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 2011

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Exploring the Diversity of Plant DNA Viruses and Their Satellites Using Vector-Enabled Metagenomics on Whiteflies, Terry Fei Fan Ng, Siobain Duffy, Jane Polston, Elise Bixby, Gary Vallad, and Mya Breitbart

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Metagenomic Identification of a Novel Anellovirus in Pacific Harbor Seal (Phoca vitulina richardsii) Lung Samples and its Detection in Samples from Multiple Years, Terry Fei Fan Ng, Elizabeth Wheeler, Denise Greig, Thomas Waltzek, Frances Gulland, and Mya Breitbart

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Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes, Terry Fei Fan Ng, Dana Willner, Yan Wei Lim, Robert Schmieder, Betty Chau, Christina Nilsson, Simon Anthony, Yijun Ruan, Forest Rohwer, and Mya Breitbart

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Exploring the Viral World Through Metagenomics, Karyna Rosario and Mya Breitbart

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Dragonfly Cyclovirus, a Novel Single-stranded DNA Virus Discovered in Dragonflies (Odonata: Anisoptera), Karyna Rosario, Milen Marinov, Daisy Stainton, Simona Kraberger, Elizabeth Wiltshire, David Collings, Matthew Walters, Darren Martin, Mya Breitbart, and Arvind Varsani

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Comparative Metagenomics of Microbial Traits Within Oceanic Viral Communities, Itai Sharon, Natalia Battchikova, Eva-Mari Aro, Carmela Giglione, Thierry Meinnel, Fabian Glaser, Ron Pinter, Mya Breitbart, Forest Rohwer, and Oded Be ́ja

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A Regional Testbed for Storm Surge and Coastal Inundation Models - an Overview, Y. P. Sheng, Justin R. Davis, Renato Figueiredo, Bin Liu, Huiqing Liu, Rick Luettich, Vladimir A. Paramygin, Robert Weaver, Robert H. Weisberg, Lian Xie, and Lianyuan Zheng

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Holocene Southern Ocean Surface Temperature Variability West of the Antarctic Peninsula, Amelia E. Shevenell, A. E. Ingalls, E. W. Domack, and C. Kelly

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Diversity of Virus–host Systems in Hypersaline Lake Retba, Senegal, Télesphore Sime‐Ngando, Soizick Lucas, Agnès Robin, Kimberly Pause Tucker, Jonathan Colombet, Yvan Bettarel, Elie Desmond, Simonetta Gribaldo, Patrick Forterre, Mya Breitbart, and David Prangishvili

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Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System, Connor Skennerton, Florent Angly, Mya Breitbart, Lauren Bragg, Shaomei He, Katherine McMahon, Philip Hugenholtz, and Gene Tyson

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Sea Surface Temperature Variability in the Florida Keys and Its Relationship to Coral Cover, I. M. Soto, Frank E. Muller-Karger, Pamela Hallock, and C. Hu

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Closed ranks in Oceanography, LuAnne Thompson, Renellys C. Perez, and Amelia E. Shevenell

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Reply to 'Not Just Family Matters', LuAnne Thompson, Renellys C. Perez, and Amelia E. Shevenell

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Diversity and Distribution of Single-stranded DNA Phages in the North Atlantic Ocean, Kimberly Tucker, Rachel Parsons, Erin Symonds, and Mya Breitbart

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Photosynthesis and Respiration in Five Species of Benthic Foraminifera that Host Algal Endosymbionts, Robert A. Walker, Pamela Hallock, Joseph J. Torres, and Gabriel A. Vargo

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Imprudent Fishing Harvests and Consequent Trophic Cascades on the West Florida Shelf Over the Last Half Century: a Harbinger of Increased Human Deaths from Paralytic Shellfish Poisoning along the Southeastern United States, in Response to Oligotrophication?, John J. Walsh, C. R. Thomas, K. A. Steidinger, J. M. Lenes, F. R. Chen, Robert H. Weisberg, Lianyuan Zheng, J. H. Landsberg, Gabriel A. Vargo, and C. A. Heil

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Coastal Ocean Pollution, Water Quality, and Ecology, Robert H. Weisberg

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Shoreline Changes in West-Central Florida between 1987 and 2008 from Landsat Observations, K. Yu, C. Hu, Frank E. Muller-Karger, D. Lu, and I. Soto

Submissions from 2010

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In Situ Nutrient Sensors for Ocean Observing Systems, Lori Adornato, Andres Cardenas-Valencia, Eric Kaltenbacher, Robert H. Byrne, Kendra L. Daly, Kate Larkin, Sue Hartman, Matt Mowlem, Ralf D. Prien, and Veronique Garcon

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Transposases Are the Most Abundant, Most Ubiquitous Genes in Nature, Ramy Aziz, Mya Breitbart, and Robert Edwards

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Iron-binding Ligand Production and Copper Speciation in an Incubation Experiment of Antarctic Peninsula Shelf Waters From the Bransfield Strait, Southern Ocean, Kristen N. Buck, Karen Selph, and Katherine Barbeau

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Partitioning of Food Resources in Bathypelagic Micronekton in the Eastern Gulf of Mexico, Scott E. Burghart, Thomas L. Hopkins, and Joseph J. Torres

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Ocean Mass from GRACE and Glacial Isostatic Adjustment, D. Chambers, John Wahr, Mark E. Tamisea, and R Steven Nerem

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A Global Evaluation of Ocean Bottom Pressure from GRACE, OMCT, and Steric-Corrected Altimetry, D. Chambers and Josh K. Willis

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Short-Term Variability of Suspended Sediment and Phytoplankton in Tampa Bay, Florida: Observations from a Coastal Oceanographic Tower and Ocean Color Satellites, Zhiqiang Chen, Chuanmin M. Hu, Frank E. Muller-Karger, and Mark E. Luther

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Short-Term Variability of Suspended Sediment and Phytoplankton in Tampa Bay, Florida: Observations from a Coastal Oceanographic Tower and Ocean Color Satellites, Z. Chen, C. Hu, Frank E. Muller-Karger, and E. E. Luther

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A Preliminary Carbon Budget for the Gulf of Mexico, Paula G. Coble, Lisa L. Robbins, Kendra L. Daly, Wei-Jun Cai, Katja Fennel, and Steven E. Lorenz

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Low Oxygen Regions in the Oceans, Kendra L. Daly, Francis Chan, and Nancy Rabalais

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Nickel Utilization in Phytoplankton Assemblages From Contrasting Oceanic Regimes, Christopher Dupont, Kristen N. Buck, Brian Palenik, and Katherine Barbeau

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Ecological Impacts of the 2005 Red Tide on Artificial Reef Epibenthic Macroinvertebrate and Fish Communities in the Eastern Gulf of Mexico, Jennifer M. Dupont, Pamela Hallock-Muller, and Walter C. Jaap

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Monitoring Coral Reefs from Space, C. M. Eakin, C. J. Nim, R. E. Brainard, C. Aubrecht, C. Elvidge, D. K. Gledhill, Frank E. Muller-Karger, P. J. Mumby, W. J. Skirving, A. E. Strong, M. Wang, S. Weeks, F. Wentz, and D. Ziskin

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West Florida Shelf: A Natural Laboratory for the Study of Ocean Acidification, Pamela Hallock, Lisa L. Robbins, Rebekka Larson, Tanya Beck, Patrick Schwing, Michael Martínez-Colón, and Brad Gooch

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Lagrangian Particle Tracking of a Toxic Dinoflagellate Bloom within the Tampa Bay Estuary, Heather Havens, Mark E. Luther, Steven D. Meyers, and Cynthia A. Heil

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Coupling of Surge and Waves for an Ivan-like Hurricane Impacting the Tampa Bay, Florida Region, Yong Huang, Robert H. Weisberg, and Lianyuan Zheng

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Remote Detection of Trichodesmium Blooms in Optically Complex Coastal Waters: Examples with Modis Full-Spectral Data, C. Hu, Jennifer Cannizzaro, Kendall L. Carder, Frank E. Muller-Karger, and R. Hardy

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Moderate Resolution Imaging Spectroradiometer (MODIS) Observations of Cyanobacteria Blooms in Taihu Lake, China, Chuanmin Hu, Zhongping Lee, Ronghua Ma, Kun Yu, Daqiu Li, and Shaoling Shang

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On the Recurrent Ulva prolifera Blooms in the Yellow Sea and East China Sea, Chuanmin Hu, Daqiu Li, Changsheng Chen, Jianzhong Ge, Frank E. Muller-Karger, Junpeng Liu, Feng Yu, and Ming-Xia He

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Hydrological and Oceanic Effects on Polar Motion from GRACE and Models, Shaunggen Jin, Don Chambers, and Byron D. Tapley

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Time Series of Bio-Optical Properties in a Subtropical Gyre: Implications for the Evaluation of Interannual Trends of Biogeochemical Properties, ZhongPing Lee, Shaoling Shang, Chuanmin Hu, Marlon Lewis, Robert Arnone, Yonghong Li, and Bertrand Lubac

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HF Radar Performance in a Low-Energy Environment: CODAR SeaSonde Experience on the West Florida Shelf, Yonggang Liu, Robert H. Weisberg, and Clifford R. Merz

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Preliminary Survey on Foraminiferal Responses to Pollutants in Torrecillas Lagoon Puerto Rico, Michael Martínez-Colón and Pamela Hallock

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Local and Regional Geochemical Signatures of Surface Sediments from the Cariaco Basin and Orinoco Delta, Venezuela, N. C. Martinez, R. W. Murray, R. C. Thunell, L. C. Peterson, Frank E. Muller-Karger, Laura Lorenzoni, Y. Astor, and R. Varela

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Using the Surface Reflectance Modis Terra Product to Estimate Turbidity in Tampa Bay, Florida, M. J. Moreno-Madrinan, M. Z. Al-Hamdan, D. L. Rickman, and Frank E. Muller-Karger

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The Cariaco Basin: CARIACO Oceanographic Time Series, Frank Muller-Karger, Ramon Varela, Robert Thunell, Mary I. Scranton, Gordon Taylor, Yrene Astor, Claudia Benitez-Nelson, Laura Lorenzoni, Eric Tappa, Miguel A. Goñi, Digna T. Rueda-Roa, and Chuanmin Hu

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Estimating Mean Sea Level Change from the TOPEX and Jason Altimeter Missions, R. S. Nerem, Don P. Chambers, C. Choe, and Gary T. Mitchum

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Viral and Microbial Community Dynamics in Four Aquatic Environments, Beltran Rodriguez-Brito, LinLin Li, Linda Wegley, Mike Furlan, Florent Angly, Mya Breitbart, John Buchanan, Christelle Desnues, Elizabeth Dinsdale, and Robert Edwards

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A radiogeochemical, land-use archive of the Manatee River Watershed, FL, Patrick Schwing, Ashanti Johnson, and Charles W. Holmes

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Shell Anomalies Observed in a Population of Archaias Angulatus (Foraminifera) from the Florida Keys (USA) Sampled in 1982-83 and 2006-07, Heidi C. Souder, Bryan McCloskey, Pamela Hallock, and Robert H. Byrne

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Metagenomic Sequencing for Virus Identification in a Public-health Setting, Sanela Svraka, Karyna Rosario, Erwin Duizer, Harrie van der Avoort, Mya Breitbart, and Marion Koopmans

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Satellite-based Global-ocean Mass Balance Estimates of Interannual Variability and Emerging Trends in Continental Freshwater Discharge, Tajdarul H. Syed, James S. Famiglietti, Don P. Chambers, Josh K. Willis, and Kyle Hilburn

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Measuring Progress Toward Global Marine Conservation Targets, C. C. Wabnitz, S. Andréfouët, and Frank E. Muller-Karger

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Deglacial Abrupt Climate Change in the Atlantic Warm Pool: A Gulf of Mexico Perspective, Carlie Williams, Benjamin P. Flower, David W. Hastings, Thomas P. Guilderson, Kelly A. Quinn, and Ethan A. Goddard

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Global Sea Level Rise: Recent Progress and Challenges for the Decade to Come, Josh K. Willis, Don P. Chambers, C. K. Shum, and Chung-Yen Kuo

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Analysis of Seasonal Ocean Bottom Pressure Variability in the Gulf of Thailand from GRACE, B. Wouters and Don P. Chambers

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Rookery Bay and Naples Bay Circulation Simulations: Applications to Tides and Fresh Water Inflow Regulation, Lianyuan Zheng and Robert H. Weisberg

Submissions from 2009

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A Nested Model of the Cariaco Basin (Venezuela): Description of the Basin'S Interior Hydrography and Interactions with the Open Ocean, Aida Alvera-Azcarate, Alexander Barth, and Robert H. Weisberg

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The Surface Circulation of the Caribbean Sea and the Gulf of Mexico as Inferred from Satellite Altimetry, Aida Alvera-Azcarate, Alexander Barth, and Robert H. Weisberg

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Genomic Analysis of Multiple Roseophage SIO1 Strains, Florent Angly, Merry Youle, Bahador Nosrat, Shailaja Srinagesh, Beltran Rodriguez‐Brito, Patrick McNairnie, Gordafaried Deyanat‐Yazdi, Mya Breitbart, and Forest Rohwer

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Larger Foraminifers of the Florida Reef Tract, USA: Distribution Patterns on Reef-Rubble Habitats, Rebekah D. Baker, Pamela Hallock, Elizabeth F. Moses, Dana E. Williams, and Alexa Ramirez

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Dynamically Constrained Ensemble Perturbations - Application to Tides on Thewest Florida Shelf, Alexander Barth, Aida Alvera-Azcarate, J. M. Beckers, Robert H. Weisberg, L. Vandenbulcke, F. Lenartz, and M. Rixen

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Dynamically Constrained Ensemble Perturbations: Application to Tides on the West Florida Shelf, Alexander Barth, Aida Alvera-Azcarate, J. M. Beckers, Robert H. Weisberg, L. Vandenbulcke, F. Lenartz, and M. Rixen

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Frequent Detection of Highly Diverse Variants of Cardiovirus, Cosavirus, Bocavirus, and Circovirus in Sewage Samples Collected in the United States, O. Blinkova, Karyna Rosario, A. Kapoor, B. Slikas, F. Bernardin, Mya Breitbart, and E. Delwart

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Comparison of Inherent Optical Properties as Surrogate for Particulate Matter Concentration in Coastal Waters, Emmanuel Boss, Lisa Taylor, Sherryl Gilbert, Kjell Gundersen, Nathan Hawley, Carol Janzen, Tom Johengen, Heidi Purcell, Charles Robertson, Daniel Schar, G. Jason Smith, and Mario Tamburri

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Metagenomic and Stable Isotopic Analyses of Modern Freshwater Microbialites in Cuatro Ciénegas, Mexico, Mya Breitbart, Ana Maria Hoare, Anthony G. Nitti, Janet Siefert, Matthew Haynes, Elizabeth Dinsdale, Robert Edwards, Valeria Souza, Forest Rohwer, and David Hollander

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Surface and Subsurface Geostrophic Current Variability in the Indian Ocean From Altimetry, Dara D. H. Cadden, Bulusu Subrahmanyam, D. Chambers, and V.S. N. Murty

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Detection of Karenia Brevis Blooms on the West Florida Shelf Using in Situ Backscattering and Fluorescence Data, Jennifer P. Cannizzaro, C. Hu, D. C. English, Kendall L. Carder, C. Heil, and Frank E. Muller-Karger

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Foraminiferal Assemblages in Biscayne Bay, Florida, USA: Responses to Urban and Agricultural Influence in a Subtropical Estuary, Elizabeth A. Carnahan, A. M. Hoare, Pamela Hallock, Barbara H. Lidz, and Christopher D. Reich

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Calculating Trends from GRACE in the Presence of Large Changes in Continental Ice Storage and Ocean Mass, D. Chambers

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Measuring Mean Ocean Mass Variability with GRACE, Don P. Chambers

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Low-Frequency Exchange of Mass Between Ocean Basins, Don P. Chambers and Josh K. Willis

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US GODAE: Global Ocean Prediction with the HYbrid Coordinate Ocean Model (HYCOM), Eric P. Chassignet, Harley E. Hurlburt, E. J. Metzger, Ole-Martin Smedstad, James Cummings, George R. Halliwell Jr., Rainer Bleck, Remy Baraille, and Robert H. Weisberg

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Influence of Extreme Storm Events on West Florida Shelf CDOM Distributions, Robyn N. Conmy, Paula G. Coble, Jennifer P. Cannizzaro, and Cynthia A. Heil

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Observing the 3-Dimensional Distribution of Bio-Optical Properties of West Florida Shelf Waters using Gliders and Autonomous Platforms, David English, Chuanmin M. Hu, Chad Lembke, Robert H. Weisberg, David Edwards, Laura Lorenzoni, Gino Gonzalez, and Frank E. Muller-Karger

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Observing the 3-Dimensional Distribution of Bio-Optical Properties of West Florida Shelf Waters Using Gliders and Autonomous Platforms, D. English, C. Hu, C. Lembke, R. Weisberg, D. Edwards, Laura Lorenzoni, G. Gonzalez, and Frank E. Muller-Karger

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Autonomous Buoy Platform for Low-Cost Visual Maritime Surveillance: Design and Initial Deployment, Sergiy Fefilatyev, Dmitry Goldgof, and Chad Lembke

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Oceanographic and Climatologic Controls on the Compositions and Fluxes of Biogenic Materials in the Water Column and Sediments of the Cariaco Basin Over the Late Holocene, M. A. Goni, H. Aceves, B. Benitez-Nelson, E. Tappa, R. Thunell, D. E. Black, Frank E. Muller-Karger, Y. Astor, and R. Varela

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Impact of GODAE Products on Nested HYCOM Simulations of the West Florida Shelf, George R. Halliwell Jr., Alexander Barth, Robert H. Weisberg, Patrick J. Hogan, Ole-Martin Smedstad, and James Cummings

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A Coastal Prediction System as an Event Response Tool: Particle Tracking Simulation of an Anhydrous Ammonia Spill in Tampa Bay, Heather Havens, Mark E. Luther, and Steven D. Meyers

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Results from US Southern Ocean GLOBEC Synthesis Studies, Eileen E. Hofmann, Daniel P. Costa, Kendra L. Daly, Michael S. Dinniman, John M. Klinck, Marina Marrari, Laurie Padman, and Andrea Piñones

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Detection of Natural Oil Slicks in the Nw Gulf of Mexico Using Modis Imagery, C. Hu, X. Li, W. G. Pichel, and Frank E. Muller-Karger

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Building an Automated Integrated Observing System to Detect Sea Surface Temperature Anomaly Events in the Florida Keys, C. Hu, Frank E. Muller-Karger, Brock Murch, D. Myhre, J. Taylor, R. Luerssen, C. Moses, Mingrui Zhang, L. Gramer, and J. Hendee

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Building an Automated Integrated Observing System to Detect Sea Surface Temperature Anomaly Events in the Florida Keys, C. Hu, Frank E. Muller-Karger, Brock Murch, D. Myhre, J. Taylor, R. Luerssen, C. Moses, Mingrui Zhang, L. Gramer, and J. Hendee

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Evaluation of Global Ocean Data Assimilation Experiment Products on South Florida Nested Simulations with the Hybrid Coordinate Ocean Model, Vassiliki H. Kourafalou, Ge Peng, HeeSook Kang, Patrick J. Hogan, Ole-Martin Smedstad, and Robert H. Weisberg

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Natural and Anthropogenic Sources of East Asian Dust, Geojun Li, Jun Chen, Junfeng Ji, Jiedong Yang, and Tim M. Conway

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The Importance of Subsurface Nepheloid Layers in Transport and Delivery of Sediments to the Eastern Cariaco Basin, Venezuela, Laura Lorenzoni, R. C. Thunell, C. R. Benitez-Nelson, D. Hollander, N. Martinez, E. Tappa, R. Varela, Y. Astor, and Frank E. Muller-Karger

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Short-Term Upwelling Events Modulate Fish Sound Production at a Mid-Atlantic Ocean Observatory, David A. Mann and T. M. Grothues

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Strategies for Using Shallow-Water Benthic Foraminifers as Bioindicators of Potentially Toxic Elements: A Review, Michael Martínez-Colón, Pamela Hallock, and Carlos Green-Ruíz

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Test-Shape Variability of Amphistegina D’Orbigny, 1826 as a Paleobathymetric Proxy: Application to Two Miocene Examples, Guillem Mateu-Vicens, Pamela Hallock, and Marco Brandano

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Mean Dynamic Topography of the Ocean Derived from Satellite and Drifting Buoy Data Using Three Different Techniques, Nikolai Maximenko, Peter Niiler, Marie-Helene Rio, Oleg Melnichenko, Luca Centurioni, Boris Galperin, Don. P. Chambers, and Victor Zlotnicki

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Regional Estimates of Reef Carbonate Dynamics and Productivity Using Landsat 7 ETM+, and Potential Impacts from Ocean Acidification, Christopher S. Moses, Serge Andrefouet, Christine J. Kranenburg, and Frank E. Muller-Karger

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Discovery of a Novel Single-Stranded DNA Virus from a Sea Turtle Fibropapilloma by Using Viral Metagenomics, Terry Fei Fan Ng, Charles Manire, Kelly Borrowman, Tammy Langer, Llewellyn Ehrhart, and Mya Breitbart

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Novel Anellovirus Discovered From a Mortality Event of Captive California Sea Lions, Terry Fei Fan Ng, Wm Kirk Suedmeyer, Elizabeth Wheeler, Frances Gulland, and Mya Breitbart

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Sailfish (Istiophorus Platypterus) Spawning and Larval Environment in a Florida Current Frontal Eddy, D. E. Richardson, J. K. Llopiz, K. D. Leaman, P. S. Vertes, Frank E. Muller-Karger, and R. K. Cowen

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Diverse Circovirus-like Genome Architectures Revealed by Environmental Metagenomics, Karyna Rosario, Siobain Duffy, and Mya Breitbart

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Metagenomic Analysis of Viruses in Reclaimed Water, Karyna Rosario, Christina Nilsson, Yan Wei Lim, Yijun Ruan, and Mya Breitbart

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Pepper Mild Mottle Virus as an Indicator of Fecal Pollution, Karyna Rosario, Erin M. Symonds, C. D. Sinigalliano, Jill Stewart, and Mya Breitbart

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Towards a Regional Coastal Ocean Observing System: an Initial Design for the Southeast Coastal Ocean Observing Regional Association, Harvey E. Seim, M. Fletcher, C. N. K. Mooers, James R. Nelson, and Robert H. Weisberg

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Physical Connectivity in the Mesoamerican Barrier Reef System Inferred from 9 Years of Ocean Color Observations, I. Soto, S. Andréfouët, C. Hu, Frank E. Muller-Karger, C. C. Wall, J. Sheng, and B. G. Hatcher

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Progress in Developing a New Detection Method for the Harmful Algal Bloom Species, Karenia brevis, through Multiwavelength Spectroscopy, Adam H. Spear, Kendra L. Daly, Debra Huffman, and Luis Garcia-Rubio

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Evaluation of Groundwater Storage Monitoring with the GRACE Satellite: Case Study High Plains Aquifer, Central United States, Gil Strassberg, Bridget Scanlon, and D. Chambers