Publications from the faculty and research scientists of the Graduate School of Oceanography.

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Manuscripts from 2013

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SCIMPI: A New Borehole Observatory, T. Lado-Insua, K. Moran, I. Kulin, S. Farrington, and J. B. Newman

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Vertical Eddy Diffusion as a Key Mechanism for Removing Perfluorooctanic Acid (PFOA) from the Global Surface Oceans, Rainer Lohmann, Elena Jurado, Henk A. Dijkstra, and Jordi Dachs

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Concentrations, Fluxes and Residence Time of PBDEs Across the Tropical Atlantic Ocean, Rainer Lohmann, Jana Klanova, Petr Kukucka, Shifra Yonis, and Kevyn Bollinger

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(Viewpoint): Science Should Guide TSCA Reform, Rainer Lohmann, Heather M. Stapleton, and Ronald A. Hites

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Fluid Interactions That Enable Stealth Predation by the Upstream-Foraging Hydromedusa Craspedacusta sowerbyi, K. Lucas, S. P. Colin, J. H. Costello, K. Katja, and E. Klos

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Climatic Variability of the Circulation in the Rhode Island Sound: A Modeling Study, Yiyong Luo, Lew Rothstein, Qianqian Liu, and Shuwen Zhang

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Water as a New Matrix for Global Assessment of Hydrophilic POPs, Derek Muir and Rainer Lohmann

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Microbial activity in the marine deep biosphere: progress and prospects, Beth N. Orcutt, Douglas E. LaRowe, Jennifer F. Biddle, Frederick S. Colwell, Brian T. Glazer, Brandi Kiel Reese, John B. Kirkpatrick, Laura L. Lapham, Heath J. Mills, Jason B. Sylvan, Scott D. Wankel, and C. Geoff Wheat

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Heterogeneities from the first 100 million years recorded in deep mantle noble gases from the Northern Lau Back-arc Basin, Maria K. Peto, Sujoy Mukhopadhyay, and Katherine A. Kelley

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The challenges of using polyethylene passive samplers to determine dissolved concentrations of parent and alkylated PAHs under cold and saline conditions, Pamela J. Reitsma, Dave Adelman, and Rainer Lohmann

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Geodynamic Evolution of a Forearc Rift in the Southernmost Mariana Arc, Julia M. Ribeiro, Robert J. Stern, Fernando Martinez, Osamu Ishizuka, Susan G. Merle, Katherine Kelley, Elizabeth Y. Anthony, Minghua Ren, Yasuhiko Ohara, Mark Reagan, Guillaume Girard, and Sherman Bloomer

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How Do Fishing and Environmental Effects Propagate Among and Within Functional Groups?, Marie-Joëlle Rochet, Jeremy Collie, and Verena M. Trenkel

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Conservation in the Context of Climate Change: Practical Guidelines for Land Protection at Local Scales, Kevin Ruddock, Peter V. August, Christopher Damon, Charles LaBash, Pamela Rubinoff, and Donald Robadue Jr.

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Analysis of Energy Flow in US GLOBEC Ecosystems Using End-to-End Models, James J. Ruzicka, John H. Steele, Sarah K. Gaichas, Tosca Ballerini, Dian J. Gifford, Richard D. Brodeur, and Eileen E. Hofmann

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Using Hierarchical Bayes to Understand Movement, Health, and Survival in the Endangered North Atlantic Right Whale, Robert S. Schick, Scott D. Kraus, Rosalind M. Rolland, Amy R. Knowlton, Philip K. Hamilton, Heather M. Pettis, Robert D. Kenney, and James S. Clark

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Impact of Breaking Wave Form Drag on Near-Surface Turbulence and Drag Coefficient over Young Seas at High Winds, Nobuhiro Suzuki, Tetsu Hara, and Peter P. Sullivan

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John H. Steele, 1926–2013, Elizabeth Turner, Eileen E. Hofmann, Dian J. Gifford, and Dale B. Haidvogel

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Processing of Underway CTD Data, D. S. Ullman and David Hebert

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Four Current Meter Models Compared in Strong Currents in Drake Passage, D. Randolph Watts, Maureen A. Kennelly, Kathleen A. Donohue, Karen L. Tracey, Teresa K. Chereskin, Robert A. Weller, and Ivan Victoria

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Organochlorine Pollutants in Western Antarctic Peninsula Sediments and Benthic Deposit Feeders, Lin Zhang, Rebecca Dickhut, Dave DeMaster, Kari Pohl, and Rainer Lohmann

Manuscripts from 2012

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Identifying Reference Genes with Stable Expression from High Throughput Sequence Data, Harriet Alexander, Bethany D. Jenkins, Tatiana A. Rynearson, Mak A. Saito, Melissa L. Mercier, and Sonya T. Dyhrman

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Continued Exploration of the Santorini Volcanic Field and Cretan Basin, Aegean Sea, Katherine L. C. Bell, Paraskevi Nomikou, Steven N. Carey, Eleni Stathopoulou, Paraskevi Polymenakou, Athanasios Godelitsas, Chris Roman, and Michelle Parks

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Evidence of Bottom-Trapped Currents in the Kuroshio Extension Region, Stuart P. Bishop, D. Randolph Watts, Jae-Hun Park, and Nelson G. Hogg

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Coastal Exploration of the Southern Black Sea Off Ereğli and Sinop, Turkey, Michael L. Brennan, Dan Davis, Chris Roman, Ilya V. Buynevich, Alexis Catsambis, Meko Kofahl, Maureen Merrigan, Suna Tuzun, Muhammet Duman, Derya Urkmez, J. Ian Vaughn, and Tufan Turanli

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Submarine Volcanism in the Straits of Sicily, Steven N. Carey, Katherine L. C. Bell, Michael Marani, Mauro Rosi, Edward T. Baker, Chris Roman, Marco Pistolesi, and Joshua Kelly

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Airborne lidar detection and characterization of internal waves in a shallow fjord, James H. Churnside, Richard D. Marchbanks, Jennifer H. Lee, Joseph A. Shaw, Alan Weidmann, and Percy L. Donaghay

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A Quantitative Comparison between 1D and 3D Source Inversion Methodologies: Application to the Middle East, Brian M. Covellone and Brian K. Savage

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Vibrio parahaemolyticus in Rhode Island Coastal Ponds and the Estuarine Environment of Narragansett Bay, Annie M. Cox and Marta Gomez-Chiarri

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Introduction to special section on Recent Advances in the Study of Optical Variability in the Near‐Surface and Upper Ocean, T. Dickey, David Farmer, and et al

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Influence of Volatile Degassing on Initial Flow Structure and Entrainment During Undersea Volcanic Fire Fountaining Eruptions, P. D. Friedman, Steven Carey, and M. Raessi

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Validation of Shear‐Wave Velocity Models of the Pacific Northwest, Haiying Gao and Yang Shen

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Recent Arctic Climate Change and Its Remote Forcing of Northwest Atlantic Shelf Ecosystems, Charles H. Greene, Bruce C. Monger, Louise P. McGarry, Matthew D. Connelly, Neesha R. Schnepf, Andrew J. Pershing, Igor M. Belkin, Paula S. Ftratantoni, David G. Mountain, Robert S. Pickart, Rubao Ji, James J. Bisagni, Changsheng Chen, Sirpa M. A. Hakkinen, Dale B. Haidvogel, Jia Wang, Erica Head, Peter Smith, and Alessandra Conversi

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Predator-Induced Fleeing Behaviors in Phytoplankton: A New Mechanism for Harmful Algal Bloom Formation?, Elizabeth L. Harvey and Susanne Menden-Deuer

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Dominant eukaryotic export production during ocean anoxic events reflects the importance of recycled NH4+, Meytal B. Higgins, Rebecca S. Robinson, Jonathan M. Husson, Susan J. Carter, and Ann Pearson

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A pipeline for structured light bathymetric mapping, Gabrielle Inglis, Clara Smart, Ian Vaughn, and Chris Roman

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Global Distribution of Microbial Abundance and Biomass in Subseafloor Sediment, Jens Kallmeyer, Robert Pockalny, Rishi Ram Adhikari, David C. Smith, and Steven D'Hondt

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Concurrent activity of anammox and denitrifying bacteria in the Black Sea, John B. Kirkpatrick, Clara A. Fuchsman, Evgeniy Yakushev, James T. Staley, and James W. Murray

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Mantle dynamics beneath the Pacific Northwest and the generation of voluminous back‐arc volcanism, Maureen D. Long, Christy B. Till, Kelsey A. Drunken, Richard W. Carlson, Lara S. Wagner, Matthew J. Fouch, David E. James, Timothy L. Grove, Nicholas Schmerr, and Christopher R. Kincaid

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The Metabolic Response of Pteropods to Acidification Reflects Natural CO2-Exposure in Oxygen Minimum Zones, A. E. Maas, K. F. Wishner, and B. A. Seibel

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A serpentinite-hosted ecosystem in the Southern Mariana Forearc, Yashuiko Ohara, Mark K. Reagan, Katsunori Fujikura, Hiromi Watanabe, Katsuyoshi Michibayahi, Teruaki Ishii, Robert J. Stern, Ignacio Pujana, Fernando Martinez, Guillaume Girard, Julia Ribeiro, Maryjo Brounce, Naoaki Komori, and Masashi Kino

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A review of nitrogen isotopic alteration in marine sediments, Rebecca S. Robinson, Markus Kienast, Ana Luiza Albuquerque, Mark Altabet, Sergio Contreras, Ricardo De Pol Holz, Nathalie Dubois, Roger Francois, Eric Galbraith, Ting-Chang Hsu, Tara Ivanochko, Samuel Jaccard, Shuh-Ji Kao, Thorsten Kiefer, Stephanie Kienkast, Moritz Lehmann, Philippe Martinez, Matthew McCarthy, Jürgen Möbius, Tom Pedersen, Tracey M. Quan, Evgeniya Ryabenko, Andreas Schmittner, Ralph Schneider, Aya Schneider-Mor, Masahito Shigemitsu, Dan Sinclair, Christopher Somes, Anja Studer, Robert Thunell, and Jin-Yu Yang

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The Development of High-Resolution Seafloor Mapping Techniques, Chris Roman, Gabrielle Inglis, J. Ian Vaughn, Clara Smart, Bertrand Douillard, and Stefan Williams

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Shelf‐basin exchange times of Arctic surface waters estimated from 228TH/228Ra disequilibrium, M. Rutgers van der Loeff, P. Cai, I. Stimac, D. Bauch, C. Hanfland, T. Roeske, and S. Bradley Moran

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Changing polar environments: Interdisciplinary challenges, Paul B. Shepson, Parisa A. Ariya, Clara J. Deal, D. James Donaldson, Thomas A. Douglas, Brice Loose, Ted Maksym, Patricia A. Matrai, Lynn M. Russell, Benjamin Saenz, Jacqueline Stefels, and Nadja Steiner

Erratum: Changing polar environments: Interdisciplinary challenges (Eos 93:11 (117-118) DOI: 10.1029/2012EO110001), Paul B. Shepson, Parisa A. Ariya, Clara J. Deal, D. James Donaldson, Thomas A. Douglas, Brice Loose, Ted Maksym, Patricia A. Matrai, Lynn M. Russell, Benjamin Saenz, Jacqueline Stefels, and Nadja Steiner

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An Adaptive Framework for Selecting Environmental Monitoring Protocols to Support Ocean Renewable Energy Development, Emily J. Shumchenia, Sarah L. Smith, Jennifer McCann, Michelle Carnevale, Grover Fugate, Robert D. Kenney, John W. King, Peter W. C. Paton, Malia Schwartz, Malcolm Spaulding, and Kritopher J. Winiarski

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Propagation of Kuroshio Extension Meanders between 143° and 149°E, Karen L. Tracey, D. Randolph Watts, Kathleen A. Donohue, and Hiroshi Ichikawa

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Molecular Subdivision of the Marine Diatom Thalassiosira rotula in Relation to Geographic Distribution, Genome Size, and Physiology, Kerry A. Whittaker, Dayna R. Rignanese, Robert J. Olson, and Tatiana A. Rynearson

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Three-dimensional anisotropic seismic wave modelling in spherical coordinates by a collocated-grid finite-difference method, Wei Zhang, Yang Shen, and Li Zhao

Manuscripts from 2011

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Pacific Atmospheric Sulfur Experiment (PASE): dynamics and chemistry of the south Pacific tropical trade wind regime, Alan Bandy, Ian C. Faloona, Byron W. Blomquist, Barry J. Huebert, Antony D. Clarke, Steven G. Howell, R. L. Mauldin, Christopher A. Cantrell, James G. Hudson, Brian G. Heikes, John T. Merrill, Yuhang Wang, Daniel W. O'Sullivan, Wolfgang Nadler, and Douglas D. Davis

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High resolution regional seismic attenuation tomography in eastern Tibetan Plateau and adjacent regions, Xueyang Bao, Eric Sandvol, James Ni, Thomas Hearn, Yongshun John Chen, and Yang Shen

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An International Quiet Ocean Experiment, Ian L. Boyd, George Frisk, Ed Urban, Peter Tyack, Jesse Ausubel, Sophie Seeyave, Doug Cato, Brandon Southall, Michael Weise, Rex Andrew, Tomonari Akamatsu, René Dekeling, Christine Erbe, David Farmer, Roger Gentry, Tom Gross, Anthony Hawkins, Fenghua Li, Kathy Metcalf, James H. Miller, David Moretti, Cristian Rodrigo, and Tomio Shinke

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Maritime History of ANZAC Cove, Michael L. Brennan, Dwight Coleman, Christopher N. Roman, Tufan Turanli, Dan Davis, Alexis Catsambis, James Moore, Maureen Merrigan, Brennan Bajdek, Daniel Whitesell, and Robert Ballard

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Landscape Imaging of the Southeast Aegean Sea, Michael L. Brennan, Tufan Turanli, Bridget Buxton, Katherine L. Croff Bell, Christopher N. Roman, Meko Kofahl, Orkan Koyagasioglu, Daniel Whitesell, Thomas Chamberlain, Richard Sullivan, and Robert Ballard

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Exploration of the Kolumbo Volcanic Rift Zone, Steven Carey, Katherine L. Croff Bell, Paraskevi Nomikou, Georges Vougioukalakis, Christopher N. Roman, Kathleen Cantner, Konstantina Bejelou, Maria Bourbouli, and Julie Fero Martin

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Improvements to the methods used to measure bubble attenuation using an underwater acoustical resonator, Helen Czerski, Svein Vagle, David M. Farmer, and Nick Hall-Patch

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Detailed Comparisons of Airborne Formaldehyde Measurements with Box Models during the 2006 INTEX-B and MILAGRO Campaigns: Potential Evidence for Significant Impacts of Unmeasured and Multi-Generation Volatile Organic Carbon Compounds, A. Fried, B. G. Heikes, and et al

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Experimental Tropical Cyclone Prediction Using the GFDL 25-km-Resolution Global Atmospheric Model, Jeffrey S. Gall, Isaac Ginis, Shian-Jiann Lin, Timothy P. Marchok, and Jan-Huey Chen

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Northeast US precipitation variability and North American climate teleconnections interpreted from late Holocene varved sediments, J. Bradford Hubeny, John W. King, and Mike Reddin

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Detection of Diffuse Sea Floor Venting Using Structured Light Imaging, Gabrielle Inglis, Clara Smart, Christopher Roman, and Steven Carey

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Development of High Resolution Sea Floor Mapping Tools and Techniques, Gabrielle Inglis, J. Ian Vaughn, Clara Smart, and Christopher N. Roman

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Biodiversity and Ecosystem Function in the Gulf of Maine: Pattern and Role of Zooplankton and Pelagic Nekton, Catherine L. Johnson, Jeffrey A. Runge, K. Alexandra Curtis, Edward G. Durbin, Jonathan A. Hare, Lewis S. Incze, Jason S. Link, Gary D. Melvin, Todd D. O'Brien, and Lou Van Guelpen

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Instabilities in an Internal Solitary-like Wave on the Oregon Shelf, Levin G. Lamb and David M. Farmer

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Tidal Effects on Intermediate Waters: A Case Study in the East/Japan Sea, Ho Jin Lee, Jae-Hun Park, Mark Wimbush, Kyung Tae Jung, Chan Joo Jang, Yang-Ki Cho, Young-Kyo Seo, and Jong Ho Nam

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Crustal and mantle velocity models of southern Tibet from finite frequency tomography, Xiaofeng Liang, Yang Shen, Yongshun John Chen, and Yong Ren

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Planktonic Microbes in the Gulf of Maine Area, William K.W. Li, Robert A. Andersen, Dian J. Gifford, Lewis S. Incze, Jennifer L. Martin, Cynthia H. Pilskaln, Juliette N. Rooney-Varga, Michael E. Sieracki, William H. Wilson, and Nicholas H. Wolff

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Evidence for aggregation and export of cyanobacteria and nano-eukaryotes from the Sargasso Sea euphotic zone, M. W. Lomas and S. Bradley Moran

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Sustained Monitoring of the Southern Ocean at Drake Passage: Past Achievements and Future Priorities, Michael P. Meredith, Philip L. Woodworth, Teresa K. Chereskin, David P. Marshall, Lesley C. Allison, Grant R. Bigg, Kathleen A. Donohue, Karen J. Heywood, Chris W. Hughes, Angela Hibbert, Andrew McC. Hogg, Helen L. Johnson, Loic Jullion, Brian A. King, Harry Leach, Yueng-Djern Lenn, Miguel A. Morales Maqueda, David R. Munday, Alberto C. Naveira Garabato, Christine Provost, Jean-Baptiste Sallée, and Janet Sprintall

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Concept Tests for a New Wire Flying Vehicle Designed to Achieve High Horizontal Resolution Profiling in Deep Water, Chris Roman and Dave Hebert

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Lagrangian floats as sea floor imaging platforms, Chris Roman, Gabrielle Inglis, and Bryan McGilvray

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Development of High-Resolution Underwater Mapping Techniques, Christopher N. Roman, Gabrielle Inglis, J. Ian Vaughn, Stefan Williams, Oscar Pizarro, Ariell Friedman, and Daniel Steinberg

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Exploration of the Anaximander Mud Volcanoes, Timothy M. Shank, Santiago Herrera, Walter Cho, Christopher N. Roman, and Katherine L. Croff Bell

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Remote Analysis of Grain Size Characteristic in Submarine Pyroclastic Deposits from Kolumbo Volcano, Greece, Clara Smart, D. P. Whitesell, Christopher N. Roman, and Steven Carey

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Comparing species and ecosystem-based estimates of fisheries yields, John H. Steele, Dian J. Gifford, and Jeremy S. Collie

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Mapping Shallow Coastal Ecosystems: A Case Study of a Rhode Island Lagoon, Mark Stolt, Michael Bradley, Jim Turenne, Maggie Payne, Eric Scherer, Giancarlo Cicchetti, Emily Shumchenia, Marisa Guarinello, John W. King, Jon Boothroyd, Bryan Oakley, Carol Thornber, and Pete August

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On the Geostrophic Adjustment of an Isolated Lens: Dependence on Burger Number and Initial Geometry, Grant A. Stuart, Miles A. Sundermeyer, and Dave Hebert

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Turbulent Airflow at Young Sea States with Frequent Wave Breaking Events: Large-Eddy Simulation, Nobuhiro Suzuki, Tetsu Hara, and Peter P. Sullivan

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Simulating the time-dependent diffusion coefficient in mixed-pore-size materials, Zhigang Zhang, David L. Johnson, and Lawrence M. Schwartz

Manuscripts from 2010

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A Regional Scale Modeling Analysis of Aerosol and Trace Gas Distributions over the Eastern Pacific During the INTEX-B Field Campaign, B. Adhikary, B. G. Heikes, and et al

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Climate Variability, Oceanography, Bowhead Whale Distribution, and Iñupiat Subsistence Whaling near Barrow, Alaska, Carin J. Ashjian, Stephen R. Braund, Robert Campbell, J. C. "Craig" George, Jack Kruse, Wieslaw Maslowski, Sue E. Moore, Craig R. Nicolson, Stephen R. Okkonen, Barry F. Sherr, Evelyn B. Sherr, and Yvette H. Spitz

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Transformation of an Agulhas eddy near the continental slope, S. Baker-Yeboah, G. R. Flieri, Georgi G. Sutyrin, and Y. Zhang

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Robotic tools for deep water archaeology: Surveying an ancient shipwreck with an autonomous underwater vehicle, Brian Bingham, Brendan Foley, Hanumant Singh, Richard Camilli, Katerina Delaporta, Ryan Eustice, Angelos Mallios, David Mindell, Christopher Roman, and Dimitris Sakellariou

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Short- and Medium-Range Prediction of Tropical and Transitioning Cyclone Tracks within the NCEP Global Ensemble Forecasting System, Christian E. Buckingham, Timothy Marchok, Isaac Ginis, Lewis M. Rothstein, and Dail Rowe

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Toward linking ocean models to fish population dynamics, Lawrence J. Buckley and Lauren B. Buckley

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Mapping Circulation in the Kuroshio Extension with an Array of Current and Pressure Recording Inverted Echo Sounders, Kathleen A. Donohue, D. Randolph Watts, Karen L. Tracey, Andrew D. Greene, and Maureen A. Kennelly

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Impact of Mexico City Emissions on Regional Air Quality from MOZART-4 Simulations, L. K. Emmons, E. C. Apel, J. -F. Lamarque, P. G. Hess, M. Avery, D. Blake, W. Brune, T. Campos, J. Crawford, P. F. DeCarlo, S. Hall, B. G. Heikes, J. Holloway, J. L. Jimenez, D. J. Knapp, G. Kok, M. Mena-Carrasco, J. Olson, D. O'Sullivan, G. Sachse, J. Walega, P. Weibring, A. Weinheimer, and C. Wiedinmyer

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Momentum Flux Budget across the Air–Sea Interface under Uniform and Tropical Cyclone Winds, Yalin Fan, Isaac Ginis, and Tetsu Hara

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Field‐derived Henry's law constants for polychlorinated biphenyls in oceanic waters, Rosalinda Gioia, Kevin C. Jones, Rainer Lohmann, Luca Nizzetto, and Jordi Dachs

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Seasonal movement of the American horseshoe crab Limulus polyphemus in a semi-enclosed bay on Cape Cod, Massachusetts (USA) as determined by acoustic telemetry, Mary-Jane James-Pirri

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Increase in water column denitrification during the last deglaciation: the influence of oxygen demand in the eastern equatorial Pacific, P. Martinez and Rebecca S. Robinson

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Seasonal distribution of dissolved inorganic carbon and net community production on the Bering Sea shelf, J. T. Mathis, J. N. Cross, N. R. Bates, S. Bradley Moran, M. W. Lomas, C. W. Mordy, and P. J. Stabeno

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Control system performance and efficiency for a mid-depth Lagrangian profiling float, Bryan McGilvray and Chris Roman

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Inherent High Correlation of Individual Motility Enhances Population Dispersal in a Heterotrophic, Planktonic Protist, Susanne Menden-Deuer

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PAH mineralization and bacterial organotolerance in surface sediments of the Charleston Harbor estuary, Michael T. Montgomery, Thomas J. Boyd, Christopher L. Osburn, and David C. Smith

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Fore‐arc basalts and subduction initiation in the Izu‐Bonin‐ Mariana system, Mark K. Reagan, Osamu Ishizuka, Robert J. Stern, Katherine A. Kelley, Yasuhiko Ohara, Janne Blichert-Toft, Sherman H. Bloomer, Jennifer Cash, Patricia Fryer, Barry B. Hanan, Rosemary Hickey-Vargas, Teruaki Ishii, Jun-Ichi Kimura, David W. Peate, Michael C. Rowe, and Melinda Woods

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South Atlantic mass transports obtained from subsurface float and hydrographic data, Regina R. Rodrigues, Mark Wimbush, D. Randolph Watts, Lewis M. Rothstein, and Michel Ollitrault

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Application of Structured Light Imaging for High Resolution Mapping of Underwater Archaeological Sites, Chris Roman, Gabrielle Inglis, and James Rutter

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Autonomous Underwater Vehicles as Tools for Deep-Submergence Archaeology, Christopher N. Roman and Ian Roderick Mather

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Coastal New England pilot study to determine fossil and biogenic formaldehyde source contributions using radiocarbon, Haiwei Shen, Brian G. Heikes, John T. Merrill, Ann P. McNichol, and Li Xu

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Impacts of Climate Change on Narragansett Bay, Leslie Smith, Sandra Whitehouse, and Candace A. Oviatt