A data structure for improved gp analysis via efficient computation and visualisation of population measures

Population measures for genetic programs are defined and analysed in an attempt to better understand the behaviour of genetic programming. Some measures are simple, but do not provide sufficient insight. The more meaningful ones are complex and take extra computation time. Here we present a unified view on the computation of population measures through an information hypertree (iTree). The iTree allows for a unified and efficient calculation of population measures via a basic tree traversal. © Springer-Verlag 2004.

An investigation of thin amorphous carbon-based sputtered coatings for MEMS and micro-engineering applications

The work presented in this thesis describes an investigation into the production and properties of thin amorphous C films, with and without Cr doping, as a low wear / friction coating applicable to MEMS and other micro- and nano-engineering applications. Firstly, an assessment was made of the available testing techniques. Secondly, the optimised test methods were applied to a series of sputtered films of thickness 10 - 2000 nm in order to: (i) investigate the effect of thickness on the properties of coatingslcoating process (ii) investigate fundamental tribology at the nano-scale and (iii) provide a starting point for nanotribological coating optimisation at ultra low thickness. The use of XPS was investigated for the determination of Sp3/Sp2 carbon bonding. Under C 1s peak analysis, significant errors were identified and this was attributed to the absence of sufficient instrument resolution to guide the component peak structure (even with a high resolution instrument). A simple peak width analysis and correlation work with C KLL D value confirmed the errors. The use of XPS for Sp3/Sp2 was therefore limited to initial tentative estimations. Nanoindentation was shown to provide consistent hardness and reduced modulus results with depth (to < 7nm) when replicate data was suitably statistically processed. No significant pile-up or cracking of the films was identified under nanoindentation. Nanowear experimentation by multiple nanoscratching provided some useful information, however the conditions of test were very different to those expect for MEMS and micro- / nano-engineering systems. A novel 'sample oscillated nanoindentation' system was developed for testing nanowear under more relevant conditions. The films were produced in an industrial production coating line. In order to maximise the available information and to take account of uncontrolled process variation a statistical design of experiment procedure was used to investigate the effect of four key process control parameters. Cr doping was the most significant control parameter at all thicknesses tested and produced a softening effect and thus increased nanowear. Substrate bias voltage was also a significant parameter and produced hardening and a wear reducing effect at all thicknesses tested. The use of a Cr adhesion layer produced beneficial results at 150 nm thickness, but was ineffective at 50 nm. Argon flow to the coating chamber produced a complex effect. All effects reduced significantly with reducing film thickness. Classic fretting wear was produced at low amplitude under nanowear testing. Reciprocating sliding was produced at higher amplitude which generated three body abrasive wear and this was generally consistent with the Archard model. Specific wear rates were very low (typically 10-16 - 10-18 m3N-1m-1). Wear rates reduced exponentially with reduced film thickness and below (approx.) 20 nm, thickness was identified as the most important control of wear.

Advances in characterisation, calibration and data processing speed of optical coherence tomography systems

This thesis describes advances in the characterisation, calibration and data processing of optical coherence tomography (OCT) systems. Femtosecond (fs) laser inscription was used for producing OCT-phantoms. Transparent materials are generally inert to infra-red radiations, but with fs lasers material modification occurs via non-linear processes when the highly focused light source interacts with the materials. This modification is confined to the focal volume and is highly reproducible. In order to select the best inscription parameters, combination of different inscription parameters were tested, using three fs laser systems, with different operating properties, on a variety of materials. This facilitated the understanding of the key characteristics of the produced structures with the aim of producing viable OCT-phantoms. Finally, OCT-phantoms were successfully designed and fabricated in fused silica. The use of these phantoms to characterise many properties (resolution, distortion, sensitivity decay, scan linearity) of an OCT system was demonstrated. Quantitative methods were developed to support the characterisation of an OCT system collecting images from phantoms and also to improve the quality of the OCT images. Characterisation methods include the measurement of the spatially variant resolution (point spread function (PSF) and modulation transfer function (MTF)), sensitivity and distortion. Processing of OCT data is a computer intensive process. Standard central processing unit (CPU) based processing might take several minutes to a few hours to process acquired data, thus data processing is a significant bottleneck. An alternative choice is to use expensive hardware-based processing such as field programmable gate arrays (FPGAs). However, recently graphics processing unit (GPU) based data processing methods have been developed to minimize this data processing and rendering time. These processing techniques include standard-processing methods which includes a set of algorithms to process the raw data (interference) obtained by the detector and generate A-scans. The work presented here describes accelerated data processing and post processing techniques for OCT systems. The GPU based processing developed, during the PhD, was later implemented into a custom built Fourier domain optical coherence tomography (FD-OCT) system. This system currently processes and renders data in real time. Processing throughput of this system is currently limited by the camera capture rate. OCTphantoms have been heavily used for the qualitative characterization and adjustment/ fine tuning of the operating conditions of OCT system. Currently, investigations are under way to characterize OCT systems using our phantoms. The work presented in this thesis demonstrate several novel techniques of fabricating OCT-phantoms and accelerating OCT data processing using GPUs. In the process of developing phantoms and quantitative methods, a thorough understanding and practical knowledge of OCT and fs laser processing systems was developed. This understanding leads to several novel pieces of research that are not only relevant to OCT but have broader importance. For example, extensive understanding of the properties of fs inscribed structures will be useful in other photonic application such as making of phase mask, wave guides and microfluidic channels. Acceleration of data processing with GPUs is also useful in other fields.

Novel ageing-biomarker discovery using data-intensive technologies

Ageing is accompanied by many visible characteristics. Other biological and physiological markers are also well-described e.g. loss of circulating sex hormones and increased inflammatory cytokines. Biomarkers for healthy ageing studies are presently predicated on existing knowledge of ageing traits. The increasing availability of data-intensive methods enables deep-analysis of biological samples for novel biomarkers. We have adopted two discrete approaches in MARK-AGE Work Package 7 for biomarker discovery; (1) microarray analyses and/or proteomics in cell systems e.g. endothelial progenitor cells or T cell ageing including a stress model; and (2) investigation of cellular material and plasma directly from tightly-defined proband subsets of different ages using proteomic, transcriptomic and miR array. The first approach provided longitudinal insight into endothelial progenitor and T cell ageing.This review describes the strategy and use of hypothesis-free, data-intensive approaches to explore cellular proteins, miR, mRNA and plasma proteins as healthy ageing biomarkers, using ageing models and directly within samples from adults of different ages. It considers the challenges associated with integrating multiple models and pilot studies as rational biomarkers for a large cohort study. From this approach, a number of high-throughput methods were developed to evaluate novel, putative biomarkers of ageing in the MARK-AGE cohort.

Quantifying the pathology of neurodegenerative disorders:Quantitative measurements, sampling strategies and data analysis

The use of quantitative methods has become increasingly important in the study of neurodegenerative disease. Disorders such as Alzheimer's disease (AD) are characterized by the formation of discrete, microscopic, pathological lesions which play an important role in pathological diagnosis. This article reviews the advantages and limitations of the different methods of quantifying the abundance of pathological lesions in histological sections, including estimates of density, frequency, coverage, and the use of semiquantitative scores. The major sampling methods by which these quantitative measures can be obtained from histological sections, including plot or quadrat sampling, transect sampling, and point-quarter sampling, are also described. In addition, the data analysis methods commonly used to analyse quantitative data in neuropathology, including analyses of variance (ANOVA) and principal components analysis (PCA), are discussed. These methods are illustrated with reference to particular problems in the pathological diagnosis of AD and dementia with Lewy bodies (DLB).

Simultaneous clock recovery and data regeneration using a nonlinear optical loop mirror as an all-optical mixer

High-speed optical clock recovery, demultiplexing and data regeneration will be integral parts of any future photonic network based on high bit-rate OTDM. Much research has been conducted on devices that perform these functions, however to date each process has been demonstrated independently. A very promising method of all-optical switching is that of a semiconductor optical amplifier-based nonlinear optical loop mirror (SOA-NOLM). This has various advantages compared with the standard fiber NOLM, most notably low switching power, compact size and stability. We use the SOA-NOLM as an all-optical mixer in a classical phase-locked loop arrangement to achieve optical clock recovery, while at the same time achieving data regeneration in a single compact device

A new method for microwave generation and data transmission using DFB laser based on fiber Bragg gratings

A novel architecture for microwave/millimeter-wave signal generation and data modulation using a fiber-grating-based distributed feedback laser has been proposed in this letter. For demonstration, a 155.52-Mb/s data stream on a 16.9-GHz subcarrier has been transmitted and recovered successfully. It has been proved that this technology would be of benefit to future microwave data transmission systems.

Recent advances in fibre grating devices and their sensing applications

Over the last twenty years, we have been continuously seeing R&D efforts and activities in developing optical fibre grating devices and technologies and exploring their applications for telecommunications, optical signal processing and smart sensing, and recently for medical care and biophotonics. In addition, we have also witnessed successful commercialisation of these R&Ds, especially in the area of fibre Bragg grating (FBG) based distributed sensor network systems and technologies for engineering structure monitoring in industrial sectors such as oil, energy and civil engineering. Despite countless published reports and papers and commercial realisation, we are still seeing significant and novel research activities in this area. This invited paper will give an overview on recent advances in fibre grating devices and their sensing applications with a focus on novel fibre gratings and their functions and grating structures in speciality fibres. The most recent developments in (i) femtosecond inscription for microfluidic/grating devices, (2) tilted grating based novel polarisation devices and (3) dual-peak long-period grating based DNA hybridisation sensors will be discussed.

Quasi-lossless optical links for broad-band transmission and data processing

We present the first experimental implementation of a recently designed quasi-lossless fiber span with strongly reduced signal power excursion. The resulting fiber waveguide medium can be advantageously used both in lightwave communications and in all-optical nonlinear data processing.

Quasi-lossless spans for broadband transmission and data processing

We present the first experimental implementation of a recently designed quasi-lossless fibre span with strongly reduced signal power excursion. The resulting fibre waveguide medium can be advantageously used both in lightwave communications and in all-optical nonlinear data processing.

Spatial contrast sensitivity and external noise: applications to optical and neural modulation transfer functions

The thesis will show how to equalise the effect of quantal noise across spatial frequencies by keeping the retinal flux (If-2) constant. In addition, quantal noise is used to study the effect of grating area and spatial frequency on contrast sensitivity resulting in the extension of the new contrast detection model describing the human contrast detection system as a simple image processor. According to the model the human contrast detection system comprises low-pass filtering due to ocular optics, addition of light dependent noise at the event of quantal absorption, high-pass filtering due to the neural visual pathways, addition of internal neural noise, after which detection takes place by a local matched filter, whose sampling efficiency decreases as grating area is increased. Furthermore, this work will demonstrate how to extract both the optical and neural modulation transfer functions of the human eye. The neural transfer function is found to be proportional to spatial frequency up to the local cut-off frequency at eccentricities of 0 - 37 deg across the visual field. The optical transfer function of the human eye is proposed to be more affected by the Stiles-Crawford -effect than generally assumed in the literature. Similarly, this work questions the prevailing ideas about the factors limiting peripheral vision by showing that peripheral optical acts as a low-pass filter in normal viewing conditions, and therefore the effect of peripheral optics is worse than generally assumed.

A new method for microwave generation and data transmission using DFB laser based on fiber bragg gratings

A novel architecture for microwave/millimeter-wave signal generation and data modulation using a fiber-grating-based distributed feedback laser has been proposed in this letter. For demonstration, a 155.52-Mb/s data stream on a 16.9-GHz subcarrier has been transmitted and recovered successfully. It has been proved that this technology would be of benefit to future microwave data transmission systems. © 2006 IEEE.

Theory and data for area summation of contrast with and without uncertainty:evidence for a noisy energy model

Contrast sensitivity improves with the area of a sine-wave grating, but why? Here we assess this phenomenon against contemporary models involving spatial summation, probability summation, uncertainty, and stochastic noise. Using a two-interval forced-choice procedure we measured contrast sensitivity for circular patches of sine-wave gratings with various diameters that were blocked or interleaved across trials to produce low and high extrinsic uncertainty, respectively. Summation curves were steep initially, becoming shallower thereafter. For the smaller stimuli, sensitivity was slightly worse for the interleaved design than for the blocked design. Neither area nor blocking affected the slope of the psychometric function. We derived model predictions for noisy mechanisms and extrinsic uncertainty that was either low or high. The contrast transducer was either linear (c1.0) or nonlinear (c2.0), and pooling was either linear or a MAX operation. There was either no intrinsic uncertainty, or it was fixed or proportional to stimulus size. Of these 10 canonical models, only the nonlinear transducer with linear pooling (the noisy energy model) described the main forms of the data for both experimental designs. We also show how a cross-correlator can be modified to fit our results and provide a contemporary presentation of the relation between summation and the slope of the psychometric function.