Profluorescent protease substrates: intramolecular dimers described by the exciton model.

Xanthene dyes are known to form dimers with spectral characteristics that have been interpreted in terms of exciton theory. A unique aspect of H-type dimers is the fluorescence quenching that accompanies their formation. Using the principles of exciton theory as a guide, a series of protease substrates was synthesized with a xanthene dye on each side of the cleavage site. To bring the attached dyes into spatial proximity to form a dimer, the molecular design included structure determinant regions in the amino acid sequence. In addition, chromophores were chosen such that changes in absorption spectra indicative of exciton splitting were anticipated. Cleavage of the peptides by a protease resulted in disruption of the dimers and indeed significant absorption spectral changes were observed. Furthermore, substrate cleavage was accompanied by at least an order of magnitude increase in fluorescence intensity. This has allowed determination of intracellular elastase activity using a fluorescence microscope equipped with standard optics.

3XMM J185246.6+003317: another low magnetic field magnetar

We study the outburst of the newly discovered X-ray transient 3XMMJ185246.6+003317, re-analyzing all available XMM-Newton observations of the source to perform a phase-coherent timing analysis, and derive updated values of the period and period derivative. We find the source rotating at P = 11.55871346(6) s (90% confidence level; at epoch MJD 54728.7) but no evidence for a period derivative in the seven months of outburst decay spanned by the observations. This translates to a 3σ upper limit for the period derivative of ˙ P <1.4×10−13 s s−1, which, assuming the classical magneto-dipolar braking model, gives a limit on the dipolar magnetic field of Bdip < 4.1×1013 G. The X-ray outburst and spectral characteristics of 3XMM J185246.6+003317 confirm its identification as a magnetar, but the magnetic field upper limit we derive defines it as the third “low-B” magnetar discovered in the past 3 yr, after SGR 0418+5729 and Swift J1822.3−1606. We have also obtained an upper limit to the quiescent luminosity (<4×1033 erg s−1), in line with the expectations for an old magnetar. The discovery of this new low field magnetar reaffirms the prediction of about one outburst per year from the hidden population of aged magnetars.

Quiescent state and outburst evolution of SGR 0501+4516

We report on the quiescent state of the soft gamma repeater SGR 0501+4516 observed by XMM–Newton on 2009 August 30. The source exhibits an absorbed flux ∼75 times lower than that measured at the peak of the 2008 outburst, and a rather soft spectrum, with the same value of the blackbody temperature observed with ROSAT back in 1992. This new observation is put into the context of all existing X-ray data since its discovery in 2008 August, allowing us to complete the study of the timing and spectral evolution of the source from outburst until its quiescent state. The set of deep XMM–Newton observations performed during the few years time-scale of its outburst allows us to monitor the spectral characteristics of this magnetar as a function of its rotational period, and their evolution along these years. After the first ∼10 d, the initially hot and bright surface spot progressively cooled down during the decay. We discuss the behaviour of this magnetar in the context of its simulated secular evolution, inferring a plausible dipolar field at birth of 3 × 1014 G, and a current (magnetothermal) age of ∼10 kyr.

The variable colours of the fiddler crab Uca vomeris and their relation to background and predation

Colour changes in fiddler crabs have long been noted, but a functional interpretation is still lacking. Here we report that neighbouring populations of Uca vomeris in Australia exhibit different degrees of carapace colours, which range from dull mottled to brilliant blue and white. We determined the spectral characteristics of the mud substratum and of the carapace colours of U. vomeris and found that the mottled colours of crabs are cryptic against this background, while display colours provide strong colour contrast for both birds and crabs, but luminance contrast only for a crab visual system. We tested whether crab populations may become cryptic under the influence of bird predation by counting birds overflying or feeding on differently coloured colonies. Colonies with cryptically coloured crabs indeed experience a much higher level of bird presence, compared to colourful colonies. We show in addition that colourful crab individuals subjected to dummy bird predation do change their body colouration over a matter of days. The crabs thus appear to modify their social signalling system depending on their assessment of predation risk.

Coarse threat images reveal theta oscillations in the amygdala: a magnetoencephalography study

Neurocognitive models propose a specialized neural system for processing threat-related information, in which the amygdala plays a key role in the analysis of threat cues. fMRI research indicates that the amygdala is sensitive to coarse visual threat relevant information—for example, low spatial frequency (LSF) fearful faces. However, fMRI cannot determine the temporal or spectral characteristics of neural responses. Consequently, we used magnetoencephalography to explore spatiotemporal patterns of activity in the amygdala and cortical regions with blurry (LSF) and normal angry, fearful, and neutral faces. Results demonstrated differences in amygdala activity between LSF threat-related and LSF neutral faces (50-250 msec after face onset). These differences were evident in the theta range (4-8 Hz) and were accompanied by power changes within visual and frontal regions. Our results support the view that the amygdala is involved in the early processing of coarse threat related information and that theta is important in integrating activity within emotion-processing networks.

Advanced UV inscribed fibre grating structures and applications in optical sensing and laser systems

This thesis presents detailed investigation of UV inscribed fibre grating based devices and novel developments in the applications of such devices in optical sensing and fibre laser systems. The major contribution of this PhD programme includes the systematic study on fabrication, spectral characteristics and applications of different types of UV written in-fibre gratings such as Type I and IA Fibre Bragg Gratings (FBGs), Chirped Fibre Bragg Gratings (CFBGs) and Tilted Fibre Gratings (TFGs) with small, large and 45º tilted structures inscribed in normal silica fibre. Three fabrication techniques including holographic, phase-mask and blank beam exposure scanning, which were employed to fabricate a range of gratings in standard single mode fibre, are fully discussed. The thesis reports the creation of smart structures with self-sensing capability by embedding FBG-array sensors in Al matrix composite. In another part of this study, we have demonstrated the particular significant improvements made in sensitising standard FBGs to the chemical surrounding medium by inducing microstructure to the grating by femtosecond (fs) patterning assisted chemical etching technique. Also, a major work is presented for the investigation on the structures, inscription methods and spectral Polarisation Dependent Loss (PDL) and thermal characteristics of different angle TFGs. Finally, a very novel application in realising stable single polarisation and multiwavelength switchable Erbium Doped Fibre Lasers (EDFLs) using intracavity polarisation selective filters based on TFG devices with tilted structures at small, large and exact 45° angles forms another important contribution of this thesis.

Soliton switching using cascaded nonlinear-optical loop mirrors

We demonstrate multiple-peaked switching in a nonlinear-optical loop mirror and present an experimental investigation of device cascading in the soliton regime based on a sequence of two independent nonlinear-optical loop mirrors. Cascading leads to an enhanced switching response with sharper switching edges, flattened peaks, and increased interpeak extinction ratios. We observe that pulses emerging from the cascade retain the sech2 temporal profile of a soliton with minimal degradation in the spectral characteristics.

Advanced fibre gratings fabricated in standard and infrared glass fibres by ultraviolet and near-infrared-femtosecond lasers

In this thesis, I describe studies on fabrication, spectral characteristics and applications of tilted fibre gratings (TFGs) with small, large and 45° tilted structures and novel developments in fabrication of fibre Bragg gratings (FBGs) and long period gratings (LPGs) in normal silica and mid-infrared (mid-IR) glass fibres using near-IR femtosecond laser. One of the major contributions presented in this thesis is the systematic investigation of structures, inscription methods and spectral, polarisation dependent loss (PDL) and thermal characteristics of TFGs with small (<45°), large (>45°) and 45° tilted structures. I have experimentally characterised TFGs, obtaining relationships between the radiation angle, central wavelength of the radiation profile, Bragg resonance and the tilt angle, which are consistent with theoretical simulation based on the mode-coupling theory. Furthermore, thermal responses have been measured for these three types of TFGs, showing the transmission spectra of large and 45° TFGs are insensitive to the temperature change, unlike the normal and small angle tilted FBGs. Based on the distinctive optical properties, TFGs have been developed into interrogation system and sensors, which form the other significant contributions of the work presented in this thesis. The 10°-TFG based 800nm WDM interrogation system can function not just as an in-fibre spectrum analyser but also possess refractive index sensing capability. By utilising the unique polarisation properties, the 81 °-TFG based sensors are capable of sensing the transverse loading and twisting with sensitivities of 2.04pW/(kg/m) and 145.90pW/rad, repectively. The final but the most important contribution from the research work presented in this thesis is the development of novel grating inscription techniques using near-IR femtosecond laser. A number of LPGs and FBGs were successfully fabricated in normal silica and mid-IR glass fibres using point-by-point and phase-mask techniques. LPGs and 1st and 2nd order FBGs have been fabricated in these mid-IR glass fibres showing resonances covering the wavelength range from 1200 to 1700nm with the strengths up to 13dB. In addition, the thermal and strain sensitivities of these gratings have been systematically investigated. All the results from these initial but systematic works will provide useful function characteristics information for future fibre grating based devices and applications in mid-IR range.

The application of remote sensing to water resources

Techniques are developed for the visual interpretation of drainage features from satellite imagery. The process of interpretation is formalised by the introduction of objective criteria. Problems of assessing the accuracy of maps are recognized, and a method is developed for quantifying the correctness of an interpretation, in which the more important features are given an appropriate weight. A study was made of imagery from a variety of landscapes in Britain and overseas, from which maps of drainage networks were drawn. The accuracy of the mapping was assessed in absolute terms, and also in relation to the geomorphic parameters used in hydrologic models. Results are presented relating the accuracy of interpretation to image quality, subjectivity and the effects of topography. It is concluded that the visual interpretation of satellite imagery gives maps of sufficient accuracy for the preliminary assessment of water resources, and for the estimation of geomorphic parameters. An examination is made of the use of remotely sensed data in hydrologic models. It is proposed that the spectral properties of a scene are holistic, and are therefore more efficient than conventional catchment characteristics. Key hydrologic parameters were identified, and were estimated from streamflow records. The correlation between hydrologic variables and spectral characteristics was examined, and regression models for streamflow were developed, based solely on spectral data. Regression models were also developed using conventional catchment characteristics, whose values were estimated using satellite imagery. It was concluded that models based primarily on variables derived from remotely sensed data give results which are as good as, or better than, models using conventional map data. The holistic properties of remotely sensed data are realised only in undeveloped areas. In developed areas an assessment of current land-use is a more useful indication of hydrologic response.

The application of fibre Bragg grating networks as strain sensors and as phased array antenna true time delay elements

The fabrication of in-fibre Bragg gratings, and the application of arrays of such gratings as strain sensors and as true time delay elements for the control of phased array antennas is reported. Chirped period Bragg gratings were produced using the fibre deformation fabrication technique, with chirps of between 2.9nm and 17.3nm achieved. Arrays of 5mm and 2mm long uniform period Bragg gratings were fabricated using the inscription method, for use as true time delay elements,dissimilar wavefronts and their spectral characteristics recorded. The uniform period grating arrays were used to create minimum time delays of 9.09ps, 19.02ps and 31ps; making them suitable for controlling phased array antennas operating at RF frequencies of up to 3GHz, with 10° phase resolution. Four 4mm long chirped gratings were produced using the dissimilar wavefronts fabrication method, having chirps of 7nm, 12nm, 20nm and 30nm, and were used to create time delays of between 0.3ps and 59ps. Hence they are suitable for controlling phased array antennas at RF frequencies of up to 48GHz. The application of in fibre Bragg gratings as strain sensors within smart structure materials was investigated, with their sensitivity to applied strain and compression measured for both embedded and surface mounted uniform period and fibre Fabry-Perot filter gratings. A fibre Bragg grating sensor demultiplexing scheme based on a liquid crystal filled Fabry-Perot etalon tuneable transmission filter was proposed, successfully constructed and fully characterised. Three characteristics of the LCFP etalon were found to pose operational limitations to its application in a Bragg grating sensor system; most significantly, the resonance peak wavelength was highly (-2,77nm/°C) temperature dependent. Several methods for minimising this temperature sensitivity were investigated, but enjoyed only limited success. It was therefore concluded that this type (E7 filled) of LCFP etalon is unsuitable for use as a Bragg grating sensor demultiplexing element.

Disconnected brains:what is the role of fMRI in connectivity research?

In this paper we consider how functional Magnetic Resonance Imaging (fMRI) has been used to study cortical connectivity in autism and autistic spectrum disorders (ASD). We discuss those studies that have contributed to the evidence supporting a model of disordered cortical connectivity in autism and (ASD), with a focusing emphasis on the application to research into the underconnectivity model. We note that the analytical techniques employed are limited and do not allow interpretation in terms of effective, or directional connectivity, nor do they provide information about the temporal or spectral characteristics of the functional networks being studied. We highlight how currently the features of neural generators that are being assessed by functional connectivity in fMRI are unclear. In addition, we note the importance in clinical studies of considering the consequences of task choice for the nature of the imaging data that can be collected and also of individual differences in participant state and trait characteristics for the accurate interpretation of imaging data. We discuss how alternative techniques such as EEG/MEG may address the limitations of fMRI in assessing brain connectivity, and additionally consider the potential of multimodal approaches. We conclude that fMRI has made significant contributions towards our understanding of the brain in terms of neural systems but that the conclusions drawn from its application in the sphere of autism research need to be approached with caution. It is important in research of this kind that we are aware of the need to examine the methodological and analytical techniques closely when applying findings in clinical populations, not only when they are used to support the development of theoretical models but also to inform diagnostic or treatment decisions.

Impact of FBGs reflectivity shape on spectra of radiation in 10 km Raman fibre laser

We study the impact of the shape of fibre Bragg gratings spectral reflectivity on spectral broadening in a 10 km Raman fibre laser. We show that, at high powers, spectral characteristics are determined by intra-cavity processes rather than by the gratings profile.

Gratings in novel fibre geometry for applications in shape sensing

A long period grating (LPG) fabricated in progressive three-layered (PTL) fibre is described. The grating with a period of 391µm, had dual attenuation bands associated with a particular cladding mode. The dual attenuation bands have been experimentally characterised for their spectral sensitivity to bending, which resulted in the highest sensitivity to bending seen for this particular fibre and temperature. The spectral characteristics of the fibre have been modelled giving good agreement to the experimental data as well as showing that the attenuation bands are both associated with the second order HE/EH2,n cladding mode.

Multiplexers and demultiplexers based on fibre Bragg gratings and optical circulators for DWDM systems

Two different architectures of multiplexers/demultiplexers based on 4×1 and 1×4 configurations are discussed. These architectures are implemented using apodized fibre Bragg gratings as optical filters and optical circulators. The spectral characteristics of the devices for channel separations of 100 GHz and 50 GHz are analysed and their performance is evaluated. Optical switch and cross-connect configurations are also demonstrated.

Impact of FBGs reflectivity shape on spectra of radiation in 10 km Raman fibre laser

We study the impact of the shape of fibre Bragg gratings spectral reflectivity on spectral broadening in a 10 km Raman fibre laser. We show that, at high powers, spectral characteristics are determined by intra-cavity processes rather than by the gratings profile.