Implementation of optical chemsensors based on HF-etched fibre Bragg grating structures

High-sensitivity optical chemsensors have been implemented by exploiting fibre Bragg grating structures UV-inscribed in D-shape, single-mode and multimode fibres and post-sensitized by hydrofluoric acid (HF) etching treatment. We have demonstrated that the Bragg grating structures which are intrinsically insensitive to chemicals can be sensitized by effective etching. All etched devices possess refractive index sensing capability that offers an encoding function to chemical concentrations. Most etched devices have been used to measure the concentrations of sugar solutions, showing a potential capability of detecting concentration changes as small as 0.1–0.5%.

Schematic structure and the modulation of propositions in economics forecasting text

Working within the framework of the branch of Linguistics known as discourse analysis, and more specifically within the current approach of genre analysis, this thesis presents an analysis of the English of economic forecasting. The language of economic forecasting is highly specialised and follows certain conventions of structure and style. This research project identifies these characteristics and explains them in terms of their communicative function. The work is based on a corpus of texts published in economic reports and surveys by major corporate bodies. These documents are targeted at an international expert readership familiar with this genre. The data is analysed at two broad levels: firstly, the macro-level of text structure which is described in terms of schema-theory, a currently influential model of analysis, and, secondly, the micro-level of authors' strategies for modulating the predictions which form the key move in the forecasting schema. The thesis aims to contribute to the newly developing field of genre analysis in a number of ways: firstly, by a coverage of a hitherto neglected but intrinsically interesting and important genre (Economic Forecasting); secondly, by testing the applicability of existing models of analysis at the level of schematic structure and proposing a genre-specific model; thirdly by offering insights into the nature of modulation of propositions which is often broadly classified as `hedging' or `modality', and which has been recently described as lq`an area for prolonged fieldwork'. This phenomenon is shown to be a key feature of this particular genre. It is suggested that this thesis, in addition to its contribution to the theory of genre analysis, provides a useful basis for work by teachers of English for Economics, an important area of English for Specific Purposes.

Uncertainty and topographic visualisations

This thesis is a study of low-dimensional visualisation methods for data visualisation under certainty of the input data. It focuses on the two main feed-forward neural network algorithms which are NeuroScale and Generative Topographic Mapping (GTM) by trying to make both algorithms able to accommodate the uncertainty. The two models are shown not to work well under high levels of noise within the data and need to be modified. The modification of both models, NeuroScale and GTM, are verified by using synthetic data to show their ability to accommodate the noise. The thesis is interested in the controversy surrounding the non-uniqueness of predictive gene lists (PGL) of predicting prognosis outcome of breast cancer patients as available in DNA microarray experiments. Many of these studies have ignored the uncertainty issue resulting in random correlations of sparse model selection in high dimensional spaces. The visualisation techniques are used to confirm that the patients involved in such medical studies are intrinsically unclassifiable on the basis of provided PGL evidence. This additional category of ‘unclassifiable’ should be accommodated within medical decision support systems if serious errors and unnecessary adjuvant therapy are to be avoided.

Beta frequency neuronal network activity in the primary motor cortex

In this study I investigated the mechanisms of neuronal network oscillatory activity in rat M1 using pharmacological manipulations and electrical stimulation protocols, employing the in vitro brain slice technique in rat and magnetoencephalography (MEG) in man. Co-application of kainic acid and carbachol generated in vitro beta oscillatory activity in all layers in M1. Analyses indicated that oscillations originated from deep layers and indicated significant involvement of GABAA receptors and gap junctions. A modulatory role of GABAB, NMDA, and dopamine receptors was also evident. Intracellular recordings from fast-spiking (FS) GABAergic inhibitory cells revealed phase-locked action potentials (APs) on every beta cycle. Glutamatergic excitatory regular-spiking (RS) and intrinsically-bursting (IB) cells both received phase locked inhibitory postsynaptic potentials, but did not fire APs on every cycle, suggesting the dynamic involvement of different pools of neurones in the overall population oscillations. Stimulation evoked activity at high frequency (HFS; 125Hz) evoked gamma oscillations and reduced ongoing beta activity. 20Hz stimulation promoted theta or gamma oscillations whilst 4Hz stimulation enhanced beta power at theta frequency. I also investigated the modulation of pathological slow wave (theta and beta) oscillatory activity using magnetoencephalography. Abnormal activity was suppressed by sub-sedative doses of GABAA receptor modulator zolpidem and the observed desynchronising effect correlated well with improved sensorimotor function. These studies indicate a fundamental role for inhibitory neuronal networks in the patterning beta activity and suggest that cortical HFS in PD re-patterns abnormally enhanced M1 network activity by modulating the activity of FS cells. Furthermore, pathological oscillation may be common to many neuropathologies and may be an important future therapeutic target.

Predictive gene lists for breast cancer prognosis: a topographic visualisation study

Background: The controversy surrounding the non-uniqueness of predictive gene lists (PGL) of small selected subsets of genes from very large potential candidates as available in DNA microarray experiments is now widely acknowledged 1. Many of these studies have focused on constructing discriminative semi-parametric models and as such are also subject to the issue of random correlations of sparse model selection in high dimensional spaces. In this work we outline a different approach based around an unsupervised patient-specific nonlinear topographic projection in predictive gene lists. Methods: We construct nonlinear topographic projection maps based on inter-patient gene-list relative dissimilarities. The Neuroscale, the Stochastic Neighbor Embedding(SNE) and the Locally Linear Embedding(LLE) techniques have been used to construct two-dimensional projective visualisation plots of 70 dimensional PGLs per patient, classifiers are also constructed to identify the prognosis indicator of each patient using the resulting projections from those visualisation techniques and investigate whether a-posteriori two prognosis groups are separable on the evidence of the gene lists. A literature-proposed predictive gene list for breast cancer is benchmarked against a separate gene list using the above methods. Generalisation ability is investigated by using the mapping capability of Neuroscale to visualise the follow-up study, but based on the projections derived from the original dataset. Results: The results indicate that small subsets of patient-specific PGLs have insufficient prognostic dissimilarity to permit a distinction between two prognosis patients. Uncertainty and diversity across multiple gene expressions prevents unambiguous or even confident patient grouping. Comparative projections across different PGLs provide similar results. Conclusion: The random correlation effect to an arbitrary outcome induced by small subset selection from very high dimensional interrelated gene expression profiles leads to an outcome with associated uncertainty. This continuum and uncertainty precludes any attempts at constructing discriminative classifiers. However a patient's gene expression profile could possibly be used in treatment planning, based on knowledge of other patients' responses. We conclude that many of the patients involved in such medical studies are intrinsically unclassifiable on the basis of provided PGL evidence. This additional category of 'unclassifiable' should be accommodated within medical decision support systems if serious errors and unnecessary adjuvant therapy are to be avoided.

A study of the formation of amorphous calcium phosphate and hydroxyapatite on melt quenched Bioglass(A (R)) using surface sensitive shallow angle X-ray diffraction

Melt quenched silicate glasses containing calcium, phosphorous and alkali metals have the ability to promote bone regeneration and to fuse to living bone. These glasses, including 45S5 Bioglass(A (R)) [(CaO)(26.9)(Na2O)(24.4)(SiO2)(46.1)(P2O5)(2.6)], are routinely used as clinical implants. Consequently there have been numerous studies on the structure of these glasses using conventional diffraction techniques. These studies have provided important information on the atomic structure of Bioglass(A (R)) but are of course intrinsically limited in the sense that they probe the bulk material and cannot be as sensitive to thin layers of near-surface dissolution/growth. The present study therefore uses surface sensitive shallow angle X-ray diffraction to study the formation of amorphous calcium phosphate and hydroxyapatite on Bioglass(A (R)) samples, pre-reacted in simulated body fluid (SBF). Unreacted Bioglass(A (R)) is dominated by a broad amorphous feature around 2.2 A...(-1) which is characteristic of sodium calcium silicate glass. After reacting Bioglass(A (R)) in SBF a second broad amorphous feature evolves similar to 1.6 A...(-1) which is attributed to amorphous calcium phosphate. This feature is evident for samples after only 4 h reacting in SBF and by 8 h the amorphous feature becomes comparable in magnitude to the background signal of the bulk Bioglass(A (R)). Bragg peaks characteristic of hydroxyapatite form after 1-3 days of reacting in SBF.

Methodology of photic stimulation revisited:updated European algorithm for visual stimulation in the EEG laboratory

Intermittent photic stimulation (IPS) is a common procedure performed in the electroencephalography (EEG) laboratory in children and adults to detect abnormal epileptogenic sensitivity to flickering light (i.e., photosensitivity). In practice, substantial variability in outcome is anecdotally found due to the many different methods used per laboratory and country. We believe that standardization of procedure, based on scientific and clinical data, should permit reproducible identification and quantification of photosensitivity. We hope that the use of our new algorithm will help in standardizing the IPS procedure, which in turn may more clearly identify and assist monitoring of patients with epilepsy and photosensitivity. Our algorithm goes far beyond that published in 1999 (Epilepsia, 1999a, 40, 75; Neurophysiol Clin, 1999b, 29, 318): it has substantially increased content, detailing technical and logistical aspects of IPS testing and the rationale for many of the steps in the IPS procedure. Furthermore, our latest algorithm incorporates the consensus of repeated scientific meetings of European experts in this field over a period of 6 years with feedback from general neurologists and epileptologists to improve its validity and utility. Accordingly, our European group has provided herein updated algorithms for two different levels of methodology: (1) requirements for defining photosensitivity in patients and in family members of known photosensitive patients and (2) requirements for tailored studies in patients with a clear history of visually induced seizures or complaints, and in those already known to be photosensitive.

Characterisation of femtosecond laser inscribed long period gratings in photonic crystal fibre

The use of high intensity femtosecond laser sources for inscribing fibre gratings has attained significant interest. The principal advantage of high-energy pulses is their ability for grating inscription in any material type without preprocessing or special core doping - the inscription process is controlled multi-photon absorption, void generation and subsequent local refractive index changes. The formation of grating structures in photonics crystal fibre has proven difficult, as the presence of holes within the fibre that allow wave-guidance impair and scatter the femtosecond inscription beam. Here we report on the consistent manufacture of long period gratings in endlessly single mode microstructure fibre and on their characterisation to external perturbations. Long period gratings are currently the subject of considerable research interest due to their potential applications as filters and as sensing devices, responsive to strain, temperature, bending and refractive index. Compared to the more mature fibre Bragg grating sensors, LPGs have more complex spectra, usually with broader spectral features. On the other hand they are intrinsically sensitive to bending and refractive index. Perhaps more importantly, the fibre design and choice of grating period can have a considerable influence over the sensitivity to the various parameters, for example allowing the creation of a bend sensor with minimal temperature cross-sensitivity. This control is not possible with FBG sensors. Here we compare the effects of symmetric and asymmetric femtosecond laser inscription.

Highly radiation sensitive type IA FBGs for future dosimetry applications

We have studied Co60 gamma-irradiation effect on the characteristics of Type IA fiber Bragg gratings. A record Bragg peak shift of 190 pm was observed for a grating written in Fibercore PS-1250/1500 photosensitive fiber at a radiation dose of 116 kGy. Type IA and Type I gratings show different kinetics under radiation and during post-radiation annealing, which can be used for the design of a grating based dosimetry system.

Highly radiation sensitive type IA FBGs for dosimetry applications

We have studied Co60 ionizing radiation effect on the characteristics of Type IA fiber Bragg gratings. A record Bragg peak shift of 190 pm was observed for a grating written in Fibercore PS-1250/1500 photosensitive fiber at a radiation dose of 116 kGy. Type IA and Type I gratings show different kinetics under radiation and during post-radiation annealing, which can be used for the design of a grating based dosimetry system.

Robust spatially resolved pressure measurements using MRI with novel buoyant advection-free preparations of stable microbubbles in polysaccharide gels

MRI of fluids containing lipid coated microbubbles has been shown to be an effective toot for measuring the local fluid pressure. However, the intrinsically buoyant nature of these microbubbles precludes lengthy measurements due to their vertical migration under gravity and pressure-induced coalescence. A novel preparation is presented which is shown to minimize both these effects for at least 25 min. By using a 2% polysaccharide gel base with a small concentration of glycerol and 1,2-distearoyl-sn-glycero-3-phosphocholine coated gas microbubbles, MR measurements are made for pressures between 0.95 and 1.44 bar. The signal drifts due to migration and amalgamation are shown to be minimized for such an experiment whilst yielding very high NMR sensitivities up to 38% signal change per bar.

3D culture of bone-derived cells immobilised in alginate following light-triggered gelation

Photoreactive liposomes have been exploited as a means of developing 3D tissue constructs. Liposomes formulated using the photosensitive lipid 1,2-bis(4-(n-butyl)phenylazo-4′-phenylbutyroyl)phosphatidylcholine (Bis Azo PC), which undergoes conformational change on stimulation with long wavelength ultraviolet light, were prepared with entrapped CaCl2 before being incorporated into a 4% alginate solution. It was shown that stimulation of the photosensitive lipid using a light emitting diode (LED) (peak emission at 385 nm, dose equivalent to 9 mJ/cm2) caused the release of liposome-entrapped CaCl2, resulting in cross-linking of the alginate solution and immobilisation of bone-derived cells over a range of seeding densities, approximately 97% of which remained viable for periods of up to 14 days in culture. Entrapment volumes of a variety of liposome types were evaluated and interdigitating fusion vesicles were identified as having the highest payload (24%), however the inclusion of cholesterol as a means of shifting Bis Azo PC sensitivity into the visible light wavelengths resulted in an approximately 10-fold reduction in calcium entrapment. This application of light-sensitised liposomes offers the potential to create complex tissue engineering substrates containing cells immobilised in precise locations, in contrast with substrates onto which cells are seeded post-production. © 2007 Elsevier B.V. All rights reserved.

Extracting protein-protein interactions from MEDLINE using the hidden vector state model

A major challenge in text mining for biomedicine is automatically extracting protein-protein interactions from the vast amount of biomedical literature. We have constructed an information extraction system based on the Hidden Vector State (HVS) model for protein-protein interactions. The HVS model can be trained using only lightly annotated data whilst simultaneously retaining sufficient ability to capture the hierarchical structure. When applied in extracting protein-protein interactions, we found that it performed better than other established statistical methods and achieved 61.5% in F-score with balanced recall and precision values. Moreover, the statistical nature of the pure data-driven HVS model makes it intrinsically robust and it can be easily adapted to other domains.

Enhanced spectral sensitivity of fibre long period gratings to refractive index of aqueous solutions utilising copper patterned coatings

A set of long period grating devices have been fabricated in photosensitive single mode fibre coated with a series of copper rings (period of 380μm, 50% duty cycle and length of 4cm). The long period gratings were inscribed with a uniform UV-laser exposure across the entire length of the copper ring patterned coating. The devices ranged in copper thickness from 0.5μm to 1.5μm. In addition, a control long period grating was fabricated in the same type of fibre with the same period for comparison. The refractive index and temperature spectral sensitivity of these devices were investigated and it was found that the index and temperature sensitivity is a function of the thickness of the copper rings, as supported by theoretical modelling. Furthermore, the index sensitivity of these devices in the 1.333 index region is greater than the control long period grating. The patterned 0.5μm coated long period grating gave a sensitivity of Δλ/Δn = -74 nm leading to a resolution of 1.4×10-3 compared to the control which had a sensitivity of Δλ/Δn = -32 nm with a resolution of 3.2×10-3 in the index region of 1.320 to 1.380 (aqueous solution regime). This demonstrates a two fold increase in the sensitivity. This novel fibre long period grating device shows potential for increasing the resolution of measurements of the index of aqueous solutions.

Coupling between counterpropagating cladding modes in fiber Bragg gratings

We present an experimental demonstration of energy transfer between counterpropagating cladding modes in a fiber Bragg grating (FBG). A strong FBG written in a standard photosensitive optical fiber is illuminated with a single cladding mode, and the power transferred between the forward propagating cladding mode and different backward propagating cladding modes is measured by using two auxiliary long period gratings. Resonances between cladding modes having 30 pm bandwidth and 8 dB rejection have been observed.