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

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Submissions from 2013

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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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Effects of chronic bottom fishing on the benthic epifauna and diets of demersal fishes on northern georges bank, Brian E. Smith, Jeremy S. Collie, and Nicole L. Lengyel

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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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Impact of a warm ocean Eddy's circulation on hurricane-induced sea surface cooling with implications for hurricane intensity, Richard M. Yablonsky and Isaac Ginis

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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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Changes in the biomass of chambo in the southeast arm of Lake Malawi: A stock assessment of Oreochromis spp., Richard J. Bell, Jeremy S. Collie, Daniel Jamu, and Moses Banda

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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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Krill feeding on sediment in the Gulf of Maine (North Atlantic), Alison C. Cleary, Edward G. Durbin, and Tatiana A. Rynearson

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A fisheries risk-assessment framework to evaluate trade-offs among management options in the presence of time-varying productivity, Jeremy S. Collie, Randall M. Peterman, and Brett M. Zuehlke

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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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Fracture of a ridged multi-year Arctic sea ice floe, J. P. Dempsey, Y. Xie, R. M. Adamson, and D. M. Farmer

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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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Copepod feeding and digestion rates using prey DNA and qPCR, Edward G. Durbin, Maria C. Casas, and Tatiana A. Rynearson

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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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Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment, Bente Aa Lomstein, Alice T. Langerhuus, Steven D'Hondt, Bo B. Jørgensen, and Arthur J. Spivack

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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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Near 13 day barotropic ocean response to the atmospheric forcing in the North Pacific, Hanna Na, Jae Hun Park, D. Randolph Watts, Kathleen A. Donohue, and Ho Jin Lee

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Submarine volcanoes of the Kolumbo volcanic zone NE of Santorini Caldera, Greece, P. Nomikou, S. Carey, D. Papanikolaou, K. Croff Bell, D. Sakellariou, M. Alexandri, and K. Bejelou

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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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Comparisons of sea surface height variability observed by pressure-recording inverted echo sounders and satellite altimetry in the Kuroshio Extension, Jae Hun Park, D. R. Watts, Kathleen A. Donohue, and Karen L. Tracey

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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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Aerosol effects on microstructure and intensity of tropical cyclones, Daniel Rosenfeld, William L. Woodley, Alexander Khain, William R. Cotton, Gustavo Carrió, Isaac Ginis, and Joseph H. Golden

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Aerobic microbial respiration in 86-million-year-old deep-sea red clay, Hans Røy, Jens Kallmeyer, Rishi Ram Adhikari, Robert Pockalny, Bo Barker Jørgensen, and Steven D'Hondt

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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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Tsunami triggering mechanisms associated with the 17th cent. BC Minoan eruption of thera Volcano, Greece, Dimitris Sakellariou, Grigoris Rousakis, Paraskevi Nomikou, Kathy Croff Bell, Steve Carey, and Haraldur Sigurdsson

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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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Geochemistry of basalts from IODP site U1365: Implications for magmatism and mantle source signatures of the mid-Cretaceous Osbourn Trough, Guoliang Zhang, Christopher Smith-Duque, Suohan Tang, He Li, Carlos Zarikian, Steven D'Hondt, and Fumio Inagaki

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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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Volcaniclastic processes and deposits in the deep-sea, Steven N. Carey and Jean Luc Schneider

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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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Heterotrophic organisms dominate nitrogen fixation in the south pacific gyre, Hannah Halm, Phyllis Lam, Timothy G. Ferdelman, Gaute Lavik, Thorsten Dittmar, Julie Laroche, Steven D’Hondt, and Marcel M.M. Kuypers

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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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The generation and evolution of nonlinear internal waves in the deep basin of the South China Sea, Qiang Li and David M. Farmer

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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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Inferred growth of juvenile French grunts, Haemulon flavolineatum, and schoolmaster, Lutjanus apodus, in mangrove and seagrass habitats, Ivan Mateo, Edward Durbin, Richard Appeldoorn, Aaron Adams, Francis Juanes, and Daisy Durant

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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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Does selective fishing conserve community biodiversity? Predictions from a length-based multispecies model, Marie Joëlle Rochet, Jeremy S. Collie, Simon Jennings, and Stephen J. Hall

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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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Sensing the ocean, Thomas B. Sanford, Kathryn A. Kelly, and David M. Farmer

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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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Coupled organic and inorganic carbon cycling in the deep subseafloor sediment of the northeastern Bering Sea Slope (IODP Exp. 323), Laura M. Wehrmann, Nils Risgaard-Petersen, Heather N. Schrum, Emily A. Walsh, Youngsook Huh, Minoru Ikehara, Catherine Pierre, Steven D'Hondt, Timothy G. Ferdelman, Ana Christina Ravelo, Kozo Takahashi, and Carlos Alvarez Zarikian

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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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Workflows and extensions to the Kepler scientific workflow system to support environmental sensor data access and analysis, Derik Barseghian, Ilkay Altintas, Matthew B. Jones, Daniel Crawl, Nathan Potter, James Gallagher, Peter Cornillon, Mark Schildhauer, Elizabeth T. Borer, Eric W. Seabloom, and Parviez R. Hosseini

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Gas bubbles as oceanographic tracers, Burkard Baschek and David M. Farmer

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Identification and determination of trinitrotoluenes and their degradation products using liquid chromatography-electrospray ionization mass spectrometry, Jitka Bečanová, Zdeněk Friedl, and Zdeněk Šimek

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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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Preliminary and novel estimates of CO2 gas transfer using a satellite scatterometer during the 2001GasEx experiment, Darek Bogucki, Mary Elena Carr, William M. Drennan, Peter Woiceshyn, Tetsu Hara, and Marjorie Schmeltz

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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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The past, present, and future of the AVHRR pathfinder SST program, Kenneth S. Casey, Tess B. Brandon, Peter Cornillon, and Robert Evans

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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