Identification, mutagenesis, and transcriptional analysis of the methanesulfonate transport operon of methylosulfonomonas methylovora

Recently identified genes located downstream (3') of the msmEF (transport encoding) gene cluster, msmGH, and located 5' of the structural genes for methanesulfonate monooxygenase (MSAMO) are described from Methylosulfonomonas methylovora. Sequence analysis of the derived polypeptide sequences encoded by these genes revealed a high degree of identity to ABC-type transporters. MsmE showed similarity to a putative periplasmic substrate binding protein, MsmF resembled an integral membraneassociated protein, and MsmG was a putative ATP-binding enzyme. MsmH was thought to be the cognate permease component of the sulfonate transport system. The close association of these putative transport genes to the MSAMO structural genes msmABCD suggested a role for these genes in transport of methanesulfonic acid (MSA) into M. methylovora. msmEFGH and msmABCD constituted two operons for the coordinated expression of MSAMO and the MSA transporter systems. Reverse-transcription-PCR analysis of msmABCD and msmEFGH revealed differential expression of these genes during growth on MSA and methanol. The msmEFGH operon was constitutively expressed, whereas MSA induced expression of msmABCD. A mutant defective in msmE had considerably slower growth rates than the wild type, thus supporting the proposed role of MsmE in the transport of MSA into M. methylovora.

Adaptive message rate control of infrastructured DSRC vehicle networks for coexisting road safety and non-safety applications

Intelligent transport system (ITS) has large potentials on road safety applications as well as nonsafety applications. One of the big challenges for ITS is on the reliable and cost-effective vehicle communications due to the large quantity of vehicles, high mobility, and bursty traffic from the safety and non-safety applications. In this paper, we investigate the use of dedicated short-range communications (DSRC) for coexisting safety and non-safety applications over infrastructured vehicle networks. The main objective of this work is to improve the scalability of communications for vehicles networks, ensure QoS for safety applications, and leave as much as possible bandwidth for non-safety applications. A two-level adaptive control scheme is proposed to find appropriate message rate and control channel interval for safety applications. Simulation results demonstrated that this adaptive method outperforms the fixed control method under varying number of vehicles. © 2012 Wenyang Guan et al.

Strongly localized moving discrete dissipative breather-solitons in Kerr nonlinear media supported by intrinsic gain

We investigate the mobility of nonlinear localized modes in a generalized discrete Ginzburg-Landau-type model, describing a one-dimensional waveguide array in an active Kerr medium with intrinsic, saturable gain and damping. It is shown that exponentially localized, traveling discrete dissipative breather-solitons may exist as stable attractors supported only by intrinsic properties of the medium, i.e., in the absence of any external field or symmetry-breaking perturbations. Through an interplay by the gain and damping effects, the moving soliton may overcome the Peierls-Nabarro barrier, present in the corresponding conservative system, by self-induced time-periodic oscillations of its power (norm) and energy (Hamiltonian), yielding exponential decays to zero with different rates in the forward and backward directions. In certain parameter windows, bistability appears between fast modes with small oscillations and slower, large-oscillation modes. The velocities and the oscillation periods are typically related by lattice commensurability and exhibit period-doubling bifurcations to chaotically "walking" modes under parameter variations. If the model is augmented by intersite Kerr nonlinearity, thereby reducing the Peierls-Nabarro barrier of the conservative system, the existence regime for moving solitons increases considerably, and a richer scenario appears including Hopf bifurcations to incommensurately moving solutions and phase-locking intervals. Stable moving breathers also survive in the presence of weak disorder. © 2014 American Physical Society.

Mode-locking intracavity dynamics:modeling nonlinear power and energy fluctuations

Modern high-power, pulsed lasers are driven by strong intracavity fluctuations. Critical in driving the intracavity dynamics is the nontrivial phase profiles generated and their periodic modification from either nonlinear mode-coupling, spectral filtering or dispersion management. Understanding the theoretical origins of the intracavity fluctuations helps guide the design, optimization and construction of efficient, high-power and high-energy pulsed laser cavities. Three specific mode-locking component are presented for enhancing laser energy: waveguide arrays, spectral filtering and dispersion management. Each component drives a strong intracavity dynamics that is captured through various modeling and analytic techniques.

Tin oxide based composites derived using electrostatic spray deposition technique as anodes for lithium-ion batteries

Recent advances in the electric & hybrid electric vehicles and rapid developments in the electronic devices have increased the demand for high power and high energy density lithium ion batteries. Graphite (theoretical specific capacity: 372 mAh/g) used in commercial anodes cannot meet these demands. Amorphous SnO2 anodes (theoretical specific capacity: 781 mAh/g) have been proposed as alternative anode materials. But these materials have poor conductivity, undergo a large volume change during charging and discharging, large irreversible capacity loss leading to poor cycle performances. To solve the issues related to SnO2 anodes, we propose to synthesize porous SnO2 composites using electrostatic spray deposition technique. First, porous SnO2/CNT composites were fabricated and the effects of the deposition temperature (200, 250, 300 °C) & CNT content (10, 20, 30, 40 wt %) on the electrochemical performance of the anodes were studied. Compared to pure SnO2 and pure CNT, the composite materials as anodes showed better discharge capacity and cyclability. 30 wt% CNT content and 250 °C deposition temperature were found to be the optimal conditions with regard to energy capacity whereas the sample with 20% CNT deposited at 250 °C exhibited good capacity retention. This can be ascribed to the porous nature of the anodes and the improvement in the conductivity by the addition of CNT. Electrochemical impedance spectroscopy studies were carried out to study in detail the change in the surface film resistance with cycling. By fitting EIS data to an equivalent circuit model, the values of the circuit components, which represent surface film resistance, were obtained. The higher the CNT content in the composite, lower the change in surface film resistance at certain voltage upon cycling. The surface resistance increased with the depth of discharge and decreased slightly at fully lithiated state. Graphene was also added to improve the performance of pure SnO2 anodes. The composites heated at 280 °C showed better energy capacity and energy density. The specific capacities of as deposited and post heat-treated samples were 534 and 737 mAh/g after 70 cycles. At the 70th cycle, the energy density of the composites at 195 °C and 280 °C were 1240 and 1760 Wh/kg, respectively, which are much higher than the commercially used graphite electrodes (37.2–74.4 Wh/kg). Both SnO2/CNTand SnO2/grapheme based composites with improved energy densities and capacities than pure SnO2 can make a significant impact on the development of new batteries for electric vehicles and portable electronics applications.

Field programmable gate array based target detection and gesture recognition

The move from Standard Definition (SD) to High Definition (HD) represents a six times increases in data, which needs to be processed. With expanding resolutions and evolving compression, there is a need for high performance with flexible architectures to allow for quick upgrade ability. The technology advances in image display resolutions, advanced compression techniques, and video intelligence. Software implementation of these systems can attain accuracy with tradeoffs among processing performance (to achieve specified frame rates, working on large image data sets), power and cost constraints. There is a need for new architectures to be in pace with the fast innovations in video and imaging. It contains dedicated hardware implementation of the pixel and frame rate processes on Field Programmable Gate Array (FPGA) to achieve the real-time performance. ^ The following outlines the contributions of the dissertation. (1) We develop a target detection system by applying a novel running average mean threshold (RAMT) approach to globalize the threshold required for background subtraction. This approach adapts the threshold automatically to different environments (indoor and outdoor) and different targets (humans and vehicles). For low power consumption and better performance, we design the complete system on FPGA. (2) We introduce a safe distance factor and develop an algorithm for occlusion occurrence detection during target tracking. A novel mean-threshold is calculated by motion-position analysis. (3) A new strategy for gesture recognition is developed using Combinational Neural Networks (CNN) based on a tree structure. Analysis of the method is done on American Sign Language (ASL) gestures. We introduce novel point of interests approach to reduce the feature vector size and gradient threshold approach for accurate classification. (4) We design a gesture recognition system using a hardware/ software co-simulation neural network for high speed and low memory storage requirements provided by the FPGA. We develop an innovative maximum distant algorithm which uses only 0.39% of the image as the feature vector to train and test the system design. Database set gestures involved in different applications may vary. Therefore, it is highly essential to keep the feature vector as low as possible while maintaining the same accuracy and performance^

The Development of an Optimized System of Narcotic and Explosive Contraband Mimics for Calibration and Training of Biological Detectors

Current commercially available mimics contain varying amounts of either the actual explosive/drug or the chemical compound of suspected interest by biological detectors. As a result, there is significant interest in determining the dominant chemical odor signatures of the mimics, often referred to as pseudos, particularly when compared to the genuine contraband material. This dissertation discusses results obtained from the analysis of drug and explosive headspace related to the odor profiles as recognized by trained detection canines. Analysis was performed through the use of headspace solid phase microextraction in conjunction with gas chromatography mass spectrometry (HS-SPME-GC-MS). Upon determination of specific odors, field trials were held using a combination of the target odors with COMPS. Piperonal was shown to be a dominant odor compound in the headspace of some ecstasy samples and a recognizable odor mimic by trained detection canines. It was also shown that detection canines could be imprinted on piperonal COMPS and correctly identify ecstasy samples at a threshold level of approximately 100ng/s. Isosafrole and/or MDP-2-POH show potential as training aid mimics for non-piperonal based MDMA. Acetic acid was shown to be dominant in the headspace of heroin samples and verified as a dominant odor in commercial vinegar samples; however, no common, secondary compound was detected in the headspace of either. Because of the similarities detected within respective explosive classes, several compounds were chosen for explosive mimics. A single based smokeless powder with a detectable level of 2,4-dinitrotoluene, a double based smokeless powder with a detectable level of nitroglycerine, 2-ethyl-1-hexanol, DMNB, ethyl centralite and diphenylamine were shown to be accurate mimics for TNT-based explosives, NG-based explosives, plastic explosives, tagged explosives, and smokeless powders, respectively. The combination of these six odors represents a comprehensive explosive odor kit with positive results for imprint on detection canines. As a proof of concept, the chemical compound PFTBA showed promise as a possible universal, non-target odor compound for comparison and calibration of detection canines and instrumentation. In a comparison study of shape versus vibration odor theory, the detection of d-methyl benzoate and methyl benzoate was explored using canine detectors. While results did not overwhelmingly substantiate either theory, shape odor theory provides a better explanation of the canine and human subject responses.

Effects of ocean acidification on the swimming ability, development and biochemical responses of sand smelt larvae

Ocean acidification, recognized as a major threat to marine ecosystems, has developed into one of the fastest growing fields of research in marine sciences. Several studies on fish larval stages point to abnormal behaviours, malformations and increased mortality rates as a result of exposure to increased levels of CO2. However, other studies fail to recognize any consequence, suggesting species-specific sensitivity to increased levels of CO2, highlighting the need of further research. In this study we investigated the effects of exposure to elevated pCO2 on behaviour, development, oxidative stress and energy metabolism of sand smelt larvae, Atherina presbyter. Larvae were caught at Arrábida Marine Park (Portugal) and exposed to different pCO2 levels (control: 600 µatm, pH = 8.03; medium: 1000 µatm, pH = 7.85; high: 1800 µatm, pH = 7.64) up to 15 days, after which critical swimming speed (Ucrit), morphometric traits and biochemical biomarkers were determined. Measured biomarkers were related with: 1) oxidative stress-superoxide dismutase and catalase enzyme activities, levels of lipid peroxidation and DNA damage, and levels of superoxide anion production; 2) energy metabolism - total carbohydrate levels, electron transport system activity, lactate dehydrogenase and isocitrate dehydrogenase enzyme activities. Swimming speed was not affected by treatment, but exposure to increasing levels of pCO2 leads to higher energetic costs and morphometric changes, with larger larvae in high pCO2 treatment and smaller larvae in medium pCO2 treatment. The efficient antioxidant response capacity and increase in energetic metabolism only registered at the medium pCO2 treatment may indicate that at higher pCO2 levels the capacity of larvae to restore their internal balance can be impaired. Our findings illustrate the need of using multiple approaches to explore the consequences of future pCO2 levels on organisms.

Catalysing the Irish Energy Transition: Capacities and Challenges

The transition to a “low carbon, climate resilient and environmentally sustainable economy by the end of the 
year 2050” has been conceptualised as the “national transition objective” in the Irish Climate Action and Low Carbon Development Bill, passed in late 2015. This has raised a myriad of questions over how this can be operationalised and resourced and whether it can maintain political momentum. This paper assesses the utility of framings informed by the transitions (MLP) and technological innovation systems perspectives in contributing to transformative societal processes, by examining their application in an Irish case study on policy and technology. Through a qualitative exploration of the broader societal and policy context of the energy sector and a more detailed examination of the innovation systems of selected niche technologies (bioenergy and electric vehicles), the Irish case study sought to identify potential catalysts for a sustainability transition in the energy sector in Ireland: where these exist, how these are being built or enabled, and barriers to change. Following a discussion on the theoretical approaches used, a description will be given of how these were applied in the conducting of the research on transition in Ireland case study and the key findings which emerged. A critical reflection will then be made on the utility of these perspectives (as applied) to contribute to broader processes of societal transformation in Ireland.

Improved Real-time State-of-Charge Estimation of LiFePO4 Battery Based on a Novel Thermoelectric Model

Li-ion batteries have been widely used in electric vehicles, and battery internal state estimation plays an important role in the battery management system. However, it is technically challenging, in particular, for the estimation of the battery internal temperature and state-ofcharge (SOC), which are two key state variables affecting the battery performance. In this paper, a novel method is proposed for realtime simultaneous estimation of these two internal states, thus leading to a significantly improved battery model for realtime SOC estimation. To achieve this, a simplified battery thermoelectric model is firstly built, which couples a thermal submodel and an electrical submodel. The interactions between the battery thermal and electrical behaviours are captured, thus offering a comprehensive description of the battery thermal and electrical behaviour. To achieve more accurate internal state estimations, the model is trained by the simulation error minimization method, and model parameters are optimized by a hybrid optimization method combining a meta-heuristic algorithm and the least square approach. Further, timevarying model parameters under different heat dissipation conditions are considered, and a joint extended Kalman filter is used to simultaneously estimate both the battery internal states and time-varying model parameters in realtime. Experimental results based on the testing data of LiFePO4 batteries confirm the efficacy of the proposed method.

Analysis of Automotive Cybersecurity - Attack surfaces and users’ privacy concerns

Modern automobiles are no longer just mechanical tools. The electronics and computing services they are shipping with are making them not less than a computer. They are massive kinetic devices with sophisticated computing power. Most of the modern vehicles are made with the added connectivity in mind which may be vulnerable to outside attack. Researchers have shown that it is possible to infiltrate into a vehicle’s internal system remotely and control the physical entities such as steering and brakes. It is quite possible to experience such attacks on a moving vehicle and unable to use the controls. These massive connected computers can be life threatening as they are related to everyday lifestyle. First part of this research studied the attack surfaces in the automotive cybersecurity domain. It also illustrated the attack methods and capabilities of the damages. Online survey has been deployed as data collection tool to learn about the consumers’ usage of such vulnerable automotive services. The second part of the research portrayed the consumers’ privacy in automotive world. It has been found that almost hundred percent of modern vehicles has the capabilities to send vehicle diagnostic data as well as user generated data to their manufacturers, and almost thirty five percent automotive companies are collecting them already. Internet privacy has been studies before in many related domain but no privacy scale were matched for automotive consumers. It created the research gap and motivation for this thesis. A study has been performed to use well established consumers privacy scale – IUIPC to match with the automotive consumers’ privacy situation. Hypotheses were developed based on the IUIPC model for internet consumers’ privacy and they were studied by the finding from the data collection methods. Based on the key findings of the research, all the hypotheses were accepted and hence it is found that automotive consumers’ privacy did follow the IUIPC model under certain conditions. It is also found that a majority of automotive consumers use the services and devices that are vulnerable and prone to cyber-attacks. It is also established that there is a market for automotive cybersecurity services and consumers are willing to pay certain fees to avail that.

Functional studies of lignin biosynthesis genes and putative flowering gene in Miscanthus x giganteus and studies on indolyl glucosinolate biosynthesis and translocation in Brassica oleracea

The first topic area of this thesis involved studies on the accumulation and translocation of glucosinolates (GSs), bioactive secondary plant compounds, in broccoli plants. Changes in GS accumulation and gene expression levels in response to exogeneous methyl jasmonate (MeJA) treatment were analyzed in different tissue types at different developmental stages of broccoli. Greater accumulation of GSs with MeJA treatment was observed in apical leaves of broccoli seedlings and florets of plants at harvest maturity. Increases in indolyl GS in apical leaves of seedlings and florets were coupled with the up-regulation of indolyl GS biosynthesis genes. The accumulation of indolyl GSs appears to be modulated by MeJA treatment in an organ-specific manner for optimal distribution of defense substances in the plant. Metabolic profiling of hydrophilic metabolites using GC-MS demonstrated increased accumulation of various phenolics, ascorbates and amino acids in broccoli tissues after MeJA treatment. Distinct changes in carbohydrate levels observed between different tissues (vegetative leaves and floret tissues) of broccoli plants after treatment suggest that carbon metabolism is differentially modulated by MeJA treatment in different tissue types depending on sink-source relationships. Reduced levels of hexose sugars and tricarboxylic acid intermediates after MeJA treatment may reflect the increased requirement for carbon and energy needed to drive secondary product biosynthesis to accumulate metabolites for defense against insects and other herbivores. Substantial increases of indolyl and aromatic GSs after exogenous treatment with MeJA in stem and petioles of seedlings and the existence of intact indolyl-GS forms in phloem exudates suggest enhanced de novo synthesis in combination with active transport. Indoly GSs share structural similarities with the auxin, IAA, and may interact with components of the auxin transport system for intra- and extra-cellular transport or translocation. Application of the auxin efflux inhibitor, 1-naphthylphthalamic acid (NPA) reduced MeJA-mediated accumulation of indolyl GSs in broccoli florets and seedling tissues. NPA did not inhibit expression of indolyl GS biosynthesis genes shown to be upregulated by MeJA treatment or the accumulation of tryptophan, the amino acid precursor of indolyl GSs. Exogenous application of benzyl GS to Arabidopsis roots induced ectopic expression of the PIN1 protein associated with the auxin transport system similar to treatment with NPA, again suggesting GS interaction with the auxin efflux carrier system. The inhibitory effect of NPA on MeJA-mediated accumulation of GS may be due to competitive binding of NPA to auxin efflux carrier components and that GS transport is mediated by the auxin transport system. The inhibitory effect of NPA on indolyl and aromatic GS accumulation and the bioactivity of exogenous treatment of these GS compounds in PIN1 localization, Arabidopsis root growth, and gravitrophic response suggest that indolyl and aromatic GSs may be antagonistic to IAA transport and biosynthesis. Indolyl and aromatic GSs can also be potentially converted into IAA by hydrolysis. This intrinsic feature of GSs may be the part of a sophisticated regulatory process where the metabolic pathways in the plant shift from active growth to a reversible defense posture in response to biotic or abiotic stress. It seems likely that indolyl and aromatic GSs are important compounds that provide connections between jasmonate and auxin signaling. Further studies are required to reveal the regulatory mechanism for crosstalk between the two hormones. The third part of this research was to investigate effect of selenium fertilization and MeJA treatment on accumulation of GSs in broccoli florets. Increasing dietary intake of the element selenium (Se) has been shown to reduce the risk of cancer. Simultaneous enhancement of both Se and GS concentrations in broccoli floret tissue were conducted through the combined treatment of MeJA with Se fertilization. A low level of Se fertilization (concentration) with MeJA treatment displayed no significant changes in total aliphatic GS concentrations with 90% and 50% increases in indolyl and total GSs concentrations, respectively. This result suggests that Se- and GS-enriched broccoli with improved health-promoting properties can be generated by this combined treatment. The second topic of this thesis was conducted to provide basic information required to improve biomass quality and productivity and develop tools for gene transformation in Miscanthus x giganteus. The perennial rhizomatous grass, Miscanthus x giganteus is an ideal biomass crop due to its rapid vegetative growth and high biomass yield potential. As a naturally occurring sterile hybrid, M. x giganteus must be propagated vegetatively by mechanicalling divided rhizomes or from micropropagated plantlets. The effect of callus type, age and culture methods on regeneration competence was studied to improve regeneration efficiency and shorten the period of tissue culture in M. x giganteus propagation. Seven lignin biosynthesis genes and one putative flowering gene were isolated from M. x giganteus by PCR reactions using maize othologous sequences. Southern hybridization and nuclear DNA content analysis indicated that the genes isolated from M. x giganteus exist in the genome of other Miscanthus species as multiple copies. Analysis of lignin content and histological staining of lignin deposition indicated that higher lignin content is found in mature stem node tissues compared to young leaves and apical stem nodal tissues. Cell wall lignification is associated with increasing tissue maturity in Miscanthus species. RNAi and antisense constructs harboring sequences of these genes were developed to generate Miscanthus transgenic plants with suppressed of lignin biosynthesis and delayed flowering.

Dendritic Cells for Real-Time Anomaly Detection

Dendritic Cells (DCs) are innate immune system cells which have the power to activate or suppress the immune system. The behaviour of human DCs is abstracted to form an algorithm suitable for anomaly detection. We test this algorithm on the real-time problem of port scan detection. Our results show a significant difference in artificial DC behaviour for an outgoing portscan when compared to behaviour for normal processes.

Comunidades energéticas sustentáveis: estudo de Implementação de uma comunidade eólica no Algarve

Tese de Doutoramento, Gestão da Inovação e do Território, Faculdade de Economia, Universidade do Algarve, 2016

Railgun

Com a presente evolução das railguns na Marinha dos Estados Unidos da América e possível instalação em seus navios num futuro muito próximo, outras marinhas se seguirão. Creio que será do interesse da Marinha Portuguesa acompanhar esta evolução tecnológica, considerando as vantagens que advém da adoção deste tipo de armamento. Neste documento são abordados os princípios básicos subjacentes ao funcionamento da railgun, com principal foco nas questões eletrodinâmicas. Pretende-se adquirir familiaridade com este novo tipo de armamento através do estudo crítico dos seus princípios de funcionamento. O princípio básico de funcionamento de uma railgun, à primeira vista, parece bastante simples, à luz da aplicação imediata da expressão da força de Lorentz sobre um condutor percorrido por corrente elétrica. No entanto, tudo se torna mais complicado no caso de uma variação rápida dos parâmetros envolvidos (regime transitório), que exige uma análise mais aprofundada do comportamento da corrente, campos elétrico e magnético, e todos os materiais envolvidos neste sistema. Este trabalho envolveu ainda a construção de duas railguns, uma primeira de dimensões mais pequenas para ganhar familiaridade com o sistema, e uma última de dimensões de laboratório na qual foram feitos vários disparos para testar diferentes tipos de material e dimensões de projétil. Em suma, é demonstrado neste documento uma análise, no domínio do tempo, da distribuição espacial do campo eletromagnético, corrente elétrica e consequente fluxo de energia, complementados por uma parte experimental.