@article{morey_he_chassignet_sheinbaum_2024, title={Editorial: Understanding and predicting the Gulf of Mexico ocean dynamics}, volume={11}, ISSN={["2296-7745"]}, DOI={10.3389/fmars.2024.1400560}, abstractNote={The Gulf of Mexico circulation has been a focus of oceanographic research for well over a century due 16 to its early importance in maritime transportation and naval interests, expansion of petroleum industry 17 activity since the mid-20 th century, and emerging understanding of its importance to regional 18 ecosystems, weather and climate. Over the past several years, a number of research programs have 19 funded significant efforts to advance understanding of and forecasting capabilities for the Gulf of 20 Mexico circulation, including the Loop Current (LC) and its associated eddies (comprising the Loop 21Current System -LCS), and deep-water dynamics. The editors thank all authors that contributed to this research topic and the Frontiers editorial staff that 96 made this issue possible. The editors hope that the readers find this collection of articles useful for 97 continued advancement toward a greater understanding and skillful prediction of the Gulf of Mexico 98 system. 99}, journal={FRONTIERS IN MARINE SCIENCE}, author={Morey, Steven L. and He, Ruoying and Chassignet, Eric P. and Sheinbaum, Julio}, year={2024}, month={Mar} }
 @article{chaichitehrani_he_2024, title={Investigation of ocean environmental variables and their variations associated with major Loop Current eddy-shedding events in the Gulf of Mexico}, volume={213}, ISSN={["1879-0100"]}, DOI={10.1016/j.dsr2.2023.105354}, abstractNote={The eddy kinetic energy (EKE) variability associated with 26 major Loop Current eddies (LCEs) in the Gulf of Mexico from 1994 through 2019 was investigated. We employed 3D multivariate observation-based ARMOR3D monthly ocean analyses of salinity, temperature, and geostrophic velocity field data. In addition, we used ERA5 wind data, the fifth generation of the European Centre for Medium-Range Weather Forecasts (ECMWF) atmospheric global climate reanalysis, to analyze internal and external forcing processes affecting the evolution of these LCEs. The energy analysis was performed to understand the role of barotropic (BT) and baroclinic (BC) instabilities and their associated energy conversion mechanisms in EKE generation. Our results suggest that BT instabilities are the primary source of EKE variability in the upper water column of the LC system. Furthermore, BT was positively correlated with Yucatan Channel (YC) transport during these major LCE shedding events. YC transport plays a significant role in energy conversion from mean kinetic energy to EKE, Loop Current growth, and generation of LCEs. BC instability was inversely correlated with buoyancy frequency, and a decrease in stratification triggers the development of BC instability, which favors eddy shedding. An eddy shedding index (ESI) was developed to quantify EKE evolution. Major LCE shedding occurs when ESI ≥0.46.}, journal={DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY}, author={Chaichitehrani, Nazanin and He, Ruoying}, year={2024}, month={Feb} }
 @article{moulton_zambon_xue_warner_bao_yin_defne_he_hegermiller_2024, title={Modeled Coastal-Ocean Pathways of Land-Sourced Contaminants in the Aftermath of Hurricane Florence}, volume={129}, ISSN={["2169-9291"]}, url={https://doi.org/10.1029/2023JC019685}, DOI={10.1029/2023JC019685}, abstractNote={Abstract}, number={3}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, author={Moulton, Melissa and Zambon, Joseph B. and Xue, Z. George and Warner, John C. and Bao, Daoyang and Yin, Dongxiao and Defne, Zafer and He, Ruoying and Hegermiller, Christie}, year={2024}, month={Mar} }
 @article{mao_he_bane_gawarkiewicz_todd_2023, title={A data-assimilative modeling investigation of Gulf Stream variability}, volume={211}, ISSN={["1879-0100"]}, url={https://doi.org/10.1016/j.dsr2.2023.105319}, DOI={10.1016/j.dsr2.2023.105319}, abstractNote={An advanced data-assimilative ocean circulation model is used to investigate Gulf Stream (GS) variability during 2017–2018. The modeling system applies a strong-constraint, 4D variational data assimilation algorithm. It assimilates satellite-based sea surface height and sea surface temperature measurements and in situ temperature and salinity profiles. Model skill assessment metrics along with comparisons of GS position and GS's three-dimensional mean kinetic energy with historical observations are applied to validate the data-assimilative model. The resulting time- and space-continuous ocean state estimates are used to diagnose eddy kinetic energy conversion and cross-stream eddy heat and salt fluxes over the two-year study period. The processes leading to kinetic energy conversion are primarily due to GS meanders. Significant inverse energy cascading (EKE→MKE and EKE→EPE) can occur during GS-eddy interactions, particularly during onshore intrusions or offshore meanderings of the GS. Throughout the two-year study period, the cross-stream eddy heat and salt fluxes off Cape Hatteras were predominantly positive (onshore). Both GS offshore meandering (occurring 44% of the time and associated with shelf/slope water export) and GS intrusion (occurring 56% of the time) contribute to onshore heat and salt transport. Improved understanding of these processes and dynamics requires strong integration of an advanced observational infrastructure that combines remote sensing; fixed, mobile, and shore-based observing components; and high-resolution data assimilative models.}, journal={DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY}, author={Mao, Shun and He, Ruoying and Bane, John and Gawarkiewicz, Glen and Todd, Robert E.}, year={2023}, month={Oct} }
 @article{bane_seim_haines_han_he_zambon_2023, title={Atmospheric forcing of the Hatteras coastal ocean during 2017-2018: The PEACH program}, volume={102}, ISSN={["1872-6879"]}, DOI={10.1016/j.dynatmoce.2023.101364}, abstractNote={The Hatteras coastal ocean is centrally located along the east coast of the 48 contiguous United States, offshore of Cape Hatteras in a complex land/ocean/atmosphere region where major ocean currents of differing temperatures and salinities meet and interact, where the atmosphere fluctuates on a wide range of time scales, and where atmosphere-ocean interactions vary both spatially and temporally. The Gulf Stream current typically leaves its contact with the continental margin here. Continental shelf currents from the north and from the south converge here, resulting in a net shelf-to-ocean transport of shelf waters that carry important water properties and constituents. The two major drivers of these shelf currents and exchanges are the atmosphere and the oceanic Gulf Stream. Atmospheric driving of the Hatteras coastal ocean is through surface wind stress and heat flux across the air-sea interface. The complexity and importance of this region motivated the NSF-sponsored PEACH research program during 2017–2018 (PEACH: Processes driving Exchange At Cape Hatteras). In this paper, we utilize the substantial number of observations available during PEACH to describe the atmospheric forcing of the ocean then. Atmospheric conditions are described in terms of two seasons: the warm season (May to mid-September), with predominantly mild northeastward winds punctuated by occasional tropical cyclones (TCs); and the cool season (mid-September through April), with a nearly continuous, northeastward progression of energetic extratropical cyclones (ETCs) through the region. Cool season ETCs force the region with strong wind stress and ocean-to-atmosphere heat flux episodes, each with a time-scale of several days. Wind stress fluctuation magnitudes typically exceed mean stress magnitudes in each season by a factor of 3–5. These stresses account for just over 40% of the total current variability in the region, showing the wind to be a major driver of the ocean here. Atmosphere-ocean heat flux is typically into the ocean throughout the warm season (~100 W m-2); it is essentially always out of the ocean during the cool season (~500 W m-2 or more). New results herein include: southward intraseasonal oscillations of the jet stream’s position drove the strongest ETCs (including one “bomb” cyclone); and during the 41 years leading up to and including PEACH, the season-averaged number and strength of atmospheric cyclones passing over the Hatteras coastal ocean have shown little long-term change. Looking ahead, the NSF Pioneer Array is scheduled to be relocated to the northern portion of the Hatteras coastal ocean in 2024, and the NASA SWOT satellite has begun its ocean topography mission, which has a ground-track cross-over here.}, journal={DYNAMICS OF ATMOSPHERES AND OCEANS}, author={Bane, John and Seim, Harvey and Haines, Sara and Han, Lu and He, Ruoying and Zambon, Joseph}, year={2023}, month={Jun} }
 @article{allahdadi_he_neary_2023, title={Impact of the Gulf Stream on ocean waves}, volume={208}, ISSN={["1879-0100"]}, DOI={10.1016/j.dsr2.2022.105239}, abstractNote={Surface wave propagation and the modulations of wave parametric and spectral properties over the Gulf Stream (GS) are studied using a high spatial resolution (1 km) wave model that considers an idealized GS. While simulation results are generally consistent with a previous modelling study, we found that for following-current (FC) cases, reflection from the GS substantially increases wave height on the offshore side of the GS center by up to 25%, and decreases wave height on the landward side of the GS by as much as 80%. In the counter-current (CC) cases, the wave height profile is more symmetrical relative to the GS centerline, and the maximum 33% increase of wave height is predominantly driven by straining. The GS also causes an increase (decrease) in wavelength and directional spreading in the FC (CC) case. Additional model sensitivity experiments that further consider realistic shelf-ocean topography show that current modulation and bottom dissipation work in concert as low- and high-pass filters on the wave frequency spectra. Wave parameters and spectral modulations imposed by the GS have significant impacts on ocean-atmosphere momentum flux and wave energy resource.}, journal={DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY}, author={Allahdadi, Mohammad Nabi and He, Ruoying and Neary, Vincent S.}, year={2023}, month={Apr} }
 @article{mao_he_andres_2023, title={Modes of North Atlantic Western boundary current variability at 36° N}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-45889-4}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Mao, Shun and He, Ruoying and Andres, Magdalena}, year={2023}, month={Oct} }
 @article{bao_xue_warner_moulton_yin_hegermiller_zambon_he_2022, title={A Numerical Investigation of Hurricane Florence-Induced Compound Flooding in the Cape Fear Estuary Using a Dynamically Coupled Hydrological-Ocean Model}, volume={14}, ISSN={["1942-2466"]}, url={https://doi.org/10.1029/2022MS003131}, DOI={10.1029/2022MS003131}, abstractNote={Abstract}, number={11}, journal={JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS}, author={Bao, Daoyang and Xue, Z. George and Warner, John C. C. and Moulton, Melissa and Yin, Dongxiao and Hegermiller, Christie A. A. and Zambon, Joseph B. B. and He, Ruoying}, year={2022}, month={Nov} }
 @article{ahn_neary_allahdadi_he_2022, title={A framework for feasibility-level validation of high-resolution wave hindcast models}, volume={263}, ISSN={["1873-5258"]}, DOI={10.1016/j.oceaneng.2022.112193}, abstractNote={The value of long-term wave hindcasts for investigating wave climates, wave energy resources, and extreme wave conditions has motivated research developing, calibrating and validating wave hindcast models. Past hindcast model validation studies examined the accuracy in modeling bulk wave parameters of overall sea states without considering the dependency of the model's skill within different sea states. In the present study, a framework for wave hindcast model validation is developed by examining the model accuracy for the most frequently occurring sea states, sea states contributing the most energy to total wave power, sea states associated with hurricane events, and those with the largest model error. Validations using bulk wave parameters and frequency-directional spectra at these key sea states and extreme wave conditions based on univariate and bivariate-contour methods provide insights to improve model accuracy, identifying the model's strong and weak points, and pathways for improvement, e.g., modeling wave-current interactions and adjusting wind data. This study adds to a growing body of research demonstrating that a carefully calibrated and verified spectral wave hindcast model can be used to estimate key wave energy parameters over a wide range of wave energy climates, as well as their spatial, temporal, frequency, directional, and probabilistic distributions.}, journal={OCEAN ENGINEERING}, author={Ahn, Seongho and Neary, Vincent S. and Allahdadi, Mohammad Nabi and He, Ruoying}, year={2022}, month={Nov} }
 @article{mcgee_he_2022, title={Hurricane-Induced Oceanic Carbon Changes in the Upper Ocean}, volume={3}, url={https://www.mdpi.com/2673-1924/3/2/10}, DOI={10.3390/oceans3020010}, abstractNote={Changes in marine carbon cycling due to hurricanes with different intensity and translation speeds have not been systematically investigated. This study uses an idealized coupled physical-biogeochemical model and a suite of model sensitivity analyses to better quantify the relationship between hurricane characteristics and marine property changes, including variations in air-sea carbon flux and partial pressure of carbon dioxide in water (pCO2w). We find that strong (category 4–5), mid-speed (5–8 m/s) storms cause the most carbon flux from the atmosphere to the ocean, and that the relationship between air-sea carbon flux and hurricane properties is non-linear. Climate models that do not consider synoptic-scale, storm-induced physical-biogeochemical coupling may underestimate regional carbon sinks.}, number={2}, journal={Oceans}, publisher={MDPI AG}, author={McGee, Laura and He, Ruoying}, year={2022}, month={Mar}, pages={114–124} }
 @article{mcgovern_bostrom_davis_demuth_ebert-uphoff_he_hickey_ii_snook_stewart_et al._2022, title={NSF AI Institute for Research on Trustworthy AI in Weather, Climate, and Coastal Oceanography (AI2ES)}, volume={103}, ISSN={["1520-0477"]}, DOI={10.1175/BAMS-D-21-0020.1}, abstractNote={Abstract}, number={7}, journal={BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY}, author={McGovern, Amy and Bostrom, Ann and Davis, Phillip and Demuth, Julie L. and Ebert-Uphoff, Imme and He, Ruoying and Hickey, Jason and Ii, David John Gagne and Snook, Nathan and Stewart, Jebb Q. and et al.}, year={2022}, month={Jul}, pages={E1658–E1668} }
 @article{seim_savidge_andres_bane_edwards_gawarkiewicz_he_todd_muglia_zambon_et al._2022, title={OVERVIEW OF THE PROCESSES DRIVING EXCHANGE AT CAPE HATTERAS(PROGRAM)}, volume={35}, ISSN={["1042-8275"]}, url={https://doi.org/10.5670/oceanog.2022.205}, DOI={10.5670/oceanog.2022.205}, abstractNote={The Processes driving Exchange At Cape Hatteras (PEACH) program seeks to better understand seawater exchanges between the continental shelf and the open ocean near Cape Hatteras, North Carolina. This location is where the Gulf Stream transitions from a boundary-trapped current to a free jet, and where robust along-shelf convergence brings cool, relatively fresh Middle Atlantic Bight and warm, salty South Atlantic Bight shelf waters together, forming an important and dynamic biogeographic boundary. The magnitude of this convergence implies large export of shelf water to the open ocean here. Background on the oceanography of the region provides motivation for the study and gives context for the measurements that were made. Science questions focus on the roles that wind forcing, Gulf Stream forcing, and lateral density gradients play in driving exchange. PEACH observational efforts include a variety of fixed and mobile observing platforms, and PEACH modeling included two different resolutions and data assimilation schemes. Findings to date on mean circulation, the nature of export from the southern Middle Atlantic Bight shelf, Gulf Stream variability, and position variability of the Hatteras Front are summarized, together with a look ahead to forthcoming analyses.}, number={2}, journal={OCEANOGRAPHY}, author={Seim, Harvey E. and Savidge, Dana and Andres, Magdalena and Bane, John and Edwards, Catherine and Gawarkiewicz, Glen and He, Ruoying and Todd, Robert E. and Muglia, Michael and Zambon, Joseph and et al.}, year={2022}, month={Sep}, pages={6–17} }
 @article{karnauskas_shertzer_paris_farmer_switzer_lowerre-barbieri_kellison_he_vaz_2022, title={Source-sink recruitment of red snapper: Connectivity between the Gulf of Mexico and Atlantic Ocean}, volume={8}, ISSN={["1365-2419"]}, DOI={10.1111/fog.12607}, abstractNote={Abstract}, journal={FISHERIES OCEANOGRAPHY}, author={Karnauskas, Mandy and Shertzer, Kyle W. and Paris, Claire B. and Farmer, Nicholas A. and Switzer, Theodore S. and Lowerre-Barbieri, Susan K. and Kellison, G. Todd and He, Ruoying and Vaz, Ana C.}, year={2022}, month={Aug} }
 @article{he_li_he_2022, title={Variability of Remotely Sensed Solar-Induced Chlorophyll Fluorescence in Relation to Climate Indices}, volume={9}, ISSN={["2076-3298"]}, DOI={10.3390/environments9090121}, abstractNote={Global remote sensing of solar-induced fluorescence (SIF), a proxy for plant photosynthetic activity, represents a breakthrough in the systematic observation of global-scale gross primary production and other ecosystem functions. Here, we hypothesize that all earth ecosystem variabilities, including SIF, are affected by climate variations. The main contribution of this study is to apply a global empirical orthogonal function (EOF) analysis of SIF to quantify the relations between the large-scale GPP variability and climate variations. We used 2007–2019 SIF data derived from the Global Ozone Monitoring Experiment-2 (GOME-2) satellite sensor observations and a rotated empirical orthogonal function (EOF) analysis to explore global SIF variability over years and decades. The first leading EOF mode captures the well-known ENSO pattern, with most of the variance over continents in the tropical Pacific and Indian Oceans. The second and third leading EOF modes in SIF variability are significantly related to the NAO and PDO climate indices, respectively. Our analysis also shows that the 2011 La Niña (2015 El Niño) elevated (decreased) global SIF.}, number={9}, journal={ENVIRONMENTS}, author={He, Katherine and Li, Wenhong and He, Ruoying}, year={2022}, month={Sep} }
 @misc{du_he_liu_huang_wang_yuan_xu_wang_dai_2021, title={Climatology of nutrient distributions in the South China Sea based on a large data set derived from a new algorithm}, volume={195}, ISSN={["1873-4472"]}, DOI={10.1016/j.pocean.2021.102586}, abstractNote={Nutrients are typically the most important determinant of the productivity of marine ecosystems. Hence, nutrients have been an essential variable of ocean observations in the modern oceanography era. Understanding of marine ecosystems and biogeochemistry, however, is largely limited by the spatiotemporal coverage of nutrient data. Herein, we developed a novel algorithm based on a large observational dataset of nutrients and their relationship with water masses indexed by temperature and salinity in the South China Sea (SCS). The algorithm yielded errors of ≤ 1.3, ≤ 0.10 and ≤ 3.5 μmol L−1 for NO3– + NO2– (N + N), phosphate and silicate, respectively. It is then applied to reconstruct nutrient concentrations primarily using temperature and salinity data archived in the World Ocean Database and Argo database during 1940–2018. It increases the nutrient data to ~ 5 million, by ca. three orders of magnitude compared to direct measurements in the SCS. This allows for a full examination of the seasonal climatology of nutrients in the SCS. In summer, in the upper 200 m, nutrient concentrations in the northwest and southernmost SCS are higher than in the rest of the SCS. An overall reversed pattern is revealed in winter, when higher nutrient concentrations are found in the central basin rather than basin margins. The Kuroshio intrusion and the vertical displacement of the nutricline, driven by upwelling/downwelling induced by horizontal convergences/divergences at both meso- and basin scales, determine the spatial and seasonal variation of nutrients. Seasonally, the Kuroshio intrusion and vertical displacements of the nutricline tend to offset the spatial variation of nutrient concentrations in spring, while they show an additive effect in the fall.}, journal={PROGRESS IN OCEANOGRAPHY}, author={Du, Chuanjun and He, Ruoying and Liu, Zhiyu and Huang, Tao and Wang, Lifang and Yuan, Zhongwei and Xu, Yanping and Wang, Zhe and Dai, Minhan}, year={2021}, month={Jul} }
 @article{allahdadi_he_ahn_chartrand_neary_2021, title={Development and calibration of a high-resolution model for the Gulf of Mexico, Puerto Rico, and the US Virgin Islands: Implication for wave energy resource characterization}, volume={235}, ISSN={["1873-5258"]}, url={https://doi.org/10.1016/j.oceaneng.2021.109304}, DOI={10.1016/j.oceaneng.2021.109304}, abstractNote={A high-resolution, unstructured Simulating WAves Nearshore (SWAN) model with a resolution of 200 m within 20 km of the coast was developed to provide a reliable setting for a long-term wave energy characterization of the Gulf of Mexico, Puerto Rico, and the U.S. Virgin Islands. A thorough model parameter sensitivity analysis, as well as a calibration process for selecting the whitecapping dissipation formulation, were conducted. Sensitivity analyses for the simulation timestep and number of iterations highlighted the less-studied interplay between these parameters in SWAN, which can substantially affect simulation accuracy and cost and is vital for the next step long-term simulation of the wave energy resources. For the present study, a 3 min timestep and three iterations are optimum. The "Garden Sprinkling" effect and the cut-off frequency were also investigated. Using 36 directional bins and a larger cut-off frequency (1.0 Hz) enable the best agreement between the model simulation and the in situ wave observations. This subsequently leads to improved model skill and performance in resolving the observed International Electrotechnical Commission (IEC) wave energy resource parameters that are highly non-linear functions of wave spectral moments.}, journal={OCEAN ENGINEERING}, publisher={Elsevier BV}, author={Allahdadi, Mohammad Nabi and He, Ruoying and Ahn, Seongho and Chartrand, Chris and Neary, Vincent S.}, year={2021}, month={Sep} }
 @article{liu_he_lee_2021, title={Effects of Ocean Optical Properties and Solar Attenuation on the Northwestern Atlantic Ocean Heat Content and Hurricane Intensity}, volume={48}, ISSN={["1944-8007"]}, url={https://doi.org/10.1029/2021GL094171}, DOI={10.1029/2021GL094171}, abstractNote={Abstract}, number={13}, journal={GEOPHYSICAL RESEARCH LETTERS}, author={Liu, Yangyang and He, Ruoying and Lee, Zhongping}, year={2021}, month={Jul} }
 @article{zambon_he_warner_hegermiller_2021, title={Impact of SST and Surface Waves on Hurricane Florence (2018): A Coupled Modeling Investigation}, volume={36}, ISSN={0882-8156 1520-0434}, url={http://dx.doi.org/10.1175/WAF-D-20-0171.1}, DOI={10.1175/WAF-D-20-0171.1}, abstractNote={Abstract}, number={5}, journal={Weather and Forecasting}, publisher={American Meteorological Society}, author={Zambon, Joseph B. and He, Ruoying and Warner, John C. and Hegermiller, Christie A.}, year={2021}, month={May}, pages={1713–1734} }
 @article{ahn_neary_allahdadi_he_2021, title={Nearshore wave energy resource characterization along the East Coast of the United States}, volume={172}, ISBN={1879-0682}, DOI={10.1016/j.renene.2021.03.037}, abstractNote={A feasibility level nearshore wave energy resource characterization is conducted for the East Coast of the United States using a 32-year (1979–2010) hindcast from a high-resolution unstructured-grid Simulating Waves Nearshore (SWAN) model with a spatial resolution of 200 m along the coastline. Wave energy resource attributes including wave energy potentials, seasonal variability, frequency and directional spreading, and extreme sea states are characterized using a broad range of resource parameters from which opportunities, risks, and constraints for wave energy conversion (WEC) projects are assessed. Cross-shore and alongshore variations of these parameters due to varying wave energy climate and coastline orientation relative to the dominant wave systems are examined. The present study also introduces a zero-crossing method for delineating wave energy climate regions based on a broad range of resource attributes beyond just wave power. Applying this method, eight nearshore wave energy climate regions are delineated for the East Coast; each region with a unique set of resource attributes to inform regional energy planning, WEC project development, conceptual WEC design, and the operation and maintenance of WEC projects.}, journal={RENEWABLE ENERGY}, author={Ahn, Seongho and Neary, Vincent S. and Allahdadi, Mohammad Nabi and He, Ruoying}, year={2021}, month={Jul}, pages={1212–1224} }
 @article{solo-gabriele_fiddaman_mauritzen_ainsworth_abramson_berenshtein_chassignet_chen_conmy_court_et al._2021, title={Towards integrated modeling of the long-term impacts of oil spills}, volume={131}, ISSN={["1872-9460"]}, DOI={10.1016/j.marpol.2021.104554}, abstractNote={Although great progress has been made to advance the scientific understanding of oil spills, tools for integrated assessment modeling of the long-term impacts on ecosystems, socioeconomics and human health are lacking. The objective of this study was to develop a conceptual framework that could be used to answer stakeholder questions about oil spill impacts and to identify knowledge gaps and future integration priorities. The framework was initially separated into four knowledge domains (ocean environment, biological ecosystems, socioeconomics, and human health) whose interactions were explored by gathering stakeholder questions through public engagement, assimilating expert input about existing models, and consolidating information through a system dynamics approach. This synthesis resulted in a causal loop diagram from which the interconnectivity of the system could be visualized. Results of this analysis indicate that the system naturally separates into two tiers, ocean environment and biological ecosystems versus socioeconomics and human health. As a result, ocean environment and ecosystem models could be used to provide input to explore human health and socioeconomic variables in hypothetical scenarios. At decadal-plus time scales, the analysis emphasized that human domains influence the natural domains through changes in oil-spill related laws and regulations. Although data gaps were identified in all four model domains, the socioeconomics and human health domains are the least established. Considerable future work is needed to address research gaps and to create fully coupled quantitative integrative assessment models that can be used in strategic decision-making that will optimize recoveries from future large oil spills.}, journal={MARINE POLICY}, author={Solo-Gabriele, Helena M. and Fiddaman, Tom and Mauritzen, Cecilie and Ainsworth, Cameron and Abramson, David M. and Berenshtein, Igal and Chassignet, Eric P. and Chen, Shuyi S. and Conmy, Robyn N. and Court, Christa D. and et al.}, year={2021}, month={Sep} }
 @article{neary_ahn_seng_allahdadi_wang_yang_he_2020, title={Characterization of Extreme Wave Conditions for Wave Energy Converter Design and Project Risk Assessment}, volume={8}, ISSN={["2077-1312"]}, DOI={10.3390/jmse8040289}, abstractNote={Best practices and international standards for determining n-year return period extreme wave (sea states) conditions allow wave energy converter designers and project developers the option to apply simple univariate or more complex bivariate extreme value analysis methods. The present study compares extreme sea state estimates derived from univariate and bivariate methods and investigates the performance of spectral wave models for predicting extreme sea states at buoy locations within several regional wave climates along the US East and West Coasts. Two common third-generation spectral wave models are evaluated, a WAVEWATCH III® model with a grid resolution of 4 arc-minutes (6–7 km), and a Simulating WAves Nearshore model, with a coastal resolution of 200–300 m. Both models are used to generate multi-year hindcasts, from which extreme sea state statistics used for wave conditions characterization can be derived and compared to those based on in-situ observations at National Data Buoy Center stations. Comparison of results using different univariate and bivariate methods from the same data source indicates reasonable agreement on average. Discrepancies are predominantly random. Large discrepancies are common and increase with return period. There is a systematic underbias for extreme significant wave heights derived from model hindcasts compared to those derived from buoy measurements. This underbias is dependent on model spatial resolution. However, simple linear corrections can effectively compensate for this bias. A similar approach is not possible for correcting model-derived environmental contours, but other methods, e.g., machine learning, should be explored.}, number={4}, journal={JOURNAL OF MARINE SCIENCE AND ENGINEERING}, author={Neary, Vincent S. and Ahn, Seongho and Seng, Bibiana E. and Allahdadi, Mohammad Nabi and Wang, Taiping and Yang, Zhaoqing and He, Ruoying}, year={2020}, month={Apr} }
 @article{li_stumpf_mcgillicuddy_he_2020, title={Dynamics of an intense Alexandrium catenella red tide in the Gulf of Maine: satellite observations and numerical modeling}, volume={99}, ISSN={["1878-1470"]}, DOI={10.1016/j.hal.2020.101927}, abstractNote={In July 2009, an unusually intense bloom of the toxic dinoflagellate Alexandrium catenella occurred in the Gulf of Maine. The bloom reached high concentrations (from hundreds of thousands to one million cells L−1) that discolored the water and exceeded normal bloom concentrations by a factor of 1000. Using Medium Resolution Imaging Spectrometer (MERIS) imagery processed to target chlorophyll concentrations (>2 µg L−1), patches of intense A. catenella concentration were identified that were consistent with the highly localized cell concentrations observed from ship surveys. The bloom patches were generally aligned with the edge of coastal waters with high-absorption. Dense bloom patches moved onshore in response to a downwelling event, persisted for approximately one week, then dispersed rapidly over a few days and did not reappear. Coupled physical-biological model simulations showed that wind forcing was an important factor in transporting cells onshore. Upward swimming behavior facilitated the horizontal cell aggregation, increasing the simulated maximum depth-integrated cell concentration by up to a factor of 40. Vertical convergence of cells, due to active swimming of A. catenella from the subsurface to the top layer, could explain the additional 25-fold intensification (25 × 40=1000-fold) needed to reach the bloom concentrations that discolored the water. A model simulation that considered upward swimming overestimated cell concentrations downstream of the intense aggregation. This discrepancy between model and observed concentrations suggested a loss of cells from the water column at a time that corresponded to the start of encystment. These results indicated that the joint effect of upward swimming, horizontal convergence, and wind-driven flow contributed to the red water event, which might have promoted the sexual reproduction event that preceded the encystment process.}, journal={HARMFUL ALGAE}, author={Li, Yizhen and Stumpf, Richard P. and McGillicuddy, D. J., Jr. and He, Ruoying}, year={2020}, month={Nov} }
 @article{mcgee_he_2020, title={Mesoscale and submesoscale mechanisms behind asymmetric cooling and phytoplankton blooms induced by hurricanes: a comparison between an open ocean case and a continental shelf sea case (vol 68, pg 1443, 2018)}, volume={70}, ISSN={["1616-7228"]}, url={https://doi.org/10.1007/s10236-020-01371-7}, DOI={10.1007/s10236-020-01371-7}, abstractNote={The original version of this article unfortunately contained a mistake. The following data attribution statement per our research sponsors requirement has been omitted.}, number={6}, journal={OCEAN DYNAMICS}, publisher={Springer Science and Business Media LLC}, author={McGee, Laura and He, Ruoying}, year={2020}, month={Jun}, pages={843–843} }
 @article{allandadi_gunawan_lai_he_neary_2019, title={Development and validation of a regional-scale high-resolution unstructured model for wave energy resource characterization along the US East Coast}, volume={136}, ISSN={["0960-1481"]}, url={https://doi.org/10.1016/j.renene.2019.01.020}, DOI={10.1016/j.renene.2019.01.020}, abstractNote={Leveraging the high-performance computing capability at one of the US Department of Energy's (USDOE) National Laboratories, an ultra-high-resolution Simulating WAves Nearshore (SWAN) model suitable for wave energy project feasibility studies is developed for the US East Coast Region. This model uses an unstructured mesh with a coastal resolution of 200 m. It is forced by Climate Forecast System Reanalysis wind fields with spatial and temporal resolutions of 0.312° and 1 h at the surface, and by wave parameters from the global WAVEWATCH III model along the model's open boundaries. It is the first USDOE regional wave hindcast model for the US East Coast developed according to International Electrotechnical Commission standards for wave energy resource assessment and characterization. The present study focuses on the development and validation of this ultra-high resolution large-scale model, including source model selection, sensitivity studies, and model performance evaluation for a wave energy resource characterization application.}, journal={RENEWABLE ENERGY}, publisher={Elsevier BV}, author={Allandadi, M. Nabi and Gunawan, Budi and Lai, Jonathan and He, Ruoying and Neary, Vincent S.}, year={2019}, month={Jun}, pages={500–511} }
 @inproceedings{shay_brewster_jaimes_gordon_fennel_furze_fargher_he_2019, title={Physical and Biochemical Structure Measured by APEX-EM Floats}, url={https://doi.org/10.1109/CWTM43797.2019.8955168}, DOI={10.1109/CWTM43797.2019.8955168}, abstractNote={Technology for measuring the deep ocean currents (including temperature and salinity) is now available using the recently Autonomous Profiling Explorer floats with electromagnetic sensors (APEX-EM) recently developed by Teledyne Webb Research. The float acquires temperature and salinity profiles using a Seabird sensor. In addition, the APEX-EM profiling floats were equipped with chemical and bio-optical sensors: Aanderaa Optode sensor measuring dissolved oxygen, and the WET Labs ECO Puck sensor which combines measurement of chlorophyll fluorescence (proxy of phytoplankton abundance), measurement of backscatter (as proxy of particle concentration) and colored dissolved organic matter (CDOM) fluorescence (incl. fluorophoric oil components). The ECO Puck was specifically designed to minimize space and power requirements for applications in autonomous measuring platforms, and is rated for sampling to 2000 m depth. Such technological advancements bringing together the physical and biochemical measurements have relevance on the response to subsurface oil spills such as Deepwater Horizon. Here we explore the impacts of wind-driven current on the biochemical response during the passage of a cold front in early May 2017 using profiles from multiple floats and shipboard data. During the frontal passage, surface friction velocity associated with the wind stress approached values of 0.6 m/s that forced strong near-inertial currents in the upper ocean of 0.75 m/s. The associated shear forced layer deepening of more than 20 m over the two days of frontal passage. The biochemical response indicated a dissolved oxygen and chlorophyll fluorescence maxima at depths of 90–100 m during the event. This deep chlorophyll maximum tends to correspond to the oxycline lying between the 24–25 isopycnal in temperature and salinity space. During this period the floats resolved these responses as continuous measurements were acquired over time scales of a few hours. Thus, this float technology enables investigators to look more closely at the upper ocean response to strong forcing events that impacts biochemistry and hydrocarbon dispersion. Note that sampling rates can changed by updating mission profiles from continuous to profiling modes between specific depths to once every five to ten days to depths of up to 2000 m by changing the piston counts on the missions.}, booktitle={2019 IEEE/OES Twelfth Current, Waves and Turbulence Measurement (CWTM)}, publisher={IEEE}, author={Shay, Lynn K. and Brewster, Jodi K. and Jaimes, Benjamin and Gordon, Christopher and Fennel, Katja and Furze, Peter and Fargher, Hugh and He, Ruoying}, year={2019}, month={Mar} }
 @article{zeng_adams_roffer_he_2019, title={Potential connectivity among spatially distinct management zones for Bonefish (Albula vulpes) via larval dispersal}, volume={102}, ISSN={["1573-5133"]}, DOI={10.1007/s10641-018-0826-z}, number={2}, journal={ENVIRONMENTAL BIOLOGY OF FISHES}, author={Zeng, Xiangming and Adams, Aaron and Roffer, Mitchell and He, Ruoying}, year={2019}, month={Feb}, pages={233–252} }
 @article{allandadi_he_neary_2019, title={Predicting ocean waves along the US east coast during energetic winter storms: sensitivity to whitecapping parameterizations}, volume={15}, ISSN={["1812-0784"]}, DOI={10.5194/os-15-691-2019}, abstractNote={Abstract. The performance of two methods for quantifying whitecapping
dissipation incorporated in the Simulating Waves Nearshore (SWAN) wave model is evaluated for waves
generated along and off the US east coast under energetic winter storms
with a predominantly westerly wind. Parameterizing the whitecapping effect
can be done using the Komen-type schemes, which are based on mean spectral
parameters, or the saturation-based (SB) approach of van der Westhuysen (2007), which is based on local wave parameters and the saturation level
concept of the wave spectrum (we use “Komen” and “Westhuysen” to denote
these two approaches). Observations of wave parameters and frequency spectra
at four National Data Buoy Center (NDBC) buoys are used to evaluate simulation results. Model–data
comparisons show that when using the default parameters in SWAN, both Komen
and Westhuysen methods underestimate wave height. Simulations of mean wave
period using the Komen method agree with observations, but those using the
Westhuysen method are substantially lower. Examination of source terms shows
that the Westhuysen method underestimates the total energy transferred into
the wave action equations, especially in the lower frequency bands that
contain higher spectral energy. Several causes for this underestimation are
identified. The primary reason is the difference between the wave growth
conditions along the east coast during winter storms and the conditions used
for the original whitecapping formula calibration. In addition, some
deficiencies in simulation results are caused along the coast by the
“slanting fetch” effect that adds low-frequency components to the 2-D wave
spectra. These components cannot be simulated partly or entirely by
available source terms (wind input, whitecapping, and quadruplet) in models
and their interaction. Further, the effect of boundary layer instability
that is not considered in the Komen and Westhuysen whitecapping wind input
formulas may cause additional underestimation.
                    }, number={3}, journal={OCEAN SCIENCE}, author={Allandadi, Mohammad Nabi and He, Ruoying and Neary, Vincent S.}, year={2019}, month={Jun}, pages={691–715} }
 @article{lohrenz_cai_chakraborty_he_tian_2019, title={SATELLITE ESTIMATION OF COASTAL PCO2 AND AIR-SEA FLUX OF CARBON DIOXIDE IN THE NORTHERN GULF OF MEXICO}, volume={1}, url={https://doi.org/10.1002/essoar.10500459.1}, DOI={10.1002/essoar.10500459.1}, abstractNote={A key to better constraining estimates of the ocean sink for fossil fuel emissions of carbon dioxide is reducing uncertainties in coastal carbon fluxes. A contributing factor in uncertainties in coastal carbon fluxes stems from the under sampling of seasonality and spatial heterogeneity. Our objectives were to i) assess satellite-based approaches that would expand the spatial and temporal coverage of the surface ocean pCO2 and sea-air CO2 flux for the northern Gulf of Mexico, and ii) investigate the seasonal and interannual variations in CO2 dynamics and possible environmental drivers. Regression tree analysis was effective in directly relating surface ocean pCO2 to satellite-retrieved (MODIS Aqua) products including chlorophyll, sea surface temperature, and dissolved/detrital absorption. Satellite-based assessments of sea surface pCO2 were made spanning the period from 2006-2010 and were used in conjunction with estimates of wind fields and atmospheric pCO2 to produce regional-scale estimates of air-sea fluxes. Seasonality was evident in air-sea fluxes of CO2, with an estimated annual average CO2 flux for the study region of -4.3 + 1.1 Tg C y-1, confirming prior findings that the Gulf of Mexico was a net CO2 sink. Interannual variability in fluxes was related to Mississippi River dissolved inorganic nitrogen inputs, an indication that human- and climate-related changes in river exports will impact coastal carbon budgets. This is the first multi-year assessment of pCO2 and air-sea flux of CO2 using satellite-derived environmental data for the northern Gulf of Mexico.}, publisher={Wiley}, author={Lohrenz, Steven and Cai, Wei-Jun and Chakraborty, Sumit and He, Ruoying and Tian, Hanqin}, year={2019}, month={Jan} }
 @misc{fringer_dawson_he_ralston_zhang_2019, title={The future of coastal and estuarine modeling: Findings from a workshop}, volume={143}, ISSN={["1463-5011"]}, DOI={10.1016/j.ocemod.2019.101458}, abstractNote={This paper summarizes the findings of a workshop convened in the United States in 2018 to discuss methods in coastal and estuarine modeling and to propose key areas of research and development needed to improve their accuracy and reliability. The focus of this paper is on physical processes, and we provide an overview of the current state-of-the-art based on presentations and discussions at the meeting, which revolved around the four primary themes of parameterizations, numerical methods, in-situ and remote-sensing measurements, and high-performance computing. A primary outcome of the workshop was agreement on the need to reduce subjectivity and improve reproducibility in modeling of physical processes in the coastal ocean. Reduction of subjectivity can be accomplished through development of standards for benchmarks, grid generation, and validation, and reproducibility can be improved through development of standards for input/output, coupling and model nesting, and reporting. Subjectivity can also be reduced through more engagement with the applied mathematics and computer science communities to develop methods for robust parameter estimation and uncertainty quantification. Such engagement could be encouraged through more collaboration between the forward and inverse modeling communities and integration of more applied math and computer science into oceanography curricula. Another outcome of the workshop was agreement on the need to develop high-resolution models that scale on advanced HPC systems to resolve, rather than parameterize, processes with horizontal scales that range between the depth and the internal Rossby deformation scale. Unsurprisingly, more research is needed on parameterizations of processes at scales smaller than the depth, including parameterizations for drag (including bottom roughness, bedforms, vegetation and corals), wave breaking, and air–sea interactions under strong wind conditions. Other topics that require significantly more work to better parameterize include nearshore wave modeling, sediment transport modeling, and morphodynamics. Finally, it was agreed that coastal models should be considered as key infrastructure needed to support research, just like laboratory facilities, field instrumentation, and research vessels. This will require a shift in the way proposals related to coastal ocean modeling are reviewed and funded.}, journal={OCEAN MODELLING}, author={Fringer, Oliver B. and Dawson, Clint N. and He, Ruoying and Ralston, David K. and Zhang, Y. Joseph}, year={2019}, month={Nov} }
 @article{ye_zhang_he_wang_wang_du_2019, title={Third-order WENO transport scheme for simulating the baroclinic eddying ocean on an unstructured grid}, volume={143}, ISSN={["1463-5011"]}, DOI={10.1016/j.ocemod.2019.101466}, abstractNote={Despite the recent success achieved by the unstructured-grid SCHISM (Semi-implicit Cross-scale Hydroscience Integrated System Model) in multi-resolution studies, its skill in simulating the baroclinic eddying ocean needs to be further improved. In particular, the classical 2nd-order transport schemes for estuaries and coastal zones are too dissipative to resolve the baroclinic dynamics associated with strong boundary currents, such as meso-scale meanders and eddies. To close this gap, this paper presents a newly designed 3rd-order finite volume transport scheme, based on the Weighted Essentially Non-Oscillatory (WENO) formalism. This new scheme strikes a delicate balance among accuracy, efficiency, and monotonicity for the transport in the eddying regime. Idealized numerical benchmark experiments demonstrate that the WENO scheme is very effective in limiting numerical diffusion. The scheme is then applied in a realistic simulation of the Gulf Stream and the surrounding circulation, further confirming its capability of resolving baroclinic meso-scale eddies and meanders. This new high-order transport scheme is therefore ideal for extending the ability of SCHISM to study cross-scale baroclinic applications that range from the river dynamics to the eddying ocean processes.}, journal={OCEAN MODELLING}, author={Ye, Fei and Zhang, Yinglong J. and He, Ruoying and Wang, Zhengui and Wang, Harry V. and Du, Jiabi}, year={2019}, month={Nov} }
 @article{he_he_zhang_2018, title={Impacts of Air-sea Interactions on Regional Air Quality Predictions Using a Coupled Atmosphere-ocean Model in Southeastern US}, volume={18}, ISSN={["2071-1409"]}, DOI={10.4209/aaqr.2016.12.0570}, abstractNote={Air-sea interactions have significant impacts on coastal convection and surface fluxes exchange. They are important for the spatial and vertical distributions of air pollutants that affect public health, particularly in densely populated coastal areas. To understand the impacts of air-sea interactions on coastal air quality predictions, sensitivity simulations with different atmosphere-ocean coupling are conducted in this work over southeastern U.S. in July 2010 using the Weather Research and Forecasting Model with Chemistry (WRF/Chem). The results show that comparing to WRF/Chem without air-sea interactions, WRF/Chem with a 1-D ocean mixed layer model (WRF/Chem-OML) and WRF/Chem coupled with a 3-D Regional Ocean Modeling System (WRF/Chem-ROMS) predict the domain averaged changes in the sea surface temperature of 0.06°C and 0.94°C, respectively for July average. The simulated differences in the surface concentrations of O3 and PM2.5 between WRF/Chem-ROMS and WRF/Chem can be as large as 17.3 ppb and 7.9 µg m–3, respectively, with the largest changes occurring not only along coast and remote ocean, but also over some inland areas. Extensive validations against observations show that WRF/Chem-ROMS improves the predictions of most cloud and radiative variables, and surface concentrations of some chemical species such as SO2, NO2, maximum 1-h and 8-h O3, SO42–, NH4+, NO3–, and PM10. This illustrates the benefits and needs of using coupled atmosphere-ocean model with advanced model representations of air-sea interactions for regional air quality modeling.}, number={4}, journal={AEROSOL AND AIR QUALITY RESEARCH}, publisher={Taiwan Association for Aerosol Research}, author={He, Jian and He, Ruoying and Zhang, Yang}, year={2018}, month={Apr}, pages={1044–1067} }
 @article{mcgee_he_2018, title={Mesoscale and submesoscale mechanisms behind asymmetric cooling and phytoplankton blooms induced by hurricanes: a comparison between an open ocean case and a continental shelf sea case}, volume={68}, url={https://doi.org/10.1007/s10236-018-1203-3}, DOI={10.1007/s10236-018-1203-3}, abstractNote={Right-side bias in both sea surface cooling and phytoplankton blooms is often observed in the wake of hurricanes in the Northern Hemisphere. This idealized hurricane modeling study uses a coupled biological-physical model to understand the underlying mechanisms behind hurricane-induced cooling and phytoplankton bloom asymmetry. Both a deep ocean case and a continental shelf sea case are considered and contrasted. Model analyses show that while right-side asymmetric mixing due to inertial oscillations and restratification from strong right-side recirculation cells contributes to bloom asymmetry in the open ocean, the well-mixed condition in the continental shelf sea inhibits formation of recirculation cells, and the convergence of water onto the shelf is a more important process for bloom asymmetry.}, number={11}, journal={Ocean Dynamics}, publisher={Springer Science and Business Media LLC}, author={McGee, Laura and He, Ruoying}, year={2018}, month={Nov}, pages={1443–1456} }
 @article{lohrenz_cai_chakraborty_huang_guo_he_xue_fennel_howden_tian_2018, title={Satellite estimation of coastal pCO(2) and air-sea flux of carbon dioxide in the northern Gulf of Mexico}, volume={207}, ISSN={["1879-0704"]}, DOI={10.1016/j.rse.2017.12.039}, abstractNote={Satellite approaches for estimation of the partial pressure of CO2 (pCO2) and air-sea flux of CO2 in coastal regions offer the potential to reduce uncertainties in coastal carbon budgets and improve understanding of spatial and temporal patterns and the factors influencing them. We used satellite-derived products in combination with an extensive data set of ship-based observations to develop an unprecedented multi-year time-series of pCO2 and air-sea flux of CO2 in the northern Gulf of Mexico for the period 2006–2010. A regression tree algorithm was used to relate satellite-derived products for chlorophyll, sea surface temperature, and dissolved and detrital organic matter to ship observations of pCO2. The resulting relationship had an r2 of 0.827 and a prediction error of 31.7 μatm pCO2 (root mean-squared error of the relationship was 28.8 μatm). Using a wind speed and gas exchange relationship along with satellite winds, estimates of air-sea flux of CO2 were derived yielding an average annual flux over the period 2006–2010 of − 0.8 to − 1.5 (annual mean = − 1.1 ± 0.3) mol C m− 2 y− 1, where the negative value indicates net ocean uptake. The estimated total annual CO2 flux for the study region was − 4.3 + 1.1 Tg C y− 1. Relationships of satellite-derived pCO2 with salinity were consistent with shipboard observations and exhibited a concave relationship with low values at mid- and low salinities attributed to strong biological drawdown of CO2 in the high productivity river-mixing zone. The time-series of satellite-derived pCO2 was characterized by a seasonal pattern with values lower during winter and spring, low to intermediate values during fall, and higher and more variable values during summer. These findings were similar to simulations from a coupled physical-biogeochemical model. A seasonal pattern was also evident in the air-sea flux of CO2 with generally more negative fluxes (i.e., ocean uptake) during winter and spring, and positive fluxes during summer months with fall being a period of transition. Interannual variations in annual means of both air-sea flux of CO2 and DIN loading were significant, with higher DIN loading coinciding in some cases with more negative air-sea flux of CO2 (i.e., net ocean uptake). Spatial patterns of pCO2 reflected regional environmental forcing including effects of river discharge, wind forcing, and shelf-slope circulation. Our study also illustrates the utility of satellite extrapolation for highlighting areas that may contribute significantly to regional signals and for guiding prioritization of locations for acquiring further observations. The approach should be readily applicable to other regions given adequate availability of in situ observations for algorithm development.}, journal={REMOTE SENSING OF ENVIRONMENT}, author={Lohrenz, S. E. and Cai, W. -J. and Chakraborty, S. and Huang, W. -J. and Guo, X. and He, R. and Xue, Z. and Fennel, K. and Howden, S. and Tian, H.}, year={2018}, month={Mar}, pages={71–83} }
 @article{robbins_daly_barbero_wanninkhof_he_zong_lisle_cai_smith_2018, title={Spatial and Temporal Variability of pCO(2), Carbon Fluxes, and Saturation State on the West Florida Shelf}, volume={123}, ISSN={["2169-9291"]}, url={https://doi.org/10.1029/2018JC014195}, DOI={10.1029/2018JC014195}, abstractNote={Abstract}, number={9}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, author={Robbins, L. L. and Daly, K. L. and Barbero, L. and Wanninkhof, R. and He, R. and Zong, H. and Lisle, J. T. and Cai, W. -J. and Smith, C. G.}, year={2018}, month={Sep}, pages={6174–6188} }
 @article{wilkin_rosenfeld_allen_baltes_baptista_he_hogan_kurapov_mehra_quintrell_et al._2017, title={Advancing coastal ocean modelling, analysis, and prediction for the US Integrated Ocean Observing System}, volume={10}, ISSN={["1755-8778"]}, url={https://doi.org/10.1080/1755876X.2017.1322026}, DOI={10.1080/1755876x.2017.1322026}, abstractNote={ABSTRACT This paper outlines strategies that would advance coastal ocean modelling, analysis and prediction as a complement to the observing and data management activities of the coastal components of the US Integrated Ocean Observing System (IOOS®) and the Global Ocean Observing System (GOOS). The views presented are the consensus of a group of US-based researchers with a cross-section of coastal oceanography and ocean modelling expertise and community representation drawn from Regional and US Federal partners in IOOS. Priorities for research and development are suggested that would enhance the value of IOOS observations through model-based synthesis, deliver better model-based information products, and assist the design, evaluation, and operation of the observing system itself. The proposed priorities are: model coupling, data assimilation, nearshore processes, cyberinfrastructure and model skill assessment, modelling for observing system design, evaluation and operation, ensemble prediction, and fast predictors. Approaches are suggested to accomplish substantial progress in a 3–8-year timeframe. In addition, the group proposes steps to promote collaboration between research and operations groups in Regional Associations, US Federal Agencies, and the international ocean research community in general that would foster coordination on scientific and technical issues, and strengthen federal–academic partnerships benefiting IOOS stakeholders and end users.}, number={2}, journal={JOURNAL OF OPERATIONAL OCEANOGRAPHY}, publisher={Informa UK Limited}, author={Wilkin, John and Rosenfeld, Leslie and Allen, Arthur and Baltes, Rebecca and Baptista, Antonio and He, Ruoying and Hogan, Patrick and Kurapov, Alexander and Mehra, Avichal and Quintrell, Josie and et al.}, year={2017}, pages={115–126} }
 @article{yao_xue_he_bao_xie_ge_2017, title={Climate projections of spatial variations in coastal storm surges along the Gulf of Mexico and U.S. east coast}, volume={16}, ISSN={1672-5182 1993-5021}, url={http://dx.doi.org/10.1007/S11802-017-3012-6}, DOI={10.1007/S11802-017-3012-6}, number={1}, journal={Journal of Ocean University of China}, publisher={Springer Nature}, author={Yao, Zhigang and Xue, Zuo and He, Ruoying and Bao, Xianwen and Xie, Jun and Ge, Qian}, year={2017}, month={Jan}, pages={1–7} }
 @article{ruoying he_li_2017, title={Cloud free Sea Surface Temperature and Chlorophyll-a analysis (2003-2012)}, url={https://doi.org/10.7266/N73R0R8M}, DOI={10.7266/N73R0R8M}, publisher={Harte Research Institute}, author={Ruoying He, Taylor Shropshire and Li, Yizhen}, year={2017} }
 @article{zuo xue_zhigang yao_he_2017, title={Dataset for: An Integrated ocean circulation, wave, atmosphere and marine ecosystem prediction system for the South Atlantic Might and Gulf of Mexico}, url={https://doi.org/10.7266/N7MP51QM}, DOI={10.7266/N7MP51QM}, publisher={Harte Research Institute}, author={Zuo Xue, Joseph Zambon and Zhigang Yao, Yuchuan Liu and He, Ruoying}, year={2017} }
 @article{yin_lin_he_hou_2017, title={Impact of mesoscale eddies on Kuroshio intrusion variability northeast of Taiwan}, volume={122}, ISSN={["2169-9291"]}, url={https://doi.org/10.1002/2016JC012263}, DOI={10.1002/2016jc012263}, abstractNote={Abstract}, number={4}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, author={Yin, Yuqi and Lin, Xiaopei and He, Ruoying and Hou, Yijun}, year={2017}, month={Apr}, pages={3021–3040} }
 @article{wall_mann_lembke_taylor_he_kellison_2017, title={Mapping the Soundscape Off the Southeastern USA by Using Passive Acoustic Glider Technology}, volume={9}, ISSN={["1942-5120"]}, url={https://doi.org/10.1080/19425120.2016.1255685}, DOI={10.1080/19425120.2016.1255685}, abstractNote={Abstract}, number={1}, journal={MARINE AND COASTAL FISHERIES}, publisher={Wiley}, author={Wall, Carrie C. and Mann, David A. and Lembke, Chad and Taylor, Chris and He, Ruoying and Kellison, Todd}, year={2017}, pages={23–37} }
 @book{wall_mann_lembke_taylor_he_kellison_2017, title={Mapping the Soundscape Off the Southeastern USA by Using Passive Acoustic Glider Technology}, url={https://doi.org/10.6084/m9.figshare.4632199.v1}, DOI={10.6084/m9.figshare.4632199.v1}, note={Abstract ; The purpose of this study was to explore the soundscape of shelf-edge Atlantic waters of the southeastern USA (SEUS) during winter by using passive acoustic and autonomous glider technologies, with a focus on the distribution of groupers. An autonomous glider was deployed off the SEUS coast near Cape Canaveral, Florida, on March 3, 2014, and transited to Cape Fear, North Carolina, where it was retrieved on April 1, 2014. Using satellite and hydrodynamic model data for guidance, the glider piloted in and out of the Gulf Stream, taking advantage of the high currents to reach the targeted sampling area. Ambient noise was recorded by an integrated passive acoustic recorder during the 29-d mission, in which the glider traveled 895 km and reached waters 267 m deep. A variety of sounds was identified in the acoustic recordings, including sounds generated by Red Grouper Epinephelus morio and toadfishes Opsanus sp.; two sounds previously documented in the Gulf of Mexico that were suspected to be produced by fish; whistles and echolocation from marine mammals; and extensive vessel noise. Numerous sounds from previously undocumented sources were also recorded. The Red Grouper was the only serranid that was consistently identified from the sound data, with detections occurring within and outside of South Atlantic Fishery Management Council marine protected areas. This research demonstrates the potential utility of a glider-based passive acoustic approach as a component of a program to map fish, marine mammal, and vessel distributions over large scales. Received February 16, 2016; accepted October 20, 2016}, institution={Figshare}, author={Wall, Carrie C. and Mann, David A. and Lembke, Chad and Taylor, Chris and He, Ruoying and Kellison, Todd}, year={2017} }
 @book{wall_mann_lembke_taylor_he_kellison_2017, title={Mapping the Soundscape Off the Southeastern USA by Using Passive Acoustic Glider Technology}, url={https://doi.org/10.6084/m9.figshare.4632199}, DOI={10.6084/m9.figshare.4632199}, note={Abstract ; The purpose of this study was to explore the soundscape of shelf-edge Atlantic waters of the southeastern USA (SEUS) during winter by using passive acoustic and autonomous glider technologies, with a focus on the distribution of groupers. An autonomous glider was deployed off the SEUS coast near Cape Canaveral, Florida, on March 3, 2014, and transited to Cape Fear, North Carolina, where it was retrieved on April 1, 2014. Using satellite and hydrodynamic model data for guidance, the glider piloted in and out of the Gulf Stream, taking advantage of the high currents to reach the targeted sampling area. Ambient noise was recorded by an integrated passive acoustic recorder during the 29-d mission, in which the glider traveled 895 km and reached waters 267 m deep. A variety of sounds was identified in the acoustic recordings, including sounds generated by Red Grouper Epinephelus morio and toadfishes Opsanus sp.; two sounds previously documented in the Gulf of Mexico that were suspected to be produced by fish; whistles and echolocation from marine mammals; and extensive vessel noise. Numerous sounds from previously undocumented sources were also recorded. The Red Grouper was the only serranid that was consistently identified from the sound data, with detections occurring within and outside of South Atlantic Fishery Management Council marine protected areas. This research demonstrates the potential utility of a glider-based passive acoustic approach as a component of a program to map fish, marine mammal, and vessel distributions over large scales. Received February 16, 2016; accepted October 20, 2016}, institution={Figshare}, author={Wall, Carrie C. and Mann, David A. and Lembke, Chad and Taylor, Chris and He, Ruoying and Kellison, Todd}, year={2017} }
 @article{bane_he_muglia_lowcher_gong_haines_2017, title={Marine Hydrokinetic Energy from Western Boundary Currents}, volume={9}, ISSN={["1941-1405"]}, DOI={10.1146/annurev-marine-010816-060423}, abstractNote={ The kinetic energy in ocean currents, or marine hydrokinetic (MHK) energy, is a renewable energy resource that can help meet global energy requirements. An ocean circulation model–based census shows that subtropical surface western boundary currents (WBCs) are the only nearshore, large-scale currents swift enough to drive large electricity-generating ocean turbines envisioned for future use. We review several WBCs in the context of kinetic energy extraction. The power density in the Gulf Stream off North Carolina at times reaches several thousand watts per square meter at 75 m below the surface, and the annual average power is approximately 500–1,000 W m−2. Significant fluctuations occur with periods of 3–20 days (Gulf Stream meanders) and weeks to months (Gulf Stream path shifts). Interannual variations in annual average power occur because of year-to-year changes in these WBC motions. No large-scale turbines presently exist, and the road to establishing MHK facilities in WBCs will encounter challenges that are similar in many aspects to those associated with the development of offshore wind power. }, number={1}, journal={ANNUAL REVIEW OF MARINE SCIENCE, VOL 9}, publisher={Annual Reviews}, author={Bane, John M. and He, Ruoying and Muglia, Michael and Lowcher, Caroline F. and Gong, Yanlin and Haines, Sara M.}, year={2017}, pages={105–123} }
 @article{lowcher_muglia_bane_he_gong_haines_2017, title={Marine Hydrokinetic Energy in the Gulf Stream Off North Carolina: An Assessment Using Observations and Ocean Circulation Models}, DOI={10.1007/978-3-319-53536-4_10}, journal={Marine Renewable Energy}, publisher={Springer International Publishing}, author={Lowcher, Caroline F. and Muglia, Michael and Bane, John M. and He, Ruoying and Gong, Yanlin and Haines, Sara M.}, year={2017}, pages={237–258} }
 @inbook{lowcher_muglia_bane_he_gong_haines_2017, title={Marine Hydrokinetic Energy in the Gulf Stream Off North Carolina: An Assessment Using Observations and Ocean Circulation Models}, booktitle={Marine Renewable Energy}, publisher={Springer, Cham}, author={Lowcher, Caroline F and Muglia, Michael and Bane, John M and He, Ruoying and Gong, Yanlin and Haines, Sara M}, year={2017}, pages={237–258} }
 @article{rempe_lenaghan_burris_stewart_2017, title={Metabolomic analysis of the mechanism of action of yerba mate aqueous extract on Salmonella enterica serovar Typhimurium}, volume={13}, ISSN={["1573-3890"]}, DOI={10.1007/s11306-016-1159-6}, number={2}, journal={METABOLOMICS}, author={Rempe, Caroline S. and Lenaghan, Scott C. and Burris, Kellie P. and Stewart, C. Neal, Jr.}, year={2017}, month={Feb} }
 @article{pringle_byers_he_pappalardo_wares_2017, title={Ocean currents and competitive strength interact to cluster benthic species range boundaries in the coastal ocean}, volume={567}, ISSN={["1616-1599"]}, DOI={10.3354/meps12065}, abstractNote={Dispersal of many coastal marine species is mediated by flows with strong directionality; bathymetric and topographic effects lead to strong alongshore variability in this transport. Using a simple model of the population dynamics of competing benthic species in a coastal ocean, we found that alongshore variability in dispersal can lead to clustering of species range boundaries for species whose dispersal is dominated by coastal currents. Furthermore, species can be absent from areas where they would have a relative competitive advantage because the presence or absence of a species is determined not only by local conditions but also by propagule supply, which is often affected by larval transport from far upstream. Our model demonstrates the quanti tative linkages between alongshore variation in coastal currents, spatial gradients in competitive strength, and the geographic extent of a species. We show that the predictions of the model are consistent with observed species distributions in the Gulf of Maine and Mid-Atlantic Bight, USA. A mechanism for extensive coexistence of competing species where range boundaries cluster is described. The implication of the clustering highlighted by our model suggests that for species whose dispersal is dominated by long-distance planktonic periods, climate change induced changes in the relative competitiveness of species will lead to abrupt changes in species range boundaries and not gradual range extension.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Pringle, James M. and Byers, James E. and He, Ruoying and Pappalardo, Paula and Wares, John}, year={2017}, month={Mar}, pages={29–40} }
 @article{li_queiroz_decarolis_bane_he_keeler_neary_2017, title={The economics of electricity generation from Gulf Stream currents}, volume={134}, ISSN={["1873-6785"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85020893529&partnerID=MN8TOARS}, DOI={10.1016/j.energy.2017.06.048}, abstractNote={Hydrokinetic turbines harnessing energy from ocean currents represent a potential low carbon electricity source. This study provides a detailed techno-economic assessment of ocean turbines operating in the Gulf Stream off the North Carolina coast. Using hindcast data from a high-resolution ocean circulation model in conjunction with the US Department of Energy's reference model 4 (RM4) for ocean turbines, we examine resource quality and apply portfolio optimization to identify the best candidate sites for ocean turbine deployment. We find that the lowest average levelized cost of electricity (LCOE) from a single site can reach 400 $/MWh. By optimally selecting geographically dispersed sites and taking advantage of economies of scale, the variations in total energy output can be reduced by an order of magnitude while keeping the LCOE below 300 $/MWh. Power take-off and transmission infrastructure are the largest cost drivers, and variation in resource quality can have a significant influence on the project LCOE. While this study focuses on a limited spatial domain, it provides a framework to assess the techno-economic feasibility of ocean current energy in other western boundary currents.}, journal={ENERGY}, publisher={Elsevier BV}, author={Li, Binghui and Queiroz, Anderson Rodrigo and DeCarolis, Joseph F. and Bane, John and He, Ruoying and Keeler, Andrew G. and Neary, Vincent S.}, year={2017}, month={Sep}, pages={649–658} }
 @article{mcveigh_eggleston_todd_young_he_2017, title={The influence of larval migration and dispersal depth on potential larval trajectories of a deep-sea bivalve}, volume={127}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2017.08.002}, abstractNote={Abstract Many fundamental questions in marine ecology require an understanding of larval dispersal and connectivity, yet direct observations of larval trajectories are difficult or impossible to obtain. Although biophysical models provide an alternative approach, in the deep sea, essential biological parameters for these models have seldom been measured empirically. In this study, we used a biophysical model to explore the role of behaviorally mediated migration from two methane seep sites in the Gulf of Mexico on potential larval dispersal patterns and population connectivity of the deep-sea mussel “ Bathymodiolus” childressi , a species for which some biological information is available. Three possible larval dispersal strategies were evaluated for larvae with a Planktonic Larval Duration (PLD) of 395 days: (1) demersal drift, (2) dispersal near the surface early in larval life followed by an extended demersal period before settlement, and (3) dispersal near the surface until just before settlement. Upward swimming speeds varied in the model based on the best data available. Average dispersal distances for simulated larvae varied between 16 km and 1488 km. Dispersal in the upper water column resulted in the greatest dispersal distance (1173 km ± 2.00), followed by mixed dispersal depth (921 km ± 2.00). Larvae originating in the Gulf of Mexico can potentially seed most known seep metapopulations on the Atlantic continental margin, whereas larvae drifting demersally cannot (237 km ± 1.43). Depth of dispersal is therefore shown to be a critical parameter for models of deep-sea connectivity.}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, publisher={Elsevier BV}, author={McVeigh, Doreen M. and Eggleston, David B. and Todd, Austin C. and Young, Craig M. and He, Ruoying}, year={2017}, month={Sep}, pages={57–64} }
 @article{yuan_castelao_he_2017, title={Variability in along-shelf and cross-shelf circulation in the South Atlantic Bight}, volume={134}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2017.01.006}, abstractNote={Variability in along-shelf and cross-shelf circulation in the South Atlantic Bight (SAB) is investigated using altimetry observations. Satellite-derived along-shelf velocity anomalies are in good agreement with independent near-surface current measurements from moored acoustic Doppler current profilers and surface velocities from high frequency radar at adjacent locations. This is especially true if wind-driven Ekman velocities are added to the geostrophic velocities, suggesting that the influence of Ekman dynamics to surface along-shelf flow in the SAB is unusually large. The decade-long time series reveals substantial seasonal variability in surface velocities, with peak poleward anomalies during late spring and summer and strong equatorward flow during autumn. Convergences and divergences in the along-shelf transport between two cross-sections are compared with three-dimensional numerical model results and used to estimate cross-shelf transport across the 50 m isobath in the SAB. The calculation suggests a pattern of weak offshore flow during spring followed by prolonged and relatively stronger offshore flow during summer and early autumn, while cross-shelf velocity anomalies during winter are weak and slightly onshore. Prolonged offshore flow following the peak in river discharge that generally occurs in spring indicates the potential for the establishment of a conduit for offshore export of riverine material. The long-term time series also reveals several large events of interannual variability, including the 2003 cold event observed in the SAB.}, journal={CONTINENTAL SHELF RESEARCH}, author={Yuan, Yeping and Castelao, Renato M. and He, Ruoying}, year={2017}, month={Feb}, pages={52–62} }
 @article{zeng_he_zong_2017, title={Variability of Changjiang Diluted Water revealed by a 45-year long-term ocean hindcast and Self-Organizing Maps analysis}, volume={146}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2017.08.010}, abstractNote={Based on long-term realistic ocean circulation hindcast for in the Bohai, Yellow, and East China Seas, 45 years (1961–2005) of sea surface salinity data were analyzed using Self-Organizing Maps (SOM) to have a better understanding of the Changjiang Diluted Water (CDW) variation. Three spatial patterns were revealed by the SOM: normal, transition, and extension. The normal pattern mainly occurs from December to May while the CDW hugs China's east coast closely and flows southward. The extension pattern is dominant from June to October when the CDW extends northwestward toward Jeju Island in an omega shape. The transition pattern prevails for the rest of the year. Pattern-averaged temperature, circulation, and chlorophyll-a concentration show significant differences. CDW area and its eastern most extension were explored as a function of the Changjiang runoff and regional upwelling index. We found that Changjiang runoff and upwelling index can be reasonable predictors for the overall CDW area, while ambient circulation determines the distribution and structure of the CDW, and thus the CDW eastern most extension.}, journal={CONTINENTAL SHELF RESEARCH}, publisher={Elsevier BV}, author={Zeng, Xiangming and He, Ruoying and Zong, Haibo}, year={2017}, month={Aug}, pages={37–46} }
 @inproceedings{tian_yang_zhang_pan_lohrenz_cai_he_xue_lu_ren_et al._2016, title={Anthropogenic and climatic controls on carbon and nitrogen exports from Mississippi river basin to Gulf of Mexico during 1800-2100: Implications for hypoxia and ocean acidification}, booktitle={AGU Fall Meeting Abstracts}, author={Tian, H and Yang, J and Zhang, B and Pan, S and Lohrenz, SE and Cai, WJ and He, R and Xue, ZG and Lu, C and Ren, W and et al.}, year={2016} }
 @article{wang_wang_herdrich_tsai_solihin_2016, title={CAF: Core to Core Communication Acceleration Framework}, DOI={10.1145/2967938.2967954}, abstractNote={As the number of cores in a multicore system increases, core-to-core (C2C) communication is increasingly limiting the performance scaling of workloads that share data frequently. The traditional way cores communicate is by using shared memory space between them. However, shared memory communication fundamentally involves coherence invalidations and cache misses, which cause large performance overheads and incur a high amount of network traffic. Many important workloads incur significant C2C communication and are affected significantly by the costs, including pipelined packet processing which is widely used in software-based networking solutions. In these workloads, threads run on different cores and pass packets from one core to another for different stages of processing using software queues. In this paper, we analyze the behavior and overheads of software queue management. Based on this analysis, we propose a novel C2C Communication Acceleration Framework (CAF) to optimize C2C communication. CAF offloads substantial communication burdens from cores and memory to a designated, efficient hardware device we refer to as Queue Management Device (QMD) attached to the Network on Chip. CAF combines hardware and software optimizations to effectively reduce the queue-induced communication overheads and improve the overall system performance by up to 2-12× over traditional software queue implementations.}, journal={2016 INTERNATIONAL CONFERENCE ON PARALLEL ARCHITECTURE AND COMPILATION TECHNIQUES (PACT)}, author={Wang, Yipeng and Wang, Ren and Herdrich, Andrew and Tsai, James and Solihin, Yan}, year={2016}, pages={351–362} }
 @article{ren_tian_cai_lohrenz_hopkinson_huang_yang_tao_pan_he_2016, title={Century-long increasing trend and variability of dissolved organic carbon export from the Mississippi River basin driven by natural and anthropogenic forcing}, volume={30}, ISSN={["1944-9224"]}, DOI={10.1002/2016gb005395}, abstractNote={Abstract}, number={9}, journal={GLOBAL BIOGEOCHEMICAL CYCLES}, author={Ren, Wei and Tian, Hanqin and Cai, Wei-Jun and Lohrenz, Steven E. and Hopkinson, Charles S. and Huang, Wei-Jen and Yang, Jia and Tao, Bo and Pan, Shufen and He, Ruoying}, year={2016}, month={Sep}, pages={1288–1299} }
 @inproceedings{xue_he_fennel_cai_lohrenz_huang_tian_ren_2016, title={Connecting the Mississippi River with Carbon Variability in the Gulf of Mexico}, booktitle={American Geophysical Union, Ocean Sciences Meeting 2016, abstract# AH33A-04}, author={Xue, ZG and He, R and Fennel, K and Cai, WJ and Lohrenz, SE and Huang, WJ and Tian, H and Ren, W}, year={2016} }
 @article{ledwell_he_xue_dimarco_spencer_chapman_2016, title={Dispersion of a tracer in the deep Gulf of Mexico}, volume={121}, ISSN={["2169-9291"]}, DOI={10.1002/2015jc011405}, abstractNote={Abstract}, number={2}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, publisher={Wiley-Blackwell}, author={Ledwell, James R. and He, Ruoying and Xue, Zuo and DiMarco, Steven F. and Spencer, Laura J. and Chapman, Piers}, year={2016}, month={Feb}, pages={1110–1132} }
 @article{zeng_he_2016, title={Gulf Stream variability and a triggering mechanism of its large meander in the South Atlantic Bight}, volume={121}, ISSN={["2169-9291"]}, DOI={10.1002/2016jc012077}, abstractNote={The Gulf Stream (GS) variability has an important impact on coastal circulation, shelf ecosystem, and regional weather and climate systems. Here we focus on the variability of the GS south of Cape Hatteras in the South Atlantic Bight (SAB). Statistical analysis on the 21 year satellite altimetry data reveals that the GS path in the SAB has two patterns: weakly and strongly deflected. The strongly deflected pattern is more likely to occur in winter. Over the last two decades, the largest GS offshore meander occurred in November 2009 to April 2010. Realistic ocean hindcast simulation and adjoint sensitivity analysis are used to investigate the triggering mechanisms for this extreme event. Our analyses show that a net increase of relative vorticity near the Charleston Bump was generated by strong interaction between increased GS velocity and local bathymetry, pushing the GS further offshore by virtue of conserving the potential vorticity. Quantitative vorticity analysis confirms this finding.}, number={11}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, publisher={Wiley}, author={Zeng, Xiangming and He, Ruoying}, year={2016}, month={Nov}, pages={8021–8038} }
 @inproceedings{he_bane_muglia_haines_lowcher_gong_taylor_2016, title={Gulf stream marine hydrokinetic energy resource characterization off Cape Hatteras, North Carolina USA}, DOI={10.1109/oceansap.2016.7485538}, abstractNote={The Gulf Stream off North Carolina (NC), USA has current velocities that approach 2 ms-1 and average volume transports of 90 Sv (1 Sv= 106 m3s-1) off of Cape Hatteras, making it the most abundant MHK (Marine Hydrokinetic Energy) resource for the state. Resource availability at a specified location depends primarily on the variability in Gulf Stream position, which is least offshore of Cape Hatteras after the stream exits the Florida Straits. Proximity to land and high current velocities in relatively shallow waters on the shelf slope make this an optimal location to quantify the MHK energy resource for NC. Multi-years of consistent current measurements beginning in August of 2013 from a moored 150 kHz ADCP at an optimal location for energy extraction quantify the available energy resource and its variability, and establish the skill of a regional ocean circulation model in predicting the MHK energy resource. The model agrees well with long term observed current averages and weekly to monthly fluctuations in the currents. Comparisons between the model and ADCP observed currents, and power density demonstrate the significant inter-annual variability in the Gulf Stream power density.}, booktitle={OCEANS 2016 - Shanghai}, publisher={IEEE}, author={He, Ruoying and Bane, John and Muglia, Mike and Haines, Sara and Lowcher, Caroline and Gong, Yanlin and Taylor, Patterson}, year={2016}, month={Apr} }
 @article{xue_he_fennel_wei-jun_lohrenz_huang_tian_ren_zang_2016, title={Modeling p CO 2 variability in the Gulf of Mexico}, volume={13}, number={15}, journal={Biogeosciences}, publisher={Copernicus GmbH}, author={Xue, Zuo and He, Ruoying and Fennel, Katja and Wei-Jun, Cai and Lohrenz, Steven and Huang, Wei-Jen and Tian, Hanqin and Ren, Wei and Zang, Zhengchen}, year={2016}, pages={4359} }
 @article{xue_he_fennel_cai_lohrenz_huang_tian_ren_zang_2016, title={Modeling pCO(2) variability in the Gulf of Mexico}, volume={13}, ISSN={["1726-4189"]}, DOI={10.5194/bg-13-4359-2016}, abstractNote={Abstract. A three-dimensional coupled physical–biogeochemical model was used to simulate and examine temporal and spatial variability of sea surface pCO2 in the Gulf of Mexico (GoM). The model was driven by realistic atmospheric forcing, open boundary conditions from a data-assimilative global ocean circulation model, and observed freshwater and terrestrial nutrient and carbon input from major rivers. A 7-year model hindcast (2004–2010) was performed and validated against ship measurements. Model results revealed clear seasonality in surface pCO2 and were used to estimate carbon budgets in the Gulf. Based on the average of model simulations, the GoM was a net CO2 sink with a flux of 1.11 ± 0.84  ×  1012 mol C yr−1, which, together with the enormous fluvial inorganic carbon input, was comparable to the inorganic carbon export through the Loop Current. Two model sensitivity experiments were performed: one without biological sources and sinks and the other using river input from the 1904–1910 period as simulated by the Dynamic Land Ecosystem Model (DLEM). It was found that biological uptake was the primary driver making GoM an overall CO2 sink and that the carbon flux in the northern GoM was very susceptible to changes in river forcing. Large uncertainties in model simulations warrant further process-based investigations.}, number={15}, journal={BIOGEOSCIENCES}, publisher={Copernicus GmbH}, author={Xue, Zuo and He, Ruoying and Fennel, Katja and Cai, Wei-Jun and Lohrenz, Steven and Huang, Wei-Jen and Tian, Hanqin and Ren, Wei and Zang, Zhengchen}, year={2016}, month={Aug}, pages={4359–4377} }
 @article{testa_adams_north_he_2016, title={Modeling the influence of deep water application of dispersants on the surface expression of oil: A sensitivity study}, volume={121}, ISSN={["2169-9291"]}, DOI={10.1002/2015jc011571}, abstractNote={Abstract}, number={8}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, author={Testa, Jeremy M. and Adams, E. Eric and North, Elizabeth W. and He, Ruoying}, year={2016}, month={Aug}, pages={5995–6008} }
 @inproceedings{he_woods_zambon_xue_2016, title={Monitoring the Gulf Stream and shelf environment in the South Atlantic Bight through integrated autonomous underwater glider observations and data assimilative ocean model predictions}, DOI={10.1109/oceansap.2016.7485539}, abstractNote={Gliders are the state-of-the-art autonomous underwater vehicles (AUV) that can operate unattended for roughly a month-long period in the ocean. Given a forward horizontal speed of 0.25 ms-1, gliders can cover ~ 25 km per day. They trace sawtooth profiles in the ocean by changing buoyancy, observing subsurface temperature, conductivity, and other water properties versus depth, and at the surface, fix position via Global Positioning System. Onshore team monitor and direct glider trajectories using two-way Iridium satellite communications, which permit near real-time delivery of observations and re-direction of mission/adaptive sampling. NCSU Ocean Observing and Modeling Group group has been running glider surveys in the South Atlantic Bight on a seasonal basis. Active research are being carried out to assimilate glider data along with other coastal ocean observations (satellite SST and SSH, mooring time series, HF Radar surface currents) into high resolution regional ocean model using advanced variational data assimilation schemes, providing a new look at along-shelf and cross-shelf exchanges associated with Gulf Stream dynamics.}, booktitle={OCEANS 2016 - Shanghai}, publisher={IEEE}, author={He, Ruoying and Woods, Wendy and Zambon, Joseph B. and Xue, Zuo}, year={2016}, month={Apr}, pages={1–4} }
 @article{zhigang_zuo_ruoying_xianwen_jun_2016, title={Statistical downscaling of IPCC sea surface wind and wind energy predictions for US east coastal ocean, Gulf of Mexico and Caribbean Sea}, volume={15}, ISSN={["1993-5021"]}, DOI={10.1007/s11802-016-2869-0}, number={4}, journal={JOURNAL OF OCEAN UNIVERSITY OF CHINA}, publisher={Springer Nature}, author={Zhigang, Yao and Zuo, Xue and Ruoying, He and Xianwen, Bao and Jun, Song}, year={2016}, month={Aug}, pages={577–582} }
 @article{shropshire_li_he_2016, title={Storm impact on sea surface temperature and chlorophyll a
 in the Gulf of Mexico and Sargasso Sea based on daily cloud-free satellite data reconstructions}, volume={43}, ISSN={0094-8276}, url={http://dx.doi.org/10.1002/2016GL071178}, DOI={10.1002/2016GL071178}, abstractNote={Abstract}, number={23}, journal={Geophysical Research Letters}, publisher={American Geophysical Union (AGU)}, author={Shropshire, Taylor and Li, Yizhen and He, Ruoying}, year={2016}, month={Dec}, pages={12,199–12,207} }
 @article{xue_zambon_yao_liu_he_2015, title={An integrated ocean circulation, wave, atmosphere, and marine ecosystem prediction system for the South Atlantic Bight and Gulf of Mexico}, volume={8}, ISSN={1755-876X 1755-8778}, url={http://dx.doi.org/10.1080/1755876X.2015.1014667}, DOI={10.1080/1755876x.2015.1014667}, abstractNote={An integrated nowcast/forecast modelling system covering the South Atlantic Bight and Gulf of Mexico (SABGOM) is in operation, utilizing sophisticated model coupling and parallel computing techniques. This three-dimensional, high-resolution, regional nowcast/forecast system provides a nowcast and an 84 h forecast of marine weather, ocean waves and circulation, and basic marine ecosystem conditions to the public via a Google Map interface. The SABGOM system runs automatically daily and supports a series of user-defined online applications. Extensive model validations were performed online against in situ and satellite-observed ocean conditions. The SABGOM system exhibits a reliable capability of providing valuable forecasts.}, number={1}, journal={Journal of Operational Oceanography}, publisher={Informa UK Limited}, author={Xue, Zuo and Zambon, Joseph and Yao, Zhigang and Liu, Yuchuan and He, Ruoying}, year={2015}, month={Jan}, pages={80–91} }
 @article{tian_ren_yang_tao_cai_lohrenz_hopkinson_liu_yang_lu_et al._2015, title={Climate extremes dominating seasonal and interannual variations in carbon export from the Mississippi River Basin}, volume={29}, ISSN={["1944-9224"]}, DOI={10.1002/2014gb005068}, abstractNote={Abstract}, number={9}, journal={GLOBAL BIOGEOCHEMICAL CYCLES}, author={Tian, Hanqin and Ren, Wei and Yang, Jia and Tao, Bo and Cai, Wei-Jun and Lohrenz, Steven E. and Hopkinson, Charles S. and Liu, Mingliang and Yang, Qichun and Lu, Chaoqun and et al.}, year={2015}, month={Sep}, pages={1333–1347} }
 @article{tian_ren_yang_tao_cai_lohrenz_hopkinson_liu_yang_lu_et al._2015, title={Climate extremes dominating seasonal and interannual variations in carbon export from the Mississippi River Basin}, volume={29}, number={9}, journal={Global Biogeochemical Cycles}, author={Tian, Hanqin and Ren, Wei and Yang, Jia and Tao, Bo and Cai, Wei-Jun and Lohrenz, Steven E and Hopkinson, Charles S and Liu, Mingliang and Yang, Qichun and Lu, Chaoqun and et al.}, year={2015}, pages={1333–1347} }
 @article{zeng_li_he_yin_2015, title={Clustering of Loop Current patterns based on the satellite-observed sea surface height and self-organizing map}, volume={6}, ISSN={["2150-7058"]}, DOI={10.1080/2150704x.2014.998347}, abstractNote={The self-organizing map is used to investigate variations of the Loop Current (LC) in the Gulf of Mexico from 1992 to 2013 based on satellite-observed sea surface height data. It is found that LC variations can be characterized by three spatial patterns: normal, extension and retraction. The corresponding temporal variations confirm that LC eddy shedding generally occurs during the transition from the extension to retraction patterns. On the weekly time scale, the wind stress curl (WSC) in the Caribbean Sea has a major influence on LC eddy shedding. The increase of Caribbean WSC from June to November favours more frequent LC eddy shedding during that period. On the interannual time scale, there is also a potential linkage between the frequency of LC eddy shedding and El Niño activities.}, number={1}, journal={REMOTE SENSING LETTERS}, publisher={Informa UK Limited}, author={Zeng, Xiangming and Li, Yizhen and He, Ruoying and Yin, Yuqi}, year={2015}, pages={11–19} }
 @article{kourafalou_de mey_le henaff_charria_edwards_he_herzfeld_pascual_stanev_tintore_et al._2015, title={Coastal Ocean Forecasting: system integration and evaluation}, volume={8}, ISSN={["1755-8778"]}, DOI={10.1080/1755876x.2015.1022336}, abstractNote={Recent advances in Coastal Ocean Forecasting Systems (COFS) are discussed. Emphasis is given to the integration of the observational and modeling components, each developed in the context of monitoring and forecasting in the coastal seas. These integrated systems must be linked to larger scale systems toward seamless data sets, nowcasts and forecasts (from the global ocean, through the continental shelf and to the nearshore regions). Emerging capabilities include: methods to optimize coastal/regional observational networks; and probabilistic approaches to address both science and applications related to COFS. International collaboration is essential to exchange best practices, achieve common frameworks and establish standards.}, journal={JOURNAL OF OPERATIONAL OCEANOGRAPHY}, author={Kourafalou, V. H. and De Mey, P. and Le Henaff, M. and Charria, G. and Edwards, C. A. and He, R. and Herzfeld, M. and Pascual, A. and Stanev, E. V. and Tintore, J. and et al.}, year={2015}, pages={S127–S146} }
 @article{qian_li_he_eggleston_2015, title={Connectivity in the Intra-American Seas and implications for potential larval transport}, volume={34}, ISSN={0722-4028 1432-0975}, url={http://dx.doi.org/10.1007/S00338-014-1244-0}, DOI={10.1007/S00338-014-1244-0}, number={2}, journal={Coral Reefs}, publisher={Springer Science and Business Media LLC}, author={Qian, H. and Li, Y. and He, R. and Eggleston, D. B.}, year={2015}, month={Jun}, pages={403–417} }
 @article{he_zhang_glotfelty_he_bennartz_rausch_sartelet_2015, title={Decadal simulation and comprehensive evaluation of CESM/CAM5.1 with advanced chemistry, aerosol microphysics, and aerosol-cloud interactions}, volume={7}, ISSN={["1942-2466"]}, DOI={10.1002/2014ms000360}, abstractNote={Abstract}, number={1}, journal={JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS}, publisher={American Geophysical Union (AGU)}, author={He, Jian and Zhang, Yang and Glotfelty, Tim and He, Ruoying and Bennartz, Ralf and Rausch, John and Sartelet, Karine}, year={2015}, month={Mar}, pages={110–141} }
 @inproceedings{muglia_he_lowcher_bane_gong_taylor_2015, title={Gulf Stream marine hydrokinetic energy resource characterization off Cape Hatteras, North Carolina}, booktitle={AGU Fall Meeting Abstracts}, author={Muglia, M and He, R and Lowcher, C and Bane, J and Gong, Y and Taylor, P}, year={2015} }
 @article{ren_tian_tao_yang_pan_cai_lohrenz_he_hopkinson_2015, title={Large increase in dissolved inorganic carbon flux from the Mississippi River to Gulf of Mexico due to climatic and anthropogenic changes over the 21st century}, volume={120}, DOI={10.1002/2014jg002761}, abstractNote={Abstract}, number={4}, journal={Journal of Geophysical Research-Biogeosciences}, author={Ren, W. and Tian, H. Q. and Tao, B. and Yang, J. and Pan, S. F. and Cai, W. J. and Lohrenz, S. E. and He, Ruoying and Hopkinson, C. S.}, year={2015}, pages={724–736} }
 @article{kapule_2015, title={MINISTRY OF FISHERIES AND MARINE RESOURCES LIBRARY: ITS DEVELOPMENT, IMPORTANCE, POTENTIAL, STRENGTHS & WEAKNESSES AND CHALLENGES}, publisher={IAMSLIC}, author={Kapule, Ataban}, year={2015} }
 @article{chen_he_2015, title={Mean circulation in the coastal ocean off northeastern North America from a regional-scale ocean model}, volume={11}, ISSN={["1812-0784"]}, DOI={10.5194/os-11-503-2015}, abstractNote={Abstract. A regional-scale ocean model was used to hindcast the coastal circulation over the Middle Atlantic Bight (MAB) and Gulf of Maine (GOM) from 2004 to 2013. The model was nested inside a data assimilative global ocean model that provided initial and open boundary conditions. Realistic atmospheric forcing, tides and observed river runoff were also used to drive the model. Hindcast solutions were compared against observations, which included coastal sea levels, satellite altimetry sea surface height, in situ temperature and salinity measurements in the GOM, and observed mean depth-averaged velocities. Good agreements with observations suggest that the hindcast model is capable of capturing the major circulation variability in the MAB and GOM. Time- and space-continuous hindcast fields were used to depict the mean circulation, along- and cross-shelf transport and the associated momentum balances. The hindcast confirms the presence of the equatorward mean shelf circulation, which varies from 2.33 Sv over the Scotian Shelf to 0.22 Sv near Cape Hatteras. Using the 200 m isobath as the shelf/slope boundary, the mean cross-shelf transport calculations indicate that the shelfbreak segments off the Gulf of Maine (including the southern flank of Georges Bank and the Northeast Channel) and Cape Hatteras are the major sites for shelf water export. The momentum analysis reveals that the along-shelf sea level difference from Nova Scotia to Cape Hatteras is about 0.36 m. The nonlinear advection, stress, and horizontal viscosity terms all contribute to the ageostrophic circulation in the along-isobath direction, whereas the nonlinear advection plays a dominant role in determining the ageostrophic current in the cross-isobath direction.
                    }, number={4}, journal={OCEAN SCIENCE}, author={Chen, K. and He, R.}, year={2015}, pages={503–517} }
 @article{gong_he_gawarkiewicz_savidge_2015, title={Numerical investigation of coastal circulation dynamics near Cape Hatteras, North Carolina, in January 2005}, volume={65}, ISSN={["1616-7228"]}, DOI={10.1007/s10236-014-0778-6}, abstractNote={A realistic regional ocean model is used to hindcast and diagnose coastal circulation variability near Cape Hatteras, North Carolina, in January 2005. Strong extratropical winter storms passed through the area during the second half of the month (January 15–31), leading to significantly different circulation conditions compared to those during the first half of the month (January 1–14). Model results were validated against sea level, temperature, salinity, and velocity observations. Analyses of along-shelf and cross-shelf transport, momentum, and kinetic energy balances were further performed to investigate circulation dynamics near Cape Hatteras. Our results show that during the strong winter storm period, both along-shelf (southward) and cross-shelf (seaward) transport increased significantly, mainly due to increases in geostrophic velocity associated with coastal sea level setup. In terms of momentum balance, the wind stress was mainly balanced by bottom friction. During the first half of month, the dominant kinetic energy (KE) balance on the shelf was between the time rate of KE change and the pressure work, whereas during the stormy second half of month, the main shelf KE balance was achieved between wind stress work and dissipation.}, number={1}, journal={OCEAN DYNAMICS}, publisher={Springer Nature}, author={Gong, Yanlin and He, Ruoying and Gawarkiewicz, Glen G. and Savidge, Dana K.}, year={2015}, month={Jan}, pages={1–15} }
 @inproceedings{muglia_lowcher_taylor_he_seim_bane_edge_2015, title={Observation and regional model based Gulf Stream marine hydrokinetic energy resource estimates for North Carolina}, DOI={10.23919/oceans.2015.7404508}, abstractNote={North Carolina and Florida are likely the only two states on the US east coast that have practical access to energy extraction from the Gulf Stream. After leaving the Florida Straits, the Gulf Stream in the region offshore of Cape Hatteras, NC exhibits the least variability in position of any location on the east coast, while simultaneously being closest to land. Gulf Stream current speeds exceed 2 m/s. These important characteristics have made this area the focus of observations and regional model estimates to quantify the hydrokinetic energy that may be available from the Gulf Stream for the state of North Carolina. Three types of observations to quantify the energy resource off NC began in 2013. A 150 kHz Acoustic Doppler Current Profiler (ADCP) was moored on the 225 isobath at the location estimated to be best for energy extraction, and recovered after two consecutive nineand ten-month deployments, respectively. Another ADCP was moored in nearly the same location to continue observations, and will be retrieved in August 2015. Currents from the first deployment averaged 1.15 m/s, and the power density was 779 W/m2 at a depth of 30m over the 9-month duration. Significant variability in current speed, and thus power, occurred over the deployment period. Additionally, current measurements from a vessel mounted 300 kHz ADCP were made from water depths of 100m to 1000 m on a crossisobath transect that passed over the location of the ADCP mooring. Currents measured from the vessel compare favorably with those from the moored 150 kHz ADCP in both magnitude and direction, and provide valuable information about the spatial variability of the current and its dependence on depth. In 2013, a coastal ocean radar (Codar) was added to an existing radar network that had been measuring ocean surface currents for more than a decade in the region to expand coverage over the entire study area. The radar current measurements provide consistent spatial and temporal coverage throughout the Gulf Stream cyclonic shear zone, and are being used to measure the variability in Gulf Stream position off of Cape Hatteras, NC. One method being developed using measurements from individual radars assumes the landward Gulf Stream front lies along selected maxima in the radial current shears chosen for consistency over the time period sampled, and magnitude. The locations where the Gulf Stream first enters and exits the radar coverage area are apparent in the large radial speeds measured by the radar, and the width and variability of the Gulf Stream cyclonic shear zone is estimated using maxima in velocity and velocity shears. Favorable comparisons between the three current observations will provide confidence that power estimates can be extrapolated from the radar surface currents alone over long time periods when ADCP information may not be available. Finally, observations are being compared with a regional specific Mid-Atlantic Bight and South Atlantic Bight (MABSAB) Model. Moored ADCP current measurements compared favorably with the model, demonstrating the skill of the model for power estimates in this area. Averaged current measurements 30 m below the surface from the ADCP mooring made between August 2013 - April 2014 and model estimates at the same location were nearly identical, both having average current speeds of 1.15 m/s. The model is more conservative than the observations with respect to higher frequency fluctuations in speed and direction.}, booktitle={OCEANS 2015 - MTS/IEEE Washington}, publisher={IEEE}, author={Muglia, Mike and Lowcher, Caroline and Taylor, Patterson and He, Ruoying and Seim, Harvey and Bane, John and Edge, Billy}, year={2015}, month={Oct} }
 @inproceedings{muglia_he_lowcher_bane_taylor_edge_2015, title={Observation and regional model based Gulf Stream marine hydrokinetic energy resource estimates for North Carolina}, DOI={10.1109/oceans-genova.2015.7271441}, abstractNote={North Carolina and Florida are likely the only two states on the US east coast that have practical access to energy extraction from the Gulf Stream. After leaving the Florida Straits, the Gulf Stream in the region offshore of Cape Hatteras, NC exhibits the least variability in position of any location on the east coast, while simultaneously being closest to land. Gulf Stream current speeds exceed 2 m/s. These important characteristics have made this area the focus of observations and regional model estimates to quantify the hydrokinetic energy that may be available from the Gulf Stream for the state of North Carolina. Three types of observations to quantify the energy resource off NC began in 2013. A 150 kHz Acoustic Doppler Current Profiler (ADCP) was moored on the 225-m isobath at the location estimated to be best for energy extraction, and recovered after two consecutive nine- and ten-month deployments, respectively. Another ADCP was moored in nearly the same location to continue observations, and will be retrieved in August 2015. Currents from the first deployment averaged 1.15 m/s, and the power density was 779 W/m2 at a depth of 30m over the 9-month duration. Significant variability in current speed, and thus power, occurred over the deployment period. Additionally, current measurements from a vessel mounted 300 kHz ADCP were made from water depths of 100m to 1000 m on a cross-isobath transect that passed over the location of the ADCP mooring. Currents measured from the vessel compare favorably with those from the moored 150 kHz ADCP in both magnitude and direction, and provide valuable information about the spatial variability of the current and its dependence on depth. In 2013, a coastal ocean radar (Codar) was added to an existing radar network that had been measuring ocean surface currents for more than a decade in the region to expand coverage over the entire study area. The radar current measurements provide consistent spatial and temporal coverage throughout the Gulf Stream cyclonic shear zone, and are being used to measure the variability in Gulf Stream position off of Cape Hatteras, NC. One method being developed using measurements from individual radars assumes the landward Gulf Stream front lies along selected maxima in the radial current shears chosen for consistency over the time period sampled, and magnitude. The locations where the Gulf Stream first enters and exits the radar coverage area are apparent in the large radial speeds measured by the radar, and the width and variability of the Gulf Stream cyclonic shear zone is estimated using maxima in velocity and velocity shears. Favorable comparisons between the three current observations will provide confidence that power estimates can be extrapolated from the radar surface currents alone over long time periods when ADCP information may not be available. Finally, observations are being compared with a regional specific Mid-Atlantic Bight and South Atlantic Bight (MABSAB) Model. Moored ADCP current measurements compared favorably with the model, demonstrating the skill of the model for power estimates in this area. Averaged current measurements 30 m below the surface from the ADCP mooring made between August 2013-April 2014 and model estimates at the same location were nearly identical, both having average current speeds of 1.15 m/s. The model is more conservative than the observations with respect to higher frequency fluctuations in speed and direction.}, booktitle={OCEANS 2015 - Genova}, publisher={IEEE}, author={Muglia, Mike and He, Ruoying and Lowcher, Caroline and Bane, John and Taylor, Patterson and Edge, Billy}, year={2015}, month={May} }
 @article{zeng_li_he_2015, title={Predictability of the Loop Current Variation and Eddy Shedding Process in the Gulf of Mexico Using an Artificial Neural Network Approach}, volume={32}, ISSN={["1520-0426"]}, DOI={10.1175/jtech-d-14-00176.1}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF ATMOSPHERIC AND OCEANIC TECHNOLOGY}, publisher={American Meteorological Society}, author={Zeng, Xiangming and Li, Yizhen and He, Ruoying}, year={2015}, month={May}, pages={1098–1111} }
 @article{zeng_he_xue_wang_wang_yao_guan_warrillow_2015, title={River-derived sediment suspension and transport in the Bohai, Yellow, and East China Seas: A preliminary modeling study}, volume={111}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2015.08.015}, abstractNote={Coastal circulation and transport of sediment derived from the Huanghe and Changjiang Rivers in the Bohai, Yellow, and East China Seas (BYECS) over the past 48 years (1958–2005) were simulated and analyzed using the Coupled Ocean–Atmosphere–Wave–Sediment Transport modeling system. Model skill assessments against in situ wave and hydrographical observations indicate the model simulation can reasonably well reproduce the hydrodynamic environment of the BYECS. Model-simulated regions of high fine sediment accumulation rate correlate well with the observed regions, which are known as "muddy patches." Bottom stress analysis further indicates that the formation of muddy patches near river mouths is largely due to their proximity to the sediment source. Muddy patches formed in regions farther away from river mouths are results of local weak bottom stress and associated circulation pattern. Simulated seabed sediment distribution reveals that most of the Huanghe-derived sediment stays inside the Bohai Sea, whereas the Changjiang-derived sediment can spread into both the Yellow and East China Seas. Strong seasonal variations exist in the river-derived sediment transport with stronger (weaker) offshore sediment transport occurring in the winter (summer).}, journal={CONTINENTAL SHELF RESEARCH}, publisher={Elsevier BV}, author={Zeng, Xiangming and He, Ruoying and Xue, Zuo and Wang, Houjie and Wang, Yue and Yao, Zhigang and Guan, Weibing and Warrillow, Jennifer}, year={2015}, month={Dec}, pages={112–125} }
 @article{north_adams_thessen_schlag_he_socolofsky_masutani_peckham_2015, title={The influence of droplet size and biodegradation on the transport of subsurface oil droplets during the Deepwater Horizon spill: a model sensitivity study}, volume={10}, ISSN={["1748-9326"]}, DOI={10.1088/1748-9326/10/2/024016}, abstractNote={A better understanding of oil droplet formation, degradation, and dispersal in deep waters is needed to enhance prediction of the fate and transport of subsurface oil spills. This research evaluates the influence of initial droplet size and rates of biodegradation on the subsurface transport of oil droplets, specifically those from the Deepwater Horizon oil spill. A three-dimensional coupled model was employed with components that included analytical multiphase plume, hydrodynamic and Lagrangian models. Oil droplet biodegradation was simulated based on first order decay rates of alkanes. The initial diameter of droplets (10–300 μm) spanned a range of sizes expected from dispersant-treated oil. Results indicate that model predictions are sensitive to biodegradation processes, with depth distributions deepening by hundreds of meters, horizontal distributions decreasing by hundreds to thousands of kilometers, and mass decreasing by 92–99% when biodegradation is applied compared to simulations without biodegradation. In addition, there are two- to four-fold changes in the area of the seafloor contacted by oil droplets among scenarios with different biodegradation rates. The spatial distributions of hydrocarbons predicted by the model with biodegradation are similar to those observed in the sediment and water column, although the model predicts hydrocarbons to the northeast and east of the well where no observations were made. This study indicates that improvement in knowledge of droplet sizes and biodegradation processes is important for accurate prediction of subsurface oil spills.}, number={2}, journal={ENVIRONMENTAL RESEARCH LETTERS}, author={North, Elizabeth W. and Adams, E. Eric and Thessen, Anne E. and Schlag, Zachary and He, Ruoying and Socolofsky, Scott A. and Masutani, Stephen M. and Peckham, Scott D.}, year={2015}, month={Feb} }
 @article{huang_cai_wang_hu_chen_lohrenz_chakraborty_he_brandes_hopkinson_2015, title={The response of inorganic carbon distributions and dynamics to upwelling-favorable winds on the northern Gulf of Mexico during summer}, volume={111}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2015.08.020}, abstractNote={Upwelling-favorable winds and an offshore-distributed Mississippi and Atchafalaya River plume trajectory were observed in summer 2009 in contrast to the mean conditions from 2002 to 2010 (upwelling-unfavorable winds and an alongshore river plume trajectory), a set of conditions which was also observed in summer 2007. The responses of dissolved inorganic carbon (DIC) distributions and dynamics to upwelling-favorable winds are studied by comparing the contrasting conditions between summer 2009 and summer 2007 on the northern Gulf of Mexico. Patterns of surface water partial pressure of CO2 (pCO2), DIC, δ13C in DIC, and total alkalinity (TA) determined in July 2009 and August 2007 were strongly related to river plume trajectories, and differed between the two summers. The slope of the relationship between dissolved oxygen (DO) and DIC in summer 2007 was comparable to the Redfield O/C ratio of 1.3, which was attributed to respiration of organic matter in the bottom water. The slope of the DO and DIC relationship and δ13CDIC values in bottom waters during July 2009 were clearly affected by mixing since their salinities were <35. A three end-member mixing model was used to remove mixing effects in (1) δ13CDIC, to estimate the organic source of respiration, and (2) in DIC concentrations, to calculate DIC removal and release. δ13CDIC results in both summers were consistent with an apparent release of DIC in hypoxic waters (DO less than 2 mg L−1) associated with respiration of surface organic matter. The area-weighted surface DIC removal (i.e., biological production) was lower in 2009 than in 2007 on the shelf, as the plume was distributed offshore. The release of DIC in bottom waters was higher over the shelf in 2009 and was surmised to be related to stronger mixing, which was favorable for the DO supply for respiration. Overall, surface waters on the continental shelf in the region of study in July 2009 acted as a weak CO2 source to the atmosphere, but a weak CO2 sink in August 2007. We contend that the inorganic carbon distribution and concentrations on the shelf were related to regional wind forcing, through its influence on the distribution of coastal currents and plume trajectories and their subsequent impact on biogeochemical processes.}, journal={CONTINENTAL SHELF RESEARCH}, author={Huang, W. -J. and Cai, W. -J and Wang, Y. and Hu, X. and Chen, B. and Lohrenz, S. E. and Chakraborty, S. and He, R. and Brandes, J. and Hopkinson, C. S.}, year={2015}, month={Dec}, pages={211–222} }
 @article{li_he_chen_mcgillicuddy_2015, title={Variational data assimilative modeling of the Gulf of Maine in spring and summer 2010}, volume={120}, ISSN={["2169-9291"]}, DOI={10.1002/2014jc010492}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, author={Li, Yizhen and He, Ruoying and Chen, Ke and McGillicuddy, Dennis J.}, year={2015}, month={May}, pages={3522–3541} }
 @article{li_he_chen_mcgillicuddy_2015, title={Variational data assimilative modeling of the Gulf of Maine in spring and summer 2010}, volume={120}, number={5}, journal={Journal of Geophysical Research: Oceans}, author={Li, Yizhen and He, Ruoying and Chen, Ke and McGillicuddy, Dennis J}, year={2015}, pages={3522–3541} }
 @article{mcgillicuddy_brosnahan_couture_he_keafer_manning_martin_pilskaln_townsend_anderson_2014, title={A red tide of Alexandrium fundyense in the Gulf of Maine}, volume={103}, ISSN={["1879-0100"]}, DOI={10.1016/j.dsr2.2013.05.011}, abstractNote={In early July 2009, an unusually high concentration of the toxic dinoflagellate Alexandrium fundyense occurred in the western Gulf of Maine, causing surface waters to appear reddish brown to the human eye. The discolored water appeared to be the southern terminus of a large-scale event that caused shellfish toxicity along the entire coast of Maine to the Canadian border. Rapid-response shipboard sampling efforts together with satellite data suggest the water discoloration in the western Gulf of Maine was a highly ephemeral feature of less than two weeks in duration. Flow cytometric analysis of surface samples from the red water indicated the population was undergoing sexual reproduction. Cyst fluxes downstream of the discolored water were the highest ever measured in the Gulf of Maine, and a large deposit of new cysts was observed that fall. Although the mechanisms causing this event remain unknown, its timing coincided with an anomalous period of downwelling-favorable winds that could have played a role in aggregating upward-swimming cells. Regardless of the underlying causes, this event highlights the importance of short-term episodic phenomena on regional population dynamics of A. fundyense.}, journal={DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY}, author={McGillicuddy, D. J., Jr. and Brosnahan, M. L. and Couture, D. A. and He, R. and Keafer, B. A. and Manning, J. P. and Martin, J. L. and Pilskaln, C. H. and Townsend, D. W. and Anderson, D. M.}, year={2014}, month={May}, pages={174–184} }
 @article{a red tide of alexandrium fundyense in the gulf of maine_2014, volume={103}, journal={Deep Sea Research Part II: Topical Studies in Oceanography}, publisher={Pergamon}, year={2014}, pages={174–184} }
 @article{a red tide of alexandrium fundyense in the gulf of maine_2014, volume={103}, journal={Deep Sea Research Part II: Topical Studies in Oceanography}, publisher={Pergamon}, year={2014}, pages={174–184} }
 @article{nelson_he_warner_bane_2014, title={Air–sea interactions during strong winter extratropical storms}, volume={64}, DOI={10.1007/s10236-014-0745-2}, number={9}, journal={Ocean Dynamics}, publisher={Springer Nature}, author={Nelson, Jill and He, Ruoying and Warner, John C. and Bane, John}, year={2014}, month={Jul}, pages={1233–1246} }
 @article{li_he_manning_2014, title={Coastal connectivity in the Gulf of Maine in spring and summer of 2004--2009}, volume={103}, journal={Deep Sea Research Part II: Topical Studies in Oceanography}, publisher={Pergamon}, author={Li, Yizhen and He, Ruoying and Manning, James P}, year={2014}, pages={199–209} }
 @article{li_he_manning_2014, title={Coastal connectivity in the Gulf of Maine in spring and summer of 2004-2009}, volume={103}, ISSN={["1879-0100"]}, DOI={10.1016/j.dsr2.2013.01.037}, abstractNote={Coastal ocean connectivity associated with the Gulf of Maine (GOM) surface flows in spring and summer seasons of 2004–2009 is studied using surface numerical particle tracking based on realistic regional ocean circulation hindcast solutions. Seven initial particle release sites are selected in key gulf regions often affected by harmful algal (Alexandrium fundyense) blooms, including Massachusetts Bay, the western GOM coastal area, the eastern GOM coastal area, the Bay of Fundy, Wilkinson Basin, the Jordan Basin, and a region seaward of Penobscot Bay. Surface particles are released every 5 days between February 1st and August 1st in each year, and the variability in their trajectories on interannual time scales is quantified by Lagrangian probability density function calculations. Coastal connectivity is further quantified using a connectivity matrix, identifying source and destination functions. Our results suggest that the interannual variability in coastal connectivity has strong impact on the spatial distribution of A. fundyense blooms in each year.}, journal={DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY}, publisher={Pergamon}, author={Li, Yizhen and He, Ruoying and Manning, James P.}, year={2014}, month={May}, pages={199–209} }
 @article{chen_he_powell_gawarkiewicz_moore_arango_2014, title={Data assimilative modeling investigation of Gulf Stream Warm Core Ring interaction with continental shelf and slope circulation}, volume={119}, ISSN={["2169-9291"]}, DOI={10.1002/2014jc009898}, abstractNote={Abstract}, number={9}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, author={Chen, Ke and He, Ruoying and Powell, Brian S. and Gawarkiewicz, Glen G. and Moore, Andrew M. and Arango, Hernan G.}, year={2014}, month={Sep}, pages={5968–5991} }
 @article{tao_tian_ren_yang_yang_he_cai_lohrenz_2014, title={Increasing Mississippi river discharge throughout the 21st century influenced by changes in climate, land use, and atmospheric CO2}, volume={41}, ISSN={["1944-8007"]}, DOI={10.1002/2014gl060361}, abstractNote={Abstract}, number={14}, journal={GEOPHYSICAL RESEARCH LETTERS}, publisher={American Geophysical Union (AGU)}, author={Tao, Bo and Tian, Hanqin and Ren, Wei and Yang, Jia and Yang, Qichun and He, Ruoying and Cai, Weijun and Lohrenz, Steven}, year={2014}, month={Jul}, pages={4978–4986} }
 @article{zambon_he_warner_2014, title={Investigation of hurricane Ivan using the coupled ocean–atmosphere–wave–sediment transport (COAWST) model}, volume={64}, ISSN={1616-7341 1616-7228}, url={http://dx.doi.org/10.1007/s10236-014-0777-7}, DOI={10.1007/s10236-014-0777-7}, number={11}, journal={Ocean Dynamics}, publisher={Springer Science and Business Media LLC}, author={Zambon, Joseph B. and He, Ruoying and Warner, John C.}, year={2014}, month={Oct}, pages={1535–1554} }
 @article{seasonal and interannual variability in gulf of maine hydrodynamics: 2002--2011_2014, volume={103}, journal={Deep Sea Research Part II: Topical Studies in Oceanography}, publisher={Pergamon}, year={2014}, pages={210–222} }
 @article{seasonal and interannual variability in gulf of maine hydrodynamics: 2002--2011_2014, volume={103}, journal={Deep Sea Research Part II: Topical Studies in Oceanography}, publisher={Pergamon}, year={2014}, pages={210–222} }
 @article{li_he_mcgillicuddy_2014, title={Seasonal and interannual variability in Gulf of Maine hydrodynamics: 2002-2011}, volume={103}, ISSN={["1879-0100"]}, DOI={10.1016/j.dsr2.2013.03.001}, abstractNote={In situ observations including long-term moored meteorological and oceanographic measurements and multi-year gulf-wide ship survey data are used to quantify interannual variability of surface wind, river runoff, and hydrographic conditions in the Gulf of Maine during summers 2002-2011. The cumulative upwelling index shows that upwelling (downwelling)-favorable wind conditions were most persistent in 2010 (2005) over the 10-year study period. River discharge was highest in 2005; peak runoff occurred in early April in 2010 as opposed to late April to middle May in other years. Moored time series show that coastal water temperature was 0.5-2 °C warmer than average in summer 2010, and about 2 °C colder than average in 2004. Coastal salinity in April 2010 was the lowest in the 10-year study period. Both moored Acoustic Doppler Current Profiler (ADCP) current measurements and dynamic height/geostrophic velocity calculations based on gulf-wide ship survey data show May-June 2010 had one of the weakest alongshore transports in the western Gulf of Maine during the 10-year study period, likely associated with intrusions of warm slope water and fresher-than-usual Scotian Shelf water. Comparisons of coastal currents to the Paralytic Shellfish Poisoning (PSP) closure maps resulting from A. fundyense blooms suggest a linkage between alongshore transport and the downstream extent of toxicity.}, journal={DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY}, author={Li, Yizhen and He, Ruoying and McGillicuddy, Dennis J., Jr.}, year={2014}, month={May}, pages={210–222} }
 @article{mann_wall_lembke_lindemuth_he_taylor_kellison_2014, title={Shelf-scale mapping of fish sound production with ocean gliders}, volume={136}, DOI={10.1121/1.4899624}, abstractNote={Ocean gliders are a powerful platform for collecting large-scale data on the distribution of sound-producing animals while also collecting environmental data that may influence their distribution. Since 2009, we have performed extensive mapping on the West Florida Shelf with ocean gliders equipped with passive acoustic recorders. These missions have revealed the distribution of red grouper as well as identified several unknown sounds likely produced by fishes. In March 2014, we ran a mission along the shelf edge from Cape Canaveral, FL to North Carolina to map fish sound production. The Gulf Stream and its strong currents necessitated a team effort with ocean modeling to guide the glider successfully to two marine protected areas. This mission also revealed large distributions of unknown sounds, especially on the shallower portions of the shelf. Gliders provide valuable spatial coverage, but because they are moving and most fish have strong diurnal sound production patterns, data analysis on presence and absence must be made carefully. In many of these cases, it is best to use a combination of platforms, including fixed recorders and ocean profilers to measure temporal patterns of sound production.}, number={4}, journal={The Journal of the Acoustical Society of America}, publisher={Acoustical Society of America (ASA)}, author={Mann, David and Wall, Carrie and Lembke, Chad and Lindemuth, Michael and He, Ruoying and Taylor, Chris and Kellison, Todd}, year={2014}, month={Oct}, pages={2117–2117} }
 @article{li_he_2014, title={Spatial and temporal variability of SST and ocean color in the Gulf of Maine based on cloud-free SST and chlorophyll reconstructions in 2003-2012}, volume={144}, ISSN={["1879-0704"]}, DOI={10.1016/j.rse.2014.01.019}, abstractNote={The spatial and temporal variability of sea surface temperature (SST) and Chlorophyll-a (Chl-a) in the Gulf of Maine (GOM) is examined using daily, cloud-free Data INterpolating Empirical Orthogonal Function (DINEOF) reconstructions during 2003–2012. The utility of the DINEOF SST and Chl-a is demonstrated through direct comparisons with buoy- and ship-based observations. EOF analyses of cloud-free products are further used to quantify the SST and Chl-a variability on seasonal to inter-annual timescales. The first mode of SST is dominated by an annual cycle in response to net surface heat flux, with SST lagging surface flux by ~ 57 days. The second mode of SST underscores interactions between GOM, the Scotian Shelf, and the slope sea in response to the basin scale atmospheric forcing represented by the North Atlantic Oscillation. The third mode correlates well with the evolution of Scotian Shelf-slope frontal displacement. The first EOF mode of Chl-a is dominated by a winter–spring bloom and a fall bloom, with a spatial distribution modified by the tidal mixing that facilitates nutrient delivery from the deep ocean. The second EOF mode is likely associated with a winter bloom in the warm slope sea, where the low-frequency variations of second modes of SST and Chl-a are in phase, suggesting a possible coupling between physical and biological responses to atmospheric forcing. The third mode of the Chl-a is likely associated with freshening events associated with advection of the Scotian Shelf Water, which enhance stratifications in the eastern GOM.}, journal={REMOTE SENSING OF ENVIRONMENT}, publisher={Elsevier BV}, author={Li, Yizhen and He, Ruoying}, year={2014}, month={Mar}, pages={98–108} }
 @article{zambon_he_warner_2014, title={Tropical to extratropical: Marine environmental changes associated with Superstorm Sandy prior to its landfall}, volume={41}, ISSN={0094-8276}, url={http://dx.doi.org/10.1002/2014GL061357}, DOI={10.1002/2014gl061357}, abstractNote={Abstract}, number={24}, journal={Geophysical Research Letters}, publisher={American Geophysical Union (AGU)}, author={Zambon, Joseph B. and He, Ruoying and Warner, John C.}, year={2014}, month={Dec}, pages={8935–8943} }
 @article{oey_ezer_qiu_berntsen_he_2013, title={Editorial-The 3rd International Workshop on Modeling the Ocean (IWMO 2011)}, volume={63}, ISSN={["1616-7228"]}, DOI={10.1007/s10236-013-0595-3}, number={2-3}, journal={OCEAN DYNAMICS}, publisher={Springer Nature}, author={Oey, Lie-Yauw and Ezer, Tal and Qiu, Bo and Berntsen, Jarle and He, Ruoying}, year={2013}, month={Mar}, pages={307–309} }
 @article{castelao_he_2013, title={Mesoscale eddies in the South Atlantic Bight}, volume={118}, ISSN={["2169-9291"]}, DOI={10.1002/jgrc.20415}, abstractNote={[1] Satellite-derived sea level anomaly fields constructed by combining measurements from simultaneously operating altimeters are used to quantify properties and propagation characteristics of eddies in the South Atlantic Bight (SAB). Eddy detection and eddy tracking algorithms are applied to 19 years of high-resolution observations available at weekly intervals. Inshore of the 800 m isobath, eddies are most frequently observed at and downstream of the Charleston Bump (a major topographic feature located at 31–32°N), a region where the amplitude of most eddies is increased. The bump is also a preferred region for eddy generation. The amplitude of eddies is found to increase with water depth. Eddies generated in the SAB tend to propagate westward toward the coast and to the northeast, presumably due to the influence of the strong mean northeastward flow of the Gulf Stream. Those eddies are highly nonlinear, with potential to trap water in their interior as they propagate. Since a large fraction of the eddies that at some point in their histories are found inshore of the 800 m isobath experience large bathymetric changes along their trajectories, they can potentially serve as efficient mechanisms for cross-isobath transport in the SAB. Analysis of temporal variability in eddy activity suggests that cross-isobath transport due to nonlinear eddies may be significant during all seasons, but will likely be characterized by large interannual variability.}, number={10}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, publisher={Wiley-Blackwell}, author={Castelao, Renato M. and He, Ruoying}, year={2013}, month={Oct}, pages={5720–5731} }
 @article{xue_he_fennel_cai_lohrenz_hopkinson_2013, title={Modeling ocean circulation and biogeochemical variability in the Gulf of Mexico}, volume={10}, number={11}, journal={Biogeosciences}, publisher={Copernicus GmbH}, author={Xue, Zuo and He, Ruoying and Fennel, Katja and Cai, W-J and Lohrenz, Steven and Hopkinson, C}, year={2013}, pages={7219} }
 @article{putman_mansfield_he_shaver_verley_2013, title={Predicting the distribution of oceanic-stage Kemp's ridley sea turtles}, volume={9}, number={5}, journal={Biology letters}, publisher={The Royal Society}, author={Putman, Nathan F and Mansfield, Katherine L and He, Ruoying and Shaver, Donna J and Verley, Philippe}, year={2013}, pages={20130345} }
 @article{putman_he_2013, title={Tracking the long-distance dispersal of marine organisms}, author={Putman, Nathan F and He, Ruoying}, year={2013} }
 @article{putman_he_2013, title={Tracking the long-distance dispersal of marine organisms: sensitivity to ocean model resolution}, volume={10}, number={81}, journal={Journal of the Royal Society Interface}, publisher={The Royal Society}, author={Putman, Nathan F and He, Ruoying}, year={2013}, pages={20120979} }
 @article{weisberg_he_liu_virmani_2013, title={West Florida Shelf Circulation on Synoptic, Seasonal, and Interannual Time Scales}, DOI={10.1029/161gm23}, abstractNote={The continental shelf ocean circulation is driven by a combination of local and deep ocean forcing, where the local forcing is by surface momentum and buoyancy (heat and fresh water) fluxes and by land-derived fresh water fluxes, and the deep ocean forcing is by momentum and buoyancy fluxes transmitted across the shelf break. While all continental shelves share the same response physics, their geometries, river distributions, and boundary currents make their individual behaviors unique. Here we consider the responses of the West Florida Continental Shelf (WFS) to external forcing on time scales ranging from the passage of synoptic scale weather systems to interannual anomalies. Our approach is to combine measurements made over several years with applied numerical model experiments, and we describe several features of the time and space varying circulation that may have relevance to the ecological workings of the WFS. These include the role of the bottom Ekman layer in transporting cold, nutrient-rich waters of deep-ocean origin to the nearshore; seasonal reversals of the inner shelf currents; seasonal reversals of the outer-shelf currents that can occur independent of the Gulf of Mexico Loop Current to provide a WFS pathway for Mississippi River water in spring and summer; the formation of a spring cold tongue and the associated Green River phenomenon; and ventilations by deep-ocean water that may occur interannually.}, journal={Circulation in the Gulf of Mexico: Observations and Models}, publisher={American Geophysical Union}, author={Weisberg, Robert H. and He, Ruoying and Liu, Yonggang and Virmani, Jyotika I.}, year={2013}, month={Mar}, pages={325–347} }
 @article{zhao_he_2012, title={Cloud-free sea surface temperature and colour reconstruction for the Gulf of Mexico: 2003-2009}, volume={3}, ISSN={["2150-7058"]}, DOI={10.1080/01431161.2012.666638}, abstractNote={The data interpolating empirical orthogonal function (DINEOF) method is applied to concurrent MODIS sea surface temperature (SST) and chlorophyll-a (chl-a) data to produce daily, 4 km, cloud-free SST and chl-a analyses for the Gulf of Mexico (GOM) from 2003 to 2009. Comparisons between SST analysis and in situ buoy temperature measurements indicate that the DINEOF method can accurately resolve temperature variability and solve the cloud-cover problem, which is a typical issue of remote-sensing observations. Based on significant correlations between cloud-free chl-a, SST and sea surface height (SSH) data in the GOM, a simple chl-a statistical prediction model is further developed. Favourable comparisons between model solutions and independent satellite chl-a observations indicate that the statistical model provides a feasible means to predict GOM chl-a field based on existing SST and SSH information, allowing for observational gap fillings when concurrent chl-a data were not available.}, number={8}, journal={REMOTE SENSING LETTERS}, publisher={Informa UK Limited}, author={Zhao, Yao and He, Ruoying}, year={2012}, pages={697–706} }
 @article{young_he_emlet_li_qian_arellano_van gaest_bennett_wolf_smart_et al._2012, title={Dispersal of Deep-Sea Larvae from the Intra-American Seas: Simulations of Trajectories using Ocean Models}, volume={52}, ISSN={["1557-7023"]}, DOI={10.1093/icb/ics090}, abstractNote={Using data on ocean circulation with a Lagrangian larval transport model, we modeled the potential dispersal distances for seven species of bathyal invertebrates whose durations of larval life have been estimated from laboratory rearing, MOCNESS plankton sampling, spawning times, and recruitment. Species associated with methane seeps in the Gulf of Mexico and/or Barbados included the bivalve "Bathymodiolus" childressi, the gastropod Bathynerita naticoidea, the siboglinid polychaete tube worm Lamellibrachia luymesi, and the asteroid Sclerasterias tanneri. Non-seep species included the echinoids Cidaris blakei and Stylocidaris lineata from sedimented slopes in the Bahamas and the wood-dwelling sipunculan Phascolosoma turnerae, found in Barbados, the Bahamas, and the Gulf of Mexico. Durations of the planktonic larval stages ranged from 3 weeks in lecithotrophic tubeworms to more than 2 years in planktotrophic starfish. Planktotrophic sipunculan larvae from the northern Gulf of Mexico were capable of reaching the mid-Atlantic off Newfoundland, a distance of more than 3000 km, during a 7- to 14-month drifting period, but the proportion retained in the Gulf of Mexico varied significantly among years. Larvae drifting in the upper water column often had longer median dispersal distances than larvae drifting for the same amount of time below the permanent thermocline, although the shapes of the distance-frequency curves varied with depth only in the species with the longest larval trajectories. Even species drifting for >2 years did not cross the ocean in the North Atlantic Drift.}, number={4}, journal={INTEGRATIVE AND COMPARATIVE BIOLOGY}, author={Young, Craig M. and He, Ruoying and Emlet, Richard B. and Li, Yizhen and Qian, Hui and Arellano, Shawn M. and Van Gaest, Ahna and Bennett, Kathleen C. and Wolf, Maya and Smart, Tracey I. and et al.}, year={2012}, month={Oct}, pages={483–496} }
 @article{young_he_emlet_li_qian_arellano_van gaest_bennett_wolf_smart_et al._2012, title={Dispersal of deep-sea larvae from the intra-American seas: simulations of trajectories using ocean models}, publisher={Oxford University Press}, author={Young, Craig M and He, Ruoying and Emlet, Richard B and Li, Yizhen and Qian, Hui and Arellano, Shawn M and Van Gaest, Ahna and Bennett, Kathleen C and Wolf, Maya and Smart, Tracey I and et al.}, year={2012} }
 @article{nelson_he_2012, title={Effect of the Gulf Stream on winter extratropical cyclone outbreaks}, volume={13}, ISSN={["1530-261X"]}, DOI={10.1002/asl.400}, abstractNote={Abstract}, number={4}, journal={ATMOSPHERIC SCIENCE LETTERS}, publisher={Wiley-Blackwell}, author={Nelson, Jill and He, Ruoying}, year={2012}, pages={311–316} }
 @article{nelson_he_2012, title={Effect of the Gulf Stream on winter extratropical cyclone outbreaks}, volume={13}, number={4}, journal={Atmospheric Science Letters}, publisher={Wiley Online Library}, author={Nelson, Jill and He, Ruoying}, year={2012}, pages={311–316} }
 @inproceedings{young_he_emlet_li_qian_arellano_van gaest_bennett_smart_wolf_et al._2012, title={Larval life and dispersal potential of deep-sea animals from the Intra-American Seas}, volume={52}, booktitle={INTEGRATIVE AND COMPARATIVE BIOLOGY}, author={Young, CM and He, R and Emlet, RB and Li, Y and Qian, H and Arellano, SM and Van Gaest, AL and Bennett, K and Smart, T and Wolf, M and et al.}, year={2012}, pages={E198–E198} }
 @article{yao_he_bao_wu_song_2012, title={M2 tidal dynamics in Bohai and Yellow Seas: a hybrid data assimilative modeling study}, volume={62}, DOI={10.1007/s10236-011-0517-1}, number={5}, journal={Ocean Dynamics}, publisher={Springer Nature}, author={Yao, Zhigang and He, Ruoying and Bao, Xianwen and Wu, Dexing and Song, Jun}, year={2012}, month={Feb}, pages={753–769} }
 @article{xue_he_liu_warner_2012, title={Modeling transport and deposition of the Mekong River sediment}, volume={37}, ISSN={0278-4343}, url={http://dx.doi.org/10.1016/j.csr.2012.02.010}, DOI={10.1016/j.csr.2012.02.010}, abstractNote={A Coupled Wave–Ocean–Sediment Transport Model was used to hindcast coastal circulation and fine sediment transport on the Mekong shelf in southeastern Asian in 2005. Comparisons with limited observations showed that the model simulation captured the regional patterns and temporal variability of surface wave, sea level, and suspended sediment concentration reasonably well. Significant seasonality in sediment transport was revealed. In summer, a large amount of fluvial sediments was delivered and deposited near the Mekong River mouth. In the following winter, strong ocean mixing, and coastal current lead to resuspension and southwestward dispersal of a small fraction of previously deposited sediments. Model sensitivity experiments (with reduced physics) were performed to investigate the impact of tides, waves, and remotely forced ambient currents on the transport and dispersal of the fluvial sediment. Strong wave mixing and downwelling-favorable coastal current associated with the more energetic northeast monsoon in the winter season are the main factors controlling the southwestward along-shelf transport.}, journal={Continental Shelf Research}, publisher={Elsevier BV}, author={Xue, Zuo and He, Ruoying and Liu, J.Paul and Warner, John C.}, year={2012}, month={Apr}, pages={66–78} }
 @article{olabarrieta_warner_armstrong_zambon_he_2012, title={Ocean–atmosphere dynamics during Hurricane Ida and Nor’Ida: An application of the coupled ocean–atmosphere–wave–sediment transport (COAWST) modeling system}, volume={43-44}, ISSN={1463-5003}, url={http://dx.doi.org/10.1016/j.ocemod.2011.12.008}, DOI={10.1016/j.ocemod.2011.12.008}, abstractNote={The coupled ocean–atmosphere–wave–sediment transport (COAWST) modeling system was used to investigate atmosphere–ocean–wave interactions in November 2009 during Hurricane Ida and its subsequent evolution to Nor'Ida, which was one of the most costly storm systems of the past two decades. One interesting aspect of this event is that it included two unique atmospheric extreme conditions, a hurricane and a nor'easter storm, which developed in regions with different oceanographic characteristics. Our modeled results were compared with several data sources, including GOES satellite infrared data, JASON-1 and JASON-2 altimeter data, CODAR measurements, and wave and tidal information from the National Data Buoy Center (NDBC) and the National Tidal Database. By performing a series of numerical runs, we were able to isolate the effect of the interaction terms between the atmosphere (modeled with Weather Research and Forecasting, the WRF model), the ocean (modeled with Regional Ocean Modeling System (ROMS)), and the wave propagation and generation model (modeled with Simulating Waves Nearshore (SWAN)). Special attention was given to the role of the ocean surface roughness. Three different ocean roughness closure models were analyzed: DGHQ (which is based on wave age), TY2001 (which is based on wave steepness), and OOST (which considers both the effects of wave age and steepness). Including the ocean roughness in the atmospheric module improved the wind intensity estimation and therefore also the wind waves, surface currents, and storm surge amplitude. For example, during the passage of Hurricane Ida through the Gulf of Mexico, the wind speeds were reduced due to wave-induced ocean roughness, resulting in better agreement with the measured winds. During Nor'Ida, including the wave-induced surface roughness changed the form and dimension of the main low pressure cell, affecting the intensity and direction of the winds. The combined wave age- and wave steepness-based parameterization (OOST) provided the best results for wind and wave growth prediction. However, the best agreement between the measured (CODAR) and computed surface currents and storm surge values was obtained with the wave steepness-based roughness parameterization (TY2001), although the differences obtained with respect to DGHQ were not significant. The influence of sea surface temperature (SST) fields on the atmospheric boundary layer dynamics was examined; in particular, we evaluated how the SST affects wind wave generation, surface currents and storm surges. The integrated hydrograph and integrated wave height, parameters that are highly correlated with the storm damage potential, were found to be highly sensitive to the ocean surface roughness parameterization.}, journal={Ocean Modelling}, publisher={Elsevier BV}, author={Olabarrieta, Maitane and Warner, John C. and Armstrong, Brandy and Zambon, Joseph B. and He, Ruoying}, year={2012}, month={Jan}, pages={112–137} }
 @inproceedings{lohrenz_cai_tian_he_liu_hopkinson_2011, title={Climate and Land Use Change Impacts on Terrestrial-Ocean Fluxes of Carbon and Nutrients and Associated Biogeochemical Cycling in the Northern Gulf of Mexico Coastal Ecosystem}, booktitle={AGU Fall Meeting Abstracts}, author={Lohrenz, SE and Cai, W and Tian, H and He, R and Liu, M and Hopkinson, C}, year={2011} }
 @article{nelson_others_2011, title={Numerical Investigation of Air-Sea Interactions During Winter Extratropical Storms.}, author={Nelson, Jill and others}, year={2011} }
 @article{he_chen_fennel_gawarkiewicz_mcgillicuddy_2011, title={Seasonal and interannual variability of physical and biological dynamics at the shelfbreak front of the Middle Atlantic Bight: nutrient supply mechanisms}, volume={8}, number={10}, journal={Biogeosciences}, author={He, R. and Chen, K. and Fennel, K. and Gawarkiewicz, G. G. and McGillicuddy, D. J.}, year={2011}, pages={2935–2946} }
 @article{seasonal and interannual variability of physical and biological dynamics at the shelfbreak front of the middle atlantic bight: nutrient supply mechanisms_2011, volume={8}, number={10}, journal={Biogeosciences}, publisher={Copernicus GmbH}, year={2011}, pages={2935} }
 @article{gawarkiewicz_nelson_he_fulweiler_goff_grothues_labrecque_2011, title={Shelf/Slope Processes: Science Opportunities and Issues Relating to the OOI Pioneer Array}, author={Gawarkiewicz, Glen and Nelson, James and He, Ruoying and Fulweiler, RW and Goff, John and Grothues, Thomas and LaBrecque, Erin}, year={2011} }
 @article{north_adams_schlag_sherwood_he_hyun_socolofsky_2011, title={Simulating Oil Droplet Dispersal From the Deepwater Horizon Spill With a Lagrangian Approach}, DOI={10.1029/2011gm001102}, abstractNote={An analytical multiphase plume model, combined with time-varying flow and hydrographic fields generated by the 3-D South Atlantic Bight and Gulf of Mexico model (SABGOM) hydrodynamic model, were used as input to a Lagrangian transport model (LTRANS), to simulate transport of oil droplets dispersed at depth from the recent Deepwater Horizon MC 252 oil spill. The plume model predicts a stratification-dominated near field, in which small oil droplets detrain from the central plume containing faster rising large oil droplets and gas bubbles and become trapped by density stratification. Simulated intrusion (trap) heights of ~ 310–370 m agree well with the midrange of Q1 conductivity-temperature-depth observations, though the simulated variation in trap height was lower than observed, presumably in part due to unresolved variability in source composition (percentage oil versus gas) and location (multiple leaks during first half of spill). Simulated droplet trajectories by the SABGOM-LTRANS modeling system showed that droplets with diameters between 10 and 50 μm formed a distinct subsurface plume, which was transported horizontally and remained in the subsurface for >1 month. In contrast, droplets with diameters ≥90 μm rose rapidly to the surface. Simulated trajectories of droplets ≤50 μ mi n diameter were found to be consistent with field observations of a southwest-tending subsurface plume in late June 2010 reported by Camilli et al. [2010]. Model results suggest that the subsurface plume looped around to the east, with potential subsurface oil transport to the northeast and southeast. Ongoing work is focusing on adding degradation processes to the model to constrain droplet dispersal.}, journal={Monitoring and Modeling the Deepwater Horizon Oil Spill: A Record-Breaking Enterprise}, publisher={American Geophysical Union}, author={North, Elizabeth W. and Adams, E. Eric and Schlag, Zachary and Sherwood, Christopher R. and He, Ruoying and Hyun, Kyung Hoon and Socolofsky, Scott A.}, year={2011}, pages={217–226} }
 @article{north_adams_schlag_sherwood_he_hyun_socolofsky_2011, title={Simulating oil droplet dispersal from the Deepwater Horizon spill with a Lagrangian approach}, journal={Monitoring and Modeling the Deepwater Horizon Oil Spill: A Record-Breaking Enterprise}, publisher={American Geophysical Union}, author={North, Elizabeth WEW and Adams, E and Schlag, Zachary Z and Sherwood, Christopher RCR and He, Ruoying R and Hyun, Kyung Hoon KH and Socolofsky, Scott ASA}, year={2011}, pages={217–226} }
 @article{mcgillicuddy_townsend_he_keafer_kleindinst_li_manning_mountain_thomas_anderson_2011, title={Suppression of the 2010 Alexandrium fundyense bloom by changes in physical, biological, and chemical properties of the Gulf of Maine}, volume={56}, ISSN={["0024-3590"]}, DOI={10.4319/lo.2011.56.6.2411}, abstractNote={For the period 2005–2009, the abundance of resting cysts in bottom sediments from the preceding autumn was a first‐order predictor of the overall severity of spring–summer blooms of Alexandrium fundyense in the western Gulf of Maine and southern New England. Cyst abundance off mid‐coast Maine was significantly higher in autumn 2009 than it was preceding a major regional bloom in 2005. A seasonal ensemble forecast was computed using a range of forcing conditions for the period 2004–2009, suggesting that a large bloom was likely in the western Gulf of Maine in 2010. This did not materialize, perhaps because environmental conditions in spring–summer 2010 were not favorable for growth of A. fundyense. Water mass anomalies indicate a regional‐scale change in circulation with direct influence on A. fundyense's niche. Specifically, near‐surface waters were warmer, fresher, more stratified, and had lower nutrients than during the period of observations used to construct the ensemble forecast. Moreover, a weaker‐than‐normal coastal current lessened A. fundyense transport into the western Gulf of Maine and Massachusetts Bay. Satellite ocean color observations indicate the 2010 spring phytoplankton bloom was more intense than usual. Early season nutrient depletion may have caused a temporal mismatch with A. fundyense's endogenous clock that regulates the timing of cyst germination. These findings highlight the difficulties of ecological forecasting in a changing oceanographic environment, and underscore the need for a sustained observational network to drive such forecasts.}, number={6}, journal={LIMNOLOGY AND OCEANOGRAPHY}, author={McGillicuddy, D. J., Jr. and Townsend, D. W. and He, R. and Keafer, B. A. and Kleindinst, J. L. and Li, Y. and Manning, J. P. and Mountain, D. G. and Thomas, M. A. and Anderson, D. M.}, year={2011}, month={Nov}, pages={2411–2426} }
 @article{suppression of the 2010 alexandrium fundyense bloom by changes in physical, biological, and chemical properties of the gulf of maine_2011, volume={56}, number={6}, journal={Limnology and Oceanography}, year={2011}, pages={2411–2426} }
 @article{suppression of the 2010 alexandrium fundyense bloom by changes in physical, biological, and chemical properties of the gulf of maine_2011, volume={56}, number={6}, journal={Limnology and Oceanography}, year={2011}, pages={2411–2426} }
 @article{hyun_he_2010, title={Coastal upwelling in the South Atlantic Bight: A revisit of the 2003 cold event using long term observations and model hindcast solutions}, volume={83}, ISSN={["1879-1573"]}, DOI={10.1016/j.jmarsys.2010.05.014}, abstractNote={Long-term (2002–2008) buoy observations, satellite imagery, and regional ocean circulation hindcast solutions were used to investigate the South Atlantic Bight (SAB) cold event that occurred in summer 2003. Observations confirmed that SAB shelf water temperature during the event was significantly colder than their 7-year (2002–2008) mean states. The cold event consisted of 6 distinctive cold wakes, which were likely related with intra-seasonal oscillations in wind fields. The upwelling index analyses based on both in situ buoy wind and North American Regional Reanalysis (NARR) highlighted that the upwelling favorable winds in 2003 were the strongest and most persistent over the 7-year study period. The regional circulation model hindcast driven by the large scale data assimilative model, NARR surface meteorological forcing and coastal river runoff generally reproduced observed hydrodynamic variability during the event. Further model analyses revealed a close relationship between the cold bottom water intrusion and the Gulf Stream (GS) core intensity and its position relative to the shelf break. Being more intensive and shoreward located, the GS worked in concert with strong upwelling favorable wind field to produce abnormal upwelling in summer 2003.}, number={1-2}, journal={JOURNAL OF MARINE SYSTEMS}, publisher={Elsevier BV}, author={Hyun, Kyung Hoon and He, Ruoying}, year={2010}, month={Oct}, pages={1–13} }
 @article{warner_armstrong_he_zambon_2010, title={Development of a Coupled Ocean–Atmosphere–Wave–Sediment Transport (COAWST) Modeling System}, volume={35}, ISSN={1463-5003}, url={http://dx.doi.org/10.1016/j.ocemod.2010.07.010}, DOI={10.1016/j.ocemod.2010.07.010}, abstractNote={Understanding the processes responsible for coastal change is important for managing our coastal resources, both natural and economic. The current scientific understanding of coastal sediment transport and geology suggests that examining coastal processes at regional scales can lead to significant insight into how the coastal zone evolves. To better identify the significant processes affecting our coastlines and how those processes create coastal change we developed a Coupled Ocean–Atmosphere–Wave–Sediment Transport (COAWST) Modeling System, which is comprised of the Model Coupling Toolkit to exchange data fields between the ocean model ROMS, the atmosphere model WRF, the wave model SWAN, and the sediment capabilities of the Community Sediment Transport Model. This formulation builds upon previous developments by coupling the atmospheric model to the ocean and wave models, providing one-way grid refinement in the ocean model, one-way grid refinement in the wave model, and coupling on refined levels. Herein we describe the modeling components and the data fields exchanged. The modeling system is used to identify model sensitivity by exchanging prognostic variable fields between different model components during an application to simulate Hurricane Isabel during September 2003. Results identify that hurricane intensity is extremely sensitive to sea surface temperature. Intensity is reduced when coupled to the ocean model although the coupling provides a more realistic simulation of the sea surface temperature. Coupling of the ocean to the atmosphere also results in decreased boundary layer stress and coupling of the waves to the atmosphere results in increased bottom stress. Wave results are sensitive to both ocean and atmospheric coupling due to wave–current interactions with the ocean and wave growth from the atmosphere wind stress. Sediment resuspension at regional scale during the hurricane is controlled by shelf width and wave propagation during hurricane approach.}, number={3}, journal={Ocean Modelling}, publisher={Elsevier BV}, author={Warner, John C. and Armstrong, Brandy and He, Ruoying and Zambon, Joseph B.}, year={2010}, month={Jan}, pages={230–244} }
 @book{he_2010, title={Eddy-Wind-Topography Interaction Dynamics}, DOI={10.21236/ada542451}, abstractNote={Abstract : This research is seeking to advance the fundamental understanding of eddy-wind-topography interaction dynamics, thereby improving our ability of predicting meso- and sub-mesoscale eddy variability.}, institution={Defense Technical Information Center}, author={He, Ruoying}, year={2010}, month={Sep} }
 @inproceedings{zambon_he_warner_armstrong_2010, title={Investigation of Hurricane Ivan Using the Three-Way Coupled Ocean-Atmosphere-Wave Sediment Transport (COAWST) Model}, booktitle={AGU Fall Meeting Abstracts}, author={Zambon, JB and He, R and Warner, JC and Armstrong, BN}, year={2010} }
 @article{he_chen_moore_li_2010, title={Mesoscale variations of sea surface temperature and ocean color patterns at the Mid-Atlantic Bight shelfbreak}, volume={37}, ISSN={0094-8276}, url={http://dx.doi.org/10.1029/2010GL042658}, DOI={10.1029/2010GL042658}, abstractNote={Concurrent sea surface temperature (SST) and color observations obtained by MODIS (Moderate Resolution Imaging Spectra‐radiometer) provide an excellent opportunity to investigate simultaneous mesoscale variations in SST and surface pigment at the Mid‐Atlantic Bight (MAB) shelf‐break. Cloud‐free MODIS images that clearly reveal mesoscale signals are used to estimate the dominant spatial scales of MAB shelfbreak water properties. Along‐shelfbreak decorrelation scales for SST and surface pigment are 45 and 40 km, respectively, whereas the across‐shelfbreak scales are much shorter, ranging from 19 km for SST to 25 km for pigment. The shelfbreak SST and surface pigment are generally inversely correlated. Cold (warm) SST corresponds to high (low) pigment concentration. Mesoscale variations account for 30% of the total variance in shelfbreak SST. For the shelfbreak surface pigment, the mesoscale variation is much larger, reaching 60–90% of its total variance.}, number={9}, journal={Geophysical Research Letters}, publisher={American Geophysical Union (AGU)}, author={He, Ruoying and Chen, Ke and Moore, Timothy and Li, Mingkui}, year={2010}, month={May}, pages={n/a-n/a} }
 @article{chen_he_2010, title={Numerical Investigation of the Middle Atlantic Bight Shelfbreak Frontal Circulation Using a High-Resolution Ocean Hindcast Model}, volume={40}, ISSN={["1520-0485"]}, DOI={10.1175/2009jpo4262.1}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF PHYSICAL OCEANOGRAPHY}, publisher={American Meteorological Society}, author={Chen, Ke and He, Ruoying}, year={2010}, month={May}, pages={949–964} }
 @article{population dynamics of alexandrium fundyense in the gulf of maine: outlook for improved management and forecasting_2010, journal={KALLIOPI A. PAGOU}, year={2010}, pages={57} }
 @article{population dynamics of alexandrium fundyense in the gulf of maine: outlook for improved management and forecasting_2010, journal={KALLIOPI A. PAGOU}, year={2010}, pages={57} }
 @inproceedings{gawarkiewicz_churchill_he_gong_2010, title={Shelfbreak Frontal Structure and Gulf Stream Interaction north of Cape Hatteras: High resolution observations and regional modeling}, booktitle={AGU Fall Meeting Abstracts}, author={Gawarkiewicz, G and Churchill, JH and He, R and Gong, Y}, year={2010} }
 @article{miles_he_2010, title={Temporal and spatial variability of Chl-a and SST on the South Atlantic Bight Revisiting with cloud-free reconstructions of MODIS satellite imagery}, volume={30}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2010.08.016}, abstractNote={Daily, cloud-free data interpolating empirical orthogonal function (DINEOF) reconstructions of sea-surface temperature (SST) and chlorophyll (Chl-a) satellite imagery are compiled into monthly mean images for a six-year period (2003–2008) and used to identify their spatial and temporal variability on the South Atlantic Bight. Monthly-mean SST has the highest variability on the inner-shelf, decreasing seaward approaching the more stable temperatures of the Gulf Stream (GS). Monthly-mean Chl-a concentrations are similarly highest on the inner shelf throughout the year and decrease cross-shelf toward the nutrient depleted open ocean. Empirical orthogonal function (EOF) analyses on SST and Chl-a show a clear seasonal cycle in their 1st mode of variability, with SST lagging behind Chl-a by approximately one month. The 1st EOF modes account for 95.8% and 46.4% variance of SST and Chl-a, respectively. Chl-a EOF mode 1 in particular shows a highly regionalized spatial pattern with values on the central SAB clearly out of phase with the southern and northern SAB. This regional difference is likely a result of shelf geometry and stratification, which modulate GS influence on the shelf. SST EOF mode 2 exhibits a seasonal cycle as well, which previous studies have shown to be a function of local wind. Chl-a EOF mode 2 is well correlated with the cumulative river transport onto the SAB, but accounts for a relatively small 10.8% of Chl-a variability.}, number={18}, journal={CONTINENTAL SHELF RESEARCH}, publisher={Elsevier BV}, author={Miles, Travis N. and He, Ruoying}, year={2010}, month={Oct}, pages={1951–1962} }
 @article{miles_he_li_2009, title={Characterizing the South Atlantic Bight seasonal variability and cold-water event in 2003 using a daily cloud-free SST and chlorophyll analysis}, volume={36}, ISSN={0094-8276}, url={http://dx.doi.org/10.1029/2008GL036396}, DOI={10.1029/2008GL036396}, abstractNote={Concurrent MODIS sea surface temperature (SST) and chlorophyll‐a (Chl‐a) data are used with a new technique: Data Interpolating Empirical Orthogonal Function (DINEOF) method to produce daily, 4‐km, cloud‐free SST and Chl‐a analyses for the South Atlantic Bight in 2003. Comparisons between SST analysis and in situ buoy temperature demonstrate the utility of DINEOF. To quantify linkages between surface wind, SST, and Chl‐a variations, Empirical Orthogonal Function (EOF) analysis is applied to North American Regional Reanalysis winds, and cloud‐free DINEOF SST and Chl‐a analyses. Wind EOF modes highlight upwelling winds from June to September. While the first SST mode represents seasonal heat flux variations, the second SST mode shows a direct response to upwelling winds with an abrupt drop in SST. The top two Chl‐a EOF modes show less connection with wind. More subsurface Chl‐a and nutrient observations are needed to quantify its relation with surface wind.}, number={2}, journal={Geophysical Research Letters}, publisher={American Geophysical Union (AGU)}, author={Miles, Travis N. and He, Ruoying and Li, Mingkui}, year={2009}, month={Jan}, pages={n/a-n/a} }
 @article{miles_he_li_2009, title={Characterizing the South Atlantic Bight seasonal variability and cold-water event in 2003 using a daily cloud-free SST and chlorophyll analysis}, volume={36}, number={2}, journal={Geophysical Research Letters}, author={Miles, Travis N and He, Ruoying and Li, Mingkui}, year={2009} }
 @article{kim_2009, title={Internal Tides and Internal Solitary Waves in the Northern South China Sea}, url={http://www.lib.ncsu.edu/resolver/1840.16/1758}, note={Large-amplitude internal solitary waves (ISWs) are frequently observed in the northern South China Sea (SCS). In a project sponsored by the US Office of Naval Research, four moorings were deployed between the Luzon Strait and the Chinese continental shelf by Steve Ramp of the Naval Postgraduate School and David Tang of National Taiwan University from late April 2005 to May 2006. Several CTD sections were taken during April and July in 2005. Satellite pictures were also collected during that period. In this study, these data were used to examine the characteristics, generation, and propagation of ISWs. In the satellite images, monthly change in stratification may cause northward shift of the propagation path, and ISWs are more frequently observed in July than in April and May. Speed estimation shows that ISWs propagate faster in the deep basin than over the continental margin and near the ridge. The generation of internal tides correlates with the eastward tidal flow over the ridge, while ISWs are produced by northwestward tidal currents over the ridges in the Luzon Strait.}, author={Kim, Sungphil}, year={2009} }
 @article{li_he_mcgillicuddy_anderson_keafer_2009, title={Investigation of the 2006 Alexandrium fundyense bloom in the Gulf of Maine: In-situ observations and numerical modeling}, volume={29}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2009.07.012}, abstractNote={In-situ observations and a coupled bio-physical model were used to study the germination, initiation, and development of the Gulf of Maine (GOM) Alexandrium fundyense bloom in 2006. Hydrographic measurements and comparisons with GOM climatology indicate that 2006 was a year with normal coastal water temperature, salinity, current and river runoff conditions. A. fundyense cyst abundance in bottom sediments preceding the 2006 bloom was at a moderate level compared to other recent annual cyst survey data. We used the coupled bio-physical model to hindcast coastal circulation and A. fundyense cell concentrations. Field data including water temperature, salinity, velocity time series and surface A. fundyense cell concentration maps were applied to gauge the model's fidelity. The coupled model is capable of reproducing the hydrodynamics and the temporal and spatial distributions of A. fundyense cell concentration reasonably well. Model hindcast solutions were further used to diagnose physical and biological factors controlling the bloom dynamics. Surface wind fields modulated the bloom's horizontal and vertical distribution. The initial cyst distribution was found to be the dominant factor affecting the severity and the interannual variability of the A. fundyense bloom. Initial cyst abundance for the 2006 bloom was about 50% of that prior to the 2005 bloom. As the result, the time-averaged gulf-wide cell concentration in 2006 was also only about 60% of that in 2005. In addition, weaker alongshore currents and episodic upwelling-favorable winds in 2006 reduced the spatial extent of the bloom as compared with 2005.}, number={17}, journal={CONTINENTAL SHELF RESEARCH}, publisher={Elsevier BV}, author={Li, Yizhen and He, Ruoying and McGillicuddy, Dennis J., Jr. and Anderson, Donald M. and Keafer, Bruce A.}, year={2009}, month={Sep}, pages={2069–2082} }
 @article{investigation of the 2006 alexandrium fundyense bloom in the gulf of maine: in-situ observations and numerical modeling_2009, volume={29}, number={17}, journal={Continental shelf research}, publisher={Pergamon}, year={2009}, pages={2069–2082} }
 @misc{walsh_weisberg_lenes_chen_dieterle_zheng_carder_vargo_havens_peebles_et al._2009, title={Isotopic evidence for dead fish maintenance of Florida red tides, with implications for coastal fisheries over both source regions of the West Florida shelf and within downstream waters of the South Atlantic Bight}, volume={80}, ISSN={["0079-6611"]}, DOI={10.1016/j.pocean.2008.12.005}, abstractNote={Toxic Florida red tides of the dinoflagellate Karenia brevis have downstream consequences of 500–1000 km spatial extent. Fish stocks, shellfish beds, and harmful algal blooms of similar species occupy the same continental shelf waters of the southeastern United States, amounting to economic losses of more than 25 million dollars in some years. Under the aegis of the Center for Prediction of Red tides, we are now developing coupled biophysical models of the conditions that lead to red tides and impacted coastal fisheries, from the Florida Panhandle to Cape Hatteras. Here, a nitrogen isotope budget of the coastal food web of the West Florida shelf (WFS) and the downstream South Atlantic Bight (SAB) reaffirms that diazotrophs are the initial nutrient source for onset of red tides and now identifies clupeid fish as the major recycled nutrient source for their maintenance. The recent isotope budget of WFS and SAB coastal waters during 1998–2001 indicates that since prehistoric times of Timacua Indian settlements along the Georgia coast during 1075, ∼50% of the nutrients required for large red tides of >1 μg chl l−1 of K. brevis have been derived from nitrogen-fixers, with the other half from decomposing dead sardines and herrings. During 2001, >90% of the harvest of WFS clupeids was by large ichthyotoxic red tides of >10 μg chl l−1 of K. brevis, rather than by fishermen. After onset of the usual red tides in summer of 2006 and 2007, the simulated subsequent fall exports of Florida red tides in September 2007 to North Carolina shelf waters replicate observations of just ∼1 μg chl l−1 on the WFS that year. In contrast, the earlier red tides of >10 μg chl l−1 left behind off West Florida during 2006, with less physical export, are instead 10-fold larger than those of 2007. Earlier, 55 fish kills were associated with these coastal red tides during September 2006, between Tampa and Naples. Yet, only six fish kills were reported there in September 2007. With little export of red tides and their fish prey during the former year, the computed larger nutrient-sated, fish-fed growth rates of the model's dinoflagellates also replicate satellite-observed daily increments of K. brevis during fall maintenance in 2006, compared to simulated smaller fish-starved growth rates of decanted red tides during fall 2007. During the last few decades, K. brevis has remained a "prudent predator" of some clupeids, i.e. Spanish sardine, whereas humans have now overfished other Florida stocks of both thread herring and Atlantic shad. Thus, future operational forecasts of the land falls and durations of Florida red tides, from Louisiana to North Carolina, as well as prudent management of regional fisheries of the southeastern United States, require consideration of negelected fish losses, at intermediate trophic levels, to algal predators. Some clupeids are harvested by K. brevis, but these fish are separately supported by a longer parallel diatom-based food chain of calanoid copepods, feeding the zooplanktivores and thence other piscivore fish predators, while intersecting the shorter food chain of just diazotrophs and red tide dinoflagellates, poorly grazed in turn by harpactacoid copepods. The distinct phytoplankton functional groups, different herbivores, as well as zoophagous and piscivore fishes, must all be formulated as explicit state variables of the next set of complex ecological models, cued by satellite data and driven by nested circulation models, within an ecosystem-based management paradigm of commercial and sport harvests of biotic marine resources at higher trophic levels of the WFS and SAB.}, number={1-2}, journal={PROGRESS IN OCEANOGRAPHY}, author={Walsh, J. J. and Weisberg, R. H. and Lenes, J. M. and Chen, F. R. and Dieterle, D. A. and Zheng, L. and Carder, K. L. and Vargo, G. A. and Havens, J. A. and Peebles, E. and et al.}, year={2009}, pages={51–73} }
 @article{isotopic evidence for dead fish maintenance of florida red tides, with implications for coastal fisheries over both source regions of the west florida shelf and within downstream waters of the south atlantic bight_2009, volume={80}, number={1-2}, journal={Progress in Oceanography}, publisher={Pergamon}, year={2009}, pages={51–73} }
 @article{isotopic evidence for dead fish maintenance of florida red tides, with implications for coastal fisheries over both source regions of the west florida shelf and within downstream waters of the south atlantic bight_2009, volume={80}, number={1-2}, journal={Progress in Oceanography}, publisher={Pergamon}, year={2009}, pages={51–73} }
 @article{lehmann_fennel_he_2009, title={Statistical validation of a 3-D bio-physical model of the western North Atlantic}, volume={6}, ISSN={["1726-4189"]}, DOI={10.5194/bg-6-1961-2009}, abstractNote={Abstract. High-resolution, physical-biological models of coastal and shelf regions typically use a single functional phytoplankton group, which limits their ability to represent ecological gradients (e.g. highly productive shelf systems adjacent to oligotrophic regions), as these are dominated by different functional phytoplankton groups. We implemented a size-structured ecosystem model in a high-resolution, regional circulation model of the northeast North American shelf and adjacent deep ocean in order to assess whether the added functional complexity of two functional phytoplankton groups improves the model's ability to represent surface chlorophyll concentrations along an ecological gradient encompassing five distinct regions. We used satellite-derived SST and sea-surface chlorophyll for our model assessment, as these allow investigation of spatial variability and temporal variations from monthly to interannual, and analyzed three complimentary statistical measures of model-data agreement: model bias, root mean square error and model efficiency (or skill). All three measures were integrated for the whole domain, for distinct subregions and were calculated in a spatially explicit manner. Comparison with a previously published simulation that used a model with a single phytoplankton functional group indicates that the inclusion of an additional phytoplankton group representing picoplankton markedly improves the model's skill.
                    }, number={10}, journal={BIOGEOSCIENCES}, publisher={Copernicus GmbH}, author={Lehmann, M. K. and Fennel, K. and He, R.}, year={2009}, pages={1961–1974} }
 @article{chassignet_hurlburt_metzger_smedstad_cummings_halliwell_bleck_baraille_wallcraft_lozano_et al._2009, title={US GODAE global ocean prediction with the Hybrid Coordinate Ocean Model (HYCOM)}, volume={22}, DOI={10.5670/oceanog.2009}, number={2}, journal={Oceanography}, author={Chassignet, E. P. and Hurlburt, H. E. and Metzger, E. J. and Smedstad, O. M. and Cummings, J. A. and Halliwell, G. R. and Bleck, R. and Baraille, R. and Wallcraft, A. J. and Lozano, C. and et al.}, year={2009}, pages={64–75} }
 @article{chassignet_hurlburt_metzger_smedstad_cummings_halliwell_bleck_baraille_wallcraft_lozano_et al._2009, title={US GODAE: Global Ocean Prediction with the HYbrid Coordinate Ocean Model (HYCOM)}, volume={22}, DOI={10.5670/oceanog.2009.39}, abstractNote={Abstract : The main objective is to use the HYbrid Coordinate Ocean Model (HYCOM) with data assimilation in an eddy-resolving, fully global ocean prediction system with transition to the Naval Oceanographic Office (NAVOCEANO) at .08 deg equatorial (~7 km mid-latitude) resolution in 2007 and .04 deg resolution by 2011. The model will include shallow water to a minimum depth of 5 m and provide boundary conditions to finer resolution coastal and regional models that may use HYCOM or a different model. In addition, HYCOM will be coupled to atmospheric, ice and bio-chemical models, with transition to the Fleet Numerical Meteorology and Oceanography Center (FNMOC) for the coupled ocean-atmosphere prediction. Basin-scale configurations will also form the backbone of the NOAA/NCEP/MMAB Ocean Forecast System. All the systems will be transitioned with assimilation of sea surface height (SSH) from satellite altimeters, sea surface temperature (SST) and temperature (T)/salinity (S) profiles, including profiles from ARGO floats. In addition, 30-day forecasts are planned once a week. The global system will include two-way coupling to an ice model and a version with two-way coupling to an atmospheric model for transition to FNMOC. The project will ensure that an accurate and generalized ocean model nesting capability is in place to support regional and littoral applications when global HYCOM becomes operational. This will include the capability to provide boundary conditions to nested models with fixed depth z-level coordinates, terrain following coordinates, generalized coordinates (HYCOM), and unstructured grids. To facilitate this goal, HYCOM will be developed into a full-featured coastal ocean model in collaboration with a partnering project. The project will participate in the multinational Global Ocean Data Assimilation Experiment (GODAE) and international GODAE-related ocean prediction system intercomparison projects.}, number={2}, journal={Oceanography}, publisher={The Oceanography Society}, author={Chassignet, Eric and Hurlburt, Harley and Metzger, E. Joseph and Smedstad, Ole and Cummings, James and Halliwell, George and Bleck, Rainer and Baraille, Remy and Wallcraft, Alan and Lozano, Carlos and et al.}, year={2009}, month={Jun}, pages={64–75} }
 @article{milroy_dieterle_he_kirkpatrick_lester_steidinger_vargo_walsh_weisberg_2008, title={A three-dimensional biophysical model of Karenia brevis dynamics on the west Florida shelf: A look at physical transport and potential zooplankton grazing controls}, volume={28}, ISSN={0278-4343}, url={http://dx.doi.org/10.1016/j.csr.2007.04.013}, DOI={10.1016/j.csr.2007.04.013}, abstractNote={Abstract The development of accurate predictive models of toxic dinoflagellate blooms is of great ecological importance, particularly in regions that are most susceptible to their detrimental effects. This is especially true along the west Florida shelf (WFS) and coast, where episodic bloom events of the toxic dinoflagellate Karenia brevis often wreak havoc on the valuable commercial fisheries and tourism industries of west Florida. In an effort to explain the dynamics at work within the maintenance and termination phases of a red tide, a simple three-dimensional coupled biophysical model was used in the analysis of the October 1999 red tide offshore Sarasota, Florida. Results of the numerical experiments indicate that: (1) measured and modeled flowfields were capable of transporting the observed offshore inoculum of K. brevis to within 16 km of the coastal boundary; (2) background concentrations (1000 cells L−1) of K. brevis could grow to a red tide of over 2×106 cells L−1 in little more than a month, assuming an estuarine initiation site with negligible offshore advection, no grazing losses, negligible competition from other phytoplankton groups, and no nutrient limitation; (3) maximal grazing pressure could not prevent the initiation of a red tide or cause its termination, assuming no other losses to algal biomass and a zooplankton community ingestion rate similar to that of Acartia tonsa; and (4) the light-cued ascent behavior of K. brevis served as an aggregational mechanism, concentrating K. brevis at the 55 μE m−2 s−1 isolume when mean concentrations of K. brevis exceeded 100,000 cells L−1. Further improvements in model fidelity will be accomplished by the future inclusion of phytoplankton competitors, disparate nutrient availability and limitation schemes, a more realistic rendering of the spectral light field and the attendant effects of photo-inhibition and compensation, and a mixed community of vertically-migrating proto- and metazoan grazers. These model refinements are currently under development and shall be used to aid progress toward an operational model of red tide forecasting along the WFS.}, number={1}, journal={Continental Shelf Research}, publisher={Elsevier BV}, author={Milroy, Scott P. and Dieterle, Dwight A. and He, Ruoying and Kirkpatrick, Gary J. and Lester, Kristen M. and Steidinger, Karen A. and Vargo, Gabriel A. and Walsh, John J. and Weisberg, Robert H.}, year={2008}, month={Jan}, pages={112–136} }
 @article{he_mcgillicuddy_keafer_anderson_2008, title={Gulf of Maine harmful algal bloom in summer 2005--Part 2: Coupled bio-physical numerical modeling}, volume={113}, number={C7}, journal={Journal of geophysical research}, publisher={NIH Public Access}, author={He, Ruoying and McGillicuddy, Dennis J and Keafer, Bruce A and Anderson, Donald M}, year={2008} }
 @article{he_mcgillicuddy_keafer_anderson_2008, title={Historic 2005 toxic bloom of Alexandrium fundyense in the western Gulf of Maine: 2. Coupled biophysical numerical modeling}, volume={113}, ISSN={["2169-9291"]}, DOI={10.1029/2007jc004602}, abstractNote={A coupled physical/biological modeling system was used to hindcast a massive Alexandrium fundyense bloom that occurred in the western Gulf of Maine in 2005 and to investigate the relative importance of factors governing the bloom's initiation and development. The coupled system consists of a state‐of‐the‐art, free‐surface primitive equation Regional Ocean Modeling System (ROMS) tailored for the Gulf of Maine (GOM) using a multinested configuration, and a population dynamics model for A. fundyense. The system was forced by realistic momentum and buoyancy fluxes, tides, river runoff, observed A. fundyense benthic cyst abundance, and climatological nutrient fields. Extensive comparisons were made between simulated (both physical and biological) fields and in situ observations, revealing that the hindcast model is capable of reproducing the temporal evolution and spatial distribution of the 2005 bloom. Sensitivity experiments were then performed to distinguish the roles of three major factors hypothesized to contribute to the bloom: (1) the high abundance of cysts in western GOM sediments; (2) strong ‘northeaster' storms with prevailing downwelling‐favorable winds; and (3) a large amount of fresh water input due to abundant rainfall and heavy snowmelt. Model results suggest the following. (1) The high abundance of cysts in western GOM was the primary factor of the 2005 bloom. (2) Wind‐forcing was an important regulator, as episodic bursts of northeast winds caused onshore advection of offshore populations. These downwelling favorable winds accelerated the alongshore flow, resulting in transport of high cell concentrations into Massachusetts Bay. A large regional bloom would still have happened, however, even with normal or typical winds for that period. (3) Anomalously high river runoff in 2005 resulted in stronger buoyant plumes/currents, which facilitated the transport of cell population to the western GOM. While affecting nearshore cell abundance in Massachusetts Bay, the buoyant plumes were confined near to the coast, and had limited impact on the gulf‐wide bloom distribution.}, number={C7}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, publisher={American Geophysical Union (AGU)}, author={He, Ruoying and McGillicuddy, Dennis J., Jr. and Keafer, Bruce A. and Anderson, Donald M.}, year={2008}, month={Jul} }
 @article{he_mcgillicuddy_keafer_anderson_2008, title={Historic 2005 toxic bloom of Alexandrium fundyense in the western Gulf of Maine: 2. Coupled biophysical numerical modeling}, volume={113}, number={C7}, journal={Journal of Geophysical Research: Oceans}, author={He, Ruoying and McGillicuddy, Dennis J and Keafer, Bruce A and Anderson, Donald M}, year={2008} }
 @article{he_mcgillicuddy_2008, title={Historic 2005 toxic bloom ofAlexandrium fundyensein the west Gulf of Maine: 1. In situ observations of coastal hydrography and circulation}, volume={113}, DOI={10.1029/2007jc004601}, abstractNote={An extensive Alexandrium fundyense bloom occurred along the coast of the Gulf of Maine in late spring and early summer 2005. To understand the physical aspects of bloom's initiation and development, in situ observations from both a coast‐wide ship survey and the coastal observing network were used to characterize coastal circulation and hydrography during that time period. Comparisons between these in situ observations and their respective long‐term means revealed anomalous ocean conditions during May 2005: waters were warmer and fresher coast‐wide owing to more surface heating and river runoff; coastal currents were at least 2 times stronger than their climatological means. Surface winds were also anomalous in the form of both episodic bursts of northeast winds and a downwelling‐favorable mean condition. These factors may have favored more vigorous along‐shore transport and nearshore aggregation of toxic A. fundyense cells (a red tide) in 2005.}, number={C7}, journal={Journal of Geophysical Research}, publisher={American Geophysical Union (AGU)}, author={He, Ruoying and McGillicuddy, Dennis J.}, year={2008}, month={Jul} }
 @inproceedings{he_warner_armstrong_zambon_2008, title={Investigation of Coastal Ocean Response to Landfalling hurricane using Coupled Ocean Atmosphere Wave Sediment Transport (COAWST) Model: Realistic Hindcast}, booktitle={AGU Fall Meeting Abstracts}, author={He, R and Warner, JC and Armstrong, B and Zambon, JB}, year={2008} }
 @misc{lenes_darrow_walsh_prospero_he_weisberg_vargo_heil_2008, title={Saharan dust and phosphatic fidelity: A three-dimensional biogeochemical model of Trichodesmium as a nutrient source for red tides on the West Florida Shelf}, volume={28}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2008.02.009}, abstractNote={The availability of iron within the surface waters of the broad, oligotrophic West Florida Shelf (WFS) controls periodic blooms of the pelagic marine cyanobacterium Trichodesmium. Summer delivery of Saharan dust provided adequate iron (Fe) to shift limitation of growth to the availability of phosphorus (P). Florida's rivers drain Miocene phosphorus deposits to provide the WFS with freshwater nutrient supplies at molar dissolved inorganic nitrogen/phosphate (DIN/PO4) ratios of <6. These diazotrophs draw upon ubiquitous stocks of dissolved nitrogen gas, once stimulated by Fe-deposition within P-replete waters of the WFS. An extensive in situ data set collected between 1998 and 2001 (NEGOM/ECOHAB) provided plankton taxonomy, hydrographic, nutrient, dissolved organic matter (DOM), pigment, and optical properties on the shelf. We constructed a three-dimensional numerical model to analyze the impact of iron fertilization of the diazotroph Trichodesmium and the resultant effect upon the elemental cycles of N, P, and Fe. The coupled physical and ecological models show that the wet deposition of Fe-rich Saharan dust was necessary to stimulate enough nitrogen fixation to initialize the toxic red tide (Karenia brevis) of ∼20 μg chl a l−1 that occurred in October 1999. The simulation suggests that the magnitude and longevity of the Trichodesmium population, and therefore this source of ‘new’ nitrogen, was controlled by both phosphorus and iron availability.}, number={9}, journal={CONTINENTAL SHELF RESEARCH}, author={Lenes, J. M. and Darrow, B. A. and Walsh, J. J. and Prospero, J. M. and He, R. and Weisberg, R. H. and Vargo, G. A. and Heil, C. A.}, year={2008}, month={May}, pages={1091–1115} }
 @article{lenes_darrow_walsh_prospero_he_weisberg_vargo_heil_2008, title={Saharan dust and phosphatic fidelity: A three-dimensional biogeochemical model of Trichodesmium as a nutrient source for red tides on the West Florida Shelf}, volume={28}, number={9}, journal={Continental Shelf Research}, publisher={Pergamon}, author={Lenes, JM and Darrow, BA and Walsh, JJ and Prospero, JM and He, R and Weisberg, RH and Vargo, GA and Heil, CA}, year={2008}, pages={1091–1115} }
 @inproceedings{warner_armstrong_he_zambon_2008, title={Using a Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Modeling System to investigate impacts of storms on coastal systems}, booktitle={AGU Fall Meeting Abstracts}, author={Warner, J and Armstrong, B and He, R and Zambon, J}, year={2008} }
 @inproceedings{armstrong_warner_he_2008, title={Using a coupled wave and ocean circulation modeling system to investigate the impacts of Hurricane Isabel}, booktitle={AGU Fall Meeting Abstracts}, author={Armstrong, BN and Warner, JC and He, R}, year={2008} }
 @article{he_wilkin_2006, title={Barotropic tides on the southeast New England shelf: A view from a hybrid data assimilative modeling approach}, volume={111}, DOI={10.1029/2005jc003254}, abstractNote={A high‐resolution hybrid data assimilative (DA) modeling system is used to study barotropic tides and tidal dynamics on the southeast New England shelf. In situ observations include tidal harmonics of 5 major tidal constituents [M2, S2, N2, O1, and K1] analyzed from coastal sea level and bottom pressure gauges. The DA system consists of both forward and inverse models. The former is the three‐dimensional, finite difference, nonlinear Regional Ocean Modeling System (ROMS). The latter is a three‐dimensional linearized, frequency domain, finite element model TRUXTON. The DA system assimilates in situ observations via the inversion for the barotropic tidal open boundary conditions (OBCs). Model skill is evaluated by comparing the misfits between the observed and modeled tidal harmonics. The assimilation scheme is found effective and efficient in correcting the tidal OBCs, which in turn improve ROMS tidal solutions. Up to 50% decreases of model/data misfits are achieved after inverse data assimilation. Co‐amplitude and co‐phase maps and tidal current ellipses for each of 5 tidal constituents are generated, revealing complex tidal variability in this transition region between the tidally amplified Gulf of Maine in the northeast and the tidally much less energetic Middle Atlantic Bight in the southwest. Detailed examinations on the residual circulation, energetics, and momentum balances of the M2 tide reveal the key roles of the unique bottom bathymetry of Nantucket Shoals and the complex coastal geometry in affecting the regional tidal dynamics.}, number={C8}, journal={Journal of Geophysical Research}, publisher={American Geophysical Union (AGU)}, author={He, Ruoying and Wilkin, John L.}, year={2006} }
 @article{barth_alvera-azcarate_weisberg_he_2006, title={Hindcast Experiment of a Nested a Baroclinic West Florida Shelf Model}, author={Barth, Alexander and Alvera-Azcarate, Aida and Weisberg, Robert H and He, Ruoying}, year={2006} }
 @article{alvera azcarate aı̈da_barth_helber_he_weisberg_2006, title={Mapped fields of surface geostrophic currents based on altimetry, and fields of sea surface winds, cloud-free sea surface temperature and chlorophyll concentration using monovariate OI and a multivariate EOF technique}, author={Alvera Azcarate Aı̈da and Barth, Alexander and Helber, RW and He, R and Weisberg, RH}, year={2006} }
 @article{liu_weisberg_he_2006, title={Sea Surface Temperature Patterns on the West Florida Shelf Using Growing Hierarchical Self-Organizing Maps}, volume={23}, DOI={10.1175/jtech1848.1}, abstractNote={Abstract}, number={2}, journal={Journal of Atmospheric and Oceanic Technology}, publisher={American Meteorological Society}, author={Liu, Yonggang and Weisberg, Robert H. and He, Ruoying}, year={2006}, month={Feb}, pages={325–338} }
 @inproceedings{barth_alvera-azcárate aı̈da_he_helber_weisberg_2005, title={A Hindcast Experiment Nesting a Baroclinic West Florida Shelf Model in the 1/12th Degree Operational North Atlantic HYCOM Model}, booktitle={AGU Spring Meeting Abstracts}, author={Barth, Alexander and Alvera-Azcárate Aı̈da and He, R and Helber, RW and Weisberg, RH}, year={2005} }
 @article{sturges_lugo-fernandez_2005, title={Circulation in the Gulf of Mexico: observations and models}, volume={161}, journal={Washington DC American Geophysical Union Geophysical Monograph Series}, author={Sturges, Wilton and Lugo-Fernandez, Alexis}, year={2005} }
 @article{he_bang_edwards_mooers_weisberg_werner_2005, title={Coastal ocean response to extratropical storms in March 2001: A retrospective analysis using sub-regional coastal ocean models of the Southeast Atlantic Coastal Ocean Observing System (SEACOOS)}, journal={Journal of Atmospheric and Oceanic Technology, Submitted}, author={He, Ruoying and Bang, Inkweon and Edwards, Karen P and Mooers, Christopher NK and Weisberg, Robert H and Werner, Francisco}, year={2005} }
 @article{he_2005, title={Data assimilative hindcast of the Gulf of Maine coastal circulation}, volume={110}, DOI={10.1029/2004jc002807}, abstractNote={A data assimilative model hindcast of the Gulf of Maine (GOM) coastal circulation during an 11 day field survey in early summer 2003 is presented. In situ observations include surface winds, coastal sea levels, and shelf hydrography as well as moored and shipboard acoustic Doppler D current profiler (ADCP) currents. The hindcast system consists of both forward and inverse models. The forward model is a three‐dimensional, nonlinear finite element ocean circulation model, and the inverse models are its linearized frequency domain and time domain counterparts. The model hindcast assimilates both coastal sea levels and ADCP current measurements via the inversion for the unknown sea level open boundary conditions. Model skill is evaluated by the divergence of the observed and modeled drifter trajectories. A mean drifter divergence rate (1.78 km d−1) is found, demonstrating the utility of the inverse data assimilation modeling system in the coastal ocean setting. Model hindcast also reveals complicated hydrodynamic structures and synoptic variability in the GOM coastal circulation and their influences on coastal water material property transport. The complex bottom bathymetric setting offshore of Penobscot and Casco bays is shown to be able to generate local upwelling and downwelling that may be important in local plankton dynamics.}, number={C10}, journal={Journal of Geophysical Research}, publisher={American Geophysical Union (AGU)}, author={He, Ruoying}, year={2005} }
 @article{he_mcgillicuddy_lynch_smith_stock_manning_2005, title={Data assimilative hindcast of the Gulf of Maine coastal circulation}, volume={110}, number={C10}, journal={Journal of Geophysical Research: Oceans}, author={He, Ruoying and McGillicuddy, Dennis J and Lynch, Daniel R and Smith, Keston W and Stock, Charles A and Manning, James P}, year={2005} }
 @article{anderson_keafer_mcgillicuddy_mickelson_keay_scott libby_manning_mayo_whittaker_michael hickey_et al._2005, title={Initial observations of the 2005 Alexandrium fundyense bloom in southern New England: General patterns and mechanisms}, volume={52}, ISSN={0967-0645}, url={http://dx.doi.org/10.1016/j.dsr2.2005.09.004}, DOI={10.1016/j.dsr2.2005.09.004}, abstractNote={From May to July, 2005, an extensive bloom of Alexandrium fundyense occurred along the coast of southern New England. The outbreak eventually closed shellfish beds from central Maine to Massachusetts, including Nantucket Island and portions of Martha's Vineyard, and resulted in the closure of 40,000 km2 of offshore federal waters as well. The coastal Alexandrium bloom was exceptional in several ways: high toxin levels were measured farther south than ever before in New England; levels of toxicity in many locations were higher than previously observed at those stations; for the first time toxicity at some locations was above quarantine levels; cell concentrations far exceeded those observed in the coastal waters of southern New England in the past; and for the first time in the region the governors of Maine and Massachusetts officially declared the red tide to be a disaster, clearing the way for federal assistance. Initial observations suggest that several factors contributed to this bloom. Abundant rainfall and heavy snowmelt substantially increased the amount of fresh water entering the Gulf of Maine. Combined with other freshwater inputs, we hypothesize that this provided macro- and micro-nutrients, a stratified water column, and a transport mechanism that led to high cell abundances and broad, region-wide dispersal of the organism. Warm temperatures in western waters also would have favored A. fundyense growth. In addition, several storms with strong winds out of the northeast occurred at times when cells were abundant and in locations where the winds could advect them into Massachusetts and Cape Cod Bays and keep them there, leading to high cell concentrations and toxicity. Another contributing factor may have been the high abundance of newly deposited cysts in western Gulf of Maine sediments, as documented in a fall 2004 survey. Here, we evaluate this bloom and the patterns of toxicity in light of the conceptual models for A. fundyense dynamics developed during the Ecology and Oceanography of Harmful Algal Blooms (ECOHAB)–Gulf of Maine (GOM) program. Several features of the 2005 bloom conform to the mechanisms proposed in those models, including the alongshore transport of cells in major water masses and episodic intrusions of cells toward shore due to downwelling-favorable wind forcings. The models need to be refined and expanded, however, based on new data and observations. For example, it is now clear that cells and bloom patches can reach the outer side of Cape Cod and even Nantucket and Martha's Vineyard. Transport to the coastal waters of Rhode Island and even Connecticut/Long Island is also possible. A critical modification also may be necessary in terms of mechanisms through which A. fundyense cells occur in Massachusetts Bay. In the past, toxicity only developed when blooms were transported from the north and into the bay via the western segment of the Maine Coastal Current. Now, it is possible that the bay might serve as a source of cells through the germination of cysts deposited in those waters during the 2005 bloom. If proven in subsequent surveys, this potential for in situ bloom development could have major implications on the timing and extent of toxicity within Massachusetts Bay and southern New England waters in future years.}, number={19-21}, journal={Deep Sea Research Part II: Topical Studies in Oceanography}, publisher={Elsevier BV}, author={Anderson, Donald M. and Keafer, Bruce A. and McGillicuddy, Dennis J., Jr. and Mickelson, Michael J. and Keay, Kenneth E. and Scott Libby, P. and Manning, James P. and Mayo, Charles A. and Whittaker, David K. and Michael Hickey, J. and et al.}, year={2005}, month={Sep}, pages={2856–2876} }
 @article{initial observations of the 2005 alexandrium fundyense bloom in southern new england: general patterns and mechanisms_2005, volume={52}, number={19-21}, journal={Deep Sea Research Part II: Topical Studies in Oceanography}, publisher={Pergamon}, year={2005}, pages={2856–2876} }
 @article{initial observations of the 2005 alexandrium fundyense bloom in southern new england: general patterns and mechanisms_2005, volume={52}, number={19-21}, journal={Deep Sea Research Part II: Topical Studies in Oceanography}, publisher={Pergamon}, year={2005}, pages={2856–2876} }
 @article{weisberg_he_liu_virmani_2005, title={West Florida shelf circulation on synoptic, seasonal, and interannual time scales}, journal={Circulation in the Gulf of Mexico: Observations and models}, publisher={American Geophysical Union}, author={Weisberg, Robert H and He, Ruoying and Liu, Yonggang and Virmani, Jyotika I}, year={2005}, pages={325–347} }
 @inproceedings{adjoint data assimilative model study of the gulf of maine coastal circulation_2004, booktitle={AGU Fall Meeting Abstracts}, year={2004} }
 @article{weisberg_he_kirkpatrick_muller-karger_walsh_2004, title={Coastal Ocean Circulation Influences on Remotely Sensed Optical Properties: A West Florida Shelf Case Study}, volume={17}, DOI={10.5670/oceanog.2004.49}, abstractNote={Author Posting. © Oceanography Society, 2004. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 17, 2 (2004): 68-75.}, number={2}, journal={Oceanography}, publisher={The Oceanography Society}, author={Weisberg, Robert and He, Ruoying and Kirkpatrick, Gary and Muller-Karger, Frank and Walsh, John}, year={2004}, month={Jun}, pages={68–75} }
 @article{weisberg_he_kirkpatrick_muller-karger_walsh_2004, title={Coastal ocean circulation influences on remotely sensed optical properties: a west Florida shelf case study}, publisher={Oceanography Society}, author={Weisberg, Robert H and He, Ruoying and Kirkpatrick, Gary and Muller-Karger, Frank E and Walsh, John J}, year={2004} }
 @article{he_2004, title={Coastal ocean wind fields gauged against the performance of an ocean circulation model}, volume={31}, ISSN={0094-8276}, url={http://dx.doi.org/10.1029/2003GL019261}, DOI={10.1029/2003GL019261}, abstractNote={Atmosphere model‐derived flux fields are used to force coastal ocean models. Coarse resolution and incomplete boundary layer dynamics limit the accuracy of these forcing fields and hence the performance of the ocean models. We address this limitation for the west Florida shelf using optimal interpolation to blend winds measured in situ with winds produced by model analyses. By improving the coastal wind field we improve the fidelity between currents modeled and currents observed. Comparisons between momentum analyses performed independently from the model and the data demonstrate the fidelity to be of a correct dynamical basis. We conclude that the primary limitation to coastal ocean model performance lies with the boundary conditions.}, number={14}, journal={Geophysical Research Letters}, publisher={American Geophysical Union (AGU)}, author={He, Ruoying}, year={2004} }
 @article{he_liu_weisberg_2004, title={Coastal ocean wind fields gauged against the performance of an ocean circulation model}, volume={31}, number={14}, journal={Geophysical research letters}, author={He, Ruoying and Liu, Yonggang and Weisberg, Robert H}, year={2004} }
 @inproceedings{walsh_dieterle_darrow_milroy_jolliff_lenes_weisberg_he_2004, title={Coupled biophysical models of Florida red tides}, booktitle={Harmful Algae 2002, Proceedings of the Tenth International Conference on Harmful Algae. Florida Fish and Wildlife Conservation Commission, Florida Institute of Oceanography and Intergovernmental Oceanographic Commission of UNESCO, Paris}, author={Walsh, John J and Dieterle, Dwight A and Darrow, Brian P and Milroy, Scott P and Jolliff, Jason K and Lenes, Jason M and Weisberg, Robert H and He, Ruoying}, year={2004}, pages={519–521} }
 @article{alvera-azcárate_barth_he_helber_law_weisberg_2004, title={Data Analyses in Support of West Florida Shelf Modeling}, author={Alvera-Azcárate, Aida and Barth, Alexander and He, Ruoying and Helber, Robert W and Law, Jay and Weisberg, Robert H}, year={2004} }
 @inproceedings{weisberg_he_liu_2004, title={Improving Coastal Ocean Modeling Using In-Situ Data}, booktitle={8th Symposium on Integrated Observing and Assimilation Systems for Atmosphere, Oceans and Land Surfaces, 84th AMS Annual Meeting}, author={Weisberg, Robert H and He, R and Liu, Y}, year={2004} }
 @article{he_weisberg_2003, title={A Loop Current Intrusion Case Study on the West Florida Shelf*}, volume={33}, DOI={10.1175/1520-0485(2003)033<0465:alcics>2.0.co;2}, abstractNote={The Gulf of Mexico Loop Current intruded upon the West Florida continental shelf in June 2000. In situ currents and hydrography along with satellite temperature and altimetry measurements are used to describe this event and its effects on the shelf. A strong southward current is observed to flow along the shelf slope seaward of the intruded water boundary. This current transported cold, nutrient-rich water from the north, thereby producing anomalous hydrographic features near the shelf break (80-m isobath). An array of moored velocity profilers reveals that the currents landward of the intruded water are independent of the Loop Current and primarily driven by local winds. A series of idealized numerical model simulations inclusive of forcing by both the Loop Current and local winds confirm the observational findings that the shelfbreak currents are largely Loop Current controlled while the shelf currents are largely controlled by the local winds.}, number={2}, journal={Journal of Physical Oceanography}, publisher={American Meteorological Society}, author={He, Ruoying and Weisberg, Robert H.}, year={2003}, month={Feb}, pages={465–477} }
 @article{he_weisberg_zhang_muller-karger_helber_2003, title={A cloud-free, satellite-derived, sea surface temperature analysis for the West Florida Shelf}, volume={30}, DOI={10.1029/2003gl017673}, abstractNote={Clouds are problematic in using Advanced Very High Resolution Radiometer (AVHRR) imagery for describing sea surface temperature (SST). The Tropical Rainfall Measuring Mission Microwave Imager (TMI) observes SST through clouds, providing daily, 1/4° maps under all weather conditions excepting rain. A TMI limitation, however, is coarse resolution. Optimal interpolation (OI) is used to generate a cloud‐free, 5‐km, daily SST analysis for the West Florida Shelf (WFS) by merging the high‐resolution (cloud‐covered) AVHRR with the coarse‐resolution (cloud‐free) TMI SST products. Comparisons with in‐situ data show good agreements. Given large spatial gradients by coastal ocean processes, this regional analysis has advantage over the global, weekly, 1° Reynolds SST. A 5‐year (1998–2002) OI SST analysis is diagnosed using Empirical Orthogonal Functions. The first two modes represent annual cycles, one by surface heat flux and another by shelf circulation dynamics.}, number={15}, journal={Geophysical Research Letters}, publisher={American Geophysical Union (AGU)}, author={He, Ruoying and Weisberg, Robert H. and Zhang, Haiying and Muller-Karger, Frank E. and Helber, Robert W.}, year={2003}, month={Aug} }
 @inproceedings{kelly_bonner_perez_trujillo_weisberg_luther_he_2003, title={A comparison of near-surface current measurements by ADCP and HF-radar on the West Florida Shelf}, booktitle={Current Measurement Technology, 2003. Proceedings of the IEEE/OES Seventh Working Conference on}, author={Kelly, FJ and Bonner, JS and Perez, JC and Trujillo, D and Weisberg, RH and Luther, ME and He, R}, year={2003}, pages={70–74} }
 @article{weisberg_he_2003, title={Local and deep-ocean forcing contributions to anomalous water properties on the west Florida shelf}, volume={108}, number={C6}, journal={Journal of Geophysical Research: Oceans}, author={Weisberg, Robert H and He, Ruoying}, year={2003} }
 @article{walsh_weisberg_dieterle_he_darrow_jolliff_lester_vargo_kirkpatrick_fanning_et al._2003, title={Phytoplankton response to intrusions of slope water on the West Florida Shelf: Models and observations}, volume={108}, number={C6}, journal={Journal of Geophysical Research: Oceans}, author={Walsh, John J and Weisberg, Robert H and Dieterle, Dwight A and He, Ruoying and Darrow, Brian P and Jolliff, Jason K and Lester, Kristen M and Vargo, Gabriel A and Kirkpatrick, Gary J and Fanning, Kent A and et al.}, year={2003} }
 @article{he_weisberg_2003, title={West Florida shelf circulation and temperature budget for the 1998 fall transition}, volume={23}, DOI={10.1016/s0278-4343(03)00028-1}, abstractNote={Mid-latitude continental shelves undergo a fall transition as the net heat flux changes from warming to cooling. Using in situ data and a numerical model we investigate the circulation on the west Florida shelf (WFS) for the fall transition of 1998. The model is a regional adaptation of the primitive equation, Princeton Ocean Model forced by NCEP reanalysis wind, air pressure, and heat flux fields, plus river inflows. After comparison with observations the model is used to draw inferences on the seasonal and synoptic scale features of the shelf circulation. By running twin experiments, one without and the other with an idealized Loop Current (LC), we explore the relative importance of local versus deep-ocean forcing. We find that local forcing largely controls the inner-shelf circulation, including changes from the Florida Panhandle in the north to regions farther south. The effects of the LC in fall 1998 are to reinforce the mid-shelf currents and to increase the across-shelf transports in the bottom Ekman layer, thereby accentuating the shoreward transport of cold, nutrient rich water of deep-ocean origin. A three-dimensional analysis of the temperature budget reveals that surface heat flux largely controls both the seasonal and synoptic scale temperature variations. Surface cooling leads to convective mixing that rapidly alters temperature gradients. One interesting consequence is that upwelling can result in near-shore warming as warmer offshore waters are advected landward. The temperature balances on the shelf are complex and fully three-dimensional.}, number={8}, journal={Continental Shelf Research}, publisher={Elsevier BV}, author={He, Ruoying and Weisberg, Robert H}, year={2003}, month={May}, pages={777–800} }
 @inproceedings{weisberg_he_luther_walsh_cole_donovan_merz_subramanian_2002, title={A coastal ocean observing system and modeling program for the West Florida Shelf}, volume={1}, booktitle={OCEANS'02 MTS/IEEE}, author={Weisberg, Robert and He, Ruoying and Luther, Mark and Walsh, John and Cole, Rick and Donovan, Jeff and Merz, Cliff and Subramanian, Vembu}, year={2002}, pages={530–534} }
 @inproceedings{kelly_bonner_perez_adams_prouty_trujillo_weisberg_luther_he_cole_et al._2002, title={An HF-Radar test deployment amidst an ADCP array on the West Florida shelf}, volume={2}, booktitle={OCEANS'02 MTS/IEEE}, author={Kelly, FJ and Bonner, JS and Perez, JC and Adams, JS and Prouty, D and Trujillo, D and Weisberg, RH and Luther, ME and He, R and Cole, R and et al.}, year={2002}, pages={692–698} }
 @inproceedings{he_weisberg_2002, title={Modeling of West Florida Shelf Circulation for Spring 1999}, DOI={10.1061/40628(268)3}, abstractNote={Mid-latitude continental shelves undergo a spring transition as the net surface heat flux changes from cooling to warming. Using in-situ data and a numerical circulation model we investigate the circulation and temperature budget on the West Florida Continental Shelf (WFS) for the spring transition of 1999. The model is a regional adaptation of the primitive equation, Princeton Ocean Model forced by NCEP re-analysis wind and heat flux fields and by river inflows. Based on agreements between the modeled and observed fields we use the model to draw inferences on how the surface momentum and heat fluxes affect the seasonal and synoptic scale variability, We account for a strong southeastward current at mid-shelf by the baroclinic response to combined wind and buoyancy forcing, and we show how this local forcing leads to annually occurring cold and low salinity tongues. Through term-by-term analyses of the temperature budget we describe the WFS temperature evolution in spring. Heat flux largely controls the seasonal transition, whereas ocean circulation largely controls the synoptic scale variability. Rivers contribute to the local hydrography and are important ecologically. Along with upwelling, river inflows facilitate frontal aggregation of nutrients and the spring formation of a high concentration chlorophyll plume near the shelf break (the so-called 'Green River'), coinciding with the cold, low salinity tongues. These features originate by local, shelf-wide forcing; the Loop Current is not an essential ingredient for spring transition of 1999.}, booktitle={Estuarine and Coastal Modeling (2001)}, publisher={American Society of Civil Engineers}, author={He, Ruoying and Weisberg, Robert H.}, year={2002}, month={Jul} }
 @article{he_weisberg_2002, title={Tides on the West Florida Shelf}, volume={32}, DOI={10.1175/1520-0485(2002)032<3455:totwfs>2.0.co;2}, abstractNote={The principal semidiurnal (M2 and S2) and diurnal (K1 and O1) tidal constituents are described on the west Florida continental shelf (WFS) using a combination of in situ measurements and a three-dimensional, primitive equation numerical model. The measurements are of sea level and currents along the coastline and across the shelf, respectively. The model extends from west of the Mississippi River to the Florida Keys with an open boundary arcing between. It is along this open boundary that the regional model is forced by a global tide model. Standard barotropic tidal analyses are performed for both the data and the model, and quantifiable metrics are provided for comparison. Based on these comparisons, the authors present coamplitude and cophase charts for sea level and velocity hodographs for currents. The semidiurnal constituents show marked spatial variability, whereas the diurnal constituents are spatially more uniform. Apalachicola Bay is a demarcation point for the semidiurnal tides that are well developed to the southeast along the WFS but are minimal to the west. The largest semidiurnal tides are in the Florida Big Bend and Florida Bay regions with a relative minimum in between just to the south of Tampa Bay. These spatial distributions may be explained on the basis of local geometry. A Lagrangian Stokes drift, coherently directed toward the northwest, is identified but is of relatively small magnitude when compared with the potential for particle transport by seasonal and synoptic-scale forcing. Bottom stressinduced tidal mixing is examined and estimates are made of the bottom logarithmic layer height by the M2 tidal currents.}, number={12}, journal={Journal of Physical Oceanography}, publisher={American Meteorological Society}, author={He, Ruoying and Weisberg, Robert H.}, year={2002}, pages={3455–3473} }
 @article{he_weisberg_2002, title={West Florida shelf circulation and temperature budget for the 1999 spring transition}, volume={22}, DOI={10.1016/s0278-4343(01)00085-1}, abstractNote={Mid-latitude continental shelves undergo a spring transition as the net surface heat flux changes from cooling to warming. Using in situ data and a numerical circulation model we investigate the circulation and temperature budget on the West Florida Continental Shelf (WFS) for the spring transition of 1999. The model is a regional adaptation of the primitive equation, Princeton Ocean Model forced by NCEP reanalysis wind and heat flux fields and by river inflows. Based on agreements between the modeled and observed fields we use the model to draw inferences on how the surface momentum and heat fluxes affect the seasonal and synoptic scale variability. We account for a strong southeastward current at mid-shelf by the baroclinic response to combined wind and buoyancy forcing, and we show how this local forcing leads to annually occurring cold and low salinity tongues. Through term-by-term analyses of the temperature budget we describe the WFS temperature evolution in spring. Heat flux largely controls the seasonal transition, whereas ocean circulation largely controls the synoptic scale variability. These two processes, however, are closely linked. Bottom topography and coastline geometry are important in generating regions of convergence and divergence. Rivers contribute to the local hydrography and are important ecologically. Along with upwelling, river inflows facilitate frontal aggregation of nutrients and the spring formation of a high concentration chlorophyll plume near the shelf break (the so-called 'Green River') coinciding with the cold, low salinity tongues. These features originate by local, shelf-wide forcing; the Loop Current is not an essential ingredient.}, number={5}, journal={Continental Shelf Research}, publisher={Elsevier BV}, author={He, Ruoying and Weisberg, Robert H.}, year={2002}, month={Mar}, pages={719–748} }
 @inproceedings{weisberg_he_luther_2001, title={Real Time Monitoring and Circulation Modeling on the West Florida Shelf}, booktitle={AGU Fall Meeting Abstracts}, author={Weisberg, RH and He, R and Luther, M}, year={2001} }
 @article{he_robert_weisberg_2001, title={q 2002 American Meteorological Society Tides on the West Florida Shelf}, url={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.665.7889}, note={The principal semidiurnal (M2 and S2) and diurnal (K1 and O1) tidal constituents are described on the west Florida continental shelf (WFS) using a combination of in situ measurements and a three-dimensional, primitive equation numerical model. The measurements are of sea level and currents along the coastline and across the shelf, respectively. The model extends from west of the Mississippi River to the Florida Keys with an open boundary arcing between. It is along this open boundary that the regional model is forced by a global tide model. Standard barotropic tidal analyses are performed for both the data and the model, and quantifiable metrics are provided for comparison. Based on these comparisons, the authors present coamplitude and cophase charts for sea level and velocity hodographs for currents. The semidiurnal constituents show marked spatial variability, whereas the diurnal constituents are spatially more uniform. Apalachicola Bay is a demarcation point for the semidiurnal tides that are well developed to the southeast along the WFS but are minimal to the west. The largest semidiurnal tides are in the Florida Big Bend and Florida Bay regions with a relative minimum in between just to the south of Tampa Bay. These spatial distributions may be explained on the basis of local geometry. A Lagrangian Stokes drift, coherently directed toward the northwest, is identified but is of relatively small magnitude when compared with the potential for particle transport by seasonal and synoptic-scale forcing. Bottom stress-induced tidal mixing is examined and estimates are made of the bottom logarithmic layer height by the M2 tidal currents. 1.}, author={He, Ruoying and Robert and Weisberg, H.}, year={2001} }
 @article{liu_weisberg_he, title={2.4 SEA SURFACE TEMPERATURE PATTERNS ON THE WEST FLORIDA SHELF USING GROWING HIERARCHICAL SELF-ORGANIZING MAPS}, url={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.122.2511}, note={The West Florida Shelf (WFS) is a broad, gently sloping continental margin that is influenced by the Gulf of Mexico Loop Current system located seaward of the}, author={Liu, Yonggang and Weisberg, Robert H. and He, Ruoying} }
 @article{he_weisberg, title={2002b. West Florida shelf circulation and temperature budget for the 1999 spring transition}, url={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.661.2929}, note={Mid-latitude continental shelves undergo a spring transition as the net surface heat flux changes from cooling to warming. Using in situ data and a numerical circulation model we investigate the circulation and temperature budget on the West Florida Continental Shelf (WFS) for the spring transition of 1999. The model is a regional adaptation of the primitive equation, Princeton Ocean Model forced by NCEP reanalysis wind and heat flux fields and by river inflows. Based on agreements between the modeled and observed fields we use the model to draw inferences on how the surface momentum and heat fluxes affect the seasonal and synoptic scale variability. We account for a strong southeastward current at mid-shelf by the baroclinic response to combined wind and buoyancy forcing, and we show how this local forcing leads to annually occurring cold and low salinity tongues. Through term-by-term analyses of the temperature budget we describe the WFS temperature evolution in spring. Heat flux largely controls the seasonal transition, whereas ocean circulation largely controls the synoptic scale variability. These two processes, however, are closely linked. Bottom topography and coastline geometry are important in generating regions of convergence and divergence. Rivers contribute to the local hydrography and are important ecologically. Along with upwelling, river inflows facilitate frontal aggregation of nutrients and the spring formation of a high concentration chlorophyll plume near the shelf break (the so-called ‘Green River’) coinciding with the cold, low salinity tongues. These features originate by local}, author={He, Ruoying and Weisberg, Robert H.} }
 @inproceedings{weisberg_he_luther_walsh_cole_donovan_merz_subramanian, title={A coastal ocean observing system and modeling program for the West Florida Shelf}, DOI={10.1109/oceans.2002.1193324}, abstractNote={The Coastal Ocean Monitoring and Prediction System (COMPS) is a real-time, web-based (http://comps.marine.usf.edu) coastal ocean observing and modeling system for the west coast of Florida. COMPS observations consist of coastal and offshore stations, each with in-situ ocean and air-sea interaction measurements. Some of these stations are maintained by the University of South Florida and others are maintained by various local, state and federal agencies. Our web-site imports and serves all available real-time data. The COMPS array also provides a backbone for process experimentation, inclusive of other non-realtime data sets, and it is supported by a numerical circulation modeling program for process experiment hindcasts and for nowcasts and forecasts. Through this coordinated program of in-situ measurements and models we are making headway in understanding material property distributions on the West Florida Shelf and how these impact shelf ecology. The COMPS in situ data and modeling program and some of its principal scientific findings are discussed. Based on these we provide recommendations on a basic set of measurements for future integrated sustained coastal ocean observing systems.}, booktitle={Oceans '02 MTS/IEEE}, publisher={IEEE}, author={Weisberg, R. and He, Ruoying and Luther, M. and Walsh, J. and Cole, R. and Donovan, J. and Merz, C. and Subramanian, V.} }
 @article{weisberg_luther_he_cole_donovan_merz, title={An HF-Radar Test Deployment Amidst an ADCP Array on the West Florida Shelf}, author={Weisberg, RH and Luther, ME and He, R and Cole, R and Donovan, J and Merz, CR} }
 @article{hyun_he, title={Eddy-wind-topography interaction dynamics: A modeling study}, author={Hyun, Kyung Hoon and He, Ruoying} }
 @article{ezer_qiu_berntsen_he, title={Editorial--The 3 rd International Workshop on Modeling the Ocean (IWMO 2011) Special Issue in Ocean Dynamics Lie-Yauw Oey (Corresponding Author: lyo@ princeton. edu) Atmospheric & Oceanic Science Program Princeton University, Princeton, NJ 08544, USA}, author={Ezer, Tal and Qiu, Bo and Berntsen, Jarle and He, Ruoying} }
 @article{he_weisberg, title={Florida shelf circulation and temperature budget for the 1999 spring transition}, url={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.470.8542}, note={Mid-latitude continental shelves undergo a fall transition as the net heat flux changes from warming to cooling. Using in situ data and a numerical model we investigate the circulation on the west Florida shelf (WFS) for the fall transition of 1998. The model is a regional adaptation of the primitive equation, Princeton Ocean Model forced by NCEP reanalysis wind, air pressure, and heat flux fields, plus river inflows. After comparison with observations the model is used to draw inferences on the seasonal and synoptic scale features of the shelf circulation. By running twin experiments, one without and the other with an idealized Loop Current (LC), we explore the relative importance of local versus deep-ocean forcing. We find that local forcing largely controls the inner-shelf circulation, including changes from the Florida Panhandle in the north to regions farther south. The effects of the LC in fall 1998 are to reinforce the mid-shelf currents and to increase the across-shelf transports in the bottom Ekman layer, thereby accentuating the shoreward transport of cold, nutrient rich water of deep-ocean origin. A three-dimensional analysis of the temperature budget reveals that surface heat flux largely controls both the seasonal and synoptic scale temperature variations. Surface cooling leads to convective mixing that rapidly alters temperature gradients. One interesting consequence is that upwelling can result in near-shore warming as warmer offshore waters are advected landward. The temperature balances on the shelf are complex and fully three-dimensional.}, author={He, Ruoying and Weisberg, Robert H.} }
 @article{zambon_he_warner, title={Investigation of Hurricane Sandy Dynamics Using the 3-Way Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Model}, author={Zambon, Joseph B and He, Ruoying and Warner, John C} }
 @article{he_mcgillicuddy, title={Maine: 1. In situ observations of coastal hydrography and circulation}, url={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.412.1800}, note={[1] An extensive Alexandrium fundyense bloom occurred along the coast of the Gulf of Maine in late spring and early summer 2005. To understand the physical aspects of bloom’s initiation and development, in situ observations from both a coast-wide ship survey and the coastal observing network were used to characterize coastal circulation and hydrography during that time period. Comparisons between these in situ observations and their respective long-term means revealed anomalous ocean conditions during May 2005: waters were warmer and fresher coast-wide owing to more surface heating and river runoff; coastal currents were at least 2 times stronger than their climatological means. Surface winds were also anomalous in the form of both episodic bursts of northeast winds and a downwelling-favorable mean condition. These factors may have favored more vigorous along-shore transport and nearshore aggregation of toxic A. fundyense cells (a red tide) in 2005.}, author={He, Ruoying and Mcgillicuddy, Dennis J.} }
 @article{anderson_sengco_doucette_bauer_cox_gulland_etheridge_he_hudnell_larkin_et al., title={Prevention, Control, and Mitigation Workgroup Report}, journal={HAB RDDTT}, author={Anderson, D and Sengco, M and Doucette, G and Bauer, MB and Cox, F and Gulland, F and Etheridge, S and He, R and Hudnell, K and Larkin, S and et al.}, pages={13} }
 @article{anderson_sengco_doucette_bauer_cox_gulland_etheridge_he_hudnell_larkin_et al., title={Prevention, Control, and Mitigation Workgroup Report}, journal={HAB RDDTT}, author={Anderson, D and Sengco, M and Doucette, G and Bauer, MB and Cox, F and Gulland, F and Etheridge, S and He, R and Hudnell, K and Larkin, S and et al.}, pages={13} }
 @article{hu, title={oTHERS. 2002. Satellite images track ��Black Water��event off Florida coast}, volume={83}, journal={EOS, Trans. Am. Geophys. U}, author={Hu, C}, pages={281–285} }
 @article{hu, title={oTHERS. 2002. Satellite images track ��Black Water��event off Florida coast}, volume={83}, journal={EOS, Trans. Am. Geophys. U}, author={Hu, C}, pages={281–285} }