Influences of tidal and slower (subtidal) oceanic flows over the continental shelf and slope off Oregon are studied using a high-resolution ocean circulation model and comparative model-data analyses. The model is based on the Regional Ocean Modeling System (ROMS), a fully nonlinear, three-dimensional model (using hydrostatic and Boussinesq approximations). The...
Currently, forecasts produced by the Oregon-Washington (OR-WA) Coastal Ocean Forecast System are constrained by assimilation of only surface observations. The 4-dimensional variational (4DVAR) data assimilation (DA) algorithm is utilized to combine the model and the data, with the time-independent forecast ("background'') error covariance B. In this study, two possible improvements...
We examined high-resolution cross-shelf distributions of particulate organic carbon
(POC) and dissolved O₂ during the upwelling season off the Oregon coast. Oxygen
concentrations were supersaturated in surface waters, and hypoxic in near-bottom
waters, with greatly expanded hypoxic conditions late in the season. Simplified time-dependent
mass balances on cross-shelf integrated concentrations...
Sea surface temperature (SST) is a critical control on the atmosphere(1), and numerical models of atmosphere-ocean circulation emphasize its accurate prediction. Yet many models demonstrate large, systematic biases in simulated SST in the equatorial 'cold tongues' (expansive regions of net heat uptake from the atmosphere) of the Atlantic(2) and Pacific(3)...
Barotropic tidal currents flowing over rough topography may be slowed by two bottom boundary–related processes: tangential stress of the bottom boundary layer, which is generally well represented by a quadratic drag law, and normal stress from bottom pressure, known as form drag. Form drag is rarely estimated from oceanic observations...
Directly wind-coherent near-inertial surface currents off the Oregon coast are investigated with a statistical parameterization of observations and outputs of a regional numerical ocean model and three one-dimensional analytical models including the slab layer, Ekman, and near-surface averaged Ekman models. The
transfer functions and response functions, statistically estimated from observed...
We measured iron concentrations off the Oregon coast in spring (May–June) and summer (August) of 2001 as part of the Coastal Ocean Advances in Shelf Transport (COAST) program. Dissolvable and total dissolvable iron levels in surface waters were generally higher in spring (mean of 2.1 and 33.9 nmol L¯¹, respectively)...
Measurements of suspended sediment concentration, velocity, salinity, and turbulent
microscale shear in the near-field region of the Columbia River plume are used to investigate
the mechanisms of sediment resuspension and entrainment into the plume. An east-west
transect was occupied during spring and neap tide periods in August 2005 and May...
Horizontal current measurements from an array of moored acoustic Doppler profilers are assimilated sequentially into a model of coastal wind-driven circulation off Oregon during the upwelling season of May–August 2001. Model results are compared against independent moored and ship survey data to document a positive effect of velocity data assimilation...
The Oregon Coastal Transition Zone (OCTZ) extends several hundred
kilometers offshore where shelf flows interact with the northern California Current. A
primitive-equation numerical ocean model is used to study the upwelling circulation in this
region from 1 May to 1 November 2001. This OCTZ model obtains initial and boundary
conditions...
In this study, uncoupled and coupled ocean–atmosphere simulations are carried out for the California Upwelling System to assess the dynamic ocean–atmosphere interactions, namely, the ocean surface current feedback to the atmosphere. The authors show the current feedback, by modulating the energy transfer from the atmosphere to the ocean, controls the...
Mixia osmundae (Basidiomycota, Pucciniomycotina) represents a monotypic class containing
an unusual fern pathogen with incompletely understood biology. We sequenced and analyzed
the genome of M. osmundae, focusing on genes that may provide some insight into its
mode of pathogenicity and reproductive biology.
Mixia osmundae has the smallest plant pathogenic basidiomycete...
Full Text:
, Timothy Y. James3, Katherine L. Lazarus3, Bernard Henrissat4,
Sebastian Albu5, Alexander Boyd6, Julianna
A single nonlinear internal wave tracked more than 100 wavelengths across Oregon’s continental shelf over a 12-h period exhibited nearly constant wave speed, c = 0.75 m s⁻¹, and amplitude, a = 15 m. The wavelength L gradually decreased from 220 m in 170-m water depth to 60 m in...
A sequence of three internal solitary waves of
elevation were observed propagating shoreward along a
near-bottom density interface over Oregon’s continental
shelf. These waves are highly turbulent and coincide with
enhanced optical backscatter, consistent with increased
suspended sediments in the bottom boundary layer. Nonlinear
solitary wave solutions are employed to...
A low-power (<10 mW), physically small (15.6 cm long × 3.2 cm diameter), lightweight (600 g Cu; alternatively, 200 g Al), robust, and simply calibrated pitot-static tube to measure mean speed and turbulence dissipation (ε ) is described and evaluated. The measurement of speed is derived from differential pressure via...
Highly resolved pressure measurements on the seafloor over New Jersey’s continental shelf reveal the pressure signature of nonlinear internal waves of depression as negative pressure perturbations. The sign of the perturbation is determined by the dominance of the internal hydrostatic pressure (p⁰Wh) due to isopycnal displacement over the contributions of...
Full Text:
Emily Shroyer, Sam Kelly, and Greg Avi-
cola for help in obtaining the data, to AlexanderPerlin
for
In the northern California Current, the onset of the 2005
upwelling season was five weeks later than usual, and well established
upwelling with a cold surface signature did not
occur until about seven weeks after this. As part of the joint
US-Canada Pacific hake survey, from 14–16 July 2005 we...
Results from a model of wind-driven circulation are analyzed to study spatial and temporal variability in
the bottom mixed layer (BML) on the mid-Oregon shelf in summer 2001. The model assimilates acoustic
Doppler profiler velocities from two cross-shore lines of moorings 90 km apart to provide improved
accuracy of near-bottom...
In this investigation the addition of hydrogen bromide
to 3-methylcyclohexene has been studied in order to see if
the theory of hyperconjugation could be extended to include
olefins of this type. Since the olefin has an equal number
of hydrogens on both carbons carrying the double bond, a
mixture of...
Comprehensive observations of velocity, density, and
turbulent dissipation permit quantification of the nonlinear
internal wave (NLIW) contribution to vertical heat flux and
lateral mass transport over New Jersey’s shelf. The effect of
NLIWs on the shelf heat budget was significant. On
average, heat flux in NLIWs was 10 times larger...
In 2005, the onset of spring conditions in the physics
of the coastal ocean (lowered sea level, spin-up of
vertically-sheared equatorward coastal jet) came about 50
days later than average off Newport Oregon, on May 24.
There was a further delay of 50 days before the subsurface
upwelled water penetrated...
Comprehensive observations of velocity, density, and
turbulent dissipation permit quantification of the nonlinear
internal wave (NLIW) contribution to vertical heat flux and
lateral mass transport over New Jersey’s shelf. The effect of
NLIWs on the shelf heat budget was significant. On
average, heat flux in NLIWs was 10 times larger...
Regional ocean circulation along the Oregon coast is studied numerically for forcing fields derived from year 2005 and climatological-mean conditions. The primary object is to study directly the Lagrangian pathways by which fluid arrives in the Oregon upwelling zone. Roughly half of the upwelling fluid is found to arrive in...
A sharp temperature front, oriented along the south-west corner of the leading edge of a Tropical Instability Wave (TIW) warm trough, was encountered at 0°N, 140°W on November 2, 2008 and detected by a 0.45°C increase in SST that occurred over 7 s. The distinct SST signal was observed at...
Extended measurements of temperature fluctuations that include the turbulence wavenumber band have now been made using rapidly sampled fast thermistors at multiple depths above the core of the Equatorial Undercurrent on the Tropical Atmosphere Ocean (TAO) mooring at 0°, 140°W. These measurements include the signature of narrowband oscillations as well...
Transportation infrastructure provides a vital service for the functionality of a
city. The efficient design of road networks poses an interesting topic in computer
science for digital content developers. For civil engineers, the visualization of
analysis results on infrastructure both efficiently and intuitively is crucial. The
following contributions are made...
A new theory of shear instability in a turbulent environment is applied to eight days of velocity and density profiles from the upper-equatorial Pacific. This period featured a regular diurnal cycle of surface forcing, together with a clear response in upper-ocean mixing. During the day, a layer of stable stratification...
Strong modulation of turbulent mixing by a westward-propagating tropical instability wave (TIW) was observed in the stratified shear layer between the equatorial undercurrent (EUC) and the surface mixed layer during October and November 2008 at 0°N 140°W. The unique deep diurnal-cycle mixing in the stratified layer beneath the equatorial cold...
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...
Vaned, internally recording instruments that measure temperature fluctuations using FP07 thermistors, including fluctuations in the turbulence wavenumber band, have been built, tested, and deployed on a Tropical Atmosphere Ocean (TAO) mooring at 0°, 140°W. These were supplemented with motion packages that measure linear accelerations, from which an assessment of cable...
Since the end of the Cold War, the US Navy has had an increasing interest in continental shelves and slopes as
operational areas. To work in such areas
requires a good understanding of ocean
acoustics, coastal physical oceanography,
and, in the modern era, autonomous
underwater vehicle (AUV) operations.
Each area...
The properties and evolution of nonlinear internal waves (NLIWs) depend
upon the background conditions within which waves form, propagate, and dissipate. As a result, the NLIW field on the New Jersey shelf displayed dramatic variability during the Shallow Water 2006 experiment. Wave variability was exhibited by 1) amplitudes that ranged...
Childhood cancers are rare diseases that affect 188 children in Texas for every million born. Leukemia is the most common childhood cancer and accounts for roughly one third of childhood cancer cases. However, it is estimated that only 10% of childhood cancer cases can be explained by known risk factors....
Packets of nonlinear internal waves (NLIWs) in a small area of the Mid-Atlantic Bight were 10 times more energetic during a local neap tide than during the preceding spring tide. This counterintuitive result cannot be explained if the waves are generated near the shelf break by the local barotropic tide...
As currents flow over rough topography, the pressure difference between the up-and downstream sides results in form drag-a force that opposes the flow. Measuring form drag is valuable because it can be used to estimate the loss of energy from currents as they interact with topography. An array of bottom...
The energetics of large amplitude, high-frequency nonlinear internal waves (NLIWs) observed over the New Jersey continental shelf are summarized from ship and mooring data acquired in August 2006. NLIW energy was typically on the order of 10⁵ Jm⁻¹, and the wave dissipative loss was near 50 W m⁻¹. However, wave...
Ship and mooring data collected off the coast of New Jersey are used to describe the nonlinear internal wave (NLIW) field and the background oceanographic conditions that formed the waveguide on the shelf. The subinertial, inertial, and tidal circulation are described in detail, and the background fluid state is characterized...
We use density and microstructure data to characterize the properties and physical setting of optical thin layers observed over the New Jersey shelf in the summer of 2006. Layers were differentiated into two types by their vertical position in the water column, fluorescence intensity, and possibly community composition or cell...
Clouds and the Earth’s Radiant Energy System (CERES) uses a suite of instruments on the Terra and Aqua satellites combined with analyzed weather data and information on surface conditions to estimate surface radiative fluxes. CERES estimates for the Terra satellite were compared with measurements of the surface radiative fluxes collected...
Shoreward propagating, mode 2 nonlinear waves appear sporadically in mooring records obtained off the coast of New Jersey in the summer of 2006. Individual mode 2 packets were tracked between two moorings separated by 1 km; however, packets could not be tracked between moorings separated by greater distances from one...
Shore-based video remote sensing is used to observe and continually monitor nonlinear internal waves
propagating across the inner shelf. Month-long measurements of velocity from bottom-mounted acoustic
Doppler current profilers and temperature from thermistor chains at the 10- and 20-m isobaths are combined
with sea surface imagery from a suite of...
Measurements of currents and turbulence beneath a geostationary ship in the equatorial Indian Ocean during a period of weak surface forcing revealed unexpectedly strong turbulence beneath the surface mixed layer. Coincident with the turbulence was a marked reduction of the current speeds registered by shipboard Doppler current profilers, and an...
Shipboard current measurements in the equatorial Indian Ocean in October and November of 2011 revealed oscillations in the meridional velocity with amplitude ~0.10 m/s. These were clearest in a layer extending from ~300 to 600 m depth and had periods near 3 weeks. Phase propagation was upward. Measurements from two...
Observations of mixing over the continental slope using a towed body reveal a great lateral extent (several kilometers) of continuously turbulent fluid within a few hundred meters of the boundary at depth 1600 m. The largest turbulent dissipation rates were observed over a 5 km horizontal region near a slope...
Horizontal tow measurements of internal waves are rare and have been largely supplanted in recent
decades by vertical profile measurements. Here, estimates of isotherm displacements and turbulence dissipation
rate from a towed vehicle deployed near Hawaii are presented. The displacement data are interpreted
in terms of horizontal wavenumber spectra of...
Surf zone eddies (f < 0.01 Hz) are important in nearshore mixing, shoreline erosion, the distribution of pollutants, and ecological processes, such as offshore transport of larvae. Surf zone eddies have traditionally been treated as two-dimensional features with horizontal length scales larger than the local water depth. Studies by Lippmann...
Background: Prenatal care (PNC) is an important preventive health service that can influence the health of the four million women who give birth annually in the United States, and the health their infants. Despite efforts to increase women’s access to PNC services, significant disparities in PNC utilization and maternal/child health...
Thorough understanding of the mechanisms controlling the temperature structure in the surface mixed layer of the ocean and, in particular, accurate values of sea surface temperature are critical for properly parameterizing air-sea heat exchange and quantifying the amount of heat redistributed below the surface. It is however difficult to obtain...
DNA microarray technology is a powerful tool for analyzing patterns in gene expression data for thousands of genes. Due to a number of systematic variations in microarray experiments, the raw gene expression data is often obfuscated by undesirable technical noises. Various normalization techniques were designed in an attempt to remove...
The growth of secondary vortices on the braids separating Kelvin–Helmholtz billows is investigated via numerical simulations. The similarity theory of Corcos & Sherman (1976) is extended to include mixing processes with Prandtl number greater than unity, and is shown to provide a useful description of the physics of the braid...
An integrated analysis of turbulence observations from four unique instrument platforms obtained over
the Hawaiian Ridge leads to an assessment of the vertical, cross-ridge, and along-ridge structure of turbulence
dissipation rate and diffusivity. The diffusivity near the seafloor was, on average, 15 times that in the
midwater column. At 1000-m...
Satellite-derived data provide the temporal means and seasonal and nonseasonal
variability of four physical and biological parameters off Oregon and Washington
(41°–48.5°N). Eight years of data (1998–2005) are available for surface chlorophyll
concentrations, sea surface temperature (SST), and sea surface height, while six years of
data (2000–2005) are available for...
An impediment to use of exotic and bioengineered trees in many places is their propensity for spread by pollen and/or seeds. Our laboratory has been using gene editing to induce mutations in floral genes as means to impart stable and reliable genetic containment when this is desirable from social (markets,...
The Columbia River delivers the greatest amount of freshwater to the coastal ocean along the U.S. Pacific coast. This freshwater forms the Columbia River plume, a mesoscale plume with significant implications on coastal ocean physical, biological, chemical, and geological processes. The plume is transported south and offshore during the upwelling...
Tide-topography coupling is important for understanding surface-tide energy loss, the intermittency of internal tides, and the cascade of internal-tide energy from large to small scales. Although tide-topography coupling has been observed and modeled for 50 years, the identification of surface and internal tides over arbitrary topography has not been standardized....
In this dissertation, a series of studies in the field of terahertz (THz) science are presented, specifically using nonlinear THz spectroscopy. We exploit huge field enhancement and subwavelength confinement in plasmonic structures. There are three distinct projects which will be discussed: nonlinear THz spectroscopy using plasmonic induced transparency (PIT), THz-triggered...
A carefully calibrated primitive-equation model from 41°N to 48°N is used to study the poleward undercurrent off the US west coast. Chapter 2 describes poleward flow over the slope from Eulerian and Lagrangian perspectives. The model is robust, in the sense of several characteristics being qualitatively consistent with observational and...
Automatic painterly rendering systems have been proposed but they opted for selecting a single style to generate paintings from images, which lacks the ability of creatively using multiple styles to focus important objects and deemphasize unimportant part of the scenes. We provide a multi-style painting framework to
address this issue...
Declarative visual programming languages (VPLs), including spreadsheets, make up a large portion of both research and commercial VPLs. Spreadsheets in particular enjoy a wide audience, including end users. Unfortunately, spreadsheets and most other declarative VPLs still suffer from some of the problems that have been solved in other languages, such...
Changes in climate caused by increased concentrations of carbon dioxide (CO₂) in the Earth’s atmosphere have led land and ocean surface temperatures to increase by 0.85°C and sea level to increase by 19 cm relative to preindustrial times. Global climate change will lead to further alterations in mean temperature and...
Continental shelves located along eastern boundary currents occupy relatively small volumes of the world’s oceans, yet are responsible for a large proportion of global primary production. The Oregon coast is among these ecosystems. Recent analyses of dissolved oxygen at shallow depths in the water column has suggested increasing episodes of...
This dissertation investigates the dynamics of the tidally modulated outflow from the Columbia River mouth using high resolution measurements of velocity, density and turbulent microstructure. At high tide, flow through the river mouth reverses from flood (onshore) to ebb (offshore). During ebb, buoyant fluid issues from the river mouth and...
Two research questions are posed: (1) How have ecosystem conditions changed through time in southwestern Oregon? (2) How have culture-driven and climate-driven processes contributed to ecosystem change in southwestern Oregon? A brief introduction to the Little River study area is followed by a cultural and ecological history of the watershed....
Rhizopogon vesiculosus is a common ectomycorrhizal (EM) symbiont of Pseudotusga menziesii (Douglas-fir) in the coast range of the Pacific Northwest. The species has been studied for its systematics, genet size, population structure, and competitive ability in several field and experimental studies. This thesis seeks to provide a more thorough characterization...
Analogous to ocean surface waves, waves in the ocean interior also experience steepening, breaking, and dissipation as they approach the coastline. Much less is known about this internal beach. In this work, extensive moored Acoustic Doppler Current Profiler and temperature/salinity data together with optical remote sensing are combined to describe...
Internal waves and tides are a dominant source of current variability, and they are intermittent and hard to predict. Internal waves can have significant variability in alongshore structure. However, previous studies on internal waves have focused primarily on their cross-shore structure and propagation. For example, while alongshore-propagating superinertial internal tides...
Obesity and metabolic syndrome (MetS) affect over 1.9 billion adults and 12.7 million youth in the US. If all of today’s obese American youth become obese adults, the total societal costs over their lifetime may exceed $1.1 trillion. We show that feeding rodents a high-fat diet supplemented with xanthohumol (XN)...
The Mars Pathfinder (MPF) arrived on the Martian surface on 4 July 1997 to become only the third successful landed mission to Mars, recording surface meteorological data intermittently over a period of 83 Martian days ("sols"). The in situ observations made by the MPF meteorology (MET) experiment were recorded at...
In eastern boundary current upwelling ecosystems, mesoscale circulation features such as eddies and upwelling filaments play a prominent role in the transfer of water and the associated plankton from the productive nearshore to the oligotrophic deep sea. The relationship between mesoscale circulation, zooplankton distributions, and the across-shelf transport of coastal...
The group of scientists that make up the Intergovernmental Panel on Climate Change found in 2007 that the warming of Earth’s climate is unequivocal and largely due to human activity. Earth’s climate has changed in the past, though the recent magnitude and pace of changes are unprecedented in human existence....
In this report, three studies are presented that utilize computations to predict transformations, identities, and properties of environmental organic molecules. Each study shows how computations can lead to models of chemical behavior. The importance of this research is rooted in the need for understanding how human behavior and health intersect...