Plankton imaging systems such as SIPPER produce a large quantity of data in the form of plankton images from a variety of classes. A system known as PICES was developed to quickly extract, classify and manage the millions of images produced from a single one-week research cruise. A new fast technique for parameter tuning and feature selection for Support Vector Machines using Wrappers was created. This technique allows for faster feature selection, while at the same time maintaining and sometimes improving classification accuracy. It also gives the user greater flexibility in the management of class contents in existing training libraries. Support vector machines are binary classifiers that can implement multi-class classifiers by creating a classifier for each possible combination of classes or for each class using a one class versus all strategy. Feature selection searches for a single set of features to be used by each of the binary classifiers. This ignores the fact that features that may be good discriminators for two particular classes might not do well for other class combinations. As a result, the feature selection process may not include these features in the common set to be used by all support vector machines. It is shown through experimentation that by selecting features for each binary class combination, overall classification accuracy can be improved and the time required for training a multi-class support vector machine can be reduced. Another benefit of this approach is that significantly less time is required for feature selection when additional classes are added to the training data. This is because the features selected for the existing class combinations are still valid, so that feature selection only needs to be run for the new combination added. This work resulted in a system called PICES, a GUI based user friendly system, which aids in the classification management of over 55 million images of plankton split amongst 180 classes. PICES embodies an improved means of performing Wrapper based feature selection that creates classifiers that train faster and are just as accurate and sometimes more accurate, while reducing the feature selection time.

Thesis (M.S.)--Oregon State University, 2009. / Printout. Includes bibliographical references (leaves 190-195). Also available on the World Wide Web.

Land, water and natural resources are under increasing pressure due to rising demands for food and energy from the rapidly growing global population. Across a catchment there can be multiple stakeholders with conflicting opinions over how space and resources should be used and managed. Consequently, it is important to consider the suitability of a catchment for a particular purpose to optimise use of the area and minimise potential conflicts and impacts on the wider environment. Aquaculture is a significant contributor to world food supply and as fisheries are unlikely to increase it is expected that the industry will continue to grow and expand in the future to help meet food security requirements. As a result, it is essential that the sector aims for sustainable development within the most suitable locations. However, it can be difficult to assess the suitability of multiple large catchments and some issues may not be immediately apparent. This project aimed to show how spatial models could be used as decision support tools to evaluate the suitability of large catchments for sustainable aquaculture. Four large areas of importance to aquaculture were selected; covering 10,148km2, 26,225km2, 48,319km2 and 66,283km2 in Bangladesh, China, Thailand and Vietnam respectively. Asia is by far the most dominant aquaculture region in the world and each of the four study areas contribute to local, regional and global food supplies. The study area in Bangladesh was located in Khulna region in the south west of the country and the main species of focus were prawn and shrimp. The Chinese study area was located in the south eastern province of Guangdong and the main species covered were tilapia and shrimp. Similarly, in Thailand, the main species evaluated were tilapia and shrimp whilst the study area extended across the Central region. Finally, the largest study area was the Mekong Delta in Vietnam and the main species of focus in this area were pangasius catfish and shrimp. One of the challenges in modelling large catchments is model applicability and data availability. Often, the required data are not available (or accessible) and it would be difficult, time consuming and expensive to collect new information. Furthermore, when assessing multiple areas is it vital that a representative and unbiased approach is used where no one catchment is favoured over the other due to higher quality data. Therefore, this study used data that are available for almost any area in the world; allowing future application of the models and enabling effective and unbiased decision support. Four modelling stages were employed in this study to evaluate the suitability of large catchments for sustainable aquaculture development. The first stage was the classification of seasonal land use models from satellite imagery. This provides information on what the land is used for and how aquaculture could impact or be impacted by the wider environment. The second step was the development of seasonal models of site suitability using optimal values within a GIS-based multi-stage framework. These models identify which locations are best for culture and can also be used to estimate the availability of areas for food production. The next stage investigated the use of Maxent as a novel approach in site suitability modelling to evaluate the conditions experienced by existing farms. The information from Maxent can be used to identify trends, opportunities and concerns related to sustainable management and farm locations. Finally, qualitative models of non-point source pollution (NPSP) were developed which assess the risk of NPSP within a catchment. NPSP is an issue which can impact both aquaculture and the wider environment. Thus, it is important to understand the areas within a catchment where NPSP risk is higher enabling the establishment of monitoring and/or mitigation procedures. The models support the ecosystem approach to aquaculture (EAA) and enable objective planning and management strategies to enhance productivity across large catchments without negatively impacting the environment. In order to meet growing food requirements, large areas will need to be used for agriculture and aquaculture; therefore, analysis at a wider catchment level, which complements assessment at a local scale, is required as it allows a holistic view of the situation. The work presented here illustrates the potential use of spatial models across large catchments and considers the suitability of the areas for aquaculture development.

Title from PDF of title page. / Document formatted into pages; contains 112 pages. / Thesis (M.S.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: The Florida Keys Coral Reef Monitoring Project (CRMP) began video transect sampling in 1996 and has continuously monitored 107 Florida Keys stations through 2002. The video was downward pointing and produced images from which planar projection data were calculated to determine percent cover of living benthic organisms. An absence of data assessing correlation between octocoral percent cover and octocoral abundance motivated a study to compare octocoral percent cover with abundance data acquired from the same video transects. The methods employed to extract octocoral abundance data from videotape were validated. Temporal changes in octocoral abundance, size and taxonomic group were determined by examination of video transects of 28 randomly selected stations from 1996, 1998, 1999, and 2002. Size classes were defined as [10cm, 10-40cm, ]40cm (short, medium and tall respectively). / ABSTRACT: Taxonomic groups were Gorgonia ventalina and "other octocorals" in three size classes, and Scleraxonia. An in situ study assessed the accuracy of video-derived counts. Average densities of G. ventalina and Scleraxonia were consistently about one colony/m2. Other octocoral as a group averaged 7-9 colonies/m2. When summarized by height, short and tall averaged about 1-2 colonies/m2, while colonies between 10 and 40 cm in height consistently averaged about 6 colonies/m2. Hurricane Georges, in September 1998, impacted the octocoral assemblage. Abundance declined most at stations near the storm center and stations in shallower water. Storm impact was related to octocoral height. Tall octocorals were removed more frequently than medium, short and encrusting forms. A dramatic increase of short individuals in 2002 is indicative of successful post-hurricane recruitment. By 2002, octocoral abundance had recovered to pre-hurricane levels. / ABSTRACT: This study demonstrated that abundance data can reliably be derived from archived video data, reinforcing the value of standardized video data archives. Octocoral abundance and octocoral percent cover are not strongly correlated because tall individuals disproportionately influence percent cover estimates. Nevertheless, trends in octocoral percent cover are reliable indicators of the trends in octocoral abundance. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Includes vita. / Title from PDF of title page. / Document formatted into pages; contains 329 pages. / Thesis (Ph.D.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: River discharge leads to extensive phytoplankton blooms often observed in ocean color satellite images to extend far into the open ocean as high chlorophyll plumes. We investigated diversity, distribution and ecology of phytoplankton populations in the Mississippi River plume, both spatially and in the water column using molecular tools. A method was developed for the quantification of diatom/pelagophyte rbcL (large subunit of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase) mRNA using quantitative PCR and applied to cultures and in the plume. The vertical structure of phytoplankton species in the Mississippi River plume was described by flow cytometry, pigments, rbcL mRNA and rbcL cDNA libraries. High productivity in the plume was associated with a large population of Synechococcus and elevated levels of cellular form IA rbcL mRNA. / ABSTRACT: rbcL cDNA libraries indicated two vertically separated clades of Prochlorococcus (high-light and low-light adapted) in addition to a diverse group of prymnesiophytes and a microdiverse clade of prasinophytes, which may have dominated the SCM (Subsurface Chlorophyll Maximum). In situ sampling and satellite image analysis were used to estimate that the plume accounted for 41% and 13% of all surface water column ix productivity in the oligotrophic Gulf of Mexico, while covering less than 3% of its area. Coastally the plume is dominated by diatoms, which are replaced by a bloom of Synechococcus as the plume moves offshore. Diatoms as indicated by pigments and rbcL clone libraries again dominated the offshore, least productive plume. 15N uptake measurements indicated that rapid recycling of ammonium despite higher levels of nitrate primarily drives production in the offshore plume. / ABSTRACT: rbcL mRNA levels and photosynthetic capacity displayed strong diel patters in three out of four time series sampled during the GRIST (Geochemical Rate/mRNA Integrated Study). In addition it was demonstrated that transcriptional regulation of the global nitrogen regulatory protein NtcA in Synechococcus WH7803 may involve a small cis-encoded anti-sense mRNA. Methods for the generation of large insert BAC (Bacterial Artificial Chromosome) from cultures and the environment were refined. Partial sequencing and genomic comparison of an ntcA containing BAC clone obtained from Synechococcus WH7803 indicated that ntcA is not part of a larger nitrogen assimilation operon in cyanobacteria. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Title from PDF of title page. / Document formatted into pages; contains 322 pages. / Thesis (Ph.D.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: Ground water resources are heavily used for drinking water supply and often as a receptacle for waste water. One concern is the possible contamination of wetland areas by ground water receiving septic system infiltration. To investigate this, two tracer studies were performed using the bacteriophage PRD-1 by seeding septic systems adjacent to wetlands with the phage and monitoring migration towards wetland areas. Transport velocities were evaluated based on appearance of tracer in sampling wells at various distances from the injection point. Velocities were estimated to be 0.25 m/d and 0.4 m/d at the two sites. Some retardation with respect to the conservative tracer SF6 was observed, with a factor of about 1.5. Due to dry conditions, the water table was well below surface, so transport of the virus into surface water was not observed. Survival of public-health-related microorganisms in ground water is also a concern. / ABSTRACT: The effects of temperature and total dissolved solids (TDS) on survival of 5 groups of indicator organisms were evaluated in controlled experiments. TDS did not have significant effects on inactivation of these microbes up to 1000 mg/l, but there was indication of reduced inactivation of enterococci at TDS concentrations of 3000 mg/l. Increased temperature consistently resulted in more rapid inactivation. Survival in aquifer and reservoir water samples was also evaluated, and significant effects due to water type, temperature, and pasteurization treatment were observed. Inactivation was more rapid in surface water sources, and pasteurization enhanced survival. For enterococci and DNA coliphage, pasteurization effects were more pronounced in surface water. DNA coliphage and perhaps fecal coliform appeared to be the more-conservative indicator organisms for aquifer injection monitoring. / ABSTRACT: Lastly, it was observed that inactivation rates were considerably slower in pore water of saturated limestone than in the bulk water column of similar water sources and conditions, particularly for enterococci and fecal coliform. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Outreach is a small, but significant component to modern research. Developing an exhibit for public display can be an effective way to communicate science to broad audiences, although it may be a less familiar method to scientists than writing papers or giving presentations. I outline the process of developing an interactive exhibit for outreach, and evaluate and discuss the effectiveness of a computer exhibit designed to communicate estuary currents and scientific modeling using Olympia Oyster restoration in the Yaquina Bay estuary as a theme. I summarize the results of this project in three primary recommendations: 1) exhibit developers should be deliberate in the decision to use a computer and only select this media if it is determined to be the best for communicating exhibit learning outcomes, 2) the design of visualizations to convey research results should be carefully modified from their scientific forms to best meet the exhibit learning outcomes and expectations of the exhibit audience, and 3) scientists should play an integral role in the development of scientific content-based exhibits, but their expertise, and the range of expertise from other members of the exhibit development team, should be strategically utilized. / Graduation date: 2012

Title from PDF of title page. / Document formatted into pages; contains 79 pages. / Thesis (M.S.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: Monthly d18O and Sr/Ca records generated from modern and fossil corals from Southwestern Pacific Ocean sites in the Republic of Vanuatu are used to assess the differences in mean climate state, seasonality, and interannual variability between a glacial and interglacial period. The modern coral contains a well-defined annual signal in d18O and Sr/Ca. The top 40 cm of the coral used in this study has a mean d18O value of -4.99+/-0.13%VPDB (2s) and a mean Sr/Ca value of 8.691+/-0.015mmol/mol (2s). El Nino-Southern Oscillation (ENSO) events are characterized by positive d18O and Sr/Ca anomalies, consistent with cooler temperatures and reduced rainfall that typifies ENSO at Vanuatu. The 12cm long fossil coral is dated to 346 ka + 25, - 9, based on uranium-series analysis and stratigraphic forward modeling, indicating that the fossil coral grew during MIS10 - a glacial period. / ABSTRACT: X-ray diffraction, petrographic inspection, SEM analysis, and geochemical considerations indicate excellent preservation. The mean d18O value is enriched by 0.74%, and the mean Sr/Ca value is equivalent, compared to the modern coral. Mathematical modeling of Pleistocene mean SST and SSS results in temperature estimates up to 2?C warmer and salinity up to 2 psu saltier than present-day conditions, if seawater Sr/Ca were 1-2% higher in MIS10. Our fossil coral data and modeling results preclude colder SST and lower SSS at Vanuatu during MIS10. Accurate estimates of past values of seawater Sr/Ca remain the largest obstacle to accurately reconstructing past tropical SST using pristine fossil corals. The fossil coral Sr/Ca annual range is similar to the modern range, indicating that seasonal SST ranges were similar, whereas the d18O annual range is about half that of the modern coral, indicating weaker past seasonal salinity variations. / ABSTRACT: The reduced seasonal SSS variations and increased SSTs near Vanuatu are interpreted as evidence that the SPCZ was displaced from its present location while the fossil coral lived. The geochemical response to El Nino events in the modern coral is observed twice in the fossil coral record, indicating that ENSO-like processes are not unique to interglacial time periods, but characterize the tropical Pacific at least back to MIS 10. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Title from PDF of title page. / Document formatted into pages; contains 84 pages. / Thesis (M.S.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: Hurricane hazards result from the combined processes of wind, waves, storm surge, and overwash (Lennon et al., 1996). Predicting the severity of these hazards requires immense effort to quantify the processes and then predict how different coastal regions respond to them. A somewhat simpler, but no less daunting task is to begin to predict the hazards due to potential erosion of barrier islands. A four-part scale has been developed by Sallenger (2000) to provide a framework for understanding how barrier islands might respond during extreme storm events. These four regimes describe how beach and dune elevations interact with surge and wave runup. This study will produce estimates of potential hazards through combining lidar surveys of dune elevation with modeled elevations of storm water levels. Direct measurements of maximum wave heights during hurricanes are rare. / ABSTRACT: We evaluated three simple equations proposed by Kjerfve (1986), Young (1988), and Hsu (1998) to forecast the maximum wave height (Hmax) generated by three 1999 hurricanes. Model results were compared to wave data recorded by the National Oceanic and Atmospheric Administration (NOAA) wave rider buoys. The radius of maximum winds, wind speed, forward velocity, distance from buoy to the storm's eye-wall (r), and buoy's position relative to the quadrant of the storm (Q) were found to have significant and direct roles in evaluating recorded hurricane induced wave heights (H) and thus, were individually examined for each comparison. The implications of the r and Q on H were assessed when determining the overall effectiveness of the modelers' equations. Linear regression analyses tested the accuracy of each modeled prediction of the Hmax, comparing it to the observed wave heights. Three statistical criteria were used to quantify model performance. / ABSTRACT: Hsu's model was the most reliable and useful forecasting technique. Despite the predictive skill of Hsu's model, direct observations of the maximum wave conditions, when available and appropriate, are preferred as inputs for SWAN, a 3rd generation shoaling wave model. Outputs from SWAN are used to calculate the empirical relationships for wave runup. For our test case, pre and post-storm topographies were surveyed as part of a joint USGS-NASA program using lidar technology. These data sets were used to calculate changes in the elevation and location of the dune crest (Dhigh) and dune base (Dlow) for the North Carolina Outer Banks. We hindcast potential coastal hazards (erosional hot spots) using the pre-storm morphology and modeled wave runup and compare those estimates to the measured results from the post-storm survey. / ABSTRACT: Links among the existing topography and spatial variations in wave runup were found to be 95% correlated for the north-south and east-west facing barrier islands. Application of Sallenger's (2000) four-part Storm Impact Scale to the pre-storm Dhigh elevation survey and wave runup extremes (Rhigh and Rlow) were found to accurately predict zones of overwash and showed potential to forecast the inundation regime. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

The Cal Poly Pier (Pier) Master/Facility Plan (FP) document provides the vision of the future for the Pier, a marine science research facility. The Plan facilitates project development and management of the Pier while meeting university and department research goals. Specifically, the FP document establishes goals and strategies to direct long-term development of the Pier, streamlines agency approval and permit requirements, provides context for pier management, and assists the permitting process for future development as it relates to regulatory permits and programmatic growth on the Cal Poly Pier to help meet goals of the Center for Coastal Marine Sciences (CCMS). The Cal Poly Pier is the marine field station for the California Polytechnic State University San Luis Obispo (Cal Poly) CCMS and is one of several facilities that supports research and educational activities. The CCMS is a CSU Campus Center research organization that provides research and education activities as a part of Cal Poly’s overall mission while offering opportunities to interested parties beyond Cal Poly, such as private and public entities. The 3,057-foot long pier provides students, faculty, researchers, and other users unrivaled access to the marine environment of the Central Coast and fosters hands-on learning opportunities to progress marine research and science. The Master Plan name was changed to Facility Plan to streamline the plan approval process and to minimize the potential for errors.