Biological Impacts and Uses of Black Bass Competitive Fishing Tournaments on Large Lake Systems

Thesis (Master, Biology) -- Queen's University, 2016-09-28 15:06:46.124

Classifying And Predicting Software Security Vulnerabilities based on Reproducibility

Security defects are common in large software systems because of their size and complexity. Although efficient development processes, testing, and maintenance policies are applied to software systems, there are still a large number of vulnerabilities that can remain, despite these measures. Some vulnerabilities stay in a system from one release to the next one because they cannot be easily reproduced through testing. These vulnerabilities endanger the security of the systems. We propose vulnerability classification and prediction frameworks based on vulnerability reproducibility. The frameworks are effective to identify the types and locations of vulnerabilities in the earlier stage, and improve the security of software in the next versions (referred to as releases). We expand an existing concept of software bug classification to vulnerability classification (easily reproducible and hard to reproduce) to develop a classification framework for differentiating between these vulnerabilities based on code fixes and textual reports. We then investigate the potential correlations between the vulnerability categories and the classical software metrics and some other runtime environmental factors of reproducibility to develop a vulnerability prediction framework. The classification and prediction frameworks help developers adopt corresponding mitigation or elimination actions and develop appropriate test cases. Also, the vulnerability prediction framework is of great help for security experts focus their effort on the top-ranked vulnerability-prone files. As a result, the frameworks decrease the number of attacks that exploit security vulnerabilities in the next versions of the software. To build the classification and prediction frameworks, different machine learning techniques (C4.5 Decision Tree, Random Forest, Logistic Regression, and Naive Bayes) are employed. The effectiveness of the proposed frameworks is assessed based on collected software security defects of Mozilla Firefox.

Development of molecular approaches to assess the diversity and abundance of marine nematodes assemblages for assessment of Good Environmental Status of the estuarine and marine ecosystems

In Europe, the concerns with the status of marine ecosystems have increased, and the Marine Directive has as main goal the achievement of Good Environmental Status (GES) of EU marine waters by 2020. Molecular tools are seen as promising and emerging approaches to improve ecosystem monitoring, and have led ecology into a new era, representing perhaps the most source of innovation in marine monitoring techniques. Benthic nematodes are considered ideal organisms to be used as biological indicator of natural and anthropogenic disturbances in aquatic ecosystems underpinning monitoring programmes on the ecological quality of marine ecosystems, very useful to assess the GES of the marine environment. dT-RFLP (directed Terminal-Restriction Fragment Length Polymorphism) allows to assess the diversity of nematode communities, but also allows studying the functioning of the ecosystem, and combined with relative real-time PCR (qPCR), provides a high-throughput semi-quantitative characterization of nematode communities. These characteristics make the two molecular tools good descriptors for the good environmental status assessment. The main aim of this study is to develop and optimize the dT-RFLP and qPCR in Mira estuary (SW coast, Portugal). A molecular phylogenetic analysis of marine and estuarine nematodes is being performed combining morphological and molecular analysis to evaluate the diversity of free-living marine nematodes in Mira estuary. After morphological identification, barcoding of 18S rDNA and COI genes are being determined for each nematode species morphologically identified. So far we generated 40 new sequences belonging to 32 different genus and 17 families, and the study has shown a good degree of concordance between traditional morphology-based identification and DNA sequences. These results will improve the assessment of marine nematode diversity and contribute to a more robust nematode taxonomy. The DNA sequences are being used to develop the dT-RFLP with the ability to easily process large sample numbers (hundreds and thousands), rather than typical of classical taxonomic or low throughput molecular analyses. A preliminary study showed that the digest enzymes used in dT-RFLP for terrestrial assemblages separated poorly the marine nematodes at taxonomic level for functional group analysis. A new digest combination was designed using the software tool DRAT (Directed Terminal Restriction Analysis Tool) to distinguished marine nematode taxa. Several solutions were provided by DRAT and tested empirically to select the solution that cuts most efficiently. A combination of three enzymes and a single digest showed to be the best solution to separate the different clusters. Parallel to this, another tool is being developed to estimate the population size (qPCR). An improvement in qPCR estimation of gene copy number using an artificial reference is being performed for marine nematodes communities to quantify the abundance. Once developed, it is proposed to validate both methodologies by determining the spatial and temporal variability of benthic nematodes assemblages across different environments. The application of these high-throughput molecular approaches for benthic nematodes will improve sample throughput and their implementation more efficient and faster as indicator of ecological status of marine ecosystems.

Design and Development of a Research Framework for Prototyping Control Tower Augmented Reality Tools

The purpose of the air traffic management system is to ensure the safe and efficient flow of air traffic. Therefore, while augmenting efficiency, throughput and capacity in airport operations, attention has rightly been placed on doing it in a safe manner. In the control tower, many advances in operational safety have come in the form of visualization tools for tower controllers. However, there is a paradox in developing such systems to increase controllers' situational awareness: by creating additional computer displays, the controller's vision is pulled away from the outside view and the time spent looking down at the monitors is increased. This reduces their situational awareness by forcing them to mentally and physically switch between the head-down equipment and the outside view. This research is based on the idea that augmented reality may be able to address this issue. The augmented reality concept has become increasingly popular over the past decade and is being proficiently used in many fields, such as entertainment, cultural heritage, aviation, military & defense. This know-how could be transferred to air traffic control with a relatively low effort and substantial benefits for controllers’ situation awareness. Research on this topic is consistent with SESAR objectives of increasing air traffic controllers’ situation awareness and enable up to 10 % of additional flights at congested airports while still increasing safety and efficiency. During the Ph.D., a research framework for prototyping augmented reality tools was set up. This framework consists of methodological tools for designing the augmented reality overlays, as well as of hardware and software equipment to test them. Several overlays have been designed and implemented in a simulated tower environment, which is a virtual reconstruction of Bologna airport control tower. The positive impact of such tools was preliminary assessed by means of the proposed methodology.

Development of methodologies supporting the sustainable and safe integration of offshore conventional and renewable energy production

Against a backdrop of rapidly increasing worldwide population and growing energy demand, the development of renewable energy technologies has become of primary importance in the effort to reduce greenhouse gas emissions. However, it is often technically and economically infeasible to transport discontinuous renewable electricity for long distances to the shore. Another shortcoming of non-programmable renewable power is its integration into the onshore grid without affecting the dispatching process. On the other hand, the offshore oil & gas industry is striving to reduce overall carbon footprint from onsite power generators and limiting large expenses associated to carrying electricity from remote offshore facilities. Furthermore, the increased complexity and expansion towards challenging areas of offshore hydrocarbons operations call for higher attention to safety and environmental protection issues from major accident hazards. Innovative hybrid energy systems, as Power-to-Gas (P2G), Power-to-Liquid (P2L) and Gas-to-Power (G2P) options, implemented at offshore locations, would offer the opportunity to overcome challenges of both renewable and oil & gas sectors. This study aims at the development of systematic methodologies based on proper sustainability and safety performance indicators supporting the choice of P2G, P2L and G2P hybrid energy options for offshore green projects in early design phases. An in-depth analysis of the different offshore hybrid strategies was performed. The literature reviews on existing methods proposing metrics to assess sustainability of hybrid energy systems, inherent safety of process routes in conceptual design stage and environmental protection of installations from oil and chemical accidental spills were carried out. To fill the gaps, a suite of specific decision-making methodologies was developed, based on representative multi-criteria indicators addressing technical, economic, environmental and societal aspects of alternative options. A set of five case-studies was defined, covering different offshore scenarios of concern, to provide an assessment of the effectiveness and value of the developed tools.

Development of a Predictive Control Function for a Plug-in Hybrid Electric Vehicle with Electrically-heated Catalyst

This master thesis work is focused on the development of a predictive EHC control function for a diesel plug-in hybrid electric vehicle equipped with a EURO 7 compliant exhaust aftertreatment system (EATS), with the purpose of showing the advantages provided by the implementation of a predictive control strategy with respect to a rule-based one. A preliminary step will be the definition of an accurate powertrain and EATS physical model, starting from already existing and validated applications. Then, a rule-based control strategy managing the torque split between the electric motor (EM) and the internal combustion engine (ICE) will be developed and calibrated, with the main target of limiting tailpipe NOx emission by taking into account EM and ICE operating conditions together with EATS conversion efficiency. The information available from vehicle connectivity will be used to reconstruct the future driving scenario, also referred to as electronic horizon (eHorizon), and in particular to predict ICE first start. Based on this knowledge, an EATS pre-heating phase can be planned to avoid low pollutant conversion efficiencies, thus preventing high NOx emission due to engine cold start. Consequently, the final NOx emission over the complete driving cycle will be strongly reduced, allowing to comply with the limits potentially set by the incoming EURO 7 regulation. Moreover, given the same NOx emission target, the gain achieved thanks to the implementation of an EHC predictive control function will allow to consider a simplified EATS layout, thus reducing the related manufacturing cost. The promising results achieved in terms of NOx emission reduction show the effectiveness of the application of a predictive control strategy focused on EATS thermal management and highlight the potential of a complete integration and parallel development of involved vehicle physical systems, control software and connectivity data management.

Optimization and development of low environmental impact propulsion systems

The aim of the Ph.D. research project was to explore Dual Fuel combustion and hybridization. Natural gas-diesel Dual Fuel combustion was experimentally investigated on a 4-Stroke, 2.8 L, turbocharged, light-duty Diesel engine, considering four operating points in the range between low to medium-high loads at 3000 rpm. Then, a numerical analysis was carried out using a customized version of the KIVA-3V code, in order to optimize the diesel injection strategy of the highest investigated load. A second KIVA-3V model was used to analyse the interchangeability between natural gas and biogas on an intermediate operating point. Since natural gas-diesel Dual Fuel combustion suffers from poor combustion efficiency at low loads, the effects of hydrogen enriched natural gas on Dual Fuel combustion were investigated using a validated Ansys Forte model, followed by an optimization of the diesel injection strategy and a sensitivity analysis to the swirl ratio, on the lowest investigated load. Since one of the main issues of Low Temperature Combustion engines is the low power density, 2-Stroke engines, thanks to the double frequency compared to 4-Stroke engines, may be more suitable to operate in Dual Fuel mode. Therefore, the application of gasoline-diesel Dual Fuel combustion to a modern 2-Stroke Diesel engine was analysed, starting from the investigation of gasoline injection and mixture formation. As far as hybridization is concerned, a MATLAB-Simulink model was built to compare a conventional (combustion) and a parallel-hybrid powertrain applied to a Formula SAE race car.

Development of JADE, a new software for the verification and validation of nuclear data libraries

Nuclear cross sections are the pillars onto which the transport simulation of particles and radiations is built on. Since the nuclear data libraries production chain is extremely complex and made of different steps, it is mandatory to foresee stringent verification and validation procedures to be applied to it. The work here presented has been focused on the development of a new python based software called JADE, whose objective is to give a significant help in increasing the level of automation and standardization of these procedures in order to reduce the time passing between new libraries releases and, at the same time, increasing their quality. After an introduction to nuclear fusion (which is the field where the majority of the V\&V action was concentrated for the time being) and to the simulation of particles and radiations transport, the motivations leading to JADE development are discussed. Subsequently, the code general architecture and the implemented benchmarks (both experimental and computational) are described. After that, the results coming from the major application of JADE during the research years are presented. At last, after a final discussion on the objective reached by JADE, the possible brief, mid and long time developments for the project are discussed.

Development of a Whole-Genome Sequencing (WGS) approach for the characterization of Legionella environmental isolates in water systems

Legionella is a Gram-negative bacterium that represent a public health issue, with heavy social and economic impact. Therefore, it is mandatory to provide a proper environmental surveillance and risk assessment plan to perform Legionella control in water distribution systems in hospital and community buildings. The thesis joins several methodologies in a unique workflow applied for the identification of non-pneumophila Legionella species (n-pL), starting from standard methods as culture and gene sequencing (mip and rpoB), and passing through innovative approaches as MALDI-TOF MS technique and whole genome sequencing (WGS). The results obtained, were compared to identify the Legionella isolates, and lead to four presumptive novel Legionella species identification. One of these four new isolates was characterized and recognized at taxonomy level with the name of Legionella bononiensis (the 64th Legionella species). The workflow applied in this thesis, help to increase the knowledge of Legionella environmental species, improving the description of the environment itself and the events that promote the growth of Legionella in their ecological niche. The correct identification and characterization of the isolates permit to prevent their spread in man-made environment and contain the occurrence of cases, clusters, or outbreaks. Therefore, the experimental work undertaken, could support the preventive measures during environmental and clinical surveillance, improving the study of species often underestimated or still unknown.

Mars delivery service - development of the electro-mechanical systems of the Sample Fetch Rover for the Mars Sample Return Campaign

This thesis describes the development of the Sample Fetch Rover (SFR), studied for Mars Sample Return (MSR), an international campaign carried out in cooperation between the National Aeronautics and Space Administration (NASA) and the European Space Agency (ESA). The focus of this document is the design of the electro-mechanical systems of the rover. After placing this work into the general context of robotic planetary exploration and summarising the state of the art for what concerns Mars rovers, the architecture of the Mars Sample Return Campaign is presented. A complete overview of the current SFR architecture is provided, touching upon all the main subsystems of the spacecraft. For each area, it is discussed what are the design drivers, the chosen solutions and whether they use heritage technology (in particular from the ExoMars Rover) or new developments. This research focuses on two topics of particular interest, due to their relevance for the mission and the novelty of their design: locomotion and sample acquisition, which are discussed in depth. The early SFR locomotion concepts are summarised, covering the initial trade-offs and discarded designs for higher traverse performance. Once a consolidated architecture was reached, the locomotion subsystem was developed further, defining the details of the suspension, actuators, deployment mechanisms and wheels. This technology is presented here in detail, including some key analysis and test results that support the design and demonstrate how it responds to the mission requirements. Another major electro-mechanical system developed as part of this work is the one dedicated to sample tube acquisition. The concept of operations of this machinery was defined to be robust against the unknown conditions that characterise the mission. The design process led to a highly automated robotic system which is described here in its main components: vision system, robotic arm and tube storage.

Network assimilation methodology and sectorization of water distribution systems by graph mining and optimization algorithm

Water Distribution Networks (WDNs) play a vital importance rule in communities, ensuring well-being band supporting economic growth and productivity. The need for greater investment requires design choices will impact on the efficiency of management in the coming decades. This thesis proposes an algorithmic approach to address two related problems:(i) identify the fundamental asset of large WDNs in terms of main infrastructure;(ii) sectorize large WDNs into isolated sectors in order to respect the minimum service to be guaranteed to users. Two methodologies have been developed to meet these objectives and subsequently they were integrated to guarantee an overall process which allows to optimize the sectorized configuration of WDN taking into account the needs to integrated in a global vision the two problems (i) and (ii). With regards to the problem (i), the methodology developed introduces the concept of primary network to give an answer with a dual approach, of connecting main nodes of WDN in terms of hydraulic infrastructures (reservoirs, tanks, pumps stations) and identifying hypothetical paths with the minimal energy losses. This primary network thus identified can be used as an initial basis to design the sectors. The sectorization problem (ii) has been faced using optimization techniques by the development of a new dedicated Tabu Search algorithm able to deal with real case studies of WDNs. For this reason, three new large WDNs models have been developed in order to test the capabilities of the algorithm on different and complex real cases. The developed methodology also allows to automatically identify the deficient parts of the primary network and dynamically includes new edges in order to support a sectorized configuration of the WDN. The application of the overall algorithm to the new real case studies and to others from literature has given applicable solutions even in specific complex situations.

Development and testing of methodologies for the control and diagnosis of innovative combustion systems

In pursuit of aligning with the European Union's ambitious target of achieving a carbon-neutral economy by 2050, researchers, vehicle manufacturers, and original equipment manufacturers have been at the forefront of exploring cutting-edge technologies for internal combustion engines. The introduction of these technologies has significantly increased the effort required to calibrate the models implemented in the engine control units. Consequently the development of tools that reduce costs and the time required during the experimental phases, has become imperative. Additionally, to comply with ever-stricter limits on 〖"CO" 〗_"2" emissions, it is crucial to develop advanced control systems that enhance traditional engine management systems in order to reduce fuel consumption. Furthermore, the introduction of new homologation cycles, such as the real driving emissions cycle, compels manufacturers to bridge the gap between engine operation in laboratory tests and real-world conditions. Within this context, this thesis showcases the performance and cost benefits achievable through the implementation of an auto-adaptive closed-loop control system, leveraging in-cylinder pressure sensors in a heavy-duty diesel engine designed for mining applications. Additionally, the thesis explores the promising prospect of real-time self-adaptive machine learning models, particularly neural networks, to develop an automatic system, using in-cylinder pressure sensors for the precise calibration of the target combustion phase and optimal spark advance in a spark-ignition engines. To facilitate the application of these combustion process feedback-based algorithms in production applications, the thesis discusses the results obtained from the development of a cost-effective sensor for indirect cylinder pressure measurement. Finally, to ensure the quality control of the proposed affordable sensor, the thesis provides a comprehensive account of the design and validation process for a piezoelectric washer test system.

Axis control optimization: autotuning techniques and frequency response analysis of industrial mechatronic systems

In the field of industrial automation, there is an increasing need to use optimal control systems that have low tracking errors and low power and energy consumption. The motors we are dealing with are mainly Permanent Magnet Synchronous Motors (PMSMs), controlled by 3 different types of controllers: a position controller, a speed controller, and a current controller. In this thesis, therefore, we are going to act on the gains of the first two controllers by going to find, through the TwinCAT 3 software, what might be the best set of parameters. To do this, starting with the default parameters recommended by TwinCAT, two main methods were used and then compared: the method of Ziegler and Nichols, which is a tabular method, and advanced tuning, an auto-tuning software method of TwinCAT. Therefore, in order to analyse which set of parameters was the best,several experiments were performed for each case, using the Motion Control Function Blocks. Moreover, some machines, such as large robotic arms, have vibration problems. To analyse them in detail, it was necessary to use the Bode Plot tool, which, through Bode plots, highlights in which frequencies there are resonance and anti-resonance peaks. This tool also makes it easier to figure out which and where to apply filters to improve control.

Development Of Egg Pc/cholesterol/α-tocopherol Liposomes With Ionic Gradients To Deliver Ropivacaine.

Ropivacaine (RVC) is an aminoamide local anesthetic widely used in surgical procedures. Studies with RVC encapsulated in liposomes and complexed in cyclodextrins have shown good results, but in order to use RVC for lengthy procedures and during the postoperative period, a still more prolonged anesthetic effect is required. This study therefore aimed to provide extended RVC release and increased upload using modified liposomes. Three types of vesicles were studied: (i) large multilamellar vesicle (LMV), (ii) large multivesicular vesicle (LMVV) and (iii) large unilamellar vesicle (LUV), prepared with egg phosphatidylcholine/cholesterol/α-tocopherol (4:3:0.07 mol%) at pH 7.4. Ionic gradient liposomes (inside: pH 5.5, pH 5.5 + (NH4)2SO4 and pH 7.4 + (NH4)2SO4) were prepared and showed improved RVC loading, compared to conventional liposomes (inside: pH 7.4). An high-performance liquid chromatography analytical method was validated for RVC quantification. The liposomes were characterized in terms of their size, zeta potential, polydispersion, morphology, RVC encapsulation efficiency (EE(%)) and in vitro RVC release. LMVV liposomes provided better performance than LMV or LUV. The best formulations were prepared using pH 5.5 (LMVV 5.5in) or pH 7.4 with 250 mM (NH4)2SO4 in the inner aqueous core (LMVV 7.4in + ammonium sulfate), enabling encapsulation of as much as 2% RVC, with high uptake (EE(%) ∼70%) and sustained release (∼25 h). The encapsulation of RVC in ionic gradient liposomes significantly extended the duration of release of the anesthetic, showing that this strategy could be a viable means of promoting longer-term anesthesia during surgical procedures and during the postoperative period.

Two-dimensional gel electrophoretic protein profile analysis during seed development of Ocotea catharinensis: a recalcitrant seed species

The aim of the present work was to characterize changes in the protein profile throughout seed development in O. catharinensis, a recalcitrant species, by two-dimensional gel electrophoresis. Protein extraction was undertaken by using a thiourea/urea buffer, followed by a precipitation step with 10% TCA. Comparative analysis during seed development showed that a large number of proteins were exclusively detected in each developmental stage. The cotyledonary stage, which represents the transition phase between embryogenesis and the beginning of metabolism related to maturation, presents the highest number of stage-specific spots. Protein identification, through MS/MS analysis, resulted in the identification of proteins mainly related to oxidative metabolism and storage synthesis. These findings contribute to a better understanding of protein metabolism during seed development in recalcitrant seeds, besides providing information on established markers that could be useful in defining and improving somatic embryogenesis protocols, besides monitoring the development of somatic embryos in this species.