The metabolism and physiology of Pseudomonas putida strain LS46 was investigated using biodiesel-derived waste streams as potential low cost substrates for production of medium chain length polyhydroxyalkanoates (mcl-PHA). Proteomic and trranscriptomic analyses were used to correlate specific gene and gene product expression patterns with differences in phenotypes of mcl-PHA biosynthesis by P. putida LS46. Growth and mcl-PHA content of P. putida LS46 were similar in cultures containing biodiesel-derived waste glycerol versus pure glycerol, and mcl-PHA synthesis occurred during stationary phase after nitrogen concentrations in the medium were exhausted. Waste glycerol cultures contained elevated concentrations of heavy metal ions, such as copper, which induced significant changes in gene expression levels related to heavy metal resistance. Several membrane-bound proteins, such as CusABC efflux and CopAB were identified and putatively play a role in regulating cellular copper concentrations. Cultures containing waste free fatty acids synthesized mcl-PHA throughout the exponential growth phase. Protein expression levels of two mcl-PHA synthases were suppressed during exponential phase growth in waste glycerol cultures, putatively via post-transcriptional regulation. Culture specific expression of monomer supplying proteins (PhaJ1 and PhaG), and sets of fatty acid oxidation enzymes were observed, and may have contributed to differences in the composition of polymers synthesized by P. putida LS46 cultured on the two substrates. Expression levels of the majority of mcl-PHA biosynthesis pathway genes were stable during active polymer synthesis in waste glycerol cultures. However, variations in protein expression levels, and in some cases their corresponding mRNAs, were observed in a number of other metabolic patheays, such as glycerol transportation, partial glycolysis, pyruvate metabolism, the TCA cycle, and fatty acid biosynthesis. These data suggest potential regulatory points that may determine carbon flux during mcl-PHA biosynthesis. Evaluation of identified genetic targets in P. putida LS46 that putatively influence mcl-PHA biosynthesis and monomer composition merit further studies. / February 2016

Bed connected support structures such as monopiles are expected to be impractical for water depths greater than 30 m and so there is increasing interest in alternative structure concepts to enable cost-effective deployment of wind and tidal stream turbines. Floating, moored platforms supporting multiple rotors are being considered for this purpose. This thesis investigates the dynamic response of such floating structures, taking into account the coupling between loading due to both turbulent flow and waves and the dynamic response of the system. The performance and loading of a single rotor in steady and quasi-steady flows are quantified with a Blade Element Momentum Theory (BEMT) code. This model is validated for steady flow against published data for two 0.8 m diameter rotors (Bahaj, Batten, et al., 2007; Galloway et al., 2011) and a 0.27 m diameter rotor (Whelan and Stallard, 2011). Time-averaged coefficients of thrust and power measured by experiment in steady turbulent flow were in agreement with BEMT predictions over a range of angular speeds. The standard deviation of force on the rotor is comparable to that on a porous grid for comparable turbulence characteristics. Drag and added mass coefficients are determined for a porous disc forced to oscillate normal to the rotor plane in quiescent flow and in the streamwise axis in turbulent flow. Added mass is negligible for the Keulegan Carpenter number range considered ( less than 1). The drag coefficient in turbulent flow was found to decay exponentially with number, to 2±10% for values greater than 0.5. These coefficients were found to be in good agreement with those for a rotor in the same turbulent flow with disc drag coefficient within 12.5% for less than 0.65. An extreme-value analysis is applied to the measured time-varying thrust due to turbulent flow and turbulent flow with waves to obtain forces with 1%, 0.1% and 0.01% probability of exceedance during operating conditions. The 1% exceedance force in turbulent flow with turbulence intensity of 12% is around 40% greater than the mean thrust. The peak force in turbulent flow with opposing waves was predicted to within 6% by superposition of the extreme force due to turbulence only with a drag force based on the relative wave-induced velocity at hub-height estimated by linear wave theory and with drag coefficient of 2.0. Response of a floating structure in surge and pitch is studied due to both wave- forcing on the platform defined by the linear diffraction code WAMIT and due to loading of the operating turbine defined by a thrust coefficient and drag coefficient. Platform response can either increase or decrease the loading on the rotor and this was dependant on the hydrodynamic characteristics of the support platform. A reduction of the force on the rotor is attained when the phase difference between the wave force on the support and the surface elevation is close to ± and when the damping of the support is increased. For a typical support and for a wave condition with phase difference close to , the 1% rotor forces were reduced by 8% when compared to the force obtained with a rotor supported on a stiff tower.

Large text streams are commonplace; news organisations are constantly producing stories and people are constantly writing social media posts. These streams should be analysed in real-time so useful information can be extracted and acted upon instantly. When natural disasters occur people want to be informed, when companies announce new products financial institutions want to know and when celebrities do things their legions of fans want to feel involved. In all these examples people care about getting information in real-time (low latency). These streams are massively varied, people’s interests are typically classified by the entities they are interested in. Organising a stream by the entity being referred to would help people extract the information useful to them. This is a difficult task: fans of ‘Captain America’ films will not want to be incorrectly told that ‘Chris Evans’ (the main actor) was appointed to host ‘Top Gear’ when it was a different ‘Chris Evans’. People who use local idiosyncrasies such as referring to their home county (‘Cornwall’) as ‘Kernow’ (the Cornish for ‘Cornwall’ that has entered the local lexicon) should not be forced to change their language when finding out information about their home. This thesis addresses a core problem for real-time entity-specific NLP: Streaming cross document coreference resolution (CDC), how to automatically identify all the entities mentioned in a stream in real-time. This thesis address two significant problems for streaming CDC: There is no representative dataset and existing systems consume more resources over time. A new technique to create datasets is introduced and it was applied to social media (Twitter) to create a large (6M mentions) and challenging new CDC dataset that contains a much more variend range of entities than typical newswire streams. Existing systems are not able to keep up with large data streams. This problem is addressed with a streaming CDC system that stores a constant sized set of mentions. New techniques to maintain the sample are introduced significantly out-performing existing ones maintaining 95% of the performance of a non-streaming system while only using 20% of the memory.

The classification task requires learning a decision boundary between classes by making use of training examples from each. A potential challenge for this task is the class imbalance problem, which occurs when there are many training instances available for a single class, the majority class, and few training instances for the other, the minority class [58]. In this case, it is no longer clear how to separate the majority class from something for which we have little to no knowledge. More worrying, often the minority class is the class of interest, e.g. for detecting abnormal conditions from streaming sensor data. The one-class classification (OCC) paradigm addresses this scenario by casting the task as learning a decision boundary around the majority class with no need for minority class instances [110]. OCC has been thoroughly investigated, e.g. [20, 60, 90, 110], and many one-class classifiers have been proposed. One approach for improving one-class classifier performance on static data sets is learning in the context of concepts: the majority class is broken down into its constituent sub-concepts and a classifier is induced over each [100]. Modern machine learning research, however, is concerned with data streams: where potentially infinite amounts of data arrive quickly and need to be processed as they arrive. In these cases it is not possible to store all of the instances in memory, nor is it practical to wait until “the end of the data stream” before learning. An example is network intrusion detection: detecting an attack on the computer network should occur as soon as practicable. Many one-class classifiers for data streams have been described in the literature, e.g. [33, 108], and it is worth investigating whether the approach of learning in the context of concepts can be successfully applied to the OCC task for data streams as well. This thesis identifies that the idea of breaking the majority class into subconcepts to simplify the OCC problem has been demonstrated for static data sets, [100], but has not been applied in data streams. The primary contribution to the literature made by this thesis is the identification of how the majority class’s sub-concept structure can be used to improve the classification performance of streaming one-class classifiers while mitigating the challenges posed by the data stream environment. Three frameworks are developed, each using this knowledge to a different degree. These are applied with a selection of streaming one-class classifiers to both synthetic and benchmark data streams with performance compared to that of the one-class classifier learning independently. These results are analyzed and it is shown that scenarios exist where knowledge of sub-concepts can be used to improve one-class classifier performance.

The Internet of Things (IoT) technology is undergoing expansion into different aspects of our life, changing the way businesses operate and bringing in efficiency and reliability of digital controls on various levels. Processing large amount of data from connected sensor networks becomes a challenging task. Specific part of it related to fleet management requires processing of the data on boards of vehicles equipped with multiple electronic devices and sensors for maintenance and operation of such vehicles. Herewith the efficiency of various configurations of employing Kalman filter algorithm for on-the-fly pre-processing of the sensory network originated data streams in IoT systems is investigated. Contextual grouping of the data streams for pre-processing by specialized Kalman filter units is found to be able to satisfy the logistics of IoT system operations. It is demonstrated that interconnection of the elementary Kalman filters into an organized network, the compositional Kalman filter, allows to take advantage of the redundancy of data streams to accomplish IoT pre-processing of the raw data. This includes intermittent data imputation, missing data replacement, lost data recovery, as well as error events detection and correction. Architectures are proposed and tested for the interaction of elementary Kalman filters in detection of GPS outage events and their compensation via data replacement procedure, as well as GPS offset occurrence detection and its compensation via data correction routine. Demonstrated is the efficiency of the suggested compositional designs of elementary Kalman filter networks for the purpose of data pre-processing in IoT systems.

abstract: Humans have dramatically increased phosphorus (P) availability in terrestrial and aquatic ecosystems. As P is often a limiting nutrient of primary production, changes in its availability can have dramatic effects on ecosystem processes. I examined the effects of calcium carbonate (CaCO3) deposition, which can lower P concentrations via coprecipitation of phosphate, on P availability in two systems: streams in the Huachuca Mountains, Arizona, and a stream, Río Mesquites, in Cuatro Ciénegas, México. Calcium carbonate forms as travertine in the former and within the microbialites of the latter. Despite these differences, CaCO3 deposition led to lowered P availability in both systems. By analyzing a three-year dataset of water chemistry from the Huachuca Mountain streams, I determined that P concentrations were negatively related to CaCO3 deposition rates. I also discovered that CaCO3 was positively correlated with nitrogen concentrations, suggesting that the stoichiometric effect of CaCO3 deposition on nutrient availability is due not only to coprecipitation of phosphate, but also to P-related constraints on biotic nitrogen uptake. Building from these observations, bioassays of nutrient limitation of periphyton growth suggest that P limitation is more prevalent in streams with active CaCO3 deposition than those without. Furthermore, when I experimentally reduced rates of CaCO3 deposition within one of the streams by partial light-exclusion, areal P uptake lengths decreased, periphyton P content and growth increased, and periphyton nutrient limitation by P decreased. In Río Mesquites, CaCO3 deposition was also associated with P limitation of microbial growth. There, I investigated the consequences of reductions in CaCO3 deposition with several methods. Calcium removal led to increased concentrations of P in the microbial biomass while light reductions decreased microbial biomass and chemical inhibition had no effect. These results suggest that CaCO3 deposition in microbialites does limit biological uptake of P, that photoautotrophs play an important role in nutrient acquisition, and, combined with other experimental observations, that sulfate reduction may support CaCO3 deposition in the microbialite communities of Río Mesquites. Overall, my results suggest that the effects of CaCO3 deposition on P availability are general and this process should be considered when managing nutrient flows across aquatic ecosystems. / Dissertation/Thesis / Doctoral Dissertation Biology 2015

Submitted by Carlos Humberto Biagolini (professorcarlosciencias@zipmail.com.br) on 2018-04-21T00:24:14Z No. of bitstreams: 1 Método avaliativo e qualitativo de parques lineares da cidade de São Paulo, (SP).pdf: 5058241 bytes, checksum: eb72f992878a44965256105f4ca22e71 (MD5) / Approved for entry into archive by Lucimara Kurokawa Shinoda null (lucimaraks@sorocaba.unesp.br) on 2018-04-23T20:25:32Z (GMT) No. of bitstreams: 1 biagolini_ch_dr_soro.pdf: 5058241 bytes, checksum: eb72f992878a44965256105f4ca22e71 (MD5) / Made available in DSpace on 2018-04-23T20:25:32Z (GMT). No. of bitstreams: 1 biagolini_ch_dr_soro.pdf: 5058241 bytes, checksum: eb72f992878a44965256105f4ca22e71 (MD5) Previous issue date: 2018-03-16 / Parques lineares são áreas estruturadas às margens de córregos e rios que apresentam a importante finalidade de revitalizar áreas degradadas, preservar áreas de várzea responsáveis pela absorção de água pluvial e, ainda, criar espaços de lazer e socialização. O objetivo deste trabalho foi o de desenvolver uma metodologia capaz de avaliar de forma quali-quantitativa 10 parques lineares entre os 24 parques existentes na cidade de São Paulo, além de identificar os principais elementos da avifauna e flora. Os parques lineares escolhidos foram: Aricanduva, Canivete, do Fogo, Gamelinha, Ipiranguinha, Itaim, Parelheiros, Rapadura, Sapé e Tiquatira. Com relação aos resultados, o parque lineare Itaim foi classificado apenas como regular enquanto que os parques lineares Aricanduva, Canivete, do Fogo, Gamelinha, Ipiranguinha, Parelheiros, Rapadura e Sapé foram classificados como bons e somente o parque linear Tiquatira foi classificado como excelente pela metodologia proposta neste trabalho. Quanto à avifauna e flora, foram identificadas 23 espécies de aves e 151 espécies vegetais. A utilização deste sistema de avaliação de parques lineares pode ser de grande importância para a avaliação destes espaços, dado que por meio desta é possível apontar as áreas que necessitam de intervenções e ações imediatas a fim de equalizar a qualidade destes espaços, melhorando seus serviços prestados ao meio ambiente e consequentemente para a qualidade de vida da população usuária. / Linear parks are structured areas along the banks of streams and rivers that have the important purpose of revitalizing degraded areas, preserving floodplain areas responsible for the absorption of rainwater, and creating leisure and socialization spaces. The objective of this work was to develop a methodology capable of qualitatively and quantitatively evaluating 10 linear parks among the 24 existing parks in the city of São Paulo, in addition to identifying the main elements of the flora and fauna. The linear parks chosen were: Aricanduva, Canivete, Fogo, Gamelinha, Ipiranguinha, Itaim, Parelheiros, Rapadura, Sapé and Tiquatira. Regarding the results, the Itaim linear park were classified as regular, while the Aricanduva, Canivete, do Fogo, Gamelinha, Ipiranguinha, Parelheiros, Rapadura e Sapé linear parks were classified as good and only Tiquatira linear park was classified as excellent by methodology proposed in this work. Regarding fauna and flora, 151 plant species and 23 bird species were identified. The use of this system of evaluation of linear parks can be of great importance, since it is possible to point out the areas that need interventions and immediate actions in order to equalize the quality of these spaces, improving their services rendered and consequently the quality of life of the user population.

abstract: Ephemeral streams in Arizona that are perpendicularly intersected by the Central Arizona Project (CAP) canal have been altered due to partial or complete damming of the stream channel. The dammed upstream channels have experienced decades long cycles of sediment deposition and waterlogging during storm events causing the development of "green-up" zones. This dissertation examines the biogeomorphological effects of damming ephemeral streams caused by the CAP canal by investigating: (1) changes in the preexisting spatial cover of riparian vegetation and how these changes are affected by stream geometry; (2) green-up initiation and evolution; and (3) changes in plant species and community level changes. To the author's knowledge, this is the only study that undertakes an interdisciplinary approach to understanding the environmental responses to anthropogenically-altered ephemeral stream channels. The results presented herein show that vegetation along the upstream section increased by an average of 200,872 m2 per kilometer of the CAP canal over a 28 year period. Vegetation growth was compared to channel widths which share a quasi-linear relationship. Remote sensing analysis of Landsat TM images using an object-oriented approach shows that riparian vegetation cover gradually increased over 28 years. Field studies reveal that the increases in vegetation are attributed to the artificial rise in local base-level upstream created by the canal, which causes water to spill laterally onto the desert floor. Vegetation within the green-up zone varies considerably in comparison to pre-canal construction. Changes are most notable in vegetation community shifts and abundance. The wettest section of the green-up zone contains the greatest density of woody plant stems, the greatest vegetation volume, and a high percentage of herbaceous cover. Vegetation within wetter zones changed from a tree-shrub to a predominantly tree-herb assemblage, whereas desert shrubs located in zones with intermediate moisture have developed larger stems. Results from this study lend valuable insight to green-up processes associated with damming ephemeral streams, which can be applied to planning future canal or dam projects in drylands. Also, understanding the development of the green-up zones provide awareness to potentially avoiding flood damage to infrastructure that may be unknowingly constructed within the slow-growing green-up zone. / Dissertation/Thesis / Ph.D. Geography 2014

O presente trabalho teve como objetivo fazer um estudo taxonômico da fauna de Plecoptera (Perlidae) da região Sul do Brasil. Nós estudamos material depositado em diferentes coleções, e também novos espécimes coletados ao longo do desenvolvimento deste trabalho. Os adultos foram capturados com puçás na vegetação das margens dos riachos e através de atração luminosa. As ninfas foram coletadas dentro de riachos com o auxílio de redes D. A genitália dos adultos foi diafanizada usando KOH. Como resultado, três novas espécies foram descritas, duas possuem novos registros de ocorrência e quatro tiveram o registro de suas distribuições ampliadas para esta região. / This work aimed to make a taxonomic study of the Plecoptera (Perlidae) fauna from southern Brazil. We studied material deposited in different collections, and also new specimens collected along the development of this work. Adults were captured with D-nets in vegetation from the banks of streams and through light attraction. Nymphs were collected in streams with a D-net. The genitalia of adults were diaphanized by KOH. The adults genitalia was cleared using KOH. As a result, three new species were described, two have new records of occurrence and four had record their distributions expanded to this region.

O zooplâncton possui grande sensibilidade ambiental e responde rapidamente a alterações ambientais com alterações na abundância e riqueza de organismos. Ainda se conhece muito pouco sobre os organismos aquáticos do Cerrado, assim como há poucos estudos sobre o zooplâncton de ambientes lóticos no Brasil. Esse trabalho teve como objetivo caracterizar dois córregos da bacia do Rio Preto, médio São Francisco, pela avaliação de comunidades zooplanctônicas e suas relações com características físicas, químicas e biológicas da água, comparando córregos em áreas de vegetação nativa conservada e sob influência de áreas agrícolas. Foram amostradas duas sub-bacias do Rio Preto, localizadas em área de Cerrado (DF e GO) durante quatro semanas nos períodos seco e chuvoso. Em dois pontos de amostragem por córrego, foram coletadas amostras de zooplâncton e de água. Variáveis físicas e químicas da água e a concentração de a clorofila a foram determinadas. Os dois córregos apresentaram tendência de aumento de íons no período chuvoso. O córrego Estanislau (em área agrícola) apresentou maiores concentrações de nitrato, sódio, cloreto e clorofila a em relação ao córrego Pindaíba (em área de vegetação nativa). O zooplâncton se caracterizou por densidades muito baixas e alta riqueza de espécies, com 63 táxons registrados ao todo. A riqueza de espécies e a densidade de organismos do zooplâncton foram maiores no córrego Pindaíba. O córrego Estanislau possui indícios de estar sofrendo impactos negativos do uso rural de sua bacia. / The zooplankton community has high environmental sensitivity and quickly responds to changes in the environment with changes in its abundance and diversity. Yet, little is known about the aquatic organisms of the Cerrado, as well there had been few investigations on the zooplankton of Brazilian lotic environments. This work had the aims to characterize two streams of Rio Preto watershed, part of the Rio São Francisco watershed; to assess their zooplankton communities and the relationships between chlorophyll a and physical and chemical characteristics of water; and to contrast forested and agricultural streams. Two streams, located in the Cerrado Biome (Federal District and the state of Goiás), were sampled for four weeks in dry and rainy seasons. Zooplankton and water samples were taken in two sampling points per stream. Physical and chemical characteristics of water and chlorophyll a concentration were determined. Ionic concentration was higher on rainy season in both streams. The agricultural stream (Estanislau) had higher concentrations of nitrate, sodium, chloride, and chlorophyll a than the forested stream (Pindaiba). Zooplankton was characterized by very low densities and high species richness, with a total of 63 taxa recorded on both streams. Zooplankton density and species richness were higher in Pindaiba stream. Estanislau stream has signs to be suffering negative impacts from the agricultural land use of its watershed.