VictorJuiz/thesis huggingface dataset:
Automatic analysis of magnetic resonance images of speech articulation

Magnetic resonance imaging (MRI) technology has facilitated capturing the dynamics of speech production at fine temporal and spatial resolutions, thus generating substantial quantities of images to be analysed. Manual processing of large MRI databases is labour intensive and time consuming. Hence, to study articulation on large scale, techniques for automatic feature extraction are needed.
This thesis investigates approaches for automatic information extraction from an MRI database of dynamic articulation. We first study the articulation by observing the pixel intensity variations in image sequences. The correspondence between acoustic segments and images is established by forced alignment of speech signals recorded during the articulation. We obtain speaker-specific typical phoneme articulations that represent general articulatory configurations in running speech. Articulation dynamics are parametrised by measuring the magnitude of change in intensities over time. We demonstrate a direct correlation between the dynamics of articulation thus measured and the energy of the generated acoustic signals.
For more sophisticated applications, a parametric description of vocal tract shape is desired. We investigate different shape extraction techniques and present a framework that can automatically identify and extract the vocal tract shapes. The framework incorporates shape prior information and intensity features in recognising and delineating the shape. The new framework is a promising new tool for automatic identification of vocal tract boundaries in large MRI databases, as demonstrated through extensive assessments.
The segmentation framework proposed in this thesis is, to the best of our knowledge, novel in the field of speech production. The methods investigated in this thesis facilitate automatic information extraction from images, either for studying the dynamics of articulation or for vocal tract shape modelling. This thesis advances the state-of-the-art by bringing new perspectives to studying articulation, and introducing a segmentation framework that is automatic, does not require extensive initialisation, and reports a minimum number of failures.

Keywords: Magnetic Resonance Imaging
Automatic Image Segmentation
Acoustics
ASR
Speech Production
Articulation
Advisor: Coleman, J
Understanding journeys of transformation – Exploring new paradigms in strategic change and enterprise transformation

This thesis seeks to study the phenomenon of transformational journeys in major organisations, defined as a process of radical change delivering dramatic and sustained improvement in market competitive performance within an aggressive timescale. This is characterised by strategic repositioning, alongside shifts in both strategic and organisational architecture, and is observable as periodic in the life of an organisation.
A research framework for observation and explanation is taken from theories and research in strategic change, strategic intent and competitive advantage, strategic and organisational architecture, management process in transformation and typologies of transformational journeys. The primary research question, “how do top managers in different organisations lead and manage transformational change?” was addressed with an overall qualitative dual approach: firstly a pilot cross-company study with executives from 23 organisations to develop a high level typology and compare and contrast aspects of process; secondly longitudinally to examine in detail the complex interrelationships and aspects of emergent process. The prime empirical work was a main case study of Thames Water Utilities on a 7 year journey. Limited or secondary data was used from around 7 other longitudinal cases.
The thesis conclusions make a number of specific propositions: around effective use of the descriptive framework and metaphor of a journey; on dependencies between aspects of context, content and process of change in transformation; on typologies of different journey management styles; on perceived conditions for success; and on practical applicability. Specifically, the adoption of “navigational leadership” capability, defined by a number of dimensions and characteristics, is explored as a new and emergent style appropriate in future business circumstances of increasing change and uncertainty. The research also concludes that such styles can be learnt and adopted by top teams.

Keywords: top teams
leadership
transformation
change
enterprise
Advisor: McGee, J
A study of interferometric distance measurement systems on a prototype rapid tunnel reference surveyor and the effects of reference network errors at the International Linear Collider

The International Linear Collider (ILC) aims to collide electrons and positrons with a centre of mass energy of 500GeV and a luminosity of 2×1034 cm−2 s−1. To achieve this luminosity, the nominal final emittance of the electron and positron beams have to be below 10μm.rad horizontally and 0.04μm.rad vertically. To prevent the emittance from becoming too large, the main linacs will require alignment at an unprecedented level. The ILC main linacs will be aligned with respect to a reference network which runs along the entire length of the tunnel. The Linear Collider Alignment and Survey (LiCAS) Rapid Tunnel Reference Surveyor (RTRS) is the prototype of a device proposed to survey the ILC reference network. The LiCAS RTRS has several measurement systems; its Frequency Scanning Interferometry (FSI) measurement system is studied in this thesis. The FSI system has three distinct sub-systems: the reference interferometers, the external FSI measurement system and the internal FSI measurement system. The errors on the length of the reference interferometers are shown to be of the order of 1.1μm (0.3ppm). The external FSI measurement system is shown to measure distances close to 0.42m with errors of &pm;1.9μm stat &pm;0.16μm syst and the internal FSI measurement system is shown to measure distances close to 4.2m with errors of &pm;0.24μm stat &pm;1.6μm syst.
A survey of the ILC reference network using laser trackers is simulated without taking account of systematic measurement errors from refraction in the tunnel air. The simulated networks are used to misalign the simulated accelerators in Dispersion Matched Steering (DMS) simulations. The DMS simulations show that only 30% of the simulated accelerators produce an acceptable final corrected vertical emittance. It is further shown that the introduction of long range distance measurements between primary reference markers (PRMs) using GPS, reduces the long range error growth in the network, and that 95% of simulated accelerators give acceptable performance. A simplified network simulation model, which is capable of simulating reference networks surveyed by conventional and novel devices, is produced and compares favorably to full simulations.

Keywords: Particle Accelerator Alignment
Advisor: Reichold, A
Social change along the Middle Yangzi river: re-configurations of late Neolithic society

Through the case study of the Shijiahe site, Tianmen, Hubei, this thesis investigates the dynamics of enclosures along the Middle Yangzi River during the third millennium BC. During the early third millennium over a dozen of enclosures were constructed in this region, earlier than elsewhere in China during this millennium. All were abandoned and some re-settled around 2000 BC, followed by another episode of abandonment. The major theoretical paradigms dominating the field are culture history and social complexity. The thesis argues that these are insufficient to fully appreciate the actual details and dynamics of the developments at the Middle Yangzi sites. As an alternative, this thesis employs a combination of approaches. A detailed practice-based analysis of the biography of Shijiahe reveals dynamics of identity formation and changes to tradition not observed before. The techniques of enclosure construction, reasons for their construction and abandonment will also be discussed.
The thesis acknowledges the central importance of religion and interaction as two essential underlying currents of prehistoric lives that, in the case of China, have largely been ignored. From this angle a series of objects, such as red pottery cups, pottery pointed-bottom vessels and jade ornaments, from Shijiahe are investigated and their religious significance established. They and the practices they were used in are also mapped according to their find spots, which show the connection of Shijiahe with regions even beyond the Middle Yangzi, such as the Yellow and Huai river regions. These interactions were probably also stimulated by religious practices. The northward connections are of particular importance, as they confirm that the Yangzi, and the giant swamp of the Yunmengze in the Jianghan Plain, were formidable barriers southwards. The usually posited direction of movements from the Yellow River into the south must be challenged on the basis of this thesis, which argues for multiple directions of interaction and transmission of objects and ideas.

Keywords: Neolithic
Archaeology
Yangzi River
China
Advisor: Rawson, J
Silicon isotopes and the development of the Earth

Silicon (Si) isotopes have been extensively studied in low temperature environments but the science of Si isotopes in igneous material has been comparatively ignored. This is because the degree of isotopic fractionation at high temperatures is relatively small, making the accurate measurement of these variations extremely challenging. Using state-of-the-art analytical techniques and instrumentation, which deliver high levels of precision, the objective of this research is to rectify this omission. Specifically, this study aims to investigate whether there are systematic Si isotope variations within, and provide robust Si isotopic compositions for, the major silicate reservoirs on Earth. To this end, a broad range of mantle and crustal lithologies, sourced globally and from various tectonic regimes, have been analysed using high resolution MC-ICP-MS.
Analyses indicate that the Si isotopic compositions of mantle-derived mafic and ultramafic material are extremely homogeneous. These data are used to calculate a Bulk Silicate Earth (BSE) average of δ30Si = -0.29 ± 0.08 ‰ (2 s.d.). The degree of Si isotopic fractionation as a result of magmatic differentiation has also been assessed, and found to be small but resolvable between basalt and rhyolitic end-members. Finally, this research shows that, although igneous rocks and sediments derived from the continental crust can be relatively heterogeneous with respect to Si isotopes, bulk averages calculated for the upper, middle and lower continental crust are all very similar to that of BSE. Providing robust estimates for these reservoirs has greatly improved our knowledge of the behaviour of Si isotopes in silicate lithologies and provides a framework for further Si isotopic investigations of such material.

Keywords: terrestrial
continental crust
silicon isotopes
Advisor: Halliday, A
Georg, R
Williams, H
The Holland family, Dukes of Exeter, Earls of Kent and Huntingdon, 1352-1475

At the turn of the fourteenth century, the Hollands were a knightly family of no great import in Lancashire. In 1475, Henry Holland died as the Lancastrian claimant to the throne. Such a transformation, in itself, deserves explanation. This will reveal the dramatic rise of a family through the beneficence of noble and then royal patronage and, even more so, through the fortune of a good marriage being compounded by a conbination of fortuitous heirless deaths and a significant remarriage to bring an inheritance and royal kinship. That was the means of ascension through the ranks of the nobility, and it was sustained by consistent service to the crown at court and in the field. The Hollands were not a family of local power who built on this to thrust themselves into the nobility; their local basis almost verged on the nomadic and it is within the context of the court that they must be viewed, they were curialist nobility. Therefore, the absence of family and estate papers is not such a blow to their study as the records of central administration have much to reveal of their activities and their estates were not of such concern to them as they were for other families.
This chronological survey of their rise, significance and disappearance provides something of a commentary on the political, and military, events of later medieval England. It helps further to fill in our picture of England's nobility, confirming its great individuality and providing an example of how a rapid rise through its ranks was possible.
High fidelity readout of trapped ion qubits

This thesis describes experimental demonstrations of high-fidelity readout of trapped ion quantum bits ("qubits") for quantum information processing. We present direct single-shot measurement of an "optical" qubit stored in a single calcium-40 ion by the process of resonance fluorescence with a fidelity of 99.991(1)% (surpassing the level necessary for fault-tolerant quantum computation). A time-resolved maximum likelihood method is used to discriminate efficiently between the two qubit states based on photon-counting information, even in the presence of qubit decay from one state to the other. It also screens out errors due to cosmic ray events in the detector, a phenomenon investigated in this work. An adaptive method allows the 99.99% level to be reached in 145us average detection time. The readout fidelity is asymmetric: 99.9998% is possible for the "bright" qubit state, while retaining 99.98% for the "dark" state. This asymmetry could be exploited in quantum error correction (by encoding the "no-error" syndrome of the ancilla qubits in the "bright" state), as could the likelihood values computed (which quantify confidence in the measurement outcome). We then extend the work to parallel readout of a four-ion string using a CCD camera and achieve the same 99.99% net fidelity, limited by qubit decay in the 400us exposure time. The behaviour of the camera is characterised by fitting experimental data with a model. The additional readout error due to cross-talk between ion images on the CCD is measured in an experiment designed to remove the effect of qubit decay; a spatial maximum likelihood technique is used to reduce this error to only 0.2(1)x10^{-4} per qubit, despite the presence of ~4% optical cross-talk between neighbouring qubits. Studies of the cross-talk indicate that the readout method would scale with negligible loss of fidelity to parallel readout of ~10,000 qubits with a readout time of ~3us per qubit. Monte-Carlo simulations of the readout process are presented for comparison with experimental data; these are also used to explore the parameter space associated with fluorescence detection and to optimise experimental and analysis parameters. Applications of the analysis methods to readout of other atomic and solid-state qubits are discussed.

Keywords: measurement
trapped ions
qubit
readout
quantum computing
quantum computation
quantum information
ion trap
Advisor: Lucas, D
Pricing exotic options using improved strong convergence

Today, better numerical approximations are required for multi-dimensional SDEs to improve on the poor performance of the standard Monte Carlo integration. With this aim in mind, the material in the thesis is divided into two main categories, stochastic calculus and mathematical finance. In the former, we introduce a new scheme or discrete time approximation based on an idea of Paul Malliavin where, for some conditions, a better strong convergence order is obtained than the standard Milstein scheme without the expensive simulation of the Lévy Area. We demonstrate when the conditions of the 2−Dimensional problem permit this and give an exact solution for the orthogonal transformation (θ Scheme or OrthogonalMilstein Scheme). Our applications are focused on continuous time diffusion models for the volatility and variance with their discrete time approximations (ARV). Two theorems that measure with confidence the order of strong and weak convergence of schemes without an exact solution or expectation of the system are formally proved and tested with numerical examples. In addition, some methods for simulating the double integrals or Lévy Area in the Milstein approximation are introduced. For mathematical finance, we review evidence of non-constant volatility and consider the implications for option pricing using stochastic volatility models. A general stochastic volatility model that represents most of the stochastic volatility models that are outlined in the literature is proposed. This was necessary in order to both study and understand the option price properties. The analytic closed-form solution for a European/Digital option for both the Square Root Model and the 3/2 Model are given. We present the Multilevel Monte Carlo path simulation method which is a powerful tool for pricing exotic options. An improved/updated version of the ML-MC algorithm using multi-schemes and a non-zero starting level is introduced. To link the contents of the thesis, we present a wide variety of pricing exotic option examples where considerable computational savings are demonstrated using the new θ Scheme and the improved Multischeme Multilevel Monte Carlo method (MSL-MC). The computational cost to achieve an an accuracy of O(ϵ) is reduced from O(ϵ−3) to O(ϵ−2) for some applications.
Single molecule studies of seven transmembrane domain proteins

This work aimed at studying biophysical properties of two membrane proteins, one of potential nanotechnological use, bacteriorhodopsin, and one potential drug target, the NTS1 neurotensin receptor, at the single molecule scale.
Bacteriorhodopsin (BR) is the only protein in the purple membrane (PM) of the halophilic organism Halobacterium salinarium. It is a light-driven proton pump converting light into a transmembrane proton gradient through isomerization of its retinal chromophore. Its stability, as well as its photoactivity remaining in dry protein layers, has made BR an attractive material for biomolecular devices. Numerous studies have been published on this topic; however, they have all used BR within the PM, on relatively large (µm-wide) surfaces.
Here, conducting-probe atomic force microscopy (C-AFM) analysis was performed after removing most of the membrane lipids. For the first time, it was shown that the molecular conductance of BR can be reversibly photoswitched with predictable wavelength sensitivity. Intimate and robust coupling to gold electrodes was achieved by using a strategically engineered cysteine which, combined with partial delipidation, generated protein trimers homogenously orientated on the surface. Numerous controls using biophysical (SPR, ellipsometry, Kelvin-probe AFM) and chemical (photocurrent, cyclic voltammetry) techniques confirmed the wavelength specificity of the photoswitch, the anchoring role of the mutation and the homogenous orientation of the protein on the gold surface.
Neurotensin is a brain and gastrointestinal 13 amino acid peptide acting as a neuromodulator in the central nervous system and as a hormone in the periphery. Its wide range of biological activities is primarily mediated through its binding to the neurotensin type 1 receptor (NTS1). NTS1 expressed in E.coli was purified and inserted into 100 nm brain polar lipid liposomes in a conformation which retained its ligand-binding capabilities. Initial AFM characterisation was performed as a prelude for ligand-receptor interaction studies, including high resolution imaging, force spectroscopy and solid state NMR approaches.

Keywords: conducting atomic force microscopy (C-AFM)
wavelength-sensitivity
molecular conductance photoswitching
bacteriorhodopsin (BR)
Advisor: Watts, A
Subsequent use of documents disclosed in civil proceedings

Rule 31.22 of the Civil Procedure Rules 1998 provides, as a general rule, that those who receive documents through disclosure during civil proceedings may use them only for the purpose of the proceedings at hand. The general rule is subject to three exceptions, and judges have discretion to authorise subsequent use for other purposes. However, the foundational presupposition underpinning CPR 31.22 is that subsequent use, generally speaking, is improper.
The thesis has two primary aims: (1) to demonstrate that the rule governing subsequent use (as developed in the case law) is theoretically and practically flawed, and that maintaining a blanket, general rule against subsequent use is unsound in principle, unjust, and procedurally inefficient; and (2) to generate a normative and procedural framework suitable for reform.
Part I outlines the content, origins and operation of CPR 31.22. Through historical analysis, it suggests that presumptively categorising as improper all forms of subsequent use beyond the original litigation contradicts traditional authority. By identifying and examining the three principal rationales said to justify the modern rule, it argues that none affords sound justification. By analysing the exceptions to the rule, including judicial discretion, it seeks to show that such measures are incapable of remedying the defects in the underlying rule.
Part II attempts to formulate a theoretically defensible, procedurally viable model for reforming CPR 31.22. It suggests that the presumption against subsequent use should be abolished, and the law reoriented around two central norms: the harm principle and a balancing approach. It tests this theoretical model by applying it to seven paradigmatic categories of subsequent use. Finally, it outlines a possible structure for procedural reform.

Keywords: Civil Procedure
Disclosure
Subsequent use
Discovery of documents
Advisor: Zuckerman, A
Tapper, C
Characterisation of the transcriptomes of Leishmania mexicana promastigotes and amastigotes

Leishmania spp. undergo substantial adaptations from being promastigotes, found in sandflies, to being amastigotes, residing in parasitophorous vacuoles within mammalian macrophages. In the past, microarray studies have sought to elucidate these adaptations using axenic amastigote systems or amastigotes purified from host-cells, raising the question whether the observed transcriptomic signatures were a true reflection of intracellular amastigotes. Moreover, with ever-improving genome annotations being available, it is clear that these studies failed to address the transcriptomic behaviour of a considerable number of transcripts.
In the work presented herein, I employed RNA-sequencing to obtain transcriptomic profiles of Leishmania mexicana axenic promastigotes (PRO), axenic amastigotes (AXA) and intracellular amastigotes (AMA) in murine bone-marrow derived macrophages. The intracellular amastigotes were not purified from host cells, but instead sequencing reads assigned to a hybrid L. mexicana - Mus musculus genome and the transcriptomes separated in silico. We were able to map pre-mRNA processing sites, thereby defining transcript boundaries, proposing 184 truncations and 1253 extensions of existing gene models as well as discovering 936 novel genes. Mass-spectrometric evidence was obtained for both proposed extended and novel proteins. Using this improved genome annotation, we generated gene expression profiles for AMA, AXA and PRO, identifying 3832 differentially expressed transcripts between PRO and AMA as well as 2176 between PRO and AXA and 1234 between AXA and AMA. Transcripts differentially expressed between AMA and PRO correlated well with previous reports, were enriched for novel transcripts identified in this study and contained an unprecedented wealth of yet uncharacterised transcripts.
Guided by these data, I performed a GFP-tagging screen identifying two proteins which may play an important role in L. mexicana biology, LmxM.16.0500, a member of a small, divergent, amastin-derived gene family, which appears to be released from the cell body of PRO, and LmxM.09.1330 a specific marker of the amastigote flagellar pocket.

Keywords: leishmania
dual RNA seq
amastigote
trypanosoma
differentiation
RNA sequencing
trypanosomatids
Leishmania mexicana
promastigote
macrophage
Advisor: Gluenz, E
Gull, K