Flexible Gaussian process wind field models

This technical report builds on previous reports to derive the likelihood and its derivatives for a Gaussian Process with a modified Bessel function based covariance function. The full derivation is shown. The likelihood (with gradient information) can be used in maximum likelihood procedures (i.e. gradient based optimisation) and in Hybrid Monte Carlo sampling (i.e. within a Bayesian framework).

Non-zero mean Gaussian process prior wind field models

This report outlines the derivation and application of a non-zero mean, polynomial-exponential covariance function based Gaussian process which forms the prior wind field model used in 'autonomous' disambiguation. It is principally used since the non-zero mean permits the computation of realistic local wind vector prior probabilities which are required when applying the scaled-likelihood trick, as the marginals of the full wind field prior. As the full prior is multi-variate normal, these marginals are very simple to compute.

GLM-beamformer method demonstrates stationary field, alpha ERD and gamma ERS co-localisation with fMRI BOLD response in visual cortex

Recently, we introduced a new 'GLM-beamformer' technique for MEG analysis that enables accurate localisation of both phase-locked and non-phase-locked neuromagnetic effects, and their representation as statistical parametric maps (SPMs). This provides a useful framework for comparison of the full range of MEG responses with fMRI BOLD results. This paper reports a 'proof of principle' study using a simple visual paradigm (static checkerboard). The five subjects each underwent both MEG and fMRI paradigms. We demonstrate, for the first time, the presence of a sustained (DC) field in the visual cortex, and its co-localisation with the visual BOLD response. The GLM-beamformer analysis method is also used to investigate the main non-phase-locked oscillatory effects: an event-related desynchronisation (ERD) in the alpha band (8-13 Hz) and an event-related synchronisation (ERS) in the gamma band (55-70 Hz). We show, using SPMs and virtual electrode traces, the spatio-temporal covariance of these effects with the visual BOLD response. Comparisons between MEG and fMRI data sets generally focus on the relationship between the BOLD response and the transient evoked response. Here, we show that the stationary field and changes in oscillatory power are also important contributors to the BOLD response, and should be included in future studies on the relationship between neuronal activation and the haemodynamic response. © 2005 Elsevier Inc. All rights reserved.

Applications of differential geometry to high spin field theories

The main aim of this thesis is to investigate the application of methods of differential geometry to the constraint analysis of relativistic high spin field theories. As a starting point the coordinate dependent descriptions of the Lagrangian and Dirac-Bergmann constraint algorithms are reviewed for general second order systems. These two algorithms are then respectively employed to analyse the constraint structure of the massive spin-1 Proca field from the Lagrangian and Hamiltonian viewpoints. As an example of a coupled field theoretic system the constraint analysis of the massive Rarita-Schwinger spin-3/2 field coupled to an external electromagnetic field is then reviewed in terms of the coordinate dependent Dirac-Bergmann algorithm for first order systems. The standard Velo-Zwanziger and Johnson-Sudarshan inconsistencies that this coupled system seemingly suffers from are then discussed in light of this full constraint analysis and it is found that both these pathologies degenerate to a field-induced loss of degrees of freedom. A description of the geometrical version of the Dirac-Bergmann algorithm developed by Gotay, Nester and Hinds begins the geometrical examination of high spin field theories. This geometric constraint algorithm is then applied to the free Proca field and to two Proca field couplings; the first of which is the minimal coupling to an external electromagnetic field whilst the second is the coupling to an external symmetric tensor field. The onset of acausality in this latter coupled case is then considered in relation to the geometric constraint algorithm.

Spatial tuning studies of the pattern evoked electroretinogram

The locus of origin of the pattern evoked electroretinogram, (PERG), has been the subject of considerable discussion. A novel approach was adopted in this study to further elaborate the nature of the PERG evoked by pattern onset/offset presentation. The PERG was found to be linearly related to stimulus contrast and in particular was linearly related to the temporal contrast of the retinal image, when elicited by patterns of low spatial frequency. At high spatial frequencies the retinal image contrast is significantly reduced because of optical degradation. This is described by the eye's modulation transfer function (MTF). The retinal contrast of square wave grating and chequerboard patterns of increasing spatial frequency were found by filtering their Fourier transforms by the MTF. The filtered pattern harmonics were then resynthesised to constitute a profile of retinal image illuminance from which the temporal and spatial contrast of the image could be calculated. If the PERG is a pure illuminance response it should be spatially insensitive and dependent upon the temporal contrast of stimulation. The calculated loss of temporal contrast for finer patterns was expressed as a space-averaged temporal contrast attentuation factor. This factor, applied to PERGs evoked by low spatial frequency patterns, was used to predict the retinal illuminance response elicited by a finer pattern. The predicted response was subtracted from the recorded signal and residual waveform was proposed to represent specific activity. An additional correction for the attenuation of spatial contrast was applied to the extracted pattern specific response. Pattern specific responses computed for different spatial frequency patterns in this way are the predicted result of iso-contrast pattern stimulation. The pattern specific responses demonstrate a striking bandpass spatial selectivity which peaks at higher spatial frequencies in the more central retina. The variation of spatial sensitivity with eccentricity corresponds closely with estimated ganglion receptive field centre separation and psychophysical data. The variation of retinal structure with eccentricity, in the form of the volumes of the nuclear layers, was compared with the amplitudes of the computed retinal illuminance and pattern specific responses. The retinal illuminance response corresponds more closely to the outer and inner nuclear layers whilst the pattern specific response appears more closely related to the ganglion cell layer. In general the negative response transients correspond to the more proximal retinal layers. This thesis therefore supports the proposed contribution of proximal retinal cell activity to the PERG and describes techniques which may be further elaborated for more detailed studies of retinal receptive field dimensions.

The attenuation surface for contrast sensitivity has the form of a witch’s hat within the central visual field

Over the full visual field, contrast sensitivity is fairly well described by a linear decline in log sensitivity as a function of eccentricity (expressed in grating cycles). However, many psychophysical studies of spatial visual function concentrate on the central ±4.5 deg (or so) of the visual field. As the details of the variation in sensitivity have not been well documented in this region we did so for small patches of target contrast at several spatial frequencies (0.7–4 c/deg), meridians (horizontal, vertical, and oblique), orientations (horizontal, vertical, and oblique), and eccentricities (0–18 cycles). To reduce the potential effects of stimulus uncertainty, circular markers surrounded the targets. Our analysis shows that the decline in binocular log sensitivity within the central visual field is bilinear: The initial decline is steep, whereas the later decline is shallow and much closer to the classical results. The bilinear decline was approximately symmetrical in the horizontal meridian and declined most steeply in the superior visual field. Further analyses showed our results to be scale-invariant and that this property could not be predicted from cone densities. We used the results from the cardinal meridians to radially interpolate an attenuation surface with the shape of a witch's hat that provided good predictions for the results from the oblique meridians. The witch's hat provides a convenient starting point from which to build models of contrast sensitivity, including those designed to investigate signal summation and neuronal convergence of the image contrast signal. Finally, we provide Matlab code for constructing the witch's hat.

Ophthalmic engineering:the development of novel instrumentation to further research in the field

The principle theme of this thesis is the advancement and expansion of ophthalmic research via the collaboration between professional Engineers and professional Optometrists. The aim has been to develop new and novel approaches and solutions to contemporary problems in the field. The work is sub divided into three areas of investigation; 1) High technology systems, 2) Modification of current systems to increase functionality, and 3) Development of smaller more portable and cost effective systems. High Technology Systems: A novel high speed Optical Coherence Tomography (OCT) system with integrated simultaneous high speed photography was developed achieving better operational speed than is currently available commercially. The mechanical design of the system featured a novel 8 axis alignment system. A full set of capture, analysis, and post processing software was developed providing custom analysis systems for ophthalmic OCT imaging, expanding the current capabilities of the technology. A large clinical trial was undertaken to test the dynamics of contact lens edge interaction with the cornea in-vivo. The interaction between lens edge design, lens base curvature, post insertion times and edge positions was investigated. A novel method for correction of optical distortion when assessing lens indentation was also demonstrated. Modification of Current Systems: A commercial autorefractor, the WAM-5500, was modified with the addition of extra hardware and a custom software and firmware solution to produce a system that was capable of measuring dynamic accommodative response to various stimuli in real time. A novel software package to control the data capture process was developed allowing real time monitoring of data by the practitioner, adding considerable functionality of the instrument further to the standard system. The device was used to assess the accommodative response differences between subjects who had worn UV blocking contact lens for 5 years, verses a control group that had not worn UV blocking lenses. While the standard static measurement of accommodation showed no differences between the two groups, it was determined that the UV blocking group did show better accommodative rise and fall times (faster), thus demonstrating the benefits of the modification of this commercially available instrumentation. Portable and Cost effective Systems: A new instrument was developed to expand the capability of the now defunct Keeler Tearscope. A device was developed that provided a similar capability in allowing observation of the reflected mires from the tear film surface, but with the added advantage of being able to record the observations. The device was tested comparatively with the tearscope and other tear film break-up techniques, demonstrating its potential. In Conclusion: This work has successfully demonstrated the advantages of interdisciplinary research between engineering and ophthalmic research has provided new and novel instrumented solutions as well as having added to the sum of scientific understanding in the ophthalmic field.

Does the Swedish Interactive Threshold Algorithm (SITA) accurately map visual field loss attributed to vigabatrin?

Background: Vigabatrin (VGB) is an anti-epileptic medication which has been linked to peripheral constriction of the visual field. Documenting the natural history associated with continued VGB exposure is important when making decisions about the risk and benefits associated with the treatment. Due to its speed the Swedish Interactive Threshold Algorithm (SITA) has become the algorithm of choice when carrying out Full Threshold automated static perimetry. SITA uses prior distributions of normal and glaucomatous visual field behaviour to estimate threshold sensitivity. As the abnormal model is based on glaucomatous behaviour this algorithm has not been validated for VGB recipients. We aim to assess the clinical utility of the SITA algorithm for accurately mapping VGB attributed field loss. Methods: The sample comprised one randomly selected eye of 16 patients diagnosed with epilepsy, exposed to VGB therapy. A clinical diagnosis of VGB attributed visual field loss was documented in 44% of the group. The mean age was 39.3 years∈±∈14.5 years and the mean deviation was -4.76 dB ±4.34 dB. Each patient was examined with the Full Threshold, SITA Standard and SITA Fast algorithm. Results: SITA Standard was on average approximately twice as fast (7.6 minutes) and SITA Fast approximately 3 times as fast (4.7 minutes) as examinations completed using the Full Threshold algorithm (15.8 minutes). In the clinical environment, the visual field outcome with both SITA algorithms was equivalent to visual field examination using the Full Threshold algorithm in terms of visual inspection of the grey scale plots, defect area and defect severity. Conclusions: Our research shows that both SITA algorithms are able to accurately map visual field loss attributed to VGB. As patients diagnosed with epilepsy are often vulnerable to fatigue, the time saving offered by SITA Fast means that this algorithm has a significant advantage for use with VGB recipients.

Field Testing and Development of Novel SHM systems at Queen’s University Belfast

Ageing and deterioration of infrastructure is a challenge facing transport authorities. In
particular, there is a need for increased bridge monitoring in order to provide adequate
maintenance and to guarantee acceptable levels of transport safety. The Intelligent
Infrastructure group at Queens University Belfast (QUB) are working on a number of aspects
of infrastructure monitoring and this paper presents summarised results from three distinct
monitoring projects carried out by this group. Firstly the findings from a project on next
generation Bridge Weight in Motion (B-WIM) are reported, this includes full scale field testing
using fibre optic strain sensors. Secondly, results from early phase testing of a computer
vision system for bridge deflection monitoring are reported on. This research seeks to exploit
recent advances in image processing technology with a view to developing contactless
bridge monitoring approaches. Considering the logistical difficulty of installing sensors on a
‘live’ bridge, contactless monitoring has some inherent advantages over conventional
contact based sensing systems. Finally the last section of the paper presents some recent
findings on drive by bridge monitoring. In practice a drive-by monitoring system will likely
require GPS to allow the response of a given bridge to be identified; this study looks at the
feasibility of using low-cost GPS sensors for this purpose, via field trials. The three topics
outlined above cover a spectrum of SHM approaches namely, wired monitoring, contactless
monitoring and drive by monitoring

Modelling the Sun's small scale global photospheric magnetic field

We present a new model for the Sun's global photospheric magnetic field during a deep minimum of activity, in which no active regions emerge. The emergence and subsequent evolution of small- scale magnetic features across the full solar surface is simulated, subject to the influence of a global supergranular flow pattern. Visually, the resulting simulated magnetograms reproduce the typical structure and scale observed in quiet Sun magnetograms. Quantitatively, the simulation quickly reaches a steady state, resulting in a mean field and flux distribution that are in good agreement with those determined from observations. A potential coronal magnetic field is extrapolated from the simulated full Sun magnetograms, to consider the implications of such a quiet photospheric magnetic field on the corona and inner heliosphere. The bulk of the coronal magnetic field closes very low down, in short connections between small-scale features in the simulated magnetic network. Just 0.1% of the photospheric magnetic flux is found to be open at 2:5 Rʘ, around 10 - 100 times less than that determined for typical HMI synoptic map observations. If such conditions were to exist on the Sun, this would lead to a significantly weaker interplanetary magnetic field than is presently observed, and hence a much higher cosmic ray flux at Earth.

Modeling electrocortical activity through improved local approximations of integral neural field equations

Neural field models of firing rate activity typically take the form of integral equations with space-dependent axonal delays. Under natural assumptions on the synaptic connectivity we show how one can derive an equivalent partial differential equation (PDE) model that properly treats the axonal delay terms of the integral formulation. Our analysis avoids the so-called long-wavelength approximation that has previously been used to formulate PDE models for neural activity in two spatial dimensions. Direct numerical simulations of this PDE model show instabilities of the homogeneous steady state that are in full agreement with a Turing instability analysis of the original integral model. We discuss the benefits of such a local model and its usefulness in modeling electrocortical activity. In particular we are able to treat "patchy'" connections, whereby a homogeneous and isotropic system is modulated in a spatially periodic fashion. In this case the emergence of a "lattice-directed" traveling wave predicted by a linear instability analysis is confirmed by the numerical simulation of an appropriate set of coupled PDEs. Article published and (c) American Physical Society 2007

In situ characterization of sediment oxygen demand across the spectrum of non-resuspension to full resuspension with varying bed shear stress

Sediment oxygen demand (SOD) can be a significant oxygen sink in various types of water bodies, particularly slow-moving waters with substantial organic sediment accumulation. In most settings where SOD is a concern, the prevailing hydraulic conditions are such that the impact of sediment resuspension on SOD is not considered. However, in the case of Bubbly Creek in Chicago, Illinois, the prevailing slack water conditions are interrupted by infrequent intervals of very high flow rates associated with pumped combined sewer overflow (CSO) during intense hydrologic events. These events can cause resuspension of the highly organic, nutrient-rich bottom sediments, resulting in precipitous drawdown of dissolved oxygen (DO) in the water column. While many past studies have addressed the dependence of SOD on near-bed velocity and bed shear stress prior to the point of sediment resuspension, there has been limited research that has attempted to characterize the complex and dynamic phenomenon of resuspended-sediment oxygen demand. To address this issue, a new in situ experimental apparatus referred to as the U of I Hydrodynamic SOD Sampler was designed to achieve a broad range of velocities and associated bed shear stresses. This allowed SOD to be analyzed across the spectrum of no sediment resuspension associated with low velocity/ bed shear stress through full sediment resuspension associated with high velocity / bed shear stress. The current study split SOD into two separate components: (1) SODNR is the sediment oxygen demand associated with non-resuspension conditions and is a surface sink calculated using traditional methods to yield a value with units (g/m2/day); and (2) SODR is the oxygen demand associated with resuspension conditions, which is a volumetric sink most accurately characterized using non-traditional methods and units that reflect suspension in the water column (mg/L/day). In the case of resuspension, the suspended sediment concentration was analyzed as a function of bed shear stress, and a formulation was developed to characterize SODR as a function of suspended sediment concentration in a form similar to first-order biochemical oxygen demand (BOD) kinetics with Monod DO term. The results obtained are intended to be implemented into a numerical model containing hydrodynamic, sediment transport, and water quality components to yield oxygen demand varying in both space and time for specific flow events. Such implementation will allow evaluation of proposed Bubbly Creek water quality improvement alternatives which take into account the impact of SOD under various flow conditions. Although the findings were based on experiments specific to the conditions in Bubbly Creek, the techniques and formulations developed in this study should be applicable to similar sites.

Catalytic CO2 hydrogenation: study at the molecular scale using field emission techniques

An accurate characterization of the rhodium specimen was obtained via FIM experiments. Reaction behaviors between H2 and CO2 were observed in FEM mode at 700 K. At this temperature, CO desorption occurs, preventing CO+H2 reaction. Surface is mainly recovered by oxygen; reaction with hydrogen occurs. Finally, we can identify the reaction as the Reverse Water Gas Shift.

A field study to describe diel, tidal and semilunar rhythms of larval release in an assemblage of tropical rocky shore crabs

Available information on the larval release rhythms of brachyurans is biased to temperate estuarine species and outcomes resulting from some sort of artificial manipulation of ovigerous females. In this study we applied field methods to describe the larval release rhythms of an assemblage of tropical rocky shore crabs. Sampling the broods of ovigerous females of Pachygrapsus transversus at two different shores indicated a spatially consistent semilunar pattern, with larval release maxima around the full and new moon. Yet, synchronism between populations varied considerably, with the pattern obtained at the site exposed to a lower wave action far more apparent. Breeding cohorts at one of the sampled shores apparently belonged to actual age groups composing the ovigerous population. The data suggest that these breeding groups release their larvae in alternate syzygy periods, responding to a lunar cycle instead of the semilunar pattern observed for the whole population. For the description of shorter-term rhythms, temporal series at hour intervals were obtained by sampling the plankton and confinement boxes where ovigerous females were held. Unexpectedly, diurnal release activity prevailed over nocturnal hatching. Yet, only grapsids living higher on the shore exhibited strong preferences over the diel cycle, with P. transversus releasing their larvae during the day and Geograpsus lividus during the night. The pea crab Dissodactylus crinitichelis, the spider crab Epialtus brasiliensis and a suite of xanthoids undertook considerable releasing activity in both periods. Apart from the commensal pea crab D. crinitichelis, all other taxa revealed tide-related rhythms of larval release, with average estimates of the time of maximum hatching always around the time of high tides; usually during the flooding and slack, rather than the ebbing tide. Data obtained for P. transversus females held in confinement boxes indicated that early larval release is mostly due to nocturnal hatching, while zoeal release in diurnal groups took place at the time of high tide. Since nocturnal high tides at the study area occurred late, sometimes close to dusk, early release would allow more time for offshore transport of larvae when the action of potential predators is reduced.

Translation Studies on an Annular Field Reversed Configuration Device for Space Propulsion

This research investigated annular field reversed configuration (AFRC)devices for high power electric propulsion by demonstrating the acceleration of these plasmoids using an experimental prototype and measuring the plasmoid's velocity, impulse, and energy efficiency. The AFRC plasmoid translation experiment was design and constructed with the aid of a dynamic circuit model. Two versions of the experiment were built, using underdamped RLC circuits at 10 kHz and 20 kHz. Input energies were varied from 100 J/pulse to 1000 J/pulse for the 10 kHz bank and 100 J/pulse for the 20 kHz bank. The plasmoids were formed in static gas fill of argon, from 1 mTorr to 50 mTorr. The translation of the plasmoid was accomplished by incorporating a small taper into the outer coil, with a half angle of 2°. Magnetic field diagnostics, plasma probes, and single-frame imaging were used to measure the plasmoid's velocity and to diagnose plasmoid behavior. Full details of the device design, construction, and diagnostics are provided in this dissertation. The results from the experiment demonstrated that a repeatable AFRC plasmoid was produced between the coils, yet failed to translate for all tested conditions. The data revealed the plasmoid was limited in lifetime to only a few (4-10) μs, too short for translation at low energy. A global stability study showed that the plasma suffered a radial collapse onto the inner wall early in its lifecycle. The radial collapse was traced to a magnetic pressure imbalance. A correction made to the circuit was successful in restoring an equilibrium pressure balance and prolonging radial stability by an additional 2.5 μs. The equilibrium state was sufficient to confirm that the plasmoid current in an AFRC reaches a steady-state prior to the peak of the coil currents. This implies that the plasmoid will always be driven to the inner wall, unless it translates from the coils prior to peak coil currents. However, ejection of the plasmoid before the peak coil currents results in severe efficiency losses. These results demonstrate the difficulty in designing an AFRC experiment for translation as balancing the different requirements for stability, balance, and efficient translation can have competing consequences.