Red tides pose a significant economic and environmental threat in the Gulf of Mexico. Detecting red tide is important for understanding this phenomenon. In this thesis, machine learning approaches based on Random Forests, Support Vector Machines and K-Nearest Neighbors have been evaluated for red tide detection from MODIS satellite images. Detection results using machine learning algorithms were compared to ship collected ground truth red tide data. This work has three major contributions. First, machine learning approaches outperformed two of the latest thresholding red tide detection algorithms based on bio-optical characterization by more than 10% in terms of F measure and more than 4% in terms of area under the ROC curve. Machine Learning approaches are effective in more locations on the West Florida Shelf. Second, the thresholds developed in recent thresholding methods were introduced as input attributes to the machine learning approaches and this strategy improved Random Forests and KNearest Neighbors approaches' F-measures. Third, voting the machine learning and thresholding methods could achieve the better performance compared with using machine learning alone, which implied a combination between machine learning models and biocharacterization thresholding methods can be used to obtain effective red tide detection results.

An appreciation of the extent of syndepositional fracturing, faulting, and cementation of carbonate platform margins is essential to understanding the role of early diagenesis and compaction in margin deformation. This study uses integrated lidar and outcrop data along the Capitan Reef from an area encompassing the mouths of both Rattlesnake and Walnut Canyons. Mapping geomorphic expressions of syndepositional faults and fractures at multiple scales of observation was the main approach to delineating zones of syndepositional fractures. Ridge- groove couplets visible in exposures of the Capitan Reef throughout the Guadalupe Mountains were targeted because the ability to identify these as signs of syndepositional fracture development would have implications for the entire reef complex. Results show that these ridgegroove couplets are the product of differential weathering of syndepositional as well as burial-related fractures. Recessive grooves have an average syndepositional fracture spacing of ~13 m whereas ridges have a spacing of ~33 m. vi Smaller (~5-20 m-wide) scale erosional lineaments common in the study area and mappable on airborne lidar are formed by differential erosion of planes of syndepositional faults. Maps of these fault lineaments on the lidar show that syndepositional faults extend laterally for 300 m - 2000 m and relay near the terminations of the faults at each end. Faults can be further grouped into fault systems consisting of sets of faults connected by fault relays that extend for at least the entire length (~12 km) of the study area. Although vertical displacement along faults is typically less than 11 m, syndepositional faults result in changes in structural dip domain of 1-6 degrees across an individual fault. Even smaller erosional lineaments (10 cm-1 m) are visible on the airborne lidar that form as a result of differential erosion of individual fractures. Larger fractures (> 20 cm) can be reliably mapped on the lidar, but smaller features (< 20 cm) cannot be reliably mapped with currently available data and can only be captured using field studies. Fracture fill types are heterogeneous along strike as shown by comparisons of field study locations. Siliciclastic-dominated fills are likely sourced from overlying siliciclastic units of the shelf, which, in this area, were from the Ocotillo Siltstone. These silt-filled fractures are broadly distributed, indicating preferential development and infill of syndepositional fractures during the deposition of the Ocotillo Siltstone in the G27/28 high-frequency sequences. Development of early fractures is also shown to have been influenced by mechanical stratigraphy with changes in fracture spacing between massive to thick-bedded shelf-margin (~17 m fracture spacing) and outer-shelf facies tracts versus thin-bedded outer-shelf and shelf-crest (~28 m fracture spacing). Ultimately, this study demonstrated that the Capitan shelf margin was ubiquitously overprinted by syndepositional fracturing and faulting and that this nearsurface structural modification influenced early diagenetic patterns and internal vii sedimentation throughout the reef margin. Before this study, the extent and nature of syndepositional fracture/fault development within the margin were largely unquantified. Here, by integrating field observations and surface weathering reflections of these fractures as observed in the lidar, we can demonstrate a widespread impact of early fracturing more akin to analogous early-lithified margins such as the Devonian of the Canning Basin of Australia. / text

Component based software engineering has been perceived to have immense reuse potential. This area has evoked wide interest and has led to considerable investment in research and development efforts. Most of these investigations have explored internal characteristics of software components such as correctness, reliability, modularity, interoperability, understandability, maintainability, readability, portability and generality for promoting reuse. But experience over the past decade and a half has demonstrated that the usefulness of a component depends as much on the context into which it fits as it does on the internal characteristics of the component. Software architecture descriptions that take into account the requirements of the domain can be used to serve as this context. While the Perry, Wolf definition of software architecture has been widely acknowledged, a number of architectural description languages (ADL) have emerged that aim to capture various facets of a software, using varying degrees of formalism. There is currently no agreement towards a standard approach for documenting software architectures which would help define the vocabulary for architectural semantics. In spite of lack of any specification standards for components, Software Product Lines (SPL) and Commercial Off The Shelf (COTS) components do provide a rich supporting base for creating software architectures and promise significant improvements in the quality of software configurations that can be composed from pre-built components. However, further research is needed for evaluation of architectural merits of such component based configurations. In this research, we identify the key aspects of software that need to be specified to enable useful analysis at an architectural level. We also propose a set of metrics that enable objective evaluation of reusability potential. Architectural research has established that software architectural styles provide a way for achieving a desired coherence for component-based architectures. Different architectural styles enforce different quality attributes for a system. Thus, if the architectural style of an emergent system could be predicted, a person playing the role of a system integrator could make necessary changes to ensure that the quality attributes dictated by the system requirements were satisfied before the actual system is built and deployed, thus somewhat mitigating project risks. As part of this research, we propose a model for predicting architectural styles based on use cases that need to be satisfied by a system configuration and demonstrate how our approach can be used to determine stylistic conformance. We also propose objective methods for assessing architectural divergence, erosion and drift during system evolution and maintenance. / text

Bacterial responses to environmental stresses may be easily observed and predicted under controlled laboratory conditions. However, realistic conditions encountered during manufacturing, in retail or in households may cause unpredicted responses of spoilage or pathogenic bacteria. Therefore it is essential to identify and understand the microbial dynamics under such conditions. The overall aim of the present study was to simulate the most common environmental conditions and consumer-style practices during storage or preparation of Ready-to-Eat (RTE) and Ready-to-Cook (RTC) products in the domestic environment, and predict the microbial dynamics which may deteriorate the quality or compromise the safety of these foods. Aiming to develop a unified mathematical model for the prediction of the growth of the specific spoilage microorganisms (SSOs), the spoilage pattern of three RTE acidic spreads of low pH was described in relation to microbial, physicochemical and molecular changes during storage. Results showed that the spoilage profile of the products was primarily affected by the initial pH and the storage temperature, despite the differences in their formulation. These findings enabled the assessment of two unified models (polynomial and Ratkowsky) for the prediction of the growth of lactic acid bacteria (LAB; SSOs) in such acidic spreads, using only the initial pH, the concentration of undissociated acetic acid and the storage temperature. The models were validated under realistic conditions in household refrigerators. Despite the abrupt fluctuations of the temperature during validation procedure, they both were able to adequately predict the growth of LAB in the spreads. However, the initial contamination level was proved to be necessary and crucial for the accurate prediction of microbial dynamics. The time-temperature profiles of the validation procedure revealed that the suggested storage conditions were not followed promptly and, therefore, concerns were raised on the effect of such consumer mishandlings on the safety of foods. Therefore, the responses of Salmonella spp. and Escherichia coli O157:H7 to the stresses encountered during frozen storage, thawing and cooking of ground beef, simulating typical scenarios followed by the consumers, were evaluated. The results revealed that the guidelines issued by the food safety authorities lack of some specific points that may affect the safety of the final product, such as the duration of frozen storage and the method of cooking. In particular, it was found that the heat resistance of E. coli O157:H7 was likely increased after long term frozen storage, while cooking in pan-grill did not ensure the safety of the final product, even when cooked at the suggested temperature. As shown in the first study, the initial contamination level played a significant role on the predictions of the models and further on the shelf-life of the products. Therefore, the dynamics of realistically low initial populations of Listeria monocytogenes and Salmonella Typhimurium versus higher levels of the pathogens (such those used during in vitro trials) in RTE fresh-cut salads were compared. In addition, any potential uncertainty sources for the growth potential of the pathogens in broth-based simulations were investigated. Results showed that the growth variability of low inocula is highly affected by the marginal storage temperatures, the indigenous microflora and the availability of nutrients. Because of this, growth from low populations showed the likelihood to exceed the growth derived from unrealistically high inocula, suggesting that ―fail-dangerous‖ implications may derive from such challenge tests. Data derived from this part were compared with broth-based simulations and the results showed that high uncertainty should be expected when extrapolating such predictions from low initial populations in fresh-cut salads, due to the various factors affecting the microbial growth on a real food, which are (inevitably) ignored by broth-based models. Overall, the present Thesis highlights the significant impact of consumer mishandlings on the food safety and quality of foods and contributes to the identification of unpredicted potential risk origins in the domestic environment.

A quasi-two dimensional model for the southern Vancouver Island shelf was developed with the Regional Ocean Modelling System (ROMS) to study coupling of the carbon, oxygen, and nitrogen cycles in a summer wind-driven upwelling region. The physical model is coupled to an ecosystem module that includes a simple representation of a sediment layer and considers non-fixed C:N ratios for detritus and dissolved organic matter (i.e., explicitly modelled pools of carbon and nitrogen for those variables). The model accounts for denitrification within the sediments as well as within the water column when oxygen concentrations are low (below 5 mmol-O2 m-3). The objective is to identify the dominant processes controlling the cycles, their coupling, and their sensitivity to changes in environmental forcing. Results demonstrate how low oxygen and low pH events are tightly coupled in the coastal study region, especially through local ecosystem processes. In particular, exchange with the sediments plays a dominant role in consuming oxygen from and releasing inorganic carbon to the bottom waters on the shelf. Two key features distinguish the southern Vancouver Island shelf from other coastal regions in the California Current System and protect inner shelf waters from severe hypoxia and corrosive (i.e., undersaturated in aragonite) conditions. First, the greater width of the shelf reduces the penetration of subsurface offshore high-carbon and low-oxygen waters into shallower waters; and second, the relatively fresh Vancouver Island Coastal Current (VICC) brings oxygen-rich and carbon-poor waters to the bottom layer over the inner shelf. Sensitivity experiments show that carbon and oxygen cycles on the southern Vancouver Island shelf may be significantly affected by an altered upwelling season, a shallower offshore Oxygen Minimum Zone, a warmer ocean, and a carbon-enriched environment. Combinations of these scenarios suggest a potential increasing risk for the development of coastal hypoxia and corrosive conditions in the future. Further sensitivity simulations indicate that sedimentary denitrification provides an additional coupling between the carbon, oxygen, and nitrogen cycles. Total alkalinity generated by sediment denitrification has the potential to buffer anthropogenic ocean acidification. However, this alkalinity effect over the Vancouver Island shelf in late spring and summer simulations is small compared with studies for other locations at annual scales. Longer time scales need to be examined in this region to confirm whether the role of alkalinity generation in the sediments is significant. In conclusion, this dissertation not only demonstrates the coupled nature of biogeochemical cycles in the coastal ocean, but also the importance of this coupling as we try to estimate how coastal ecosystems will respond to human modifications of shelf waters and the climate.

In this thesis, COTS-software requirements elicitation, which is an input for RFP in software intensive automation system&rsquo / s acquisition, is examined. Business Process Models are used for COTS-software requirements elicitation. A new method, namely CREB, is developed to meet the requirements of COTS-software. A software intensive system acquisition of a military organization is used to validate the method.

Marine nitrogen (N) is an essential nutrient for all oceanic organisms. The cycling of N between biologically available and unavailable forms occurs through numerous reactions. Because of the vast number of reactions and chemical species involved, the N cycle is still not well understood. This dissertation focuses on understanding some of the reactions involved in the cycling of marine N, as well as improving techniques used to measure dissolved N2 gas. The largest loss term for global marine N is a reaction called denitrification. In this work, denitrification was measured in the sandy sediments of the Georgia continental shelf, an area where this reaction was thought to be unlikely because of the physical properties of the sediments. Nitrogen fixation, which is a reaction that produces biologically available N, was detected in Georgia estuarine sediments. N fixation was measured concurrently with denitrification in these sediments, resulting in a much smaller net loss of marine N than previously thought. Lastly, membrane inlet mass spectrometry (MIMS) is a technique that measures dissolved N2, the end product of denitrification and a reactant in N fixation reactions. This study suggests that N2 measurements by MIMS are influenced by O2 concentrations due to pressure differences inside of the ion source of the mass spectrometer. These findings seek to improve denitrification measurements using MIMS on samples with varying O2 concentrations. In conclusion, this dissertation suggests that the marine N cycle is more dynamic than has been suggested, due to the recognition of input and loss reactions in a wider range of marine and estuarine environments. However, improvements in the understanding of MIMS will help with direct measurements with reactions involved in the global marine N cycle.

[Truncated abstract] The Northern Bonaparte Basin and adjacent Darwin Shelf form part of a major petroleum province on the northwestern margin of Australia. The middle to Late Cretaceous Bathurst Island Group consists of siliciclastic and pelagic carbonate strata that form the regional seal to underlying Upper Jurassic and Lower Cretaceous reservoir sandstones. The Bathurst Island Group has previously been subdivided into four stratigraphic sequences or ‘play intervals’ bound by regional disconformities in the Valanginian (KV horizon), Lower Aptian (KA horizon), upper Lower Cenomanian (KC horizon), Middle Campanian (KSC horizon), and at the CretaceousPaleocene boundary (T horizon). Correlation of these sedimentary packages and stratigraphic surfaces requires high-resolution calcareous microfossil biostratigraphy, while palaeobathymetric determinations based on benthonic foraminiferal assemblages are important for determining the subsidence history of the area and relative sea-level changes. This study presents the first detailed stratigraphic distributions, taxonomic lists and illustrations of foraminifera and calcareous nannofossils from the Bathurst Island Group of the Northern Bonaparte Basin and Darwin Shelf. A biostratigraphic framework has been constructed for the study area incorporating ‘standard’ (Tethyan) Cretaceous planktonic foraminiferal and calcareous nannofossil events where applicable, and integrating locally defined events where necessary. This framework allows Cretaceous strata to be correlated regionally across the study area and to the global chronostratigraphic scale. Correlation of the Northern Bonaparte Basin and Darwin Shelf strata to the Cretaceous Stages and international time scale is based on recent ties of nannofossil and foraminiferal events to macrofossil zones and palaeomagnetic polarity chrons at ratified and proposed Global Stratotype Sections and Points (GSSPs). Calcareous nannofossil events recorded in the study area that are critical for defining stage boundaries include the lowest occurrences of Prediscosphaera columnata, Micula decussata, Lithastrinus grillii, and Aspidolithus parcus parcus, and the highest occurrences of Helenea chiastia, Lithastrinus moratus, Aspidolithus parcus constrictus, and Eiffellithus eximius. Important planktonic foraminiferal events for correlation include the lowest occurrences of Rotalipora gr. globotruncanoides, and Dicarinella asymetrica, and the highest occurrences of Planomalina buxtorfi, Rotalipora cushmani, and Dicarinella asymetrica. During the middle to Late Cretaceous the Northern Bonaparte Basin and Darwin Shelf occupied mid-high palaeolatitudes between 35ºS to 45ºS. These palaeolatitudes are reflected in the transitional character of the planktonic microfossil assemblages, which combine elements of the low-latitude, warm-water Tethyan Province to the north and the cool-water high-latitude Austral Province to the south. ‘Standard’ Tethyan zonations are most applicable for uppermost AlbianMiddle Campanian strata because equator-to-pole temperature gradients were weakly developed, and global climate was warm and equable during this interval. These conditions resulted in broad latitudinal distributions for Tethyan marker species, and consequently most UC calcareous nannofossil zones and European-Mediterranean planktonic foraminiferal zones are recognised. In contrast, the EarlyLate Albian and the late Middle CampanianMaastrichtian were intervals of greater bioprovinciality and stronger palaeotemperature gradients. In these intervals application of the Tethyan zonations is more difficult, and a number of the Tethyan biostratigraphic markers are absent from the study area (e.g. Ticinella species in the Albian and Radotruncana calcarata in the Late Campanian). Cretaceous palaeobathymetric reconstruction of the study area is based on comparison of the foraminiferal assemblages with those of previous Cretaceous palaeobathymetric studies. Marginal marine assemblages consist solely of low diversity siliceous agglutinated foraminifera (e.g. Trochammina). Inner and middle neritic water depths (0-100 m) contain rare to common planktonic foraminifera (mainly globigerine forms), robertinids (e.g. Epistomina), siliceous agglutinates, lagenids, buliminids (e.g. Neobulimina), and rotaliids. The outer neritic zone (100-200 m water depth) contains abundant planktonic foraminifera (keeled and globigerine), calcareous agglutinates (e.g. Dorothia), and diverse lagenids, buliminids, and rotaliids. Upper-middle bathyal water depths (200-1000 m) are characterised by abundant planktonic foraminifera, common siliceous agglutinated taxa (e.g. Glomospira), rare to common Osangularia, and globular species of Gyroidinoides, Pullenia, and Paralabamina.

Made available in DSpace on 2015-04-17T14:49:21Z (GMT). No. of bitstreams: 1 Arquivototal.pdf: 939298 bytes, checksum: 4db0a28a49a01afe330ae2fff4b91cc0 (MD5) Previous issue date: 2011-08-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The shelf life of foods is the time allowed for food to be consumed safely on the microbiological aspects, physicochemical and sensory characteristics, and is a determining factor in production logistics, trade and consumption, considered in the cost of the product, especially when it comes to perishable foods, for the presence and growth of micro-organisms during production to consumption are inevitable and their study is essential for the development of conservation technologies as well as determining with regard to the risk which consumers are exposed to. In this work we simulated the conditions of time (fifteen days) and temperature (<2.0 ° C) as indicated by the manufacturer shelf life of the product analyzed and the evaluations performed microbiological and physico-chemical properties during times of 0, 5, 10 and 15 days for raw and under cooling (1.4 ± 0.6 ° C) chicken breast without skin. The samples were analyzed for the presence / absence of the microorganism Salmonella spp., quantification of mesophilic microorganisms, MPN- most probable number for the group of coliform bacteria, the presence / absence of the Escherichia coli and pH analysis. None of the samples showed the presence of Salmonella spp. during the study , however, 10 days time was the limit for guaranteeing the quality of the microorganism Fecal samples at 45 ° C, and 70% of samples unfit for human consumption and at odds with the precepts of sanitary legislation in force. It was found that the microbiological quality of chicken flesh had flaws, as demonstrated by the high number of mesophilic aerobic bacteria, coliforms at 35 ° C and the confirmed presence of E. coli in 20% of the samples, which may therefore be a potential risk for the occurrence of foodborne illnesses DVA. / A vida de prateleira dos alimentos é o tempo estabelecido para que o alimento seja consumido com segurança quanto aos aspectos microbiológicos, físico-químicos e sensoriais, sendo fator determinante na logística de produção, comércio e consumo, sendo considerado no custo do produto, principalmente quando se trata de alimentos perecíveis, pois a presença e o crescimento de micro-organismos durante a produção até o consumo são inevitáveis e seu estudo é essencial para o desenvolvimento de tecnologias de conservação e determinante quanto ao risco em que os consumidores estão expostos. Neste trabalho foram simuladas as condições de tempo (quinze dias) e temperatura (< 2,0°C) indicados pelo fabricante como vida de prateleira do produto analisado e realizadas as avaliações microbiológicas e físicoquímicas durante os tempos de 0, 5, 10 e 15 dias para peito de frango sem pele, cru e sobrefrigeração(1,4 ± 0,6 ºC). As amostras foram analisadas quanto a presença/ausência do microorganismo Salmonella spp., contagem de micro organismos mesófilos, NMP - número mais provável para o grupo de coliformes, presença/ausência de E. coli e análise de pH. Em nenhuma das amostras foi detectada a presença de Salmonella spp., durante o tempo de estudo, porém, o tempo de 10 dias mostrou-se como limite para garantia da qualidade das amostras para o microorganismo Coliformes a 45°C, estando com 70% das amostras impróprias ao consumo humano e em desacordo com o que preceitua a legislação sanitária vigente. Foi possível constatar que a qualidade microbiológica da carne de frango apresentou falhas, como demonstrado pelo elevado número de bactérias aeróbias mesófilas, coliformes a 35°C e confirmação da presença de E. coli em 20% das amostras, podendo, portanto, ser um risco em potencial para ocorrência de Doenças Veiculadas por Alimentos - DVA.

Made available in DSpace on 2015-04-17T14:49:36Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 2092428 bytes, checksum: 9f2660b1eca5b207292adc4d196cdd59 (MD5) Previous issue date: 2014-02-26 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The success of the food industry depends not only on sure foods are safety for consumers, but also the capacity to innovate and supply the market trends, like the demand for food products made from health benefits ingredients. In this way, this research aimed to develop and characterize a yogurt-like fermented beverage made from a mixture of goat s milk and water-soluble soy extract (WSSE), supplemented with inulin. To established the most suitable formulation, a Central Composite Design (CCD) in conjunction with Response Surface Methodology (RSM) was used, having as independent variables the concentrations of WSSE and inulin. The response variables were water holding capacity (WHC), syneresis index, pH, acidity, and rheological and sensory properties. By using that methodology was observed that increasing WSSE concentration was related to better results for rheological properties, WHC and syneresis index, whereas, a negative influence was observed on overall acceptability of the product. Inulin concentration, at the levels studied, showed a positive influence on apparent viscosity and overall acceptability of the beverages. By using the models obtained for response variables was elaborated a treatment containing the concentrations of WSSE and inulin that promoted the most suitable result. The fermented beverage elaborated was characterized for physicochemical and sensory properties and the refrigerated storage stability was analyzed during 28 days by evaluating microbiological, chemical and physical parameters. The results obtained from this treatment were compared with the results obtained from a control treatment made using goat s milk only and without inulin supplementation. The treatment containing WSSE and inulin showed better results for physical and chemical properties, showing better stability during refrigerated storage. However, control treatment showed a better overall acceptability, presenting aroma and taste more pleasant. Regarding to microbiological parameters, no significative differences were observed for these two treatments. / O sucesso da indústria de alimentos não depende apenas da certeza de que os alimentos são seguros para o consumo, mas também da habilidade para inovar e para atender as atuais tendências de mercado, como a demanda por alimentos elaborados a partir de ingredientes que, além de nutrir, trazem benefícios adicionais a saúde. Neste contexto, este trabalho objetivou desenvolver e caracterizar uma bebida fermentada tipo iogurte elaborada a partir de uma mistura composta por leite de cabra e extrato hidrossolúvel de soja (EHS), adicionada de inulina. Para a definição da formulação mais adequada foi utilizado um Delineamento Composto Central Rotacional (DCCR) em conjunto com a Metodologia de Superfície de Resposta (MSR), tendo como variáveis independentes as concentrações de EHS e inulina e como variáveis dependentes a capacidade de retenção de água, o índice de sinerese, pH, acidez e as propriedades reológicas e sensoriais. A partir desta metodologia, foi verificado que o aumento na concentração de EHS favoreceu a obtenção de melhores resultados para as propriedades reológicas, para a capacidade de retenção de água e para o índice de sinerese, no entanto, apresentou uma influência negativa sobre a aceitação sensorial do produto. A concentração de inulina, dentro dos níveis utilizados, influenciou de forma positiva sobre a viscosidade aparente e sobre a aceitação sensorial do produto. A partir dos modelos obtidos para as variáveis dependentes estudadas, foi elaborado um tratamento contendo as concentrações de EHS e inulina que forneceram os resultados mais satisfatórios. A bebida fermentada elaborada foi caracterizada quanto as propriedades físico-químicas e sensoriais e sua estabilidade foi avaliada durante um período de armazenamento refrigerado de 28 dias com relação a parâmetros microbiológicos, físicos e químicos. Os resultados obtidos a partir deste tratamento otimizado foram comparados com os resultados de um tratamento controle elaborado apenas com leite de cabra e sem a adição de inulina. O tratamento contendo EHS e inulina obteve melhores resultados com relação as propriedades físicas e químicas, apresentando melhor estabilidade durante o armazenamento. No entanto, o tratamento controle obteve uma melhor aceitação sensorial, apresentando sabor e aroma mais agradáveis. Com relação aos parâmetros microbiológicos, diferenças significativas não foram observadas entre estes dois tratamentos.