STRATEGIES FOR TARGETING LENTIVIRAL VECTORS

Lentiviral gene therapy has held great promise for treating a wide range of neurological disorders due to its ability to stably integrate into the genome of nondividing cells like neurons, in addition to dividing cells. The nervous system is a complex and highly heterogeneous system, and while a therapeutic intervention may have beneficial effects in one population of cells it may have severe side effects in another. For this reason, specific targeting of lentiviral vectors is crucial for their ultimate utility for research and clinical research use. Two different approaches for focusing the targeting of lentiviral vectors were employed in these studies. The first method involved assessing the effects of vector production strategies on the resulting virus’s tropism both in vivo and in vitro. The changes in vector transduction were determined via flow cytometry on cells in culture and immunohistochemistry following brain injections. Results from these experiments suggest that while the production conditions do impact the vectors efficacy, there is not a distinct effect on their tropism. A unique characteristic of retroviral and lentiviral vectors is their capacity for being pseudotyped, conferring a new tropism on the vector. Native tropisms are generally not specific beyond very broad cell types, which may not be sufficient for all applications. In this case, chimeric targeting molecules can provide an even more refined targeting profile compared to native pseudotypes. The second approach utilizes novel chimeric glycoproteins made from nerve growth factor and the vesicular stomatitis virus glycoprotein. These chimeras are designed to pseudotype lentiviral vectors to target nociceptive sensory neurons for a variety of disorders. While these chimeras were successfully produced as protein, they were misfolded and sequestered in the endoplasmic reticulum and therefore unavailable to produce lentivirus. While neither strategy was completely successful, they do provide interesting information for the design and creation of lentiviral vectors. This research shows that small differences in the steps followed as part of a lentivirus production protocol can greatly impact the resulting vectors efficacy. It also shows that while VSV has been used to create chimeric glycoproteins, not all targeting molecules are suitable for this purpose

Phase-Change Meta-Devices for Tuneable Bandpass Filtering in the Infrared

Tuneable light filters, especially those which are compact and fast to tune, are essential in a wide range of technologies, especially for multispectral imaging applications. However, state-of-the-art approaches to create such filters all possess drawbacks, with many wavelength regions poorly served. This thesis attempts to address this problem by combining metasurfaces which support extraordinary optical transmission (ultra-thin band-pass filters) with chalcogenide phase-change materials (adding dynamic tuneability). The optical properties of phase-change materials are very different in their amorphous and crystalline states and switching between such states can be rapidly controlled via thermal excitations. In this work nine different phase-change materials, including alloys of GeTe, GeSbTe, GeSbSeTe and GaLaS, were optically and elementally characterised and assessed for their application-specific suitability. The resulting materials data was used to computationally design and evaluate a range of tuneable infrared filter device designs both optically and thermally. These filters exhibit high transmission (≈80% at best) with large spectral tuning ranges of approximately +50% relative to their shortest wavelength; this range is sufficient to cover entire atmospheric transmission windows. This is the first such combination of phase-change materials and extraordinary optical transmission for application from the visible through to long-wave infrared (14 μm) regions of the spectrum. A rigorous computational study was conducted to produce comprehensive design guidelines for such filters, and confirm the viability of in-situ electrical switching. Several filter devices were experimentally fabricated, and the viability for a number of applications, including tuneable filtering, chemical sensing and infrared displays, was investigated and confirmed computationally.Engineering and Physical Sciences Research Council (EPSRC

The Effect Of Affirming Scientific Belief On Existential Anxiety

A Research Methods Project supervised by Dr. Hilary Stebbins (Spring 2021)

Controlling the nature of a charged impurity in a bath of Feshbach dimers

We theoretically study the dynamics of a trapped ion that is immersed in an ultracold gas of weakly bound atomic dimers created by a Feshbach resonance. Using quasi-classical simulations, we find a crossover from dimer dissociation to molecular ion formation depending on the binding energy of the dimers. The location of the crossover strongly depends on the collision energy and the time-dependent fields of the Paul trap. Deeply bound dimers lead to fast molecular ion formation, with rates approaching the Langevin collision rate $\Gamma'_\text{L}\approx4.8\times10^{-9}\,$cm$^3$s$^{-1}$. The kinetic energies of the created molecular ions have a median below $1\,$mK, such that they will stay confined in the ion trap. We conclude that interacting ions and Feshbach molecules may provide a novel approach towards the creation of ultracold molecular ions with applications in precision spectroscopy and quantum chemistry.Comment: 9 pages and 12 figures including appendice

Phase-change band-pass filters for multispectral imaging

This is the author accepted manuscript. The final version is available from SPIE via the DOI in this recordPhase-change materials (PCMs) provide a route to adding dynamic tunability and reconfigurability to many types of photonic devices by changing the phase-state of the PCM itself. In this work we discuss the use of the phase-change alloy GeSbTe (GST) in the design of dynamically tunable filters operating in the infrared. GST is used to manipulate the extraordinary optical transmission of a periodic hole-array in a metallic layer, so creating ultra-thin, tunable band-pass filters. We discuss the use of such filters for multispectral imaging, suggest some approaches to overcome various practical challenges, and, finally, show that through the use of appropriate post processing algorithms this tunable filter could provide a cheap, ultra-thin, real-time, and relatively high performance multispectral imaging device.CDW acknowledges funding via the US Naval Research Laboratories ONRG programme (#N62909-16-1-2174) and the EPSRC ChAMP and WAFT grants (EP/M015130/1 and EP/M015173/1). LT acknowledges funding via the EPSRC CDT in Metamaterials (EP/L015331/1) and via QinetiQ PL

Engine cylinder pressure reconstruction using crank kinematics, block vibrations, and time-delay neural networks

Time-delay feed-forward Artificial Neural Networks are examined for gasoline engine cylinder pressure reconstruction using both measured crank kinematics obtained from a shaft encoder, and measured engine cylinder block vibrations obtained from a production knock sensor. Initially, the study focuses on the information content associated with measured data, which is considered to be of equal importance to the particular network architecture and the training methodology. Several hypotheses are constructed, which when tested, reveal the influence of the data information content on the reconstruction potential and limitations. These hypotheses are tested on real data from a 3-cylinder (DISI) engine. Three distinct ideas emerge through this testing process, which are combined to produce a single pressure reconstruction methodology. Reconstruction results obtained via this methodology, applied to crank kinematics associated with steady-state engine operation, show a marked improvement over previously published reconstruction accuracy. Moreover, in steady-state engine operation, the application of this methodology to acceleration measurements of cylinder block vibration, obtained from a knock sensor, show very significant improvements over previous attempts. But the direct application of this same reconstruction methodology to transient engine operation, proves to be problematic. However, a novel generalisation of the approach in the form of a time-dependent feed-forward neural network is proposed and the required adaptation made to the use of the Levenberg-Marquardt training algorithm. This time-dependent approach has been tested under limited transient conditions and shown in the thesis to give good results, therefore offering considerable potential for use with real engine operation. Overall, the thesis shows that by careful processing of measured engine data, standard neural network architectures and standard training algorithms can be used to reconstruct engine cylinder pressure

Engine cylinder pressure reconstruction using crank kinematics and recurrently-trained neural networks

A recurrent non-linear autoregressive with exogenous input (NARX) neural network is proposed, and a suitable fully-recurrent training methodology is adapted and tuned, for reconstructing cylinder pressure in multi-cylinder IC engines using measured crank kinematics. This type of indirect sensing is important for cost effective closed-loop combustion control and for On-Board Diagnostics. The challenge addressed is to accurately predict cylinder pressure traces within the cycle under generalisation conditions: i.e. using data not previously seen by the network during training. This involves direct construction and calibration of a suitable inverse crank dynamic model, which owing to singular behaviour at top-dead-centre (TDC), has proved difficult via physical model construction, calibration, and inversion. The NARX architecture is specialised and adapted to cylinder pressure reconstruction, using a fully-recurrent training methodology which is needed because the alternatives are too slow and unreliable for practical network training on production engines. The fully-recurrent Robust Adaptive Gradient Descent (RAGD) algorithm, is tuned initially using synthesised crank kinematics, and then tested on real engine data to assess the reconstruction capability. Real data is obtained from a 1.125 litre, 3-cylinder, in-line, direct injection spark ignition (DISI) engine involving synchronised measurements of crank kinematics and cylinder pressure across a range of steady-state speed and load conditions. The paper shows that a RAGD-trained NARX network using both crank velocity and crank acceleration as input information, provides fast and robust training. By using the optimum epoch identified during RAGD training, acceptably accurate cylinder pressures, and especially accurate location-of-peak-pressure, can be reconstructed robustly under generalisation conditions, making it the most practical NARX configuration and recurrent training methodology for use on production engines

Grain‐scale dependency of metamorphic reaction on crystal plastic strain

The Breaksea Orthogneiss in Fiordland, New Zealand preserves water‐poor intermediate and mafic igneous rocks that were partially recrystallized to omphacite granulite and eclogite, respectively, at P ≈ 1.8 GPa and T ≈ 850°C. Metamorphic reaction consumed plagioclase and produced grossular‐rich garnet, jadeite‐rich omphacite, clinozoisite and kyanite. The extent of metamorphic reaction, identified by major and trace element composition and microstructural features, is patchy on the grain and outcrop scale. Domains of re‐equilibration coincide with areas that exhibit higher strain suggesting a causal link between crystal plastic strain and metamorphic reaction. Quantitative orientation analysis (EBSD) identifies gradual and stepped changes in crystal lattice orientations of igneous phenocrysts that are surrounded by homophase areas of neoblasts, characterized by high grain boundary to volume ratios and little to no internal lattice distortion. The narrow, peripheral compositional modification of less deformed garnet and omphacite phenocrysts reflects limited lattice diffusion in areas that lacked three‐dimensional networks of interconnected low‐angle boundaries. Low‐angle boundaries acted as elemental pathways (pipe diffusion) that enhanced in‐grain element diffusion. The scale of pipe diffusion is pronounced in garnet relatively to clinopyroxene. Strain‐induced mineral transformation largely controlled the extent of high‐T metamorphic reaction under relatively fluid‐poor conditions

Quantitative characterization of plastic deformation of zircon and geological implications

The deformation-related microstructure of an Indian Ocean zircon hosted in a gabbro deformed at amphibolite grade has been quantified by electron backscatter diffraction. Orientation mapping reveals progressive variations in intragrain crystallographic orientations that accommodate 20° of misorientation in the zircon crystal. These variations are manifested by discrete low-angle (<4°) boundaries that separate domains recording no resolvable orientation variation. The progressive nature of orientation change is documented by crystallographic pole figures which show systematic small circle distributions, and disorientation axes associated with 0.5–4° disorientation angles, which lie parallel to rational low index crystallographic axes. In the most distorted part of the grain (area A), this is the [100] crystal direction. A quaternion analysis of orientation correlations confirms the [100] rotation axis inferred by stereographic inspection, and reveals subtle orientation variations related to the local boundary structure. Microstructural characteristics and orientation data are consistent with the low-angle boundaries having a tilt boundary geometry with dislocation line [100]. This tilt boundary is most likely to have formed by accumulation of edge dislocations associated with a 〈001〉{100} slip system. Analysis of the energy associated with these dislocations suggest they are energetically more favorable than TEM verified 〈010〉{100} slip. Analysis of minor boundaries in area A indicates deformation by either [01¯0] (001) edge, or [100](100) and [001](100) screw dislocations. In other parts of the grain, [11¯0] cross slip on (111), (111¯) and (112) planes seems likely. These data provide the first detailed microstructural analysis of naturally deformed zircon and indicate ductile crystal-plastic deformation of zircon by the formation and migration of dislocations into low-angle boundaries. Minimum estimates of dislocation density in the low-angle boundaries are of the order of ∼3.1010 cm−2. This value is sufficiently high to have a marked effect on the geochemical behavior of zircon, via enhanced bulk diffusion and increased dissolution rates. Therefore, crystal plasticity in zircon may have significant implications for the interpretation of radiometric ages, isotopic discordance and trace element mobility during high-grade metamorphism and melting of the crust