Background: Short RNAs, and in particular microRNAs, are important regulators of gene
expression both within defined regulatory pathways and at the epigenetic scale. We investigated
the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the
sequenced Populus trichocarpa using a concatenation strategy in combination with...
Since 1958 when Alfred C. Redfield (1) recognized the similarity between the ratios of elements in living biomass and those dissolved in the surrounding seawater, we have understood that microorganisms largely control the concentrations, distribution, and molecular makeup of nutritional resources in the ocean. The primary elemental ingredients for life,...
Recent natural disasters around the world including
both tsunamis and hurricanes, have highlighted the inability
of wood buildings to withstand wave and surge
loading during these extreme events. Little is known
about the interaction between coastal residential light-frame
wood buildings and wave and surge loading because
often little is left...
This study quantifies the short-term effects of low-, moderate-, and high-severity fire on carbon pools and fluxes in the Eastern Cascades of Oregon. We surveyed 64 forest stands across four fires that burned 41,000 ha (35%) of the Metolius Watershed in 2002 and 2003, stratifying the landscape by burn severity...
Pretreatment of male C57BL/6 mice with low doses of the persistent organochlorine
(OC) pesticide, chlordecone (CD), stimulated biliary excretion of exogenous CH up to 3-fold. Increased biliary excretion occurred without changes in hepatic ATP-binding
cassette transporter G8 (ABCG8) of the bile canaliculus or scavenger receptor class B
type I (SR-BI)...
Tsunami force and pressure distributions on a rigid
wall fronted by a small seawall were determined experimentally
in a large-scale wave flume. Six different
seawall heights were examined, two of which were exposed
to a range of solitary wave heights. The same
experiment was done without a seawall for comparison....
A definition is suggested for affine symmetry tensors, which generalize the notion of affine vectors in the same way that (conformal) Killing tensors generalize (conformal) Killing vectors. An identity for these tensors is proven, which gives the second derivative of the tensor in terms of the curvature tensor, generalizing a...
The eastern South Pacific (ESP) oxygen minimum zone (OMZ) is a permanent hydrographic feature located directly off the coasts of northern Chile and Peru. The ESP OMZ reaches from coastal waters out to thousands of kilometers offshore, and can extend from the near surface to depths greater than 700 m....
Recent work by S. Lentz et al. documents offshore transport in the inner shelf due to a wave-driven return
flow associated with the Hasselmann wave stress (the Stokes–Coriolis force). This analysis is extended using
observations from the central Oregon coast to identify the wave-driven return flow present and quantify the...
Observations, primarily from satellites, have shown a statistical relationship between the surface wind stress and underlying sea surface temperature (SST) on intermediate space and time scales, in many regions inclusive of eastern boundary upwelling current systems. In this paper, this empirical SST–wind stress relationship is utilized to provide a simple...
Successfully shifting to a more piscivorous diet may be an important factor in the growth and survival of juvenile coho salmon Oncorhynchus kisutch and Chinook salmon O. tshawytscha during their first summer in the northern California Current. Nonmetric multidimensional scaling and cluster analysis of diets by size showed several distinct...
Surface tensions of high-salinity solutions are significantly different from those of pure water. Our objective was to develop and test a methodology to determine whether these surface tension effects predictably alter imbibition into dry and moist porous media. Static and dynamic experiments were performed using four grades of quartz sand...
This work compares the Weather Research and Forecasting (WRF) and Hadley Centre Regional Model (HadRM) simulations with the observed daily maximum and minimum temperature (Tmax and Tmin) and precipitation at Historical Climatology Network (HCN) stations over the U.S. Pacific Northwest for 2003–07. The WRF and HadRM runs were driven by...
Analytical methods capable of trace measurement of semi-volatile organic
compounds (SOCs) are necessary to assess the exposure of tadpoles to contaminants as a
result of long-range and regional atmospheric transport and deposition. The following
study compares the results of two analytical methods, one using pressurized liquid
extraction (PLE) and the...
A reexamination of turbulence dissipation measurements from the equatorial Pacific shows that the turbulence diffusivities are not a simple function of the gradient Richardson number. A widely used mixing scheme, the K-profile parameterization, overpredicts the turbulent vertical heat flux by roughly a factor of 4 in the stably stratified region...
Field trials in four distinct agricultural soils were conducted to examine changes to total recoverable and labile soil Cd and Ni concentrations with applications of commercial phosphate fertilizers. The edible portion of wheat and potato crops grown at the field plots were analyzed for recoverable Cd and Ni. Total recoverable...
To directly determine mortality and predation in the endangered western Steller sea lion Eumetopias jubatus, we deployed implanted, satellite-linked post-mortem data transmitters in 21 juveniles. Data recovered from 4 of 5 detected mortalities exhibited precipitous drops in ambient temperatures followed by immediate onset of transmissions (N = 3), or gradual...
"... One goal of this document is to synthesize the literature on the effects of mechanical thinning on understory plant species. A second goal is to document the effect of prescribed burning on rare, threatened, or endangered species. We review current literature on studies that address effects of prescribed fire...
Cadmium is a common impurity in phosphatic fertilizers and may contribute to soil Cd accumulation. Changes in total and bioavailable Cd burdens to agricultural soils and the potential for plant Cd accumulation resulting from fertilizer input was investigated. Three year field studies were conducted using three dose levels of cadmium-rich,...
Fluctuations of the low frequency sound field in the presence of an internal solitary wave packet during the Shallow Water ’06 experiment are analyzed. Acoustic, environmental, and on-board ship radar image data were collected simultaneously before, during, and after a strong internal solitary wave packet passed through the acoustic track....
Chemical and biological sensor technologies have advanced rapidly in the past five years. Sensors that require low power and operate for multiple years are now available for oxygen, nitrate, and a variety of bio-optional properties that serve as proxies for important components of the carbon cycle (e.g., particulate organic carbon)....
Applying concepts from the behavioral complexity literature (Ashby, 1952; Denison, Hooijberg, and Quinn, 1995) we examine if supply managers’ multiple roles and the ability to shift among these roles is related to their interpersonal relationship with their key contact within the strategic suppliers’ organization and ultimately with the firm-to-firm relationship....
The predictability of coastal ocean circulation over the central Oregon shelf, a region of strong wind-driven
currents and variable topography, is studied using ensembles of 50-day primitive equation ocean model
simulations with realistic topography, simplified lateral boundary conditions, and forcing from both idealized
and observed wind time series representative of...
The materiality and neutrality of neutral density and several forms of orthobaric density are calculated and compared using a simple idealization of the warm-sphere water mass properties of the Atlantic Ocean. Materiality is the value of the material derivative, expressed as a quasi-vertical velocity, following the motion of each of...
The synthesis of isoindazoles bearing α-ketoester and α-hydroxyester groups via the coarctate cyclization of ester terminated azo-ene-yne precursors is described. Whereas previous studies on isoindazole formation have shown the reaction to proceed through a kinetic coarctate pathway, functionalization of the terminal acetylene with a methyl ester sufficiently stabilizes the carbene...
Multiplicative random cascades (MRCs) can parsimoniously generate highly intermittent patterns similar to those in rainfall. The elemental MRC model parameter is the cascade weight, which determines how rainfall at one scale is partitioned at the next smallest scale in the cascade. While it is known that the probability density of...
Lipid classes, fatty acids (FAs), and stable carbon isotopes of FAs were used to investi-
gate dietary sources of organic carbon for juvenile Atlantic cod
Gadus morhua
during settlement into
eelgrass
Zostera marina
. Primary producers, epibenthic prey, zooplankton, and fish were collected
from August to November 2002 in shallow...
Objective: Millions of US households experienced food insecurity in 2005.
Research indicates that low wages and little social support contribute to food
insecurity. The present study aimed to examine whether social support moderates
the relationship between income and food insecurity.
Design: Using a mail survey, we collected data on social...
The spatial and temporal variability of inner-shelf circulation along the central Oregon coast during the
2004 upwelling season is described using a 70-km-long array of moorings along the 15-m isobath. Circulation
at three stations located onshore of a submarine bank differed from that of a station north of the bank,...
Horizontal ice-core sites, where ancient ice is exposed at the glacier surface, offer unique opportunities for paleo-studies of trace components requiring large sample volumes. Following previous work at the Pâkitsoq ice margin in West Greenland, we use a combination of geochemical parameters measured in the ice matrix (δ¹⁸O[subscript ice]) and...
This is the synthesis of a series of studies to evaluate perceptions of U.S. Department of Agriculture Forest Service (USFS) law enforcement and investigations (LEI). Five groups were evaluated: four groups of employees from different positions within LEI, and a group of customers of LEI, the line officers of the...
The zebrafish has become an important model for cancer research. Several cancer models have
been established by transgenic expression of human or mouse oncogenes in zebrafish. Since it is
amenable to efficient transgenesis, zebrafish have immense potential to be used for studying
interaction of oncogenes and pathways at the organismal...
The nature of the teleconnection linking ENSO variability with Atlantic basin tropical storm formation is investigated. Solutions of the linearized barotropic vorticity equation forced with August–October El Niño event divergence produce upper-tropospheric vorticity anomalies over the Sahel and at the mouth of the North African–Asian (NAA) jet over the tropical...
The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA
populations. However, these methods have been limited by several factors, including representational artifacts and lack of
established statistical methods of analysis. Furthermore, massive HTS data sets present new problems related to data processing
and...
The dependence of mixing efficiency on time-varying forcing is studied by direct numerical simulation
(DNS) of Kelvin–Helmholtz (KH) instability. Time-dependent forcing fields are designed to reproduce a
wavelike oscillation by solving the equations of motion in a tilted coordinate frame and allowing the tilt angle
to vary in time. Mixing...
After hatchery-reared salmonids are released into the wild, their survival and performance are
frequently lower than those of wild conspecifics. Additionally, negative effects of hatchery fish on wild fish are cited as factors affecting the recovery of salmonid populations. Alternative hatchery rearing environments and release practices have been proposed to...
A snowpack model sensitivity study, observed changes of snow cover in the NOAA satellite dataset, and snow cover simulations from the Coupled Model Intercomparison Project phase 3 (CMIP3) multimodel dataset are used to provide new insights into the climate response of Northern Hemisphere (NH) snow cover. Under conditions of warming...
The Library of Congress (LC) decided to suspend creating series authority records on May 1, 2006 and to transcribe all future series statements as untraced. To evaluate the impact on cataloging workload at Oregon State University (OSU), bibliographic records were examined for untraced series statements from June 1, 2006 to...
Little is known about how people living with HIV in low prevalence contexts face the challenges of stigma and
discrimination. Low prevalence and rural communities are unique environments in which HIV-related stigma
and discrimination may be intensified due to lower tolerance of differences among people and greater fear of
HIV....
The potential for moisture sorption by boron and fluoride rods following application of rods to wood to affect subsequent chemical diffusion was investigated in small Douglas-fir blocks conditioned to 30, 60, or 90 percent target moisture content (MC). MCs tended to decline over the 180-day test period, but there was...
The temporal response of the length of a partially mixed estuary to changes in freshwater discharge Q𝒻 and
tidal amplitude Uₜ is studied using a 108-day time series collected along the length of the Hudson River
estuary in the spring and summer of 2004 and a long-term (13.4 yr) record...
Influenza A incidence peaks during winter in temperate regions. The basis for this pronounced seasonality is not understood, nor is it well documented how influenza A transmission principally occurs. Previous studies indicate that relative humidity (RH) affects both influenza virus transmission (IVT) and influenza virus survival (IVS). Here, we reanalyze...
Chromosomal rearrangements may complicate construction of Arabidopsis with multiple TDNA-insertion mutations. Here, crossing two lines homozygous for insertions in AtREV3 and AtPOLH (chromosomes I and V, respectively) and selfing F1 plants yielded non-Mendelian F2 genotype distributions: frequencies of +/++/+ and 1/1 2/2 progeny were only 0.42 and 0.25%. However, the...
Hop (Humulus lupulus L.) is cultivated for the female flowers, or “cones,” which traditionally have been used as a bittering and flavoring agent in beer. Hop breeding historically relied on relatively simple selection techniques within established breeding lines. Supplementing current breeding material with new genetic sources would enhance a hop...
Observations off the New Jersey coast document the shoaling of three groups of nonlinear internal waves of depression over 35 km across the shelf. Each wave group experienced changing background conditions along its shoreward transit. Despite different wave environments, a clear pattern emerges. Nearly symmetric waves propagating into shallow water...
The Oregon 4-H Carcass of Merit Program offers recognition to Oregon State University Extension 4-H members who breed and/or buy, feed, and raise animals whose carcasses meet the “ideal” for red meat: lean, early maturing, high yielding, and containing minimal external fat. This
publication was prepared for 4-H leaders and...
The event-scale variability of across-shelf transport was investigated using observations made in 15 m of
water on the central Oregon inner shelf. In a study area with intermittently upwelling-favorable winds and
significant density stratification, hydrographic and velocity observations show rapid across-shelf movement of
water masses over event time scales of...
Land-associated, sound-scattering layers of mesopelagic micronekton surround the Hawaiian Islands. These animals undergo diel
migrations during which they split into multiple, distinct layers that have differences in animal density, taxonomic composition,
and size. A video-camera system capable of quantitatively estimating the biological constituency of the layers was combined with
a...
Ceratomyxa shasta is a myxozoan parasite identified as a contributor to salmon mortality in the Klamath River, USA. The parasite has a complex life cycle involving a freshwater polychaete, Manayunkia speciosa and a salmonid. As part of ongoing research on how environmental parameters influence parasite establishment and replication, we designed...
Raman spectra distributed temperature sensing (DTS) by fiber-optic cables has
recently shown considerable promise for the measuring and monitoring of surface and
near-surface hydrologic processes such as groundwater–surface water interaction,
borehole circulation, snow hydrology, soil moisture studies, and land surface energy
exchanges. DTS systems uniquely provide the opportunity to monitor...
Epitaxial LaRh₁/₂Mn₁/₂O₃ thin films have been grown on (001)-oriented LaAlO₃ and SrTiO₃ substrates using pulsed laser deposition. The optimized thin film samples are semiconducting and ferromagnetic with a Curie temperature close to 100 K, a coercive field of 1200 Oe, and a saturation magnetization of 1.7μB per formula unit. The...
Optical closure is essential for the determination of biogeochemical properties from ocean color remote sensing information. Mie scattering theory, a radiative transfer model, and a semi-analytical inversion algorithm were used to investigate the influence of particles and their properties on optical closure. Closure results were generally poor. Absorption coefficient (at)...
The forces exerted on light-frame wood buildings as a result of surge and waves are not fully understood. With a better understanding of these types of forces, it may eventually be possible to build coastal structures to better withstand the loads. In this paper, a recent two part experimental study...
We investigated the response of hyporheic exchange flow (HEF) to wood removal in a small, low-gradient, gravel bed stream in southeast Alaska using a series of groundwater models built to simulate HEF for the initial conditions immediately after wood removal and 1 month, 2 years, 4 years, and 16 years...
Primula sect. Parryi comprises five species endemic to western North America: P. parryi, P. angustifolia, P. rusbyi, P. capillaris, and P. cusickiana with four varieties. This section, derived from a clade with representatives in Asia and Europe, exemplifies a phytogeographic pattern in which a widespread species is accompanied by multiple...
The placement of ‘Pseudomonas butanovora’ in the genus Thauera was proposed previously, based on 16S rRNA gene sequence analysis, upon further studies of taxonomical characteristics. In this study, physiological characteristics and DNA–DNA reassociation data are presented and the transfer of ‘P. butanovora’ to the genus Thauera is proposed. The original...
In Fall 2006, a faculty member in George Washington University's University Writing 20 (UW20) program began incorporating service learning into her theme-based first-year writing course. Along with her librarian partner, they linked two research assignments to the service work of the students. An end-of-semester survey was administrated over three semesters...
This study evaluates the impacts of sea surface temperature (SST) specification and grid resolution on numerical simulations of air–sea coupling near oceanic fronts through analyses of surface winds from the European Centre for Medium-Range Weather Forecasts (ECMWF) model. The 9 May 2001 change of the boundary condition from the Reynolds...
The global biogeochemical cycle of methane has received wide attention because of methane's role as a greenhouse gas. Measurements of methane in air trapped in Greenland ice cores provide a high-resolution record of methane levels in the atmosphere over the past ~100 ka, providing clues about what controls the methane...
In the blink of an eye, unconscious bias was visible to me, an African American. A man saw my face as I walked into the store and unconsciously checked his wallet. On the street, a woman catches my eye a half block away and moves her purse from the handle...
Oregon State University has trained paraprofessionals to assign subject headings to theses and dissertations. This article describes the training program for the paraprofessionals and the ongoing support provided by weekly meetings to discuss works that are difficult to analyze. The transition from copy cataloging to subject analysis is a major...
Yutian (Cry to Heaven) is the third Chinese stage adaptation of Harriet Beecher Stowe’s novel Uncle Tom’s Cabin between 1907 and 2007. The first, Heinu yutian lu (Black Slave’s Cry to Heaven) by Zeng Xiaogu, was staged by Chinese students in Tokyo in 1907; the second, Heinu hen (Regret of...
The diel feeding periodicity of juvenile Chinook salmon Oncorhynchus tshawytscha was determined from stomachs collected in coastal waters off Oregon in 2000 and 2003. Juvenile Chinook salmon exhibited a diurnal feeding pattern with morning and evening feeding periods. There were differences in the duration and magnitude of the dawn and...
Measurement of soil hydraulic retention and conduction parameters using tension infiltrometers has been found to be useful but has suffered from unreliable instrument membranes at the soil interface and the need for manual control, which limits the range of boundary conditions that can feasibly be established. An automated design is...
The most important step in deciding whether to start a vineyard is to learn as much as possible about vineyard establishment, vine growth and development, and requirements of vineyards. Considerations include vine
physiology, vineyard inputs, and crop management. By having some understanding of winegrape production, you can avoid many mistakes...
Dynein light chain LC8 is a small, dimeric, and very highly conserved globular protein that is an integral part of the dynein and myosin molecular motors but appears to have a broader role in multiple protein complexes unrelated to molecular motors. LC8 binds to two families of targets: those having...
A method for measuring whole-tree interception of precipitation is presented which employs mechanical displacement sensors to measure trunk compression caused by the water captured by the tree. This direct and nondestructive method is demonstrated to be sensitive to less than 5 kg of interception field tests in Netherlands and Ghana.
Varied observations over Oregon’s continental shelf illustrate the
beauty and complexity of geophysical flows in coastal waters. Rapid, creative, and
sometimes fortuitous sampling from ships and moorings has allowed detailed looks
at boundary layer processes, internal waves (some extremely nonlinear), and coastal
currents, including how they interact. These processes drive...
Snowpack base temperatures vary during accumulation and diurnally. Their measurement
provides insight into physical, biological and chemical processes occurring at the snow/soil interface.
Recent advances in Raman-spectra instruments, which use the scattered light in a standard
telecommunications fiber-optic cable to infer absolute temperature along the entire length of the fiber,...
Fatty acid esters extractable from the surface of honey bee, Apis mellifera L. (Hymenoptera: Apidae), larvae, called brood pheromone, significantly increase rate of colony growth in the spring and summer when flowering plant pollen is available in the foraging environment. Increased colony growth rate occurs as a consequence of increased...
One common assumption in interpreting ice-core CO₂ records is that diffusion in the ice does not affect the concentration profile. However, this assumption remains untested because the extremely small CO₂ diffusion coefficient in ice has not been accurately determined in the laboratory. In this study we take advantage of high...
Earth's climate and the concentrations of the atmospheric greenhouse gases carbon dioxide (CO2) and nitrous oxide (N2O) varied strongly on millennial timescales during past glacial periods. Large and rapid warming events in Greenland and the North Atlantic were followed by more gradual cooling, and are highly correlated with fluctuations of...
Global seasonal cycles of the wind and wind stress fields estimated from the 8-yr record (September 1999–August 2007) of wind measurements by the NASA Quick Scatterometer (QuikSCAT) are presented. While this atlas, referred to here as the Scatterometer Climatology of Ocean Winds (SCOW), consists of 12 variables, the focus here...
The term “downwelling currents” refers to currents with a downslope mass flux in the bottom boundary layer. Examples are the Malvinas and Southland Currents in the Southern Hemisphere and the Oyashio in the Northern Hemisphere. Although many of these currents generate the same type of highly productive ecosystems that is...
A high-resolution primitive equation model simulation is used to form an energy budget for the principal semidiurnal tide (M₂) over a region of the Hawaiian Ridge from Niihau to Maui. This region includes the Kaena Ridge, one of the three main internal tide generation sites along the Hawaiian Ridge and...
In order to better understand the general problem of satellite cloud top height retrievals for low clouds, observations made by NOAA research vessels in the stratocumulus region in the southeastern Pacific during cruises in 2001 and 2003 to 2006 were matched with near-coincident retrievals from the Moderate Resolution Imaging Spectroradiometer...
Preliminary results are presented from an analysis of mid-frequency acoustic transmission data collected at range 550m during the Shallow Water 2006 Experiment. The acoustic data were collected on a vertical array immediately before, during, and after the passage of a nonlinear internal wave on 18 August, 2006. Using oceanographic data...
Many industrially important reactions use immobilized enzymes in non-aqueous, organic
systems, particularly for the production of chiral compounds such as pharmaceutical precursors.
The addition of a spacer molecule (“tether”) between a supporting surface and enzyme often
substantially improves the activity and stability of enzymes in aqueous solution. Most “long”
linkers...
Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for...
Pesticides, including insecticides, acaricides, fungicides, bactericides, and herbicides are essential for maintaining healthy grape crops with reliable
yields and quality. In many instances, pesticides have become less effective as target organisms have developed resistance. The first record of resistance dates to 1897, when orchardists began having problems controlling San Jose...