VictorJuiz/thesis huggingface dataset:
Distributed anytime generic inference in valuation algebras

In this thesis, we construct a general theoretical framework for anytime inference which automatically gives us instantiations of inference in various important domains, such as Bayesian networks, relational algebras, disjunctive normal forms and set potentials in Dempster-Shafer theory. Our framework is based on local computation schemes for inference, which perform inference by message-passing on junction trees. We also undertake an analysis of distributed inference. Our theoretical framework is implemented as a software library to illustrate examples of anytime inference using the theoretical framework.
Exact inference in general is a #P-hard problem. Due to the prohibitive computational complexity, approximate inference is well-studied. In many applications a coarse approximation is sufficient. Ideally we would like such an approximation process to be anytime. In an anytime algorithm, the approximation improves monotonically with time, and the process can be interrupted and resumed without restarting. This is especially useful in domains where time may be limited such as continuous learning and robotics. While there are several domain-specific anytime algorithms, little work has been done on generalisation. It is advantageous to develop a theoretical framework which can work for several domains, including statistical and logical inference. We use the theory of generic inference, a unification of prior local computation schemes, as a starting point for our framework. In generic inference, information is represented as elements of an algebra called a valuation algebra, with certain axioms for approximate and exact inference. We introduce axioms and operations on valuation algebras to support anytime inference. We illustrate anytime inference with applications to several domains.
Computational overhead can also be reduced by making the algorithm distributed. For our algorithm, we analyse the tradeoffs between computational, communication and synchronisation costs. We give bounds on the number of processors for maximum concurrency and describe a processor assignment algorithm for optimisation of communication costs.
The overall aim of the thesis is to contribute to the study of anytime inference, and to do so in a manner that enables some measure of control over the degree of approximation and easy applicability to a wide range of domains.

Advisor: Abramsky, S
Making and manipulating nanowires inside carbon nanotubes

This thesis summaries the study of various aspects related to the growth of multi-wall carbon nanotubes (MWCNTs) filled with metals and their post-synthesis processing to form macroscopic papers, known as buckypapers (BPs). Fe-filled MWCNTs (Fe@MWCNTs) and Fe/Co-filled MWCNTs (Fe/Co@MWCNTs) were produced by chemical vapour deposition (CVD), with the objective of growing sufficient quantities of these materials, whilst retaining their quality. A systematic study was carried out to investigate the effects of changing the synthesis parameters (sublimation and pyrolysis temperature, furnace gap and Ar flow) on the quality of Fe@MWCNTs produced. Crucially, this systematic study revealed the conditions to produce Fe@MWCNTs of high enough quality and quantity for post-synthesis processing. In situ residual gas analysis (RGA) revealed that regardless of pyrolysis temperature, the detected high mass fragments were broken down over the course of the reaction to ethene and methane, which continued to break down and release H2 even after exhaustion of ferrocene. In situ TEM studied passing current through a Co- NP decorated Fe@MWCNT and emphasised the importance of discerning the affects of current on the structure of the metal filling before utilising them in electrical applications. Fe@MWCNTs were processed to form BPs (4 cm diameter), constructed by depositing layers of Fe@MWCNTs and conventional MWCNTs. Strips of these BPs were successfully prototyped as the moving component in a non-metallic electromechanical relay. I/V measurements showed these ferromagnetic BPs were capable of consistently carrying the same current at a given voltage, up to 3 V, for a minimum of 50 cycles. Selectively depositing the Fe@MWCNTs produced BPs which responded in pre-selected regions to external magnetic stimuli. Tensile tests performed on BPs formed of conventional and N-doped MWCNTs, of two different lengths each, revealed that CNT length and type influence different aspects of the BP’s mechanical properties.

Advisor: Grobert, N
Dillon, F
Ergodic and algebraic properties of transfer operators for products of random matrices

A recent paper by Pollicott in 2010 presented an efficient algorithm for computing the Lyapunov exponent of i.i.d. random products of positive matrices. The aim of this thesis is to generalise some of the aspects of Pollicott's approach to Markovian and more general matrix products using the theory of transfer operators. Some minor mistakes in Pollicott's original paper are corrected in the thesis. The possibility of further generalising the algorithm using the theory of operator algebras is discussed in the last chapter.

Keywords: Transfer operators
Lyapunov exponent
Products of random matrices
Operator algebra
Advisor: Steinsaltz, D
Material mnemonics and social relationships in the Diocese of London, 1467-1524

This study is an analysis of objects as a conduit for social communication in the later medieval diocese of London. Although the giving of tokens did not constitute a legal proof of marital consent, the frequency and detail with which they were recalled by litigants and witnesses is testament to their importance as socially-meaningful proofs of courtship and consent. Such gifts, however, were not fixed or irrefutable proofs of matrimony. Rather, the meaning associated with particular objects was dependent on how people perceived they had been exchanged. I contend that people were aware of this flexibility of meaning and framed their arguments about an exchange of gifts according to personal, social, and legal agendas.
The chapters of this thesis demonstrate how the exchange of tokens reflected a relationship’s progression: from courtship to married life. Chapter 1 examines what tokens were exchanged during negotiations of marriage and places these objects within a wider cultural and archaeological context. Chapter 2 focuses on courtship tokens, and how they were used to navigate potential marital relationships. Chapter 3 discusses how contract gifts were given to mark the new marital identity of a contracting couple. The final chapter examines the exchange of things across the marital life course. Letters written between recently married couples show how the exchange of objects was used by couples to communicate their desires and emotions during times of separation. The objects bequeathed in last wills and testaments are further evidence of the importance of objects not just in the creation of a marriage but also in the conservation of marital and personal identity. This thesis shows that the exchange of gifts was socially and culturally recognised as a powerful and emotive expression of marital intention, even if the law and its systems denied it.

Advisor: Forrest, I
Reproductive microbiotas of the red junglefowl, Gallus gallus: Patterns and drivers of variation

Organisms host diverse and complex bacterial communities (microbiotas), often with fundamental roles in host ecology and evolution. While microbiotas of the gut have received considerable research focus, relatively little is known about reproductive microbiotas, (i.e. those communities living within the reproductive tract and potentially transmitted at mating), despite the potentially critical role they may play in host sexual selection and mating system evolution. This thesis seeks to address this gap by laying the foundations for the systematic study of reproductive microbiotas in bird populations, and the patterns and drivers of intra- and inter-individual variation. I studied a captive population of red junglefowl, Gallus gallus, a sexually promiscuous species with well-characterised mating systems. Developing a pipeline based on a next-generation sequencing approach I show that junglefowl ejaculates contain diverse bacterial communities of bacteria (seminal microbiotas), which reflect the gut microbiota and vary in structure across males. I then use in vitro culturing to demonstrate that seminal microbiotas are alive and ecologically complex. Next, focusing on patterns of variation in seminal microbiotas, I show an association between inter-male variation in composition and aspects of the male immune-genotype, and find evidence that variation in seminal microbiota structure might be influenced by the sexual dynamics of social groups. Finally, I focus on the female cloacal microbiota and the potential effects that insemination of male semen might have on these communities. Using a series of controlled artificial insemination experiments, I show some evidence that the microbiota of the female cloaca appears to be disrupted by the first inseminations, but might revert back to its initial structure following cessation of inseminations. These effects might be due to the disruption caused by the insemination, rather than by the transmission, and subsequent colonisation of male bacteria. Collectively, these results demonstrate an ecologically complex and dynamic avian reproductive microbiota, providing a platform and direction for future work, by emphasising the need for an understanding of composition, function and variation in reproductive microbiota in order to better understand microbiotas and contextualise the evolutionary ecology of host mating systems.

Keywords: Microbial Ecology
Red Junglefowl
Seminal Microbiota
Behavioural Ecology
Reproductive Microbiota
Cloacal Microbiota
Microbiota
Advisor: Pizzari, T
Biomarkers for Parkinson’s disease and Alzheimer’s disease

Alzheimer’s Disease (AD) and Parkinson’s Disease (PD) represent the two most prevalent neurodegenerative diseases in the world, affecting 30 million and 5 million people, respectively. As populations age, the global burden of AD and PD will increase, resulting in significant societal and economic implications. By 2050, it is estimated that 1 in 85 people will have AD. Biomarkers, surrogate indicators of physiological or pathophysiological states, can be used to guide the diagnosis of diseases, evaluate risk or prognosis, and track therapeutic interventions. In neurodegenerative diseases such as PD and AD, biomarkers can play a crucial role by facilitating earlier diagnosis and the screening of individuals into clinical trials.
Given its function to track various disease states, biomarkers will be fundamentally important as we develop and assess disease-modifying therapies and preventative strategies. (3) The advent of high-throughput sequencing technologies and advancements in omics— genomics, proteomics, and transcriptomics—has enabled the exploration of biomarkers for disease with unprecedented scale. Investigators can now move beyond candidate biomarker discovery approaches based upon a priori hypotheses. This presents an opportunity to utilize biomarkers to develop more sensitive and specific diagnostics and identify molecular targets that may have been overlooked through candidate approaches. Researchers can also use biomarkers to better define subgroups within PD or AD. These endophenotypes can help characterize the different etiologies that contribute to the development of the diseases, reveal distinct subpopulations within disease categories, and thereby uncover potential therapeutic targets.
The work presented here leverages these new advancements in high variable capture approaches, specifically proteomics, to identify novel biomarkers and signatures of disease states for PD and AD. My thesis also demonstrates how multivariate analytical tools can be used to interrogate and validate distinguishing signatures found between disease and control states. In the first chapter, I will review the pathophysiology and clinical management of AD and PD. I will also review the AD and PD biomarkers and the various proteomic and computational approaches that enable biomarker discovery at scale. In the second chapter, I introduce a novel biomarker discovery approach that combines the advantages of hypothesis-driven and high variable capture approaches. The third chapter explores biomarkers for PD, using data from plasma and brain. In the fourth chapter, I identify proteins correlated across CSF and plasma and demonstrate how this data may be used in biomarker identification. In summary, I have identified novel biomarker signatures for the diagnosis and prognosis of PD and AD using high variable data capture methods and multivariate computational approaches.

Advisor: Lovestone, S
Radiolabelled Bacillus anthracis toxin-based probes for molecular imaging of MMP activity in tumour models

Increased activity of matrix metalloproteinases (MMPs) is associated with poor prognosis and metastasis in different cancer types. To exploit this feature and target cancer cells, the protective antigen (PAWT) of the binary anthrax lethal toxin (LT) was modified to form pores in cell membranes only when cleaved by MMPs (PAL1). Anthrax lethal factor (LF) is then able to translocate through these pores into the cytosol of tumour cells. The aim of this work was to develop a novel non-invasive imaging agent for the detection of matrix metalloproteinase (MMP) activity based on engineered variants of LT. Here, 111In- radiolabelled form of LF was used with the PAL1/LF system to allow non-invasive in vivo imaging and quantification of MMP activity in tumour tissue by SPECT.
Initially, PAL1 MMP-activation was tested in a cell free assay. Subsequently, the activation of PAL1 was evaluated by a cytotoxic assay in a range of cancer cell lines, with or without a broad spectrum MMP inhibitor. MMP2 and MMP9 activity in the different cancer cells was assessed by gelatin zymography. Expression levels of MMP14, and LT native receptors (TEM8 and CMG2) were evaluated by western blot analysis. LT components were radiolabelled with 111In. Cell abundance of TEM8 and CMG2 was determined by saturation binding assays using 111In-radiolabelled PAWT. After 111In-radiolabelling non-toxic variants of LF, their cell uptake was evaluated in the presence or not of PAL1. Evaluation of the in vivo pharmacokinetics and biodistribution of 111In-radiolabelled LT components was performed by SPECT/CT in naive mice or MMP-expressing MDA-MB-231 tumour-bearing mice.
PAL1 MMP-cleavage was confirmed in a cell free assay. Notably, PAL1 capacity to cause cytotoxicity in a panel of cancer cells correlated with anthrax toxin receptor and MMP14 expression. Additionally, in the presence of MMP inhibitors PAL1 mediated cytotoxicity was prevented. Selective delivery of 111In-radiolabelled LF variants to MMP-expressing cells by PAL1 was demonstrated in vitro, and corroborated using confocal microscopy with fluorescently labelled variants of LF. Dynamic SPECT imaging demonstrated superior and selective uptake of radiolabelled PAL1 in tumour tissue when compared to radiolabelled PAWT. Finally, a radiolabelled LF variant was selectively delivered to MMP-positive MDA-MB-231 tumour bearing mice by PAL1, presenting excellent target-to-background contrast.
Taken together, these results indicate that radiolabelled forms of mutated anthrax lethal toxin hold promise for non-invasive imaging of MMP activity in tumour tissue.

Keywords: Matrix metalloproteinases activity
cancer
anthrax lethal toxin
SPECT
Advisor: Cornelissen, B
Statistical physics interpretation of southern ocean mesoscale turbulence

Ocean mesoscale (10-100km) turbulence is integral to the complex and interconnected climate system. Many of the assumptions made in classical turbulence theory are inappropriate for describing the characteristic features of geophysical flows. In particular, when the fluid flow is both forced and dissipative. With increased interest in stochastic parameterization of ocean eddies, it becomes pertinent to consider what the statistics of ocean turbulence should look like as well as consider what statistical physics concepts can be used to further the theoretical understanding of the ocean mesoscale. In this thesis, we examine mesoscale turbulence from both a theoretical and empirical perspective employing both idealized models and realistic ocean model data. The statistical nature of a turbulent barotropic jet is explored empirically in the context of an idealized model as well as for realistic ocean model data. Additionally, an entropic and statistical mechanics framework is investigated in the context of force-dissipative flow. It is shown that: ocean jets which exhibit strong mixing barriers have a profound effect on the statistics, leading to multi-modal probability distributions and pointing to the importance asymmetry and extreme values in the statistics; an eddy-mixing entropy, which quantifies turbulent disorder, is a useful metric in describing turbulent motions and evidence is found for the maximization of this entropy in a forced-dissipative fluid flow. Further, across the separate studies presented in this thesis, it is shown that Lagrangian information is useful in distinguishing large-scale coherent structures from the more stochastic small-scale turbulence; and high-order Casimir invariants of motion are important for describing forced-dissipative geophysical flows in a statistical mechanics framework.

Advisor: Zanna, L
Marshall, D
Understanding occipitoparietal alpha oscillations and enhancing sustained attention using electroencephalography and transcranial alternating current stimulation

This project studied the effects of 10-Hz (alpha)-tACS, delivered over occipitoparietal cortex, on sustained attention. Poor performance on all visual tasks used in this project had previously been associated with increased EEG alpha power. I therefore assumed that alpha-tACS would reliably impair visual task performance. However, my results did not support this prediction. In my first two experiments (Chapters 4 & 5), alpha-tACS was found to reduce the slope of deteriorations in task performance that otherwise occurred during control-tACS (i.e. sham- and 50-Hz-tACS). In my third experiment, an auditory control task indicated that such effects are specific to the visual domain (Chapter 6). Furthermore, in a fourth experiment, in which tACS was delivered during a visual task where performance naturally improved over time, alpha-tACS was conversely found to limit the slope of such improvements (Chapter 7). Therefore, regardless of whether task performance improved or deteriorated naturally over time, alpha-tACS seemed to exert a consistently stabilising effect on visual attention. I tested this hypothesis in my fifth experiment, in which alpha-tACS was delivered during an audiovisual switching task. I assumed that, if alpha-tACS stabilises visual attention, this stimulation should impair switching between visual tasks, but leave switching from visual to auditory tasks unaffected. In contrast to this prediction, alpha-tACS was not found to influence visuovisual vs. audiovisual switching. However, alpha-tACS was found to exert a trend-level, impairing effect on visuoauditory switching accuracy, suggesting that this stimulation may help to focus visual attention by preventing transitions of attention away from the visual domain (Chapter 8). A final experiment indicated that 4-Hz-tACS exerts weak, but descriptively similarly effects on visual task performance to those observed during alpha-tACS in my first two experiments (Chapter 9). Throughout these studies, tACS was found to have highly variable and inconsistent effects on EEG power. Overall, these results provide intriguing evidence to suggest that low-frequency tACS can be used to stabilise performance on a range of visual attention tasks. However, the usefulness of tACS for purposes of cognitive enhancement in real-world settings may be limited by the small magnitudes of its influence on both brain activity and behaviour.

Advisor: Kadosh, R
Yeung, N
Spectral networks, abelianization, and opers

In this thesis we study a number of geometric structures arising in the study of four-dimensional supersymmetric quantum ﬁeld theories.
We study properties and applications of so-called “spectral networks” on Riemann surfaces C, focusing in particular on the “abelianization map” which we use to produce special coordinate systems on moduli spaces of local systems on C. We generalize the classical Fenchel-Nielsen coordinates and utilize these coordinates to compute superpotentials, following and generalizing a conjecture of Nekrasov-RoslyShatashvili.
Our ﬁrst result is a computation of the higher rank spectral coordinates associated to certain “generalized Fenchel-Nielsen” networks, yielding explicit formulas for the trace functions on the moduli space with two “minimal” and two “maximal” punctures. We use this result to verify the NRS conjecture at the lowest order asymptotics for a prototypical SU(3) theory, and furthermore compute the 1-instanton correction in the SU(2) case, extending previous results. In the ﬁnal chapter we include some partial results the author has obtained on the existence and uniqueness of abelianizations for certain classes of networks related to Grassmannians.

Keywords: algebraic geometry
quantum field theory
flat connections
supersymmetry
spectral networks
Advisor: Hollands, L
Dancer, A
Air-film behaviour in an air-riding face seal

Increased cycle efficiency and reduced ownership costs of gas turbine engines can be facilitated by improvements in sealing between stationary and rotating engine components. Contacting seals have already improved performance but advanced non-contacting seals offer the possibility of high performance with near-infinite service life. This thesis investigates one potential style of non-contacting face seal which uses a thin film of air to maintain clearance between engine components at all engine operating conditions. Unlike conventional face seals, the seal must be capable of operating with moderate clearances in the order of tens to hundreds of microns and be deployable over large axial movements of several millimetres if it is to operate successfully in the jet engine environment where components are light, flexible and subject to extreme thermal growths. The level of leakage for this seal is intended to be similar to a brush seal at its end of life condition.
The thesis reports experimental analytical and numerical studies of the behaviour of the air-film in the primary sealing gap over a wide range of engine representative conditions. The effect of rotor distortions causing converging and diverging coning are characterised. Experimental pressure distributions are compared to 2D modelling tools based on Reynolds flow equations, used widely to design conventional face seals. These were found to be largely inadequate. High fidelity 3D Commercial CFD however, provided highly accurate predictions of the seal face behaviour, particularly if coupled to mechanical prediction of the distortion of sealing faces under pressure loads. Detailed measurements and modelling of diverging gaps experienced during thermal transients are reported for the first time.
On the basis of these results, a large axial movement prototype face seal was designed and tested. The seal was shown to be capable of running successfully without the addition of a thin, vulnerable to damage, front face typical of gas thrust bearings. A design strategy where passive hydrostatic balancing without the use of biasing springs was seen to be generally successful, although design for tolerance to circumferential distortions was shown to be vital, as optimisation for leakage with a flat face made the seal liable to touch-down under extreme axial offset conditions. Steady state RANS 3D CFD model provided sufficient resolution to model the seal behaviour showing excellent agreement with experimental testing.

Advisor: Gillespie, D