@article {277,
	title = {Development of deep neural networks for marine mammal call detection using an open-source, user friendly tool},
	journal = {The Journal of the Acoustical Society of America},
	volume = {151},
	year = {2022},
	month = {2022/04//},
	pages = {A28},
	abstract = {As the collection of large acoustic datasets used to monitor marine mammals increases, so too does the need for expedited and reliable detection of accurately classified bioacoustic signals. Deep learning methods of detection and classification are increasingly proposed as a means of addressing this processing need. These image recognition and classification methods include the use of a neural networks that independently determine important features of bioacoustic signals from spectrograms. Recent marine mammal call detection studies report consistent performance even when used with datasets that were not included in the network training. We present here the use of DeepSqueak, a novel open-source tool originally developed to detect and classify ultrasonic vocalizations from rodents in a low-noise, laboratory setting. We have trained networks in DeepSqueak to detect marine mammal vocalizations in comparatively noisy, natural acoustic environments. DeepSqueak utilizes a regional convolutional neural network architecture within an intuitive graphical user interface that provides automated detection results independent of acoustician expertise. Using passive acoustic data from two hydrophones on the Ocean Observatories Initiative{\textquoteright}s Coastal Endurance Array, we developed networks for humpback whales, delphinids, and fin whales. We report performance and limitations for use of this detection method for each species.},
	isbn = {0001-4966},
	doi = {10.1121/10.0010547},
	url = {https://asa.scitation.org/doi/abs/10.1121/10.0010547},
	author = {Ferguson, Elizabeth L. and Sugarman, Peter and Coffey, Kevin R. and Pettis Schallert, Jennifer and Alongi, Gabriela C.}
}
@article {278,
	title = {An overview of ambient sound using Ocean Observatories Initiative hydrophones},
	journal = {The Journal of the Acoustical Society of America},
	volume = {151},
	year = {2022},
	month = {2022/03//},
	pages = {2085 - 2100},
	abstract = {The Ocean Observatories Initiative (OOI) sensor network provides a unique opportunity to study ambient sound in the north-east Pacific Ocean. The OOI sensor network has five low frequency (Fs = 200 Hz) and six broadband (Fs = 64 kHz) hydrophones that have been recording ambient sound since 2015. In this paper, we analyze acoustic data from 2015 to 2020 to identify prominent features that are present in the OOI acoustic dataset. Notable features in the acoustic dataset that are highlighted in this paper include volcanic and seismic activity, rain and wind noise, marine mammal vocalizations, and anthropogenic sound, such as shipping noise. For all low frequency hydrophones and four of the six broadband hydrophones, we will present long-term spectrograms, median time-series trends for different spectral bands, and different statistical metrics about the acoustic environment. We find that 6-yr acoustic trends vary, depending on the location of the hydrophone and the spectral band that is observed. Over the course of six years, increases in spectral levels are seen in some locations and spectral bands, while decreases are seen in other locations and spectral bands. Last, we discuss future areas of research to which the OOI dataset lends itself.},
	isbn = {0001-4966},
	doi = {10.1121/10.0009836},
	url = {https://asa.scitation.org/doi/full/10.1121/10.0009836},
	author = {Ragland, John and Schwock, Felix and Munson, Matthew and Abadi, Shima}
}
@article {281,
	title = {Particle trajectories in an eastern boundary current using a regional ocean model at two horizontal resolutions},
	journal = {Journal of Marine Systems},
	volume = {233},
	year = {2022},
	month = {2022/09/01/},
	pages = {103757},
	abstract = {Lagrangian particle tracking (LPT) models are used to study the transport and dispersal of marine organisms. In LPT studies, the accuracy of the circulation is essential for nearshore habitats of Eastern Boundary Current (EBC) regions that are areas of high productivity and economically important fisheries. We used the California Current System as an example of an EBC region, specifically the Oregon coast located in the northern California Current System because it has distinct upwelling and downwelling regimes and variable shelf width. More specifically, we developed and applied a LPT model to compare and contrast particle drift patterns during the spring transition as it is an important period for spawning. We contrasted years (2016{\textendash}18) using Regional Ocean Modeling System (ROMS) with different horizontal spatial resolutions (2~km, 250~m). Lagrangian particles experience stronger downward velocities and displacements to greater depths in the 250~m ROMS simulations that used a finer resolution bathymetry. Consequently, retention along the Oregon coast increases in the 250~m ROMS compared to the 2~km ROMS. After 10~days, 37\%{\textendash}83\% of particles forced with the 2~km ROMS remain in the model domain, compared to 61\%{\textendash}86\% of particles remaining when using the 250~m ROMS. Particles in the 250~m ROMS are advected to depth at specific times and locations for each simulated year, coinciding with the location and timing of a strong and shallow alongshore undercurrent that is not present in the 2~km ROMS. Additionally, ageostrophic dynamics close to shore, in the bottom boundary layer, and around headlands emerge in the 250~m resolution model, while they are at best poorly resolved in the 2~km resolution case. We conclude that the higher horizontal model resolution and bathymetry used in the 250~m ROMS generates well-resolved mesoscale and submesoscale features (e.g., surface, subsurface, and nearshore jet) that vary annually. These physical features are significantly different than those modeled by the 2~km model and may be responsible for these differences in particle dispersal. These results have implications for modeling the dispersal, growth, and development of coastal organisms with dispersing early life stages.},
	keywords = {coastal oceanography, Eastern boundary currents, Lagrangian particle tracking models, Oregon coast, ROMS, Spatial resolution},
	isbn = {0924-7963},
	doi = {10.1016/j.jmarsys.2022.103757},
	url = {https://www.sciencedirect.com/science/article/pii/S0924796322000586},
	author = {Wong-Ala, Jennifer A. T. K. and Ciannelli, Lorenzo and Durski, Scott M. and Spitz, Yvette}
}
@article {RN204,
	title = {Bottom boundary layer oxygen fluxes during winter on the Oregon Shelf},
	journal = {Journal of Geophysical Research - Oceans},
	year = {2021},
	type = {Journal Article},
	abstract = {In this study, lander-based eddy covariance measurements made 30 cm above a sandy seafloor are combined with ocean-observing and ship-based measurements to evaluate magnitudes of oxygen fluxes within the bottom boundary layer (BBL) during winter on the Oregon shelf. The total oxygen fluxes observed at a mid-shelf station were -12.3 {\textpm} 7.6 and -18.6 {\textpm} 16.9 mmol m-2d-1 during February 2018 and January 2019 deployments, respectively, and -51.8 {\textpm} 34.9 mmol m-2d-1 during a deployment on the inner shelf in January 2019. These mean ({\textpm}SD) flux derivations are greater than fluxes determined previously at nearly the same locations during the summer upwelling season, which points to the activation of benthic respiration by winter wave-dominated BBL dynamics. To determine the direct flux contributions (or potential bias) at wave frequencies, a phase-based method of spectral decomposition was applied to separate wave-induced and turbulence-induced components of velocity and dissolved oxygen time-series. This approach identified 25.4, 18.6, and 23.3\% of the average total EC oxygen fluxes from the three deployments as carried by waves or possibly turbulence stretched by waves. Additionally, we observed evidence of large waves regularly resuspending sediments and transporting entrained particles past the EC sensors. We apply this evidence to infer that wave frequencies must also contribute significantly to the real spectral domain of benthic oxygen fluxes and that the total fluxes of this study reflect elevated oxygen consumption rates without artifacts. This assessment may not be true for all data sets and may be dependent on wave properties and the quality and treatment of the measurements.},
	keywords = {bottom boundary layer, eddy covariance, Oregon shelf, oxygen fluxes, turbulence, waves},
	doi = {10.1029/2020jc016828},
	author = {Reimers, Clare E. and Fogaren, Kristen E.}
}
@article {RN165,
	title = {Measurement and Quality Control of MIROS Wave Radar Data at Dokdo},
	journal = {Journal of Korean Society of Coastal and Ocean Engineers},
	volume = {32},
	number = {2},
	year = {2020},
	pages = {135-145},
	type = {Journal Article},
	abstract = {Wave observation is widely used to direct observation method for observing the water surface elevation using wave buoy or pressure gauge and remote-sensing wave observation method. The wave buoy and pressure gauge can produce high-quality wave data but have disadvantages of the high risk of damage and loss of the instrument, and high maintenance cost in the offshore area. On the other hand, remote observation method such as radar is easy to maintain by installing the equipment on the land, but the accuracy is somewhat lower than the direct observation method. This study investigates the data quality of MIROS Wave and Current Radar (MWR) installed at Dokdo and improve the data quality of remote wave observation data using the wave buoy (CWB) observation data operated by the Korea Meteorological Administration. We applied and developed the three types of wave data quality control; 1) the combined use (Optimal Filter) of the filter designed by MIROS (Reduce Noise Frequency, Phillips Check, Energy Level Check), 2) Spike Test Algorithm (Spike Test) developed by OOI (Ocean Observatories Initiative) and 3) a new filter (H-Ts QC) using the significant wave height-period relationship. As a result, the wave observation data of MWR using three quality control have some reliability about the significant wave height. On the other hand, there are still some errors in the significant wave period, so improvements are required. Also, since the wave observation data of MWR is different somewhat from the CWB data in high waves of over 3 m, further research such as collection and analysis of long-term remote wave observation data and filter development is necessary.},
	keywords = {data processing, Dokdo, quality control, quality enhancement of wave data, wave and current radar},
	doi = {10.9765/kscoe.2020.32.2.135},
	url = {https://app.dimensions.ai/details/publication/pub.1127450425 http://jkscoe.or.kr/upload/pdf/jkscoe-32-2-135.pdf},
	author = {Jun, Hyunjung and Min, Yongchim and Jeong, Jin-Yong and Do, Kideok}
}
@article {RN169,
	title = {Optimal sensors placement for detecting CO2 discharges from unknown locations on the seafloor},
	journal = {International Journal of Greenhouse Gas Control},
	volume = {95},
	year = {2020},
	pages = {102951},
	type = {Journal Article},
	abstract = {Assurance monitoring of the marine environment is a required and intrinsic part of CO2 storage project. To reduce the costs related to the monitoring effort, the monitoring program must be designed with optimal use of instrumentation. Here we use solution of a classical set cover problem to design placement of an array of fixed chemical sensors with the purpose of detecting a seep of CO2 through the seafloor from an unknown location. The solution of the problem is not unique and different aspects, such as cost or existing infrastructure, can be added to define an optimal solution. We formulate an optimization problem and propose a method to generate footprints of potential seeps using an advection{\textendash}diffusion model and a stoichiometric method for detection of small seepage CO2 signals. We provide some numerical experiments to illustrate the concepts.},
	keywords = {Chemical sensors, Monitoring design, Offshore, Optimal sensor placement, Subsea CO2 seepage},
	doi = {10.1016/j.ijggc.2019.102951},
	url = {https://app.dimensions.ai/details/publication/pub.1124683604 https://doi.org/10.1016/j.ijggc.2019.102951},
	author = {Oleynik, Anna and Garc{\'\i}a-Ib{\'a}{\~n}ez, Maribel I. and Blaser, Nello and Omar, Abdirahman and Alendal, Guttorm}
}
@article {RN160,
	title = {Towards Naples Ecological REsearch for Augmented Observatories (NEREA): The NEREA-Fix Module, a Stand-Alone Platform for Long-Term Deep-Sea Ecosystem Monitoring},
	journal = {Sensors},
	volume = {20},
	number = {10},
	year = {2020},
	type = {Journal Article},
	abstract = {Deep-sea ecological monitoring is increasingly recognized as indispensable for the comprehension of the largest biome on Earth, but at the same time it is subjected to growing human impacts for the exploitation of biotic and abiotic resources. Here, we present the Naples Ecological REsearch (NEREA) stand-alone observatory concept (NEREA-fix), an integrated observatory with a modular, adaptive structure, characterized by a multiparametric video-platform to be deployed in the Dohrn canyon (Gulf of Naples, Tyrrhenian Sea) at ca. 650 m depth. The observatory integrates a seabed platform with optoacoustic and oceanographic/geochemical sensors connected to a surface transmission buoy, plus a mooring line (also equipped with depth-staged environmental sensors). This reinforced high-frequency and long-lasting ecological monitoring will integrate the historical data conducted over 40 years for the Long-Term Ecological Research (LTER) at the station {\textquotedblleft}Mare Chiara{\textquotedblright}, and ongoing vessel-assisted plankton (and future environmental DNA-eDNA) sampling. NEREA aims at expanding the observational capacity in a key area of the Mediterranean Sea, representing a first step towards the establishment of a bentho-pelagic network to enforce an end-to-end transdisciplinary approach for the monitoring of marine ecosystems across a wide range of animal sizes (from bacteria to megafauna).},
	keywords = {stand-alone observatory; optoacoustic imaging; ecological monitoring; remote data transmission; Artificial Intelligence},
	doi = {10.3390/s20102911},
	author = {Fanelli, E. and Aguzzi, J. and Marini, S. and del Rio, J. and Nogueras, M. and Canese, S. and Stefanni, S. and Danovaro, R. and Conversano, F.}
}
@article {RN67,
	title = {Better Regional Ocean Observing Through Cross-National Cooperation: A Case Study From the Northeast Pacific},
	journal = {Frontiers in Marine Science},
	volume = {6},
	year = {2019},
	pages = {93},
	type = {Journal Article},
	abstract = {The ocean knows no political borders. Ocean processes, like summertime wind-driven upwelling, stretch thousands of kilometers along the Northeast Pacific (NEP) coast. This upwelling drives marine ecosystem productivity and is modulated by weather systems and seasonal to interdecadal ocean-atmosphere variability. Major ocean currents in the NEP transport water properties such as heat, fresh water, nutrients, dissolved oxygen, pCO2, and pH close to the shore. The eastward North Pacific Current bifurcates offshore in the NEP, delivering open-ocean signals south into the California Current and north into the Gulf of Alaska. There is a large and growing number of NEP ocean observing elements operated by government agencies, Native American Tribes, First Nations groups, not-for-profit organizations, and private entities. Observing elements include moored and mobile platforms, shipboard repeat cruises, as well as land-based and estuarine stations. A wide range of multidisciplinary ocean sensors are deployed to track, for example, upwelling, downwelling, ocean productivity, harmful algal blooms, ocean acidification and hypoxia, seismic activity and tsunami wave propagation. Data delivery to shore and observatory controls are done through satellite and cell phone communication, and via seafloor cables. Remote sensing from satellites and land-based coastal radar provide broader spatial coverage, while numerical circulation and biogeochemical modeling complement ocean observing efforts. Models span from the deep ocean into the inland Salish Sea and estuaries. NEP ocean observing systems are used to understand regional processes and, together with numerical models, provide ocean forecasts. By sharing data, experiences and lessons learned, the regional ocean observatory is better than the sum of its parts.

},
	keywords = {coastal oceanography, data delivery, marine eco system, ocean model and observations comparison, Ocean observation},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00093},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00093},
	author = {Barth, John A. and Allen, Susan E. and Dever, Edward P. and Dewey, Richard K. and Evans, Wiley and Feely, Richard A. and Fisher, Jennifer L. and Fram, Jonathan P. and Hales, Burke and Ianson, Debby and Jackson, Jennifer and Juniper, Kim and Kawka, Orest and Kelley, Deborah and Klymak, Jody M. and Konovsky, John and Kosro, P. Michael and Kurapov, Alexander and Mayorga, Emilio and MacCready, Parker and Newton, Jan and Perry, R. Ian and Risien, Craig M. and Robert, Marie and Ross, Tetjana and Shearman, R. Kipp and Schumacker, Joe and Siedlecki, Samantha and Trainer, Vera L. and Waterman, Stephanie and Wingard, Christopher E.}
}
@article {RN103,
	title = {Global Perspectives on Observing Ocean Boundary Current Systems},
	journal = {Frontiers in Marine Science},
	volume = {6},
	year = {2019},
	pages = {423},
	type = {Journal Article},
	abstract = {Ocean boundary current systems are key components of the climate system, are home to highly productive ecosystems, and have numerous societal impacts. Establishment of a global network of boundary current observing systems is a critical part of ongoing development of the Global Ocean Observing System. The characteristics of boundary current systems are reviewed, focusing on scientific and societal motivations for sustained observing. Techniques currently used to observe boundary current systems are reviewed, followed by a census of the current state of boundary current observing systems globally. The next steps in the development of boundary current observing systems are considered, leading to several specific recommendations.},
	keywords = {autonomous underwater gliders, drifters, eastern boundary current systems, moorings, ocean observing systems, remote sensing, time series, western boundary current systems},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00423},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00423},
	author = {Todd, Robert E. and Chavez, Francisco P. and Clayton, Sophie and Cravatte, Sophie and Goes, Marlos and Graco, Michelle and Lin, Xiaopei and Sprintall, Janet and Zilberman, Nathalie V. and Archer, Matthew and Ar{\'\i}stegui, Javier and Balmaseda, Magdalena and Bane, John M. and Baringer, Molly O. and Barth, John A. and Beal, Lisa M. and Brandt, Peter and Calil, Paulo H. R. and Campos, Edmo and Centurioni, Luca R. and Chidichimo, Maria Paz and Cirano, Mauro and Cronin, Meghan F. and Curchitser, Enrique N. and Davis, Russ E. and Dengler, Marcus and deYoung, Brad and Dong, Shenfu and Escribano, Ruben and Fassbender, Andrea J. and Fawcett, Sarah E. and Feng, Ming and Goni, Gustavo J. and Gray, Alison R. and Guti{\'e}rrez, Dimitri and Hebert, Dave and Hummels, Rebecca and Ito, Shin-ichi and Krug, Marjorlaine and Lacan, Fran{\c c}ois and Laurindo, Lucas and Lazar, Alban and Lee, Craig M. and Lengaigne, Matthieu and Levine, Naomi M. and Middleton, John and Montes, Ivonne and Muglia, Mike and Nagai, Takeyoshi and Palevsky, Hilary I. and Palter, Jaime B. and Phillips, Helen E. and Piola, Alberto and Plueddemann, Albert J. and Qiu, Bo and Rodrigues, Regina R. and Roughan, Moninya and Rudnick, Daniel L. and Rykaczewski, Ryan R. and Saraceno, Martin and Seim, Harvey and Gupta, Alex Sen and Shannon, Lynne and Sloyan, Bernadette M. and Sutton, Adrienne J. and Thompson, LuAnne and Plas, Anja K. van der and Volkov, Denis and Wilkin, John and Zhang, Dongxiao and Zhang, Linlin}
}
@article {RN108,
	title = {Integrated Observations of Global Surface Winds, Currents, and Waves: Requirements and Challenges for the Next Decade},
	journal = {Frontiers in Marine Science},
	volume = {6},
	year = {2019},
	pages = {425},
	type = {Journal Article},
	abstract = {Ocean surface winds, currents, and waves play a crucial role in exchanges of momentum, energy, heat, freshwater, gases, and other tracers between the ocean, atmosphere, and ice. Despite surface waves being strongly coupled to the upper ocean circulation and the overlying atmosphere, efforts to improve ocean, atmospheric, and wave observations and models have evolved somewhat independently. From an observational point of view, community efforts to bridge this gap have led to proposals for satellite Doppler oceanography mission concepts, which could provide unprecedented measurements of absolute surface velocity and directional wave spectrum at global scales. This paper reviews the present state of observations of surface winds, currents, and waves, and it outlines observational gaps that limit our current understanding of coupled processes that happen at the air-sea-ice interface. A significant challenge for the coming decade of wind, current, and wave observations will come in combining and interpreting measurements from (a) wave-buoys and high-frequency radars in coastal regions, (b) surface drifters and wave-enabled drifters in the open-ocean, marginal ice zones, and wave-current interaction {\textquotedblleft}hot-spots,{\textquotedblright} and (c) simultaneous measurements of absolute surface currents, ocean surface wind vector, and directional wave spectrum from Doppler satellite sensors.},
	keywords = {absolute surface velocity, air-sea interactions, Doppler oceanography from space, ocean surface winds, surface waves},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00425},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00425},
	author = {Villas B{\^o}as, Ana B. and Ardhuin, Fabrice and Ayet, Alex and Bourassa, Mark A. and Brandt, Peter and Chapron, Betrand and Cornuelle, Bruce D. and Farrar, J. T. and Fewings, Melanie R. and Fox-Kemper, Baylor and Gille, Sarah T. and Gommenginger, Christine and Heimbach, Patrick and Hell, Momme C. and Li, Qing and Mazloff, Matthew R. and Merrifield, Sophia T. and Mouche, Alexis and Rio, Marie H. and Rodriguez, Ernesto and Shutler, Jamie D. and Subramanian, Aneesh C. and Terrill, Eric J. and Tsamados, Michel and Ubelmann, Clement and van Sebille, Erik}
}
@article {RN75,
	title = {Why Gliders Appreciate Good Company: Glider Assimilation in the Oregon-Washington Coastal Ocean 4DVAR System With and Without Surface Observations},
	journal = {Journal of Geophysical Research: Oceans},
	volume = {124},
	number = {1},
	year = {2019},
	pages = {750-772},
	type = {Journal Article},
	abstract = {Gliders are low-power autonomous underwater vehicles used to obtain oceanic measurements in vertical sections. Assimilation of glider temperature and salinity into coastal ocean circulation models holds the potential to improve the ocean subsurface structure estimate. In this study, the impact of assimilation of glider observations is studied using a four-dimensional variational (4DVAR) data assimilation and forecast system set offshore of Oregon and Washington on the U.S. West Coast. Four test cases are compared: (1) no assimilation, (2) assimilation of glider temperature and salinity data alone, (3) assimilation of the glider data in combination with the surface observations including satellite sea surface temperature, sea surface height, and high-frequency radar surface velocities, and (4) assimilation of the surface data alone. It is found that the assimilation of glider observations alone creates unphysical eddies in the vicinity of the glider transect. As a consequence, the forecast errors in the surface velocity and temperature increase compared to the case without data assimilation. Assimilation of surface and subsurface observations in combination prevents these features from forming and reduces the errors in the forecasts for the subsurface fields compared to the other three experiments. These improvements persisted in 21-day forecasts run after the last data assimilation cycle.

},
	issn = {2169-9275},
	doi = {10.1029/2018JC014230},
	url = {https://doi.org/10.1029/2018JC014230},
	author = {Pasmans, I. and Kurapov, A. L. and Barth, J. A. and Ignatov, A. and Kosro, P. M. and Shearman, R. K.}
}
@article {RN39,
	title = {The impact of wave energy converter arrays on wave-induced forcing in the surf zone},
	journal = {Ocean Engineering},
	volume = {161},
	year = {2018},
	pages = {322-336},
	type = {Journal Article},
	abstract = {An alternative metric for assessing nearshore hydrodynamic impact due to Wave Energy Converter (WEC) arrays is presented that is based on the modeled changes in alongshore radiation stress gradients in the lee of the array. The metric is developed using a previously observed relationship between measured radiation stresses and alongshore current magnitudes. Next, a parametric study is conducted using the spectral model SWAN to analyze the nearshore impact of different WEC array designs. A realistic range of array configurations, locations, and incident wave conditions are examined and conditions that generate alongshore radiation stress gradients exceeding a chosen impact threshold on a uniform beach are identified. Finally, the methodology is applied to two permitted WEC test sites to assess the applicability of the results to sites with more realistic bathymetries. For these sites, the overall trends seen in the changes in wave height, direction, and radiation stress gradients in the lee of the array are similar to those seen in the parametric study. However, interactions between the wave field and real bathymetry induce additional alongshore variability in wave-induced forcing. Results indicate that array-induced changes can exceed the natural variability up to 15\% of the time with certain array designs and locations.

},
	keywords = {Nearshore impact, Radiation stress, SWAN, Wave energy, Wave farm},
	issn = {0029-8018},
	doi = {10.1016/j.oceaneng.2018.03.077},
	url = {<Go to ISI>://WOS:000437819800026},
	author = {O{\textquoteright}Dea, A. and Haller, M. C. and Ozkan-Haller, H. T.}
}
@article {RN84,
	title = {Surfzone State Estimation, with Applications to Quadcopter-Based Remote Sensing Data},
	journal = {Journal of Atmospheric and Oceanic Technology},
	volume = {35},
	number = {10},
	year = {2018},
	pages = {1881-1896},
	type = {Journal Article},
	abstract = {A one-dimensional variational data assimilation (1DVar) method is presented based on the depth- and time-averaged alongshore-uniform surfzone wave and current equations, for simultaneous estimation of three uncertain variables: bathymetry, incident wave boundary conditions, and bed roughness. The method is validated using twin tests and in situ field observations, and its results are shown to be comparable to those of an existing ensemble-based bathymetry inversion technique. Unlike existing techniques, the ability to simultaneously estimate boundary conditions and bed roughness along with bathymetry also means the 1DVar method can produce full state estimates without the requirement for additional supporting measurements (e.g., direct measurements of the incident waves). A proof-of-concept field application is shown using observations collected from an unmanned quadcopter sensor package that measures surfzone wave height from a fixed-beam lidar range finder, and time-averaged longshore current from particle image velocimetry of drifting surface foam.},
	keywords = {Bayesian methods, Coastal flows, Data assimilation, Inverse methods, Numerical analysis/modeling, Variational analysis},
	issn = {0739-0572},
	doi = {10.1175/JTECH-D-17-0205.1},
	url = {https://doi.org/10.1175/JTECH-D-17-0205.1},
	author = {Wilson, Gregory and Berezhnoy, Stephen}
}
@article {RN33,
	title = {Temporal and Spatial Dynamics of Physical and Biological Properties along the Endurance Array of the California Current Ecosystem},
	journal = {Oceanography},
	volume = {31},
	number = {1},
	year = {2018},
	pages = {80-89},
	type = {Journal Article},
	abstract = {The coastal margin of the Pacific Northwest of the United States is a highly dynamic and productive region. Here, we use satellite, high-frequency mooring, and glider estimates of biologically relevant physical and optical variables to characterize seasonal patterns and latitudinal and cross-shore gradients in particle concentrations between the Washington and Oregon shelves. Consistent with prior research, we find that the Columbia River exerts a strong seasonal influence on the Washington shelf, but smaller coastal rivers and resuspension processes also appear important in determining particle distributions nearshore during winter across the full study region. We find fluorescence-based measurements of chlorophyll to be similar in magnitude across the two shelves over the time period examined, although the much weaker wind stresses off Washington indicate that processes other than upwelling are important determinants of chlorophyll changes in those areas, as previously suggested. These in situ observations contrast with the overall differences observed from satellite data, which consistently show higher chlorophyll concentrations off the Washington coast. This research suggests that latitudinal differences in chromophoric dissolved organic matter may be a partial explanation for perceived trends in satellite-derived chlorophyll. The observations presented are nascent; maturation of temporal and spatial coverage of OOI data sets will be necessary to more conclusively link physical forcing and biogeochemical responses.},
	issn = {1042-8275},
	doi = {10.5670/oceanog.2018.113},
	url = {<Go to ISI>://WOS:000427367300013},
	author = {Freitas, F. H. and Saldias, G. S. and Goni, M. and Shearman, R. K. and White, A. E.}
}
@article {RN34,
	title = {Warm Blobs, Low-Oxygen Events, and an Eclipse THE OCEAN OBSERVATORIES INITIATIVE ENDURANCE ARRAY CAPTURES THEM ALL},
	journal = {Oceanography},
	volume = {31},
	number = {1},
	year = {2018},
	pages = {90-97},
	type = {Journal Article},
	abstract = {The Ocean Observatories Initiative (OOI) Endurance Array in the Northeast Pacific off the coasts of Oregon and Washington is designed to measure changes in the ocean on timescales from hours to decades. The Endurance Array is located halfway between the pole and the equator in one of the major coastal upwelling systems on our planet, the California Current System. This area is forced locally by winds, waves, tides, and freshwater inputs from rivers and, more broadly, by large-scale ocean-atmosphere phenomena from both the south, for example, the El Ni{\~n}o-Southern Oscillation, and the north, for example, changes originating in the subarctic Gulf of Alaska. The Endurance Array spans the continental shelf and slope and hosts a variety of platforms and sensors for measuring physical-biogeochemical oceanographic processes. After briefly introducing the unique OOI platforms and range of sensors that make up the Endurance Array, we describe three phenomena with durations spanning hours to years. These include an ocean response to the total eclipse of the Sun on August 21, 2017, the devastating effects of a low-oxygen event off central Oregon, and the appearance of an anomalously warm upper-ocean feature off the Pacific Northwest in recent years.},
	issn = {1042-8275},
	doi = {10.5670/oceanog.2018.114},
	url = {<Go to ISI>://WOS:000427367300014},
	author = {Barth, J. A. and Fram, J. P. and Dever, E. P. and Risien, C. M. and Wingard, C. E. and Collier, R. W. and Kearney, T. D.}
}
@article {RN35,
	title = {Intraseasonal Cross-Shelf Variability of Hypoxia along the Newport, Oregon, Hydrographic Line},
	journal = {Journal of Physical Oceanography},
	volume = {46},
	number = {7},
	year = {2016},
	pages = {2219-2238},
	type = {Journal Article},
	abstract = {Observations of hypoxia, dissolved oxygen (DO) concentrations < 1.4 ml L-1, off the central Oregon coast vary in duration and spatial extent throughout each upwelling season. Underwater glider measurements along the Newport hydrographic line (NH-Line) reveal cross-shelf DO gradients at a horizontal resolution nearly 30 times greater than previous ship-based station sampling. Two prevalent hypoxic locations are identified along the NH-Line, as is a midshelf region with less severe hypoxia north of Stonewall Bank. Intraseasonal cross-shelf variability is investigated with 10 sequential glider lines and a midshelf mooring time series during the 2011 upwelling season. The cross-sectional area of hypoxia observed in the glider lines ranges from 0 to 1.41 km2. The vertical extent of hypoxia in the water column agrees well with the bottom mixed layer height. Midshelf mooring water velocities show that cross-shelf advection cannot account for the increase in outer-shelf hypoxia observed in the glider sequence. This change is attributed to an along-shelf DO gradient of -0.72 ml L-1 over 2.58 km or 0.28 ml L-1 km-1. In early July of the 2011 upwelling season, near-bottom cross-shelf currents reverse direction as an onshore flow at 30-m depth is observed. This shoaling of the return flow depth throughout the season, as the equatorward coastal jet moves offshore, results in a more retentive near-bottom environment more vulnerable to hypoxia. Slope Burger numbers calculated across the season do not reconcile this return flow depth change, providing evidence that simplified two-dimensional upwelling model assumptions do not hold in this location.},
	keywords = {Circulation/Dynamics, Coastal flows, Upwelling/downwelling},
	issn = {0022-3670},
	doi = {10.1175/Jpo-D-15-0119.1},
	author = {Adams, K. A. and Barth, J. A. and Shearman, R. K.}
}
@article {RN36,
	title = {Optics of the offshore Columbia River plume from glider observations and satellite imagery},
	journal = {Journal of Geophysical Research: Oceans},
	volume = {121},
	number = {4},
	year = {2016},
	pages = {2367-2384},
	type = {Journal Article},
	abstract = {The Columbia River (CR) is the largest source of freshwater along the U.S. Pacific coast. The resultant plume is often transported southward and offshore forming a large buoyant feature off Oregon and northern California in spring-summer{\textemdash}the offshore CR plume. Observations from autonomous underwater gliders and Moderate Resolution Imaging Spectroradiometer (MODIS) satellite imagery are used to characterize the optics of the offshore CR plume off Newport, Oregon. Vertical sections, under contrasting river flow conditions, reveal a low-salinity and warm surface layer of \~{}20{\textendash}25 m (fresher in spring and warmer in summer), high Colored Dissolved Organic Matter (CDOM) concentration, and backscatter, and associated with the base of the plume high chlorophyll fluorescence. Plume characteristics vary in the offshore direction as the warm and fresh surface layer thickens progressively to an average 30{\textendash}40 m of depth 270{\textendash}310 km offshore; CDOM, backscatter, and chlorophyll fluorescence decrease in the upper 20 m and increase at subsurface levels (30{\textendash}50 m depth). MODIS normalized water-leaving radiance (nLw(λ)) spectra for CR plume cases show enhanced water-leaving radiance at green bands (as compared to no-CR plume cases) up to \~{}154 km from shore. Farther offshore, the spectral shapes for both cases are very similar, and consequently, a contrasting color signature of low-salinity plume water is practically imperceptible from ocean color remote sensing. Empirical algorithms based on multivariate regression analyses of nLw(λ) plus SST data produce more accurate results detecting offshore plume waters than previous studies using single visible bands (e.g., adg(412) or nLw(555)).},
	issn = {21699275},
	doi = {10.1002/2015jc011431},
	url = {https://staging-ddpp.dimensions.ai/details/publication/pub.1044838771},
	author = {Sald{\'\i}as, Gonzalo S. and Kipp Shearman, R. and Barth, John A. and Tufillaro, Nicholas}
}
@article {RN52,
	title = {Anomalous Near-Surface Low-Salinity Pulses off the Central Oregon Coast},
	journal = {Sci Rep},
	volume = {5},
	year = {2015},
	pages = {17145},
	type = {Journal Article},
	abstract = {From mid-May to August 2011, extreme runoff in the Columbia River ranged from 14,000 to over 17,000 m(3)/s, more than two standard deviations above the mean for this period. The extreme runoff was the direct result of both melting of anomalously high snowpack and rainfall associated with the 2010-2011 La Ni{\~n}a. The effects of this increased freshwater discharge were observed off Newport, Oregon, 180 km south of the Columbia River mouth. Salinity values as low as 22, nine standard deviations below the climatological value for this period, were registered at the mid-shelf. Using a network of ocean observing sensors and platforms, it was possible to capture the onshore advection of the Columbia River plume from the mid-shelf, 20 km offshore, to the coast and eventually into Yaquina Bay (Newport) during a sustained wind reversal event. Increased freshwater delivery can influence coastal ocean ecosystems and delivery of offshore, river-influenced water may influence estuarine biogeochemistry.},
	issn = {2045-2322 (Electronic) 2045-2322 (Linking)},
	doi = {10.1038/srep17145},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26607750},
	author = {Mazzini, P. L. and Risien, C. M. and Barth, J. A. and Pierce, S. D. and Erofeev, A. and Dever, E. P. and Kosro, P. M. and Levine, M. D. and Shearman, R. K. and Vardaro, M. F.}
}
@article {RN37,
	title = {Dynamics of the benthic boundary layer and seafloor contributions to oxygen depletion on the Oregon inner shelf},
	journal = {Continental Shelf Research},
	volume = {84},
	year = {2014},
	pages = {93-106},
	type = {Journal Article},
	abstract = {
Outline
Highlights
Abstract
Keywords
1. Introduction
2. Material and methods
3. Results
4. Discussion
Acknowledgements
Appendix A. Supplementary materials
References
Figures (11)
Fig. 1. Bathymetric and multibeam backscatter map of study site (prepared by C
Fig. 2. Digital images of seafloor taken by BOXER camera system in (A) September 2009{\textellipsis}
Fig. 3. Stacked measurements of (A) chlorophyll-α and phaeophytin-α contents and (B){\textellipsis}
Fig. 4. Sediment formation factor (FF) and O2 microprofiles measured in situ
Fig. 5. EC time-series data from April 2009 with date and local time along the top{\textellipsis}
Fig. 6. EC time-series data from June 2009
Tables (3)
Table 1
Table 2
Table 3
Extras (1)
Supplementary material
Elsevier
Continental Shelf Research
Volume 84, 1 August 2014, Pages 93-106
Continental Shelf Research
Research papers
Dynamics of the benthic boundary layer and seafloor contributions to oxygen depletion on the Oregon inner shelf
Author links open overlay panelKristinaMcCann-GrosvenorClare E.ReimersRhea D.Sanders
https://doi.org/10.1016/j.csr.2014.05.010Get rights and content
Highlights
{\textbullet}
Eddy correlation O2 fluxes were measured in 2009 at a 30 m site off Newport, OR.

{\textbullet}
High flux contributions occurred at times at the frequencies of surface waves.

{\textbullet}
The rate of change of O2 concentration was negatively correlated with fluxes.

{\textbullet}
The benthic O2 flux was primarily into the bed (-18{\textpm}3 mmol m-2 d-1).

{\textbullet}
Inner shelf benthic O2 fluxes were 2{\textendash}5 times greater than fluxes on the mid-shelf.


Abstract
Measurement of in situ O2 consumption and production within permeable sediments, such as those found over the Oregon{\textendash}Washington inner shelf, has traditionally been done using methods that isolate the sediments from the dynamic influences of currents and wave motions. Modified from atmospheric research, the non-invasive eddy correlation technique can be used to characterize benthic boundary layer dynamics and measure O2 flux across the sediment{\textendash}water interface without excluding the natural hydrodynamic flow. In 2009, eddy correlation measurements were made in 5 discrete months with varying conditions at a 30 m site off Yaquina Head, Newport, OR. The O2 flux was found to be primarily into the bed (-18{\textpm}3 mmol m-2 d-1; mean{\textpm}SE, n=137 15-min bursts) but was sensitive to non-steady state changes in O2 concentrations caused by the differential advection of water masses with variable mean O2 concentrations. Important contributions to O2 eddy fluxes at surface wave frequencies were seen in eddy correlation cospectra and these are interpreted as being indicative of consumption enhanced by advective transport of O2 into the bed. The sediments were deposits of fine sand with permeabilities of 1.3{\textendash}4.7{\texttimes}10-11 m2 and wave-generated ripples. Sediment pigment and organic carbon concentrations were low (chlorophyll-α: 0.02{\textendash}0.45 μg g-1, phaeophytin-α: 0.38{\textendash}1.38 μg g-1 and organic carbon: 0.05{\textendash}0.39\% dry wt in discrete depth intervals from cores collected between March and October), but it was evident that during the summer fresh pigments were trapped in the sand and rapidly mixed over the uppermost 0{\textendash}13 cm. From these results it is inferred that physical forcing associated largely with waves and currents may accentuate the role of sediment-covered inner shelf habitats as a regional O2 sink compared to the middle shelf. In effect, the action of waves and currents in the benthic boundary layer enables aerobic respiration that counterbalances the oxygenation of the water column by primary production and mixing in the surface layer.},
	keywords = {Benthic boundary layer, Eddy correlation, Hypoxia, Oregon shelf, Oxygen consumption, Permeable sediments},
	issn = {0278-4343},
	doi = {10.1016/j.csr.2014.05.010},
	url = {<Go to ISI>://WOS:000339696200009},
	author = {McCann-Grosvenor, K. and Reimers, C. E. and Sanders, R. D.}
}
