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Full-Text Articles in Life Sciences

Computing For Numeracy: How Safe Is Your Covid-19 Social Bubble?, Charles Connor Jan 2021

Computing For Numeracy: How Safe Is Your Covid-19 Social Bubble?, Charles Connor

Numeracy

The COVID-19 pandemic has led many people to form social bubbles. These social bubbles are small groups of people who interact with one another but restrict interactions with the outside world. The assumption in forming social bubbles is that risk of infection and severe outcomes, like hospitalization, are reduced. How effective are social bubbles? A Bayesian event tree is developed to calculate the probabilities of specific outcomes, like hospitalization, using example rates of infection in the greater community and example prior functions describing the effectiveness of isolation by members of the social bubble. The probabilities are solved for two contrasting …


Dna Detectives: Outreach Activity Teaching Students To Identify Fish Eggs Using Dna Barcoding, Makenzie Kerr, Mya Breitbart Jan 2021

Dna Detectives: Outreach Activity Teaching Students To Identify Fish Eggs Using Dna Barcoding, Makenzie Kerr, Mya Breitbart

Marine Science Faculty Publications

Fish are an important resource worldwide and their management requires a combination of strategies, including the protection of spawning areas. However, the identification of fish early life stages, especially fish eggs, is challenging due to the lack of distinguishing morphological features. Here we present an outreach activity, named “DNA Detectives”, that allows students to discover the method of DNA barcoding, a technique used by scientists to determine which species of fish are spawning in a given location. Students will learn about fish reproduction strategies, methods used by scientists for collecting fish eggs, and how to identify these eggs using their …


The Discovery Of New Deep-Sea Hydrothermal Vent Communities In The Southern Ocean And Implications For Biogeography, Alex D. Rogers, Paul A. Tyler, Douglas P. Connelly, Jon T. Copley, Rachael James, Robert D. Larter, Katrin Linse, Rachel A. Mills, Alfredo Naveira Garabato, Richard D. Pancost, David A. Pearce, Nicholas V. Polunin, Christopher R. German, Timothy Shank, Philipp H. Boersch-Supan, Belinda J. Alker, Alfred Aquilina, Sarah A. Bennett, Andrew Clarke, Robert J. Dinley, Alastair G. C. Graham, Darryl R. Green, Jeffrey A. Hawkes, Laura Hepburn, Ana Hilario, Veerle A. Huvenne, Leigh Marsh, Eva Ramirez-Llodra, William D. Reid, Christopher N. Roterman, Christopher J. Sweeting, Sven Thatje, Katrin Zwirglmaier Jan 2021

The Discovery Of New Deep-Sea Hydrothermal Vent Communities In The Southern Ocean And Implications For Biogeography, Alex D. Rogers, Paul A. Tyler, Douglas P. Connelly, Jon T. Copley, Rachael James, Robert D. Larter, Katrin Linse, Rachel A. Mills, Alfredo Naveira Garabato, Richard D. Pancost, David A. Pearce, Nicholas V. Polunin, Christopher R. German, Timothy Shank, Philipp H. Boersch-Supan, Belinda J. Alker, Alfred Aquilina, Sarah A. Bennett, Andrew Clarke, Robert J. Dinley, Alastair G. C. Graham, Darryl R. Green, Jeffrey A. Hawkes, Laura Hepburn, Ana Hilario, Veerle A. Huvenne, Leigh Marsh, Eva Ramirez-Llodra, William D. Reid, Christopher N. Roterman, Christopher J. Sweeting, Sven Thatje, Katrin Zwirglmaier

Marine Science Faculty Publications

Since the first discovery of deep-sea hydrothermal vents along the Galápagos Rift in 1977, numerous vent sites and endemic faunal assemblages have been found along mid-ocean ridges and back-arc basins at low to mid latitudes. These discoveries have suggested the existence of separate biogeographic provinces in the Atlantic and the North West Pacific, the existence of a province including the South West Pacific and Indian Ocean, and a separation of the North East Pacific, North East Pacific Rise, and South East Pacific Rise. The Southern Ocean is known to be a region of high deep-sea species diversity and centre of …


Using Multiple Ecological Models To Inform Environmental Decision-Making, Kristy A. Lewis, Kenneth A. Rose, Mutsert, Kim De Mutsert, Shaye Sable, Cameron Ainsworth, Damian C. Brady, Howard Townsend Jan 2021

Using Multiple Ecological Models To Inform Environmental Decision-Making, Kristy A. Lewis, Kenneth A. Rose, Mutsert, Kim De Mutsert, Shaye Sable, Cameron Ainsworth, Damian C. Brady, Howard Townsend

Marine Science Faculty Publications

Coastal ecosystems are experiencing degradation from compound impacts of climate change and multiple anthropogenic disturbances. These pressures often act synergistically and complicate designing effective conservation measures; consequently, large-scale coastal restoration actions become a wicked problem. The purpose of this study was to use two different food web models in a coordinated manner to inform resource managers in their assessment of the ecological effects of a large-scale marsh restoration project. A team was formed that included the model developers and outside scientists, who were asked to use available model results of the calibrated simulations of an Ecopath with Ecosim (EwE) model …


Preparedness, Planning, And Advances In Operational Response, David G. Westerholm, Cameron H. Ainsworth, Christopher H. Barker, Peter G. Brewer, John W. Farrington, Dubravko Justic, Vassiliki H. Kourafalou, Steven A. Murawsk, Helena M. Solo-Gabriele Jan 2021

Preparedness, Planning, And Advances In Operational Response, David G. Westerholm, Cameron H. Ainsworth, Christopher H. Barker, Peter G. Brewer, John W. Farrington, Dubravko Justic, Vassiliki H. Kourafalou, Steven A. Murawsk, Helena M. Solo-Gabriele

Marine Science Faculty Publications

During the last 50 years, the numbers and sizes of oil spills have been significantly reduced through prevention. But spills still occur, and it is critical to prepare for these events through planning and exercises. Operational decisions are designed to expedite cleanup and minimize overall impacts, yet they often involve complex trade-offs between a multitude of competing interests. It is imperative to apply the best technology and science when events occur. However, while planning and response tactics have evolved over time, determining what may be most at risk is often confounded by sparse background data, modeling limitations, scalability, or research …


Impacts Of Petroleum, Petroleum Components, And Dispersants On Organisms And Populations, Steven A. Murawski, Martin Grosell, Cynthia Smith, Tracey Sutton, Kenneth M. Halanych, Richard F. Shaw, Charles A. Wilson Jan 2021

Impacts Of Petroleum, Petroleum Components, And Dispersants On Organisms And Populations, Steven A. Murawski, Martin Grosell, Cynthia Smith, Tracey Sutton, Kenneth M. Halanych, Richard F. Shaw, Charles A. Wilson

Marine Science Faculty Publications

Following the Deepwater Horizon blowout, oil, degraded oil, oil mixed with dispersants, and management responses to the spill affected a variety of Gulf of Mexico organisms. This review provides examples of various documented impacts, common patterns, and trends across organisms and/or their environments, and discusses future implications as well as directions for future research. Organism effects are generally characterized as lethal and sublethal. Sublethal can be short term, long term, or permanent and multigenerational. We present individual examples of effects on behavioral response, olfaction, vision, cardiac function, and gene shift, based on research done in laboratories, mesocosm settings, and the …


Nasa's Surface Biology And Geology Designated Observable: A Perspective On Surface Imaging Algorithms, Kerry Cawse-Nicholson, Philip A. Townsend, David Schimel, Ali M. Assiri, Pamela L. Blake, Maria Fabrizia Buongiorno, Petya Campbell, Nimrod Carmon, Kimberly A. Casey, Rosa Elvira Correa-Pabón, Kyla M. Dahlin, Hamid Dashti, Philip E. Dennison, Heidi Dierssen, Adam Erickson, Joshua B. Fisher, Robert Frouin, Charles K. Gatebe, Hamed Gholizadeh, Michelle Gierach, Nancy F. Glenn, James A. Goodman, Daniel M. Griffith, Liane Guild, Christopher R. Hakkenberg, Eric J. Hochberg, Thomas R.H. Holmes, Chuanmin Hu, Glynn Hulley, Karl F. Huemmrich, Raphael M. Kudela, Raymond F. Kokaly, Christine M. Lee, Roberta Martin, Charles E. Miller, Wesley J. Moses, Frank E. Muller-Karger, Joseph D. Ortiz, Daniel B. Otis, Nima Pahlevan, Thomas H. Painter, Ryan Pavlick, Ben Poulter, Yi Qi, Vincent J. Realmuto, Dar Roberts, Michael E. Schaepman, Fabian D. Schneider, Florian M. Schwandner, Shawn P. Serbin, Alexey N. Shiklomanov, E. Natasha Stavros, David R. Thompson, Juan L. Torres-Perez, Kevin R. Turpie, Maria Tzortziou, Susan Ustin, Qian Yu, Yusri Yusup, Qingyuan Zhang Jan 2021

Nasa's Surface Biology And Geology Designated Observable: A Perspective On Surface Imaging Algorithms, Kerry Cawse-Nicholson, Philip A. Townsend, David Schimel, Ali M. Assiri, Pamela L. Blake, Maria Fabrizia Buongiorno, Petya Campbell, Nimrod Carmon, Kimberly A. Casey, Rosa Elvira Correa-Pabón, Kyla M. Dahlin, Hamid Dashti, Philip E. Dennison, Heidi Dierssen, Adam Erickson, Joshua B. Fisher, Robert Frouin, Charles K. Gatebe, Hamed Gholizadeh, Michelle Gierach, Nancy F. Glenn, James A. Goodman, Daniel M. Griffith, Liane Guild, Christopher R. Hakkenberg, Eric J. Hochberg, Thomas R.H. Holmes, Chuanmin Hu, Glynn Hulley, Karl F. Huemmrich, Raphael M. Kudela, Raymond F. Kokaly, Christine M. Lee, Roberta Martin, Charles E. Miller, Wesley J. Moses, Frank E. Muller-Karger, Joseph D. Ortiz, Daniel B. Otis, Nima Pahlevan, Thomas H. Painter, Ryan Pavlick, Ben Poulter, Yi Qi, Vincent J. Realmuto, Dar Roberts, Michael E. Schaepman, Fabian D. Schneider, Florian M. Schwandner, Shawn P. Serbin, Alexey N. Shiklomanov, E. Natasha Stavros, David R. Thompson, Juan L. Torres-Perez, Kevin R. Turpie, Maria Tzortziou, Susan Ustin, Qian Yu, Yusri Yusup, Qingyuan Zhang

Marine Science Faculty Publications

The 2017–2027 National Academies' Decadal Survey, Thriving on Our Changing Planet, recommended Surface Biology and Geology (SBG) as a “Designated Targeted Observable” (DO). The SBG DO is based on the need for capabilities to acquire global, high spatial resolution, visible to shortwave infrared (VSWIR; 380–2500 nm; ~30 m pixel resolution) hyperspectral (imaging spectroscopy) and multispectral midwave and thermal infrared (MWIR: 3–5 μm; TIR: 8–12 μm; ~60 m pixel resolution) measurements with sub-monthly temporal revisits over terrestrial, freshwater, and coastal marine habitats. To address the various mission design needs, an SBG Algorithms Working Group of multidisciplinary researchers has been formed to …


Isotopic Fingerprinting Of Biogeochemical Processes And Iron Sources In The Iron-Limited Surface Southern Ocean, M. Sieber, T. M. Conway, G. F. De Souza, C. S. Hassler, M. J. Ellwood, D. Vance Jan 2021

Isotopic Fingerprinting Of Biogeochemical Processes And Iron Sources In The Iron-Limited Surface Southern Ocean, M. Sieber, T. M. Conway, G. F. De Souza, C. S. Hassler, M. J. Ellwood, D. Vance

Marine Science Faculty Publications

Iron (Fe) is an essential micronutrient that limits primary productivity throughout the surface of the Southern Ocean. Here, we present the first high-resolution depth profiles for dissolved Fe and Fe isotope ratios (δ56">δ56 Fe) from all major zones of the Southern Ocean, collected during the Antarctic Circumnavigation Expedition in austral summer 2017. Open-ocean surface waters are characterized by remarkably high δ56">δ56 Fe values (up to +1.6‰) and very low Fe concentrations (<0.05 nmol kg−1). We attribute the elevated δ56">δ56 Fe values above the ferricline to the effect of continuous shallow cycling processes (uptake, recycling, and binding …


Bioactive Trace Metals And Their Isotopes As Paleoproductivity Proxies: An Assessment Using Geotraces-Era Data, T. J. Horner, S. H. Little, T. M. Conway, J. R. Farmer, J. E. Hertzberg, D. J. Janssen, A. J. M. Lough, J. L. Mckay, A. Tessin, S. J. G. Galer, S. L. Jaccard, F. Lacan, A. Paytan, K. Wuttig, Geotraces–Pages Biological Productivity Working Group Members Jan 2021

Bioactive Trace Metals And Their Isotopes As Paleoproductivity Proxies: An Assessment Using Geotraces-Era Data, T. J. Horner, S. H. Little, T. M. Conway, J. R. Farmer, J. E. Hertzberg, D. J. Janssen, A. J. M. Lough, J. L. Mckay, A. Tessin, S. J. G. Galer, S. L. Jaccard, F. Lacan, A. Paytan, K. Wuttig, Geotraces–Pages Biological Productivity Working Group Members

Marine Science Faculty Publications

Phytoplankton productivity and export sequester climatically significant quantities of atmospheric carbon dioxide as particulate organic carbon through a suite of processes termed the biological pump. Constraining how the biological pump operated in the past is important for understanding past atmospheric carbon dioxide concentrations and Earth's climate history. However, reconstructing the history of the biological pump requires proxies. Due to their intimate association with biological processes, several bioactive trace metals and their isotopes are potential proxies for past phytoplankton productivity, including iron, zinc, copper, cadmium, molybdenum, barium, nickel, chromium, and silver. Here, we review the oceanic distributions, driving processes, and depositional …


Sea Surface Current Mapping With Hf Radar – A Primer, Clifford R. Merz, Yonggang Liu, Robert H. Weisberg Jan 2021

Sea Surface Current Mapping With Hf Radar – A Primer, Clifford R. Merz, Yonggang Liu, Robert H. Weisberg

Marine Science Faculty Publications

Shore-based oceanographic High Frequency (HF) radars are frequently used to remotely sense and map coastal sea surface currents. This chapter begins with a review of the development and utilization of HF radar sea-echo interactions and their relationship in the determination of the radial component of the sea surface current and vector coverage map, followed by a brief discussion of recent ongoing HF radar observations on the West Florida Shelf (WFS). Reported are HF radar performance and its complicated relationships with environmental factors.


The Genomic Processes Of Biological Invasions: From Invasive Species To Cancer Metastases And Back Again, Fargam Neinavaie, Arig Ibrahim-Hashim, Andrew M. Kramer, Joel S. Brown, Christina L. Richards Jan 2021

The Genomic Processes Of Biological Invasions: From Invasive Species To Cancer Metastases And Back Again, Fargam Neinavaie, Arig Ibrahim-Hashim, Andrew M. Kramer, Joel S. Brown, Christina L. Richards

Integrative Biology Faculty and Staff Publications

The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information …


Deep Learning For Supervised Classification Of Temporal Data In Ecology, César Capinha, Ana Ceia-Hasse, Andrew M. Kramer, Christiaan Meijer Jan 2021

Deep Learning For Supervised Classification Of Temporal Data In Ecology, César Capinha, Ana Ceia-Hasse, Andrew M. Kramer, Christiaan Meijer

Integrative Biology Faculty and Staff Publications

Temporal data is ubiquitous in ecology and ecologists often face the challenge of accurately differentiating these data into predefined classes, such as biological entities or ecological states. The usual approach consists of transforming the time series into user-defined features and then using these features as predictors in conventional statistical or machine learning models. Here we suggest the use of deep learning models as an alternative to this approach. Recent deep learning techniques can perform the classification directly from the time series, eliminating subjective and resource-consuming data transformation steps, and potentially improving classification results. We describe some of the deep learning …


Global Economic Costs Of Aquatic Invasive Alien Species, Ross N. Cuthbert, Zarah Pattison, Nigel G. Taylor, Laura Verbrugge, Christophe Diagne, Danish A. Ahmed, Boris Leroy, Elena Angulo, Elizabeta Briski, César Capinha, Jane A. Catford, Tatenda Dalu, Franz Essl, Rodolphe E. Gozlan, Phillip J. Haubrock, Melina Kourantidou, Andrew M. Kramer, David Renault, Ryan J. Wasserman, Franck Courchamp Jan 2021

Global Economic Costs Of Aquatic Invasive Alien Species, Ross N. Cuthbert, Zarah Pattison, Nigel G. Taylor, Laura Verbrugge, Christophe Diagne, Danish A. Ahmed, Boris Leroy, Elena Angulo, Elizabeta Briski, César Capinha, Jane A. Catford, Tatenda Dalu, Franz Essl, Rodolphe E. Gozlan, Phillip J. Haubrock, Melina Kourantidou, Andrew M. Kramer, David Renault, Ryan J. Wasserman, Franck Courchamp

Integrative Biology Faculty and Staff Publications

Much research effort has been invested in understanding ecological impacts of invasive alien species (IAS) across ecosystems and taxonomic groups, but empirical studies about economic effects lack synthesis. Using a comprehensive global database, we determine patterns and trends in economic costs of aquatic IAS by examining: (i) the distribution of these costs across taxa, geographic regions and cost types; (ii) the temporal dynamics of global costs; and (iii) knowledge gaps, especially compared to terrestrial IAS. Based on the costs recorded from the existing literature, the global cost of aquatic IAS conservatively summed to US$345 …


Deep Learning For Supervised Classification Of Temporal Data In Ecology, César Capinha, Ana Ceia-Hasse, Andrew M. Kramer, Christiaan Meijer Jan 2021

Deep Learning For Supervised Classification Of Temporal Data In Ecology, César Capinha, Ana Ceia-Hasse, Andrew M. Kramer, Christiaan Meijer

Integrative Biology Faculty and Staff Publications

Temporal data is ubiquitous in ecology and ecologists often face the challenge of accurately differentiating these data into predefined classes, such as biological entities or ecological states. The usual approach consists of transforming the time series into user-defined features and then using these features as predictors in conventional statistical or machine learning models. Here we suggest the use of deep learning models as an alternative to this approach. Recent deep learning techniques can perform the classification directly from the time series, eliminating subjective and resource-consuming data transformation steps, and potentially improving classification results. We describe some of the deep learning …


The 79°N Glacier Cavity Modulates Subglacial Iron Export To The Ne Greenland Shelf, Stephan Krisch, Mark James Hopwood, Janin Schaffer, Ali Al-Hashem, Juan Höfer, Rutgers Van Der Loeff, Tim M. Conway, Brent A. Summers, Pablo Lodeiro, Indah Ardiningsih, Tim Steffens, Eric Pieter Achterberg Jan 2021

The 79°N Glacier Cavity Modulates Subglacial Iron Export To The Ne Greenland Shelf, Stephan Krisch, Mark James Hopwood, Janin Schaffer, Ali Al-Hashem, Juan Höfer, Rutgers Van Der Loeff, Tim M. Conway, Brent A. Summers, Pablo Lodeiro, Indah Ardiningsih, Tim Steffens, Eric Pieter Achterberg

Marine Science Faculty Publications

Approximately half of the freshwater discharged from the Greenland and Antarctic Ice Sheets enters the ocean subsurface as a result of basal ice melt, or runoff draining via the grounding line of a deep ice shelf or marine-terminating glacier. Around Antarctica and parts of northern Greenland, this freshwater then experiences prolonged residence times in large cavities beneath floating ice tongues. Due to the inaccessibility of these cavities, it is unclear how they moderate the freshwater associated supply of nutrients such as iron (Fe) to the ocean. Here, we show that subglacial dissolved Fe export from Nioghalvfjerdsbrae (the ‘79°N Glacier’) is …


Constraints On The Cycling Of Iron Isotopes From A Global Ocean Model, D. König, T. M. Conway, M. J. Ellwood, W. B. Homoky, A. Tagliabue Jan 2021

Constraints On The Cycling Of Iron Isotopes From A Global Ocean Model, D. König, T. M. Conway, M. J. Ellwood, W. B. Homoky, A. Tagliabue

Marine Science Faculty Publications

Although iron (Fe) is a key regulator of primary production over much of the ocean, many components of the marine iron cycle are poorly constrained, which undermines our understanding of climate change impacts. In recent years, a growing number of studies (often part of GEOTRACES) have used Fe isotopic signatures (δ56Fe) to disentangle different aspects of the marine Fe cycle. Characteristic δ56Fe endmembers of external sources and assumed isotopic fractionation during biological Fe uptake or recycling have been used to estimate relative source contributions and investigate internal transformations, respectively. However, different external sources and fractionation processes …


Local People’S Perceptions Of Benefits And Costs Of Protected Areas: The Case Of Tarangire National Park And The Surrounding Ecosystem, Northern Tanzania, Felix J. Mkonyi Jan 2021

Local People’S Perceptions Of Benefits And Costs Of Protected Areas: The Case Of Tarangire National Park And The Surrounding Ecosystem, Northern Tanzania, Felix J. Mkonyi

Journal of Ecological Anthropology

A

A better understanding of the benefits and costs of conservation to people living adjacent to protected areas is fundamental to balancing their conservation goals and needs. This study, based in the Tarangire-Simanjiro ecosystem, explored the costs, benefits and attitudes of local people living adjacent to Tarangire National Park in northern Tanzania. In-depth interviews were conducted with 30 respondents which were randomly selected from the ‘population’ of 300 respondents used previously for the main survey. Results indicate mixed responses towards protected areas. The majority of respondents held positive attitudes toward the park (56.7%) and park staff (63.3%) but had negative …


Yellowtail Snapper: Human-Ecological Relationships In The South Florida Fishery, Brent Stoffle, Amanda D. Stoltz Jan 2021

Yellowtail Snapper: Human-Ecological Relationships In The South Florida Fishery, Brent Stoffle, Amanda D. Stoltz

Journal of Ecological Anthropology

In 2018 over a period of five months researchers from National Oceanographic and Atmospheric Administration’s (NOAA) Southeast Fisheries Science Center (SEFSC) conducted a study with fishermen and local business owners who participate in the South Florida Yellowtail snapper fishery. Fishermen were asked about changes in their targeting strategies over the last several decades; and they perceive these changes to have altered the health and the biology of the snapper species. The changes are perceived as partially responsible for improving both the overall abundance of Yellowtail and having sped up its the growth and reproductive cycles. This is a case where …


Tracking The Subcellular Localization Of Surface Proteins In Staphylococcus Aureus By Immunofluorescence Microscopy, Salvatore J. Scaffidi, Mac A. Shebes, Wenqi Yu Jan 2021

Tracking The Subcellular Localization Of Surface Proteins In Staphylococcus Aureus By Immunofluorescence Microscopy, Salvatore J. Scaffidi, Mac A. Shebes, Wenqi Yu

Molecular Biosciences Faculty Publications

Surface proteins of Staphylococcus aureus and other Gram-positive bacteria play essential roles in bacterial colonization and host-microbe interactions. Surface protein precursors containing a YSIRK/GXXS signal peptide are translocated across the septal membrane at mid-cell, anchored to the cell wall peptidoglycan at the cross-wall compartment, and presented on the new hemispheres of the daughter cells following cell division. After several generations of cell division, these surface proteins will eventually cover the entire cell surface. To understand how these proteins travel from the bacterial cytoplasm to the cell surface, we describe a series of immunofluorescence microscopy protocols designed to detect the stepwise …


Dcaf14 Promotes Stalled Fork Stability To Maintain Genome Integrity, Arik Townsend, Gabriella Lora, Justin Engel, Neysha Tirado-Class, Huzefa Dungrawala Jan 2021

Dcaf14 Promotes Stalled Fork Stability To Maintain Genome Integrity, Arik Townsend, Gabriella Lora, Justin Engel, Neysha Tirado-Class, Huzefa Dungrawala

Molecular Biosciences Faculty Publications

No abstract provided.


Spatial Spread Of White-Nose Syndrome In North America, 2006-2018, Andrew M. Kramer, Alex Mercier, Sean Maher, Yaw Kumi-Ansu, Sarah Bowden Jan 2021

Spatial Spread Of White-Nose Syndrome In North America, 2006-2018, Andrew M. Kramer, Alex Mercier, Sean Maher, Yaw Kumi-Ansu, Sarah Bowden

Integrative Biology Faculty and Staff Publications

White-nose syndrome has caused massive mortality in multiple bat species and spread across much of North America, making it one of the most destructive wildlife diseases on record. This has also resulted in it being one of the most well-documented wildlife disease outbreaks, making it possible to look for changes in the pattern of spatial spread over time. We fit a series of spatial interaction models to the United States county-level observations of the pathogenic fungus, Pseudogymnoascus destructans, that causes white-nose syndrome. Models included the distance between caves, cave abundance, measures of winter length and winter onset, and species …


Deep Learning For Supervised Classification Of Temporal Data In Ecology, César Capinha, Ana Ceia-Hasse, Andrew M. Kramer, Christiaan Meijer Jan 2021

Deep Learning For Supervised Classification Of Temporal Data In Ecology, César Capinha, Ana Ceia-Hasse, Andrew M. Kramer, Christiaan Meijer

Integrative Biology Faculty and Staff Publications

Temporal data is ubiquitous in ecology and ecologists often face the challenge of accurately differentiating these data into predefined classes, such as biological entities or ecological states. The usual approach consists of transforming the time series into user-defined features and then using these features as predictors in conventional statistical or machine learning models. Here we suggest the use of deep learning models as an alternative to this approach. Recent deep learning techniques can perform the classification directly from the time series, eliminating subjective and resource-consuming data transformation steps, and potentially improving classification results. We describe some of the deep learning …


A Scopus-Based Bibliometric Study Of Maritime Research Involving The Automatic Identification System, Steven D. Meyers, Laura Azevedo, Mark E. Luther Jan 2021

A Scopus-Based Bibliometric Study Of Maritime Research Involving The Automatic Identification System, Steven D. Meyers, Laura Azevedo, Mark E. Luther

Marine Science Faculty Publications

Vessel traffic records from the Automatic Identification System (AIS) are a useful source of information for maritime data analytics, and of training data for maritime artificial intelligence systems. Researchers utilizing these data are developing the foundations for operational maritime tools essential to economic expansion and security. The global growth and distribution of this research effort from 1997 to 2019 was examined through a bibliometric study of 817 Scopus-listed publications. Indications of both collaboration and accelerating competition were found by examining the number of publications and authors, national and institutional affiliations of the authors, and number of citations received. Prior …


Effects Of Petroleum By-Products And Dispersants On Ecosystems, Kenneth M. Halanych, Cameron H. Ainsworth, Erik E. Cordes, Richard E. Dodge, Markus Huettel, Irving A. Mendelssohn, Steven A. Murawski, Claire B. Paris-Limouzy, Patrick T. Schwing, Richard F. Shaw, Tracey Sutton Jan 2021

Effects Of Petroleum By-Products And Dispersants On Ecosystems, Kenneth M. Halanych, Cameron H. Ainsworth, Erik E. Cordes, Richard E. Dodge, Markus Huettel, Irving A. Mendelssohn, Steven A. Murawski, Claire B. Paris-Limouzy, Patrick T. Schwing, Richard F. Shaw, Tracey Sutton

Marine Science Faculty Publications

Gulf of Mexico ecosystems are interconnected by numerous physical and biological processes. As a result of the Deepwater Horizon (DWH) spill, some normal ecological processes including resource connectivity and trophic interactions and were damaged or broken. A considerable portion of post-DWH research has focused on higher levels of biological organization (i.e., populations, communities, and ecosystems) spanning at least four environments (onshore, coastal, open ocean, and deep benthos). Damage wrought by the oil spill and mitigation efforts varied considerably across ecosystems. Whereas all systems show prolonged impacts because of cascading effects that impacted functional connections within and between communities, deep-sea and …


Spectrophotometric Determination Of The Bicarbonate Dissociation Constant In Seawater, Katelyn M. Schockman, Robert H. Byrne Jan 2021

Spectrophotometric Determination Of The Bicarbonate Dissociation Constant In Seawater, Katelyn M. Schockman, Robert H. Byrne

Marine Science Faculty Publications

The aqueous carbon dioxide (CO2) system stoichiometric dissociation constants K1 and K2 express the relative concentrations of CO2, HCO3− (bicarbonate), and CO32− (carbonate) in terms of pH. These constants are critical in the study of seawater and the oceans because any mathematical expression that relates the four major CO2 system parameters (pH, here expressed on the total hydrogen ion concentration scale, pHT; total dissolved inorganic carbon, CT; total alkalinity, AT; and CO2 fugacity, fCO2) requires the use of …


A Synthesis Of Deepwater Horizon Impacts On Coastal And Nearshore Living Marine Resources, Steven A. Murawski, Joshua P. Kilborn, Adriana C. Bejarano, David Chagaris, David Donaldson, Frank J. Hernandez, Timothy C. Macdonald, Craig Newton, Ernst Peebles, Kelly L. Robinson Jan 2021

A Synthesis Of Deepwater Horizon Impacts On Coastal And Nearshore Living Marine Resources, Steven A. Murawski, Joshua P. Kilborn, Adriana C. Bejarano, David Chagaris, David Donaldson, Frank J. Hernandez, Timothy C. Macdonald, Craig Newton, Ernst Peebles, Kelly L. Robinson

Marine Science Faculty Publications

The 2010 Deepwater Horizon (DWH) oil blowout in the Gulf of Mexico began on April 20, originating in the deep sea 66 km off the Louisiana coast. By early June, DWH oil had spread to coastal Louisiana, Mississippi, Alabama and western Florida. An estimated 2,113 km of shoreline were oiled, making DWH the largest marine oil spill in global history by length of affected shoreline. Additionally, a series of oil spill response measures were deployed, including diversions of Mississippi River discharge to forestall oil coming ashore, and the establishment of large-scale fishery closures, with both affecting coastal resources to varying …


The Gulf Of Mexico: An Overview, Larry D. Mckinney, John G. Shepherd, Charles A. Wilson, William T T. Hogarth, Jeff Chanton, Steven A. Murawski, Paul A. Sandifer, Tracey Sutton, David Yoskowitz, Katya Wowk, Tamay M. Özgökmen, Samantha B. Joye, Rex Caffey Jan 2021

The Gulf Of Mexico: An Overview, Larry D. Mckinney, John G. Shepherd, Charles A. Wilson, William T T. Hogarth, Jeff Chanton, Steven A. Murawski, Paul A. Sandifer, Tracey Sutton, David Yoskowitz, Katya Wowk, Tamay M. Özgökmen, Samantha B. Joye, Rex Caffey

Marine Science Faculty Publications

The Gulf of Mexico is a place where the environment and the economy both coexist and contend. It is a resilient large marine ecosystem that has changed in response to many drivers and pressures that we are only now beginning to fully understand. Coastlines of the states that border the Gulf comprise about half of the US southern seaboard, and those states are capped by the vast Midwest. The Gulf drains most of North America and is both an economic keystone and an unintended waste receptacle. It is a renowned resource for seafood markets, recreational fishing, and beach destinations and …


Extreme Sea Level Variability Dominates Coastal Flood Risk Changes At Decadal Time Scales, M M. Rashid, T Wahl, D P. Chambers Jan 2021

Extreme Sea Level Variability Dominates Coastal Flood Risk Changes At Decadal Time Scales, M M. Rashid, T Wahl, D P. Chambers

Marine Science Faculty Publications

Coastal flood risk assessments typically ignore interannual to multidecadal variability stemming from mean sea level, storm surges, and long period tides (i.e. 4.4 year perigean and 18.6 year nodal cycles), although combined these can lead to significant variations in extreme sea levels (ESL). Here, we examine the effects of ESL variability on the amplification of flood frequencies and risks for 17 major U.S. coastal cities. We also quantify the relative importance of ESL variability compared to long-term relative sea level rise (RSLR). Results show that, depending on the region, observed ESL variability can lead to amplification factors of up to …


A Decade Of Gomri Dispersant Science: Lessons Learned And Recommendations For The Future, Antonietta Quigg, John W. Farrington, Sherryl Gilbert, Steven A. Murawski, Vijay T. John Jan 2021

A Decade Of Gomri Dispersant Science: Lessons Learned And Recommendations For The Future, Antonietta Quigg, John W. Farrington, Sherryl Gilbert, Steven A. Murawski, Vijay T. John

Marine Science Faculty Publications

Dispersants are among a number of options available to oil spill responders. The goals of this technique are to remove oil from surface waters in order to reduce exposure of surface-dwelling organisms, to keep oil slicks from impacting sensitive shorelines, and to protect responders from volatile organic compounds. During the Deepwater Horizon response, unprecedented volumes of dispersants (Corexit 9500 and 9527) were both sprayed on surface slicks from airplanes and applied directly at the wellhead (~1,500 m water depth). A decade of research followed, leading to a deeper understanding of dispersant effectiveness, fate, and effects. These studies resulted in new …


Dendriplex - Cyclodextrin Conjugates For Gene Delivery To Retina, Durga Deepak Puro Nov 2020

Dendriplex - Cyclodextrin Conjugates For Gene Delivery To Retina, Durga Deepak Puro

USF Tampa Graduate Theses and Dissertations

Gene therapy holds promise for treating a wide range of diseases including cancer and several other polygenic and monogenic disorder arising in different organs. Due to its immune privilege nature, eye is an ideal organ for gene therapy,as various visual pathologies arise from gene defect and can lead to partial or complete vision loss. The last decade, several nanoparticles have been developed and tested for their transfection efficiency in vitro and in vivo. Among them, dendrimers with small size, good physicochemical properties and endosomal escape activity have shown high transfection efficiency in various cell lines. In an attempt to further …