Retrotransposon expression profiling: Unveiling the hidden SINE transcriptome through Next-Generation Sequencing data analysis

Of the ~1.7 million SINE elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which SINE transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq datasets and unique SINE DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual SINE elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ~1300 Alu loci and ~1100 MIR loci corresponding to detectable transcripts, with ~120 and ~60 respectively Alu and MIR loci expressed in at least three cell lines. In vitro transcription of selected SINEs did not reflect their in vivo expression properties, and required the native 5’-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for SINEs nested within Pol II-transcribed genes raising the possibility of an underlying mechanism for Pol II gene regulation by SINE transcriptional units. Moreover the application of our bioinformatic pipeline to both RNA-seq data of cells subjected to an in vitro pro-oncogenic stimulus and of in vivo matched tumor and non-tumor samples allowed us to detect increased Alu RNA expression as well as the source loci of such deregulation. The ability to investigate SINE transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant SINE RNAs and the assessment of SINE expression alteration under pathological conditions.

Advanced receivers for next generation wireless communication systems

Despite extensive progress on the theoretical aspects of spectral efficient communication systems, hardware impairments, such as phase noise, are the key bottlenecks in next generation wireless communication systems. The presence of non-ideal oscillators at the transceiver introduces time varying phase noise and degrades the performance of the communication system. Significant research literature focuses on joint synchronization and decoding based on joint posterior distribution, which incorporate both the channel and code graph. These joint synchronization and decoding approaches operate on well designed sum-product algorithms, which involves calculating probabilistic messages iteratively passed between the channel statistical information and decoding information. Channel statistical information, generally entails a high computational complexity because its probabilistic model may involve continuous random variables. The detailed knowledge about the channel statistics for these algorithms make them an inadequate choice for real world applications due to power and computational limitations. In this thesis, novel phase estimation strategies are proposed, in which soft decision-directed iterative receivers for a separate A Posteriori Probability (APP)-based synchronization and decoding are proposed. These algorithms do not require any a priori statistical characterization of the phase noise process. The proposed approach relies on a Maximum A Posteriori (MAP)-based algorithm to perform phase noise estimation and does not depend on the considered modulation/coding scheme as it only exploits the APPs of the transmitted symbols. Different variants of APP-based phase estimation are considered. The proposed algorithm has significantly lower computational complexity with respect to joint synchronization/decoding approaches at the cost of slight performance degradation. With the aim to improve the robustness of the iterative receiver, we derive a new system model for an oversampled (more than one sample per symbol interval) phase noise channel. We extend the separate APP-based synchronization and decoding algorithm to a multi-sample receiver, which exploits the received information from the channel by exchanging the information in an iterative fashion to achieve robust convergence. Two algorithms based on sliding block-wise processing with soft ISI cancellation and detection are proposed, based on the use of reliable information from the channel decoder. Dually polarized systems provide a cost-and spatial-effective solution to increase spectral efficiency and are competitive candidates for next generation wireless communication systems. A novel soft decision-directed iterative receiver, for separate APP-based synchronization and decoding, is proposed. This algorithm relies on an Minimum Mean Square Error (MMSE)-based cancellation of the cross polarization interference (XPI) followed by phase estimation on the polarization of interest. This iterative receiver structure is motivated from Master/Slave Phase Estimation (M/S-PE), where M-PE corresponds to the polarization of interest. The operational principle of a M/S-PE block is to improve the phase tracking performance of both polarization branches: more precisely, the M-PE block tracks the co-polar phase and the S-PE block reduces the residual phase error on the cross-polar branch. Two variants of MMSE-based phase estimation are considered; BW and PLP.

Vibrational methods applied to NDT testing and fluid density measurement

A system for the NDI' testing of the integrity of conposite materials and of adhesive bonds has been developed to meet industrial requirements. The vibration techniques used were found to be applicable to the development of fluid measuring transducers. The vibrational spectra of thin rectangular bars were used for the NDT work. A machined cut in a bar had a significant effect on the spectrum but a genuine crack gave an unambiguous response at high amplitudes. This was the generation of fretting crack noise at frequencies far above that of the drive. A specially designed vibrational decrement meter which, in effect, measures mechanical energy loss enabled a numerical classification of material adhesion to be obtained. This was used to study bars which had been flame or plasma sprayed with a variety of materials. It has become a useful tool in optimising coating methods. A direct industrial application was to classify piston rings of high performance I.C. engines. Each consists of a cast iron ring with a channel into which molybdenum, a good bearing surface, is sprayed. The NDT classification agreed quite well with the destructive test normally used. The techniques and equipment used for the NOT work were applied to the development of the tuning fork transducers investigated by Hassan into commercial density and viscosity devices. Using narrowly spaced, large area tines a thin lamina of fluid is trapped between them. It stores a large fraction of the vibrational energy which, acting as an inertia load reduces the frequency. Magnetostrictive and piezoelectric effects together or in combination enable the fork to be operated through a flange. This allows it to be used in pipeline or 'dipstick' applications. Using a different tine geometry the viscosity loading can be predoninant. This as well as the signal decrement of the density transducer makes a practical viscometer.

High efficiency supercontinuum generation using ultra-long Raman fiber cavities

Supercontinuum generation in a multi-fiber ultra-long Raman fiber laser cavity is experimentally investigated for the first time. We demonstrate significantly enhanced spectral flatness and supercontinuum generation efficiency using only conventional single mode silica fiber. With a pump power of only 1.63W a ~15dB bandwidth >260 nm wide (from 1440 to >1700nm) supercontinuum source is reported with a flatness of <1dB over 180nm using an optimised hybrid TW/HNLF cavity. We address the dependence of the supercontinuum spectrum on the input pump power and ultra-long Raman cavity.

Testing incremental politics : the case of North Sea oil

In the quest to secure the much vaunted benefits of North Sea oil, highly non-incremental technologies have been adopted. Nowhere is this more the case than with the early fields of the central and northern North Sea. By focusing on the inflexible nature of North Sea hardware, in such fields, this thesis examines the problems that this sort of technology might pose for policy making. More particularly, the following issues are raised. First, the implications of non-incremental technical change for the successful conduct of oil policy is raised. Here, the focus is on the micro-economic performance of the first generation of North Sea oil fields and the manner in which this relates to government policy. Secondly, the question is posed as to whether there were more flexible, perhaps more incremental policy alternatives open to the decision makers. Conclusions drawn relate to the degree to which non-incremental shifts in policy permit decision makers to achieve their objectives at relatively low cost. To discover cases where non-incremental policy making has led to success in this way, would be to falsify the thesis that decision makers are best served by employing incremental politics as an approach to complex problem solving.

The development of a testing procedure for dry friction brakes

A description of the background to testing friction materials for automotive brakes explains the need for a rapid, inexpensive means of assessing their behaviour in a way which is both accurate and meaningful. Various methods of controlling inertia dynamometers to simulate road vehicles are rejected in favour of programming by means of a commercially available XY plotter. Investigation of brake service conditions is used to set up test schedules, and a dynamometer programming unit built to enable service conditions on vehicles to be simulated on a full scale dynamometer. A technique is developed by which accelerated testing can be achieved without operating under overload conditions, saving time and cost without sacrificing validity. The development of programming by XY plotter is described, with a method of operating one XY plotter to programme the machine, monitor its own behaviour, and plot its own results in logical sequence. Commissioning trials are described and the generation of reproducible results in frictional behaviour and material durability is discussed. Teclmiques are developed to cross check the operation of the machine in retrospect, and retrospectively correct results in the event of malfunctions. Sensitivity errors in the measuring circuits are displayed between calibrations, whilst leaving the recorded results almost unaffected by error. Typical results of brake lining tests are used to demonstrate the range of performance parameters which can be studied by use of the machine. Successful test investigations completed on the machine are reported, including comments on behaviour of cast iron drums and discs. The machine shows that materials can repeat their complex friction/ temperature/speed/pressure relationships at a reproducibility of the order of +-0.003u and +~ 0.0002 in. thickness loss during wear tests. Discussion of practical and academic implications completes the report with recommendations for further work in both fields.

Mixed-frequency testing of induction machines using inverters

This work has concentrated on the testing of induction machines to determine their temperature rise at full-load without mechanically coupling to a load machine. The achievements of this work are outlined as follows. 1. Four distinct categories of mixed-frequency test using an inverter have been identified by the author. The simulation results of these tests as well as the conventional 2-supply test have been analysed in detail. 2. Experimental work on mixed-frequency tests has been done on a small (4 kW) squirrel cage induction machine using a voltage source PWM inverter. Two out of the four categories of test suggested have been tested and the temperature rise results were found to be similar to the results of a direct loading test. Further, one of the categories of test proposed has been performed on a 3.3 kW slip-ring induction machine for the conformation of the rotor values. 3. A low current supply mixed-frequency test-rig has been proposed. For this purpose, a resonant bank was connected to the DC link of the inverter in order to maintain the exchange of power between the test machine and the resonant bank instead of between the main supply and the test machine. The resonant bank was then replaced with a special electro-mechanical energy storage unit. The current of the main power supply was then reduced in amplitude. 4. A variable inertia test for full load temperature rise testing of induction machines has been introduced. This test is purely mechanical in nature and does not require any electrical connection of the test machine to any other machine. It has the advantage of drawing very little net power from the supply.

Generation of triangular pulses in normally dispersive fibre

In this scheme, nonlinearity and dispersion in the NDF lead to various reshaping processes of an initial, conventional pulse according to the chirping value and power level at the input of the fibre. In particular, we have observed that triangular-shaped pulses can be generated for sufficiently high energies and a positive initial chirp parameter. In our experiments, 2.8 ps-FWHM, transform-limited pulses generated from a mode-locked fibre laser source at a repetition rate of 1.25 GHz were pre-chirped by propagating the pulses through different lengths of standard mono-mode fibre. The chirped pulses were then amplified to different power levels before being launched into a 2.3 km section of True Wave fibre (TWF). The corresponding numerically calculated pulse temporal intensity profile and numerical and experimental second-harmonic generation frequency-resolved optical gating (SHG FROG) spectrograms were also derived. In conclusion, we have presented numerical modelling results which show the system design parameters required for the generation of triangular-shaped pulses in a nonlinear NDF, and experimentally demonstrated triangular pulse shaping in conventional NDF.

Computationsl modelling of dimethyl ether separation and steam reforming in fluidized bed reactors

This study presents a computational fluid dynamic (CFD) study of Dimethyl Ether (DME) gas adsorptive separation and steam reforming (DME-SR) in a large scale Circulating Fluidized Bed (CFB) reactor. The CFD model is based on Eulerian-Eulerian dispersed flow and solved using commercial software (ANSYS FLUENT). Hydrogen is currently receiving increasing interest as an alternative source of clean energy and has high potential applications, including the transportation sector and power generation. Computational fluid dynamic (CFD) modelling has attracted considerable recognition in the engineering sector consequently leading to using it as a tool for process design and optimisation in many industrial processes. In most cases, these processes are difficult or expensive to conduct in lab scale experiments. The CFD provides a cost effective methodology to gain detailed information up to the microscopic level. The main objectives in this project are to: (i) develop a predictive model using ANSYS FLUENT (CFD) commercial code to simulate the flow hydrodynamics, mass transfer, reactions and heat transfer in a large scale dual fluidized bed system for combined gas separation and steam reforming processes (ii) implement a suitable adsorption models in the CFD code, through a user defined function, to predict selective separation of a gas from a mixture (iii) develop a model for dimethyl ether steam reforming (DME-SR) to predict hydrogen production (iv) carry out detailed parametric analysis in order to establish ideal operating conditions for future industrial application. The project has originated from a real industrial case problem in collaboration with the industrial partner Dow Corning (UK) and jointly funded by the Engineering and Physical Research Council (UK) and Dow Corning. The research examined gas separation by adsorption in a bubbling bed, as part of a dual fluidized bed system. The adsorption process was simulated based on the kinetics derived from the experimental data produced as part of a separate PhD project completed under the same fund. The kinetic model was incorporated in FLUENT CFD tool as a pseudo-first order rate equation; some of the parameters for the pseudo-first order kinetics were obtained using MATLAB. The modelling of the DME adsorption in the designed bubbling bed was performed for the first time in this project and highlights the novelty in the investigations. The simulation results were analysed to provide understanding of the flow hydrodynamic, reactor design and optimum operating condition for efficient separation. Bubbling bed validation by estimation of bed expansion and the solid and gas distribution from simulation agreed well with trends seen in the literatures. Parametric analysis on the adsorption process demonstrated that increasing fluidizing velocity reduced adsorption of DME. This is as a result of reduction in the gas residence time which appears to have much effect compared to the solid residence time. The removal efficiency of DME from the bed was found to be more than 88%. Simulation of the DME-SR in FLUENT CFD was conducted using selected kinetics from literature and implemented in the model using an in-house developed user defined function. The validation of the kinetics was achieved by simulating a case to replicate an experimental study of a laboratory scale bubbling bed by Vicente et al [1]. Good agreement was achieved for the validation of the models, which was then applied in the DME-SR in the large scale riser section of the dual fluidized bed system. This is the first study to use the selected DME-SR kinetics in a circulating fluidized bed (CFB) system and for the geometry size proposed for the project. As a result, the simulation produced the first detailed data on the spatial variation and final gas product in such an industrial scale fluidized bed system. The simulation results provided insight in the flow hydrodynamic, reactor design and optimum operating condition. The solid and gas distribution in the CFB was observed to show good agreement with literatures. The parametric analysis showed that the increase in temperature and steam to DME molar ratio increased the production of hydrogen due to the increased DME conversions, whereas the increase in the space velocity has been found to have an adverse effect. Increasing temperature between 200 oC to 350 oC increased DME conversion from 47% to 99% while hydrogen yield increased substantially from 11% to 100%. The CO2 selectivity decreased from 100% to 91% due to the water gas shift reaction favouring CO at higher temperatures. The higher conversions observed as the temperature increased was reflected on the quantity of unreacted DME and methanol concentrations in the product gas, where both decreased to very low values of 0.27 mol% and 0.46 mol% respectively at 350 °C. Increasing the steam to DME molar ratio from 4 to 7.68 increased the DME conversion from 69% to 87%, while the hydrogen yield increased from 40% to 59%. The CO2 selectivity decreased from 100% to 97%. The decrease in the space velocity from 37104 ml/g/h to 15394 ml/g/h increased the DME conversion from 87% to 100% while increasing the hydrogen yield from 59% to 87%. The parametric analysis suggests an operating condition for maximum hydrogen yield is in the region of 300 oC temperatures and Steam/DME molar ratio of 5. The analysis of the industrial sponsor’s case for the given flow and composition of the gas to be treated suggests that 88% of DME can be adsorbed from the bubbling and consequently producing 224.4t/y of hydrogen in the riser section of the dual fluidized bed system. The process also produces 1458.4t/y of CO2 and 127.9t/y of CO as part of the product gas. The developed models and parametric analysis carried out in this study provided essential guideline for future design of DME-SR at industrial level and in particular this work has been of tremendous importance for the industrial collaborator in order to draw conclusions and plan for future potential implementation of the process at an industrial scale.

From rogue waves to random walks:nonlinear instabilities in supercontinuum generation

The noise properties of supercontinuum generation continue to be a subject of wide interest within both pure and applied physics. Aside from immediate applications in supercontinuum source development, detailed studies of supercontinuum noise mechanisms have attracted interdisciplinary attention because of links with extreme instabilities in other physical systems, especially the infamous and destructive oceanic rogue waves. But the instabilities inherent in supercontinuum generation can also be interpreted in terms of natural links with the general field of random processes, and this raises new possibilities for applications in areas such as random number generation. In this contribution we will describe recent work where we interpret supercontinuum intensity and phase fluctuations in this way.

Generation of orange light from a PPKTP waveguide end-pumped by a quantum-dot tuneable laser

Here we present a compact all-room-temperature frequency-doubling scheme generating orange light, using a PPKTP waveguide and a quantum-dot external cavity diode laser (QD-ECDL). The maximum output power for the second harmonic generated light (SHG) was 1.43 mW at 613 nm, achieved for 70 mW of launched pump power at 1226 nm. This represents an important step towards a compact and wall-plug-efficient coherent orange light source, operating at room temperature.

Generation of tunable visible picosecond pulses by frequency-doubling of a quantum-dot laser in a PPKTP waveguide

We demonstrate a compact all-room-temperature picosecond laser source broadly tunable in the visible spectral region between 600 nm and 627 nm. The tunable radiation is obtained by frequency-doubling of a tunable quantum-dot external-cavity mode-locked laser in a periodically-poled KTP multimode waveguide. In this case, utilization of a significant difference in the effective refractive indices of the high- and low-order modes enables to match the period of poling in a very broad wavelength range. The maximum achieved second harmonic output peak power is 3.25 mW at 613 nm for 71.43 mW of launched pump peak power at 1226 nm, resulting in conversion efficiency of 4.55%. © 2013 Copyright SPIE.

Experiments on the generation of activated carbon from biomass

Activated carbon is generated from various waste biomass sources like rice straw, wheat straw, wheat straw pellets, olive stones, pistachios shells, walnut shells, beech wood and hardcoal. After drying the biomass is pyrolysed in the temperature range of 500-600 °C at low heating rates of 10 K/min. The activation of the chars is performed as steam activation at temperatures between 800 °C and 900 °C. Both the pyrolysis and activation experiments were run in lab-scale facilities. It is shown that nut shells provide high active surfaces of 1000-1300 m/g whereas the active surface of straw matters does hardly exceed 800 m/g which might be a result of the high ash content of the straws and the slightly higher carbon content of the nut shells. The active surface is detected by BET method. Besides the testing of a many types of biomass for the suitability as base material in the activated carbon production process, the experiments allow for the determination of production parameters like heating rate and pyrolysis temperature, activation time and temperature as well as steam flux which are necessary for the scale up of the process chain. © 2006 Elsevier B.V. All rights reserved.

Efficient yellow-green light generation at 561 nm by frequency-doubling of a QD-FBG laser diode in a PPLN waveguide

A compact high-power yellow-green continuous wave (CW) laser source based on second-harmonic generation (SHG) in a 5% MgO doped periodically poled congruent lithium niobate (PPLN) waveguide crystal pumped by a quantum-dot fiber Bragg grating (QD-FBG) laser diode is demonstrated. A frequency-doubled power of 90.11 mW at the wavelength of 560.68 nm with a conversion efficiency of 52.4% is reported. To the best of our knowledge, this represents the highest output power and conversion efficiency achieved to date in this spectral region from a diode-pumped PPLN waveguide crystal, which could prove extremely valuable for the deployment of such a source in a wide range of biomedical applications.

574-647 nm wavelength tuning by second-harmonic generation from diode-pumped PPKTP waveguides

We present a compact, all-room-temperature continuous-wave laser source in the visible spectral region between 574 and 647 nm by frequency doubling of a broadly tunable InAs/GaAs quantum-dot external-cavity diode laser in a periodically poled potassium titanyl phosphate crystal containing three waveguides with different cross-sectional areas (4 × 4, 3 × 5, and 2 μm × 6 μm). The influence of a waveguide's design on tunability, output power, and mode distribution of second-harmonic generated light, as well as possibilities to increase the conversion efficiency via an optimization of a waveguide's cross-sectional area, was systematically investigated. A maximum output power of 12.04 mW with a conversion efficiency of 10.29% at 605.6 nm was demonstrated in the wider waveguide with the cross-sectional area of 4 μm × 4 μm.