Analysis of phase retrieval from multiple images

This thesis considers the calculation of phase from sets of phase contrast and defocused images. An improvement to phase contrast imaging is developed that combines three phase contrast images. This method results in a reduction in the phase error by a factor of up to 20 in comparison to using a single image. Additionally the method offers the potential for optimisation and the extension to an arbitrary number of images. Phase diversity using defocused images is considered in more depth where the intensity transport equation is used to calculate the phase. First a Green's function approach to solving this equation was considered. One of the Green's functions stated in the literature is shown to be incorrect, the other two are shown to be correct both giving equivalent phase estimates. A further improvement is made to this method by removing the singularities in the phase calculation process. As an alternative to the Green's function solution a Fourier transform approach is also considered. A complete solution to the intensity transport equation is derived with inclusion of the boundary conditions. This completes the method incompletely described in the literature. Through simulation, generic key factors are identified for the potential optimisation of experimental and numerical process to improve the estimated phase. Determining 3D structural information of an object from the phase calculated in a single plane is considered using an iterative process. It is shown that this process is limited but can be used, in some cases, to generate an approximate representation of the object

Growing hydrodynamic modes in Keplerian accretion disks during secondary perturbations: Elliptical vortex effects

The origin of hydrodynamic turbulence, and in particular of an anomalously enhanced angular momentum transport, in accretion disks is still an unsolved problem. This is especially important for cold disk systems which are practically neutral in charge and therefore turbulence can not be of magnetohydrodynamic origin. While the flow must exhibit some instability and then turbulence in support of the transfer of mass inward and angular momentum outward, according to the linear perturbation theory, in absence of magnetohydrodynamic effects, it should always be stable. We demonstrate that the three-dimensional secondary disturbance to the primarily perturbed disk, consisting of elliptical vortices, gives significantly large hydrodynamic growth in such a system and hence may suggest a transition to an ultimately turbulent state. This result is essentially applicable to accretion disks around quiescent cataclysmic variables, in proto-planetary and star-forming disks, the outer region of disks in active galactic nuclei, where the gas is significantly cold and thus the magnetic Reynolds number is smaller than 10^4.Comment: 21 pages including 4 figures, aastex format; Accepted for publication in The Astrophysical Journa

Microwave control electrodes for scalable, parallel, single-qubit operations in a surface-electrode ion trap

We propose a surface ion trap design incorporating microwave control electrodes for near-field single-qubit control. The electrodes are arranged so as to provide arbitrary frequency, amplitude and polarization control of the microwave field in one trap zone, while a similar set of electrodes is used to null the residual microwave field in a neighbouring zone. The geometry is chosen to reduce the residual field to the 0.5% level without nulling fields; with nulling, the crosstalk may be kept close to the 0.01% level for realistic microwave amplitude and phase drift. Using standard photolithography and electroplating techniques, we have fabricated a proof-of-principle electrode array with two trapping zones. We discuss requirements for the microwave drive system and prospects for scalability to a large two-dimensional trap array.Comment: 8 pages, 6 figure

Dynamical energy analysis on mesh grids: a new tool for describing the vibro-acoustic response of complex mechanical structures

We present a new approach for modelling noise and vibration in complex mechanical structures in the mid-to-high frequency regime. It is based on a dynamical energy analysis (DEA) formulation which extends standard techniques such as statistical energy analysis (SEA) towards non-diffusive wave fields. DEA takes into account the full directionality of the wave field and makes sub-structuring obsolete. It can thus be implemented on mesh grids commonly used, for example, in the finite element method (FEM). The resulting mesh based formulation of DEA can be implemented very efficiently using discrete flow mapping (DFM) as detailed in [1] and described here for applications in vibro-acoustics

Older adults’ experiences of the rehabilitation process in acute health care.

Rehabilitation is a key component of nursing and allied healthcare professionals’ roles in most health and social care settings. This paper reports on stage 2 of an action research project to ascertain older adult’s experience of rehabilitation. Twenty postdischarge interviews were conducted and the interview transcripts were analysed using thematic content analysis. All older adults discharged from an acute older acute rehabilitation ward to their own homes in the community were eligible to participate. The only exclusion criterion was older adults who were thought to be unable to give consent to participate by the nurse in charge and the researcher. Whilst 92 older adults were eligible to participate in this research study, only 20 were interviewed. The findings from this study suggest that older adults valued communication with health professionals but were aware of their time constraints that hindered communication. This study suggests that both nurses and allied health professionals are not actively providing rehabilitative services to promote health and well-being which contradicts the focus of active ageing. Furthermore, there was evidence of unmet needs on discharge, and older adults unable to recall the professions that were involved in their interventions and the rationale for therapy input. It is suggested that further research is needed to explore the effectiveness of allied health rehabilitation in the acute setting. This study highlights the need for further research into older adults’ perceptions of the rehabilitation process in the acute setting

Does Colour Filling-In Account for Colour Perception in Natural Images?

It is popular to attribute the appearance of extended colour fields to a process of filling-in from the differential colour signals at colour edges, where one colour transitions to another. We ask whether such a process can account for the appearance of extended colour fields in natural images. Some form of colour filling-in must underlie the equiluminant colour Craik-O’Brien-Cornsweet effect and the Water colour Effect, but these effects are too weak to account for the appearance of extended colour fields in natural images. Moreover, the graded colour disappearance effect reported as evidence for colour filling-in does not work under natural viewing conditions. We demonstrate that natural images do not look very colourful when their colour is restricted to edge transitions . Moreover, purely chromatic images with maximally graded (‘edgeless’) transitions look fully colourful. Consequently, we conclude that colour filling-in makes no more than a minor contribution to the appearance of extended colour regions in natural images

Global Substrate Profiling of Proteases in Human Neutrophil Extracellular Traps Reveals Consensus Motif Predominantly Contributed by Elastase

Neutrophil extracellular traps (NETs) consist of antimicrobial molecules embedded in a web of extracellular DNA. Formation of NETs is considered to be a defense mechanism utilized by neutrophils to ensnare and kill invading pathogens, and has been recently termed NETosis. Neutrophils can be stimulated to undergo NETosis ex vivo, and are predicted to contain high levels of serine proteases, such as neutrophil elastase (NE), cathepsin G (CG) and proteinase 3 (PR3). Serine proteases are important effectors of neutrophil-mediated immunity, which function directly by degrading pathogenic virulent factors and indirectly via proteolytic activation or deactivation of cytokines, chemokines and receptors. In this study, we utilized a diverse and unbiased peptide library to detect and profile protease activity associated with NETs induced by phorbol-12-myristate-13-acetate (PMA). We obtained a "proteolytic signature" from NETs derived from healthy donor neutrophils and used proteomics to assist in the identification of the source of this proteolytic activity. In addition, we profiled each neutrophil serine protease and included the newly identified enzyme, neutrophil serine protease 4 (NSP4). Each enzyme had overlapping yet distinct endopeptidase activities and often cleaved at unique sites within the same peptide substrate. The dominant proteolytic activity in NETs was attributed to NE; however, cleavage sites corresponding to CG and PR3 activity were evident. When NE was immunodepleted, the remaining activity was attributed to CG and to a lesser extent PR3 and NSP4. Our results suggest that blocking NE activity would abrogate the major protease activity associated with NETs. In addition, the newly identified substrate specificity signatures will guide the design of more specific probes and inhibitors that target NET-associated proteases

Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNaV1.7

The human voltage-gated sodium channel sub-type 1.7 (hNaV1.7) is emerging as an attractive target for the development of potent and sub-type selective novel analgesics with increased potency and fewer side effects than existing therapeutics. HwTx-IV, a spider derived peptide toxin, inhibits hNaV1.7 with high potency and is therefore of great interest as an analgesic lead. In the current study we examined whether engineering a HwTx-IV analogue with increased ability to bind to lipid membranes would improve its inhibitory potency at hNaV1.7. This hypothesis was explored by comparing HwTx-IV and two analogues [E1PyrE]HwTx-IV (mHwTx-IV) and [E1G,E4G,F6W,Y30W]HwTx-IV (gHwTx-IV) on their membrane-binding affinity and hNaV1.7 inhibitory potency using a range of biophysical techniques including computational analysis, NMR spectroscopy, surface plasmon resonance, and fluorescence spectroscopy. HwTx-IV and mHwTx-IV exhibited weak affinity for lipid membranes, whereas gHwTx-IV showed improved affinity for the model membranes studied. In addition, activity assays using SH-SY5Y neuroblastoma cells expressing hNaV1.7 showed that gHwTx-IV has increased activity at hNaV1.7 compared to HwTx-IV. Based on these results we hypothesize that an increase in the affinity of HwTx-IV for lipid membranes is accompanied by improved inhibitory potency at hNaV1.7 and that increasing the affinity of gating modifier toxins to lipid bilayers is a strategy that may be useful for improving their potency at hNaV1.7

The Magnetohydrodynamic Kelvin-Helmholtz Instability: A Three-Dimensional Study of Nonlinear Evolution

We investigate through high resolution 3D simulations the nonlinear evolution of compressible magnetohydrodynamic flows subject to the Kelvin-Helmholtz instability. We confirm in 3D flows the conclusion from our 2D work that even apparently weak magnetic fields embedded in Kelvin-Helmholtz unstable plasma flows can be fundamentally important to nonlinear evolution of the instability. In fact, that statement is strengthened in 3D by this work, because it shows how field line bundles can be stretched and twisted in 3D as the quasi-2D Cat's Eye vortex forms out of the hydrodynamical motions. In our simulations twisting of the field may increase the maximum field strength by more than a factor of two over the 2D effect. If, by these developments, the Alfv\'en Mach number of flows around the Cat's Eye drops to unity or less, our simulations suggest magnetic stresses will eventually destroy the Cat's Eye and cause the plasma flow to self-organize into a relatively smooth and apparently stable flow that retains memory of the original shear. For our flow configurations the regime in 3D for such reorganization is $4\lesssim M_{Ax} \lesssim 50$, expressed in terms of the Alfv\'en Mach number of the original velocity transition and the initial Alfv\'en speed projected to the flow plan. For weaker fields the instability remains essentially hydrodynamic in early stages, and the Cat's Eye is destroyed by the hydrodynamic secondary instabilities of a 3D nature. Then, the flows evolve into chaotic structures that approach decaying isotropic turbulence. In this stage, there is considerable enhancement to the magnetic energy due to stretching, twisting, and turbulent amplification, which is retained long afterwards. The magnetic energy eventually catches up to the kinetic energy, and the nature of flows become magnetohydrodynamic.Comment: 11 pages, 12 figures in degraded jpg format (2 in color), paper with original quality figures available via ftp at ftp://ftp.msi.umn.edu/pub/users/twj/mhdkh3dd.ps.gz or ftp://canopus.chungnam.ac.kr/ryu/mhdkh3dd.ps.gz, to appear in The Astrophysical Journa