VictorJuiz/thesis huggingface dataset:
Progressive messages: tracking message progress through events

This thesis introduces the Progressive Messages model of communication. It is an event-driven framework for building scalable parallel and distributed computing applications on modern networks. In particular, the paradigm provides notification of message termination. That is, when a message succeeds or fails, the user’s application can capture an event (often through a callback) and perform a designated action.
The semantics of the Progressive Messages model are defined as an extension to the message-driven model, which is like an asynchronous RPC. Together, these models can be contrasted to the message-passing model (the basis of Sockets and MPI), which has no event notification.
Using Progressive Messages allows for a more scalable design than permitted by either the message-passing or message-driven model. In particular, Progressive Messages can handle communication concurrently with computation, which means that one process does not need to wait in order to service a request or response from another process. This overlap leads to more efficiency.
As part of the study of Progressive Messages, we create the MATE (Message Alerts Through Events) library, which is a prototype API that supports event notification in communication. This API was implemented in both MPI and InfiniBand verbs (OpenFabrics). "Unit tests" of network metrics shows that there is some latency in event-driven message handling, though it is difficult to determine if the source of the latency is hardware or software based.
The goal of the Progressive Messages model is that parallel and distributed computing applications will be easier to build and will be more scalable.

Keywords: networks
messaging
Advisor: Brent, RP
High Tc superconductors and the contact properties

Methods of processing large grained textured superconductor have been successfully developed, based on a melt texturing process. Large grained textured superconductor with grain size over 10mm along the growth direction and Jc over 3600A/cm2 (77K, 0.5 Tesla) has been produced in both one - zone and two - zone furnaces with good reproducibility.
Two kinds of design of reactive metal contacts have been proposed and investigated, aiming to make low resistivity contacts with strong mechanical strength. Three possible reactive contact metals have been tested for contact making, and the microstructures at the interfaces have been studied to find the relations between contact resistivity and contact processing conditions. Titanium/noble metal multilayer contacts is a promising type of contact technique for low resistivity and strong mechanical bonds.
Gold and silver contacts give resistivities among the best reported results in the literature, and they turned out to be extremely stable in time, could withstand repeated thermal cycling from room temperature to 10K and yield very reproducible R-T curves.
The electrochemical titration method has been used to increase the oxygen stoichiometry of bulk textured YBa2Cu3O7-x samples. The electrochemical titration method can further oxidize melt textured thick film YBa2Cu3O7-x samples in which it may be difficult to further improve oxygen content by conventional annealing. The solid state electrochemical cell has been used to study the thermodynamic properties of the Y-Ba-Cu-O system at high oxygen pressure by measuring the oxygen activity versus time continuously immediately after the electrochemical titration.
A series of computer models have been set up according to the microstructure of the contact interface to simulate the complicated contact resistivity behaviours. The nature of, and geometry of, the reaction products at the contact interfaces may be revealed by the temperature dependence of the contact resistance. This information combined with direct observations on the structure and chemistry of the contacts provided a fuller understanding of conduction mechanism at the contact interface.

Advisor: Grovenor, C
Concepts and applications of quantum measurement

In this thesis I discuss the nature of ‘measurement’ in quantum theory. ‘Measurement’ is associated with several different processes: the gradual imprinting of information about one system onto another, which is well understood; the collapse of the wavefunction, which is ill-defined and troublesome; and finally, the means by which inferences about unknown experimental parameters are made.
I present a theoretical extension to an experimental proposal from Leggett and Garg, who suggested that the quantum-or-classical reality of a macroscopic system may be probed with successive measurements arrayed in time. The extension allows for a finite level of imperfection in the protocol, and makes use of Leggett’s ‘null result’ measurement scheme. I present the results of an experiment conducted in Oxford that, up to certain loopholes, defies a non-quantum interpretation of the dynamics of phosphorous nuclei embedded in silicon.
I also present the theory of statistical parameter estimation, and discover that a recent trend to employ time symmetric ‘postselected’ measurements offers no true advantage over standard methods. The technique, known as weak-value amplification, combines a weak transfer of quantum information from system to meter with conditional data rejection, to surprising effect. The Fisher information is a powerful tool for evaluating the performance of any parameter estimation model, and it reveals the technique to be worse than ordinary, preselected only measurements. That this is true despite the presence of noise (including magnetic field fluctuations causing deco- herence, poor resolution detection, and random displacements), casts serious doubt on the utility of the method.

Keywords: Weak value
measurement
parameter estimation
Leggett-Garg
amplification
Quantum theory
venality
Fisher information
quantum measurement
weak measurement
null result measurement
Macrorealism
Advisor: Benjamin, S
Briggs, G
The development of CT urography for investigating haematuria

This thesis addresses the three principal questions concerning the development of CT urography for investigating haematuria and each question is the subject of a separate chapter. The questions are:
What is the reasoning behind using CT urography?
What is the optimum diagnostic strategy using CT urography?
What are the problems with using CT urography and how may solutions be provided?
Haematuria can signify serious disease such as urinary tract stones, renal cell cancer, upper tract urothelial cancer (UTUC) and bladder cancer (BCa).
CT urography is defined as contrast enhanced CT examination of kidneys, ureters and bladder. The technique used here includes unenhanced, nephrographic and excretory-phases for optimized diagnosis of stones, renal masses and urothelial cancer respectively.
The reasoning behind using excretory-phase CT urography for investigating haematuria is based on results showing its high diagnostic accuracy for UTUC and BCa.
Patients with haematuria are classified as low risk or high risk for UTUC and BCa, by a risk score, determined by the presence / absence of risk factors: age > 50 years, visible or nonvisible haematuria, history of smoking and occupational exposure.
The optimum diagnostic strategy for patients at high risk for urothelial cancer, uses CT urography as a replacement test for ultrasonography and intravenous urography and as a triage test for flexible and rigid cystoscopy, resulting in earlier diagnosis and potentially improving prognosis. For patients at low risk, ultrasonography, unenhanced and nephrographic-phase CT urography are proposed as initial imaging tests.
Problems with using CT urography include false positive results for UTUC, which are eliminated by retrograde ureteropyelography-guided biopsy, an innovative technique, for histopathological confirmation of diagnosis. Recommendations for the NHS and possible future developments are discussed.
CT urography, including excretory-phase imaging, is recommended as the initial diagnostic imaging test before cystoscopy for patients with haematuria at high risk for urothelial cancer.

Keywords: biomarkers
diagnostic imaging
hematuria
bladder cancer
cytology
transitional cell
educational techniques
incidental findings
ureteral calculi
prognosis
cystoscopy
neoplasm grading
x-ray
costs and cost analysis
neoplasm staging
pyelography
urography
educational assessment
kidney neoplasms
urinary calculi
diagnostic techniques and procedures
disease-free survival
early diagnosis
urological
carcinoma
computed tomography
kidney calculi
urinary bladder calculi
ultrasonography
ureteral catheterization
early detection of cancer
cost savings
urinary bladder cancer
diagnostic tests
sensitivity and specificity
diagnostic errors
biopsy
urinary bladder neoplasm
urinary bladder neoplasms
renal cell
diagnostic techniques
urolithiasis
cost effectiveness
retrograde
diagnosis
risk factors
Advisor: Harris, A
Microalgal growth and lipid production: trends, multiple regression models, and validation in a photobioreactor

Algae are a promising new source of oil for biodiesel. They are aquatic organisms that do not require cropland, and they can produce many useful side-products for bioenergy, aquaculture, and nutraceutical production. To be cost-effective, algae need high and reliable oil productivities; however, there is still a great deal to learn about the effects of culturing conditions on algae growth rates and lipid production. These culturing conditions include light intensity, gas flow, use of CO2, and culture volume. An extensive database of published research on algae growth rates and lipid contents under a wide variety of environmental conditions was prepared. By graphing data from 116 publications on 132 microalgae species, several key trends were identified relating to culturing parameters and algae biomass and lipid production. In addition, data from 131 publications on 128 microalgae species were graphed to look at presence of flagella, nutrient limitation, lipid productivity, and productivity tradeoffs. Moreover, cell size information was gathered for 146 species. The interactions between culture variables are complex, so it is difficult to quantify the degree to which each culture variable affects algae growth rates and lipid production. Therefore, several multivariate analyses were performed to generate a set of general and simple predictive models to assess specific growth rates, maximum lipid contents, and volumetric lipid productivities. These models were used to determine which culture parameters were significant predictors of algae growth rates and lipid production, and the contribution of each environmental parameter was quantified. In addition to models for algae in general, genera specific models were prepared for Chlorella, Isochrysis, Nannochloropsis, Phaeodactylum, and Tetraselmis. These models show high predictive capabilities, and they greatly extend the range of species-specific multiple regression models available. Furthermore, one Tetraselmis model was validated using Tetraselmis impellucida growth experiments in a large novel photobioreactor.

Keywords: Maximum Lipid Content
Biofuel
Algae
Energy
Biodiesel
Tetraselmis
Specific Growth Rate
Photobioreactor
Mathematical Model
Advisor: Field, R
Cui, Z
One-pot nitro-Mannich cascade reactions: new methodologies and synthetic applications

Pyrrolidine and pyrrolidinone rings are common motifs found in many biologically active natural products and drugs. Accordingly, our work focuses on the development of new methodologies for their one-pot synthesis.
An efficient diastereoselective nitro-Mannich / lactamisation reaction cascade of methyl 3-nitropropanoate with cyclic and acyclic imines for the direct preparation of trans-monocyclic and fused tricyclic pyrrolidinone derivatives was developed. The reaction is easy to perform, broad in scope and tolerates a wide variety of functional groups. For the monocyclic methodology, 28 examples with a very good average yield of 72% and excellent diastereocontrol (typical dr >98:2) were obtained using optimized conditions and varying the amine and the aldehyde reagents.
The methodology has been extended to the synthesis of 1,3,5-trisubstituted 4-nitropyrrolidinone derivatives using α-substituted 3-nitropropanoate. Using a one-pot protocol, 22 derivatives were synthesised in good yields (65% average) and diastereomeric ratios ranging from 3:1 to 30:1 in favor of the trans/trans diastereoisomer.
In addition, the nitro-Mannich / lactamisation cascade of methyl 3-nitropropanoate was developed further to allow the rapid synthesis of 5-isopropyl-4-nitropyrrolidin-2-one from reaction with ammonium acetate and 1-butyl-4-nitropyrrolidin-2-one from reaction with formaldehyde. Also, the synthetic utility of the nitro-pyrrolidinones formed was exemplified through various functional group modifications: the selective reduction of the lactam carbonyl, the reduction of the nitro group in the presence or absence of a carbonyl group and the reductive removal of the nitro group.
The development of an enantioselective version of the cascade under chiral Brönsted acid catalysis provided promising results (up to 90% ee). Moreover, various studies were undertaken to understand the mechanism of the reaction and the nitro-Mannich / latamisation cascade is now well understood. Furthermore, a formal synthesis of rac-Slaframine in 8 steps and 15% overall yield was achieved and it inspired additional work towards a nitro-Mannich / epoxide ring opening cascade.

Keywords: diastereoselective
methodology
multi-component reaction
enantioselective
nitro-Mannich
Slaframine
cascade
Advisor: Dixon, D
Polytopes, scattering amplitudes, and cohomology

We introduce a new definition of abstract polytope in any dimension and answer the question of defining and calculating its area. The entire discussion is motivated by studying the expressions arising from super-BCFW recursion on tree-level, n-point NMHV amplitudes in the planar limit of N=4 Super Yang-Mills (SYM) theory. It has recently been discovered that such expressions should be interpreted as volumes of complex projective polytopes in some sense, and here we give this interpretation explicit meaning. In doing so, we uncover a novel calculus for calculating the volumes of such polytopes. This calculus can be used on the polytopes corresponding to these BCFW representations of amplitudes to obtain new expressions that make manifest all of the known properties of the polytopes. Additionally, we show how this new calculus can be used to readily obtain the volumes of any lower-dimensional face of an arbitrary polytope.
We begin by reviewing the known results for n-point NMHV amplitudes in planar N=4 SYM. In Chapter 2 we introduce our new definition of abstract (oriented) polytopes in terms of new objects called cyclic lists, and in Chapter 3 we define the volumes of these polytopes using cyclic lists in a natural way. Chapter 4 introduces a useful calculus for calculating not only the volumes of these polytopes, but also the volumes of any of their lower dimensional bounding polytopes. Finally, in Chapter 5, we briefly explore the twistor and cohomology theory that motivates the calculus and which may provide important insight for generalization of this whole discussion to more exotic spaces.

Keywords: Scattering Amplitude
Polytope
Volume
Cohomology
Triangulation
Advisor: Hodges, A
Penrose, R
Representations of Elizabeth I

This thesis looks at three themes in representations of the Queen in Elizabethan literature. They are: the problem of representing a female ruler; the relation between the cult of Elizabeth and the cult of the Virgin Mary; and representations of Elizabeth as Cynthia, the moon-goddess. These topics are seen as focal points for problematic issues in panegyric.
The first part of the thesis looks at the problem of reconciling the "masculine" virtues of the ideal ruler with ideal "feminine" virtues, in the figure of Elizabeth. Some panegyric stressed her "masculine" qualities; but, more often, her uniqueness as perfect woman was extolled. However, apparent praise of "feminine" virtues like peacefulness and mercifulness could veil implicit criticism of the effeminisation of the state. In Elizabeth's sex can be found reasons for the proliferation and complexity of fictional personae for her: first, she had to be shown to possess all the virtues, masculine and feminine, even when those virtues were incompatible or contradictory. Secondly, a masculine idea of woman as enigma, incomprehensible and ultimately unrepresentable, was magnified in the figure of a female monarch.
The second section examines the theory, popularised by Frances Yates and Roy Strong, that Elizabeth was a Protestant "substitute" for the Virgin Mary, who filled a "psychological gap" for the populace after the Reformation. It considers the extent of contradiction between opposition to idolatry, and belief in the spiritual status of the ruler; and the longstanding exchange of imagery between secular and sacred literature. The relations between the cult of the Virgin and representations of Elizabeth were complex and various. Some apparent examples of Marian imagery in panegyric of Elizabeth were part of the use of religious imagery in the discourse of courtly love; some were attempts to appropriate the "magical" symbolic qualities of virginity in general for the Protestant cause; some were typological readings of Marian myths as narrative structures with which to mythologise contemporary history. Direct identification of Elizabeth with the Virgin only became prevalent in the later years of the reign, particularly in elegies for her death.
Finally, the thesis looks at moon-imagery in panegyric of Elizabeth as a means for apparent praise which contains undertones of criticism and disillusionment. The moon-image was particularly a means of expressing anxiety regarding mutability, as Elizabeth's advancing age added to the problem of her sex, and foregrounded the issue of her mortality.
The role of the primate frontopolar cortex in mnemonic and choice behaviour

The role of the primate frontopolar cortex (FPC) has been investigated using human neuroimaging, lesion and disruption techniques. The results of these investigations have led to a variety of theories regarding the function of this region. It has been linked to the formation of task sets, the performance of multiple tasks, reasoning, context-specific memory (including episodic memory, prospective memory and source memory), attention to internally or externally generated information, mentalising and decision-making. It has not previously been possible to study this area using animal lesion techniques. Here, behavioural experiments conducted using non-human primates (rhesus macaque monkeys) who have received lesions to the frontal pole investigate the contribution of this region to context-specific memory, decision-making and social cognition. Functional magnetic resonance imaging (fMRI) is used to investigate changes in functional network connectivity which occur after lesions to this region. A long-lasting impairment is observed in contextual memory judgements (specifically, how recently a stimulus was encountered) after lesions to the frontal pole. An analysis of the influence of the outcomes of previous choices on behaviour on an analogue to the Wisconsin Card Sorting Test (WCST) indicate that monkeys with lesions to area 10 may be less influenced by the outcomes of an extended history of rewards than control animals. Long-lasting widespread disruption to functional networks after lesions to this region indicate that indirect anatomical connections from this region to posterior areas play a crucial role in the normal functioning of posterior networks.

Keywords: frontopolar cortex
recency memory
anterior prefrontal cortex
WCST
episodic memory
social cognition
Advisor: Buckley, M
Linear Paul trap design for high-fidelity, scalable quantum information processing

We have designed and built a new linear Paul trap to expand our capability for carrying out high-fidelity quantum logic. We have identified some key limitations of our existing trap: the presence of a magnetic field gradient of 0.6 milligauss per micrometre, which limits the fidelity of Bell state preparation; a high axial micromotion amplitude, which limits the fidelity of operations on linear ion crystals; and a small numerical aperture in the imaging system, which restricts the collection efficiency and thus the performance of remote entanglement experiments.
We have carried out theoretical investigations into axial ion micromotion, including a full analysis of ion motion, using numerical simulations to understand the impact of electrode geometry. We have considered the effect of ion micromotion on the excitation spectrum, and how the micromotion sidebands can be used to selectively address ions within a linear crystal.
Based on this work, electrode design parameters have been selected for the new trap to prioritise sideband addressing while maintaining the most useful properties of the existing design. We have redesigned the mechanical structure of the trap, carefully considering manufacturing limitations, to minimise the magnetic field gradient, increase the numerical aperture to 0.6 and accurately align the electrodes. Additionally, we have considered methods of characterising the trap performance to assess how well the design criteria have been met.

Keywords: quantum computing
quantum information processing
ion trap
Paul trap
Advisor: Lucas, D
Aspects of the electroweak phase transition and baryogenesis

In this thesis we study aspects of the cosmological electroweak phase transition which are relevant to the possibility of baryogenesis at this epoch. We focus on two issues: first, requiring that the observed baryon number be of electroweak origin places strong constraints on electroweak physics, and second, baryogenesis at the electroweak scale may be driven by an asymmetry generated at the GUT scale.
We use the effective potential at finite temperature as a means of analyzing phase transitions associated with spontaneous symmetry breaking. We develop the theory with two basic examples: the scalar and Abelian Higgs models. Infrared divergences near the phase transition make the one-loop description unreliable, and indeed invalidate conventional perturbation theory. Borrowing a method from studies of QCD at high temperatures, we demonstrate that the summation of ring diagrams cures the leading infrared divergences and achieves a more reliable perturbative expansion.
We then apply this formalism to the minimal Standard Model, following previous work, and confirm weak first-order behavior at the phase transition. We show that requiring the baryon number not be erased by sphaleron processes after the phase transition places a stringent bound on the Higgs mass, which is incompatible with experiment. This cosmological bound, however, may be relaxed by extending the scalar sector of the Standard Model. We consider the two simplest such extensions, the addition of a gauge singlet and of a second doublet. We demonstrate that ring-improvement in the singlet extension alters previous arguments at the one-loop level and yields a more restrictive bound on the Higgs mass. While ring-improvement in the two-doublet model, in principle, also reduces the Higgs mass bound found earlier at one loop, the multitude of new couplings in this model does not permit a definitive statement.
We then investigate a mechanism for generating the observed baryon asymmetry (nB/S~ 10-10) at the electroweak phase transition from a pre-existing leptonic asymmetry (LT/s~ 10-5) produced at the GUT scale. This mechanism works by charge transport in a strongly first-order phase transition and avoids the need for large CP-violation at the electroweak scale.

Advisor: Sarkar, S