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

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Manuscripts from 2009

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US GODAE: Global Ocean Prediction with the HYbrid Coordinate Ocean Model (HYCOM), Eric P. Chassignet, Harley E. Hurlburt, E. Joseph Metzger, Ole Martin Smedstad, James A. Cummings, George R. Halliwell, Rainer Bleck, Remy Baraille, Alan J. Wallcraft, Carlos Lozano, Hendrik L. Tolman, Ashwanth Srinivasan, Steven Hankin, Peter C. Cornillon, Robert Weisberg, Alexander Barth, Ruoying He, Francisco Werner, and John Wilkin

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Strong bottom currents and cyclogenesis in Drake Passage, T. K. Chereskin, K. A. Donohue, D. R. Watts, K. L. Tracey, Y. L. Firing, and A. L. Cutting

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Narragansett Bay hypoxic event characteristics based on fixed-site monitoring network time series: Intermittency, geographic distribution, spatial synchronicity, and interannual variability, Daniel L. Codiga, Heather E. Stoffel, Christopher F. Deacutis, Susan Kiernan, and Candace A. Oviatt

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End-to-end foodweb control of fish production on Georges Bank, Jeremy S. Collie, Dian J. Gifford, and John H. Steele

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Recolonization of gravel habitats on Georges Bank (northwest Atlantic), Jeremy S. Collie, Jerome M. Hermsen, and Page C. Valentine

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NVODS and the Development of OPeNDAP, Peter C. Cornillon, Jennifer Adams, M. Benno Blumenthal, Eric Chassignet, Ethan Davis, Steve Hankin, James Kinter, Roy Mendelssohn, James T. Potemra, Ashwanth Srinivasan, and Joseph Sirott

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High-precision determination of iron oxidation state in silicate glasses using XANES, Elizabeth Cottrell, Katherine A. Kelley, Antonio Lanzirotti, and Rebecca A. Fischer

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Controls on sedimentary nitrogen isotopes along the Chile margin, Ricardo De Pol-Holz, Rebecca S. Robinson, Dierk Hebbeln, Daniel M. Sigman, and Osvaldo Ulloa

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Subseafloor Sedimentary Life in the South Pacific Gyre, Steven D'Hondt, Arthur J. Spivack, Robert Pockalny, Timothy G. Ferdelman, Jan P. Fischer, Jens Kallmeyer, Lewis J. Abrams, David C. Smith, Dennis Graham, Franciszek Hasiuk, Heather Schrum, and Andrea M. Stancin

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Hydrometeor‐enhanced tephra sedimentation: Constraints from the 18 May 1980 eruption of Mount St. Helens, A. J. Durant, W. I. Rose, A. M. Sarna-Wojcicki, Steven Carey, and A. C. M. Volentik

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The Effect of Wind–Wave–Current Interaction on Air–Sea Momentum Fluxes and Ocean Response in Tropical Cyclones, Yalin Fan, Isaac Ginis, and Tetsu Hara

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Numerical Simulations and Observations of Surface Wave Fields under an Extreme Tropical Cyclone, Yalin Fan, Isaac Ginis, Tetsu Hara, C. Wayne Wright, and Edward J. Walsh

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Internal wave observations in the South China sea: The role of rotation and non-linearity, David Farmer, Qiang Li, and Jae Hun Park

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Simulating the dispersal of tephra from the 1991 Pinatubo eruption: Implications for the formation of widespread ash layers, Julie Fero, Steven N. Carey, and John T. Merrill

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Oxygen penetration deep into the sediment of the South Pacific gyre, J. P. Fischer, T. G. Ferdelman, Steven D'Hondt, H. Røy, and F. Wenzhöfer

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Fisheries Overview, M. J. Fogarty and J. S. Collie

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The 2005 Chios Ancient Shipwreck Survey: New Methods for Underwater Archaeology, Brendan P. Foley, Katerina Dellaporta, Dimitris Sakellariou, Brian S. Bingham, Richard Camilli, Ryan M. Eustice, Dionysis Evagelistis, Vicki Lynn Ferrini, Kostas Katsaros, Dimitris Kourkoumelis, Aggelos Mallios, Paraskevi Micha, David A. Mindell, Christopher Roman, Hanumant Singh, David S. Switzer, and Theotokis Theodoulou

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Comparing polychaete and polyethylene uptake to assess sediment resuspension effects on PCB bioavailability, Carey L. Friedman; Robert M. Burgess; Monique M. Perron; Mark G. Cantwell; Kay T, Ho; and Rainer Lohmann

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Functional diversity in a marine fish community, Dian J. Gifford, Jeremy S. Collie, and John H. Steele

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Applications of Satellite-Derived Ocean Measurements to Tropical Cyclone Intensity Forecasting, Gustavo Goni, Mark DeMaria, John Knaff, Charles Sampson, Isaac Ginis, Francis Bringas, Alberto Mavume, Chris Lauer, I.-I. Lin, M. M. Ali, Paul Sandery, Silvana Ramos-Buarque, KiRyong Kang, Avichal Mehra, Eric Chassignet, and George Halliwell

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Turbulent supply of nutrients to phytoplankton at the New England shelf break front, Burke Hales, Dave Hebert, and John Marra

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High-resolution surveys of the biogeochemistry of the New England shelfbreak front during Summer, 2002, Burke Hales, Robert D. Vaillancourt, Laura Prieto, John Marra, Robert Houghton, and Dave Hebert

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Paleomagnetism and environmental magnetism of GLAD800 sediment cores from Bear Lake, Utah and Idaho, Clifford W. Heil, John W. King, Joseph G. Rosenbaum, Richard L. Reynolds, and Steven M. Colman

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A method for determining the nitrogen isotopic composition of porphyrins, Meytal B. Higgins, Rebecca S. Robinson, Karen L. Casciotti, Matthew R. McIlvin, and Ann Pearson

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The fissure swarm of the Askja volcanic system along the divergent plate boundary of N Iceland, Ásta Rut Hjartardóttir, Páll Einarsson, and Haraldur Sigurdsson

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Cross-shelf circulation and phytoplankton distribution at the summertime New England shelfbreak front, Robert W. Houghton, Robert D. Vaillancourt, John Marra, Dave Hebert, and Burke Hales

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Stream-coordinate structure and variability of the Kuroshio Extension, Penelope J. Howe, Kathleen A. Donohue, and D. Randolph Watts

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Anthropogenic influences on estuarine sedimentation and ecology: Examples from the varved sediments of the Pettaquamscutt River Estuary, Rhode Island, J. Bradford Hubeny, John W. King, and Mark Cantwell

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Terrain Constrained Stereo Correspondence, Gabrielle Inglis and Chris Roman

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Effects of Open Marsh Water Management on Numbers of Larval Salt Marsh Mosquitoes, Mary-Jane James-Pirri, Howard S. Ginsberg, R. Michael Erwin, and Janith Taylor

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The Kuroshio Extension and its recirculation gyres, Steven R. Jayne, Nelson G. Hogg, Stephanie N. Waterman, Luc Rainville, Kathleen A. Donohue, D. Randolph Watts, Karen L. Tracey, Julie L. McClean, Mathew E. Maltrud, Bo Qiu, Shuiming Chen, and Peter Hacker

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An improved electroelution method for separation of DNA from humic substances in marine sediment DNA extracts: Research article, Jens Kallmeyer and David C. Smith

Erratum: Water and the oxidation state of subduction zone magmas (Science (605)), K. A. Kelley and E. Cottrell

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Water and the oxidation state of subduction zone magmas, Katherine A. Kelley and Elizabeth Cottrell

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Compositional variations and magma mixing in the 1991 eruptions of Hudson volcano, Chile, David J. Kratzmann, Steven Carey, Roberto Scasso, and Jose Antonio Naranjo

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Erratum: Compositional variations and magma mixing in the 1991 eruptions of Hudson volcano, Chile (Bulletin of Volcanology 10.1007/s00445-008-0234-x), David J. Kratzmann, Steven Carey, Roberto Scasso, and Jose Antonio Naranjo

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Toward extraplanetary under-ice exploration: Robotic steps in the arctic, Clayton Kunz, Chris Murphy, Hanumant Singh, Claire Pontbriand, Robert A. Sohn, Sandipa Singh, Taichi Sato, Chris Roman, Ko Ichi Nakamura, Michael Jakuba, Ryan Eustice, Richard Camilli, and John Bailey

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The invasive colonial ascidian Didemnum vexillum on Georges Bank - Ecological effects and genetic identification, Nicole L. Lengyel, Jeremy S. Collie, and Page C. Valentine

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Large eddy simulations of Upper-Ocean response to a midlatitude storm and comparison with observations, Ming Li, Svein Vagle, and David M. Farmer

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Acoustical measurement of nonlinear internal waves using the inverted echo sounder, Qiang Li, David M. Farmer, Timothy F. Duda, and Steve Ramp

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Fluxes of soot black carbon to South Atlantic sediments, Rainer Lohmann, Kevyn Bollinger, Mark Cantwell, Johann Feichter, Irene Fischer-Bruns, and Matthias Zabel

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Organochlorine pesticides and PAHs in the surface water and atmosphere of the North Atlantic and Arctic Ocean, Rainer Lohmann, Rosalinda Gioia, Kevin C. Jones, Luca Nizzetto, Christian Temme, Zhiyong Xie, Detlef Schulz-Bull, Ines Hand, Eric Morgan, and Liisa Jantunen

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Simulated response of North Pacific Mode Waters to global warming, Yiyong Luo, Qinyu Liu, and Lewis M. Rothstein

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Response of pacific subtropical-tropical thermocine water pathways and transports to global warming, Yiyong Luo, Lewis M. Rothstein, and Rong Hua Zhang

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Airborne Measurement of OH Reactivity During INTEX-B, J. Mao, X. Ren, W. H. Brune, J. R. Olson, J. H. Crawford, A. Fried, L. G. Huey, R. C. Cohen, B. G. Heikes, H. B. Singh, D. R. Blake, G. W. Sachse, G. S. Diskin, S. R. Hall, and R. E. Shetter

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Eutrophication and the macroscope, Scott W. Nixon

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Anthropogenic enhancement of Egypt's Mediterranean fishery, Autumn J. Oczkowski, Scott W. Nixon, Stephen L. Granger, Abdel-Fattah M. El-Sayed, and Richard A. McKinney

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Intrusion of warm Bering/Chukchi waters onto the shelf in the western Beaufort Sea, Stephen R. Okkonen, Carin J. Ashjian, Robert G. Campbell, Wieslaw Maslowski, Jaclyn L. Clement-Kinney, and Rachel Potter

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Impact of the assimilation of ozone from the tropospheric emission spectrometer on surface ozone across North America, M. Parrington, D. B.A. Jones, K. W. Bowman, A. M. Thompson, D. W. Tarasick, J. Merrill, S. J. Oltmans, T. Leblanc, J. C. Witte, and D. B. Millet

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Airborne Observations of Total RONO2: New Constraints on the Yield and Lifetime of Isoprene Nitrates, A. E. Perring, T. H. Bertram, P. J. Wooldridge, A. Fried, B. G. Heikes, J. Dibb, J. D. Crounse, P. O. Wennberg, N. J. Blake, D. R. Blake, W. H. Brune, H. B. Singh, and R. C. Cohen

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Foraminiferal isotope evidence of reduced nitrogen fixation in the ice age Atlantic ocean, H. Ren, D. M. Sigman, A. N. Meckler, B. Plessen, R. S. Robinson, Y. Rosenthal, and G. H. Haug

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Effect of selected marine and freshwater microalgae on development and survival of the mosquito Aedes aegypti, Jorge R. Rey, Paul E. Hargraves, and Sheila M. O'Connell

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Nitrogen isotopic evidence for deglacial changes in nutrient supply in the eastern equatorial Pacific, Rebecca S. Robinson, P. Martinez, L. D. Pena, and I. Cacho

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An isopycnal view of the Nordic Seas hydrography with focus on properties of the Lofoten Basin, T. Rossby, Vladimir Ozhigin, Victor Ivshin, and Sheldon Bacon

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Pathways of inflow and dispersion of warm waters in the Nordic seas, T. Rossby, M. D. Prater, and H. Søiland

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Metapopulation Structure in the Planktonic Diatom Ditylum brightwellii (Bacillariophyceae), Tatiana A. Rynearson, Ellen O. Lin, and E. Virginia Armbrust

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Sulfate-reducing ammonium oxidation: A thermodynamically feasible metabolic pathway in subseafloor sediment, Heather N. Schrum, Arthur J. Spivack, Miriam Kastner, and Steven D'Hondt

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Development of a New Lagrangian Float for Studying Coastal Marine Ecosystems, Alex Schwithal and Chris Roman

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Atlantic forcing of persistent drought in West Africa, T. M. Shanahan, J. T. Overpeck, K. J. Anchukaitis, J. W. Beck, J. E. Cole, D. L. Dettman, J. A. Peck, C. A. Scholz, and J. W. King

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Radiocarbon analysis of atmospheric formaldehyde using cystamine derivatization, Haiwei Shen, Ann P. McNichol, Li Xu, Alan Gagnon, and Brian G. Heikes

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Seismic evidence for a Moho offset and south-directed thrust at the easternmost Qaidam-Kunlun boundary in the Northeast Tibetan plateau, Danian Shi, Yang Shen, Wenjin Zhao, and Aibing Li

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Hydrogenase activity in deeply buried sediments of the Arctic and North Atlantic Oceans, Bruno Soffientino, Arthur J. Spivack, David C. Smith, and Steven D'Hondt

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Rebuilding Global Fisheries, Boris Worm, Ray Hilborn, Julia K. Baum, Trevor A. Branch, Jeremy S. Collie, Christopher Costello, Michael J. Fogarty, Elizabeth A. Fulton, Jeffrey A. Hutchings, Simon Jennings, Olaf P. Jensen, Heike K. Lotze, Pamela M. Mace, Tim R. McClanahan, Cóilín Minto, Stephen R. Palumbi, Ana M. Parma, Daniel Ricard, Andrew A. Rosenberg, Reg Watson, and Dirk Zeller

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Limitation of one-dimensional ocean models for coupled hurricane-ocean model forecasts, R. M. Yablonsky and Isaac Ginis

Manuscripts from 2008

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Observations of Kuroshio flow variations in the East China Sea, Magdalena Andres, Mark Wimbush, J.-H. Park, K.-I. Chang, B.-H. Lim, D. Randolph Watts, H. Ichikawa, and W. J. Teague

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Changes in a benthic megafaunal community due to disturbance from bottom fishing and the establishment of a fishery closure, Rebecca G. Asch and Jeremy S. Collie

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Factors influencing the recruitment and abundance of Didemnum in Narragansett Bay, Rhode Island, Linda A. Auker and Candace A. Oviatt

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Age model and core‐seismic integration for the Cenozoic Arctic Coring Expedition sediments from the Lomonosov Ridge, Jan Backman, Martin Jakobsson, Martin Frank, Francesca Sangiorgi, Henk Brinkhuis, Catherine Stickley, Matthew O'Regan, Reidar Løvlie, Heiko Pälike, David Spofforth, Jérôme Gattacecca, Kate Moran, John W. King, and Chip Heil

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The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Chris Bowler, Bethany D. Jenkins, Tatiana A. Rynearson, and et al

Evaluating PAH biodegradation relative to total bacterial carbon demand in coastal ecosystems: Are PAHs truly recalcitrant?, Thomas J. Boyd, David C. Smith, Jude K. Apple, Leila J. Hamdan, Christopher L. Osburn, and Michael T. Montgomery

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Reply to comment by Yannick Garcin on "Abrupt change in tropical African climate linked to the bipolar seesaw over the past 55,000 years", E. T. Brown, T. C. Johnson, C. A. Scholz, A. S. Cohen, and J. W. King

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Winter flounder larval genetic population structure in Narragansett Bay, RI: Recruitment to juvenile young-of-the-year, Larry Buckley, Jeremy Collie, Lisa A.E. Kaplan, and Joseph Crivello

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Byzantium Beneath the Black Sea, Bridget Buxton, Robert Ballard, Michael Brennan, Dwight Coleman, Katy Croff, Christopher Roman, Dan Davis, Dennis Piechota, and Sergiy Voronov

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The response of benthic macrofauna to anthropogenic stress in Narragansett Bay, Rhode Island: A review of human stressors and assessment of community conditions, Christopher J. Calabretta and Candace A. Oviatt

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Resuspension of contaminated field and formulated reference sediments Part I: Evaluation of metal release under controlled laboratory conditions, Mark G. Cantwell, Robert M. Burgess, and John W. King

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Long-term shifts in the species composition of a coastal fish community, Jeremy S. Collie, Anthony D. Wood, and H. Perry Jeffries

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Using satellite-derived sst fronts to evaluate an eddy resolving numerical circulation model, Peter Cornillon and Andrew Eichmann

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Quaternary paleoceanography of the central Arctic based on Integrated Ocean Drilling Program Arctic Coring Expedition 302 foraminiferal assemblages, Thomas M. Cronin, Shannon A. Smith, Frédérique Eynaud, Matthew O'Regan, and John King

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Program studies the Kuroshio extension, Kathleen Donohue, D. Randolph Watts, Karen Tracey, Mark Wimbush, Jae Hun Park, Nicholas Bond, Meghan Cronin, Shuiming Chen, Bo Qiu, Peter Hacker, Nelson Hogg, Steven Jayne, Julie MCClean, Luc Rainville, Humio Mitsudera, Youichi Tanimoto, and Shang Ping Xie

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Measurement of copepod predation on nauplii using qPCR of the cytochrome oxidase I gene, Edward G. Durbin, Maria C. Casas, Tatiana A. Rynearson, and David C. Smith

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Simulation of the 1980 eruption of Mount St. Helens using the ash-tracking model PUFF, Julie Fero, Steven N. Carey, and John T. Merrill

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Variable Morphologic Expression of Volcanic, Tectonic, and Hydrothermal Processes at Six Hydrothermal Vent Fields in the Lau Back-Arc Basin, Vicki Lynn Ferrini, Margaret K. Tivey, Suzanne M. Carbotte, Fernando Martinez, and Chris Roman

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Beryllium isotopes in central Arctic Ocean sediments over the past 12.3 million years: Stratigraphic and paleoclimatic implications, Martin Frank, Jan Backman, Martin Jakobsson, Kate Moran, Matthew O'Regan, John W. King, Brian A. Haley, Peter W. Kubik, and Dieter Garbe-Schönberg

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Role of convection in redistributing formaldehyde to the upper troposphere over North America and the North Atlantic during the summer 2004 INTEX campaign, Alan Fried, Haiwei Shen, and et al

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Formaldehyde over North America and the North Atlantic during the summer 2004 INTEX campaign: Methods, observed distributions, and measurement‐model comparisons, Alan Fried, James G. Walega, Jennifer R. Olson, Jim H. Crawford, Gao Chen, Petter Weibring, Dirk Richter, Chad Roller, Frank K. Tittel, Brian G. Heikes, Julie A. Snow, Haiwei Shen, Daniel W. O'Sullivan, Michael Porter, Henry Fuelberg, Jeremy Halland, and Dylan B. Millet

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Nitrogen in Past Marine Environments, Eric D. Galbraith, Daniel M. Sigman, Rebecca S. Robinson, and Thomas F. Pedersen

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Polychlorinated biphenyls in air and water of the North Atlantic and Arctic Ocean, Rosalinda Gioia, Rainer Lohmann, Jordi Dachs, Christian Temme, Soenke Lakaschus, Stlef Schulz-Bull, Ines Hand, and Kevin C. Jones

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Polychlorinated biphenyls (PCBs) in air and seawater of the Atlantic Ocean: Sources, trends and processes, Rosalinda Gioia, Luca Nizzetto, Rainer Lohmann, Jordi Dachs, Christian Temme, and Kevin C. Jones

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Allelopathy at the land/sea interface: Microalgae and Brazilian pepper, Paul E. Hargraves

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Evaluation and application of satellite primary production models in Massachusetts Bay, Kimberly J.W. Hyde, John E. O'Reilly, and Candace A. Oviatt

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Long-baseline acoustic navigation for under-ice autonomous underwater vehicle operations, Michael V. Jakuba, Christopher N. Roman, Hanumant Singh, Christopher Murphy, Clayton Kunz, Claire Willis, Taichi Sato, and Robert A. Sohn

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Characteristics of Calanus finmarchicus dormancy patterns in the Northwest Atlantic, Catherine L. Johnson, Andrew W. Leising, Jeffrey A. Runge, Erica J.H. Head, Pierre Pepin, Stéphane Plourde, and Edward G. Durbin

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New cell extraction procedure applied to deep subsurface sediments, Jens Kallmeyer, David C. Smith, Arthur J. Spivack, and Steven D'Hondt

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The Effect of Breaking Waves on a Coupled Model of Wind and Ocean Surface Waves. Part II: Growing Seas, Tobias Kukulka and Tetsu Hara

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The Effect of Breaking Waves on a Coupled Model of Wind and Ocean Surface Waves. Part I: Mature Seas, Tobias Kukulka and Tetsu Hara

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Deep Sea Underwater Robotic Exploration in the Ice-Covered Arctic Ocean With AUVs, Clayton Kunz, Chris Murphy, Richard Camilli, Hanumant Singh, John Bailey, Ryan M. Eustice, Chris Roman, Michael Jakuba, Claire Willis, Taichi Sato, Ko-ichi Nakamura, and Robert A. Sohn

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3500 yr record of centennial-scale climate variability from the Western Pacific Warm Pool, S. J. Langton, B. K. Linsley, R. S. Robinson, Y. Rosenthal, D. W. Oppo, T. I. Eglinton, S. S. Howe, Y. S. Djajadihardja, and F. Syamsudin

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Evolution of lakes in the Huron basin: Deglaciation to present, C. F. Michael Lewis, Paul F. Karrow, Stefan M. Blasco, Francine M.G. McCarthy, John W. King, Theodore C. Moore, and David K. Rea

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Dry climate disconnected the Laurentian Great Lakes, C. F. Michael Lewis, John W. King, Stefan M. Blasco, Gregory R. Brooks, John P. Coakley, Thomas E. Croley, David L. Dettman, Thomas W.D. Edwards, Clifford W. Heil, J. Bradford Hubeny, Kathleen R. Laird, John H. McAndrews, Francine M.G. McCarthy, Barbara E. Medioli, Theodore C. Moore, David K. Rea, and Alison J. Smith

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On the size and distribution of rings and coherent vortices in the Sargasso Sea, David L. Luce and Tom Rossby