Causality and synchronisation in complex systems with applications to neuroscience

This thesis presents an investigation, of synchronisation and causality, motivated by problems in computational neuroscience. The thesis addresses both theoretical and practical signal processing issues regarding the estimation of interdependence from a set of multivariate data generated by a complex underlying dynamical system. This topic is driven by a series of problems in neuroscience, which represents the principal background motive behind the material in this work. The underlying system is the human brain and the generative process of the data is based on modern electromagnetic neuroimaging methods . In this thesis, the underlying functional of the brain mechanisms are derived from the recent mathematical formalism of dynamical systems in complex networks. This is justified principally on the grounds of the complex hierarchical and multiscale nature of the brain and it offers new methods of analysis to model its emergent phenomena. A fundamental approach to study the neural activity is to investigate the connectivity pattern developed by the brain’s complex network. Three types of connectivity are important to study: 1) anatomical connectivity refering to the physical links forming the topology of the brain network; 2) effective connectivity concerning with the way the neural elements communicate with each other using the brain’s anatomical structure, through phenomena of synchronisation and information transfer; 3) functional connectivity, presenting an epistemic concept which alludes to the interdependence between data measured from the brain network. The main contribution of this thesis is to present, apply and discuss novel algorithms of functional connectivities, which are designed to extract different specific aspects of interaction between the underlying generators of the data. Firstly, a univariate statistic is developed to allow for indirect assessment of synchronisation in the local network from a single time series. This approach is useful in inferring the coupling as in a local cortical area as observed by a single measurement electrode. Secondly, different existing methods of phase synchronisation are considered from the perspective of experimental data analysis and inference of coupling from observed data. These methods are designed to address the estimation of medium to long range connectivity and their differences are particularly relevant in the context of volume conduction, that is known to produce spurious detections of connectivity. Finally, an asymmetric temporal metric is introduced in order to detect the direction of the coupling between different regions of the brain. The method developed in this thesis is based on a machine learning extensions of the well known concept of Granger causality. The thesis discussion is developed alongside examples of synthetic and experimental real data. The synthetic data are simulations of complex dynamical systems with the intention to mimic the behaviour of simple cortical neural assemblies. They are helpful to test the techniques developed in this thesis. The real datasets are provided to illustrate the problem of brain connectivity in the case of important neurological disorders such as Epilepsy and Parkinson’s disease. The methods of functional connectivity in this thesis are applied to intracranial EEG recordings in order to extract features, which characterize underlying spatiotemporal dynamics before during and after an epileptic seizure and predict seizure location and onset prior to conventional electrographic signs. The methodology is also applied to a MEG dataset containing healthy, Parkinson’s and dementia subjects with the scope of distinguishing patterns of pathological from physiological connectivity.

Nonlinear loop mirror-based all-optical signal processing in fiber-optic communications

All-optical data processing is expected to play a major role in future optical communications. The fiber nonlinear optical loop mirror (NOLM) is a valuable tool in optical signal processing applications. This paper presents an overview of our recent advances in developing NOLM-based all-optical processing techniques for application in fiber-optic communications. The use of in-line NOLMs as a general technique for all-optical passive 2R (reamplification, reshaping) regeneration of return-to-zero (RZ) on-off keyed signals in both high-speed, ultralong-distance transmission systems and terrestrial photonic networks is reviewed. In this context, a theoretical model enabling the description of the stable propagation of carrier pulses with periodic all-optical self-regeneration in fiber systems with in-line deployment of nonlinear optical devices is presented. A novel, simple pulse processing scheme using nonlinear broadening in normal dispersion fiber and loop mirror intensity filtering is described, and its employment is demonstrated as an optical decision element at a RZ receiver as well as an in-line device to realize a transmission technique of periodic all-optical RZ-nonreturn-to-zero-like format conversion. The important issue of phase-preserving regeneration of phase-encoded signals is also addressed by presenting a new design of NOLM based on distributed Raman amplification in the loop fiber. © 2008 Elsevier Inc. All rights reserved.

Signal processing techniques for ultrasonic inspection

This thesis discusses the need for nondestructive testing and highlights some of the limitations in present day techniques. Special interest has been given to ultrasonic examination techniques and the problems encountered when they are applied to thick welded plates. Some suggestions are given using signal processing methods. Chapter 2 treats the need for nondestructive testing as seen in the light of economy and safety. A short review of present day techniques in nondestructive testing is also given. The special problems using ultrasonic techniques for welded structures is discussed in Chapter 3 with some examples of elastic wave propagation in welded steel. The limitations in applying sophisticated signal processing techniques to ultrasonic NDT~ mainly found in the transducers generating or receiving the ultrasound. Chapter 4 deals with the different transducers used. One of the difficulties with ultrasonic testing is the interpretation of the signals encountered. Similar problems might be found with SONAR/RADAR techniques and Chapter 5 draws some analogies between SONAR/RADAR and ultrasonic nondestructive testing. This chapter also includes a discussion on some on the techniques used in signal processing in general. A special signal processing technique found useful is cross-correlation detection and this technique is treated in Chapter 6. Electronic digital compute.rs have made signal processing techniques easier to implement -Chapter 7 discusses the use of digital computers in ultrasonic NDT. Experimental equipment used to test cross-correlation detection of ultrasonic signals is described in Chapter 8. Chapter 9 summarises the conclusions drawn during this investigation.

Compatibilisation of heterogeneous polymer blends by reactive processing

Functionalisation of polystyrene, PS, and ethylene-co-propylene-co-cyclopentadiene terpolymer, EPDM, with acrylic acid, AA, in a melt reactive processing procedure, in the presence of peroxide, trigonox 101, and coagents, Divinyl benzene, DVB (for PS), and trimethylolpropane triacrylate, TRIS (for EPDM), were successfully carried out. The level of grafting of the AA, as determined by infrared analysis, was significantly enhanced by the coagents. The grafting reaction of AA takes place simultaneously with homopolymerisation of the monomers, melt degradation and crosslinking reactions of the polymers. The extent of these competing reactions were inferred from measurements of melt flow index and insoluble gel content. Through a judicious use of both the peroxide and the coagent, particularly TRIS, unwanted side reactions were minimized. Five different processing methods were investigated for both functionalisation experiments; the direct addition of the pre-mixed polymer with peroxide and reactive modifiers was found to give optimum condition for grafting. The functionalised PS, F-PS, and EPDM, F-EPD, and maleinised polypropylene carrying a potential antioxidant, N-(4-anilinophenyl maleimide), F-PP were melt blended in binary mixtures of F-PS/F-EPD and F-PP/F-EPD in the presence (or absence) of organic diamines which act as an interlinking agent, e.g, Ethylene Diamine, EDA, and Hexamethylene Diamine, HEMDA. The presence of an interlinking agent, particularly HEMDA shows significant enhancement in the mechanical properties of the blend, suggesting that the copolymer formed has acted as compatibiliser to the otherwise incompatible polymer pairs. The functionalised and amidised blends, F and A-PSIEPDM (SPOI) and F and A-PPIEPDM (SPD2) were subsequently used as compatibiliser concentrates in the corresponding PSIEPDM and PPIEPDM blends containing various weight propotion of the homopolymers. The SPD1 caused general decreased in tensile strength, albeit increased in drop impact strength particularly in blend containing high PS content (80%). The SPD2 was particularly effective in enhancing impact strength in blends containing low weight ratio of PP (<70%). The SPD2 was also a good thermal antioxidant albeit less effective than commercial antioxidant. In all blends the evidence of compatibility was examined by scanning electron microscopy.

Functionalisation of polymers: reactive processing, structure and performance characteristics

The main aim of this work was to study the effect of two comonomers, trimethylolpropane trimethacrylate (TRIS) and divinylbenzene (DVB) on the nature and efficiency of grafting of two different monomers, glycidyl methacrylate (GMA) and maleic anhydride (MA) on polypropylene (P) and on natural rubber (NR) using reactive processing methods. Four different peroxides, benzoyl peroxide (BPO), dicumyl peroxide (DCP), 2,5-dimethyl-2,5-bis-(tert-butyl peroxy) hexane (t-101), and 1,1-di(tert-butylperoxy)-3,3,5-trimethyl cyclohexene (T-29B90) were examined as free radical initiators. An appropriate methodology was established and chemical composition and reactive processing parameters were examined and optimised. It was found that in the absence of the coagents DVB and TRIS, the grafting degree of GMA and MA increased with increasing peroxide concentration, but the level of grafting was low and the homopolymerisaton of GMA and the crosslinking of NR or chain scission of PP were identified as the main side reactions that competed with the desired grafting reaction in the polymers. At high concentrations of the peroxide T-101 (>0.02 mr) cross linking of NR and chain scission of PP became dominant and unacceptable. An attempt to add a reactive coagent, e.g. TRIS during grafting of GMA on natural rubber resulted in excessive crosslinking because of the very high reactivity of this comonomer with the C=C of the rubber. Therefore, the use of any multifunctional and highly reactive coagent such as TRIS, could not be applied in the grafting of GAM onto natural rubber. In the case of PP, however, the use of TRIS and DVB was shown to greatly enhance the grafting degree and reduce the chain scission with very little extent of monomer homopolymerisation taking place. The results showed that the grafting degree was increased with increasing GMA and MA concentrations. It was also found that T-101 was a suitable peroxide to initiate the grafting reaction of these monomers on NR and PP and the optimum temperature for this peroxide was =160°C. A very preliminary work was also conducted on the use of the functionalised-PP (f-PP) in the absence and presence of the two comonomers (f-PP-DVB or f-PP-TRIS) for the purpose of compatibilising PP-PBT blends through reactive blending. Examination of the morphology of the blends suggested that an effective compatibilisation has been achieved when using f-PP-DVB and f-PP-TRIS, however more work is required in this area.

The ecology of algae in relation to river water equality surveillance

The broad objectives of the work were to develop standard methods for the routine biological surveillance of river water quality, using the non-planktonic algae. Studies on sampling methodology indicated that natural substrata should be sampled directly wherever possible, but for routine purposes, only a semi-quantitative approach was found to be feasible. Artificial substrata were considered to be useful for sample collection in deeper waters, and of three different types tested, Polythene strips were selected for further investigation essentially on grounds of practicality. These were tested in the deeper reaches of a wide range of river types and water qualities: 26 pool sites in 14 different rivers were studied over a period of 9 months. At each site, the assemblages developing on 3 strips following a 4, or less commonly, an 3 week immersion period were analysed quantitatively. Where possible, the natural substrata were also sampled semi-quantitatively at each site, and at a nearby riffle. The results of this survey were very fragmentary: many strips failed to yield useful data, and the results were often difficult to interpret, and of limited value for water quality surveillance purposes. In one river, the Churnet, the natural substrata at 14 riffle sites were sampled semi-quantitatively on 14 occasions at intervals of 4 weeks. In this survey, the results were more readily interpreted in relation to water quality, and no special data processing was found to be necessary or helpful. Further studies carried out on the filamentous green alga Cladophora showed that this alga may have some value as a bioaccumulation indicator for metals, and as a bioassay organism for the assessment of the algal growth promoting potential of natural river waters.

Novel approaches in nonlinear optical fibre-based signal processing

All-optical data processing is expected to play a major role in future optical communications. Nonlinear effects in optical fibres have many attractive features and a great, not yet fully explored potential in optical signal processing. Here, we overview our recent advances in developing novel techniques and approaches to all-optical processing based on optical fibre nonlinearities.

User interface design support for the development of knowledge-based systems

The present scarcity of operational knowledge-based systems (KBS) has been attributed, in part, to an inadequate consideration shown to user interface design during development. From a human factors perspective the problem has stemmed from an overall lack of user-centred design principles. Consequently the integration of human factors principles and techniques is seen as a necessary and important precursor to ensuring the implementation of KBS which are useful to, and usable by, the end-users for whom they are intended. Focussing upon KBS work taking place within commercial and industrial environments, this research set out to assess both the extent to which human factors support was presently being utilised within development, and the future path for human factors integration. The assessment consisted of interviews conducted with a number of commercial and industrial organisations involved in KBS development; and a set of three detailed case studies of individual KBS projects. Two of the studies were carried out within a collaborative Alvey project, involving the Interdisciplinary Higher Degrees Scheme (IHD) at the University of Aston in Birmingham, BIS Applied Systems Ltd (BIS), and the British Steel Corporation. This project, which had provided the initial basis and funding for the research, was concerned with the application of KBS to the design of commercial data processing (DP) systems. The third study stemmed from involvement on a KBS project being carried out by the Technology Division of the Trustees Saving Bank Group plc. The preliminary research highlighted poor human factors integration. In particular, there was a lack of early consideration of end-user requirements definition and user-centred evaluation. Instead concentration was given to the construction of the knowledge base and prototype evaluation with the expert(s). In response to this identified problem, a set of methods was developed that was aimed at encouraging developers to consider user interface requirements early on in a project. These methods were then applied in the two further projects, and their uptake within the overall development process was monitored. Experience from the two studies demonstrated that early consideration of user interface requirements was both feasible, and instructive for guiding future development work. In particular, it was shown a user interface prototype could be used as a basis for capturing requirements at the functional (task) level, and at the interface dialogue level. Extrapolating from this experience, a KBS life-cycle model is proposed which incorporates user interface design (and within that, user evaluation) as a largely parallel, rather than subsequent, activity to knowledge base construction. Further to this, there is a discussion of several key elements which can be seen as inhibiting the integration of human factors within KBS development. These elements stem from characteristics of present KBS development practice; from constraints within the commercial and industrial development environments; and from the state of existing human factors support.

Processing and rendering of Fourier domain optical coherence tomography images at a line rate over 524 kHz using a graphics processing unit

In Fourier domain optical coherence tomography (FD-OCT), a large amount of interference data needs to be resampled from the wavelength domain to the wavenumber domain prior to Fourier transformation. We present an approach to optimize this data processing, using a graphics processing unit (GPU) and parallel processing algorithms. We demonstrate an increased processing and rendering rate over that previously reported by using GPU paged memory to render data in the GPU rather than copying back to the CPU. This avoids unnecessary and slow data transfer, enabling a processing and display rate of well over 524,000 A-scan/s for a single frame. To the best of our knowledge this is the fastest processing demonstrated to date and the first time that FD-OCT processing and rendering has been demonstrated entirely on a GPU.

Nonlinear pulse shaping in fibres for pulse generation and optical processing

The development of new all-optical technologies for data processing and signal manipulation is a field of growing importance with a strong potential for numerous applications in diverse areas of modern science. Nonlinear phenomena occurring in optical fibres have many attractive features and great, but not yet fully explored, potential in signal processing. Here, we review recent progress on the use of fibre nonlinearities for the generation and shaping of optical pulses and on the applications of advanced pulse shapes in all-optical signal processing. Amongst other topics, we will discuss ultrahigh repetition rate pulse sources, the generation of parabolic shaped pulses in active and passive fibres, the generation of pulses with triangular temporal profiles, and coherent supercontinuum sources. The signal processing applications will span optical regeneration, linear distortion compensation, optical decision at the receiver in optical communication systems, spectral and temporal signal doubling, and frequency conversion. © Copyright 2012 Sonia Boscolo and Christophe Finot.

All-optical nonlinear fibre signal processing

All-optical technologies for data processing and signal manipulation are expected to play a major role in future optical communications. Nonlinear phenomena occurring in optical fibre have many attractive features and great, but not yet fully exploited potential in optical signal processing. Here, we overview our recent results and advances in developing novel photonic techniques and approaches to all-optical processing based on fibre nonlinearities. Amongst other topics, we will discuss phase-preserving optical 2R regeneration, the possibility of using parabolic/flat-top pulses for optical signal processing and regeneration, and nonlinear optical pulse shaping. A method for passive nonlinear pulse shaping based on pulse pre-chirping and propagation in a normally dispersive fibre will be presented. The approach provides a simple way of generating various temporal waveforms of fundamental and practical interest. Particular emphasis will be given to the formation and characterization of pulses with a triangular intensity profile. A new technique of doubling/copying optical pulses in both the frequency and time domains using triangular-shaped pulses will be also introduced.

Quantitative neuropathology:data collection and statistical analysis

The use of quantitative methods has become increasingly important in the study of neuropathology and especially in neurodegenerative disease. Disorders such as Alzheimer's disease (AD) and the frontotemporal dementias (FTD) are characterized by the formation of discrete, microscopic, pathological lesions which play an important role in pathological diagnosis. This chapter reviews the advantages and limitations of the different methods of quantifying pathological lesions in histological sections including estimates of density, frequency, coverage, and the use of semi-quantitative scores. The sampling strategies by which these quantitative measures can be obtained from histological sections, including plot or quadrat sampling, transect sampling, and point-quarter sampling, are described. In addition, data analysis methods commonly used to analysis quantitative data in neuropathology, including analysis of variance (ANOVA), polynomial curve fitting, multiple regression, classification trees, and principal components analysis (PCA), are discussed. These methods are illustrated with reference to quantitative studies of a variety of neurodegenerative disorders.

Recent developments in all-optical nonlinear signal processing for fiber-optic communications

All-optical data processing is expected to play a major role in future optical communications. Nonlinear effects in optical fibers have attractive applications in optical signal processing. In this paper, we review our recent advances in developing all-optical processing techniques at high speed based on optical fiber nonlinearities.

Generalized methods and solvers for noise removal from piecewise constant signals. I. Background theory

Removing noise from piecewise constant (PWC) signals is a challenging signal processing problem arising in many practical contexts. For example, in exploration geosciences, noisy drill hole records need to be separated into stratigraphic zones, and in biophysics, jumps between molecular dwell states have to be extracted from noisy fluorescence microscopy signals. Many PWC denoising methods exist, including total variation regularization, mean shift clustering, stepwise jump placement, running medians, convex clustering shrinkage and bilateral filtering; conventional linear signal processing methods are fundamentally unsuited. This paper (part I, the first of two) shows that most of these methods are associated with a special case of a generalized functional, minimized to achieve PWC denoising. The minimizer can be obtained by diverse solver algorithms, including stepwise jump placement, convex programming, finite differences, iterated running medians, least angle regression, regularization path following and coordinate descent. In the second paper, part II, we introduce novel PWC denoising methods, and comparisons between these methods performed on synthetic and real signals, showing that the new understanding of the problem gained in part I leads to new methods that have a useful role to play.

Novel approaches in nonlinear optical fibre-based signal processing

All-optical data processing is expected to play a major role in future optical communications. Nonlinear effects in optical fibres have many attractive features and a great, not yet fully explored potential in optical signal processing. Here, we overview our recent advances in developing novel techniques and approaches to all-optical processing based on optical fibre nonlinearities.