This is a select list of works produced by the faculty of the USF College of Marine Science. Materials are included when two conditions are satisfied: 1) the creator approves inclusion and 2) the publisher allows the material to be placed in the repository. Please direct questions or requests to expand the list of materials to Jason Boczar.

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Submissions from 2016

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Linking Oceanographic Modeling and Benthic Mapping with Habitat Suitability Models for Pink Shrimp on the West Florida Shelf, Peter J. Rubec, Jesse Lewis, David Reed, Christi Santi, Robert H. Weisberg, Lianyuan Zheng, Chris Jenkins, Charles F. Ashbaugh, Curt Lashley, and Salvatore Versaggi

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An Imperative to Monitor Earth's Energy Imbalance, K. von Schuckmann, M. D. Palmer, K. E. Trenberth, A. Cazenave, D. Chambers, N. Champollion, J. Hansen, S. A. Josey, N. Loeb, P.-P. Mathieu, B. Meyssignac, and M. Wild

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Benthic Foraminifera Abundance, Stable Isotopes, Desoto Canyon Sediments, 2010-2012, Patrick Schwing

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Using Foraminifera to Assess Benthic Distribution, Impacts and Recovery following Sedimentary Oil Deposition Associated with the DWH and Ixtoc Events, Patrick Schwing, Michael Martinez-Colon, Maria Luisa Machain-Castillo, Isabel C. Romero, Jeff P. Chanton, Bryan J. O'Malley, Erika E Fridrik, Gregg Brooks, David Hastings, Rebekka A. Larson, and David J. Hollander

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Sediment Core Extrusion Method at Millimeter Resolution Using a Calibrated, Threaded-rod, Patrick Schwing, Isabel C. Romero, Rebekka A Larson, Bryan J. O'Malley, Erika E Fridrik, Ethan Goddard, Gregg R Brooks, David Hastings, Brad Rosenheim, David Hollander, Guy Grant, and Jim Mulhollan

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Cephalopod Susceptibility to Asphyxiation via Ocean Incalescence, Deoxygenation, and Acidification, Brad A. Seibel

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Hypoxia Tolerance and Metabolic Suppression in Oxygen Minimum Zone Euphausiids: Implications for Ocean Deoxygenation and Biogeochemical Cycles, Brad A. Seibel, Jillian L. Schneider, Stein Kaartvedt, Karen F. Wishner, and Kendra L. Daly

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Drilling and Modeling Studies Expose Antarctica’s Miocene Secrets, Amelia E. Shevenell

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Quantification of Boat Visitation Rates at Artificial and Natural Reefs in the Eastern Gulf of Mexico Using Acoustic Recorders, Peter Simard, Kara R. Wall, David A. Mann, Carrie C. Wall, and Christopher D. Stallings

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Clumped Isotope Composition of Cold-water Corals: A Role for Vital Effects?, Peter T. Spooner, Weifo Guo, Laura F. Robinson, Nivedita Thiagarajan, Katharine R. Hendry, Brad E. Rosenheim, and Melanie J. Leng

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Lunar periodicity in spawning of white grunt, Haemulon plumierii, Christopher D. Stallings, Ernst B. Peebles, Oscar Ayala, Joseph S. Curtis, and Kara R. Wall

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QNSE Theory of Turbulence Anisotropization And onset of the Inverse Energy Cascade by Solid Body Rotation, Semion Sukoriansky and Boris Galperin

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A Hybrid Method to Estimate Suspended Particle Sizes from Satellite Measurements over Bohai Sea and Yellow Sea, Deyong Sun, Zhongfeng Qiu, Chuanmin Hu, Shengqiang Wang, Lin Wang, Lufei Zheng, Tian Peng, and Yijun He

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Temporal Variability of Diapycnal Mixing in the Northern South China Sea, Hui Sun, Qingxuan Yang, Wei Zhao, Xinfeng Liang, and Jiwei Tian

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Sun Glint Requirement for the Remote Detection of Surface Oil Films, Shaojie Sun and Chuanmin Hu

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Oil Slick Morphology Derived from AVIRIS Measurements of the Deepwater Horizon Oil Spill: Implications for Spatial Resolution Requirements of Remote Sensors, Shaojie Sun, Chuanmin Hu, Lian Feng, Gregg A. Swayze, Jamie Holmes, George Graettinger, Ian MacDonald, Oscar Garcia, and Ira Leifer

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Faecal Pollution Along the Southeastern Coast of Florida and Insight into the Use of Pepper Mild Mottle Virus as an Indicator, E. M. Symonds, C. Sinigalliano, M. Gidley, W. Ahmed, S. M. McQuaig‐Ulrich, and Mya Breitbart

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Single-stranded DNA Phages: From Early Molecular Biology Tools to Recent Revolutions in Environmental Microbiology, Anna Székely and Mya Breitbart

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Progression of a Gulf of Mexico Food Web Supporting Atlantis Ecosystem Model Development, Joseph H. Tarnecki, Amy A. Wallace, James E. Simons, and Cameron Ainsworth

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The Impact of the QNSE-EDMF Scheme and Its Modifications on Boundary Layer Parameterization in WRF: Modelling of CASES-97, Esa-Matti Tastula, Margaret A. LeMone, Jimy Dudhia, and Boris Galperin

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Characterization of Available Light for Seagrass and Patch Reef Productivity in Sugarloaf Key, Lower Florida Keys, Gerardo Toro-Farmer, Frank E. Muller-Karger, Maria Vega-Rodriguez, Nelson Melo, Kimberly Yates, Sergio Cerdeira-Estrada, and Stanley R. Herwitz

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The Impact of a Barrier Island Loss on Extreme Events in the Tampa Bay, Marius Ulm, Arne Arns, Thomas Wahl, Steven D. Meyers, Mark E. Luther, and Jürgen Jensen

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Managing Microbial Risks from Indirect Wastewater Reuse for Irrigation in Urbanizing Watersheds, Matthew Verbyla, Erin Symonds, Ram Kafle, Maryann Cairns, Mercedes Iriarte, Alvaro Mercado Guzmán, Olver Coronado, Mya Breitbart, Carmen Ledo, and James Mihelcic

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Recent Change - North Sea, Thomas Wahl

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Climate Controls Multidecadal Variability in U. S. Extreme Sea Level Records, Thomas Wahl and Don P. Chambers

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Impacts of Combined Overfishing and Oil Spills on the Plankton Trophodynamics of the West Florida Shelf Over the Last Half Century of 1965-2011: a Two-Dimensional Simulation Analysis of Biotic State Transitions, from a Zooplankton- to a Bacterioplankton-Modulated Ecosystem, John J. Walsh, Jason M. Lenes, Brian P. Darrow, Ashley A. Parks, and Robert H. Weisberg

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Mapping and Quantifying Sargassum Distribution and Coverage in the Central West Atlantic using MODIS Observations, Mengqiu Wang and Chuanmin Hu

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An Evaluation of pH and NO3 Sensor Data from SOCCOM Floats and their Utilization to Develop Ocean Inorganic Carbon Products, R. Wanninkhof, K. Johnson, N. Williams, J. Sarmiento, S. Riser, E. Briggs, S. M. Bushinsky, B. Carter, A. G. Dickson, R. A. Feely, A. Gray, L. Juranek, R. Key, L. Talley, J. Russel, and A. Verdy

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Hercules 265 Rapid Response: Immediate Ecosystem Impacts of a Natural Gas Blowout Incident, Sarah C. Weber, Leigha Peterson, Jessica J. Battles, Brian J. Roberts, Richard N. Peterson, David J. Hollander, Jeffrey P. Chanton, Samantha Joye, and Joseph P. Montoya

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Atlantis Ecosystem Model Summit: Report from a workshop, M. Weijerman, J. S. Link, E. A. Fulton, E. Olsen, H. Townsend, S. Gaichas, C. Hansen, M. Skern-Mauritzen, I. C. Kaplan, R. Gamble, G. Fay, M. Savina, C. Ainsworth, I. van Putten, R. Gorton, R. Brainard, K. Larsen, and T. Hutton

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Atlantis Ecosystem Model Summit: Report from a Workshop, M. Weijerman, J. S. Link, E. A. Fulton, E. Olsen, H. Townsend, S. Gaichas, C. Hansen, M. Skern-Mauritzen, I. C. Kaplan, R. Gamble, G. Fay, M. Savina, C. Ainsworth, I. van Putten, R. Gorton, R. Brainard, K. Larsen, and T. Hutton

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West Florida Shelf Upwelling: Origins and Pathways, Robert H. Weisberg, Lianyuan Zheng, and Yonggang Liu

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Karenia Brevis Blooms on the West Florida Shelf: A Comparative Study of the Robust 2012 Bloom and the Nearly Null 2013 Event, Robert H. Weisberg, Lianyuan Zheng, Yonggang Liu, Alina A. Corcoran, Chad Lembke, Chuanmin Hu, Jason M. Lenes, and John J. Walsh

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Did Deepwater Horizon Hydrocarbons Transit to the West Florida Continental Shelf?, Robert H. Weisberg, Lianyuan Zheng, Yonggang Liu, Steven Murawski, Chuamin Hu, and John Paul

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Empirical Algorithms to Estimate Water Column pH in the Southern Ocean, N. L. Williams, L. W. Juranek, K. S. Johnson, R. A. Feely, S. C. Riser, L. D. Talley, J. L. Russell, J. L. Sarmiento, and R. Wanninkhof

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Processes of Multibathyal Aragonite Undersaturation in the Arctic Ocean, Jonathan G. Wynn, Lisa Robbins, and L. G. Anderson

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Mapping Macroalgal Blooms in the Yellow Sea and East China Sea using HJ-1 and Landsat Data: Application of a Virtual Baseline Reflectance Height Technique, Qianguo Xing and Chuanmin Hu

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Recent Increases in Arctic Freshwater Flux Affects Labrador Sea Convection and Atlantic Overturning Circulation, Qian Yang, Tim Dixon, Paul G. Myers, Jennifer Bonin, Don Chambers, M.R. van den Broeke, Mads H. Ribergaard, and John Mortensen

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Short-Term Changes of Remote Sensing Reflectancein a Shallow-Water Environment: Observations from Repeated Airborne Hyperspectral Measurements, Mingrui Zhang, D. English, Chuanmin Hu, P. Carlson, Frank E. Muller-Karger, G. Toro-Farmer, and S. R. Herwitz

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Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume, Brian L. Zielinski, Andrew E. Allen, Edward J. Carpenter, Victoria J. Coles, Byron C. Crump, Mary Doherty, Rachel A. Foster, Joaquim I. Goes, Helga R. Gomes, Raleigh R. Hood, John P. McCrow, Joseph P. Montoya, Ahmed Moustafa, Brandon M. Satinsky, Shalabh Sharma, Christa B. Smith, Patricia L. Yager, and John H Paul

Submissions from 2015

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Stochastic Lagrangian Trajectory Modeling of Surface Drifters Deployed during the Deepwater Horizon Oil Spill, Ana J. Abascal, Sonia Castanedo, R. Minguez, Raul Medina, Yonggang Liu, and Robert H. Weisberg

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Ratification Vote on Taxonomic Proposals to the International Committee on Taxonomy of Viruses, M. Adams, E. J. Lefkowitz, A. M. Q. King, D. H. Bamford, and Mya Breitbart

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British Columbia Marine Fisheries Catch Reconstruction: 1873 to 2011, Cameron Ainsworth

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Coral–algal Phase Shifts Alter Fish Communities and Reduce Fisheries Production, Cameron H. Ainsworth and Peter J. Mumby

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Ten Common Mistakes Made in Ecopath with Ecosim Modelling, Cameron H. Ainsworth and C. J. Walters

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An Atlantis Ecosystem Model for the Gulf of Mexico supporting Integrated Ecosystem Assessment, Cameron Ainsworth, Michael Schirripa, and Hem Nalini Morzaria-Luna

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MODIS Observations of Human-Induced Changes in the Mesopotamian Marshes in Iraq, Adil Al-Handal and Chuanmin Hu

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Assessing Carbon and Nutrient Inputs in a Spring-fed Estuary Using Fluorescence Spectroscopy and Discriminatory Classification, Ana Arellano and Paula G. Coble

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Multidimensional Metrics for Estimating Phage Abundance, Distribution, Gene Density, and Sequence Coverage in Metagenomes, Ramy Aziz, Bhakti Dwivedi, Sajia Akhter, Mya Breitbart, and Robert Edwards

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Solutions for Recovering and Sustaining the Bounty of the Ocean: Combining Fishery Reforms, Rights-Based Fisheries Management, and Marine Reserves, Allison K. Barner, Jane Lubchenco, Christopher Costello, Steven D. Gaines, Amanda Leland, Brett Jenks, Steven Murawski, Eric Schwaab, and Margaret Spring

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Prediction of Coral Bleaching in the Florida Keys Using Remotely Sensed Data, Brian B. Barnes, P. Hallock, Chuanmin Hu, Frank E. Muller-Karger, D. Palandro, C. Walter, and R. Zepp

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Cross-Sensor Continuity of Satellite-Derived Water Clarity in the Gulf of Mexico: Insights Into Temporal Aliasing and Implications for Long-Term Water Clarity Assessment, Brian B. Barnes and Chuanmin Hu

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Sediment Plumes Induced by the Port of Miami Dredging: Analysis and Interpretation using Landsat and MODIS Data, Brian B. Barnes, Chuanmin Hu, Charles Kovach, and Rachel N. Silverstein

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Influence of Temperature on Yolk Resorption in Common Snook Centropomus Undecimalis (Bloch, 1792) Larvae, Claudia C. Barón-Aguilar, Nicole R. Rhody, Nathan P. Brennan, Kevan L. Main, Ernst B. Peebles, and Frank E. Muller-Karger

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Paleoreconstruction of Organic Carbon Inputs to an Oxbow Lake in the Mississippi River Watershed: Effects of Dam Construction and Land use Change on Regional Inputs, Thomas S. Bianchi, Valier Galy, Brad E. Rosenheim, Michael Shields, Xingqian Cui, and Peter Van Metre

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Quantifying the Resolution Level Where the GRACE Satellites Can Separate Greenland's Glacial Mass Balance from Surface Mass Balance, J. A. Bonin and D. P. Chambers

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Discovery, Prevalence, and Persistence of Novel Circular Single-Stranded DNA Viruses in the Ctenophores Mnemiopsis leidyi and Beroe ovata, Mya Breitbart, Bayleigh Benner, Parker Jernigan, Karyna Rosario, Laura Birsa, Rachel Harbeitner, Sidney Fulford, Carina Graham, Anna Walters, Dawn Goldsmith, Stella Berger, and Jens Nejstgaard

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And on Top of All That… Coping with Ocean Acidification in the Midst of Many Stressors, Denise L. Breitburg, Joseph Salisbury, Joan M. Bernhard, Wei-Jun Cai, Sam Dupont, Scott C. Doney, Kristy J. Kroeker, Lisa A. Levin, W. Christopher Long, Lisa M. Milke, Seth H. Miller, Beth Phelan, Uta Passow, Brad A. Seibel, Anne E. Todgham, and Ann M. Tarrant

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The Ocean Colour Climate Change Initiative: III. A Round-robin Comparison on In-water Bio-optical Algorithms, Robert J.W. Brewin, Shubha Sathyendranath, Dagmar Müller, Carsten Brockmann, Pierre-Yves Deschamps, Emmanuel Devred, Roland Doerffer, Norman Fomferra, Bryan Franz, Mike Grant, Steve Groom, Andrew Horseman, Chuanmin Hu, Hajo Krasemann, ZhongPing Lee, Stéphane Maritorena, Frédéric Mélin, Marco Peters, Trevor Platt, Peter Regner, Tim Smyth, Francois Steinmetz, John Swinton, Jeremy Werdell, and George N. White

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Annual to Millennial Record of Sediment Delivery to US Virgin Island Coastal Environments, Gregg Brooks, Rebekka A. Larson, Barry Devine, and Patrick Schwing

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Sedimentation Pulse in the NE Gulf of Mexico following the 2010 DWH Blowout, Gregg R. Brooks, Rebekka A. Larson, Patrick Schwing, Isabel C. Romero, Christopher Moore, Gert-Jan Reichart, Tom Jilbert, Jeff P. Chanton, David W. Hastings, Will A. Overholt, Kala P. Marks, Joel E. Kostka, Charles W. Holmes, and David Hollander

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The Organic Complexation of Dissolved Iron Along the U.S. GEOTRACES (GA03) North Atlantic Section, Kristen N. Buck, Bettina Sohst, and Peter N. Sedwick

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Iron-binding Ligands and Humic Substances in the San Francisco Bay Estuary and Estuarine-influenced Shelf Regions of Coastal California, Randelle Bundy, Hussain Abdulla, Patrick Hatcher, Dondra Biller, Kristen N. Buck, and Katherine Barbeau

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Ecological Characteristics of Eucalanoid Copepods of the Eastern Tropical North Pacific Ocean: Adaptations for Life Within a Low Oxygen System, Christine J. Cass

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Temporal and Spatial Availability of Atlantic Thread Herring, Opisthonema Oglinum, in Relation to Oceanographic Drivers and Fishery Landings on the Florida Panhandle, D. Chagaris, B. Mahmoudi, Frank E. Muller-Karger, W. Cooper, and K. Fischer

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Evaluation of Empirical Mode Decomposition for Quantifying Multi-decadal Variations and Acceleration in Sea Level Records, D. P. Chambers

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Gravimetric Methods – Satellite Altimeter Measurements, D. P. Chambers

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Colored Dissolved Organic Matter in the Coastal Ocean: An Optical Tool for Coastal Zone Environmental Assessment and Management, Paula Coble, Chuanmin Hu, Richard W. Gould Jr., Grace Chang, and A. Michelle Wood

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Biogeochemical Cycling of Cadmium Isotopes along a High-Resolution Section through the North Atlantic Ocean, Tim M. Conway and Seth G. John

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The Cycling of Iron, Zinc and Cadmium in the North East Pacific Ocean – Insights from Stable Isotopes, Tim M. Conway and Seth G. John

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Constraints on Soluble Aerosol Iron Flux to the Southern Ocean at the Last Glacial Maximum, Tim M. Conway, E. W. Wolff, R. Röthlisberger, R. Mulvaney, and H. E. Elderfield

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Nutrient concentrations for the northeastern Gulf of Mexico and west Florida shelf: June 2012 – August 2014, Kendra L. Daly

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Climate Change Tightens a Metabolic Constraint on Marine Habitats, Curtis Deutsch, Aaron Ferrel, Brad Seibel, Hans-Otto Pörtner, and Raymond B. Huey

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Ecophysiological Implications of Vertical Migration into Oxygen Minimum Zones for the Hyperiid Amphipod Phronima sedentaria , Leanne E. Elder and Brad A. Seibel

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The Thermal Stress Response to Diel Vertical Migration in the Hyperiid Amphipod Phronima sedentaria , Leanne E. Elder and Brad A. Seibel

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Shell Dissolution in Larger Benthic Foraminifers Exposed to Ph and Temperature Extremes: Results from an in Situ Experiment, Brienne E. Engel, Pamela Hallock, Roy E. Price, and Thomas Brichler

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Discovery of a Novel Circular DNA Virus in the Forbes Sea Star, Asterias forbesi, Elizabeth Fahsbender, Ian Hewson, Karyna Rosario, Allison Tuttle, Arvind Varsani, and Mya Breitbart

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Development of a Serological Assay for the Sea Lion (Zalophus californianus) Anellovirus, ZcAV, Elizabeth Fahsbender, Karyna Rosario, John Cannon, Frances Gulland, Larry Dishaw, and Mya Breitbart

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An Ammonium Enrichment Event in the Surface Ocean: Wind Forcing and Potential Ramifications, Kent A. Fanning, Robert T. Masserini Jr., John J. Walsh, Rik Wanninkhof, K. Sullivan, Jyotika I. Virmani, and Cynthia A. Heil

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Long-Term Distribution Patterns of Chlorophyll-a Concentration in China’s Largest Freshwater Lake: MERIS Full-Resolution Observations with a Practical Approach, Lian Feng, Chuanmin Hu, Xingxing Han, Xiaoling Chen, and Lin Qi

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Ventilation Time Scales of the North Atlantic Subtropical Cell Revealed by Coral Radiocarbon from the Cape Verde Islands, Alvaro Fernandez, Thomas J. Lapen, Rasmus Andreasen, Peter K. Swart, Christopher D. White, and Brad E. Rosenheim

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Partitioning of Dissolved Iron and Iron Isotopes into Soluble and Colloidal Phases along the GA03 GEOTRACES North Atlantic Transect, Jessica N. Fitzsimmons, Gonzalo G. Carrasco, Jingfeng Wu, Saeed Roshan, Mariko Hatta, Christopher I. Measures, Tim M. Conway, Seth G. John, and Edward A. Boyle

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Meta-omic Signatures of Microbial Metal and Nitrogen Cycling in Marine Oxygen Minimum Zones, Jennifer B. Glass, Cecilia B. Kretz, Sangita Ganesh, Piyush Ranjan, Sherry L. Seston, Kristen N. Buck, William M. Landing, Peter L. Morton, James W. Moffett, Stephen J. Giovannoni, Kevin L. Vergin, and Frank J. Stewart

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Water Column Stratification Structures Viral Community Composition in the Sargasso Sea, Dawn Goldsmith, Jennifer Brum, Max Hopkins, Craig Carlson, and Mya Breitbart

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Deep Sequencing of the Viral phoH Gene Reveals Temporal Variation, Depth-specific Composition, and Persistent Dominance of the Same Viral phoH Genes in the Sargasso Sea, Dawn Goldsmith, Rachel Parsons, Damitu Beyene, Peter Salamon, and Mya Breitbart

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Evaluation of the Trophic Structure of the West Florida Shelf in the 2000s Using the Ecosystem Model OSMOSE, Arnaud Grüss, Michael J. Schirripa, David Chagaris, Michael Drexler, James Simons, Philippe Verley, Yunne-Jai Shin, Mandy Karnauskas, Ricardo Oliveros-Ramos, and Cameron H. Ainsworth

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Changing Influences between Life and Limestones in Earth History, Pamela Hallock

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Shelf break Exchange Events near the De Soto Canyon, Peter Hamilton, Kevin Speer, Richard Snyder, Nicolas Wienders, and Robert R. Leben

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Quantifying the Geomorphic Resiliency of Barrier Island Beaches, Cheryl J. Hapke, Owen T. Brenner, and Rachel E. Henderson

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Recent Trends in the Southern Ocean Eddy Field, Andrew McC. Hogg, Michael P. Meredith, Don P. Chambers, E. Povl Abrahamsen, Chris W. Hughes, and Adele K. Morrison

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Spectral and Spatial Requirements of Remote Measurements of Pelagic Sargassum Macroalgae, Chuamin Hu, Lian Feng, Robert F. Hardy, and Eric J. Hochberg

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A Harmful Algal Bloom of Karenia brevis in the Northeastern Gulf of Mexico as Revealed by MODIS and VIIRS: A Comparison, Chuanmin Hu, Brian B. Barnes, Lin Qi, and Alina A. Corcoran

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A Severe Red Tide (Tampa Bay, 2005) Causes an Anomalous Decrease in Biological Sound, Katherine L. Indeck, Peter Simard, Shannon Gowans, Susan Lowerre-Barbieri, and David A. Mann

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Phytoplankton Adapt to Changing Ocean Environments, A. J. Irwin, Z. V. Finkel, Frank E. Muller-Karger, and L. T. Ghinaglia

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Reply to Brun Et Al.: Fingerprint of Evolution Revealed by Shifts in Realized Phytoplankton Niches in Natural Populations, Andrew J. Irwin, Zoe V. Finkel, Frank E. Muller-Karger, and Luis Troccoli Ghinaglia

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Decadal- to Centennial-Scale East Asian Summer Monsoon Variability during the Medieval Climate Anomaly Reconstructed from an Eastern Tibet Lacustrine Sequence, Hanchao Jiang, Amelia E. Shevenell, Song Yu, Hongyan Xu, and Xue Mao

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Using Post-settlement Demography to Estimate Larval Survivorship: A Coral Reef Fish Example, D. W. Johnson, M. R. Christie, C. D. Stallings, T. J. Pusack, and M. A. Hixon

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Palaeo-ice Stream Pathways and Retreat Style in the Easternmost Amundsen Sea Embayment, West Antarctica, Revealed by Combined Multibeam Bathymetric and Seismic Data, J. P. Klages, G. Kuhn, A. G. C. Graham, C.-D. Hillenbrand, J.A. Smith, F. O. Nitsche, R. D. Larter, and K. Gohl

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Using Dispersants after Oil Spills: Impacts on the Composition and Activity of Microbial Communities, Sara Kleindienst, John H. Paul, and Samantha B. Joye

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Response of the Miliolid Archaias angulatus to Simulated Ocean Acidification, Paul O. Knorr, Lisa L. Robbins, Peter J. Harries, Pamela Hallock, and Jonathan G. Wynn