native coral-reef fish communities. © 2012 Springer Science+Business Media B.V.


Despite decades of policymaking, the U.S. has only recently made significant strides in becoming a more energy secure nation. With a focus on the executive and legislative branches, this paper investigates two possible political obstacles to achieve this policy goal. The first question it asks is whether or not the two branches have been defining energy security in the same way. As the concept itself has no universal definition, it is possible that the branches have been focusing on different aspects of the term. Results from a content analysis of presidential speeches and congressional hearings suggest that no such division has occurred. The subsequent question asks whether or not the two branches, in tandem, are providing the foundation for sound policy. Results suggest that Congress and presidents have defined and discussed energy security in a generally balanced, comprehensive and internally non-conflictual way. What policy emerges from these discussions should be the subject of future research. © 2013 Elsevier Ltd.


Xue L.,Oregon State University | Qu A.,University of Illinois at Urbana - Champaign
Journal of Machine Learning Research | Year: 2012

The varying-coefficient model is flexible and powerful for modeling the dynamic changes of regression coefficients. It is important to identify significant covariates associated with response variables, especially for high-dimensional settings where the number of covariates can be larger than the sample size. We consider model selection in the high-dimensional setting and adopt difference convex programming to approximate the L0 penalty, and we investigate the global optimality properties of the varying-coefficient estimator. The challenge of the variable selection problem here is that the dimension of the nonparametric form for the varying-coefficient modeling could be infinite, in addition to dealing with the high-dimensional linear covariates. We show that the proposed varying-coefficient estimator is consistent, enjoys the oracle property and achieves an optimal convergence rate for the non-zero nonparametric components for high-dimensional data. Our simulations and numerical examples indicate that the difference convex algorithm is efficient using the coordinate decent algorithm, and is able to select the true model at a higher frequency than the least absolute shrinkage and selection operator (LASSO), the adaptive LASSO and the smoothly clipped absolute deviation (SCAD) approaches. © 2012 Lan Xue and Annie Qu.


Kaplan R.M.,Health-U | Irvin V.L.,Oregon State University
PLoS ONE | Year: 2015

Background: We explore whether the number of null results in large National Heart Lung, and Blood Institute (NHLBI) funded trials has increased over time. Methods: We identified all large NHLBI supported RCTs between 1970 and 2012 evaluating drugs or dietary supplements for the treatment or prevention of cardiovascular disease. Trials were included if direct costs >$500,000/year, participants were adult humans, and the primary outcome was cardiovascular risk, disease or death. The 55 trials meeting these criteria were coded for whether they were published prior to or after the year 2000, whether they registered in clinicaltrials.gov prior to publication, used active or placebo comparator, and whether or not the trial had industry co-sponsorship. We tabulated whether the study reported a positive, negative, or null result on the primary outcome variable and for total mortality. Results: 17 of 30 studies (57%) published prior to 2000 showed a significant benefit of intervention on the primary outcome in comparison to only 2 among the 25 (8%) trials published after 2000 (χ2=12.2,df= 1, p=0.0005). There has been no change in the proportion of trials that compared treatment to placebo versus active comparator. Industry co-sponsorship was unrelated to the probability of reporting a significant benefit. Pre-registration in clinical trials. gov was strongly associated with the trend toward null findings. Conclusions: The number NHLBI trials reporting positive results declined after the year 2000. Prospective declaration of outcomes in RCTs, and the adoption of transparent reporting standards, as required by clinicaltrials.gov, may have contributed to the trend toward null findings.


Hollinger G.A.,Oregon State University | Sukhatme G.S.,University of Southern California
International Journal of Robotics Research | Year: 2014

We propose three sampling-based motion planning algorithms for generating informative mobile robot trajectories. The goal is to find a trajectory that maximizes an information quality metric (e.g. variance reduction, information gain, or mutual information) and also falls within a pre-specified budget constraint (e.g. fuel, energy, or time). Prior algorithms have employed combinatorial optimization techniques to solve these problems, but existing techniques are typically restricted to discrete domains and often scale poorly in the size of the problem. Our proposed rapidly exploring information gathering (RIG) algorithms combine ideas from sampling-based motion planning with branch and bound techniques to achieve efficient information gathering in continuous space with motion constraints. We provide analysis of the asymptotic optimality of our algorithms, and we present several conservative pruning strategies for modular, submodular, and time-varying information objectives. We demonstrate that our proposed techniques find optimal solutions more quickly than existing combinatorial solvers, and we provide a proof-of-concept field implementation on an autonomous surface vehicle performing a wireless signal strength monitoring task in a lake. © The Author(s) 2014.


Lachenbruch B.,Oregon State University | Mcculloh K.A.,University of Wisconsin - Madison
New Phytologist | Year: 2014

This review presents a framework for evaluating how cells, tissues, organs, and whole plants perform both hydraulic and mechanical functions. The morphological alterations that affect dual functionality are varied: individual cells can have altered morphology; tissues can have altered partitioning to functions or altered cell alignment; and organs and whole plants can differ in their allocation to different tissues, or in the geometric distribution of the tissues they have. A hierarchical model emphasizes that morphological traits influence the hydraulic or mechanical properties; the properties, combined with the plant unit's environment, then influence the performance of that plant unit. As a special case, we discuss the mechanisms by which the proxy property wood density has strong correlations to performance but without direct causality. Traits and properties influence multiple aspects of performance, and there can be mutual compensations such that similar performance occurs. This compensation emphasizes that natural selection acts on, and a plant's viability is determined by, its performance, rather than its contributing traits and properties. Continued research on the relationships among traits, and on their effects on multiple aspects of performance, will help us better predict, manage, and select plant material for success under multiple stresses in the future. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.


Manore M.M.,Oregon State University
International Journal of Sport Nutrition and Exercise Metabolism | Year: 2012

Weight-loss supplements typically fall into 1 of 4 categories depending on their hypothesized mechanism of action: products that block the absorption of fat or carbohydrate, stimulants that increase thermogenesis, products that change metabolism and improve body composition, and products that suppress appetite or give a sense of fullness. Each category is reviewed, and an overview of the current science related to their effectiveness is presented. While some weight-loss supplements produce modest effects (<2 kg weight loss), many have either no or few randomized clinical trials examining their effectiveness. A number of factors confound research results associated with the efficacy of weight-loss supplements, such as small sample sizes, short intervention periods, little or no follow-up, and whether the supplement is given in combination with an energy-restricted diet or increased exercise expenditure. There is no strong research evidence indicating that a specific supplement will produce significant weight loss (>2 kg), especially in the long term. Some foods or supplements such as green tea, fiber, and calcium supplements or dairy products may complement a healthy lifestyle to produce small weight losses or prevent weight gain over time. Weight-loss supplements containing metabolic stimulants (e.g., caffeine, ephedra, synephrine) are most likely to produce adverse side effects and should be avoided. © 2012 Human Kinetics, Inc.


Reimer J.J.,Oregon State University
Ecological Economics | Year: 2012

Virtual water trade is increasingly recognized as a useful metaphor for thinking about freshwater resources in an international context. Its legitimacy in terms of economic theory has been questioned by a number of authors, however. In this article I develop new theoretical results that place the virtual water concept on a firm economic foundation, and which correct several misconceptions within the existing literature on virtual water economics. © 2012 Elsevier B.V.


Hense B.A.,Helmholtz Center Munich | Schuster M.,Oregon State University
Microbiology and Molecular Biology Reviews | Year: 2015

Autoinduction (AI), the response to self-produced chemical signals, is widespread in the bacterial world. This process controls vastly different target functions, such as luminescence, nutrient acquisition, and biofilm formation, in different ways and integrates additional environmental and physiological cues. This diversity raises questions about unifying principles that underlie all AI systems. Here, we suggest that such core principles exist. We argue that the general purpose of AI systems is the homeostatic control of costly cooperative behaviors, including, but not limited to, secreted public goods. First, costly behaviors require preassessment of their efficiency by cheaper AI signals, which we encapsulate in a hybrid "push-pull" model. The "push" factors cell density, diffusion, and spatial clustering determine when a behavior becomes effective. The relative importance of each factor depends on each species' individual ecological context and life history. In turn, "pull" factors, often stress cues that reduce the activation threshold, determine the cellular demand for the target behavior. Second, control is homeostatic because AI systems, either themselves or through accessory mechanisms, not only initiate but also maintain the efficiency of target behaviors. Third, AI-controlled behaviors, even seemingly noncooperative ones, are generally cooperative in nature, when interpreted in the appropriate ecological context. The escape of individual cells from biofilms, for example, may be viewed as an altruistic behavior that increases the fitness of the resident population by reducing starvation stress. The framework proposed here helps appropriately categorize AIcontrolled behaviors and allows for a deeper understanding of their ecological and evolutionary functions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.


Wildenschild D.,Oregon State University | Sheppard A.P.,Australian National University
Advances in Water Resources | Year: 2013

We report here on recent developments and advances in pore-scale X-ray tomographic imaging of subsurface porous media. Our particular focus is on immiscible multi-phase fluid flow, i.e., the displacement of one immiscible fluid by another inside a porous material, which is of central importance to many natural and engineered processes. Multiphase flow and displacement can pose a rather difficult problem, both because the underlying physics is complex, and also because standard laboratory investigation reveals little about the mechanisms that control micro-scale processes. X-ray microtomographic imaging is a non-destructive technique for quantifying these processes in three dimensions within individual pores, and as we report here, with rapidly increasing spatial and temporal resolution. © 2012 Elsevier Ltd.


Bostian M.B.,Lewis And Clark College | Herlihy A.T.,Oregon State University
Ecological Economics | Year: 2014

This study uses the directional output distance function, a multi-output economic production frontier model, to value the physical tradeoffs between agricultural production and wetland condition in the U.S. Mid-Atlantic region Nanticoke River watershed. We combine detailed ecological indicator data to measure wetland condition with satellite imagery land use data on agricultural production in the watershed. Our estimation procedure adapts the bootstrap methods originally developed by Simar and Wilson (1998) for nonparametric efficiency estimates to the quadratic directional output distance function. We find substantial variation in tradeoff values across the watershed, which could be used to target wetland conservation efforts in the region. © 2014 Elsevier B.V.


Nyman M.,Sandia National Laboratories | Nyman M.,Oregon State University | Alam T.M.,Sandia National Laboratories
Journal of the American Chemical Society | Year: 2012

Discrete aqueous metal oxide polyionic clusters that include aluminum polycations, transition-metal polyoxometalates, and the actinyl peroxide clusters have captivated the interest of scientists in the realm of both their fundamental and applied chemistries. Yet the counterions for these polycations or polyanions are often ignored, even though they are imperative for solubility, crystallization, purification, and even templating cluster formation. The actinyl peroxide clusters have counterions not only external, but internal to the hollow peroxide capsules. In this study, we reveal the dynamic behavior of these internal alkali counterions via solid-state and liquid NMR experiments. These studies on two select cluster geometries, those containing 24 and 28 uranyl polyhedra, respectively, show that the capsules-like clusters are not rigid entities. Rather, the internal alkalis both have mobility inside the capsules, as well as exchange with species in the media in which they are dissolved. The alkali mobilities are affected by both what is inside the clusters as well as the composition of the dissolving medium. © 2012 American Chemical Society.


On the basis of their morphology and seasonal thermal characteristics, recurrent slope lineae (RSL) on Mars have been inferred to be a possible result of the flow of a liquid (likely a saline brine) through the upper portions of the martian regolith. In this note, we analyze repeat HiRISE imaging of RSL to show that the downslope growth rate of recurrent slope lineae is well-fit by an elementary groundwater flow model that also describes the downslope propagation of Antarctic water tracks (terrestrial analogs to RSL), and that the apparent permeability of RSL-bearing slopes is consistent with the observed sandy regolith substrate. © 2012 Elsevier Inc.


Edwards K.J.,University of Southern California | Becker K.,University of Miami | Colwell F.,Oregon State University
Annual Review of Earth and Planetary Sciences | Year: 2012

Most ecosystems on Earth exist in permanent darkness, one or more steps removed from the light-driven surface world. This collection of dark habitats is the most poorly understood on Earth, in particular the size, function, and activity of these ecosystems and what influence they have on global biogeochemical processes. The vastest of these ecosystems constitute the "deep biosphere"-habitats physically located below the surface of continents and the bottom of the ocean. The deep biosphere has been the subject of considerable-and increasing-study and scrutiny in recent years. New deep biosphere realms are being explored from deep in mines in South Africa, to sediments in the middle of oceanic gyres-and beyond. New technologies are emerging, permitting researchers to do active, manipulable experimentation in situ within the subsurface. This review highlights recent history of the research and the exciting new directions this field of research is going in, and discusses some of the most active and interesting field realms currently under scrutiny by researchers examining this deep, dark, intraterrestrial life. © 2012 by Annual Reviews. All rights reserved.


Cheong P.H.-Y.,Oregon State University | Legault C.Y.,Universite de Sherbrooke | Um J.M.,University of California at Los Angeles | Celebi-Olcum N.,University of California at Los Angeles | Houk K.N.,University of California at Los Angeles
Chemical Reviews | Year: 2011

B3LYP with modest basis sets continues to be used routinely for the study of organocatalysis, but deficiencies in this functional have been discovered. This is especially true for reaction thermochemistries and in cases where dispersion effects influence weak interactions between groups. Newer, more highly parametrized functionals such as Truhlar's M0X series, especially M06-2X and now M08 for organic reactions are being used routinely. More accurate, but also more expensive methods, like SCS-MP2, and double hybrid functionals like B2PLYP are being used with increasing frequency. Isoxazolidine-3-carboxylic Acid is an interesting choice of catalyst, due to the possibility of increased nucleophilicity originating from an α-effect. The Seebach-Eschenmoser model has been proposed to explain the origin of selectivity. This model involves the enamine carboxylate as a key reaction intermediate. Acyclic primary amino acids have also been discovered to be catalysts for the intermolecular aldol reactions.


Logendran R.,Oregon State University
Expert Systems with Applications | Year: 2013

Typically, in order to process jobs in a flowshop both machines and labor are required. However, in traditional scheduling problems, labor is assumed to be plentiful and only machine is considered to be a constraint. This assumption could be due to the lower cost of labor compared to machines or the complexity of dual-resource constrained problems. In this paper a mathematical model is developed to minimize the work-in-process inventory while maximizing the service level in a flowshop with dual resources. The model focuses on optimizing a non-permutation flowshop. There are different skill levels considered for labor and the setup times on machines are sequence-dependent. Jobs are allowed to skip one or more stages in the flowshop. Job release and machine availability times are considered to be dynamic. The problem is solved in two layers. The outer layer is a search algorithm to find the schedule of jobs on the machine (traditional flowshop scheduling problem) and the inner layer is a three-step heuristic to find a schedule of jobs on labor in accordance to the machine schedule. Three different search algorithms are developed to solve the proposed NP-hard problem. First algorithm can solve a permutation flowshop while the other two are developed to solve a non-permutation flowshop. The comparison between the optimal solution and the search algorithms in small examples shows a good performance of the algorithms with an average deviation of only 2.00%. An experimental design analyzes the effectiveness and efficiency of the algorithms statistically. The results show that non-permutation algorithms perform better than the permutation algorithm, although the former are less efficient. The effectiveness and efficiency in all three algorithms have an inverse relation. To the best of our knowledge, this research is the first of its kind to provide a comprehensive mathematical model for dual resource flowshop scheduling problem. © 2013 Elsevier Ltd. All rights reserved.


de Stefano L.,Oregon State University
Water Resources Management | Year: 2010

The recent international agreement to implement principles of Integrated Water Resources Management (IWRM) as a means to overcome the current world water crisis has brought about the need to measure countries' progress towards a new way of managing water. Several governmental and nongovernmental international organizations have taken up this challenge using different methods. This paper analyzes the methodological approaches currently applied to comparative water policy assessment, points out advantages and drawbacks of the different types of initiatives, and looks at where this relatively young field of research is heading. The technical and topical constraints of existing numerical indicators, the lack of consolidated qualitative assessments and the difficulty to measure real water policy implementation are among the main challenges to be addressed in the near future in the context of water policy assessment. © 2009 Springer Science+Business Media B.V.


Menge B.A.,Oregon State University | Menge D.N.L.,Princeton University | Menge D.N.L.,Stanford University | Menge D.N.L.,Columbia University
Ecological Monographs | Year: 2013

The intermittent upwelling hypothesis (IUH) predicts that the strength of ecological subsidies, organismal growth responses, and species interactions will vary unimodally along a gradient of upwelling from persistent downwelling to persistent upwelling, with maximal levels at an intermediate or "intermittent" state of upwelling. To test this model, we employed the comparative-experimental method to investigate these processes at 16-44 wave-exposed rocky intertidal sites in Oregon, California, and New Zealand, varying in average upwelling and/or downwelling during spring-summer. As predicted by the IUH, ecological subsidies (phytoplankton abundance, prey recruitment rates), prey responses (barnacle colonization, mussel growth), and species interactions (competition rate, predation rate and effects) were unimodally related to upwelling. On average, unimodal relationships with upwelling magnitude explained ;50% of the variance in the various processes, and unimodal and monotonic positive relationships against an index of intermittency explained ;37% of the variance. Regressions among the ecological subsidies and species interactions were used to infer potential ecological linkages that underpinned these patterns. Abundance of phytoplankton was associated with increases in rates of barnacle colonization, intensity of competition and predation, and predation effects, and rates of barnacle recruitment were associated with increases in mussel growth, barnacle colonization, and species interactions. Positive effects on interactions were also seen for rates of colonization, competition, predation, and predation effects. Several responses were saturating or exponential, suggestive of threshold effects. These results suggest that the IUH has geographic generality and are also consistent with earlier arguments that bottom-up effects and propagule subsidies are strongly linked to the dynamics of higher trophic levels, or top-down effects, as well as to nontrophic interactions. The ;50% of the variance not explained by upwelling is likely due to more regional-to-local influences on the processes examined, and future efforts should focus on incorporating such effects into the IUH. © 2013 by the Ecological Society of America.


Gombart A.F.,Oregon State University
Blood | Year: 2015

In this issue of Blood, Bartels and colleagues demonstrate that acetylation of the transcription factor CCAAT enhancer binding protein e (C/EBPe) is essential for terminal neutrophil granulocyte differentiation.1 © 2015 by The American Society of Hematology.


Anderson K.A.,Oregon State University
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2014

It is difficult to assess pollution in remote areas of less-developed regions owing to the limited availability of energy, equipment, technology, trained personnel and other key resources. Passive sampling devices (PSDs) are technologically simple analytical tools that sequester and concentrate bioavailable organic contaminants from the environment. Scientists from Oregon State University and the Centre Régional de Recherches en Ecotoxicologie et de Sécurité Environnementale (CERES) in Senegal developed a partnership to build capacity at CERES and to develop a pesticide-monitoring project using PSDs. This engagement resulted in the development of a dynamic training process applicable to capacity-building programmes. The project culminated in a field and laboratory study where paired PSD samples were simultaneously analysed in African and US laboratories with quality control evaluation and traceability. The joint study included sampling from 63 sites across six western African countries, generating a 9000 data point pesticide database with virtual access to all study participants.


Yeh H.,Oregon State University
Natural Hazards Review | Year: 2010

A tsunami casualty model is developed with criteria based on whether a person can remain standing within tsunami flow. A simplified model of a human body is made using anthropometric data. By applying the model to tsunami inundation predictions generated by analytic solution of fully nonlinear shallow-water wave theory, we demonstrate quantitatively that differences in gender and age fatalities are most pronounced when a tsunami is marginally significant; strong tsunamis wipe out population almost indiscriminately. This trend is consistent with some of the field observations. It is important to consider gender and age factors when a coastal community plans for tsunami preparedness. Because the development of the casualty model is based solely on physical mechanisms, the model results can be used to remove physical causes from field data, which then allows for further investigation of social and behavioral factors. © 2010 ASCE.


Allendorf F.W.,University of Montana | Allendorf F.W.,Victoria University of Wellington | Hohenlohe P.A.,University of Oregon | Hohenlohe P.A.,Oregon State University | And 2 more authors.
Nature Reviews Genetics | Year: 2010

We will soon have complete genome sequences from thousands of species, as well as from many individuals within species. This coming explosion of information will transform our understanding of the amount, distribution and functional significance of genetic variation in natural populations. Now is a crucial time to explore the potential implications of this information revolution for conservation genetics and to recognize limitations in applying genomic tools to conservation issues. We identify and discuss those problems for which genomics will be most valuable for curbing the accelerating worldwide loss of biodiversity. We also provide guidance on which genomics tools and approaches will be most appropriate to use for different aspects of conservation. © 2010 Macmillan Publishers Limited. All rights reserved.


Gunter K.B.,Oregon State University | Almstedt H.C.,Loyola Marymount University | Janz K.F.,University of Iowa
Exercise and Sport Sciences Reviews | Year: 2012

Physical activities undertaken in childhood, particularly activities, which apply large forces quickly convey optimal benefits to bone mass, size, and structure. Evidence is accumulating that benefits persist well beyond activity cessation. This review examines the potential for early childhood activity to improve bone mineralization and structure and explores childhood activity as prevention for osteoporosis in later life. Copyright © 2011 by the American College of Sports Medicine.


Putman N.F.,Oregon State University
Biology letters | Year: 2013

The inaccessibility of open ocean habitat and the cryptic nature of small animals are fundamental problems when assessing the distribution of oceanic-stage sea turtles and other marine animals sharing similar life-history traits. Most methods that estimate patterns of abundance cannot be applied in situations that are extremely data limited. Here, we use a movement ecology framework to generate the first predicted distributions for the oceanic stage of the Kemp's ridley sea turtle (Lepidochelys kempii). Our simulations of particle dispersal within ocean circulation models reveal substantial annual variation in distribution and survival among simulated cohorts. Such techniques can help prioritize areas for conservation, and supply inputs for more realistic demographic models attempting to characterize population trends.


Background. It is rare to find terrestrial nematode lineages parasitizing arthropods inhabiting the intertidal or littoral zone of the oceans. During an ecological study along the Oregon dunes, an allantonematid nematode (Tylenchomorpha: Allantonematidae) was discovered parasitizing the intertidal shore bug, Saldula laticollis (Reuter)(Hemiptera: Saldidae). This shore bug is adapted to an intertidal environment and can survive short periods of submergence during high tides. The present study describes the nematode parasite and discusses aspects of its development, ecology and evolution. Methods. Adults and last instar nymphs of S. laticollis (Hemiptera: Saldidae) were collected from the high intertidal zone among clumps of Juncus L. (Juncaceae) plants at Waldport, Oregon on October 3, 2011. The bugs were dissected in 1% saline solution and the nematodes killed in 1% Ringers solution and immediately fixed in 5% formalin (at 20°C). Third stage juveniles removed from infected hosts were maintained in 1% saline solution until they matured to the adult stage, molted and mated. Results. Halophilanema prolata n. gen., n. sp. (Nematoda: Allantonematidae) is described from last instar nymphs and adults of the intertidal bug, Saldula laticollis on the Oregon coast. The new genus can be distinguished from other genera in the Allantonematidae by a stylet lacking basal knobs in both sexes, an excretory pore located behind the nerve ring, ribbed spicules, a gubernaculum, the absence of a bursa and the elongate-tubular shape of the ovoviviparous parasitic females. Studies of the organogenesis of Halophilanema showed development to third stage juveniles in the uterus of parasitic females. Maturation to the free-living adults and mating occurred in the environment. The incidence of infection of S. laticollis ranged from 0% to 85% depending on the microhabitat in the intertidal zone. Conclusions. Based on the habitat and morphological characters, it is proposed that Halophilanema adapted a parasitic existence fairly recently, evolutionarily speaking. It was probably a free-living intertidal or shore nematode that fed on microorganisms, especially fungi, in the intertidal habitat and became parasitic after saldids entered the environment. Halophilanema represents the first described nematode parasite of an intertidal insect. © 2012 Poinar; licensee BioMed Central Ltd.


Wu Z.,Oregon State University | Pullman M.E.,Portland State University
Journal of Operations Management | Year: 2015

Recent studies on structural and relational embeddedness suggest that favorable position and connections in supply networks benefit a firm. While fruitful, this focus misses the motivations that prompt firms to take economic action in the first place. Understanding cultural embeddedness provides insight into why individuals and firms behave as they do and how their behavior can influence network structure. Contrary to the belief that firms act solely for profit and growth, we note that cultural contents such as values, social issues and political ideologies explain firms' motives and guide their economic activities. We explore the role of cultural embeddedness through a grounded study of Country Natural Beef, a sustainability-oriented agricultural cooperative in the western United States. This supply network demonstrates strongly competing cultural claims among its members as well as a unique institutionalized culture. Cultural interactions at the node and network levels explain the functioning of and changes to the network. Through interviews, analysis of archival information and direct observation of pivotal events over a period of 5 years, we unpack cultural embeddedness and take an incremental step toward a theory of cultural embeddedness in cooperative supply networks. © 2014 Published by Elsevier B.V.


Briggs F.,Oregon State University
The Journal of the Acoustical Society of America | Year: 2012

Although field-collected recordings typically contain multiple simultaneously vocalizing birds of different species, acoustic species classification in this setting has received little study so far. This work formulates the problem of classifying the set of species present in an audio recording using the multi-instance multi-label (MIML) framework for machine learning, and proposes a MIML bag generator for audio, i.e., an algorithm which transforms an input audio signal into a bag-of-instances representation suitable for use with MIML classifiers. The proposed representation uses a 2D time-frequency segmentation of the audio signal, which can separate bird sounds that overlap in time. Experiments using audio data containing 13 species collected with unattended omnidirectional microphones in the H. J. Andrews Experimental Forest demonstrate that the proposed methods achieve high accuracy (96.1% true positives/negatives). Automated detection of bird species occurrence using MIML has many potential applications, particularly in long-term monitoring of remote sites, species distribution modeling, and conservation planning.


Epps C.W.,Oregon State University
Condor | Year: 2014

In this issue of The Condor: Ornithological Applications, Haig et al. (2014) summarize negative impacts of lead ammunition and fishing tackle on birds and discuss strategies for mitigating risks to wildlife and human health. Their Review raises an important set of questions for hunters, wildlife managers, and conservation scientists. Effective mitigation will require careful understanding of technical, economic, and social dimensions of the problem. Here, I focus on challenges specific to adopting non-lead ammunition for hunting, particularly for large game animals. I discuss limitations of using the ban on lead ammunition for waterfowl hunting as an analog for reducing lead use for other types of hunting, explain important technical considerations in design and use of non-lead ammunition, and point out areas where effective non-lead alternatives are still lacking. I suggest that currently available economic analyses of the cost of non-lead alternatives are inadequate and do not recognize wide variation in hunter behavior. These considerations have strong implications for designing effective outreach and predicting responses of hunters asked to consider non-lead alternatives. Enforcing outright bans on using lead ammunition for all types of hunting, as recently enacted in California, may prove even more challenging than similar restrictions for waterfowl hunting. Despite this, I propose that major reductions in exposure of wildlife and people to lead bullet fragments are achievable, particularly through outreach and incentive programs that focus on the most commonly used types of firearms for big game hunting-high velocity modern rifles. Bullets from these widely used rifles typically produce the most lead fragments and have the best selection of effective non-lead options available at this time. Efforts to change hunter behavior must recognize the true costs and challenges of changing to non-lead ammunition. Likewise, hunters should recognize and accept their important role in wildlife conservation and work to embrace effective alternatives to lead as they become available. © 2014 Cooper Ornithological Society.


Horning M.,Oregon State University
Frontiers in Physiology | Year: 2012

Constraint lines-the boundaries that delimit point clouds in bivariate scattergrams-have been applied in macro-ecology to quantify the effects of limiting factors on response variables, but have not been applied to the behavioral performance and physiological ecology of individual vertebrates. I propose that behavioral scattergrams of air-breathing, diving vertebrates contain informative edges that convey insights into physiological constraints that shape the performance envelopes of divers. In the classic example of repeated cycles of apnea and eupnea in diving, air-breathing vertebrates, the need to balance oxygen consumption, and intake should differentially constrain recovery for dives within or exceeding the aerobic dive limit (ADL). However, the bulk of variance observed in recovery versus dive duration scattergrams originates from undetermined behavioral variables, and deviations from overall stasis may become increasingly apparent at progressively smaller scales of observation. As shown on dive records from 79 Galápagos fur seals, the selection of appropriate time scales of integration yields two distinct recovery boundaries for dive series within and beyond the estimated ADL. An analysis of the corresponding constraint lines is independent of central tendencies in data and avoids violating parametric assumptions for large data sets where variables of interest account for only a small portion of observed variance. I hypothesize that the intercept between these constraint lines represents the effective ADL, and present physiological and ecological considerations to support this hypothesis. © 2012 Horning.


Ruaux C.G.,Oregon State University
Veterinary Journal | Year: 2013

Measurement of the water-soluble vitamin cobalamin has long been of interest as a marker of gastrointestinal disease in companion animals due to the highly localized presence of cobalamin receptors in the ileum. An increasing body of evidence suggests that cobalamin deficiency is an important co-morbidity in many companion animal patients with gastrointestinal and pancreatic disease. Congenital disorders of cobalamin absorption and cellular metabolism are also increasingly recognized in companion animal breeds. The early recognition of these disorders and timely treatment with parenteral cobalamin can be life-saving. In this article, the normal mechanisms of cobalamin absorption, the use of cobalamin as a marker of intestinal disease and data on the prevalence of hypocobalaminemia in a variety of diseases are described. The prognostic impact of and rational therapy for hypocobalaminemia in domestic animals are discussed. © 2013 Elsevier Ltd.


O'Neil S.T.,Oregon State University | O'Neil S.T.,University of Notre Dame | Emrich S.J.,University of Notre Dame
BMC Genomics | Year: 2013

Background: Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality.Results: We simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a " perfect" and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased.Several commonly used metrics were not consistent with these expectations, including average contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways.Conclusions: Although much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies. © 2013 O'Neil and Emrich; licensee BioMed Central Ltd.


Suess E.,Leibniz Institute of Marine Science | Suess E.,Oregon State University
International Journal of Earth Sciences | Year: 2014

Characteristics of cold seeps at different geologic settings are the subject of this review primarily based on results of the Research Consortium SFB 574. Criteria are drawn from examples on the erosive convergent margin off Costa Rica, the accretionary margin off Chile supplemented by examples from the transform margin of the Golf of Cadiz and the convergent Hikurangi margin off New Zealand. Others are from well-studied passive margins of the Black Sea, the Golf of Mexico, the eastern Mediterranean Sea and the South China Sea. Seeps at all settings transport water and dissolved compounds to the ocean through the seafloor by different forcing mechanism and from different depths of the submerged geosphere (10s of meters to 10s of km). The compounds sustain oasis-type ecosystems by providing bioactive reductants sulfide, methane and hydrogen. Hereby, the interaction between fluid composition, flux rates and biota results in a diagnostic hydrocarbon–metazoan–microbe–carbonate association; currently, well over 100 active sites are known. The single most important reaction is microbially mediated anaerobic oxidation of methane with secondary reactions involving S-biogeochemistry and carbonate mineral precipitation. Seep fluids and their seafloor manifestations provide clues as to source depth, fluid–sediment/rock interaction during ascent, lifetime and cyclicity of seepage events but less so on the magnitude of return flow. At erosive margins, Cl-depleted and B-enriched fluids from clay dehydration provide criteria for source depth and temperature. The upward material flow generates mud volcanoes at the seafloor above the projected location of dehydration at depth. At accretionary margins, fluids are derived from more shallow depths by compaction of sediments as they ride on the incoming oceanic plate; they are emitted through thrust faults. At highly sedimented margins, organic-rich and evaporite-containing strata (when present) determine the final fluid composition, by emitting characteristically gas hydrate-derived methane, brine-associated non-methane hydrocarbons or leached elements and their isotopes (Li, δ7Li, B, Ba) from host sediments. Smectite–illite transformation and associated Cl-depletion from release of interlayer water is a pervasive process at these margins. Rare earth element pattern in conjunction with redox-sensitive metals retained in seep carbonates indicate whether or not they precipitated in contact with oxic bottom water or suboxic fluids; clear environmental characterization, though, currently remains inconclusive. More deeply sourced fluids as in transform margins may be characterized by their 87Sr/86Sr ratios from interaction with oceanic crustal rocks below. Quantification of flow and reliable estimates of total volatile output from fore-arcs remain a challenge to seep research, as does understanding the role of geologically derived methane in the global methane cycle. © 2014, Springer-Verlag Berlin Heidelberg.


Barbar E.,Oregon State University
Biochemical Society Transactions | Year: 2012

In the present paper, I report the molecular overlap of the linkage of three essential protein complexes that co-ordinate the formation of the mitotic spindle. These proteins are dynein, a large motor complex that moves machinery inside cells, and two of its regulators: a protein complex called dynactin, a dynein activator, and a protein called NudE whose depletion in mice produces a small brain and mental retardation. What is intriguing about the dynein-dynactin-NudE interplay is that dynactin and NudE bind to a common segment of dynein that is intrinsically disordered. Elucidating differences in their binding modes may explain how one regulator can be selected over the other even when both are present in the same cellular compartment. These results not only have a far-reaching impact on our understanding of processes essential for the formation and orientation of the spindle, but also offer a novel role for protein disorder in controlling cellular processes, and highlight the advantages of NMR spectroscopy in elucidating atomic-level characterization of extremely complex dynamic cellular assemblies. ©The Authors Journal compilation ©2012 Biochemical Society.


Murtaugh P.A.,Oregon State University
Ecology | Year: 2014

Statistical hypothesis testing has been widely criticized by ecologists in recent years. I review some of the more persistent criticisms of P values and argue that most stem from misunderstandings or incorrect interpretations, rather than from intrinsic shortcomings of the P value. I show that P values are intimately linked to confidence intervals and to differences in Akaike's information criterion (ΔAIC), two metrics that have been advocated as replacements for the P value. The choice of a threshold value of ΔAIC that breaks ties among competing models is as arbitrary as the choice of the probability of a Type I error in hypothesis testing, and several other criticisms of the P value apply equally to ΔAIC. Since P values, confidence intervals, and ΔAIC are based on the same statistical information, all have their places in modern statistical practice. The choice of which to use should be stylistic, dictated by details of the application rather than by dogmatic, a priori considerations. © 2014 by the Ecological Society of America.


Thomas C.K.,Oregon State University
Boundary-Layer Meteorology | Year: 2011

We examine the space-time structure of the wind and temperature fields, as well as that of the resulting spatial temperature gradients and horizontal advection of sensible heat, in the sub-canopy of a forest with a dense overstorey in moderately complex terrain. Data were collected from a sensor network consisting of ten stations and subject to orthogonal decomposition using the multiresolution basis set and stochastic analyses including two-point correlations, dimensional structure functions, and various other bulk measures for space and time variability. Despite some similarities, fundamental differences were found in the space-time structure of the motions dominating the variability of the sub-canopy wind and temperature fields. The dominating motions occupy similar spatial, but different temporal, scales. A conceptual space-time diagram was constructed based on the stochastic analysis that includes the important end members of the spatial and temporal scales of the observed motions of both variables. Short-lived and small-scale motions govern the variability of the wind, while the diurnal temperature oscillation driven by the surface radiative transfer is the main determinant of the variability in the temperature signal, which occupies much larger time scales. This scale mismatch renders Taylor's hypothesis for sub-canopy flow invalid and aggravates the computation of meaningful estimates of horizontal advective fluxes without dense spatial information. It may further explain the ambiguous and inconclusive results reported in numerous energy and mass balance and advection studies evaluating the hypothesis that accounting for budget components other than the change in storage term and the vertical turbulent flux improves the budget closure when turbulent diffusion is suppressed in plant canopies. Estimates of spatial temperature gradients and advective fluxes were sensitive to the network geometry and the spatial interpolation method. The assumption of linear spatial temperature gradients was not supported by the results, and leads to increased spatial and temporal variability of inferred spatial gradients and advection estimates. A method is proposed to estimate the appropriate minimum network size of wind and temperature sensors suitable for an evaluation of energy and mass balances by reducing spatial and temporal variability of the spatially sampled signals, was estimated to be on the order of 200 m at the study site. © 2011 Springer Science+Business Media B.V.


Coles P.J.,Carnegie Mellon University | Colbeck R.,Perimeter Institute for Theoretical Physics | Yu L.,Carnegie Mellon University | Zwolak M.,Oregon State University
Physical Review Letters | Year: 2012

Uncertainty relations provide constraints on how well the outcomes of incompatible measurements can be predicted, and as well as being fundamental to our understanding of quantum theory, they have practical applications such as for cryptography and witnessing entanglement. Here we shed new light on the entropic form of these relations, showing that they follow from a few simple properties, including the data-processing inequality. We prove these relations without relying on the exact expression for the entropy, and hence show that a single technique applies to several entropic quantities, including the von Neumann entropy, min- and max-entropies, and the Rényi entropies. © 2012 American Physical Society.


Niess M.L.,Oregon State University
Journal of Educational Computing Research | Year: 2013

Technological pedagogical content knowledge (TPACK) proposes a theoretical framework that incorporates four central components: an overarching conception of what it means to teach with technology, knowledge of students' thinking and understandings of specific topics with technologies, knowledge of curricular materials that incorporate technologies, and knowledge of instructional strategies and representations for teaching subject matter with technologies. This interpretive case study, conducted over a 3-year period, identified descriptors aligned with the four central components of TPACK to highlight differences in teachers' knowledge levels when integrating spreadsheets as learning tools in mathematics. © 2013, Baywood Publishing Co., Inc.


Antle J.M.,Oregon State University
American Journal of Agricultural Economics | Year: 2011

This article develops the conceptual and empirical foundations for a parsimonious, generic modeling approach to multi-dimensional (i.e., economic, environmental and social) impact assessments of agricultural technologies and environmental change. Joint distributions between technology adoption and outcome variables are characterized, and used to analyze the selection effects of adoption on a general class of impact indicators. The approach is implemented with a generic model that can be parameterized with low-order moments of outcome variables. A case study of adoption of a high-yielding maize variety in Kenya illustrates the model's use and confirms theoretical results. © TheAuthor (2011). Published by Oxford University Press on behalf of the Agricultural and Applied Economics Association. All rights reserved.


Minder J.R.,University of Washington | Mote P.W.,Oregon State University | Lundquist J.D.,University of Washington
Journal of Geophysical Research: Atmospheres | Year: 2010

The typically sparse distribution of weather stations in mountainous terrain inadequately resolves temperature variability. Accordingly, high-resolution gridding of climate data (for applications such as hydrological modeling) often relies on assumptions such as a constant surface temperature lapse rate (i.e., decrease of surface temperature with altitude) of 6.5°C km-1. Using an example of the Cascade Mountains, we describe the temporal and spatial variability of the surface temperature lapse rate, combining data from: (1) COOP stations, (2) nearby radiosonde launches, (3) a temporary dense network of sensors, (4) forecasts from the MM5 regional model, and (5) PRISM geo-statistical analyses. On the windward side of the range, the various data sources reveal annual mean lapse rates of 3.9-5.2°C km -1, substantially smaller than the often-assumed 6.5°C km -1. The data sets show similar seasonal and diurnal variability, with lapse rates smallest (2.5-3.5°C km-1) in late-summer minimum temperatures, and largest (6.5-7.5°C km-1) in spring maximum temperatures. Geographic (windward versus lee side) differences in lapse rates are found to be substantial. Using a simple runoff model, we show the appreciable implications of these results for hydrological modeling. Copyright 2010 by the American Geophysical Union.


Reynolds R.W.,National Oceanic and Atmospheric Administration | Chelton D.B.,Oregon State University
Journal of Climate | Year: 2010

Six different SST analyses are compared with each other and with buoy data for the period 2007-08. All analyses used different combinations of satellite data [for example, infrared Advanced Very High Resolution Radiometer (AVHRR) and microwave Advanced Microwave Scanning Radiometer (AMSR) instruments] with different algorithms, spatial resolution, etc. The analyses considered are the National Climatic Data Center (NCDC) AVHRR-only and AMSR1AVHRR, the Navy Coupled Ocean Data Assimilation (NCODA), the Remote Sensing Systems (RSS), the Real-Time Global High-Resolution (RTG-HR), and the Operational SST and Sea Ice Analysis (OSTIA); the spatial grid sizes were 1/4°, 1/4°, 1/9°, 1/11°, 1/12°, and 1/20°, respectively. In addition, all analyses except RSS used in situ data. Most analysis procedures and weighting functions differed. Thus, differences among analyses could be large in high-gradient and data-sparse regions. An example off the coast of South Carolina showed winter SST differences that exceeded 5°C. To help quantify SST analysis differences, wavenumber spectra were computed at several locations. These results suggested that the RSS is much noisier and that the RTG-HR analysis is much smoother than the other analyses. Further comparisons made using collocated buoys showed that RSS was especially noisy in the tropics and that RTG-HR had winter biases near the Aleutians region during January and February 2007. The correlation results show that NCODA and, to a somewhat lesser extent, OSTIA are strongly tuned locally to buoy data. The results also show that grid spacing does not always correlate with analysis resolution. The AVHRR-only analysis is useful for climate studies because it is the only daily SST analysis that extends back to September 1981. Furthermore, comparisons of the AVHRR-only analysis and the AMSR1AVHRR analysis show that AMSR data can degrade the combined AMSR and AVHRR resolution in cloud-free regions while AMSR otherwise improves the resolution. These results indicate that changes in satellite instruments over time can impact SST analysis resolution. © 2010 American Meteorological Society.


Fox D.B.,University of Missouri | Warnock J.J.,Oregon State University
Clinical Orthopaedics and Related Research | Year: 2011

Background: Avascular meniscal injuries are largely incapable of healing; the most common treatment remains partial meniscectomy despite the risk of subsequent osteoarthritis. Meniscal responses to injury are partially mediated through synovial activity and strategies have been investigated to encourage healing through stimulating or transplanting adjacent synovial lining. However, with their potential for chondrogenesis, synovial fibroblast-like stem cells hold promise for meniscal cartilage tissue engineering. Questions/purposes: Thus, specific purposes of this review were to (1) examine how the synovial intima and synoviomeniscal junction affect current meniscal treatment modalities; and (2) examine the components of tissue engineering (cells, scaffolds, bioactive agents, and bioreactors) in the specific context of how cells of synovial origin may be used for meniscal healing or regeneration. Methods: An online bibliographic search through PubMed was performed in March 2010. Studies were subjectively evaluated and reviewed if they addressed the question posed. Fifty-four resources were initially retrieved, which offered information on the chondrogenic potential of synovial-based cells that could prove valuable for meniscal fibrocartilage engineering. Results: Based on the positive effects of adjoining synovium on meniscal healing as used in some current treatment modalities, the chondrogenic potential of fibroblast-like stem cells of synovial origin make this cell source a promising candidate for cell-based tissue engineering strategies. Conclusions: The abundance of autologous synovial lining, its ability to regenerate, and the potential of synovial-derived stem cells to produce a wide spectrum of chondral matrix components make it an ideal candidate for future meniscal engineering investigations. © 2011 The Association of Bone and Joint Surgeons.


Hallowell M.R.,University of Colorado at Boulder | Gambatese J.A.,Oregon State University
Journal of Construction Engineering and Management | Year: 2010

Construction engineering and management (CEM) researchers often rely on alternative research techniques when traditional methods fail. For example, surveys, interviews, and group-brainstorming techniques may not be appropriate for research that involves confounding factors and requires access to sensitive data. In such an environment, the Delphi technique allows researchers to obtain highly reliable data from certified experts through the use of strategically designed surveys. At present, the Delphi method has not seen widespread use in CEM research. This is likely due to variation among studies that implement Delphi in CEM research and ambiguity in literature that provides guidance for the specific parameters associated with the method. Using the guidance in this paper, the reader may: (1) understand the merits, appropriate application, and appropriate procedure of the traditional Delphi process; (2) identify and qualify potential expert panelists according to objective guidelines; (3) select the appropriate parameters of the study such as the number of panelists, number of rounds, type of feedback, and measure of consensus; (4) identify potential biases that may negatively impact the quality of the results; and (5) appropriately structure the surveys and conduct the process in such a way that bias is minimized or eliminated. © 2010 ASCE.


Welsh R.M.,Oregon State University
ISME Journal | Year: 2015

In many ecological communities, predation has a key role in regulating community structure or function. Although predation has been extensively explored in animals and microbial eukaryotes, predation by bacteria is less well understood. Here we show that predatory bacteria of the genus Halobacteriovorax are prevalent and active predators on the surface of several genera of reef-building corals. Across a library of 198 16S rRNA samples spanning three coral genera, 79% were positive for carriage of Halobacteriovorax. Cultured Halobacteriovorax from Porites asteroides corals tested positive for predation on the putative coral pathogens Vibrio corallyticus and Vibrio harveyii. Co-occurrence network analysis showed that Halobacteriovorax’s interactions with other bacteria are influenced by temperature and inorganic nutrient concentration, and further suggested that this bacterial predator’s abundance may be driven by prey availability. Thus, animal microbiomes can harbor active bacterial predators, which may regulate microbiome structure and protect the host by consuming potential pathogens.The ISME Journal advance online publication, 27 November 2015; doi:10.1038/ismej.2015.219. © 2015 International Society for Microbial Ecology


Stevens A.M.,Virginia Polytechnic Institute and State University | Schuster M.,Oregon State University | Rumbaugh K.P.,Texas Tech University Health Sciences Center
Journal of Bacteriology | Year: 2012

The 4th ASM Conference on Cell-Cell Communication in Bacteria was held in Miami, FL, from 6 to 9 November 2011. This review highlights three key themes that emerged from the many exciting talks and poster presentations in the area of quorum sensing: sociomicrobiology, signal transduction mechanisms, and interspecies communication. © 2012, American Society for Microbiology.


Sher I.,Cornell University | Hanemann C.,University of Plymouth | Karplus P.,Oregon State University | Bretscher A.,Cornell University
Developmental Cell | Year: 2012

Unlike other ERM family proteins that are activated by phosphorylation, the merlin/NF2 tumor suppressor is inactivated. Sher et al. resolve this apparent contradiction by showing that the relationship between conformation and function is conserved in merlin but that the regulation of conformation-by phosphorylation and other inputs-is more complex. © 2012 Elsevier Inc.


Higdon R.L.,Oregon State University
Journal of Computational Physics | Year: 2013

This paper is part of an effort to examine the application of discontinuous Galerkin (DG) methods to the numerical modeling of the general circulation of the ocean. One step performed here is to develop an integral weak formulation of the lateral pressure forcing that is suitable for usage with a DG method and with a generalized vertical coordinate that includes level, terrain-fitted, isopycnic, and hybrid coordinates as examples. This formulation is then tested, in special cases, with analyses of dispersion relations and numerical stability and with some computational experiments. These results suggest that the advantages of DG methods may significantly outweigh their disadvantages, in the settings tested here. This paper also outlines some other issues that need to be addressed in future work. © 2013 Elsevier Inc.


Lehmann J.,Cornell University | Kleber M.,Oregon State University | Kleber M.,Leibniz Center for Agricultural Landscape Research
Nature | Year: 2015

The exchange of nutrients, energy and carbon between soil organic matter, the soil environment, aquatic systems and the atmosphere is important for agricultural productivity, water quality and climate. Long-standing theory suggests that soil organic matter is composed of inherently stable and chemically unique compounds. Here we argue that the available evidence does not support the formation of large-molecular-size and persistent € humic substances € in soils. Instead, soil organic matter is a continuum of progressively decomposing organic compounds. We discuss implications of this view of the nature of soil organic matter for aquatic health, soil carbon-climate interactions and land management. © 2015 Macmillan Publishers Limited. All rights reserved.


Sun Y.,The Interdisciplinary Center | Todorovic S.,Oregon State University | Goodison S.,Cancer Research Institute
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2010

This paper considers feature selection for data classification in the presence of a huge number of irrelevant features. We propose a new feature-selection algorithm that addresses several major issues with prior work, including problems with algorithm implementation, computational complexity, and solution accuracy. The key idea is to decompose an arbitrarily complex nonlinear problem into a set of locally linear ones through local learning, and then learn feature relevance globally within the large margin framework. The proposed algorithm is based on well-established machine learning and numerical analysis techniques, without making any assumptions about the underlying data distribution. It is capable of processing many thousands of features within minutes on a personal computer while maintaining a very high accuracy that is nearly insensitive to a growing number of irrelevant features. Theoretical analyses of the algorithm's sample complexity suggest that the algorithm has a logarithmical sample complexity with respect to the number of features. Experiments on 11 synthetic and real-world data sets demonstrate the viability of our formulation of the feature-selection problem for supervised learning and the effectiveness of our algorithm. © 2010 IEEE.


Smyth W.D.,Oregon State University | Ruddick B.,Dalhousie University
Journal of Physical Oceanography | Year: 2010

In this paper the authors investigate the action of ambient turbulence on thermohaline interleaving using both theory and numerical calculations in combination with observations from Meddy Sharon and the Faroe Front. The highly simplified models of ambient turbulence used previously are improved upon by allowing turbulent diffusivities of momentum, heat, and salt to depend on background gradients and to evolve as the instability grows. Previous studies have shown that ambient turbulence, at typical ocean levels, can quench the thermohaline interleaving instability on baroclinic fronts. These findings conflict with the observation that interleaving is common in baroclinic frontal zones despite ambient turbulence. Another challenge to the existing theory comes from numerical experiments showing that the Schmidt number for sheared salt fingers is much smaller than previously assumed. Use of the revised value in an interleaving calculation results in interleaving layers that are both weaker and thinner than those observed. This study aims to resolve those paradoxes. The authors show that, when turbulence has a Prandtl number greater than unity, turbulent momentum fluxes can compensate for the reduced Schmidt number of salt fingering. Thus, ambient turbulence determines the vertical scale of interleaving. In typical oceanic interleaving structures, the observed property gradients are insufficient to predict interleaving growth at an observable level, even when improved turbulence models are used. The deficiency is small, though: gradients sharper by a few tens of percent are sufficient to support instability. The authors suggest that this is due to the efficiency of interleaving in erasing those property gradients. A new class of mechanisms for interleaving, driven by flow-dependent fluctuations in turbulent diffusivities, is identified. The underlying mechanism is similar to the well-known Phillips layering instability; however, because of Coriolis effects, it has a well-defined vertical scale and also a tilt angle opposite to that of fingerdriven interleaving. © 2010 American Meteorological Society.


Shakun J.D.,Oregon State University | Carlson A.E.,University of Wisconsin - Madison
Quaternary Science Reviews | Year: 2010

While the abrupt climate events of the last deglaciation are well defined in ice core records from the polar regions of both hemispheres, their manifestation elsewhere is less well constrained. Here we compile 104 high-resolution paleoclimate records to characterize the timing and spatial pattern of climate change during the last deglaciation. This compilation indicates relatively concurrent timing of the Last Glacial Maximum (LGM; peak glacial conditions) and the Altithermal (peak interglacial conditions) in the Northern (22.1 ± 4.3. ka and 8.0 ± 3.2. ka) and Southern (22.3 ± 3.6. ka and 7.4 ± 3.7. ka) Hemispheres, suggesting the hemispheres were synchronized by greenhouse gases, local insolation, and/or Northern Hemisphere induced ocean circulation changes. The magnitude of the glacial-interglacial temperature change increases with latitude, reflecting the polar amplification of climate change, with a likely minimum global mean cooling of ∼-4.9 °C during the LGM relative to the Altithermal.Empirical orthogonal function (EOF) analysis of 71 records spanning 19-11ka indicates that two modes explain 72% of deglacial climate variability. EOF1 (61% of variance) shows a globally near-uniform pattern, with its principal component (PC1) strongly correlated with changes in atmospheric CO2. EOF2 (11% of variance) exhibits a bipolar seesaw pattern between the hemispheres, with its principal component (PC2) resembling changes in Atlantic meridional overturning circulation strength. EOF analysis of 90 records from 15 to 11ka indicates that northern and southern modes of climate variability characterize the Younger Dryas-Bølling/Allerød interval. These modes dominate at the higher latitudes of each hemisphere and exhibit a complex interaction in the tropics. The magnitude of the Younger Dryas climate anomaly (cooler/drier) increases with latitude in the Northern Hemisphere, with an opposite pattern (warmer/wetter) in the Southern Hemisphere reflecting a general bipolar seesaw climate response. Global mean temperature decreased by ∼0.6°C during the Younger Dryas. Therefore, our analysis supports the paradigm that while the Younger Dryas was a period of global climate change, it was not a major global cooling event but rather a manifestation of the bipolar seesaw driven by a reduction in Atlantic meridional overturning circulation strength. © 2010 Elsevier Ltd.


Kleber M.,Oregon State University
Environmental Chemistry | Year: 2010

The understanding that some natural organic molecules can resist microbial decomposition because of certain molecular properties forms the basis of the biogeochemical paradigm of 'intrinsic recalcitrance'. In this concept paper I argue that recalcitrance is an indeterminate abstraction whose semantic vagueness encumbers research on terrestrial carbon cycling. Consequently, it appears to be advantageous to view the perceived 'inherent resistance' to decomposition of some forms of organic matter not as a material property, but as a logistical problem constrained by (i) microbial ecology; (ii) enzyme kinetics; (iii) environmental drivers; and (iv) matrix protection. A consequence of this view would be that the frequently observed temperature sensitivity of the decomposition of organic matter must result from factors other than intrinsic molecular recalcitrance. © CSIRO 2010.


Mote P.W.,University of Washington | Mote P.W.,Oregon State University | Salathe Jr. E.P.,University of Washington
Climatic Change | Year: 2010

Climate models used in the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) on the whole reproduce the observed seasonal cycle and twentieth century warming trend of 0.8°C (1.5°F) in the Pacific Northwest, and point to much greater warming for the next century. These models project increases in annual temperature of, on average, 1.1°C (2.0°F) by the 2020s, 1.8°C (3.2°F) by the 2040s, and 3.0°C (5.3°F) by the 2080s, compared with the average from 1970 to 1999, averaged across all climate models. Rates of warming range from 0.1°C to 0.6°C (0.2°F to 1.0°F) per decade. Projected changes in annual precipitation, averaged over all models, are small (+1% to +2%), but some models project an enhanced seasonal cycle with changes toward wetter autumns and winters and drier summers. Changes in nearshore sea surface temperatures, though smaller than on land, are likely to substantially exceed interannual variability, but coastal upwelling changes little. Rates of twenty-first century sea level rise will depend on poorly known factors like ice sheet instability in Greenland and Antarctica, and could be as low as twentieth century values (20 cm, 8″) or as large as 1.3 m (50″). © 2010 Springer Science+Business Media B.V.


Poulsen K.P.,Oregon State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2013

Listeria monocytogenes causes several clinical manifestations in humans and domestic animals. This bacterium is a saprophyte in soil and ensiled feeds, which are sources of infection for food producing animals (i.e. ruminants). The most common route of infection for people is via ingestion of contaminated ready-to-eat food products such as produce, soft cheeses and deli meats. In the United States, L. monocytogenes causes relatively few cases of clinical disease compared to other food-borne pathogens. However, clinical listeriosis is associated with high mortality, especially in immunocompromised patients, pregnant women, neonates, and the elderly. Listeria is an intracellular pathogen, which has been widely used in basic research to elucidate mechanisms of molecular pathogenesis and protective cell-mediated immunity. Despite the sizeable knowledge on L. monocytogenes pathogenesis, key points regarding listeriosis during pregnancy and the perinatal period remain unknown. This review summarizes listeriosis in humans and domestic animals during pregnancy, and animal models used to study the pathogenesis and immune response to L. monocytogenes infection during these periods.


Mahrt L.,Oregon State University
Boundary-Layer Meteorology | Year: 2010

The relationship of turbulence quantities to mean flow quantities, such as the Richardson number, degenerates substantially for strong stability, at least in those studies that do not place restrictions on minimum turbulence or non-stationarity. This study examines the large variability of the turbulence for very stable conditions by analyzing four months of turbulence data from a site with short grass. Brief comparisons are made with three additional sites, one over short grass on flat terrain and two with tall vegetation in complex terrain. For very stable conditions, any dependence of the turbulence quantities on the mean wind speed or bulk Richardson number becomes masked by large scatter, as found in some previous studies. The large variability of the turbulence quantities is due to random variations and other physical influences not represented by the bulk Richardson number. There is no critical Richardson number above which the turbulence vanishes. For very stable conditions, the record-averaged vertical velocity variance and the drag coefficient increase with the strength of the submeso motions (wave motions, solitary waves, horizontal modes and numerous more complex signatures). The submeso motions are on time scales of minutes and not normally considered part of the mean flow. The generation of turbulence by such unpredictable motions appears to preclude universal similarity theory for predicting the surface stress for very stable conditions. Large variation of the stress direction with respect to the wind direction for the very stable regime is also examined. Needed additional work is noted. © 2009 The Author(s).


Komar P.D.,Oregon State University
Journal of Coastal Research | Year: 2010

The evolution of the coast of Hawke's Bay, New Zealand, and its erosion problems have been governed by multiple factors, including its tectonic setting with an earthquake in 1931 that altered land elevations along its shore, ranging from a 2-m uplift at its north end to 1-m subsidence at its south. Human environmental impacts have also been important, including the deforestation of the watersheds of rivers and the mining of gravel and sand from their channels, having decreased the sediment supplies to the beaches. Significant erosion has occurred at the south end of the Hawke's Bay shore, attributed in part to its subsidence in 1931, together with the net northward longshore transport of the beach sediment that is greater than the volumes being supplied by the rivers, the beach-sediment budget being significantly "in the red." Midway along the Bay's shore, the construction of the Port of Napier's breakwater in 1887-90, extending seaward from the Buff Hill headland within that city, is interpreted by some investigators to have been the cause of the erosion experienced at Westshore, a development located immediately north of the breakwater. The assumption has been that this erosion was the result of the breakwater having blocked the northward longshore transport of sediment that formerly had bypassed Bluff Hill, this being an example of down-drift beach erosion. However, a reexamination of the history of the Port's development, the resulting shoreline changes, differences in beach gravels on the shores north and south of Bluff Hill, as well as other evidence, support the conclusion that the breakwater was not the cause of the erosion; instead, the impacts to Westshore at the time of the breakwater construction can be attributed primarily to a series of major storms, which produced erosion at a number of sites along the Hawke's Bay shore. There has been minimal erosion at Westshore since the completion of the breakwater a century ago, its northward extending arm acting to shelter the development from the waves of major storms. Investigations by coastal scientists and engineers of the Hawke's Bay coast, together with a comprehensive beach-survey monitoring program, support its sound management based on an understanding of the multiple factors that are important to its responses during storms, and to its long-term changes. © 2010 Coastal Education and Research Foundation.


Samelson R.M.,Oregon State University
Ocean Modelling | Year: 2010

An effective- β vector and an accompanying mean flow advection vector are computed for linear planetary waves on a weak, horizontally uniform mean flow, for arbitrary stratification and vertical shear profiles. These vectors arise from the projections of mean flow vertical shear and horizontal advection terms onto vertical structure functions related to the rest-state linear vertical mode. As such, these vectors are independent of depth, and determine the propagation direction and speed for the linear planetary waves on the weak mean flow. The resulting dispersion relation gives the modified wave frequency as the sum of a Doppler shift term and a dispersion function that has the same form as the rest-state planetary wave dispersion function, but relative to the effective- β vector. The propagation of long-waves remains non-dispersive. A modal decomposition of the mean flow illustrates the non-Doppler effect. For two examples of climatological mean flow and stratification profiles, the theory is shown to reproduce accurately the modified long-wave zonal phase speeds from the full linear long-wave solution on a purely zonal mean flow. © 2010 Elsevier Ltd.


Rockey D.D.,Oregon State University
Journal of Experimental Medicine | Year: 2011

Chlamydial plasmids are small, highly conserved, nonconjugative, and nonintegrative DNA molecules that are nearly ubiquitous in many chlamydial species, including Chlamydia trachomatis. There has been significant recent progress in understanding chlamydial plasmid participation in host-microbe interactions, disease, and immune responses. Work in mouse model systems and, very recently, in nonhuman primates demonstrates that plasmiddeficient chlamydial strains function as live attenuated vaccines against genital and ocular infections. Collectively, these studies open new avenues of research into developing vaccines against trachoma and sexually transmitted chlamydial infections.


Mahrt L.,Oregon State University
Quarterly Journal of the Royal Meteorological Society | Year: 2010

Microfronts with abrupt changes of temperature and/or wind vector are found to be common for weak winds and thin stable boundary layers. In this study, microfronts and their parent structures on time-scales of minutes or tens of minutes are sampled from fast-response tower measurements of temperature and the three velocity components during FLOSSII. Cold microfronts are generally characterized by rising motion, followed by stronger stratification and weaker turbulence. Sinking warm air prior to the cold microfront, followed by rising cold air after the microfront passage, corresponds to conversion of kinetic energy to potential energy. This conversion requires a source of external energy for maintenance of the circulation. The shallow cold microfronts appear to be often related to deeper fast-moving disturbances in the horizontal velocity field. Warm microfronts generally lead to stronger wind and turbulence after the microfront passage. Gust microfronts induce rising motion in advance of the microfront. Solitary waves cause little net change of temperature and are systematically embedded within larger-scale deeper disturbances at this site. The sensitivity of the results to the sampling window width and sampling criteria is examined. © 2010 Royal Meteorological Society.


This chapter describes a mass spectrometry-based strategy that facilitates the unambiguous identification and characterization of proteins modified by lipid peroxidation-derived 2-alkenals. The approach employs a biotinylated hydroxyl amine derivative as an aldehyde/keto-reactive probe in conjunction with selective enrichment and tandem mass spectrometric analysis. Methodological details are given for model studies involving a distinct protein and 4-hydroxy-2-nonenal (HNE). The method was also evaluated for an exposure study of a cell culture system with HNE that yielded the major protein targets of HNE in human monocytic THP-1 cells. The application of the approach to complex biological systems is demonstrated for the identification and characterization of endogenous protein targets of aldehydic lipid peroxidation products present in cardiac mitochondria. Copyright (c) 2010 Elsevier Inc. All rights reserved.


Chelton D.B.,Oregon State University | Xie S.-P.,University of Hawaii at Manoa
Oceanography | Year: 2010

Satellite observations have revealed a remarkably strong positive correlation between sea surface temperature (SST) and surface winds on oceanic mesoscales of 10-1000 km. Although SST influence on the atmosphere had previously been identified from several in situ observational studies, its widespread existence in regions of strong SST gradients throughout the world's ocean and the detailed structure of the surface wind response to SST have only become evident over the past decade from simultaneous satellite measurements of SST and surface winds. This has stimulated considerable scientific interest in the implications of this air-sea interaction to large-scale and mesoscale circulation of the atmosphere and ocean. Convergence and divergence of surface winds in regions of spatially varying SST generate vertical motion that can penetrate deep into the atmosphere. Spatial variability of the SST field also results in a curl of the wind stress and associated upwelling and downwelling that feeds back on the ocean and alters SST itself. Significant progress has been made toward understanding the two-way coupling between the ocean and atmosphere but many exciting research opportunities remain. In addition to regional and global modeling, future research on coupled ocean-atmosphere interaction will continue to be guided by satellite observations. In particular, high-resolution measurements in the vicinity of narrow, intense SST fronts and immediately adjacent to land provided by the next-generation scatterometer will open up new areas of research that cannot be addressed from presently available data sets.


Hagmann R.K.,University of Washington | Franklin J.F.,University of Washington | Johnson K.N.,Oregon State University
Forest Ecology and Management | Year: 2013

We summarized structure and composition of dry forests from a 90-year-old timber inventory collected by the Bureau of Indian Affairs on the former Klamath Indian Reservation (now part of the Fremont-Winema National Forest). This analysis includes data from 4,24,626 conifers ≥15cmdbh on 3068 transects covering 6646ha. The data represent a 10-20% sample of 38,651ha of forest growing on sites that are classified as ponderosa pine (Pinus ponderosa) and mixed-conifer habitat types distributed within the 1,17,672ha of the study area. Large, drought- and fire-tolerant ponderosa pine dominated these forests. Large tree (>53cmdbh) basal area (13±7m2/ha) contributed 83±16% of total basal area; 81±20% of the large-tree basal area was ponderosa pine. Composition and structure of forests on mixed-conifer sites were very similar to those on ponderosa pine sites. Variability in composition and structure was recorded on all habitat types and was highest on moist mixed-conifer sites. Stand densities (trees per hectare, tph) have more than tripled over the past 90years from 68±28tph to a current density of 234±122tph recorded in Current Vegetation Survey data collected by the United States Forest Service. Mean basal area, however, increased by less than 20%. Basal area of large trees (>53cmdbh) has declined by 50%, and the abundance of large trees as a proportion of the total number of trees per hectare has decreased by more than a factor of five. This landscape-level record of historical forest conditions allows inferences about structure and composition across tens of thousands of hectares. A historical landscape emerges which supports current working hypotheses that frequent, low- to moderate-severity wildfires maintained a predominantly low-density forest dominated by large, fire- and drought-tolerant ponderosa pines across a significant moisture and productivity gradient from the driest ponderosa pine to the mixed-conifer habitat types. © 2013 Elsevier B.V.


Mendez-Luck C.A.,Oregon State University
Medical Care | Year: 2016

BACKGROUND:: The burden of informal caregiving is significant and well-documented, yet the evidence is mixed as to whether being a caregiver presents an additional barrier to receiving recommended preventive care. OBJECTIVES:: To determine whether (1) caregivers compared with noncaregivers were less likely to receive preventive health services; and (2) higher intensity caregivers were less likely to receive preventive health services than lower intensity caregivers. RESEARCH DESIGN, SUBJECTS, AND MEASURES:: Data were from a telephone survey of Latino and African American adults 50 years or older in South Los Angeles (n=702). Outcomes were flu vaccination, pneumococcal vaccination, and colorectal cancer screening. Logistic regression models adjusted for predisposing, enabling, and need factors according to the Andersen Model of Access to Health Care for Low-income Populations. RESULTS:: Caregiver type (eg, adult child, nonrelated) was associated with varying odds of receiving a preventive service. Caregivers had lower odds than noncaregivers of receiving preventive services although odds of receiving a flu vaccination improved slightly for caregivers of persons with memory loss compared with other caregivers. More weekly caregiving hours was associated with higher odds of receiving flu vaccination (adjusted odds ratios, 1.1; 95% confidence interval=1.0, 1.1) or colorectal cancer screening (adjusted odds ratios, 1.1; 95% confidence interval=1.0, 1.1). Caregivers and noncaregivers age 65 and older or with chronic conditions were more likely to receive vaccinations. CONCLUSIONS:: Preventive service use was influenced by characteristics of the caregiving situation. An opportunity may exist to leverage care recipients’ ongoing contact with health care providers to increase caregivers’ own access to preventive services. Copyright © 2016 Wolters Kluwer Health, Inc. All rights reserved.


Samelson R.M.,Oregon State University
Annual Review of Marine Science | Year: 2013

Lagrangian motion in geophysical fluids may be strongly influenced by coherent structures that support distinct regimes in a given flow. The problems of identifying and demarcating Lagrangian regime boundaries associated with dynamical coherent structures in a given velocity field can be studied using approaches originally developed in the context of the abstract geometric theory of ordinary differential equations. An essential insight is that when coherent structures exist in a flow, Lagrangian regime boundaries may often be indicated as material curves on which the Lagrangian-mean principal-axis strain is large. This insight is the foundation of many numerical techniques for identifying such features in complex observed or numerically simulated ocean flows. The basic theoretical ideas are illustrated with a simple, kinematic traveling-wave model. The corresponding numerical algorithms for identifying candidate Lagrangian regime boundaries and lines of principal Lagrangian strain (also called Lagrangian coherent structures) are divided into parcel and bundle schemes; the latter include the finite-time and finite-size Lyapunov exponent/Lagrangian strain (FTLE/FTLS and FSLE/FSLS) metrics. Some aspects and results of oceanographic studies based on these approaches are reviewed, and the results are discussed in the context of oceanographic observations of dynamical coherent structures. © 2013 by Annual Reviews. All rights reserved.


Colwell F.S.,Oregon State University | D'Hondt S.,University of Rhode Island
Reviews in Mineralogy and Geochemistry | Year: 2013

As investigators of life underground, we anticipate the chance to learn more about the unseen world of small life deep in Earth, but only if we continue to engage in essential collaborations with all those who possess complementary knowledge of the planet's history and systems. Soon, we hope, there will be more complete synthetic models of how the living and non-living aspects of Earth's uppermost layers function and integrate with one another. These models will guide our search for new deep life, its niches, capabilities, and adaptations. We look forward to new explanations for how the subsurface biosphere is sustained and how its expression matters to life at the surface.


Ziegler L.B.,Oregon State University | Stegman D.R.,University of California at San Diego
Geochemistry, Geophysics, Geosystems | Year: 2013

Observations of Earth's magnetic field extending back to 3.45 billion years ago indicate that generation by a core dynamo must be sustained over most of Earth's history. However, recent estimates of thermal and electrical conductivity of liquid iron at core conditions from mineral physics experiments indicate that adiabatic heat flux is approximately 15 TW, nearly three times larger than previously thought, exacerbating difficulties for driving a core dynamo throughout Earth history by convective core cooling alone. Here, we explore the geomagnetic consequences of a basal magma ocean layer in the lowermost mantle, hypothesized to exist in the early Earth and perhaps surviving until well after the Archean. While the modern, solid lower mantle is an electromagnetic insulator, electrical conductivities of silicate melts are known to be higher, though as yet they are unconstrained for lowermost mantle conditions. We consider a range of possible electrical conductivities and find that for the highest electrical conductivities considered, a long-lived basal magma ocean could be a primary dynamo source region. This would suggest the proposed three magnetic eras observed in paleomagnetic data originate from distinct sources for dynamo generation: from 4.5 to 2.45 Ga within a basal magma ocean, from 2.25 to 0.4 Ga within a superadiabatically cooled liquid core, and from 0.4 Ga to present within a quasi-adiabatic core that includes a solidifying inner core. ©2013. American Geophysical Union. All Rights Reserved.


Fisk M.,Oregon State University | McLoughlin N.,University of Bergen
Geosphere | Year: 2013

We provide a comprehensive photographic atlas of the intricate alteration features found in glass in igneous rocks from the ocean basins. The samples come from surface and subsurface rocks from oceanic rises and seamounts of the ocean basins and some marginal seas. These textures have previously been termed "bioalteration textures" by those who consider them as potentially biogenic in origin, or as "etch pits" by those who prefer a non-biogenic interpretation. Here, transmitted-light color photomicrographs are provided to illustrate the range of granular and tubular textures as well as their relation to fractures, minerals, vesicles, and multiple episodes of alteration in the same sample. The tubular forms are described using seven morphological characteristics: (1) length and width; (2) density; (3) curvature; (4) roughness; (5) variations in width; (6) branching; and (7) tunnel contents. The photomicrographs are a starting point for understanding the factors that control the formation of the alteration textures, for evaluating the biogenicity of the various forms, for inferring subsurface conditions during alteration, and for making comparisons to similar textures in ancient ophiolites, some of which have been attributed to the earliest life on Earth. © 2013 Geological Society of America.


Kerkvliet N.I.,Oregon State University
Toxicologic Pathology | Year: 2012

I was honored to be the keynote speaker at the 30th Annual Society of Toxicologic Pathology Symposium "Toxicologic Pathology and the Immune System." I had the opportunity to reminisce about events in the 1970s that set the stage for the birth and subsequent growth of the field of immunotoxicology and to summarize my research career that has spanned the past 40 years as well. An initial focus on the immunotoxicity of pentachlorophenol led my laboratory into the aryl hydrocarbon receptor (AHR) field and the study of its most potent ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). My research career has been devoted to trying to elucidate the immunological basis of TCDD's profound immunosuppressive activity that is mediated by activation of AHR. In recent years, my laboratory has focused on the role of CD4+ T cells as targets of TCDD, and we were the first to describe the induction of AHR-dependent regulatory T cells (Tregs). The ability to induce Tregs using an exogenous AHR ligand to activate the AHR-Treg pathway represents a novel approach to the prevention and/or treatment of autoimmune disease. We are currently searching for such ligands. © 2012 Society of Toxicologic Pathology.


Strik B.C.,Oregon State University
Acta Horticulturae | Year: 2012

Many berry crops are managed by altering growth and environment in commercial production systems, to affect time of flowering and fruiting season. The effect of photoperiod, temperature, and production system on flower bud initiation and development is reviewed for strawberry, raspberry, blackberry and blueberry. While "flowering on command" is still a challenge, research and commercial production systems have been successful at scheduling fruit harvest for many of these crops. In strawberry and biennial cropping red raspberry, pre-conditioned plants, grown to maximize flower bud development, are commonly used along with staggered planting dates (often in tunnels) to time fruit harvest date. In primocane-fruiting raspberry, annual production systems with staggered planting dates, often in combination with pruning techniques, are used to target market windows. This system of production shows promise with primocane-fruiting blackberry. In southern highbush blueberry, cultivars are grown in warm regions using evergreening systems, pruning, and fertilization methods, to produce fruit at desired times. With a good understanding of plant physiology and the factors that affect flower bud initiation and development, bud break, and the production of high-quality fruit, it is possible to manipulate many berry crops to have fruit production target desirable market windows.


Behrenfeld M.J.,Oregon State University
Ecology | Year: 2010

The Critical Depth Hypothesis formalized by Sverdrup in 1953 posits that vernal phytoplankton blooms occur when surface mixing shoals to a depth shallower than a critical depth horizon defining the point where phytoplankton growth exceeds losses. This hypothesis has since served as a cornerstone in plankton ecology and reflects the very common assumption that blooms are caused by enhanced growth rates in response to improved light, temperature, and stratification conditions, not simply correlated with them. Here, a nine-year satellite record of phytoplankton biomass in the subarctic Atlantic is used to reevaluate seasonal plankton dynamics. Results show that (1) bloom initiation occurs in the winter when mixed layer depths are maximum, not in the spring, (2) coupling between phytoplankton growth (μ) and losses increases during spring stratification, rather than decreases, (3) maxima in net population growth rates (r) are as likely to occur in midwinter as in spring, and (4) r is generally inversely related to μ, These results are incompatible with the Critical Depth Hypothesis as a functional framework for understanding bloom dynamics. In its place, a "Dilution-Recoupling Hypothesis" is described that focuses on the balance between phytoplankton growth and grazing, and the seasonally varying physical processes influencing this balance. This revised view derives from fundamental concepts applied during field dilution experiments, builds upon earlier modeling results, and is compatible with observed phytoplankton blooms in the absence of spring mixed layer shoaling. © 2010 by the Ecological Society of America.


Thomas T.D.,Oregon State University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

The effect of the Coriolis interaction upon the sharing of energy between rotational and vibrational excitation during an electronic transition is considered with particular emphasis on recoil-induced excitation during photoionization. If there is a large change in equilibrium bond length upon ionization, then Coriolis coupling leads to a significant transfer of energy between rotational and vibrational excitation. Experimental results for valence ionization of N2 and CO and for carbon 1s ionization of CO show evidence of this effect. © 2014 American Physical Society.


Stuedlein A.W.,Oregon State University | Holtz R.D.,University of Washington
Journal of Geotechnical and Geoenvironmental Engineering | Year: 2013

Aggregate piers, also known as stone columns, are a commonly used ground improvement technique to stiffen existing soils for the support of structure foundations. This paper presents an evaluation of existing analytical expressions for the bearing capacity of spread footings supported on aggregate pier reinforced clay. The accuracy of these models was investigated using a database of high-quality footing load test data. The existing models were compared using the bias (i.e., the ratio of measured and calculated bearing capacity), and they produced a wide range in predicted bearing capacities. Selected analytical models were empirically modified using the load test database, and this resulted in improved accuracy and reduced variability. Back-calculated aggregate pier bearing capacity and cavity expansion factors are shown to be inversely proportional to undrained shear strength, and therefore to the ultimate confining pressure available at failure. This finding is attributed to the curved failure envelope of the angular aggregate used in pier construction. Additionally, a multiple nonlinear regression model suitable for spread footings resting on aggregate piers under a wide range of pier configurations is presented. The regression model is shown to produce more accurate bearing capacity estimates than existing analytical models. © 2013 American Society of Civil Engineers.


Johnson K.B.,Oregon State University
Annual Review of Phytopathology | Year: 2010

Pathogen refuge is the idea that some potentially infectious pathogen propagules are not susceptible to the influence of an antagonistic microbial agent. The existence of a refuge can be attributable to one or more factors, including temporal, spatial, structural, and probabilistic, or to the pathogen's evolved ability to acquire antagonist-free space prior to ingress into a plant host. Within a specific pathosystem, refuge size can be estimated in experiments by measuring the proportion of pathogen propagules that remain infective as a function of the amount of antagonist introduced to the system. Refuge size is influenced by qualities of specific antagonists and by environment but less so by the quantity of antagonist. Consequently, most efforts to improve and optimize biological control are in essence efforts to reduce refuge size. Antagonist mixtures, optimal timing of antagonist introductions, integrated biological and chemical control, environmental optimization, and the utilization of disarmed pathogens as antagonists are strategies with potential to minimize a pathogen refuge. © 2010 by Annual Reviews. All rights reserved.


Ezenwa V.O.,University of Georgia | Jolles A.E.,Oregon State University
Science | Year: 2015

Parasitic worms modulate host immune responses in ways that affect microbial co-infections. For this reason, anthelmintic therapy may be a potent tool for indirectly controlling microbial pathogens. However, the population-level consequences of this type of intervention on co-infecting microbes are unknown. We evaluated the effects of anthelmintic treatment on bovine tuberculosis (BTB) acquisition, mortality after infection, and pathogen fitness in free-ranging African buffalo. We found that treatment had no effect on the probability of BTB infection, but buffalo survival after infection was ninefold higher among treated individuals. These contrasting effects translated into an approximately eightfold increase in the reproductive number of BTB for anthelmintic-treated compared with untreated buffalo. Our results indicate that anthelmintic treatment can enhance the spread of microbial pathogens in some real-world situations. © 2015, American Association for the Advancement of Science. All rights reserved.


Sapon-White R.E.,Oregon State University
Library Resources and Technical Services | Year: 2012

Academic and public libraries have begun to purchase e-book readers and make them available for check-out to their users. The nature of the e-books on these devices necessitates new approaches to workflow for acquisitions and catalogingdepartments. In addition the application of cataloging rules and conventions presents a number of difficulties for catalogers. At the Oregon State University Libraries, a pilot project to purchase Kindles, load them with e-books, and make them available for circulation offered an opportunity to explore and understand the various challenges that these electronic resources present for traditional technical services units. The experience resulted in several innovations. A novel workflow largely bypassed the acquisitions unit, shifting purchasing procedures to the circulation unit. Use of the Provider-Neutral E-Monograph MARC Record Guide made most cataloging straightforward, although the lack of adherence to print conventions for some titles made cataloging a time-consuming endeavor. LibraryThing provided an additional avenue of discovery of the Kindle titles for library users.


A critical constraint in the design of appropriate medical devices for the lowest-resource settings is the lack of access to maintenance or repair on instrumentation. There are numerous point-of-care applications for which quantitative readout would have clinical utility. Thus, a challenge to the device developer is to enable quantitative device readout in an equipment-free model that is appropriate for use in even the lowest-resource settings. Paper microfluidics has great potential for enabling equipment-free devices that are low-cost, operable by minimally-trained users, and provide quantitative readout. The focus of this critical review is to describe the work, starting several decades ago and continuing to the present, to enable assays with quantitative readout in a fully-disposable device. © the Partner Organisations 2014.


Cheng L.-J.,Oregon State University | Chang H.-C.,University of Notre Dame
Lab on a Chip - Miniaturisation for Chemistry and Biology | Year: 2014

We present novel strategies for reconfigurable, high-throughput microfluidic free-flow electrophoretic separation using electrically switchable pH actuators and 3D integrated salt bridges to allow rapid formation of stable pH gradients and efficient electrophoresis. The pH actuator is achieved by microfluidic integration of bipolar membranes which change electrolyte pH by injecting excess H+ or OH- ions produced by a field-enhanced water dissociation phenomenon at the membrane junction upon voltage bias. The technique does not require conventional multiple buffer inflows and leaves no gas production as experienced in electrolysis, thus providing stable pH gradients for isoelectric focusing (IEF) separation. With the pH actuator inactivated, the platform can perform zone electrophoretic (ZE) separation in a medium of constant pH. We also describe the use of 3D integrated ion conductive polymers that serve as salt bridges for improving the voltage efficiency of electrophoresis and to allow high throughput. The proof of concept was successfully demonstrated for free-flow IEF and ZE separation of protein mixtures showing the potential and the simplicity of the platform for high-throughput and high-precision sample separation. This journal is © The Royal Society of Chemistry 2014.


Keszler D.,Oregon State University
Nature Materials | Year: 2011

High annealing temperatures have limited the technological potential of solution-processed metal oxide semiconductors. it is now shown that high-quality films can be formed below 250°C using precursors that are hydrolyzed on-chip. The vivid, high-definition images of liquid-crystal displays (LCD) pervade modern society, and range from large television screens to smaller computer displays and mobile devices. The zinc indium oxide system provides a particularly clear example of the state of the art in vapor deposition, because amorphous films ranging from transparent conductors to semiconductors for stable transistors have been made. The turn-on voltage in oxide TFTs, which is given by the intrinsic densities of free charge carriers and defects in the semiconductor film, is commonly too highly positive or negative, and it drifts in time as the transistor is operated.


Yoon J.,Oregon State University
The journal of mental health policy and economics | Year: 2013

There is an on-going concern that reductions in psychiatric inpatient bed capacity beyond a critical threshold will further exacerbate the incarceration of persons with mental illness. However, research to date to assess the proposed relationship between inpatient bed capacity and jail use has been limited in several ways. In addition, mechanisms through which changes in psychiatric bed capacity may affect jail use by persons with mental illness remain unexamined empirically. The aim of this study is to test whether changes in inpatient psychiatric resources, measured by per-capita psychiatric beds, inversely affect the likelihood of jail use by persons with severe mental illness. We also examine mechanisms that link psychiatric bed supply and jail detention. We analyze unique individual-level panel data on 41,236 adults in King County, Washington who were users of jails, the public mental health system, or the Medicaid program from 1993 to 1998. Using administrative records, we identify persons ever diagnosed with severe mental illness during the study period. Our analyses build upon a system of simultaneous equations that captures mechanisms from changes in psychiatric bed supply to jail detention. We estimate a reduced-form model and calculate the total effect of a shift in psychiatric bed supply on the likelihood of jail use by persons with severe mental illness. We also estimate a semi-reduced-form equation to examine whether changes in mental health and substance use mediate the relationship between bed supply and jail detention. We estimate linear probability models with person-level fixed effects to control for individual heterogeneity. Standard errors are adjusted for intra-cluster correlations. When an equation includes an endogenous variable, we calculate generalized method of moments estimators with instrumental variables. A decrease in the supply of psychiatric hospital beds is significantly associated with a greater probability of jail detention for minor charges among persons diagnosed with severe mental illness. Substance use appears to mediate this relationship. A reduction of inpatient psychiatric beds, ceteris paribus, is associated with an increase in jail detention among persons with severe mental illness via substance use problems. Further research should examine whether the magnitude of this relationship is greater for persons who have severe mental illness but are unable to obtain necessary treatment. This study further confirms an identified relationship between the supply of inpatient psychiatric beds, substance use and jail detention among persons with severe mental illness. These important relationships should be incorporated in the policy planning process, especially at the time of psychiatric inpatient bed reductions.


Wu Z.,Oregon State University | Pagell M.,York University
Journal of Operations Management | Year: 2011

The need for environmental protection and increasing demands for natural resources are forcing companies to reconsider their business models and restructure their supply chain operations. Scholars and proactive companies have begun to create more sustainable supply chains. What has not been fully addressed is how organizations deal with short-term pressures to remain economically viable while implementing these newly modeled supply chains. In this study, we use theory-building through case studies to answer the question: how do organizations balance short-term profitability and long-term environmental sustainability when making supply chain decisions under conditions of uncertainty? We present five sets of propositions that explain how exemplars in green supply chain management make decisions and balance short and long term objectives. We also identify four environmental postures that help explain the decisions organizations make when dealing with strategic trade-offs among the economic, environmental and social elements of the triple-bottom-line. © 2010 Elsevier B.V.


Clough S.,Oregon State University
Social Science and Medicine | Year: 2011

The hygiene hypothesis offers an explanation for the correlation, well-established in the industrialized nations of North and West, between increased hygiene and sanitation, and increased rates of asthma and allergies. Recent studies have added to the scope of the hypothesis, showing a link between decreased exposure to certain bacteria and parasitic worms, and increased rates of depression and intestinal auto-immune disorders, respectively. What remains less often discussed in the research on these links is that women have higher rates than men of asthma and allergies, as well as many auto-immune disorders, and also depression. The current paper introduces a feminist understanding of gender socialization to the epidemiological and immunological picture. That standards of cleanliness are generally higher for girls than boys, especially under the age of five when children are more likely to be under close adult supervision, is a robust phenomenon in industrialized nations, and some research points to a cross-cultural pattern. I conclude that, insofar as the hygiene hypothesis successfully identifies standards of hygiene and sanitation as mediators of immune health, then attention to the relevant patterns of gender socialization is important. The review also makes clear that adding a feminist analysis of gender socialization to the hygiene hypothesis helps explain variation in morbidity rates not addressed by other sources and responds to a number of outstanding puzzles in current research. Alternative explanations for the sex differences in the relevant morbidity rates are also discussed (e.g., the effects of estrogens). Finally, new sources of evidence for the hygiene hypothesis are suggested in the form of cross-cultural and other natural experiments. © 2010 Elsevier Ltd.


Traber M.G.,Oregon State University
Advances in Nutrition | Year: 2014

It is estimated that >90% of Americans do not consume sufficient dietary vitamin E, as α-tocopherol, to meet estimated average requirements. What are the adverse consequences of inadequate dietary α-tocopherol intakes? This review discusses health aspects where inadequate vitamin E status is detrimental and additional vitamin E has reversed the symptoms. In general, plasma α-tocopherol concentrations <12 mmol/L are associated with increased infection, anemia, stunting of growth, and poor outcomes during pregnancy for both the infant and the mother. When low dietary amounts of α-tocopherol are consumed, tissue α-tocopherol needs exceed amounts available, leading to increased damage to target tissues. Seemingly, adequacy of human vitamin E status cannot be assessed from circulating α-tocopherol concentrations, but inadequacy can be determined from "low" values. Circulating α-tocopherol concentrations are very difficult to interpret because, as a person ages, plasma lipid concentrations also increase and these elevations in lipids increase the plasma carriers for α-tocopherol, leading to higher circulating α-tocopherol concentrations. However, abnormal lipoprotein metabolism does not necessarily increase α-tocopherol delivery to tissues. Additional biomarkers of inadequate vitamin E status are needed. Urinary excretion of the vitamin E metabolite a-carboxy-ethyl-hydroxychromanol may fulfill this biomarker role, but it has not been widely studied with regard to vitamin E status in humans or with regard to health benefits. This review evaluated the information available on the adverse consequences of inadequate α-tocopherol status and provides suggestions for avenues for research. © 2014 American Society for Nutrition.


Cory R.M.,University of Michigan | Ward C.P.,University of Michigan | Crump B.C.,Oregon State University | Kling G.W.,University of Michigan
Science | Year: 2014

Carbon in thawing permafrost soils may have global impacts on climate change; however, the factors that control its processing and fate are poorly understood. The dominant fate of dissolved organic carbon (DOC) released from soils to inland waters is either complete oxidation to CO2 or partial oxidation and river export to oceans. Although both processes are most often attributed to bacterial respiration, we found that photochemical oxidation exceeds rates of respiration and accounts for 70 to 95% of total DOC processed in the water column of arctic lakes and rivers. At the basin scale, photochemical processing of DOC is about one-third of the total CO2 released from surface waters and is thus an important component of the arctic carbon budget.


Zwolak M.,Oregon State University | Riedel C.J.,IBM | Zurek W.H.,Los Alamos National Laboratory
Physical Review Letters | Year: 2014

Amplification was regarded, since the early days of quantum theory, as a mysterious ingredient that endows quantum microstates with macroscopic consequences, key to the "collapse of the wave packet," and a way to avoid embarrassing problems exemplified by Schrödinger's cat. Such a bridge between the quantum microworld and the classical world of our experience was postulated ad hoc in the Copenhagen interpretation. Quantum Darwinism views amplification as replication, in many copies, of the information about quantum states. We show that such amplification is a natural consequence of a broad class of models of decoherence, including the photon environment we use to obtain most of our information. This leads to objective reality via the presence of robust and widely accessible records of selected quantum states. The resulting redundancy (the number of copies deposited in the environment) follows from the quantum Chernoff information that quantifies the information transmitted by a typical elementary subsystem of the environment. © 2014 American Physical Society.


Surfleet C.G.,California Polytechnic State University, San Luis Obispo | Tullos D.,Oregon State University
Journal of Hydrology | Year: 2013

The frequency of rain-on-snow (ROS) hydrologic events, which produce high runoff volumes and lead to large-scale flooding and avalanching, are likely to change in the future as the types and timing of precipitation change. The relationship between ROS precipitation events and peak daily flow events ≥1-year return were examined for historical and future runoff affected by climate change within the Santiam River Basin, Oregon. Historical streamflow records and modeled historical and future streamflow projections were analyzed for three sites across three elevation zones defined by the dominant precipitation types; rain, rain and snow transition, and snow. The results illustrate that, across elevation zones, historical peak daily flows ≥1-year return have a high frequency (>60%) of association with ROS. The historical association between peak daily flows and ROS is highest within the transient rain and snow elevation band (350-1100. m), with 80% and 100% of ≥1 and ≥5-year return peak flows associated with ROS, respectively. In a future with increased air temperature due to climate change, our results indicate that a decrease in the frequency of high peak flow ROS events will occur in the low and middle elevation zones while the frequency of ROS associated peak flows will increase in high elevation areas. The transition of winter precipitation from snow to rain is predicted to increase peak daily flows <5-10-year return interval and decrease peak daily flows ≥10-year return in the middle to high elevation zones. © 2012 Elsevier B.V.


Whitmire A.L.,Oregon State University
Optics express | Year: 2010

The backscattering properties of marine phytoplankton, which are assumed to vary widely with differences in size, shape, morphology and internal structure, have been directly measured in the laboratory on a very limited basis. This work presents results from laboratory analysis of the backscattering properties of thirteen phytoplankton species from five major taxa. Optical measurements include portions of the volume scattering function (VSF) and the absorption and attenuation coefficients at nine wavelengths. The VSF was used to obtain the backscattering coefficient for each species, and we focus on intra- and interspecific variability in spectral backscattering in this work. Ancillary measurements included chlorophyll-a concentration, cell concentration, and cell size, shape and morphology via microscopy for each culture. We found that the spectral backscattering properties of phytoplankton deviate from theory at wavelengths where pigment absorption is significant. We were unable to detect an effect of cell size on the spectral shape of backscattering, but we did find a relationship between cell size and both the backscattering ratio and backscattering cross-section. While particulate backscattering at 555 nm was well correlated to chlorophyll-a concentration for any given species, the relationship was highly variable between species. Results from this work indicate that phytoplankton cells may backscatter light at significantly higher efficiencies than what is predicted by Mie theory, which has important implications for closing the underwater and remotely sensed light budget.


Niemeyer K.E.,Oregon State University | Sung C.-J.,University of Connecticut
Combustion and Flame | Year: 2014

Strategies and recommendations for performing skeletal reductions of multicomponent surrogate fuels are presented, through the generation and validation of skeletal mechanisms for a three-component toluene reference fuel. Using the directed relation graph with error propagation and sensitivity analysis method followed by a further unimportant reaction elimination stage, skeletal mechanisms valid over comprehensive and high-temperature ranges of conditions were developed at varying levels of detail. These skeletal mechanisms were generated based on autoignition simulations, and validation using ignition delay predictions showed good agreement with the detailed mechanism in the target range of conditions. When validated using phenomena other than autoignition, such as perfectly stirred reactor and laminar flame propagation, tight error control or more restrictions on the reduction during the sensitivity analysis stage were needed to ensure good agreement. In addition, tight error limits were needed for close prediction of ignition delay when varying the mixture composition away from that used for the reduction. In homogeneous compression-ignition engine simulations, the skeletal mechanisms closely matched the point of ignition and accurately predicted species profiles for lean to stoichiometric conditions. Furthermore, the efficacy of generating a multicomponent skeletal mechanism was compared to combining skeletal mechanisms produced separately for neat fuel components; using the same error limits, the latter resulted in a larger skeletal mechanism size that also lacked important cross reactions between fuel components. Based on the present results, general guidelines for reducing detailed mechanisms for multicomponent fuels are discussed. © 2014 The Combustion Institute.


Pence D.,Oregon State University
Experimental Thermal and Fluid Science | Year: 2010

A variety of applications using disk-shaped fractal-like flow networks and the status of one and two-dimensional predictive models for these applications are summarized. Applications discussed include single-phase and two-phase heat sinks and heat exchangers, two-phase flow separators, desorbers, and passive micromixers. Advantages of using these fractal-like flow networks versus parallel-flow networks include lower pressure drop, lower maximum wall temperature, inlet plenum symmetry, alternate flow paths, and pressure recovery at the bifurcation. The compact nature of microscale fractal-like branching heat exchangers makes them ideal for modularity. Differences between fractal-like and constructal approaches applied to disk-shaped heat sink designs are highlighted, and the importance of including geometric constraints, including fabrication constraints, in flow network design optimization is discussed. Finally, a simple pencil and paper procedure for designing single-phase heat sinks with fractal-like flow networks based solely on geometric constraints is outlined. Benefit-to-cost ratios resulting from geometric-based designs are compared with those from flow networks determined using multivariable optimization. Results from the two network designs are within 11%. © 2009 Elsevier Inc. All rights reserved.


Perkins J.P.,University of California at Santa Cruz | Finnegan N.J.,University of California at Santa Cruz | De Silva S.L.,Oregon State University
Nature Geoscience | Year: 2015

Bedrock canyons are ubiquitous on Earth and Mars, and river canyon morphology is commonly used to interpret the climatic and tectonic histories of landscapes. On both planets, however, many bedrock canyons exist in dry, wind-dominated environments. Although wind abrasion can significantly influence the evolution of arid landscapes, the role of wind in shaping arid bedrock canyon systems is poorly understood and thus typically neglected. Here we exploit a natural experiment on the western slope of the central Andes that allows direct comparison of wind-affected and wind-protected canyons. Through a combined analysis of the morphology of 36 canyons and topographic wind simulations, we show that wind abrasion can amplify bedrock canyon incision rates by an order of magnitude above fluvial rates. Our results imply that wind can extend bedrock canyons - landforms traditionally thought to evolve only from flowing water. Furthermore, our analyses reveal a direct relationship between aerodynamics and landscape evolution on varying scales. Topographic shielding of high winds by mountains modulates the pace of canyon retreat, while individual canyon profiles become aerodynamically streamlined. We conclude that wind abrasion can significantly modify the morphology of bedrock canyons and suggest that wind may have similarly reshaped fluvial landscapes on the martian surface.


Klomsiri C.,Wake forest University | Karplus P.A.,Oregon State University | Poole L.B.,Wake forest University
Antioxidants and Redox Signaling | Year: 2011

The enzymes involved in metabolism and signaling are regulated by posttranslational modifications that influence their catalytic activity, rates of turnover, and targeting to subcellular locations. Most prominent among these has been phosphorylation/dephosphorylation, but now a distinct class of modification coming to the fore is a set of versatile redox modifications of key cysteine residues. Here we review the chemical, structural, and regulatory aspects of such redox regulation of enzymes and discuss examples of how these regulatory modifications often work in concert with phosphorylation/ dephosphorylation events, making redox dependence an integral part of many cell signaling processes. Included are the emerging roles played by peroxiredoxins, a family of cysteine-based peroxidases that now appear to be major players in both antioxidant defense and cell signaling. Copyright 2011, Mary Ann Liebert, Inc.


Pomraning K.R.,Oregon State University
Methods in molecular biology (Clifton, N.J.) | Year: 2012

High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of our protocol for constructing single- and paired-end Illumina sequencing libraries, beginning with purified genomic DNA. The present protocol can also be used for "multiplexing," i.e. the analysis of several samples in a single flowcell lane by generating "barcoded" or "indexed" Illumina sequencing libraries in a way that is independent from Illumina-supported methods. To analyze sequencing results, we suggest several independent approaches but end users should be aware that this is a quickly evolving field and that currently many alignment (or "mapping") and counting algorithms are being developed and tested.


Davy S.K.,Victoria University of Wellington | Allemand D.,Center Scientifique Of Monaco | Weis V.M.,Oregon State University
Microbiology and Molecular Biology Reviews | Year: 2012

The symbiosis between cnidarians (e.g., corals or sea anemones) and intracellular dinoflagellate algae of the genus Symbiodinium is of immense ecological importance. In particular, this symbiosis promotes the growth and survival of reef corals in nutrient-poor tropical waters; indeed, coral reefs could not exist without this symbiosis. However, our fundamental understanding of the cnidarian-dinoflagellate symbiosis and of its links to coral calcification remains poor. Here we review what we currently know about the cell biology of cnidariandinoflagellate symbiosis. In doing so, we aim to refocus attention on fundamental cellular aspects that have been somewhat neglected since the early to mid-1980s, when a more ecological approach began to dominate. We review the four major processes that we believe underlie the various phases of establishment and persistence in the cnidarian/coral-dinoflagellate symbiosis: (i) recognition and phagocytosis, (ii) regulation of host-symbiont biomass, (iii) metabolic exchange and nutrient trafficking, and (iv) calcification. Where appropriate, we draw upon examples from a range of cnidarian-alga symbioses, including the symbiosis between green Hydra and its intracellular chlorophyte symbiont, which has considerable potential to inform our understanding of the cnidarian-dinoflagellate symbiosis. Ultimately, we provide a comprehensive overview of the history of the field, its current status, and where it should be going in the future. Copyright © 2012, American Society for Microbiology. All Rights Reserved.


Hartung D.M.,Oregon State University
BMC family practice | Year: 2012

Academic detailing is an interactive, convenient, and user-friendly approach to delivering non-commercial education to healthcare clinicians. While evidence suggests academic detailing is associated with improvements in prescribing behavior, uncertainty exists about generalizability and scalability in diverse settings. Our study evaluates different models of delivering academic detailing in a rural family medicine setting. We conducted a pilot project to assess the feasibility, effectiveness, and satisfaction with academic detailing delivered face-to-face as compared to a modified approach using distance-learning technology. The recipients were four family medicine clinics within the Oregon Rural Practice-based Research Network (ORPRN). Two clinics were allocated to receive face-to-face detailing and two received outreach through video conferencing or asynchronous web-based outreach. Surveys at midpoint and completion were used to assess effectiveness and satisfaction. Each clinic received four outreach visits over an eight month period. Topics included treatment-resistant depression, management of atypical antipsychotics, drugs for insomnia, and benzodiazepine tapering. Overall, 90% of participating clinicians were satisfied with the program. Respondents who received in person detailing reported a higher likelihood of changing their behavior compared to respondents in the distance detailing group for five of seven content areas. While 90%-100% of respondents indicated they would continue to participate if the program were continued, the likelihood of participation declined if only distance approaches were offered. We found strong support and satisfaction for the program among participating clinicians. Participants favored in-person approaches to distance interactions. Future efforts will be directed at quantitative methods for evaluating the economic and clinical effectiveness of detailing in rural family practice settings.


Hurst J.W.,Oregon State University
International Journal of Humanoid Robotics | Year: 2011

This paper documents the mechanical system of the electric cable differential (ECD) leg, and its incorporation into a monopod hopping robot named "Thumper" and a bipedal robot named "Mabel." The ECD leg is designed with physical springs and other passive dynamics to match a mathematically simple, bioinspired mass-spring model, which can exhibit robust and economic walking and running gaits. With this design approach, existing spring-mass theory-based controllers can be used to control the robot. The scientific goals of this work focus on finding an energetically optimal leg stiffness for running, and results from experimentation on Thumper and on a simulation of Thumper are presented. © 2011 World Scientific Publishing Company.


Dreves A.J.,Oregon State University
Pest Management Science | Year: 2011

BACKGROUND: Spotted wing drosophila (SWD), Drosophila suzukii Matsumura, was found along the west coast of the United States, beginning in 2008 and 2009, infesting a wide variety of small and stone fruit crops. This pest is a serious economic threat, as noted in its native range (Asia), because it lays eggs within ripening fruit before harvest, leading to crop loss. The aim of this paper is to describe the process in order to create collaboration, communication routes and evaluation methods in response to a new invasive pest. RESULTS: Funding was secured and a program (SWD*IPM) was quickly developed to address social, economic and biological components. Communication routes were outlined, and a stakeholder advisory panel was established to guide program objectives. A central website was created to host up-to-date information. An online monitoring and mapping program for D. suzukii in Oregon fruit-growing regions illustrated the range, distribution and seasonal abundance of the pest. In addition, a program for backyard fruit growers was initiated to examine citizen scientists' roles in managing D. suzukii infestations in the urban setting. A monitoring kit, laminated educational cards, dry fly mounts and quick-time videos were some of the tools used to educate growers. First-year challenges for dealing with a new pest are discussed. CONCLUSION: The discovery and subsequent response to an exotic pest is information intensive and requires a well-planned, coordinated Extension and evaluation effort. © 2011 Society of Chemical Industry.


Temes G.C.,Oregon State University
IEEE Transactions on Circuits and Systems II: Express Briefs | Year: 2010

In many applications, such as in battery-operated medical devices or in habitat monitoring sensor networks, special data converters are needed, which can operate on battery or even harvested power. The available power in these devices is very limited, often only a few tens of microwatts. This tutorial discusses some of the design options for such micropower digital-to-analog and analog-to-digital converters. © 2010 IEEE.


Auth T.D.,Oregon State University
California Cooperative Oceanic Fisheries Investigations Reports | Year: 2011

The taxonomic composition, distribution, concentration, and community structure of ichthyoplankton of the Oregon and Washington coasts were examined in 2004-2009 to investigate annual, seasonal, latitudinal, and cross-shelf variability. Larval concentrations and community structure were also analyzed in relation to several local and larger-scale environmental variables. The dominant taxa, comprising 94% of the total larvae collected, were Engraulis mordax, Sebastes spp., Stenobrachius leucop-sarus, Tarletonbeania crenularis, and Lyopsetta exilis. Larval concentrations and diversity generally varied across the temporal and spatial scales. Several seasonal and cross-shelf assemblages were identified, and annual, seasonal, latitudinal, and cross-shelf gradients of taxonomic associations with significant indicator taxa were found. Distance from shore, salinity, and temperature were the local environmental factors that explained the most variability in larval fish concentrations, while Columbia River out-flow and sea-surface temperature were the larger-scale factors that explained the most variability in 2-4 month lagged larval fish concentrations and diversity.


Streck M.J.,Portland State University | Grunder A.L.,Oregon State University
Geochemistry, Geophysics, Geosystems | Year: 2012

Strongly bimodal, basalt-rhyolite volcanism of the High Lava Plains Province of Oregon followed the Middle Miocene flood basalts of the Pacific Northwest and extends to recent time. During the 8 m.y. of volcanism recorded in the central High Lava Plains, in western Harney Basin, three distinct mafic magmatic trends originate from primitive high-alumina olivine tholeiites (HAOT); they are tholeiitic, calcalkaline and ferro-trachytic. Tholeiitic basalts occur throughout the history and their compositions are derived by crystal fractionation while traversing the crust and mixing with evolved mafic magmas. Scavenging of apatite from crustal rocks and minor contamination with felsic melts accounts for P, incompatible element enrichments and increasing tilts of incompatible element patterns with differentiation. The calcalkaline mafic suite occurs in temporal association with abundant silicic volcanism and is the only suite with Fe decreasing with Mg. Calcalkaline compositions are derived from evolved tholeiitic basalt by crystal fractionation coupled with assimilation of felsic crust or crustal melts. The ferro-trachytic suite occurs mainly late, is highly enriched in incompatible element with patterns parallel to tholeiites from which it is derived by protracted fractionation and recharge. The three suites primarily reflect changes in magma flux and crustal interactions in time. High magma flux promotes crustal melting and contamination of tholeiite to make the calcalkaline suite. On the other hand, ferrotrachytic magmas erupted mainly late in the sequence, during magmatic waning and after significant basaltification of the crust. © 2012. American Geophysical Union. All Rights Reserved.


Fenberg P.B.,Oregon State University | Roy K.,University of California at San Diego
American Naturalist | Year: 2012

The importance of large breeding individuals for maintaining the health of marine fish and invertebrate populations has long been recognized. Unfortunately, decades of human harvesting that preferentially remove larger individuals have led to drastic reductions in body sizes of many of these species. Such size-selective harvesting is particularly worrisome for sequentially hermaphroditic species where the larger size classes are composed primarily of one sex. Whether these species can maintain stable sex ratios under sustained harvesting pressure depends on the level of plasticity of their life-history traits. Here, we show that populations of a marine limpet (Lottia gigantea) can adjust a fundamental aspect of their life history (the timing of sex change) when subjected to size-selective harvesting. As predicted by theoretical models, individuals from harvested populations change sex at smaller sizes and grow at slower rates compared to individuals from protected populations. In addition, the relative size at which the change from male to female occurs remains constant (∼0.75; size at sex change/maximum size) across populations, regardless of harvesting pressure. Our results show that populationlevel demographic and life-history data, in conjunction with existing theory, can be sufficient to predict the responses of sequential hermaphrodites to harvesting pressure. Furthermore, they suggest such species can potentially adapt to size-selective harvesting. © 2012 by The University of Chicago.


A major challenge for foresters in the future will be issues related to global change. Global change expresses itself in a variety of ways, depending on regional vegetation and climate patterns, small-scale topographic differences, tree species, and stand development stages. Using silviculture as an example, the variety of steps linking global change-as a general concept-and actual management decisions is explored. The first task is to relate global change aspects to silviculturally relevant scales. Second, silvicultural responses must reflect the wide variety of changes, including their interactions. A number of management recommendations have been proposed from the global scale to the application of specific silvicultural treatments. These recommendations are mostly focused on increasing the resistance of forests to perturbations. Increasing ecosystem adaptability and resilience through silvicultural practices may benefit from developments in other scientific fields. Recent advances in the complexity and ecosystem sciences may provide approaches that are better suited for a future with increased variability and uncertainty in ecological and social conditions. Specifically, managing forests as complex adaptive systems may provide a conceptual framework that can be useful for silviculture, even though much work still must be done to fully explore the implications of such a new framework for silvicultural decisionmaking. © 2011 by the Society of American Foresters.


Egbert G.D.,Oregon State University
Geophysical Journal International | Year: 2012

We describe novel hybrid algorithms for inversion of electromagnetic geophysical data, combining the computational and storage efficiency of a conjugate gradient approach with an Occam scheme for regularization and step-length control. The basic algorithm is based on the observation that iterative solution of the symmetric (Gauss-Newton) normal equations with conjugate gradients effectively generates a sequence of sensitivities for different linear combinations of the data, allowing construction of the Jacobian for a projection of the original full data space. The Occam scheme can then be applied to this projected problem, with the tradeoff parameter chosen by assessing fit to the full data set. For EM geophysical problems with multiple transmitters (either multiple frequencies or source geometries) an extension of the basic hybrid algorithm is possible. In this case multiple forward and adjoint solutions (one each for each transmitter) are required for each step in the iterative normal equation solver, and each corresponds to the sensitivity for a separate linear combination of data. From the perspective of the hybrid approach, with conjugate gradients generating an approximation to the full Jacobian, it is advantageous to save all of the component sensitivities, and use these to solve the projected problem in a larger subspace. We illustrate the algorithms on a simple problem, 2-D magnetotelluric inversion, using synthetic data. Both the basic and modified hybrid schemes produce essentially the same result as an Occam inversion based on a full calculation of the Jacobian, and the modified scheme requires significantly fewer steps (relative to the basic hybrid scheme) to converge to an adequate solution to the normal equations. The algorithms are expected to be useful primarily for 3-D inverse problems for which the computational burden is heavily dominated by solution to the forward and adjoint problems. © 2012 The Author Geophysical Journal International © 2012 RAS.


Use of crop residues for biofuel production raises concerns on how removal will impact soil organic carbon (SOC). Information on the effects on SOC is limited and requires long-term experimentation. Fortunately, Pendleton long-term experiments (LTEs), dating to the 1930s, provide some answers. This study compared crop residue inputs and SOC balance in conventional tillage (CT) winter wheat (Triticum aestivum L.)-summer fallow (WW-SF) systems with annual rotation of WW and spring pea (Pisum sativum L.). The WW-SF consisted of crop residue (CR-LTE) (0-90 N ha-1 yr-1, 11.2 Mg ha-1 yr-1 of steer (Bos taurus) manure and 1.1 Mg ha-1 yr-1of pea vines additions, residue burning, and tillage fertility (TF-LTE) (tillage- plow, disc, sweep, and N (0-180 kg ha-1)). Winter wheat- pea (WP-LTE) rotation treatments included maxi-till (MT-disc/chisel), fall plow (FP), spring plow (SP), and no-till (NT). Soils were sampled (0-60-cm depth) at 10-yr intervals, and grain yield and residue data collected every year. In WW-SF systems, SOC was maintained only by manure addition and depleted at a rate of 0.22 to 0.42 Mg ha-1 yr-1 in other treatments. In WP-LTE, MT, FP, SP, and NT treatments increased SOC at the rate of 0.10, 0.11, 0.02, and 0.89 Mg ha-1 yr-1, respectively. Minimum straw biomass to maintain soil organic carbon (MSB) in the CR-LTE, TF-LTE, and WP-LTE was 7.8, 5.8, and 5.2 Mg ha-1 yr-1, respectively. Winter wheat-SF straw production was lower than MSB, therefore residue removal would exacerbate SOC decline. Harvesting straw residues under NT continuous cropping systems is possible when MSB and conservation requirements are exceeded. © 2011 by the American Society of Agronomy.


Water management is conflict management, and has been since time immemorial. And yet models of conflict management of recent times regularly ignore the balance between rationality and spirituality that has prevailed in our thinking for millennia, relying almost entirely on the measurable. While this focus has been helpful, perhaps some part of the answer lies not in the world of rationality at all, but rather in the spiritual, ethical and moral dimensions of water conflict resolution, and that re-acknowledging the balance between the rational and the transcendent offers constructs for understanding and working with process. Acknowledging the balance between the quantifiable and the transcendent allows both for more coherent models of conflict transformation and for direct applications to water negotiations. This paper begins by setting the context of current understanding of water conflict and cooperation, then by documenting the geography of the 'Enlightenment Rift' - the process by which the global West/North has separated the worlds of rationality and spirituality - and the impact of this rift on ideas related to natural resources management. We continue with a discussion of the current clash of world views, and conclude with a section describing how the two world views might gently be interwoven, for example within a fairly universal construct of four worlds of perception, and how this construct might be employed within the framework of more effective water conflict management and transformation. © IWA Publishing & the Botín Foundation 2012.


Harris K.E.,University of Montana | DeGrandpre M.D.,University of Montana | Hales B.,Oregon State University
Geophysical Research Letters | Year: 2013

Coastal upwelling zones may be at enhanced risk from ocean acidification as upwelling brings low aragonite saturation state (ΩAr) waters to the surface that are further suppressed by anthropogenic CO2. ΩAr was calculated with pH, pCO2, and salinity-derived alkalinity time series data from autonomous pH and pCO 2 instruments moored on the Oregon shelf and shelf break during different seasons from 2007 to 2011. Surface ΩAr values ranged between 0.66 ± 0.04 and 3.9 ± 0.04 compared to an estimated pre-industrial range of 1.0 ± 0.1 to 4.7 ± 0.1. Upwelling of high-CO2 water and subsequent removal of CO2 by phytoplankton imparts a dynamic range to ΩAr from ∼1.0 to ∼4.0 between spring and autumn. Freshwater input also suppresses saturation states during the spring. Winter ΩAr is less variable than during other seasons and is controlled primarily by mixing of the water column. © 2013 American Geophysical Union. All Rights Reserved.


Objectives: (1) To understand demographic and environmental factors influencing walking trips to parks for adults with children living at home; and (2) To determine if preferences for walking environments may influence walking trips and why. Methods: Neighborhoods with varying levels of canopy coverage and access to destinations were selected within the city of Seattle, Washington and surrounding suburbs. Walking trip frequency, preferences for walking environments, and demographic information were measured through a postal survey in fall 2006 (21% response rate, N = 617; 41% adults with children living in the household, n = 250). Analysis of variance and multiple linear regressions were used to test the associations between variables. Chi-square and qualitative content analysis were used to understand preferences for walking environments. Results: Adult respondents with children living at home walked most frequently to parks compared to other destinations. Owning a dog, living within close proximity to a variety of destinations, perceptions of ample neighborhood vegetation, and preference for natural-looking environments were factors positively associated with these walking trips. Conclusions: Demographic and environmental factors influence walking trips, particularly perceived level of neighborhood vegetation and individual preferences. However, highly vegetated walking environments also elicited concerns about safety for some respondents. © 2009 Elsevier Inc. All rights reserved.


Niki E.,Japan National Institute of Advanced Industrial Science and Technology | Traber M.G.,Oregon State University
Annals of Nutrition and Metabolism | Year: 2012

Vitamin E (α-tocopherol) was discovered nearly 100 years ago because it was required to prevent fetal resorption in pregnant, vitamin E-deficient rats fed lard-containing diets that were easily oxidizable. The human diet contains eight different vitamin E-related molecules synthesized by plants; despite the fact that all of these molecules are peroxyl radical scavengers, the human body prefers α-tocopherol. The biological activity of vitamin E is highly dependent upon regulatory mechanisms that serve to retain α-tocopherol and excrete the non-α-tocopherol forms. This preference is dependent upon the combination of the function of α-tocopherol transfer protein (α-TTP) to enrich the plasma with α-tocopherol and the metabolism of non-α-tocopherols. α-TTP is critical for human health because mutations in this protein lead to severe vitamin E deficiency characterized by neurologic abnormalities, especially ataxia and eventually death if vitamin E is not provided in large quantities to overcome the lack of α-TTP. α-Tocopherol serves as a peroxyl radical scavenger that protects polyunsaturated fatty acids in membranes and lipoproteins. Although specific pathways and specific molecular targets have been sought in a variety of studies, the most likely explanation as to why humans require vitamin E is that it is a fat-soluble antioxidant. Copyright © 2012 S. Karger AG, Basel.


Wood B.D.,Oregon State University | Valdes-Parada F.J.,Metropolitan Autonomous University
Advances in Water Resources | Year: 2013

Modeling transport phenomena in discretely hierarchical systems can be carried out using any number of upscaling techniques. In this paper, we revisit the method of volume averaging as a technique to pass from a microscopic level of description to a macroscopic one. Our focus is primarily on developing a more consistent and rigorous foundation for the relation between the microscale and averaged levels of description. We have put a particular focus on (1) carefully establishing statistical representations of the length scales used in volume averaging, (2) developing a time-space nonlocal closure scheme with as few assumptions and constraints as are possible, and (3) carefully identifying a sequence of simplifications (in terms of. scaling postulates) that explain the conditions for which various upscaled models are valid. Although the approach is general for linear differential equations, we upscale the problem of linear convective diffusion as an example to help keep the discussion from becoming overly abstract. In our efforts, we have also revisited the concept of a closure variable, and explain how closure variables can be based on an integral formulation in terms of Green's functions. In such a framework, a closure variable then represents the integration (in time and space) of the associated Green's functions that describe the influence of the average sources over the spatial deviations. The approach using Green's functions has utility not only in formalizing the method of volume averaging, but by clearly identifying how the method can be extended to transient and time or space nonlocal formulations. In addition to formalizing the upscaling process using Green's functions, we also discuss the upscaling process itself in some detail to help foster improved understanding of how the process works. Discussion about the role of. scaling postulates in the upscaling process is provided, and poised, whenever possible, in terms of measurable properties of (1) the parameter fields (including the indicator fields describing the medium geometry) associated with the transport phenomenon of interest, and (2) measurable properties of the independent variable itself. To highlight the relevance of this interpretation we study the benchmark problem of linear nonlocal diffusion in porous media. © 2012 Elsevier Ltd.


Diederichs K.,University of Konstanz | Karplus P.A.,Oregon State University
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

In macromolecular X-ray crystallography, typical data sets have substantial multiplicity. This can be used to calculate the consistency of repeated measurements and thereby assess data quality. Recently, the properties of a correlation coefficient, CC1/2, that can be used for this purpose were characterized and it was shown that CC1/2 has superior properties compared with 'merging' R values. A derived quantity, CC*, links data and model quality. Using experimental data sets, the behaviour of CC1/2 and the more conventional indicators were compared in two situations of practical importance: merging data sets from different crystals and selectively rejecting weak observations or (merged) unique reflections from a data set. In these situations controlled 'paired-refinement' tests show that even though discarding the weaker data leads to improvements in the merging R values, the refined models based on these data are of lower quality. These results show the folly of such data-filtering practices aimed at improving the merging R values. Interestingly, in all of these tests CC1/2 is the one data-quality indicator for which the behaviour accurately reflects which of the alternative data-handling strategies results in the best-quality refined model. Its properties in the presence of systematic error are documented and discussed.


Loveland W.,Oregon State University
Journal of Physics: Conference Series | Year: 2013

The cross section for producing a heavy reaction product, σEVR, can be represented by the equation where σcapture (Ec.m.,J) is the capture cross section at center of mass energy Ec.m. and spin J. PCN is the probability that the projectile-target system will evolve from the contact configuration inside the fission saddle point to form a completely fused system rather than re-separating (quasifission, fast fission). Wsur is the probability that the completely fused system will de-excite by neutron emission rather than fission. I discuss results of experiments that characterize these quantities in heavy element synthesis reactions. I also discuss the possibilities of synthesizing heavy nuclei using damped collisions and reactions using radioactive beams.


Ray R.D.,NASA | Erofeeva S.Y.,Oregon State University
Journal of Geophysical Research: Solid Earth | Year: 2014

A new model of long-period tidal variations in length of day is developed. The model comprises 80 spectral lines with periods between 18.6 years and 4.7 days, and it consistently includes effects of mantle anelasticity and dynamic ocean tides for all lines. The anelastic properties followWahr and Bergen; experimental confirmation for their results now exists at the fortnightly period, but there remains uncertainty when extrapolating to the longest periods. The ocean modeling builds on recent work with the fortnightly constituent, which suggests that oceanic tidal angular momentum can be reliably predicted at these periods without data assimilation. This is a critical property when modeling most long-period tides, for which little observational data exist. Dynamic ocean effects are quite pronounced at shortest periods as out-of-phase rotation components become nearly as large as in-phase components. The model is tested against a 20 year time series of space geodetic measurements of length of day. The current international standard model is shown to leave significant residual tidal energy, and the new model is found to mostly eliminate that energy, with especially large variance reduction for constituents Sa, Ssa, Mf, and Mt. ©2014. American Geophysical Union.


Benoit-Bird K.J.,Oregon State University | McManus M.A.,University of Hawaii at Manoa
Biology Letters | Year: 2012

The importance of spatial pattern in ecosystems has long been recognized. However, incorporating patchiness into our understanding of forces regulating ecosystems has proved challenging. We used a combination of continuously sampling moored sensors, complemented by shipboard sampling, to measure the temporal variation, abundance and vertical distribution of four trophic levels in Hawaii's near shore pelagic ecosystem. Using an analysis approach from trophic dynamics, we found that the frequency and intensity of spatial aggregations-rather than total biomass-in each step of a food chain involving phytoplankton, copepods, mesopelagic micronekton and spinner dolphins (Stenella longirostris) were the most significant predictors of variation in adjacent trophic levels.Patches of organisms hadimpacts disproportionate to the biomass of organisms within them. Our results are in accordance with resource limitation- mediated by patch dynamics-regulating structure at each trophic step in this ecosystem, as well as the foraging behaviour of the top predator. Because of their high degree of heterogeneity, ecosystem-level effects of patchiness such as this may be common inmany pelagic marine systems. © 2012 The Royal Society.


Fotso S.,Oregon State University
Mini-Reviews in Organic Chemistry | Year: 2010

Pyrrolo[1,4]benzodiazepines (PBDs) are a growing group of microbial secondary metabolites that showed remarkable biological activities particularly against tumor cells. Their antitumor activity is mainly due to their specifically binding to DNA and other polydeoxynucleotides to form irreversibly polymer-bound drugs. Consequently, they have been the target of several syntheses as well as screening of natural sources to discover new members. This review provides an update on recent discoveries of PBDs as well as a compilation of spectroscopic data described in the literature. © 2010 Bentham Science Publishers Ltd.


Ver Hoef J.M.,National Oceanic and Atmospheric Administration | Temesgen H.,Oregon State University
PLoS ONE | Year: 2013

Forest surveys provide critical information for many diverse interests. Data are often collected from samples, and from these samples, maps of resources and estimates of aerial totals or averages are required. In this paper, two approaches for mapping and estimating totals; the spatial linear model (SLM) and k-NN (k-Nearest Neighbor) are compared, theoretically, through simulations, and as applied to real forestry data. While both methods have desirable properties, a review shows that the SLM has prediction optimality properties, and can be quite robust. Simulations of artificial populations and resamplings of real forestry data show that the SLM has smaller empirical root-mean-squared prediction errors (RMSPE) for a wide variety of data types, with generally less bias and better interval coverage than k-NN. These patterns held for both point predictions and for population totals or averages, with the SLM reducing RMSPE from 9% to 67% over some popular k-NN methods, with SLM also more robust to spatially imbalanced sampling. Estimating prediction standard errors remains a problem for k-NN predictors, despite recent attempts using model-based methods. Our conclusions are that the SLM should generally be used rather than k-NN if the goal is accurate mapping or estimation of population totals or averages.


Barker K.K.,Oregon State University
Social Science and Medicine | Year: 2011

Fibromyalgia syndrome is a debilitating pain disorder of unknown origins and a paradigmatic contested illness. As with other contested illnesses, the reality of fibromyalgia is disputed by many physicians. Thus, millions of individuals who are diagnosed with fibromyalgia must cope with chronic symptoms as well as medical and public skepticism. In this context, the U.S. Federal Drug Administration's approval of Lyrica, the first prescription medication specifically for the management of fibromyalgia, is of considerable interest. In this paper I examine the cultural logic whereby the existence (and marketing) of an officially approved prescription medication for a condition lends support to the biomedical existence of the condition itself. I label this logic pharmaceutical determinism and argue that it represents an important new phase in the proliferation of contested illness diagnoses. Using the case of Lyrica, I describe the role that pharmaceutical companies and pharmaceuticals themselves play in promoting and legitimating contested diagnoses and validating those who are so diagnosed. Through a narrative analysis of the Lyrica direct-to-consumer advertising campaign and the responses of fibromyalgia sufferers to the introduction and marketing of Lyrica, I demonstrate the symbiotic relationship between the interests of the pharmaceutical industry, contested illness legitimization, and medicalization. I also provide a gender analysis of this relationship, foregrounding how contested illnesses continue to be shaped by their feminization in a cultural context that equates women with irrationality. Finally, I address the consequences and limitations of relying on the pharmaceutical industry for illness validation. © 2011 Elsevier Ltd.


Goldfinger C.,Oregon State University
Annual Review of Marine Science | Year: 2011

Many of the largest earthquakes are generated at subduction zones or other plate boundary fault systems near enough to the coast that marine environments may record evidence of them. During and shortly after large earthquakes in the coastal and marine environments, a spectrum of evidence may be left behind, mirroring onshore paleoseismic evidence. Shaking or displacement of the seafloor can trigger processes such as turbidity currents, submarine landslides, tsunami (which may be recorded both onshore and offshore), and soft-sediment deformation. Marine sites may also share evidence of fault scarps, colluvial wedges, offset features, and liquefaction or fluid expulsion with their onshore counterparts. This article reviews the use of submarine turbidite deposits for paleoseismology, focuses on the dating and correlation techniques used to establish stratigraphic continuity of marine deposits, and outlines criteria for distinguishing earthquake deposits and the strategies used to acquire suitable samples and data for marine paleoseismology. Copyright © 2011 by Annual Reviews. All rights reserved.


Stearns K.M.,University of Southern California | Pollard C.D.,Oregon State University
American Journal of Sports Medicine | Year: 2013

Background: Athletes who have undergone anterior cruciate ligament reconstruction (ACLR) have a high risk of reinjury upon the return to sports participation. While the mechanisms behind this increased risk of reinjury are unknown, it has been suggested that altered knee biomechanics during sports-specific activities may be a contributing factor. Purpose/Hypothesis: To compare frontal plane knee joint angles and moments during a sidestep cutting maneuver in female soccer athletes who have undergone ACLR with those in athletes with no history of knee injury. It was hypothesized that athletes with a history of ACLR would exhibit increased knee abduction angles and knee adductor moments compared with those with no history of injury. Study Design: Controlled laboratory study. Methods: Twelve female soccer players with a history of ACLR served as the experimental group, and 12 female soccer players with no history of knee injury constituted the control group. Three-dimensional kinematics and ground-reaction forces were collected while each participant performed a sidestep cutting maneuver. Variables of interest included the knee abduction angle and knee adductor moment during the early deceleration phase of the cutting maneuver. Independent-samples t tests were used to evaluate differences between groups (P ≤ .05). Results: Participants in the ACLR group exhibited increased average knee abduction angles (ACLR: 3.8≤ vs control: 1.8≤; P = .03) and peak knee adductor moments (ACLR: 1.33 N·m/kg vs control: 0.80 N·m/kg; P = .004) compared with the control group. Conclusion: Female soccer players who have undergone ACLR and returned to sports participation exhibited increased knee abduction angles and knee adductor moments during the early deceleration phase of cutting compared with their healthy counterparts with no history of knee injury. Clinical Relevance: Even though athletes are able to return to sport after ACLR, they are at an increased risk for reinjury. It may be the case that the increased frontal plane knee angles and moments exhibited by these athletes after ACLR could be contributing to this risk for reinjury. Therefore, it is important that rehabilitation programs after ACLR include the restoration of frontal plane knee mechanics. © 2013 The Author(s).


Hamre B.,University of Virginia | Hatfield B.,Oregon State University | Pianta R.,University of Virginia | Jamil F.,Clemson University
Child Development | Year: 2014

This study evaluates a model for considering domain-general and domain-specific associations between teacher-child interactions and children's development, using a bifactor analytic strategy. Among a sample of 325 early childhood classrooms there was evidence for both general elements of teacher-child interaction (responsive teaching) and domain-specific elements related to positive management and routines and cognitive facilitation. Among a diverse population of 4-year-old children (n = 1,407) responsive teaching was modestly associated with development across social and cognitive domains, whereas positive management and routines was modestly associated with increases in inhibitory control and cognitive facilitation was associated with gains in early language and literacy skills. The conceptual and methodological contributions and challenges of this approach are discussed. © 2013 Society for Research in Child Development, Inc.


Wood B.D.,Oregon State University
Advances in Water Resources | Year: 2013

The geometric theorems reported by Quintard and Whitaker [5, Appendix B] are re-examined. We show (1) The geometrical theorems can be interpreted in terms of the raw spatial moments of the pore structure within the averaging volume. (2) For the case where the first spatial moment is aligned with the center of mass of the averaging volume, the geometric theorems can be expressed in terms of the central moments of the porous medium. (3) When the spatial moments of the pore structure are spatially stationary, the geometrical theorems allow substantial simplification of nonlocal terms arising in the averaged equations. (4) In the context of volume averaging, the geometric theorems of Quintard and Whitaker [5, Appendix B] are better interpreted as statements regarding the spatial stationarity of specific volume averaged quantities rather than an explicit statement about the media disorder. © 2013 Elsevier Ltd.


Rondon S.I.,Oregon State University
American Journal of Potato Research | Year: 2010

The potato tuberworm, Phthorimaea operculella (Zeller), is a worldwide pest of solanaceous crops especially devastating to potatoes. Adults mate and lay eggs in foliage or tubers throughout the growing season, preferring foliage over tubers. When foliage has naturally or artificially senesced and/or tubers are accessible, they deposit eggs in or near the eye buds. The larvae mine leaves, stems, and petioles causing irregular galleries, and excavate tunnels through tubers. Foliar damage to the potato crop usually does not result in significant yield losses but infested tubers may have reduced marketability and losses in storage may be up to 100% especially in non-refrigerated systems. The greatest risk of tuber damage occurs immediately before harvest while the crop is left in the field prior to digging; additional damage may occur in storage, if conditions are not maintained properly. Potatoes that are left in the field for any length of time can become infested. The pest is difficult to control and growers rely extensively on the use of insecticides and a variety of cultural practices. After harvest, the insect may continue to develop on tubers or volunteer plants remaining in the field as well as on other solanaceous plants. Incorporation of host plant resistance together with insecticides and appropriate biological and cultural practices may provide the best management options. This review addresses P. operculella bionomics, including origins, distribution, host range, life cycle and life stage behavior; seasonal dynamics; abiotic factors; cultural, biological, and chemical control methods; and host plant resistance. © 2009 The Author(s).


Mahrt L.,Oregon State University
Agricultural and Forest Meteorology | Year: 2010

With the recognition that eddy flux measurements are relatively accurate for a variety of common situations, a number of issues leading to inaccurate flux estimates and/or ambiguous interpretation of flux values are surveyed. These issues include inadvertent conversion of random errors to systematic errors, ambiguous differentiation between turbulence and other motions, and omission of transport by stationary eddies. Correcting for sonic misalignment and flow distortion in the presence of real systematic vertical motions is also problematic. Special emphasis is placed on the need for spatial information, partly to include vertical transport by stationary circulations induced by small-scale surface features. While no categorical solutions to the above problems are offered, promising approaches worthy of more investigation are discussed. © 2010 Elsevier B.V. All rights reserved.


Mundt C.C.,Oregon State University
Infection, Genetics and Evolution | Year: 2014

This review briefly addresses what has been learned about resistance durability in recent years, as well as the questions that still remain. Molecular analyses of major gene interactions have potential to contribute to both breeding for resistance and improved understanding of virulence impacts on pathogen fitness. Though the molecular basis of quantitative resistance is less clear, substantial evidence has accumulated for the relative simplicity of inheritance. There is increasing evidence for specific interactions with quantitative resistance, though implications of this for durability are still unknown. Mechanisms by which resistance gene pyramids contribute to durability remain elusive, though ideas have been generated for identifying gene combinations that may be more durable. Though cultivar mixtures and related approaches have been used successfully, identifying the diseases and conditions that are most conducive to the use of diversity has been surprisingly difficult, and the selective influence of diversity on pathogen populations is complex. The importance of considering resistance durability in a landscape context has received increasing emphasis and is an important future area of research. Experimental systems are being developed to test resistance gene deployment strategies that previously could be addressed only with logic and observation. The value of molecular markers for identifying and pyramiding major genes is quite clear, but the successful use of quantitative trait loci (QTL) for marker-assisted selection of quantitative resistance will depend greatly on the degree to which the identified QTL are expressed in different genetic backgrounds. Transgenic approaches will likely provide opportunities for control of some recalcitrant pathogens, though issues of durability for transgenes are likely to be no different than other genes for resistance. The need for high quality phenotypic analysis and screening methodologies is a priority, and field-based studies are likely to remain of signal importance in the foreseeable future. © 2014 The Authors.


Flanner M.G.,University of Michigan | Shell K.M.,Oregon State University | Barlage M.,U.S. National Center for Atmospheric Research | Perovich D.K.,U.S. Army | Tschudi M.A.,University of Colorado at Boulder
Nature Geoscience | Year: 2011

The extent of snow cover and sea ice in the Northern Hemispherehas declined since 1979, coincident with hemispheric warming and indicative of a positive feedback of surface reflectivity on climate. This albedo feedback of snow on land has been quantified from observations at seasonal timescales, and century-scale feedback has been assessed using climate models. However, the total impact of the cryosphere on radiative forcing and albedo feedback has yet to be determined from measurements. Here we assess the influence of the Northern Hemisphere cryosphere on Earth's radiation budget at the top of the atmosphere-termed cryosphere radiative forcing-by synthesizing a variety of remote sensing and field measurements. We estimate mean Northern Hemisphere forcing at -4.6 to -2.2 W m-2, with a peak in May of -9.0±2.7 W m-2. We find that cyrospheric cooling declined by 0.45 W m -2 from 1979 to 2008, with nearly equal contributions from changes in land snow cover and sea ice. On the basis of these observations, we conclude that the albedo feedback from the Northern Hemisphere cryosphere falls between 0.3 and 1.1 W m-2 K-1, substantially larger than comparable estimates obtained from 18 climate models. © 2011 Macmillan Publishers Limited. All rights reserved.


Lund D.C.,100 North University Ave | Mix A.C.,Oregon State University | Southon J.,University of California at Irvine
Nature Geoscience | Year: 2011

The rise in atmospheric carbon dioxide during the last deglaciation may have been driven by the release of carbon from the abyssal ocean 1,2. This mechanism would require a poorly ventilated deep Pacific Ocean during the Last Glacial Maximum and enhanced exchange with the atmosphere during deglaciation. Here we use radiocarbon measurements of planktonic and benthic foraminiferal shells from a core collected at 2.7 km water depth in the northeast Pacific to estimate the ventilation age of deep waters using the projection age method. In contrast to the above scenario, we show that ventilation ages during the Last Glacial Maximum were similar to today. This suggests that this part of the Pacific was not an important reservoir of carbon during glacial times. During deglaciation, ventilation ages increased by ∼1,000 years, indicating a decrease in the ventilation rate, an increase in the surface water reservoir age in the Southern Ocean, or an influx of old carbon from another source. Despite the increased ventilation age during deglaciation, the deep northeast Pacific still had a higher 14C/C ratio than intermediate waters near Baja California 3. We therefore conclude that the deep northeast Pacific was apparently not old enough to be the source of deglacial radiocarbon anomalies found shallower in the water column. © 2011 Macmillan Publishers Limited. All rights reserved.


Moseley W.G.,Macalester College | Carney J.,University of California at Los Angeles | Becker L.,Oregon State University
Proceedings of the National Academy of Sciences of the United States of America | Year: 2010

This study examines the impact of two decades of neoliberal policy reform on food production and household livelihood security in three West African countries. The rice sectors in The Gambia, Côte d'Ivoire, and Mali are scrutinized as well as cotton and its relationship to sorghum production in Mali. Although market reforms were intended to improve food production, the net result was an increasing reliance on imported rice. The vulnerability of the urban populations in The Gambia and Côte d'Ivoire became especially clear during the 2007-2008 global food crisis when world prices for rice spiked. Urban Mali was spared the worst of this crisis because the country produces more of its own rice and the poorest consumers shifted from rice to sorghum, a grain whose production increased steeply as cotton production collapsed. The findings are based on household and market surveys as well as on an analysis of national level production data.


Groce A.,Oregon State University
2011 26th IEEE/ACM International Conference on Automated Software Engineering, ASE 2011, Proceedings | Year: 2011

This paper introduces a new approach to test input generation, based on reinforcement learning via easy to use adaptation-based programming. In this approach, a test harness can be written with little more effort than is involved in naïve random testing. The harness will simply map choices made by the adaptation-based programming (ABP) library, rather than pseudo-random numbers, into operations and parameters. Realistic experimental evaluation over three important fine-grained coverage measures (path, shape, and predicate coverage) shows that ABP-based testing is typically competitive with, and sometimes superior to, other effective methods for testing container classes, including random testing and shape-based abstraction. © 2011 IEEE.


Schmittner A.,Oregon State University | Lund D.C.,University of Connecticut
Climate of the Past | Year: 2015

The reason for the initial rise in atmospheric CO2 during the last deglaciation remains unknown. Most recent hypotheses invoke Southern Hemisphere processes such as shifts in midlatitude westerly winds. Coeval changes in the Atlantic meridional overturning circulation (AMOC) are poorly quantified, and their relation to the CO2 increase is not understood. Here we compare simulations from a global, coupled climate-biogeochemistry model that includes a detailed representation of stable carbon isotopes (δ13C) with a synthesis of high-resolution δ13C reconstructions from deep-sea sediments and ice core data. In response to a prolonged AMOC shutdown initialized from a preindustrial state, modeled δ13C of dissolved inorganic carbon (δ13CDIC) decreases in most of the surface ocean and the subsurface Atlantic, with largest amplitudes (more than 1.5%‰) in the intermediate-depth North Atlantic. It increases in the intermediate and abyssal South Atlantic, as well as in the subsurface Southern, Indian, and Pacific oceans. The modeled pattern is similar and highly correlated with the available foraminiferal δ13C reconstructions spanning from the late Last Glacial Maximum (LGM, ~19.5-18.5 ka BP) to the late Heinrich stadial event 1 (HS1, ~16.5-15.5 ka BP), but the model overestimates δ13CDIC reductions in the North Atlantic. Possible reasons for the model-sediment-data differences are discussed. Changes in remineralized δ13CDIC dominate the total δ13CDIC variations in the model but preformed contributions are not negligible. Simulated changes in atmospheric CO2 and its isotopic composition (δ13CCO2) agree well with ice core data. Modeled effects of AMOC-induced wind changes on the carbon and isotope cycles are small, suggesting that Southern Hemisphere westerly wind effects may have been less important for the global carbon cycle response during HS1 than previously thought. Our results indicate that during the early deglaciation the AMOC decreased for several thousand years. We propose that the observed early deglacial rise in atmospheric CO2 and the decrease in δ13CCO2 may have been dominated by an AMOC-induced decline of the ocean's biologically sequestered carbon storage. © Author(s) 2015.


Briggs J.C.,Oregon State University
Marine Biology | Year: 2010

A review of evidence from two kinds of studies conducted in the marine environment suggests a species relationship not previously recognized as being consistent and widespread. In the first instance, observations on species invading from a more diverse ecosystem into a less diverse ecosystem indicate that successful colonizations take place because space is yielded by their ecological equivalents. In the second instance, widespread studies show that any community, rich or poor, located in tropical or cold waters, is vulnerable to invasions by species from a larger, more diverse region. Furthermore, the species richness of a community apparently depends upon that of the region to which it belongs. Together, these observations indicate the existence of a general rule which states that if an invader becomes established, it is permitted to do so by an accommodation on the part of the species that occupies the preferred ecological space. Paleontological data on invasions provide evidence of speciation following accommodation. This leads to the recognition of a three-step process: invasion to accommodation to speciation (IAS). This process, which may be called the IAS mechanism, may have contributed to historical rises of global biodiversity. © 2010 Springer-Verlag.


Zaron E.D.,Portland State University | Egbert G.D.,Oregon State University
Journal of Physical Oceanography | Year: 2014

The interaction of the dominant semidiurnal M2 internal tide with the large-scale subtidal flow is examined in an ocean model by propagating the tide through an ensemble of background fields in a domain centered on theHawaiianRidge. The background fields are taken fromthe SimpleOceanDataAssimilation (SODA) ocean analysis, at 2-month intervals from 1992 through 2001. Tides are computed with the Primitive Equation Z-coordinate Harmonic Analysis of Tides (PEZ-HAT) model by 14-day integrations using SODA initial conditions and M2 tidal forcing. Variability of the tide is found to occur primarily as the result of propagation through the nonstationary background fields, rather than via generation site variability. Generation of incoherent tidal variability is mapped and shown to occur mostly in association with waves generated at French Frigate Shoals scattering near the Musicians Seamounts to the north of the ridge. The phasecoherent internal tide loses energy at a domain-average rate of 2 m Wm-2 by scattering into the nonstationary tide. Because of the interference of waves from multiple generation sites, variability of the internal tide is spatially inhomogeneous and values of the scattering rate 10 times larger occur in localized areas. It is estimated that 20% of the baroclinic tidal energy flux is lost by adiabatic scattering (refraction) within 250 kmof the ridge, a value regarded as a lower bound because of the smoothed nature of the SODA fields used in this study. © 2014 American Meteorological Society.


This article analyzes community health workers' (CHW) capacities for empathic service within an AIDS treatment program in Addis Ababa. I show how CHWs' capacities to build relationships with stigmatized people, reconcile family disputes, and confront death draw on a constellation of values, desires, and emotions encouraged by CHWs' families and religious teachings. I then examine the ways in which the capacities of CHWs were valued by the institutions that deployed them. NGO and government officials recognized that empathic care was crucial to both saving and improving the quality of people's lives. These institutional actors also defended a policy of not financially remunerating CHWs, partly by constructing their capacities as so valuable that they become "priceless" and therefore only remunerable with immaterial satisfaction. Positive change within CHW programs requires ethnographic analysis of how CHWs exercise capacities for empathic care as well as consideration of how global health institutions value these capacities. © 2014 by the American Anthropological Association.


Jenny B.,Oregon State University
IEEE Transactions on Visualization and Computer Graphics | Year: 2012

All major web mapping services use the web Mercator projection. This is a poor choice for maps of the entire globe or areas of the size of continents or larger countries because the Mercator projection shows medium and higher latitudes with extreme areal distortion and provides an erroneous impression of distances and relative areas. The web Mercator projection is also not able to show the entire globe, as polar latitudes cannot be mapped. When selecting an alternative projection for information visualization, rivaling factors have to be taken into account, such as map scale, the geographic area shown, the mapÊs height-to-width ratio, and the type of cartographic visualization. It is impossible for a single map projection to meet the requirements for all these factors. The proposed composite map projection combines several projections that are recommended in cartographic literature and seamlessly morphs map space as the user changes map scale or the geographic region displayed. The composite projection adapts the mapÊs geometry to scale, to the mapÊs height-to-width ratio, and to the central latitude of the displayed area by replacing projections and adjusting their parameters. The composite projection shows the entire globe including poles; it portrays continents or larger countries with less distortion (optionally without areal distortion); and it can morph to the web Mercator projection for maps showing small regions. © 1995-2012 IEEE.


Kruzic J.J.,Oregon State University
Metallurgical and Materials Transactions A: Physical Metallurgy and Materials Science | Year: 2011

Early studies suggested there was a severe problem with the fatigue resistance of some bulk metallic glasses (BMGs) and BMG matrix composites, while more recent studies begin to demonstrate a wide variety of fatigue behaviors may be possible for both fully amorphous BMGs and their composites. However, in order to truly understand and control the fatigue behavior of these materials, the role of such factors as thermomechanical processing, the corresponding glass structure, environment, and defects must be understood. Additionally, it is important to understand how these factors relate to the mechanisms of fatigue. This article reviews the current understanding in this regard, and identifies some of the challenges for the future development of fatigue-resistant BMG-based materials. © 2010 The Minerals, Metals & Materials Society and ASM International.


Maddison D.R.,Oregon State University | Guralnick R.,University of Colorado at Boulder | Hill A.,University of Colorado at Boulder | Reysenbach A.-L.,Portland State University | McDade L.A.,Claremont Graduate University
Trends in Ecology and Evolution | Year: 2012

The pace of species discovery and documentation remains too slow on a human-altered planet in the midst of a massive extinction event. Increasing this pace requires altering conventional workflows. In this review, we propose that systematics needs to shift to a model of quantum contributions whereby species hypotheses are published as they are formulated and data as they are collected in web-based repositories and content-management systems. If our recommendation is followed, many species will make their first appearance on the Internet as candidate new species before documentation is complete. Acknowledging the changes that we describe may be controversial, we discuss problems that may be encountered along with possible solutions. © 2011 Elsevier Ltd.


Place S.P.,University of South Carolina | Menge B.A.,Oregon State University | Hofmann G.E.,University of California at Santa Barbara
Functional Ecology | Year: 2012

The marine intertidal zone is characterized by large variation in temperature, pH, dissolved oxygen and the supply of nutrients and food on seasonal and daily time scales. These oceanic fluctuations drive ecological processes such as recruitment, competition and consumer-prey interactions largely via physiological mechanisms. Thus, to understand coastal ecosystem dynamics and responses to climate change, it is crucial to understand these mechanisms. Here we utilize transcriptome analysis of the physiological response of the mussel Mytilus californianus at different spatial scales to gain insight into these mechanisms. We used mussels inhabiting different vertical locations within Strawberry Hill on Cape Perpetua, OR and Boiler Bay on Cape Foulweather, OR to study inter- and intra-site variation of gene expression. The results highlight two distinct gene expression signatures related to the cycling of metabolic activity and perturbations to cellular homeostasis. Intermediate spatial scales show a strong influence of oceanographical differences in food and stress environments between sites separated by c. 65km. Together, these new insights into environmental control of gene expression may allow understanding of important physiological drivers within and across populations. © 2011 The Authors. Functional Ecology © 2011 British Ecological Society.


Chouinard A.J.,Oregon State University
Behavioral Ecology and Sociobiology | Year: 2012

In the competition to acquire mates, environmental factors can be important in determining the relative quality of an individual. These aspects of quality are often conveyed through signals used for mate assessment by the most energetically invested sex. In red-backed salamanders, Plethodon cinereus, chemical signals communicate a surprising amount of information, much of which is dependent on the current condition of the sender. One such condition-dependent aspect of information conveyed via chemicals is the quality of the sender's diet, but it is unclear as to whether this information is actively advertised by the sender (i. e., a signal) or simply inferred from food-derived odors (i. e., a cue). The amount of time on different diets required for changes in signaling is also unknown. I examined how quickly gravid female salamanders could detect a difference between the scents of males on high- vs. low-quality diets without fecal cues. The amount of protein present in two known signaling glands (the mental and postcloacal glands) was also measured after experimental feeding. Gravid females were able to infer the differences in male diet quality after only 1 week. Females also responded to the male scents more quickly after differential feeding had begun. High-quality males had significantly more protein present in both signaling glands than low-quality males. This scenario highlights the ongoing interplay between the quality of an individual and its environment, with males actually advertising the status of this relationship as an honest signal for mate assessment. © 2012 Springer-Verlag.


Stein D.L.,Oregon State University
Zootaxa | Year: 2012

Snailfishes (Family Liparidae) of the Ross Sea are reviewed, keys are provided to their identification, and the utility of several taxonomic characters, including the pectoral fin and girdle and length and shape of the abdominal cavity, is discussed. New and previously unstudied specimens show that there are more than 34 Ross Sea liparid species in three genera; 18 of them are new to science and are described below. Ross Sea snailfishes include at least six Careproctus, 27 Paraliparis, and one Genioliparis species. The new species are Paraliparis alius from off Iselin Seamount at 1225-1332 m, P. amerismos from off Hillary Canyon (near Pennell Bank) at 1149-1358 m, P. camilarus from the northwest edge of Mawson Bank at 1431-1658 m, P. ekaporus from off Mawson Bank at 1431-1658 m, P. epacrognathus from off Mawson Bank at 1431-1658 m, P. haploporus from off Mawson Bank at 1954-1990 m, P. longicaecus from the NW edge of Mawson Bank at 1431-1658 m, P. macropterus from off Iselin and Mawson Banks at 1133-1990 m, P. magnoculus from off Iselin and Scott Canyon at 950-1368 m, P. mentikoilon from off Mawson Bank at 1954-1990 m, P. nigrolineatus from off Mawson Bank at 1954-1990 m, P. nullansa from off Mawson Bank at 1954-1990 m, P. orbitalis from off Cape Adare at 1110-1210 m, P. parviradialis from off Mawson Bank at 1954-1990 m, P. plicatus from off Mawson Bank at 1431-1990 m, P. posteroporus from off Mawson Bank at 1400-1600 m, P. tangaroa from Iselin Seamount at 966-1153 m, and P. voroninorum from off Mawson Bank at 1954-1990 m. In addition, one unknown Paraliparis is partially described but not named owing to its poor condition. Range extensions for P. neelovi and P. stehmanni are reported, and two more individuals of P. andriashevi, previously known from two specimens, were collected. Other species included are Careproctus ampliceps, C. catherinae, C. inflexidens, C. polarsterni, C. pseudoprofundicola, C. vladibeckeri, Genioliparis kafanovi, Paraliparis antarcticus, P. devriesi, P. fuscolingua, P. macrocephalus, P. rossi, and P. terraenovae. History and characteristics of the Ross Sea that probably led to isolation and speciation are described and discussed. The new discoveries increase the number of known Southern Hemisphere snailfish species to about 200. © 2012 Magnolia Press.


Krane K.S.,Oregon State University
Physical Review C - Nuclear Physics | Year: 2012

Radiative neutron capture cross sections have been measured for the stable isotopes of natural Os with mass numbers 184, 189, 190, and 192 by observing radioactive decays of the activation products following neutron irradiation of naturally occurring Os. From irradiations of Os samples separately with thermal and epithermal neutrons, independent values of the thermal cross sections and resonance integrals have been deduced. By observing the γ rays emitted by the activation products 185Os, 190Osm, 191Os, and 193Os, improved values for the energies and intensities of the γ rays and the decay half-lives have been obtained, enabling corresponding improvements in the energy values and β-decay feedings of levels in the daughter nuclei. © 2012 American Physical Society.


Cheyney M.,Oregon State University
Medical Anthropology Quarterly | Year: 2011

In this article, I examine the clinical practices engaged in by U.S. homebirth midwives and their clients from the beginning of pregnancy through to the immediate postpartum period, deconstructing them for their symbolic and ritual content. Using data collected from open-ended, semistructured interviews and intensive participant-observation, I describe the roles ritual plays in the construction, performance, and maintenance of birth at home as a transgressive rite of passage. As midwives ritually elaborate approaches to care to capitalize on their semiotic power to transmit a set of counterhegemonic values to participants, they are attempting, quite self-consciously, to peel away the fictions of medicalized birthing care. Their goal: to expose strong and capable women who "grow" and birth babies outside the regulatory and self-regulatory processes naturalized by modern, technocratic obstetrics. Homebirth practices are, thus, not simply evidence-based care strategies. They are intentionally manipulated rituals of technocratic subversion designed to reinscribe pregnant bodies and to reterritorialize childbirth spaces (home) and authorities (midwives and mothers). © 2011 by the American Anthropological Association.


Koppers A.A.P.,Oregon State University | Watts A.B.,University of Oxford
Oceanography | Year: 2010

Seamounts are windows into the deep Earth that are helping to elucidate various deep Earth processes. For example, thermal and mechanical properties of oceanic lithosphere can be determined from the flexing of oceanic crust caused by the growth of seamounts on top of it. Seamount trails also are excellent recorders of absolute plate tectonic motions and provide key insights into the relationships among plate motion, plume motion, whole-Earth motion, and mantle convection. And, because seamounts are created from the partial melts of deep mantle sources, they offer unique glimpses into the chemical development and heterogeneity of Earth's deepest regions. Current research efforts focus on resolving the fundamental differences between magmas generated by passive upwelling from upper mantle regions and deep mantle plumes rising from the core-mantle boundary, mapping the different modes of mantle plumes and mantle convection, reconciling fixed and nonfixed mantle plumes, and understanding the prolonged volcanic evolution of seamounts. The role of intraplate seamounts is pivotal to this research, and we must collect vast amounts more geochemical and geophysical data to advance our knowledge. These data needs leave the ocean wide open for future seamount exploration.


Wrolstad R.E.,Oregon State University | Culver C.A.,Pepsi Cola Company
Annual Review of Food Science and Technology | Year: 2012

Replacement of artificial food dyes with natural colorants is a current marketing trend, notwithstanding the fact that neither the United States nor the European Union (EU) has defined natural with respect to food colors. Consumer groups have concerns over the safety of synthetic colorants, and in addition, many of the naturally derived colorants provide health benefits. Food scientists frequently have the assignment of replacing artificial colorants with natural alternatives. This can be challenging, as naturally derived colorants are usually less stable, and all desired hues might, in fact, not be obtainable. In this review, the chemical and physical properties, limitations, and more suitable applications for those colorants that are legally available as substitutes for the synthetic colorants are summarized. Issues and challenges for certain foods are discussed, and in addition, colorants that may be available in the future are briefly described. Copyright © 2012 by Annual Reviews.


Boehlert G.W.,Oregon State University | Gill A.B.,Cranfield University
Oceanography | Year: 2010

Marine renewable energy promises to assist in the effort to reduce carbon emissions worldwide. As with any large-scale development in the marine environment, however, it comes with uncertainty about potential environmental impacts, most of which have not been adequately evaluated-in part because many of the devices have yet to be deployed and tested. We review the nature of environmental and, more specifically, ecological effects of the development of diverse types of marine renewable energy-covering marine wind, wave, tidal, ocean current, and thermal gradient-and discuss the current state of knowledge or uncertainty on how these effects may be manifested. Many of the projected effects are common with other types of development in the marine environment; for example, additional structures lead to concerns for entanglement, habitat change, and community change. Other effects are relatively unique to marine energy conversion, and specific to the type of energy being harnessed, the individual device type, or the reduction in energy in marine systems. While many potential impacts are unavoidable but measurable, we would argue it is possible (and necessary) to minimize others through careful device development and site selection; the scale of development, however, will lead to cumulative effects that we must understand to avoid environmental impacts. Renewable energy developers, regulators, scientists, engineers, and ocean stakeholders must work together to achieve the common dual objectives of clean renewable energy and a healthy marine environment. © 2010 by The Oceanography Society.


Traber M.G.,Oregon State University
Molecular Nutrition and Food Research | Year: 2010

There is growing concern based on meta-analyses of clinical trials using vitamin E supplements that these supplements increase the risk of all-cause mortality in humans. My laboratory has been investigating the metabolism and disposition of "excess" vitamin E. This review focuses on the various mechanisms that prevent vitamin E intoxication. Non-α-tocopherols are aggressively metabolized thereby preventing their tissue accumulation and limiting increases in their plasma concentrations. Moreover, "excess" α-tocopherol is also metabolized and its concentrations are limited. The mechanisms for this limitation do not seem to be specific for vitamin E, but rather are general xenobiotic pathways. We suggest that the most relevant cytochrome P450-mediated pathway is the one that is most important for the regulation and activation of vitamin K, specifically the one dependent on CYP4F2. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Pythium species are common damping-off pathogens that can cause stunting, chlorosis, and death of conifer seedlings in the Pacific Northwest (PNW) region of the United States. Despite the prevalence and importance of these pathogens in forest nurseries, relatively little is known about the identity of Pythium species associated with forest nursery soils in Washington and Oregon. A limited number of studies have reported P. aphanidermatum, P. irregulare, P. mamillatum, and P. ultimum as the predominant species in the PNW, but most studies of this genus in forest nurseries have not reported Pythium species identity. In an attempt to identify Pythium species associated with forest nursery soils, field surveys were conducted at three forest nurseries (two in Oregon and one in Washington) in 2008 using three isolation methods. Pythium species were isolated by plating soil onto a semiselective medium or by baiting soil with rhododendron leaf disks and Douglas-fir needle segments. One hundred isolates were randomly selected from each isolation method at each nursery (900 isolates total) and identified on the basis of the internal transcribed spacer (ITS) sequence. Nineteen Pythium species were identified during the survey. Species richness and abundance were strongly influenced by both nursery and isolation method. Of the 300 isolates obtained from each nursery, P. irregulare was the most commonly isolated species from nursery A in Washington (65% incidence). P. 'vipa'and P. dissotocum were the most commonly isolated species from nurseries B and C in Oregon, respectively (53 and 47% incidence, respectively). © 2011 The American Phytopathological Society.


Ray R.D.,NASA | Egbert G.D.,Oregon State University
Geophysical Journal International | Year: 2012

This study of the fortnightly Mf tide comprises three main topics: (1) a new determination of the fortnightly component of polar motion and length of day (LOD) from a multidecade time-series of observed space-geodetic data; (2) the use of the polar motion determination as one constraint in the development of a hydrodynamic ocean model of the Mf tide and (3) the use of these results to place new constraints on mantle anelasticity at the Mf tidal period. Our model of the Mf ocean tide assimilates more than 14 years of altimeter data from the Topex/Poseidon and Jason-1 satellites. Because the Mf altimetric signal-to-noise ratio is very small, it is critical that altimeter data not be overweighted. The polar motion data, plus tide-gauge data and independent altimeter data, give useful additional information, with only the polar motion putting constraints on tidal current velocities. The resulting ocean-tide model, plus the dominant elastic body tide, leaves a small residual in observed LOD caused by mantle anelasticity. The inferred effective tidal Q of the anelastic body tide is 90 and is in line with a ω α frequency dependence with α in the range 0.2-0.3. © 2012 The Authors Geophysical Journal International © 2012 RAS.


Miller J.A.,Oregon State University
Journal of Experimental Marine Biology and Ecology | Year: 2011

Analysis of naturally occurring variation in otolith elemental composition has become a common approach for retrospectively determining migratory history in diadromous fishes. Environmental factors, such as temperature, salinity, and ambient water concentration, can independently, or in an interactive manner, affect elemental incorporation rates. Furthermore, the relative importance of kinetic and metabolic (or "vital") effects on elemental incorporation remains unclear. In this study, a repeated measures design was used to: (1) quantify the effects of water temperature (9°C, 12°C, 15°C) and freshwater Ba:Ca levels (low, intermediate, and high) on elemental partitioning and otolith composition (Mg:Ca, Sr:Ca, Ba:Ca) in juvenile Chinook salmon (Oncorhynchus tshawytscha) along a salinity gradient (0, 5, 10, 14); and (2) estimate the lag time between physical exposure to chemically distinct water masses and changes in otolith composition. Additionally, relationships between elemental incorporation and somatic and otolith growth rates were evaluated across and within temperature treatments to identify potential rate effects. Otolith incorporation of Sr and Ba was positively related to water concentration whereas Mg incorporation was not. For Sr and Mg, there were significant interactions between temperature and salinity (p⇐0.01). For Ba, there were complex interactions among temperature, water Ba:Ca values, and salinity (p⇐0.01). In certain instances, interactive effects of temperature and salinity were large enough to confound interpretation of field data. Furthermore, there was evidence for negative effects of somatic growth rate on the incorporation of Ba that were consistent across temperatures (r=⇐0.32 to ⇐0.72). Observations were consistently contrary to expectations based on models of elemental incorporation for abiotic aragonite, highlighting the importance of vital effects and indicating that species-specific models of incorporation may be necessary. Changes in otolith composition were detected within 2-3. d of a change in water composition but otolith composition did not stabilize for 12-14. d, indicating that habitat transitions should be discernable in a short period of time but the otolith may not reflect ambient water levels for up to 2. weeks. These observations underscore the need to evaluate the effects of abiotic and biotic factors on otolith elemental incorporation in settings that mimic natural conditions to accurately interpret field data. © 2011 Elsevier B.V.


Lauchnor E.G.,Montana State University | Semprini L.,Oregon State University
Water Research | Year: 2013

Ammonia oxidation by Nitrosomonas europaea, an ammonia oxidizing bacterium prevalent in wastewater treatment, is inhibited in the presence of phenol, due to interaction of the phenol with the ammonia monooxygenase enzyme. Suspended cells of N. europaea were cultured in batch reactors and continuous flow reactors at dilution rates of 0.01-0.2d-1. The rate of ammonia oxidation in the continuous cultures correlated to the dilution rate in the reactor. The batch and continuous cultures were exposed to 20μM phenol and ammonia oxidation activity was measured by specific oxygen uptake rates (SOURs). Inhibition of NH3 oxidation by 20μM phenol ranged from a 77% reduction of SOUR observed with suspended cells harvested during exponential growth, to 26% in biofilms. The extent of inhibition was correlated with ammonia oxidation rates in both suspended and biofilm cells, with greater percent inhibition observed with higher initial rates of NH3 oxidation. In biofilm grown cells, an increase in activity and phenol inhibition were both observed upon dispersing the biofilm cells into fresh, liquid medium. Under higher oxygen tension, an increase in the NO2- production of the biofilms was observed and biofilms were more susceptible to phenol inhibition. Dissolved oxygen microsensor measurements showed oxygen limited conditions existed in the biofilms. The ammonia oxidation rate was much lower in biofilms, which were less inhibited during phenol exposure. The results clearly indicate in both suspended and attached cells of N. europaea that a higher extent of phenol inhibition is positively correlated with a higher rate of NH3 oxidation (enzyme turnover). © 2013 Elsevier Ltd.


The mitochondrial gene cytochrome-c oxidase subunit 1 (COI) and the nuclear ribosomal DNA region known as Internal Transcribed Spacer 1 (ITS1) are used in a phylogenetic analysis of Ridgewayia from the Galapagos Islands and of a new species, Ridgewayia tortuga, from the Florida Keys. In addition, the phylogeny of Calanoida is reconstructed based on the 18S ribosomal RNA gene. The following characters exclude R. tortuga from the three recognized species groups of Ridgewayia: the presence of only 7 setae on the terminal endopod segment of leg 2; a 20-segmented male right antennule with two geniculations, the first between segments 9 and 10 and the second between segments 16 and 17; and details of the male fifth leg, in particular the elongate, unarmed, right endopod with a bifurcated tip. The molecular analysis shows that the first half of the COI gene not only fails to differentiate the various species of Ridgewayia, but it also fails to differentiate between the families Ridgewayiidae and Pseudocyclopidae. The second half of this gene and the ITS1 region are species specific. Molecular and morphological evidence suggest that the Galapagos ridgewayiids are the result of one colonization event and that the current phylogeography of these animals can be explained by a combination of vicariance and active migration models. The 18S ribosomal RNA gene proves successful in the reconstruction of the phylogeny of Calanoida with the following main conclusions: 1) Centropagoidea is the sister branch to all other Calanoida; 2) Ridgewayiidae and Pseudocyclopidae likely share a common ancestor with Augaptiloidea; 3) Ridgewayiidae and Pseudocyclopidae should be included in the same superfamily, the Pseudocyclopoidea; and 4) Spinocalanoidea likely needs to be included in Clausocalanoidea to recover the monophyly of the latter superfamily. © The Crustacean Society.


Gamon J.A.,University of Alberta | Bond B.,Oregon State University
Remote Sensing of Environment | Year: 2013

Using the "photochemical reflectance index" (PRI) as a measure of xanthophyll pigment activity and photosynthetic light-use efficiency, we examined physiological responses to diurnal illumination in mature forest stands. In a Douglas-fir forest in Corvallis, Oregon, PRI varied primarily with illumination, which was strongly influenced by canopy aspect and time of day. Once normalized for illumination, PRI exhibited a pattern of midday depression similar to that of leaf photosynthesis and stomatal conductance. Comparable optical responses to illumination were detected at canopy and leaf scales, demonstrating that remote spectroradiometry could be applied to monitor photosynthetic downregulation in uniform, closed stands. In similar measurements at a ponderosa pine forest in Black Butte, Oregon, an old tree exhibited more suppressed midday PRI values than a young tree, once values were normalized for illumination. Unlike the PRI response in Douglas-fir, variation in the diurnal PRI response between individual ponderosa pine trees was a predominant source of PRI variation. This contrasting age effect was consistent with other studies at this site showing reduced midday photosynthesis and stomatal conductance in old trees due to hydraulic limitations. These results indicate that diurnal and spatial patterns of photosynthetic activity in structurally complex evergreen forest stands can be characterized with narrow-band spectral reflectance, provided measurements are properly normalized by illumination. These findings also support recent studies using field and satellite remote sensing that report strong effects of illumination on the PRI signal from forest stands, and provide additional evidence that individual canopy responses can reveal contrasting degrees of photosynthetic downregulation due to varying stress effects within a single forest stand. Together, these results support the hypothesis that photosynthesis is coordinately regulated, allowing PRI to detect changing levels of stomatal activity and carboxylation. While illumination patterns and photosynthetic downregulation both influenced PRI, pigment pool sizes and enhanced PRI under prolonged low light provided additional sources of PRI variation in the canopy signal. Further understanding of these multiple PRI responses could help realize the goal of remote sensing of photosynthetic activity using PRI. © 2013 Elsevier Inc.


Rosell-Mele A.,Catalan Institution for Research and Advanced Studies | Rosell-Mele A.,Autonomous University of Barcelona | Prahl F.G.,Oregon State University
Quaternary Science Reviews | Year: 2013

The seasonality of sea surface temperatures (SST) estimated from the alkenone- UK'37 index has been a debated issue since the development of the proxy. Using a compilation of sediment trap time series data from 34 sampling locations, we show that the seasonality of maximum alkenone flux in sediment traps varies markedly across the oceans, depending not only on latitude and light availability but also on local oceanographic conditions. The seasonality of the alkenone flux to sediments may also be shaped by the complexity of sedimentation processes and a consistent, globally applicable, seasonal pattern is not apparent. Nevertheless, UK'37 values display a world ocean scale correlation with mean annual SSTs (0m) that closely resembles the standard calibration equation now established for modern surface sediment records. Thus, with a few notable exceptions at oceanographic locations proximate to major hydrographic fronts, it can be concluded that the integrated sedimentation patterns for UK'37 measured in sediment trap time series provide a measure of annual mean SST. © 2013.


Sleight A.W.,Oregon State University
Physica C: Superconductivity and its Applications | Year: 2015

BaBiO3 has the perovskite structure, but tilting of the BiO6 octahedra destroy the ideal cubic symmetry except at temperatures above 820 K. BaBiO3 is a diamagnetic semiconductor due to a charge density wave (CDW), which is equivalent to a Ba2Bi3+Bi5+O6 representation. Recent calculations and experimental results confirm that there is no significant deviation from the oxidation states of 3+ and 5+. Superconductivity with a Tc as high as 13 K occurs for BaPb1-xBixO3 phases where the 6s band is about 25% filled, and superconductivity with a Tc as high as 34 K occurs for Ba1-xKxBiO3 phases where the 6s band is about 35% filled. Structures in these two solid solutions can have cubic, tetragonal, orthorhombic, or monoclinic symmetry. However, superconductivity has only been observed when the symmetry is tetragonal. © 2015 Elsevier B.V. All rights reserved.


Juranek L.W.,Oregon State University | Quay P.D.,University of Washington
Annual Review of Marine Science | Year: 2013

Since the triple isotopic composition of dissolved O2 ( 17Δ) was introduced as a natural tracer of photosynthetic gross O2 production (GOP) over 10 years ago, observations of 17Δ have been used to constrain marine productivity throughout the global ocean. This incubation-independent approach has several advantages: It allows the determination of production free from containment artifacts and reduces logistical hurdles that can make obtaining productivity with traditional incubation-dependent methods difficult. As such, GOP estimates derived from 17Δ have been used to give insight into potential biases in incubation-based approaches and to evaluate satellite-based estimates of production at the regional scale. With increased use, we have also learned more about the potential biases and uncertainties of this approach, some of which have been addressed by recent method improvements. We recap the major advances the 17Δ method has brought to improved understanding of biological carbon cycling, from incubation bottles to ocean basins. © 2013 by Annual Reviews. All rights reserved.


Climate sensitivity is generally studied using two types of models. Atmosphere-ocean general circulation models (AOGCMs) include interactive ocean dynamics and detailed heat uptake. Atmospheric GCMs (AGCMs) with slab ocean models (SOMs) cannot fully simulate the ocean's response to and influence on climate. However, AGCMs are computationally cheaper and thus are often used to quantify and understand climate feedbacks and sensitivity. Here, physical climate feedbacks are compared between AOGCMs and SOM-AGCMs from the Coupled Model Intercomparison Project phase 3 (CMIP3) using the radiative kernel technique. Both the global-average (positive) water vapor and (negative) lapse-rate feedbacks are consistently stronger in AOGCMs. Water vapor feedback differences result from an essentially constant relative humidity and peak in the tropics, where temperature changes are larger for AOGCMs. Differences in lapserate feedbacks extend to midlatitudes and correspond to a larger ratio of tropical- to global-average temperature changes. Global-average surface albedo feedbacks are similar between models types because of a near cancellation of Arctic and Antarctic differences. In AOGCMs, the northern high latitudes warm faster than the southern latitudes, resulting in interhemispheric differences in albedo, water vapor, and lapse-rate feedbacks lacking in the SOM-AGCMs. Meridional heat transport changes also depend on the model type, although there is a large intermodel spread. However, there are no consistent global or zonal differences in cloud feedbacks. Effects of the forcing scenario [Special Report on Emissions Scenarios A1B (SRESa1b) or the 1% CO2 increase per year to doubling (1%to2x) experiments] on feedbacks are model dependent and generally of lesser importance than the model type. Care should be taken when using SOM-AGCMs to understand AOGCM feedback behavior. © 2013 American Meteorological Society.


Petersen S.V.,Harvard University | Schrag D.P.,Harvard University | Clark P.U.,Oregon State University
Paleoceanography | Year: 2013

We present a new hypothesis to explain the millennial-scale temperature variability recorded in ice cores known as Dansgaard-Oeschger (DO) cycles. We propose that an ice shelf acted in concert with sea ice to set the slow and fast timescales of the DO cycle, respectively. The abrupt warming at the onset of a cycle is caused by the rapid retreat of sea ice after the collapse of an ice shelf. The gradual cooling during the subsequent interstadial phase is determined by the timescale of ice-shelf regrowth. Once the ice shelf reaches a critical size, sea ice expands, driving the climate rapidly back into stadial conditions. The stadial phase ends when warm subsurface waters penetrate beneath the ice shelf and cause it to collapse. This hypothesis explains the full shape of the DO cycle, the duration of the different phases, and the transitions between them and is supported by proxy records in the North Atlantic and Nordic Seas. © 2012 American Geophysical Union. All Rights Reserved.


Leshchinsky B.,Oregon State University | Ling H.I.,Columbia University
Geotextiles and Geomembranes | Year: 2013

Railroad foundations are geotechnical structures that are highly dependent on quality ballast to dampen impact loading and railway vibration, facilitate easy construction, distribute stresses more evenly, reduce long-term settlements and provide a competent base under low confining pressures. However, there are various instances where the use of ballast alone may not be completely adequate or could be prohibitively expensive, i.e. costly transport of select materials, weak subgrade, etc. One possible method of managing these issues is the use of geosynthetics, primarily reinforcements that utilize a confining mechanism to enhance the strength of a soil by utilizing its own internal friction: a mechanism where geocell is applicable. Based on prior large-scale laboratory tests of ballast embankments with geocell confinement and relevant numerical modeling, an acceptable material model was validated for a parametric study using finite element analysis. The purpose of the parametric study is to investigate the effects of geocell confinement on ballasted embankments when encountering a soft subgrade, weaker ballast, or varying reinforcement stiffnesses. This analysis suggests that based on numerical modeling, geocell confinement can have a significant benefit when used on a wide range of subgrade stiffnesses, when using weaker ballast and that mechanically, most polymeric materials commonly used for geosynthetic reinforcements are adequate. The composite effect of the confined ballast selected as infill also demonstrates a " mattressing" effect, distributing stresses more uniformly to the subgrade, which can provide higher bearing capacities and possibly less settlement, all while preventing significant lateral spreading. In certain situations, the benefits provided by behavior of the geocell-ballast composite may be economical by allowing for use of weaker/inferior ballast, less embankment maintenance upon problem soils, improved bearing capacity and reduced foundation settlement. © 2012 Elsevier Ltd.


Meigs A.,Oregon State University
Lithosphere | Year: 2013

A revolution in remote sensing, light detection and ranging (LiDAR) laser altimetry swath mapping, reveals the details of topographic features at such high resolution that they have transformed our understanding of tectonic forcing of the shape of the Earth's surface. Meter-scale DEMs (digital elevation models) capture fault offsets, fault zone structure, off-fault deformation, and landscape properties at microgeomorphic scale, highlighting that the surface faithfully records the complexity and sensitivity of deformation in detail.


Haley B.A.,Oregon State University | Polyak L.,Ohio State University
Geophysical Research Letters | Year: 2013

We present a survey of Nd isotopes measured from authigenic phases on surface sediments from the Arctic Ocean seafloor. Comparison with published dissolved water column Nd isotope distributions suggests that εNd from sediment leachates accurately represents bottom water circulation of the Arctic Ocean, with Atlantic (∼-11 εNd) and Pacific (∼-5 εNd) water end-members clearly distinguishable. Nd isotopic data from the Chukchi margin show several apparent deviations from the expected pattern, which imply that this margin has been a region of sustained shelf-to-basin sediment redistribution and/or a region where deep water cascades downslope, such as through brine rejection during ice formation. These data also provide insights into a pre-anthropocene "baseline" (several thousand years) for investigating Arctic Ocean circulation in a changing climate; the data presented here are indicative that these changes may be impacting the deep as well as surface ocean. © 2013. American Geophysical Union. All Rights Reserved.


Barbier E.B.,University of Wyoming | Hacker S.D.,Oregon State University | Kennedy C.,University of Wyoming | Koch E.W.,University of Cambridge | And 2 more authors.
Ecological Monographs | Year: 2011

The global decline in estuarine and coastal ecosystems (ECEs) is affecting a number of critical benefits, or ecosystem services. We review the main ecological services across a variety of ECEs, including marshes, mangroves, nearshore coral reefs, seagrass beds, and sand beaches and dunes. Where possible, we indicate estimates of the key economic values arising from these services, and discuss how the natural variability of ECEs impacts their benefits, the synergistic relationships of ECEs across seascapes, and management implications. Although reliable valuation estimates are beginning to emerge for the key services of some ECEs, such as coral reefs, salt marshes, and mangroves, many of the important benefits of seagrass beds and sand dunes and beaches have not been assessed properly. Even for coral reefs, marshes, and mangroves, important ecological services have yet to be valued reliably, such as cross-ecosystem nutrient transfer (coral reefs), erosion control (marshes), and pollution control (mangroves). An important issue for valuing certain ECE services, such as coastal protection and habitat-fishery linkages, is that the ecological functions underlying these services vary spatially and temporally. Allowing for the connectivity between ECE habitats also may have important implications for assessing the ecological functions underlying key ecosystems services, such coastal protection, control of erosion, and habitat-fishery linkages. Finally, we conclude by suggesting an action plan for protecting and/or enhancing the immediate and longer-term values of ECE services. Because the connectivity of ECEs across land-sea gradients also influences the provision of certain ecosystem services, management of the entire seascape will be necessary to preserve such synergistic effects. Other key elements of an action plan include further ecological and economic collaborative research on valuing ECE services, improving institutional and legal frameworks for management, controlling and regulating destructive economic activities, and developing ecological restoration options. © 2011 by the Ecological Society of America.


Mathews C.K.,Oregon State University
Structure | Year: 2016

Ribonucleotide reductases of the class I family are α2β2 tetramers. Like all RNRs they are subject to allosteric control mechanisms affecting activity and specificity. In this issue of Structure, Johansson et al. (2016) present a structural analysis of an unusual mode of activity site regulation. © 2016 Elsevier Ltd.


Coops N.C.,University of British Columbia | Waring R.H.,Oregon State University
Ecological Modelling | Year: 2011

In the Pacific northwestern (PNW) region of North America, climatic conditions have significantly warmed since a predominantly cool phase of the Pacific North American circulation patterns between 1950 and 1975. What are the implications of this shift in climate for the vulnerability of native tree species? To address this question, we combined mechanistic and statistical models to assess where a variety of native tree species might be more vulnerable within their recorded ranges and where they might potentially migrate. For long-lived species that are well adapted to compete, seasonal differences in photosynthesis and water use offer insights helpful in predicting their distributions. To evaluate the general response of conifers to climatic variation across the region, we previously applied a process-based model (3-PG), to simulate the growth and maximum leaf area index that Douglas-fir could attain within recognized forested areas. We then constructed automated decision tree models to define and map the ecological distributions of 15 tree species based on differences in how photosynthesis was constrained by drought, daytime temperatures, high evaporative demand, and the frequency of frost. For the baseline climate period (1950-1975), the decision tree models predicted presence and absence of each species at ∼23,000 observations with an average accuracy of 81%, with an average kappa statistic of 0.74. In this paper the same models were run annually for the period between 1976 and 2006 for each species, and the areas defined as remaining suitable or becoming vulnerable to disturbance were identified based on whether more or less than half of the years fell within the originally defined limits. Based on these criteria, 70% of the species recorded ranges remained suitable, with 30% deemed vulnerable. Results varied notably by species with western red cedar and western hemlock remaining highly adapted, with potential for range expansion in area of up to 50% relative to the baseline period. In contrast, ponderosa pine, lodgepole pine, grand, and noble fir were classified as vulnerable with potential net contractions in their ranges. The analysis was extended through the rest of the 21st century using climatic projections from the Canadian global circulation model with a high fossil fuel emission scenario (A2) and compared to other previously published species range predictions. © 2011 Elsevier B.V.


Michalakis S.,California Institute of Technology | Zwolak J.P.,Nicolaus Copernicus University | Zwolak J.P.,Oregon State University
Communications in Mathematical Physics | Year: 2013

We prove stability of the spectral gap for gapped, frustration-free Hamiltonians under general, quasi-local perturbations. We present a necessary and sufficient condition for stability, which we call Local Topological Quantum Order and show that this condition implies an area law for the entanglement entropy of the groundstate subspace. This result extends previous work by Bravyi et al. on the stability of topological quantum order for Hamiltonians composed of commuting projections with a common zero-energy subspace. We conclude with a list of open problems relevant to spectral gaps and topological quantum order. © 2013 Springer-Verlag Berlin Heidelberg.


Putman N.F.,Oregon State University
Proceedings. Biological sciences / The Royal Society | Year: 2013

Organismal movement is an essential component of ecological processes and connectivity among ecosystems. However, estimating connectivity and identifying corridors of movement are challenging in oceanic organisms such as young turtles that disperse into the open sea and remain largely unobserved during a period known as 'the lost years'. Using predictions of transport within an ocean circulation model and data from published genetic analysis, we present to our knowledge, the first basin-scale hypothesis of distribution and connectivity among major rookeries and foraging grounds (FGs) of green turtles (Chelonia mydas) during their 'lost years'. Simulations indicate that transatlantic dispersal is likely to be common and that recurrent connectivity between the southwestern Indian Ocean and the South Atlantic is possible. The predicted distribution of pelagic juvenile turtles suggests that many 'lost years hotspots' are presently unstudied and located outside protected areas. These models, therefore, provide new information on possible dispersal pathways that link nesting beaches with FGs. These pathways may be of exceptional conservation concern owing to their importance for sea turtles during a critical developmental period.


Turner D.P.,Oregon State University
Frontiers in Ecology and the Environment | Year: 2011

The concept of sustainable resource management can be applied at multiple scales. Monitoring is an essential component of sustainable natural resource management schemes, and as we begin to confront the need to manage natural resources at the global scale, the importance of monitoring at the global scale is also growing. The combination of satellite remote sensing, in situ measurements, and simulation modeling has the potential to deliver an annual assessment of status and trends for several measures of terrestrial biosphere structure and function relevant to sustainability. However, there is, as yet, no internationally coordinated effort in place to perform that analysis. Synthesis activity of that kind would support the development of global environmental governance institutions, including both non-governmental organizations and international bodies. © The Ecological Society of America.


Briggs J.C.,Oregon State University
Marine Biology | Year: 2011

In contrast to the large number of terrestrial extinctions that have taken place over the past 12,000 years, there have apparently been very few marine extinctions. But these small losses should not be reason for complacency. During the past 50 years, government supported, commercial fishing has resulted in the collapse of about a thousand populations that once supplied most of the world's seafood. For the collapsed species, now existing as small remnants of their former population sizes, the future is bleak. They suffer from loss of genetic diversity, inbreeding depression, and depensation. Because marine species were eliminated by historic climatic changes, continued global warming is likely to result in the extinction of small populations that already have a precarious existence. They may be considered evidence of an extinction debt that must be paid as the climate change becomes more severe. For some of the remnant species, extinction can be avoided if there is a rapid management conversion to the use of more marine protected areas (MPAs) and extensive ocean zoning where fishing is prohibited. © 2010 Springer-Verlag.


Nolin A.W.,Oregon State University
Journal of Glaciology | Year: 2011

Remote sensing offers local, regional and global observations of seasonal snow, providing key information on snowpack processes. This brief review highlights advancements in instrumentation and analysis techniques that have been developed over the past decade. Areas of advancement include improved algorithms for mapping snow-cover extent, snow albedo, snow grain size, snow water equivalent, melt detection and snow depth, as well as new uses of instruments such as multiangular spectroradiometers, scatterometry and lidar. Limitations and synergies of the instruments and techniques are discussed, and remaining challenges such as multisensor mapping, scaling issues, vegetation correction and data assimilation are identified.


Wirsing A.J.,University of Washington | Ripple W.J.,Oregon State University
Frontiers in Ecology and the Environment | Year: 2011

Marine and terrestrial ecologists rarely exchange information, yet comparing research from both sides of the land-sea boundary holds great potential for improving our understanding of ecological processes. For example, by comparing the interaction between tiger sharks (Galeocerdo cuvier) and dugongs (Dugong dugon) to that between gray wolves (Canis lupus) and elk (Cervus elaphus), we show that top predators in marine and terrestrial ecosystems trigger three similar types of anti-predator behavior: (1) encounter avoidance, (2) escape facilitation, and (3) increased vigilance. By implication, the ecological roles of top predators in both ecosystems may be more similar than previously thought, and studies that fail to account for multiple modes of antipredator behavior are likely to underestimate these roles and the consequences of eliminating predators from ecosystems. We encourage more communication between marine and terrestrial ecologists, in the interest of generating further insights into ecosystem dynamics and conservation. © 2011 The Ecological Society of America.


Scott M.H.,Oregon State University
Journal of Structural Engineering (United States) | Year: 2012

The direct differentiation method (DDM) has been shown to be an accurate and efficient approach to computing the sensitivity of structural response to uncertain parameters of constitutive models and finite-element formulations. Although it is well-known that the DDM should be consistent with the numerical time stepping procedure at the structural level, it is possible for element-level numerical instabilities to arise when the response sensitivity equations are inconsistent with the equations that govern the element response. Two existing formulations of DDM force-based element response sensitivity are shown to be mathematically equivalent in exact arithmetic; however, only one is consistent with the force-based response equations and possesses a low condition number for finite arithmetic. On the other hand, the inconsistent formulation has a high condition number that is equal to the product of the largest singular values of the section and element stiffness matrices. Representative examples show that the high condition number of the inconsistent formulation is innocuous for sensitivity with respect to section-level parameters but can lead to round off errors for sensitivity with respect to element-level geometric parameters. © 2012 American Society of Civil Engineers.


Moulton H.M.,Oregon State University | Moulton J.D.,Gene Tools LLC
Biochimica et Biophysica Acta - Biomembranes | Year: 2010

Exon-skipping efficacies of phosphodiamidate morpholino oligomers (PMOs) or the conjugates of PMOs with cell-penetrating peptides (PPMOs) have been tested in various animal models of Duchenne muscular dystrophy (DMD), including mdx mice, utrophin-dystrophin double-knockout mice, and CXMD dogs, as well as in DMD patients in clinical trials. The studies have shown that PMOs can diffuse into leaky muscle cells, modify splicing of DMD transcripts, induce expression of partially functional dystrophin, and improve function of some skeletal muscles. PMOs are non-toxic, with a report of mdx mice tolerating a 3 g/kg dose, and no drug-related safety issue in human has been reported. However, because of their poor cell uptake and rapid renal clearance, large and frequently repeated doses of PMOs are likely required for functional benefit in some skeletal muscles of DMD patients. In addition, PMOs do not enter cardiomyocytes sufficiently to relieve heart pathology, the efficacy of delivery to various muscles varies greatly, and delivery across the tissue of each skeletal muscle tissue is patchy. PPMOs enter cells at far lower doses, enter cardiomyocytes in useful quantities, and deliver more evenly to myocytes both when different muscles are compared and when assessed at the level of single muscle tissue sections. Compared to PMOs, far lower doses of PPMOs can restore dystrophin sufficiently to reduce disease pathology, increase skeletal and cardiac muscle functions, and prolong survival of animals. The biggest challenge for PPMO is determining safe and effective doses. The toxicity of PPMOs will require caution when moving into the clinic. The first PPMO-based DMD drug is currently in preclinical development for DMD patients who can benefit from skipping exon 50. © 2010 Elsevier B.V.


Macuga K.L.,Oregon State University | Frey S.H.,University of Missouri
NeuroImage | Year: 2014

Damage to the superior and/or inferior parietal lobules (SPL, IPL) (Sirigu et al., 1996) or cerebellum (Grealy and Lee, 2011) can selectively disrupt motor imagery, motivating the hypothesis that these regions participate in predictive (i.e., feedforward) control. If so, then the SPL, IPL, and cerebellum should show greater activity as the demands on feedforward control increase from visually-guided execution (closed-loop) to execution without visual feedback (open-loop) to motor imagery. Using fMRI and a Fitts' reciprocal aiming task with tools directed at targets in far space, we found that the SPL and cerebellum exhibited greater activity during closed-loop control. Conversely, open-loop and imagery conditions were associated with increased activity within the IPL and prefrontal areas. These results are consistent with a superior-to-inferior gradient in the representation of feedback-to-feedforward control within the posterior parietal cortex. Additionally, the anterior SPL displayed greater activity when aiming movements were performed with a stick vs. laser pointer. This may suggest that it is involved in the remapping of far into near (reachable) space (Maravita and Iriki, 2004), or in distalization of the end-effector from hand to stick (Arbib et al., 2009). © 2014 Elsevier Inc.


Loprinzi P.D.,Bellarmine University | Smit E.,Oregon State University | Mahoney S.,Bellarmine University
Mayo Clinic Proceedings | Year: 2014

Objective: To examine the association between objectively measured physical activity and dietary behavior and their combined effect on health. Patients and Methods: Data for this study were obtained from the 2003-2006 National Health and Nutrition Examination Survey cycles. The data were evaluated between September 9, 2012, and August 14, 2013. As part of the national survey, participants wore an accelerometer for 4 or more days to assess physical activity, blood samples were obtained to assess various biological markers, and interviews were conducted to assess dietary behavior. We selected a sample of 5211 participants and categorized them into 4 groups: (1) healthy diet and active, (2) unhealthy diet and active, (3) healthy diet and inactive, and (4) unhealthy diet and inactive. Results: A total of 16.5% of participants (weighted proportions) were classified as consuming a healthy diet and being sufficiently active. After adjustments, participants were 32% more likely to consume a healthy diet if they met physical activity guidelines. For nearly all biomarkers, those who consumed a healthy diet and were sufficiently active had the most favorable biomarker levels. Compared with those who consumed a healthy diet and were active, participants who consumed an unhealthy diet and were inactive were 2.4 times more likely to have metabolic syndrome. Conclusion: Our findings indicate a relationship between objectively measured physical activity and dietary behavior and that participating in regular physical activity and eating a healthy diet are associated with better health outcomes when compared with diet or physical activity alone. © 2014 Mayo Foundation for Medical Education and Research.


Ruther R.E.,University of Wisconsin - Madison | Ruther R.E.,Oregon State University | Cui Q.,University of Wisconsin - Madison | Hamers R.J.,University of Wisconsin - Madison
Journal of the American Chemical Society | Year: 2013

We have investigated the electron-transfer kinetics of ferrocene groups covalently tethered to surfaces of conductive diamond electrodes. Electrochemical measurements show that the rates are only weakly dependent on chain length but are strongly dependent on the surface coverage; these observations are contrary to what is commonly observed for self-assembled monolayers on gold, pointing to important mechanistic differences in electron transfer processes on covalently bonded materials. Molecular dynamics simulations show that dependence on chain length and molecular density can be readily explained in terms of dynamic crowding effects. At low coverage, conformational flexibility of surface-tethered alkyl chains allows the redox-active ferrocene group to dynamically approach the diamond surface, leading to facile electron transfer for all surface molecules. As the coverage is increased, steric crowding causes the average ferrocene-to-surface distance to increase, decreasing the electron transfer rate. Even at the most dense packings, the mismatch between the spacing of surface lattice sites and the optimum alkyl chain density leads to voids and inherent disorder that facilitates electron transfer. These results are significant in the design and optimization of electrocatalytically active surfaces on covalently bonded materials relevant for electro-and photocatalysis. © 2013 American Chemical Society.


Cuadros D.F.,University of Kentucky | Branscum A.J.,Oregon State University | Crowley P.H.,University of Kentucky
International Journal of Epidemiology | Year: 2011

Objective: To examine the association between malaria and HIV prevalence in East sub-Saharan Africa. Methods: Using large nationally representative samples of 19 735 sexually active adults from the 2003-04HIV/AIDS indicator surveys conducted in Kenya, Malawi and Tanzania, and the atlas malaria project, we analysed the relationship between malaria and HIV prevalence adjusting for important socioeconomic and biological cofactors. Results: In adjusted models, individuals who live in areas with high Plasmodium falciparum parasite rate (PfPR40.42) had increased estimated odds of being HIV positive than individuals who live in areas with low P. falciparum parasite rate (PfPR40.10) [men: estimated odds ratio (OR) 2.24, 95% confidence interval (CI) 1.62-3.12; women: estimated OR 2.44, 95% CI 1.85-3.21]. Conclusion: This is the first study to report malaria as a risk factor of concurrent HIV infection at the population level. According to our results, individuals who live in areas with high P. falciparum parasite rate have about twice the risk of being HIV positive compared with individuals who live in areas with low P. falciparum parasite rate. Our work emphasizes the need for field studies focused on quantifying the interaction among parasitic infections and risk of HIV infection, and studies to explore the impact of control interventions. Programmes focused on reducing malaria transmission will be important to address, especially in HIV-infected individuals. Published by Oxford University Press on behalf of the International Epidemiological Association © The Author 2011; all rights reserved.


Robbertse B.,U.S. National Center for Biotechnology Information | Spatafora J.W.,Oregon State University
PLoS Currents | Year: 2011

The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous clusters of proteins or genes, and the assembly of alignments of orthologous sequence data into individual and concatenated super alignments. Here we report the production of an automated pipeline, Hal that produces multiple alignments and trees from genomic data. These alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. In short, the Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees. The script is available at sourceforge (http://sourceforge.net/projects/bio-hal/). The results from an example analysis of Kingdom Fungi are briefly discussed.


Ebert T.A.,Oregon State University
Proceedings. Biological sciences / The Royal Society | Year: 2014

A wide variety of organisms show morphologically plastic responses to environmental stressors but in general these changes are not reversible. Though less common, reversible morphological structures are shown by a range of species in response to changes in predators, competitors or food. Theoretical analysis indicates that reversible plasticity increases fitness if organisms are long-lived relative to the frequency of changes in the stressor and morphological changes are rapid. Many sea urchin species show differences in the sizes of jaws (demi-pyramids) of the feeding apparatus, Aristotle's lantern, relative to overall body size, and these differences have been correlated with available food. The question addressed here is whether reversible changes of relative jaw size occur in the field as available food changes with season. Monthly samples of the North American Pacific coast sea urchin Strongylocentrotus purpuratus were collected from Gregory Point on the Oregon (USA) coast and showed an annual cycle of relative jaw size together with a linear trend from 2007 to 2009. Strongylocentrotus purpuratus is a long-lived species and under field conditions individuals experience multiple episodes of changes in food resources both seasonally and from year to year. Their rapid and reversible jaw plasticity fits well with theoretical expectations.


Poinar Jr. G.O.,Oregon State University
Current Biology | Year: 2012

New flea-like fossils from China provide a rare, tantalizing glimpse of bizarre insects in the Cretaceous and Jurassic. Possibly the oldest flea-like animals known, they provide a challenge to the functional morphologist to infer which animals they may have targeted. © 2012 Elsevier Ltd. All rights reserved.


While interdisciplinary research is increasingly practiced as a way to transcend the limitations of individual disciplines, our concepts, and methods are primarily rooted in the disciplines that shape the way we think about the world and how we conduct research. While natural and social scientists may share a general understanding of how science is conducted, disciplinary differences in methodologies quickly emerge during interdisciplinary research efforts. This paper briefly introduces and reviews different philosophical underpinnings of quantitative and qualitative methodological approaches and introduces the idea that a pragmatic, realistic approach may allow natural and social scientists to work together productively. While realism assumes that there is a reality that exists independently of our perceptions, the work of scientists is to explore the mechanisms by which actions cause meaningful outcomes and the conditions under which the mechanisms can act. Our task as interdisciplinary researchers is to use the insights of our disciplines in the context of the problem to co-produce an explanation for the variables of interest. Research on qualities necessary for successful interdisciplinary researchers is also discussed along with recent efforts by funding agencies and academia to increase capacities for interdisciplinary research. © 2013 Springer Science+Business Media New York.


Paredes-Sabja D.,Andres Bello University | Paredes-Sabja D.,Oregon State University | Shen A.,University of Vermont | Sorg J.A.,Texas A&M University
Trends in Microbiology | Year: 2014

Clostridium difficile is a Gram-positive, spore-forming obligate anaerobe and a major nosocomial pathogen of worldwide concern. Owing to its strict anaerobic requirements, the infectious and transmissible morphotype is the dormant spore. In susceptible patients, C. difficile spores germinate in the colon to form the vegetative cells that initiate Clostridium difficile infections (CDI). During CDI, C. difficile induces a sporulation pathway that produces more spores; these spores are responsible for the persistence of C. difficile in patients and horizontal transmission between hospitalized patients. Although important to the C. difficile lifecycle, the C. difficile spore proteome is poorly conserved when compared to members of the Bacillus genus. Further, recent studies have revealed significant differences between C. difficile and Bacillus subtilis at the level of sporulation, germination, and spore coat and exosporium morphogenesis. In this review, the regulation of the sporulation and germination pathways and the morphogenesis of the spore coat and exosporium will be discussed. © 2014 Elsevier Ltd.


De Castro M.C.,Harvard University | Fisher M.G.,Oregon State University
Malaria Journal | Year: 2012

Background: Malaria is commonly considered a disease of the poor, but there is very little evidence of a possible two-way causality in the association between malaria and poverty. Until now, limitations to examine that dual relationship were the availability of representative data on confirmed malaria cases, the use of a good proxy for poverty, and accounting for endogeneity in regression models. Methods: A simultaneous equation model was estimated with nationally representative data for Tanzania that included malaria parasite testing with RDTs for young children (six-59 months), and accounted for environmental variables assembled with the aid of GIS. A wealth index based on assets, access to utilities/infrastructure, and housing characteristics was used as a proxy for socioeconomic status. Model estimation was done with instrumental variables regression. Results: Results show that households with a child who tested positive for malaria at the time of the survey had a wealth index that was, on average, 1.9 units lower (p-value<0.001), and that an increase in the wealth index did not reveal significant effects on malaria. Conclusion: If malaria is indeed a cause of poverty, as the findings of this study suggest, then malaria control activities, and particularly the current efforts to eliminate/eradicate malaria, are much more than just a public health policy, but also a poverty alleviation strategy. However, if poverty has no causal effect on malaria, then poverty alleviation policies should not be advertised as having the potential additional effect of reducing the prevalence of malaria. © 2012 de Castro and Fisher; licensee BioMed Central Ltd.


Celebi Oncu E.,Oregon State University | Metindogan Wise A.,Bogazici University
Child Development | Year: 2010

The purpose of this exploratory study was to determine whether projective techniques could identify long-term consequences among children stemming from exposure to a traumatic event. The first group of children (n = 53; 26 female, 27 male) experienced 2 major earthquakes at age 7, 3 months apart, in Turkey, while a similarly matched control group (n = 50; 25 female, 25 male) did not. Both groups of children (current age: 9) completed a series of short stories related to disastrous events. Results indicated that the traumatized group evinced a range of trauma-related symptoms 2 years after experiencing the earthquakes. © 2010, Copyright the Author(s). Journal Compilation © 2010, Society for Research in Child Development, Inc.


Nolin A.W.,Oregon State University
Mountain Research and Development | Year: 2012

From both social and environmental perspectives, water is the main connection between highland and lowland processes in mountain watersheds: Water flows downhill while human impacts flow uphill. For example, in the Oregon Cascades mountain range, geology, vegetation, and climate influence the hydrologic connections within watersheds. Geology determines which watersheds are surface runoff-dominated and which are groundwater-dominated. In this Mediterranean climate with dry summers, surface runoff watersheds will consistently experience near-zero late summer discharge, so declining snowpacks will have little effect on low flows. This contrasts with groundwater-dominated watersheds, where a shift from snow to rain or a decline in precipitation will reduce recharge, thereby reducing late summer groundwater contributions to streamflow. Earlier snowmelt causes forests to transpire earlier, resulting in decreased springtime streamflow. Reduced snowpacks lead to soil moisture stress, making forests more vulnerable to extensive wildfires and affecting the lifespan and composition of forests. Monitoring and quantifying these complex linkages and feedbacks require appropriate measurement networks. Sampling strategies often use watershed typology to identify where measurements should be focused. Such an approach should include not only established watershed classification parameters such as topology and geology but also interannual climate variability and land cover. As concerns of water scarcity and vulnerability move to the forefront, our watershed classifications should be extended to include ecosystem and socialecological parameters. An integrated and agent-based modeling scheme called Envision has been developed to simulate alternative future landscapes at the watershed scale. Using fully coupled models of hydrology, ecosystems, and socioeconomics, decision-makers can simulate the effects of policy decisions in conjunction with other climate forcing, land use change, and economic disturbances. To understand the combined impacts of climate change and humans on water in mountain watersheds, researchers must develop integrated monitoring and modeling systems that explicitly include connections across eco-hydrologic and social-ecological systems. © 2012 by the authors.


Traber M.G.,Oregon State University
Journal of Lipid Research | Year: 2013

The liver is at the nexus of the regulation of lipoprotein uptake, synthesis, and secretion, and it is the site of xenobiotic detoxification by cytochrome P450 oxidation systems (phase I), conjugation systems (phase II), and transporters (phase III). These two major liver systems control vitamin E status. The mechanisms for the preference for α-tocopherol relative to the eight naturally occurring vitamin E forms largely depend upon the liver and include both a preferential secretion of α-tocopherol from the liver into the plasma for its transport in circulating lipoproteins for subsequent uptake by tissues, as well as the preferential hepatic metabolism of non- α-tocopherol forms. These mechanisms are the focus of this review. Copyright © 2013 by the American Society for Biochemistry and Molecular Biology, Inc.


Jepson P.C.,Oregon State University
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2014

We outline an approach to pesticide risk assessment that is based upon surveys of pesticide use throughout West Africa. We have developed and used new risk assessment models to provide, to our knowledge, the first detailed, geographically extensive, scientifically based analysis of pesticide risks for this region. Human health risks from dermal exposure to adults and children are severe enough in many crops to require long periods of up to three weeks when entry to fields should be restricted. This is impractical in terms of crop management, and regulatory action is needed to remove these pesticides from the marketplace. We also found widespread risks to terrestrial and aquatic wildlife throughout the region, and if these results were extrapolated to all similar irrigated perimeters in the Senegal and Niger River Basins, they suggest that pesticides could pose a significant threat to regional biodiversity. Our analyses are presented at the regional, national and village levels to promote regulatory advances but also local risk communication and management. Without progress in pesticide risk management, supported by participatory farmer education, West African agriculture provides a weak context for the sustainable intensification of agricultural production or for the adoption of new crop technologies.


Poinar G.O.,Oregon State University | Struwe L.,Rutgers University
Nature Plants | Year: 2016

Fossils preserved in amber may provide significant palaeoevolutionary and biogeographical data regarding the evolution of life on Earth1. Although amber is particularly noted for its detailed preservation of arthropods, the same degree of preservation can be found for vascular plant remains2. Mid-Tertiary Dominican amber is a rich source for such fossils, and representatives of several angiosperm families have been described. However, no fossilized examples of the large asterid plant clade have yet been reported. Here we describe the first fossil neotropical flowers found in amber from a representative of the asterids. The asterids are one of the largest lineages of flowering plants, containing groups such as the sunflower, potato, coffee and mint families, totalling over 80,000 species3. The new fossils are only known as flowers, more precisely corollas with stamens and styles.We here describe them as a new species, Strychnos electri sp. nov, in the plant family Loganiaceae (Gentianales). © 2016 Macmillan Publishers Limited. All rights reserved.


Lim J.,Oregon State University
Food Quality and Preference | Year: 2011

In recent years, interest in measuring hedonic responses has grown tremendously in both basic psychophysics and applied food and consumer research, resulting in the development of several new hedonic scaling methods. With these developments have come questions about theoretical and practical differences among the methods. The goal of this review is to compare and contrast these different approaches for the purpose of aiding researchers in selecting the most appropriate scaling method for their specific measurement needs. The review begins by addressing fundamental issues in scaling methodology, including the role of context effects, then moves on to describing and discussing the development of various types of hedonic scales, their specific properties, and their potential advantages and disadvantages. © 2011.


Nielsen R.L.,Oregon State University
Geochemistry, Geophysics, Geosystems | Year: 2011

Melt inclusions trapped in phenocrysts provide a unique picture of magma systems prior to modification by crustal processes. However, post-entrapment crystallization complicates their interpretation. Re-heating the phenocryst to the temperature of entrapment is a commonly applied method to recover the original melt composition. To understand the effects of re-homogenization, we compared the composition of re-heated and naturally quenched melt inclusions and inclusion compositions that had been subjected to over-heating and under-heating to examine the degree to which anomalous compositions were produced. Our results on plagioclase hosted inclusions from ocean floor basalts indicate that the general patterns represented by naturally quenched inclusions are the same as observed for rehomogenized inclusions. Most important, the range of minor elements described for plagioclase hosted inclusions from basalts is found in naturally quenched inclusions, and is therefore not a consequence of the re-homogenization process. Copyright 2011 by the American Geophysical Union.


Simonich S.M.,Oregon State University
Integrated environmental assessment and management | Year: 2013

The risks of 1,4-dioxane (dioxane) concentrations in wastewater treatment plant (WWTP) effluents, receiving primarily domestic wastewater, to downstream drinking water intakes was estimated using distributions of measured dioxane concentrations in effluents from 40 WWTPs and surface water dilution factors of 1323 drinking water intakes across the United States. Effluent samples were spiked with a d8 -1,4-dioxane internal standard in the field immediately after sample collection. Dioxane was extracted with ENVI-CARB-Plus solid phase columns and analyzed by GC/MS/MS, with a limit of quantification of 0.30 μg/L. Measured dioxane concentrations in domestic wastewater effluents ranged from <0.30 to 3.30 μg/L, with a mean concentration of 1.11 ± 0.60 μg/L. Dilution of upstream inputs of effluent were estimated for US drinking water intakes using the iSTREEM model at mean flow conditions, assuming no in-stream loss of dioxane. Dilution factors ranged from 2.6 to 48 113, with a mean of 875. The distributions of dilution factors and dioxane concentration in effluent were then combined using Monte Carlo analysis to estimate dioxane concentrations at drinking water intakes. This analysis showed the probability was negligible (p = 0.0031) that dioxane inputs from upstream WWTPs could result in intake concentrations exceeding the USEPA drinking water advisory concentration of 0.35 μg/L, before any treatment of the water for drinking use. © 2013 SETAC.


Mahrt L.,Oregon State University
Journal of Applied Meteorology and Climatology | Year: 2011

Common large shifts of wind direction in the weak-wind nocturnal boundary layer are poorly understood and are not adequately captured by numerical models and statistical parameterizations. The current study examines 15 datasets representing a variety of surface conditions to study the behavior of wind direction variability. In contrast to previous studies, the current investigation directly examines wind direction changes with emphasis on weak winds and wind direction changes over smaller time periods of minutes to tens of minutes, including large wind direction shifts. A formulation of the wind direction changes is offered that provides more realistic behavior for very weak winds and for complex terrain. © 2011 American Meteorological Society.


Lade P.V.,Catholic University of America | Yamamuro J.A.,Oregon State University
Canadian Geotechnical Journal | Year: 2011

The mechanism of instability in granular soils is explained and its requirement as a forerunner to the liquefaction of level or sloping ground is described. Case histories support the observation that it is silty sands that liquefy under static and a majority of earthquake-induced conditions. Recent experiments show that clean sands do not behave similarly to silty sands. Tests on loose, silty sand indicate a "reverse" behavior with respect to confining pressure and this violates the basic assumption that loose, silty sands behave similarly to loose, clean sands. Strong correlations between fines content, compressibility, and liquefaction potential are often found for these soils. A procedure for the analysis and evaluation of static liquefaction of slopes of fine sand and silt, such as submarine slopes, mine tailings, and spoil heaps, is presented. It involves determination of the region of instability in stress space in which potential liquefaction may be initiated and determination of the state of stress in the slope. A method of finding the state of stress is developed to predict the zone of potential liquefaction in simple slopes. Trigger mechanisms for initiation of instability followed by soil liquefaction are reviewed and mechanisms of soil strengthening are discussed.


Mahrt L.,Oregon State University
Boundary-Layer Meteorology | Year: 2011

For the near-calm stable boundary layer, nominally 2-m mean wind speed <0.5 ms-1, the time-average turbulent flux is dominated by infrequent mixing events. These events are related to accelerations associated with wave-like motions and other more complex small-scale motions. In this regime, the relationship between the fluxes and the weak mean flow breaks down. Such near-calm conditions are common at some sites. For very weak winds and strong stratification, the characteristics of the fluctuating quantities change slowly with increasing scale and the separation between the turbulence and non-turbulent motions can become ambiguous. Therefore, a new analysis strategy is developed based on the scale dependence of selected flow characteristics, such as the ratio of the fluctuating potential energy to the kinetic energy. In contrast to more developed turbulence, correlations between fluctuating quantities are small, and a significant heat flux is sometimes carried by very weak vertical motions with large temperature fluctuations. The relation of the flux events to small-scale increases of wind speed is examined. Large remaining uncertainties are noted. © 2011 The Author(s).


Hess R.,Oregon State University
MM'10 - Proceedings of the ACM Multimedia 2010 International Conference | Year: 2010

Recent years have seen an explosion in the use of invariant keypoint methods across nearly every area of computer vision research. Since its introduction, the scale-invariant feature transform (SIFT) has been one of the most effective and widely-used of these methods and has served as a major catalyst in their popularization. In this paper, I present an open-source SIFT library, implemented in C and freely available at http://eecs.oregonstate.edu/ ∼hess/sift.html, and I briefly compare its performance with that of the original SIFT executable released by David Lowe. © 2010 ACM.


Monkul M.M.,Yeditepe University | Yamamuro J.A.,Oregon State University
Canadian Geotechnical Journal | Year: 2011

This study investigates the fines content influence on liquefaction potential of a single base sand mixed with three different essentially nonplastic silts through strain-controlled monotonic undrained triaxial compression tests. Confining stress (30 kPa) and deposition method (dry funnel deposition) were kept the same, while fines content was varied, to solely focus on how different silts and their contents influence the undrained response of the sand under comparable conditions. It was found that if the mean grain diameter ratio (D50-sand/d50-silt) of the sand grains to silt grains is sufficiently small, the liquefaction potential of the sand increases steadily with increasing fines content for the studied range (0%-20%). As D50-sand/d50-silt increases, the liquefaction potential of the silty sand might actually be less than the liquefaction potential of the clean sand. Test results also revealed that commonly used comparison bases (i.e., void ratio, intergranular void ratio, relative density) are not sufficient for assessing the influence of fines on liquefaction potential of silty sands. Finally, relative size of the silt grains should also be considered in geotechnical engineering practice in addition to content and plasticity of fines to characterize the influence of silt on liquefaction potential of sands.


Samelson R.M.,Oregon State University
Journal of Physical Oceanography | Year: 2011

A recently proposed reduced-gravity model of the warm-water branch of the middepth meridional overturning circulation in a rectangular basin with a circumpolar connection is extended to include time dependence. The model describes the balance between gain of warm water through northward Ekman advection across the circumpolar current, loss of warm water through eddy fluxes southward across the current, net gain or loss of warm water through diabatic processes north of the current, and changes in the thickness of the warm-water layer. The steady solutions are the same as those found previously, when the previous parameterization of diabatic fluxes is used. Time-dependent solutions are considered for the approach of the solution to a new equilibrium when the forcing or parameters are abruptly changed and then held fixed. An initial adjustment occurs through a combination of boundary and equatorial adjustment, followed by planetary wave propagation. The longer-term adjustment to equilibrium consists primarily of the slow change in eastern boundary thickness of the warm layer, which controls the mean depth of the entire layer. An approximate analytical solution of the time-dependent equations yields an explicit expression for the intrinsic time scale of the long-term adjustment, which depends on the eddy and diabatic flux parameters and on the equilibrium solution toward which the time-dependent solution adjusts. Numerical solutions are also considered with a second, advective-diffusive diabatic flux parameterization. These solutions differ quantitatively but not qualitatively from those with the original parameterization. For the range of parameter values considered, the adjustment time scale has dimensional values of several decades to more than a century, but the meridional flux of warm water may respond to changes in external parameters or forcing much more rapidly than this time scale for equilibration of the eastern boundary thickness and thermocline structure. © 2011 American Meteorological Society.


Dascaliuc R.,Oregon State University | Grujic Z.,University of Virginia
Communications in Mathematical Physics | Year: 2013

Existence of 2D enstrophy cascade in a suitable mathematical setting, and under suitable conditions compatible with 2D turbulence phenomenology, is known both in the Fourier and in the physical scales. The goal of this paper is to show that the same geometric condition preventing the formation of singularities - 1/2-Hölder coherence of the vorticity direction - coupled with a suitable condition on a modified Kraichnan scale, and under a certain modulation assumption on evolution of the vorticity, leads to existence of 3D enstrophy cascade in physical scales of the flow. © 2012 Springer-Verlag Berlin Heidelberg.


Wiens J.A.,PRBO Conservation Science | Bachelet D.,Oregon State University | Bachelet D.,Conservation Biology Institute
Conservation Biology | Year: 2010

To anticipate the rapidly changing world resulting from global climate change, the projections of climate models must be incorporated into conservation. This requires that the scales of conservation be aligned with the scales of climate-change projections. We considered how conservation has incorporated spatial scale into protecting biodiversity, how the projections of climate-change models vary with scale, and how the two do or do not align. Conservation planners use information about past and current ecological conditions at multiple scales to identify conservation targets and threats and guide conservation actions. Projections of climate change are also made at multiple scales, from global and regional circulation models to projections downscaled to local scales. These downscaled projections carry with them the uncertainties associated with the broad-scale models from which they are derived; thus, their high resolution may be more apparent than real. Conservation at regional or global scales is about establishing priorities and influencing policy. At these scales, the coarseness and uncertainties of global and regional climate models may be less important than what they reveal about possible futures. At the ecoregional scale, the uncertainties associated with downscaling climate models become more critical because the distributions of conservation targets on which plans are founded may shift under future climates. At a local scale, variations in topography and land cover influence local climate, often overriding the projections of broad-scale climate models and increasing uncertainty. Despite the uncertainties, ecologists and conservationists must work with climate-change modelers to focus on the most likely projections. The future will be different from the past and full of surprises; judicious use of model projections at appropriate scales may help us prepare. © 2009 Society for Conservation Biology.


Goyer A.,Oregon State University
Phytochemistry | Year: 2010

Thiamine diphosphate (vitamin B1) plays a fundamental role as an enzymatic cofactor in universal metabolic pathways including glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle. In addition, thiamine diphosphate has recently been shown to have functions other than as a cofactor in response to abiotic and biotic stress in plants. Recently, several steps of the plant thiamine biosynthetic pathway have been characterized, and a mechanism of feedback regulation of thiamine biosynthesis via riboswitch has been unraveled. This review focuses on these most recent advances made in our understanding of thiamine metabolism and functions in plants. Phenotypes of plant mutants affected in thiamine biosynthesis are described, and genomics, proteomics, and metabolomics data that have increased further our knowledge of plant thiamine metabolic pathways and functions are summarized. Aspects of thiamine metabolism such as catabolism, salvage, and transport in plants are discussed. © 2010 Elsevier Ltd. All rights reserved.


Needham M.D.,Oregon State University | Vaske J.J.,Colorado State University
Leisure Sciences | Year: 2013

This article examines relationships between hunter specialization and activity substitutability. Data were obtained from a mail survey of 6,983 deer hunters in eight states and 2,584 elk hunters in three states. Activity substitutability was measured by asking what activity would provide the same satisfaction as deer or elk hunting. Between 41% and 59% of deer hunters and 38% to 46% of elk hunters reported substitutes such as fishing and other big game hunting. Cluster analyses of hunter skill, centrality, equipment, and experience revealed four specialization groups (casual, intermediate, focused, and veteran). Casual hunters were most likely to report a substitute followed by intermediates, focused, and veterans. This inverse relationship between concepts was consistent across states and species hunted. Veteran hunters were most likely to report other big game hunting as a substitute, whereas casual hunters in many states were most likely to consider fishing as a substitute. © 2013 Copyright Taylor and Francis Group, LLC.


Moulton H.M.,Oregon State University
Methods in Molecular Biology | Year: 2012

Exon-skipping efficacy of phosphorodiamidate morpholino oligomers (Morpholinos) has been demonstrated in a proof-of-concept clinical trial for Duchenne muscular dystrophy (DMD). Systemic delivery of Morpholinos can be significantly enhanced by conjugating them to cell-penetrating peptides. The improved efficacy has been demonstrated in DMD animal models, including mdx mice and utrophin-dystrophin double-knockout mice. Compared to unconjugated Morpholinos, far lower doses of the-peptide-Morpholino conjugates can restore dystrophin sufficiently to reduce disease pathology, increase skeletal and cardiac muscle functions and prolong survival of animals. In addition, the conjugates enter cardiomyocytes in useful quantities and improve heart functions. Here, an experimental protocol for making Tat peptide-Morpholino conjugate is described. © 2012 Springer Science+Business Media, LLC.


Nairn J.A.,Oregon State University
International Journal of Fracture | Year: 2011

A new approach was developed for the evaluation of energy release rate by the virtual crack closure technique in quadratic and linear elements. The generalized method allows arbitrary placement of the side nodes for quadratic elements and thus includes both standard elements, with mid-side nodes, and singularity elements, with quarter-point nodes, as special cases of one general equation. It also accounts for traction-loaded cracks. The new derivation revealed that the proper nodal forces needed for crack closure calculations should be the newly-defined "nodal edge forces," rather than the global or element forces from standard finite element analysis results. A method is derived for calculating nodal edge forces from global forces. These new forces affect energy release rate calculations for singularity elements and for problems with traction-loaded cracks. Several sample calculations show that the new approach gives improved accuracy. © 2011 Springer Science+Business Media B.V.


Mathews C.K.,Oregon State University
FASEB Journal | Year: 2014

For >35 yr, we have known that the accuracy of DNA replication is controlled in large part by the relative concentrations of the 4 canonical deoxyribonucleoside 5′-triphosphates (dNTPs) at the replisome. Since this field was last reviewed, ∼8 yr ago, there has been increased understanding of the mutagenic pathways as they occur in living cells. At the same time, aspects of deoxyribonucleotide metabolism have been shown to be critically involved in processes as diverse as cell cycle control, protooncogene expression, cellular defense against HIV infection, replication rate control, telomere length control, and mitochondrial function. Evidence supports a relationship between dNTP pools and microsatellite repeat instability. Relationships between dNTP synthesis and breakdown in controlling steady-state pools have become better defined. In addition, new experimental approaches have allowed definitive analysis of mutational pathways induced by dNTP pool abnormalities, both in Escherichia coli and in yeast. Finally, ribonucleoside triphosphate (rNTP) pools have been shown to be critical determinants of DNA replication fidelity. These developments are discussed in this review article. © FASEB.


Sampson D.B.,Oregon State University
Fisheries Research | Year: 2014

Fishery selection (selectivity for short) is the term often used to describe the phenomenon whereby a fish stock experiences mortality due to fishing that is age- or size-specific. Selectivity operates both at a local scale, as in the direct interactions of individual fish with the fishing gear (contact selection), and at a stock-wide scale (population selection), as evidenced by the differential rates of fishing mortality-at-age that are generally observed in stock assessment results. All age-structured stock assessment models have some form of fishery selection to modulate the impact of fishing mortality on differing age-classes, but selection coefficients, from a stock assessment viewpoint, generally are nuisance parameters rather than a focus of attention. This paper provides an overview of the three main processes that contribute to and influence population selection: (1) physical sorting by the fishing gear or differential behavioral responses of the fish to the gear produce the phenomenon of contact selection; (2) differing selection properties of different types of fishing gear (e.g., trawl versus longline) in turn generate a composite selection curve that is a weighted average of the different kinds of contact selection; and (3) when the fish are not well mixed spatially, then the spatial distribution of fishing relative to the spatial distribution of the fish also affects population selectivity. Fishing mortality-at-age estimates derived from a published Virtual Population Analysis of Scotian Shelf haddock are used to illustrate the diversity of shapes that can be seen in population selection curves and their considerable temporal variability. A spatial model for fishery age-selectivity is then used to demonstrate that the maximum relative yield harvested from a stock can be a function of both contact selection and the spatial distribution of fishing. © 2013 Elsevier B.V.


Bennett A.F.,Oregon State University
Annals of Physics | Year: 2014

The parametrized Dirac wave equation represents position and time as operators, and can be formulated for many particles. It thus provides, unlike field-theoretic Quantum Electrodynamics (QED), an elementary and unrestricted representation of electrons entangled in space or time. The parametrized formalism leads directly and without further conjecture to the Bethe-Salpeter equation for bound states. The formalism also yields the Uehling shift of the hydrogenic spectrum, the anomalous magnetic moment of the electron to leading order in the fine structure constant, the Lamb shift and the axial anomaly of QED. © 2014 Elsevier Inc.


Sloat M.R.,Oregon State University | Reeves G.H.,U.S. Department of Agriculture
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2014

We reared juvenile Oncorhychus mykiss with low and high standard metabolic rates (SMR) under alternative thermal regimes to determine how these proximate factors influence life histories in a partially migratory salmonid fish. High SMR significantly decreased rates of freshwater maturation and increased rates of smoltification in females, but not males, after 1 year of rearing. Warmer water temperatures significantly decreased rates of freshwater maturation and increased rates of smoltification in both sexes. Variation in individual growth influenced the probability of adopting anadromy or freshwater residency as life histories, but produced paradoxical results. Individuals with the highest growth performance within their respective temperature treatments had a higher probability of freshwater maturation, but warmer temperatures decreased freshwater maturation despite significantly increasing somatic growth. Whole-body lipid content was significantly lower for fish reared in the warm temperature treatment, which may explain the decreased probability of freshwater maturation for individuals exposed to warmer temperatures. Our results indicate that changes in somatic growth induced by altered thermal regimes can influence the relationship between body size and the probability of maturation. Accordingly, somatic growth may not be a robust predictor of shifts in the prevalence of anadromy and residency in partially migratory salmonids when compared across thermal regimes.


Tepley A.J.,Oregon State University | Swanson F.J.,U.S. Department of Agriculture | Spies T.A.,U.S. Department of Agriculture
Ecology | Year: 2013

Forests dominated by Douglas-fir and western hemlock in the Pacific Northwest of the United States have strongly influenced concepts and policy concerning old-growth forest conservation. Despite the attention to their old-growth characteristics, a tendency remains to view their disturbance ecology in relatively simple terms, emphasizing infrequent, stand-replacing (SR) fire and an associated linear pathway toward development of those old-growth characteristics. This study uses forest stand- and age-structure data from 124 stands in the central western Cascades of Oregon to construct a conceptual model of stand development under the mixed-severity fire regime that has operated extensively in this region. Hierarchical clustering of variables describing the age distributions of shade-intolerant and shade-tolerant species identified six groups, representing different influences of fire frequency and severity on stand development. Douglas-fir trees .400 years old were found in 84% of stands, yet only 18% of these stands (15% overall) lack evidence of fire since the establishment of these old trees, whereas 73% of all stands show evidence of at least one non-stand-replacing (NSR) fire. Differences in fire frequency and severity have contributed to multiple development pathways and associated variation in contemporary stand structure and the successional roles of the major tree species. Shade-intolerant species form a single cohort following SR fire, or up to four cohorts per stand in response to recurring NSR fires that left living trees at densities up to 45 trees/ha. Where the surviving trees persist at densities of 60-65 trees/ha, the postfire cohort is composed only of shade-tolerant species. This study reveals that fire history and the development of old-growth forests in this region are more complex than characterized in current stand-development models, with important implications for maintaining existing old-growth forests and restoring stands subject to timber management. © 2013 by the Ecological Society of America.